item: #1 of 1349
          id: cord-000018-amvlm09p
      author: Pauli, Eva-K.
       title: Influenza A Virus Inhibits Type I IFN Signaling via NF-κB-Dependent Induction of SOCS-3 Expression
        date: 2008-11-07
       words: 9034
      flesch: 48
     summary: To examine whether expression of SOCS genes is induced in influenza virus infected cells, A549 cells were infected with PR8 for different time points. Signalling and apoptosis in influenza virus infected cells Dual function of interleukin-1beta for the regulation of interleukin-6-induced suppressor of cytokine signaling 3 expression IKKalpha, IKKbeta, and NEMO/IKKgamma are each required for the NF-kappaB-mediated inflammatory response program NF-kappaB-dependent induction of tumor necrosis factor-related apoptosisinducing ligand (TRAIL) and Fas/FasL is crucial for efficient influenza virus propagation Activation of NF-kappa B via the ikappa B kinase complex is both essential and sufficient for proinflammatory gene expression in primary endothelial cells Multiple signaling pathways regulate NF-kappaB-dependent transcription of the monocyte chemoattractant protein-1 gene in primary endothelial cells Type 1 interferons and the virus-host relationship: A lesson in detente IL-6 induces an anti-inflammatory response in the absence of SOCS3 in macrophages NS1 protein of influenza A virus inhibits the function of intracytoplasmic pathogen sensor, RIG-I Intracellular warfare between human influenza viruses and human cells: The roles of the viral NS1 protein Regulation of a nuclear export signal by an adjacent inhibitory sequence: The effector domain of the influenza virus NS1 protein Binding of the influenza A virus NS1 protein to PKR mediates the inhibition of its activation by either PACT or double-stranded RNA Suppressors of cytokine signalling (SOCS) in the immune system Influenza viruses and
    keywords: cells; expression; figure; gene; ifn; ifnb; induction; influenza; ns1; phosphorylation; protein; rna; signaling; socs-3; stat1; type; virus
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        item: #2 of 1349
          id: cord-000063-tex6bgab
      author: Sui, Hong-Yan
       title: Small Interfering RNA Targeting M2 Gene Induces Effective and Long Term Inhibition of Influenza A Virus Replication
        date: 2009-05-22
       words: 3531
      flesch: 43
     summary: 1B showed that the siRNA NP-1496 could inhibit influenza virus replication, while siRNA NP-336 had no inhibition effect, which is consistent with the previous report [25] . In this study we found that siM2 not only decreased the level of M2 mRNA but also the level of NP mRNA, suggesting that siM2 has a broad inhibition manner in the process of influenza virus replication.
    keywords: cells; gene; h5n1; influenza; inhibition; mdck; replication; sim2; sirna; virus
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        item: #3 of 1349
          id: cord-000083-3p81yr4n
      author: None
       title: Poster Exhibition
        date: 2009-01-31
       words: 113010
      flesch: 51
     summary: From this group of HBV patients 35 (98%) have had elevated urinal Dol excreation (45,8±5,2 g/ml vs . 3% and 47.4 respectively in HCC patients, 60.3% and 39.7 in LC patients, 55% and 40 in CHB patients, 55% and 40 in ACLF patients.
    keywords: activity; acute; adefovir; adv; afp; age; aim; aims; alt; alt levels; analysis; anti; assay; associated; b virus; background; baseline; blood; cancer; carcinoma; cases; cells; chb patients; china; chronic hcv; chronic hepatitis; clinical; combination; conclusion; control; control group; copies; correlation; data; days; development; diagnosis; difference; dna levels; dose; drug; effect; efficacy; end; etv; expression; factors; fibrosis; follow; gene; genotype; group; group b; hbeag; hbv dna; hbv genotype; hbv infection; hcc cell; hcc patients; hcv; hepatic; hepatitis b; hepatitis patients; hepatocellular; hospital; ifn; increase; infected; lamivudine; levels; liver; liver biopsy; liver cirrhosis; liver disease; load; low; male; markers; mean; median; medical; methods; model; months; mrna; mutation; nafld; negative; non; p<0.05; patients; patients chronic; pcr; positive; prevalence; protein; rate; ratio; rats; recurrence; related; resistance; respectively; response; results; rfa; risk; rna; role; samples; score; seroconversion; serum alt; serum hbv; significant; specific; study; study group; subjects; survival; svr; therapy; time; total; treatment; treatment group; tumor; university; virus; weeks; years
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        item: #4 of 1349
          id: cord-000088-1xgjdhkx
      author: Faria, Nuno R
       title: Rooting human parechovirus evolution in time
        date: 2009-07-15
       words: 4012
      flesch: 46
     summary: While the latter appears to be clearly established for e.g. SARS-CoV or influenza H5N1, a zoonotic link remains to be elucidated for HPeV. Because Ljungan virus shares a close phylogenetic proximity with HPeV virus, it is likely that both species have had a common ancestor [52] . Comparison of classic and molecular approaches for the identification of untypeable enteroviruses Enteroviruses in human disease Human parechovirus types 1, 2 and 3 infections in Canada Human parechovirus 3 and neonatal infections Human parechovirus infections in Dutch children and the association between serotype and disease severity Properties of ECHO types 22, 23 and 24 viruses Human parechoviruses as an important viral cause of sepsislike illness and meningitis in young children Analysis of a new human parechovirus allows the definition of parechovirus types and the identification of RNA structural domains Fourth human parechovirus serotype Isolation and characterization of novel human parechovirus from clinical samples Human parechovirus type 1, 3, 4, 5, and 6 detection in picornavirus cultures Prevalence, types, and RNA concentrations of human parechoviruses, including a sixth parechovirus type, in stool samples from patients with acute enteritis Genomic characterization of novel human parechovirus type Novel human parechovirus from Brazil High prevalence of human Parechovirus (HPeV) genotypes in the Amsterdam region and identification of specific HPeV variants by direct genotyping of stool samples Longitudinal observation of parechovirus in stool samples from Norwegian infants The population genetics and evolutionary epidemiology of RNA viruses Unifying the epidemiological and evolutionary dynamics of pathogens A method for detecting positive selection at single amino acid sites Mutation rates among RNA viruses Rates of evolutionary change in viruses: patterns and determinants The phylogeography of human viruses Evolutionary history and phylogeography of human viruses Inference of viral evolutionary rates from molecular sequences BEAST: Bayesian evolutionary analysis by sampling trees CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Molecular evolution Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm Relaxed phylogenetics and dating with confidence Bayesian selection of continuous-time Markov chain evolutionary models Bayes empirical bayes inference of amino acid sites under positive selection Calibration of multiple poliovirus molecular clocks covering an extended evolutionary range Codon substitution in evolution and the saturation of synonymous changes Time dependency of molecular rate estimates and systematic overestimation of recent divergence times Molecular clocks and the puzzle of RNA virus origins A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution Basic concepts in RNA virus evolution Bayesian coalescent inference of hepatitis A virus populations: evolutionary rates and patterns Evolution of circulating wild poliovirus and of vaccine-derived poliovirus in an immunodeficient patient: a unifying model Molecular epidemiology and evolution of enterovirus 71 strains isolated from 1970 to 1998 Genetic diversity in the VP1 gene of foot-andmouth disease virus serotype Asia 1 Sensitivity of the relative-rate test to taxonomic sampling Molecular analysis of three Ljungan virus isolates reveals a new, close-to-root lineage of the Picornaviridae with a cluster of two unrelated 2A proteins Molecular evolution of Puumala hantavirus Outbreak of Puumala virus infection Puumala hantavirus infection in humans and in the reservoir host, Ardennes region Hantavirus outbreak Widespread recombination within human parechoviruses: analysis of temporal dynamics and constraints We are grateful to Philippe Lemey for helpful comments on the paper and for computational assistance.
    keywords: analysis; hpev; human; parechovirus; rates; rna; sequences; types; virus; vp1
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        item: #5 of 1349
          id: cord-000113-d0eur1hq
      author: Fooks, Anthony R.
       title: Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century
        date: 2009-09-29
       words: 6946
      flesch: 34
     summary: Atlanta: US Department of Health and Human Services Rabies diagnosis for developing countries The primary application of direct rapid immunohistochemical test to rabies diagnosis in China Evaluation of a direct, rapid immunohistochemical test for rabies diagnosis Simple technique for the collection and shipment of brain specimens for rabies diagnosis Evaluation of a rapid immunodiagnostic test kit for rabies virus Immunochromatographic lateral flow strip tests The polymerase chain reaction (PCR) technique for diagnosis, typing and epidemiological studies Phylogenetic comparison of the genus Lyssavirus using distal coding sequences of the glycoprotein and nucleoprotein genes Identification of regional variants of the rabies virus within the Canadian province of Ontario Polymerase chain reaction protocols for rabies virus discrimination PCR technology for lyssavirus diagnosis Rabies virus detection by RT-PCR in decomposed naturally infected brains Heminested reversetranscriptase polymerase chain reaction (hnRT-PCR) as a tool for rabies virus detection in stored and decomposed samples Rabies virus in the decomposed brain of an Ethiopian wolf detected by nested reverse transcription-polymerase chain reaction An evaluation of immunofluorescence and PCR methods for detection of rabies in archival Carnoy-fixed, paraffin-embedded brain tissue Usefulness of reverse transcriptasepolymerase chain reaction for detection of rabies RNA in archival samples Molecular diagnosis of animal diseases: some experiences over the past decade PCR technique as an alternative method for diagnosis and molecular epidemiology of rabies virus Molecular methods to distinguish between classical rabies and the rabiesrelated European bat lyssaviruses Experimental infection of big brown bats (Eptesicus fuscus) with Eurasian bat lyssaviruses Aravan, Khujand, and Irkut virus A novel method for real time quantitative RT-PCR Real time quantitative PCR Development of a Real-Time, TaqMan Reverse Transcription-PCR Assay for Detection and Differentiation of Lyssavirus Genotypes 1, 5, and 6 Evaluation of a TaqMan PCR assay to detect rabies virus RNA: influence of sequence variation and application to quantification of viral loads Nucleic-acid sequence based amplification in the rapid diagnosis of rabies Integrated microfluidic tmRNA purification and real-time NASBA device for molecular diagnostics Multi-analyte single-membrane biosensor for the serotype-specific detection of Dengue virus Parallel nanoliter detection of cancer markers using polymer microchips Isothermal amplification of rabies virus gene Loop-mediated isothermal amplification of DNA Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of West Nile virus Rapid detection and quantification of Japanese Encephalitis virus by real-time reverse transcription loop-mediated isothermal amplification Novel reverse transcription loopmediated isothermal amplification for rapid detection of foot-and-mouth disease virus Rapid and real-time detection of Chikungunya virus by reverse transcription loop-mediated isothermal amplification assay Accelerated reaction by loop-mediated isothermal amplification using loop primers Host switching in Lyssavirus history from the Chiroptera to the Carnivora orders Microarray-based detection and genotyping of viral pathogens Microarrays for rapid identification of plant viruses Microassay-based detection of viruses causing vesicular or vesicular-like lesions in livestock animals An ultrasensitive and stable potentiometric immunosensor A novel hepatitis B virus surface antigen immunoassay as sensitive as hepatitis B virus nucleic acid testing in detecting early infection A novel serological assay for the detection of rabies virus neutralising antibodies Development of a TaqMan real-time RT-PCR assay for the detection of rabies virus Intravitam diagnosis of human rabies by PCR using saliva and cerebrospinal fluid Phylogenetic relationships of Irkut and West Caucasian bat viruses within the Lyssavirus genus and suggested quantitative criteria based on the N gene sequence for lyssavirus genotype definition Bat lyssaviruses (Aravan and Khujand) from Central Asia: phylogenetic relationships according to N, P and G gene sequences Primary structure of leader RNA and nucleoprotein genes of the rabies genome: segmented homology with VSV Case report: rapid ante-mortem diagnosis of a human case of rabies imported into the UK from the Philippines Expert Consultation on Rabies Longitudinally profiling neutralizing antibody response to SARS coronavirus with pseudotypes A sensitive retroviral pseudotype assay for influenza H5N1-neutralizing antibodies Retroviral pseudotypes Survival after treatment of rabies with induction of coma Applying the Milwaukee Protocol to treat canine rabies in Equatorial Guinea. In the course of the past three decades, the application of molecular biology has aided in the development of tests that result in a more rapid detection of rabies virus.
    keywords: amplification; countries; detection; diagnosis; pcr; rabies; rabies virus; rna; samples; techniques; tests; time; use; virus
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        item: #6 of 1349
          id: cord-000125-uvf5qzfd
      author: Kenworthy, Rachael
       title: Short-hairpin RNAs delivered by lentiviral vector transduction trigger RIG-I-mediated IFN activation
        date: 2009-09-03
       words: 6664
      flesch: 43
     summary: Moreover, activation of IRF-3 ( Figure 1E ) and IFN promoters ( Figure 1F ) in 293FT cells, which do not contain a functional TLR3 signaling pathway (42) , indicates that TLR3 plays a negligible role, if any, in IFN induction by sh-B971. These results demonstrate that sh-B971 is a potent activator of IRF-3 and IRF-7, master regulators of IFN expression in human cells.
    keywords: activation; b971; cells; expression; figure; hcv; ifn; induction; promoter; rig; rna; shrnas
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        item: #7 of 1349
          id: cord-000128-t74b5j2j
      author: Laufer, S.D
       title: Peptide-Mediated Cellular Delivery of Oligonucleotide-Based Therapeutics In Vitro: Quantitative Evaluation of Overall Efficacy Employing Easy to Handle Reporter Systems
        date: 2008-12-17
       words: 11965
      flesch: 34
     summary: The versatility of oligonucleotides as potential therapeutics Gene therapy with viral vectors Gene therapy: twenty-first century medicine A pilot study of in vivo liver-directed gene transfer with an adenoviral vector in partial ornithine transcarbamylase deficiency LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1 Fatal systemic inflammatory response syndrome in a ornithine transcarbamylase deficient patient following adenoviral gene transfer Gene therapy put on hold as third child develops cancer TAT peptide on the surface of liposomes affords their efficient intracellular delivery even at low temperature and in the presence of metabolic inhibitors Comparison between the interactions of adenovirus-derived peptides with plasmid DNA and their role in gene delivery mediated by liposomepeptide-DNA virus-like nanoparticles Vectors based on reducible polycations facilitate intracellular release of nucleic acids Cell transfection in vitro and in vivo with nontoxic TAT peptide-liposome-DNA complexes HIV-1 Tat protein transduction domain peptide facilitates gene transfer in combination with cationic liposomes Unique features of a pH-sensitive fusogenic peptide that improves the transfection efficiency of cationic liposomes A versatile reducible polycation-based system for efficient delivery of a broad range of nucleic acids Tat peptide-mediated intracellular delivery of pharmaceutical nanocarriers Evaluation of transportan 10 in PEI mediated plasmid delivery assay Efficient gene transfer by histidylated polylysine/pDNA complexes Branched co-polymers of histidine and lysine are efficient carriers of plasmids A novel transfecting peptide comprising a tetrameric nuclear localization sequence Highly branched HK peptides are effective carriers of siRNA Macro-branched cell-penetrating peptide design for gene delivery Protein transduction by lipidic peptide dendrimers Tat-Conjugated PAMAM Dendrimers as Delivery Agents for Antisense and siRNA Oligonucleotides Design, synthesis, and characterization of pH-sensitive PEG-PE conjugates for stimuli-sensitive pharmaceutical nanocarriers: the effect of substitutes at the hydrazone linkage on the ph stability of PEG-PE conjugates Smart drug carriers: PEGylated TATpmodified pH-sensitive liposomes Octaarginine-modified multifunctional envelope-type nanoparticles for gene delivery Multiblock reducible copolypeptides containing histidine-rich and nuclear localization sequences for gene delivery Intracellular siRNA and precursor miRNA trafficking using bioresponsive copolypeptides Cellular uptake of the tat protein from human immunodeficiency virus Autonomous functional domains of chemically synthesized human immunodeficiency virus tat transactivator protein alpha-2,8-Polysialic acid is the neuronal surface receptor of antennapedia homeobox peptide Tat-mediated delivery of heterologous proteins into cells Prochiantz A. Downregulation of amyloid precursor protein inhibits neurite outgrowth in vitro In vivo protein transduction: delivery of a biologically active protein into the mouse Cellpenetrating peptides Cell-penetrating peptides: mechanism and kinetics of cargo delivery Handbook of Cell-Penetrating Peptides Cell penetrating peptides: intracellular pathways and pharmaceutical perspectives Cell-penetrating peptides: from molecular mechanisms to therapeutics Cell-penetrating peptides for drug delivery across membrane barriers Recent Developments in Peptidebased Nucleic Acid Delivery Conjugates of oligonucleotides and analogues with cell penetrating peptides as gene silencing agents Delivery of proteins and nucleic acids using a non-covalent peptide-based strategy Peptide-based Nanoparticle for ex vivo and in vivo drug delivery Cell internalization of the third helix of the Antennapedia homeodomain is receptor-independent A new peptide vector for efficient delivery of oligonucleotides into mammalian cells To illustrate current limitations of non-viral nucleic acid delivery systems, we present own data as an example and discuss options of how to enhance trafficking of molecules entrapped in cellular compartments.
    keywords: acid; antisense; cargo; cell; complexes; conjugates; delivery; gene; molecules; mpg; oligonucleotides; peptide; protein; sirna; splice; splicing; systems; tat; transfection; uptake; vivo
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        item: #8 of 1349
          id: cord-000143-2xvd5ogf
      author: Napthine, Sawsan
       title: Expression of the VP2 Protein of Murine Norovirus by a Translation Termination-Reinitiation Strategy
        date: 2009-12-22
       words: 6891
      flesch: 47
     summary: The mechanism of an exceptional case of reinitiation after translation of a long ORF reveals why such events do not generally occur in mammalian mRNA translation A bipartite sequence motif induces translation reinitiation in feline calicivirus RNA Expression of the ORF-2 protein of the human respiratory syncytial virus M2 gene is initiated by a ribosomal termination-dependent reinitiation mechanism Coupled translation of the respiratory syncytial virus M2 open reading frames requires upstream sequences Coupled translation of the second open reading frame of M2 mRNA is sequence dependent and differs significantly within the subfamily Pneumovirinae The importance of inter-and intramolecular base pairing for translation reinitiation on a eukaryotic bicistronic mRNA Characterization of the termination-reinitiation strategy employed in the expression of influenza B virus BM2 protein A dualluciferase reporter system for studying recoding signals Ribosome pausing and stacking during translation of a eukaryotic mRNA Dissociation of eIF1 from the 40S ribosomal subunit is a key step in start codon selection in vivo The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome Migration of 40S ribosomal subunits on messenger RNA in the presence of edeine Migration of 40S ribosomal subunits on messenger RNA when initiation is perturbed by lowering magnesium or adding drugs Mutational analysis of the RNA pseudoknot component of a coronavirus ribosomal frameshifting signal Mutational analysis of the 'slipperysequence' component of a coronavirus ribosomal frameshifting signal Generation of deletion and point mutations with one primer in a single cloning step Two-stage PCR protocol allowing introduction of multiple mutations, deletions and insertions using QuikChange Site-Directed Mutagenesis Structure-function analysis of the ribosomal frameshifting signal of two human immunodeficiency virus type 1 isolates with increased resistance to viral protease inhibitors Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Characterization of the frameshift signal of Edr, a mammalian example of programmed -1 ribosomal frameshifting Distinct protein forms are produced from alternatively spliced bicistronic glutamic acid decarboxylase However, the substantial reintiation activity displayed by MNV49.7, an mRNA in which both AUGs were changed, indicates that non-AUG codons can act as reinitiation codons, although probably at reduced efficiency.
    keywords: codon; figure; mnv; motif; mrna; orf; reinitiation; start; stop; structure; termination; translation; upstream
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        item: #9 of 1349
          id: cord-000159-8y8ho2x5
      author: Bekaert, Michaël
       title: Recode-2: new design, new search tools, and many more genes
        date: 2009-09-25
       words: 2626
      flesch: 25
     summary: As the field grows and the number of recoded genes progressively increases, it becomes harder to extract data from the relevant literature and a number of novel recoded genes may escape the database. The hurdle lies not so much in the fact that recoded genes do not obey standard rules of genetic readout but, rather, in the considerable diversity of recoded genes and sequence elements responsible for recoding.
    keywords: database; events; expression; frameshifting; genes; recoding; ribosomal; rna
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        item: #10 of 1349
          id: cord-000238-om92cx5q
      author: Ogbunugafor, C. Brandon
       title: On the possible role of robustness in the evolution of infectious diseases
        date: 2010-06-30
       words: 6721
      flesch: 34
     summary: 24 For brevity we limit our discussion to complementation that occurs during coinfection and its potential role in the evolution of virus robustness. This logic infers that the degree of coinfection-high multiplicity of infection ͑MOI; ratio of viruses to cells͒ versus low MOI-should influence evolution of robustness in virus populations.
    keywords: bacteria; evolution; host; mutation; phage; populations; resistance; rna; robustness; selection; uvc; virus; viruses
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        item: #11 of 1349
          id: cord-000248-zueoyesj
      author: Berretta, Regina
       title: Cancer Biomarker Discovery: The Entropic Hallmark
        date: 2010-08-18
       words: 33640
      flesch: 32
     summary: implications for Dunnigan-type familial partial lipodystrophy A-type lamins: guardians of the soma? Downregulation of human X-box binding protein 1 (hXBP-1) expression correlates with tumor progression in human prostate cancers The proapoptotic kinase Mst1 and its caspase cleavage products are direct inhibitors of Akt1 Gene network and canonical pathway analysis in prostate cancer: a microarray study Biomarker expression patterns that correlate with high grade features in treatment naive, organ-confined prostate cancer NF-kappaB2 processing and p52 nuclear accumulation after androgenic stimulation of LNCaP prostate cancer cells Diverse effects of zinc on NF-kappaB and AP-1 transcription factors: implications for prostate cancer progression Nuclear factor-kappaB nuclear localization is predictive of biochemical recurrence in patients with positive margin prostate cancer Id-1 expression promotes cell survival through activation of NF-kappaB signalling pathway in prostate cancer cells Suppression of hormone-refractory prostate cancer by a novel nuclear factor kappaB inhibitor in nude mice Mechanisms of constitutive NF-kappaB activation in human prostate cancer cells Bcl-2 suppresses apoptosis resulting from disruption of the NF-kappa B survival pathway Gene expression profiling of human prostate cancer stem cells reveals a proinflammatory phenotype and the importance of extracellular matrix interactions Molecular imaging of NF-kappaB in prostate tissue after systemic administration of IL-1 beta TNF/IL-1/NIK/NF-kappa B transduction pathway: a comparative study in normal and pathological human prostate (benign hyperplasia and carcinoma) Proteasome inhibitors induce apoptosis of prostate cancer cells by inducing nuclear translocation of IkappaBalpha Targeting the receptor activator of nuclear factor-kappaB (RANK) ligand in prostate cancer bone metastases Pomegranate extract inhibits androgen-independent prostate cancer growth through a nuclear factor-kappaB-dependent mechanism The nuclear factor-kappaB pathway controls the progression of prostate cancer to androgenindependent growth A new prostate cancer therapeutic approach: combination of androgen ablation with COX-2 inhibitor Inhibitory effect of snake venom toxin from Vipera lebetina turanica on hormone-refractory human prostate cancer cell growth: induction of apoptosis through inactivation of nuclear factor kappaB Prostate cancer chemoprevention by silibinin: bench to bedside Genistein inhibits radiation-induced activation of NF-kappaB in prostate cancer cells promoting apoptosis and G2/M cell cycle arrest NF-kappaB inhibition increases chemosensitivity to trichostatin A-induced cell death of Ki-Ras-transformed human prostate epithelial cells Involvement of the TNF-alpha autocrine-paracrine loop, via NF-kappaB and YY1, in the regulation of tumor cell resistance to Fas-induced apoptosis Estrogens and antiestrogens as etiological factors and therapeutics for prostate cancer NF-kappaB activation upregulates fibroblast growth factor 8 expression in prostate cancer cells Anticancer potential of silymarin: from bench to bed side Blockage of NF-kappaB induces serine 15 phosphorylation of mutant p53 by JNK kinase in prostate cancer cells Skp2 enhances polyubiquitination and degradation of TIS21/BTG2/PC3, tumor suppressor protein, at the downstream of FoxM1 Triiodothyronine modulates cell proliferation of human prostatic carcinoma cells by downregulation of the B-cell translocation gene 2 B cell translocation gene 2 enhances susceptibility of HeLa cells to doxorubicin-induced oxidative damage TIS21 (/BTG2/PC3) as a link between ageing and cancer: cell cycle regulator and endogenous cell death molecule Expression of B-cell translocation gene 2 protein in normal human tissues Antiproliferative B cell translocation gene 2 protein is down-regulated posttranscriptionally as an early event in prostate carcinogenesis Identification of genes associated with stromal hyperplasia and glandular atrophy of the prostate by mRNA differential display Role of connective tissue growth factor in fibronectin synthesis in cultured human prostate stromal cells Stromal expression of connective tissue growth factor promotes angiogenesis and prostate cancer tumorigenesis Analysis of gene expression during staurosporine-induced neuronal differentiation of human prostate cancer cells Profiling molecular targets of TGF-beta1 in prostate fibroblast-to-myofibroblast transdifferentiation Expression of androgen receptor coregulatory proteins in prostate cancer and stromal-cell culture models FHL2, a novel tissue-specific coactivator of the androgen receptor Four and a Half LIM Domain 2 alters the impact of Aryl Hydrocarbon Receptor on Androgen Receptor transcriptional activity Differently regulated androgen receptor transcriptional complex in prostate cancer compared with normal prostate Suppression of FOXO1 activity by FHL2 through SIRT1-mediated deacetylation The transcriptional coactivator FHL2 transmits Rho signals from the cell membrane into the nucleus Functional epigenomics identifies genes frequently silenced in prostate cancer Expression level and DNA methylation status of glutathione-S-transferase genes in normal murine prostate and TRAMP tumors Function of JunB in transient amplifying cell senescence and progression of human prostate cancer KAI1 promoter activity is dependent on p53, junB and AP2: evidence for a possible mechanism underlying loss of KAI1 expression in cancer cells Inhibition of prostate tumor growth by overexpression of NudC, a microtubule motorassociated protein Control of androgen receptor signaling in prostate cancer by the cochaperone small glutamine rich tetratricopeptide repeat containing protein alpha Signal transducer and activator of transcription-6 (STAT6) is a constitutively expressed survival factor in human prostate cancer Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data Molecular features of the transition from prostatic intraepithelial neoplasia (PIN) to prostate cancer: genome-wide gene-expression profiles of prostate cancers and PINs Analysis of integrin alpha7 mutations in prostate cancer, liver cancer, glioblastoma multiforme, and leiomyosarcoma The biology of cancer The chromosomal basis of cancer Gene panel model predictive of outcome in men at high-risk of systemic progression and death from prostate cancer after radical retropubic prostatectomy Aneuploidy and rapid cell proliferation in recurrent prostate cancers with androgen receptor gene amplification Prognostic value of DNA analysis of prostate adenocarcinoma: correlation to clinicopathologic predictors Heterogeneity in prostate cancer: Identification of cdk activating kinase (CAK) as an androgen receptor NH(2)-terminal associated coactivator Alphamethylacyl-CoA racemase-an 'obscure' metabolic enzyme takes centre stage Biopsy tissue microarray study of Ki-67 expression in untreated, localized prostate cancer managed by active surveillance Alpha-methylacyl-CoA racemase (P504S) expression in evolving carcinomas within benign prostatic hyperplasia and in cancers of the transition zone Expression of alpha-methylacyl-CoA racemase (P504s) in various malignant neoplasms and normal tissues: astudy of 761 cases Using an AMACR (P504S)/34betaE12/p63 cocktail for the detection of small focal prostate carcinoma in needle biopsy specimens Diagnostic utility of alpha-methylacyl CoA racemase (P504S) on prostate needle biopsy Discovery and clinical application of a novel prostate cancer marker: alpha-methylacyl CoA racemase (P504S) Alphamethylacyl-CoA racemase: a multi-institutional study of a new prostate cancer marker Quantitative immunohistochemical detection of the molecular expression patterns in proliferative inflammatory atrophy The importance of determining the aggressiveness of prostate cancer using serum and tissue molecular markers GOLPH2 protein expression as a novel tissue biomarker for prostate cancer: implications for tissue-based diagnostics Optimization of laser capture microdissection and RNA amplification for gene expression profiling of prostate cancer ) alpha-Methylacyl-CoA racemase: expression levels of this novel cancer biomarker depend on tumor differentiation Elevated alpha-methylacyl-CoA racemase enzymatic activity in prostate cancer Comparison of monoclonal antibody (P504S) and polyclonal antibody to alpha methylacyl-CoA racemase (AMACR) in the work-up of prostate cancer Immunohistochemical detection of carcinoma in radical prostatectomy specimens following hormone therapy Basal cell subpopulation as putative human prostate carcinoma stem cells A statistical method for identifying differential gene-gene co-expression patterns Alphamethylacyl-CoA racemase (AMACR/P504S) protein expression in urothelial carcinoma of the upper urinary tract correlates with tumour progression Sequence variation in alpha-methylacyl-CoA racemase and risk of early-onset and familial prostate cancer Malignant transformation of human benign prostate epithelial cells by high linear energy transfer alpha-particles Expression of alpha-methylacylcoenzyme A racemase in dysplastic Barrett's epithelium Quantitative analysis of a panel of gene expression in prostate cancer-with emphasis on NPY expression analysis The value of using an AMACR/34betaE12/p63 cocktail double staining for diagnosis of prostate carcinoma Decreased gene expression of steroid 5 alpha-reductase 2 in human prostate cancer: implications for finasteride therapy of prostate carcinoma Alpha-methylacyl-CoA racemase: a new molecular marker for prostate cancer Alpha-methylacyl-CoA racemase: a variably sensitive immunohistochemical marker for the diagnosis of small prostate cancer foci on needle biopsy Neoadjuvant docetaxel treatment for locally advanced prostate cancer: a clinicopathologic study Biomarkers for Prostate Cancer Method for quantification of a prostate cancer biomarker in urine without sample preparation Effects of the dual 5 alpha-reductase inhibitor dutasteride on apoptosis in primary cultures of prostate cancer epithelial cells and cell lines Routine immunohistochemical staining for high-molecular weight cytokeratin 34-beta and alpha-methylacyl CoA racemase (P504S) in postirradiation prostate biopsies Search for residual prostate cancer on pT0 radical prostatectomy after positive biopsy Branched fatty acids in dairy and beef products markedly enhance alpha-methylacyl-CoA racemase expression in prostate cancer cells in vitro Alpha-methyl CoA racemase expression in renal cell carcinomas Diagnostic utility of a p63/alpha-methyl-CoA-racemase (p504s) cocktail in atypical foci in the prostate Value of new prostate cancer markers: alpha methylacyl CoA racemase (P504S) and p63 Evaluation of p63 and p504s markers for the diagnosis of prostate cancer
    keywords: alpha; analysis; associated; biomarkers; cancer cells; cancer progression; cell; changes; coa; complexity; correlation; dataset; distribution; divergence; dna; expression; factor; figure; function; gene; gene expression; gleason; growth; human; information; jensen; kinase; loss; malignant; melanoma; metastasis; methylacyl; normalized; normalized shannon; novel; osteopontin; probes; profile; progression; prostate cancer; protein; racemase; regulation; results; role; samples; shannon; shannon divergence; shannon entropy; skin; study; tissue; transcriptional; tumor; values
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        item: #12 of 1349
          id: cord-000265-llilwq1u
      author: Gao, Rongbao
       title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case
        date: 2010-10-12
       words: 4904
      flesch: 41
     summary: Global public health concerns surrounding H5N1 viruses include not only individual transmission events between infected poultry and individual humans, but also their pandemic potential, should these viruses acquire genetic changes that result in sustained human-to-human transmission. Reactive hemophagocytosis in multiple organs, and occasional detection of viral antigen or viral RNA in extrapulmonary organs suggest a broader tissue distribution of H5N1 viruses compared with seasonal viruses in fatal human cases [21, 22] .
    keywords: avian; cells; gene; h5n1; human; infection; influenza; load; lung; tissues; virus; viruses
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        item: #13 of 1349
          id: cord-000269-v4jochbe
      author: Wittekindt, Nicola E.
       title: Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics
        date: 2010-10-18
       words: 5897
      flesch: 40
     summary: A comparison of the three methods used to detect bacteria in mule deer lymph node samples is shown for MD 257 in Figure 2 and for MD 80228 and MD OCT-pool in Figure S1 . The microbial community of mule deer lymph nodes Detection of protein-coding and ribosomal RNA transcripts provides strong support for the presence of viable and replicating microorganisms.
    keywords: cdna; database; deer; helicobacter; libraries; lymph; microbial; pool; rna; rrna; sequencing; tags; transcripts
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        item: #14 of 1349
          id: cord-000293-pc4x5e24
      author: Yu, Chien-Hung
       title: Stimulation of ribosomal frameshifting by antisense LNA
        date: 2010-08-06
       words: 3906
      flesch: 40
     summary: To demonstrate that the enhanced effect of LNA oligonucleotides is a general feature we designed another construct (SF462) in which the target sequence was replaced by an unrelated sequence ( Figure 4 ). However, the excellent affinity of LNA oligonucleotides could be a double-edged sword in certain cases.
    keywords: antisense; dna; efficiency; frameshifting; lna; oligonucleotides; pseudoknot; ribosomal; rna
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        item: #15 of 1349
          id: cord-000295-ft5wl70x
      author: Tomankova, Tereza
       title: Involvement of microRNAs in physiological and pathological processes in the lung
        date: 2010-11-23
       words: 4783
      flesch: 39
     summary: [102] miR-34 regulation of apoptosis in lung cancer cells (H) [66] , [67] function as tumor suppressors in lung cells.
    keywords: cancer; cells; expression; human; lung; microrna; mirnas; mrna; regulation; role; target
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        item: #16 of 1349
          id: cord-000322-8ctsa9sd
      author: Ninove, Laetitia
       title: RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests
        date: 2011-02-09
       words: 2897
      flesch: 36
     summary: Protocols for real time PCR detection of phages TA and MS2 were elaborated in various formats and are described in Supporting Information S2. When IDP was associated with negative PCR detection results, a new assay was performed using a tenfold dilution of the nucleic acid extract.
    keywords: detection; dna; pcr; rna; samples; time
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        item: #17 of 1349
          id: cord-000364-ikq38rm1
      author: Rasmuson, J.
       title: Time to revise the paradigm of hantavirus syndromes? Hantavirus pulmonary syndrome caused by European hantavirus
        date: 2011-01-15
       words: 2843
      flesch: 39
     summary: Hantavirus pulmonary syndrome caused by European hantavirus date: 2011-01-15 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-010-1141-6 sha: doc_id: 364 cord_uid: ikq38rm1 Hantaviruses have previously been recognised to cause two separate syndromes: hemorrhagic fever with renal syndrome in Eurasia, and hantavirus pulmonary syndrome (HPS) in the Americas. Pathogenesis of an emerging infectious disease Hantavirus regulation of endothelial cell functions Hantavirus infection induces a typical myocarditis that may be responsible for myocardial depression and shock in hantavirus pulmonary syndrome Pulmonary involvement in nephropathia epidemica as demonstrated by computed tomography Impaired pulmonary function in patients with hemorrhagic fever with renal syndrome Pulmonary involvement in nephropathia epidemica: radiological findings and their clinical correlations Hantavirus pulmonary syndrome in New England and Europe Puumala virus pulmonary syndrome in a Romanian immigrant Puumala virus RNA in patient with multiorgan failure Corticosteroids combined with continuous veno-venous hemodiafiltration for treatment of hantavirus pulmonary syndrome caused by Puumala virus infection Outbreak of Puumala virus infection Puumala hantavirus viremia diagnosed by real-time reverse transcriptase PCR using samples from patients with hemorrhagic fever and renal syndrome Hantavirus pulmonary syndrome, 2010 case definition Hantavirus pulmonary syndrome: the new American hemorrhagic fever Outbreak of hantavirus pulmonary syndrome Electrocardiographic changes in patients with haemorrhagic fever with renal syndrome More than half of the patients with acute Puumala hantavirus infection have abnormal cardiac findings Prospective evaluation of household contacts of persons with hantavirus cardiopulmonary syndrome in Chile Acknowledgements Irene Eriksson and Ingrid Gustafsson are greatly acknowledged for their skilled technical assistance.
    keywords: hantavirus; infection; infiltrates; patients; pulmonary; puuv; rna; syndrome
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        item: #18 of 1349
          id: cord-000372-wzwpyvll
      author: Castelló, Alfredo
       title: The Multifaceted Poliovirus 2A Protease: Regulation of Gene Expression by Picornavirus Proteases
        date: 2011-04-14
       words: 16348
      flesch: 40
     summary: However, some of the PV proteins are able to target nuclear proteins such as transcription and splicing factors and proteins involved in nuclear-cytoplasmic trafficking. PV infection strongly impacts on hostcell protein localization, giving rise to an unusual cytoplasmic distribution of nuclear proteins [188] .
    keywords: cells; cleavage; complex; cytoplasm; eif4gi; export; expression; factors; host; infection; initiation; mrna; nuclear; nucleus; poliovirus; pro; protease; protein; rna; synthesis; translation; virus
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        item: #19 of 1349
          id: cord-000435-2u49b7xo
      author: Firth, Andrew E.
       title: Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element
        date: 2011-04-27
       words: 7281
      flesch: 37
     summary: Sequence alignments of coding sequences containing RT stop codons were generated for a number of RNA virus taxa and the degree of conservation at synonymous sites was analyzed as described in the 'Materials and Methods' section. In terms of 5 0 stimulatory motifs, adenines at the À1 and À2 nucleotide positions have been shown to positively modulate RT in yeast and are a feature common to many virus RT sites, notably in the tobamoviruses, poleroviruses and luteoviruses (38) .
    keywords: codon; conservation; figure; gene; loop; rna; sequence; site; stem; stop; stop codon; structure; uga; virus
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        item: #20 of 1349
          id: cord-000482-wifs97yy
      author: Yu, Chien-Hung
       title: Stem–loop structures can effectively substitute for an RNA pseudoknot in −1 ribosomal frameshifting
        date: 2011-07-29
       words: 4794
      flesch: 47
     summary: Frameshifting efficiency was calculated by dividing the ratio of Renilla luciferase (RL) over Firefly luciferase (FL) activity of the mutant by the RL/ FL ratio of the in-frame control, multiplied by 100. Next, we investigated the role of stem length on frameshifting efficiency.
    keywords: efficiency; figure; frameshifting; hairpin; loop; pseudoknot; ribosomal; rna; stability; stem
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        item: #21 of 1349
          id: cord-000532-e18licyc
      author: Tholstrup, Jesper
       title: mRNA pseudoknot structures can act as ribosomal roadblocks
        date: 2011-09-08
       words: 5814
      flesch: 49
     summary: The ribosome uses two active mechanisms to unwind messenger RNA during translation Codon usage determines the translation rate in Escherichia coli Ribosomal movement impeded at a pseudoknot required for frameshifting Ribosomal pausing during translation of an RNA pseudoknot Ribosomal pausing at a frameshifter RNA pseudoknot is sensitive to reading phase but shows little correlation with frameshift efficiency Torsional restraint: a new twist on frameshifting pseudoknots Divergent stalling sequences sense and control cellular physiology Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting Characterization of the Mechanical Unfolding of RNA Pseudoknots Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an RNA pseudoknot Achieving a golden mean: mechanisms by which coronaviruses ensure synthesis of the correct stoichiometric ratios of viral proteins The role of RNA pseudoknot stem 1 length in the promotion of efficient -1 ribosomal frameshifting Evidence for an RNA pseudoknot loop-helix interaction essential for efficient-1 ribosomal frameshifting Culture medium for enterobacteria pknotsRG: key: cord-000532-e18licyc authors: Tholstrup, Jesper; Oddershede, Lene B.; Sørensen, Michael A. title: mRNA pseudoknot structures can act as ribosomal roadblocks date: 2011-09-08 journal: Nucleic Acids Res DOI: 10.1093/nar/gkr686 sha: doc_id: 532 cord_uid: e18licyc Several viruses utilize programmed ribosomal frameshifting mediated by mRNA pseudoknots in combination with a slippery sequence to produce a well defined stochiometric ratio of the upstream encoded to the downstream-encoded protein.
    keywords: codon; downstream; figure; frameshift; frameshifting; lacz; mrna; pseudoknot; ribosomes; stop; structure
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        item: #22 of 1349
          id: cord-000547-adfigzc1
      author: Beniac, Daniel R.
       title: The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy
        date: 2012-01-11
       words: 7821
      flesch: 47
     summary: (MOV) Physical principles in the construction of regular viruses Studies on the pleomorphism of HVJ virons Infectious bursal disease virus is an icosahedral polyploid dsRNA virus Architecture of ribonucleoprotein complexes in influenza A virus particles Ebola virus: new insights into disease aetiopathology and possible therapeutic interventions Live attenuated recombinant vaccine protects nonhuman primates against Ebola and Marburg viruses Ebola virus: from discovery to vaccine The virion glycoproteins of Ebola viruses are encoded in two reading frames and are expressed through transcriptional editing GP mRNA of Ebola virus is edited by the Ebola virus polymerase and by T7 and vaccinia virus polymerases Ebola virus glycoprotein 1: identification of residues important for binding and postbinding events Conserved receptor-binding domains of Lake Victoria marburgvirus and Zaire ebolavirus bind a common receptor Comprehensive analysis of ebola virus GP1 in viral entry Identification of two amino acid residues on Ebola virus glycoprotein 1 critical for cell entry The assembly of Ebola virus nucleocapsid requires virion-associated proteins 35 and 24 and posttranslational modification of nucleoprotein Functional mapping of the nucleoprotein of Ebola virus Nucleocapsid-like structures of Ebola virus reconstructed using electron tomography Electron tomography reveals the steps in filovirus budding GraFix: stabilization of fragile macromolecular complexes for single particle cryo-EM GraFix: sample preparation for single-particle electron cryomicroscopy Post-crystallization treatments for improving diffraction quality of protein crystals Differentiation of filoviruses by electron microscopy Ebola and Marburg viruses: I. Some ultrastructural differences between strains when grown in Vero cells Ultrastructure of Ebola virus particles in human liver On the etiology of an unknown human infection originating from monkeys Apoptosis induced in vitro and in vivo during infection by Ebola and Marburg viruses Movie S1 3-D reconstruction of Ebola virus nucleocapsid.
    keywords: analysis; cryo; ebola; ebola virus; ebov; figure; genome; image; length; nucleocapsid; particles; protein; structure; virus; vp40
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        item: #23 of 1349
          id: cord-000556-uu1oz2ei
      author: Kumar, Ranjit
       title: RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336”
        date: 2012-01-20
       words: 4410
      flesch: 43
     summary: We identified co-expression for 452 pairs (total 730 genes) of H. somni genes ( Table S2 ) that were transcribed together and constituted a minimal operon. Regions where coverage depth was greater than the lower tenth percentile of expressed genes were considered significantly expressed [21] ; in the current study, this corresponded to a coverage depth of 7 reads/bp in pileup format.
    keywords: coding; genes; genome; novel; protein; regions; rna; seq; somni; srnas; transcriptome
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        item: #24 of 1349
          id: cord-000578-jhetyd9t
      author: Kovalev, Nikolay
       title: A Co-Opted DEAD-Box RNA Helicase Enhances Tombusvirus Plus-Strand Synthesis
        date: 2012-02-16
       words: 8832
      flesch: 51
     summary: One digestion was used to confirm the replicase products: the de novo products are insensitive, while the 39TEX product changes migration after RNase treatment Yeast as a model host to explore plant virus-host interactions Organelle-like membrane compartmentalization of positive-strand RNA virus replication factories Cytoplasmic viral replication complexes Emerging picture of host chaperone and cyclophilin roles in RNA virus replication The dependence of viral RNA replication on coopted host factors Yeast as a model host to dissect functions of viral and host factors in tombusvirus replication Host factors involved in West Nile virus replication Viral and cellular proteins involved in coronavirus replication Diverse roles of host RNA binding proteins in RNA virus replication Global genomics and proteomics approaches to identify host factors as targets to induce resistance against tomato bushy stunt virus Multiple roles of viral replication proteins in plant RNA virus replication The roles of host factors in tombusvirus RNA recombination Yeast as a model host to study replication and recombination of defective interfering RNA of Tomato bushy stunt virus Purification of the cucumber necrosis virus replicase from yeast cells: role of coexpressed viral RNA in stimulation of replicase activity Role of an internal and two 39-terminal RNA elements in assembly of tombusvirus replicase Specific Binding of Tombusvirus Replication Protein p33 to an Internal Replication Element in the Viral RNA Is Essential for Replication Defining the Roles of cis-Acting RNA Elements in Tombusvirus Replicase Assembly In Vitro Systematic, genome-wide identification of host genes affecting replication of a positive-strand RNA virus Yeast genome-wide screen reveals dissimilar sets of host genes affecting replication of RNA viruses Identification of essential host factors affecting tombusvirus RNA replication based on the yeast Tet promoters Hughes Collection A temperature sensitive mutant of heat shock protein 70 reveals an essential role during the early steps of tombusvirus replication A key role for heat shock protein 70 in the localization and insertion of tombusvirus replication proteins to intracellular membranes In vitro assembly of the Tomato bushy stunt virus replicase requires the host Heat shock protein 70 Proteomics analysis of the tombusvirus replicase: Hsp70 molecular chaperone is associated with the replicase and enhances viral RNA replication Tomato bushy stunt virus Co-Opts the RNA-Binding Function of a Host Metabolic Enzyme for Viral Genomic RNA Synthesis Ubiquitin-Conjugating Enzyme Is a Component of the Tombusvirus Replicase Complex and Ubiquitinates p33 Replication Protein Translation Elongation Factor 1A Facilitates the Assembly of the Tombusvirus Replicase and Stimulates Minus-Strand Synthesis Translation elongation factor 1A is a component of the tombusvirus replicase complex and affects the stability of the p33 replication co-factor Synergistic Roles of Eukaryotic Translation Elongation Factors 1Bgamma and 1A in Stimulation of Tombusvirus Minus-Strand Synthesis
    keywords: ded1p; figure; helicase; host; p33; proteins; replicase; replication; rna; synthesis; tbsv; tombusvirus; vitro; yeast
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        item: #25 of 1349
          id: cord-000640-t0y0b0gb
      author: Sumibcay, Laarni
       title: Divergent lineage of a novel hantavirus in the banana pipistrelle (Neoromicia nanus) in Côte d'Ivoire
        date: 2012-01-26
       words: 2222
      flesch: 38
     summary: To investigate this possibility, archival tissues from 213 insectivorous bats (order Chiroptera) were analyzed for hantavirus RNA by RT-PCR. Following numerous failed attempts, hantavirus RNA was detected in ethanol-fixed liver tissue from two banana pipistrelles (Neoromicia nanus), captured near Mouyassué village in Côte d'Ivoire, West Africa, in June 2011.
    keywords: banana; bats; hantavirus; mouv; rna; shrew; tissues
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        item: #26 of 1349
          id: cord-000660-tsvzg0ax
      author: Fensterl, Volker
       title: Interferon-Induced Ifit2/ISG54 Protects Mice from Lethal VSV Neuropathogenesis
        date: 2012-05-17
       words: 8309
      flesch: 48
     summary: In wt mice, VSV RNA was present prominently in the cortex, midbrain and brainstem, but not in the cerebellum ( Figure 4C ), which is consistent with published results [24] . Ifit1 and IFN-b mRNAs were induced as strongly in OB of Ifit22/2 as in wt mice, which correlated well with similar abundance of VSV RNA in wt and Ifit2 2/2 OB (Figure 5A compared to Figure 3C ).
    keywords: 2/2; brain; d.p.i; figure; ifit2; ifn; infection; mice; protein; replication; rna; type; virus; vsv; wt mice
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        item: #27 of 1349
          id: cord-000715-zl1s82yi
      author: Shulman, Lester M.
       title: Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition
        date: 2012-07-16
       words: 4791
      flesch: 42
     summary: The number of stool suspension RNA extracts with inhibitors of MS2 rRT-PCR varied between RNA extraction protocols for randomly chosen stool suspensions. Potential inhibitors that might be incompletely removed from stool suspensions during RNA extraction include hemoglobin, immunoglobulins, bilirubin, triglycerides, complex polysaccharides, organic and phenolic compounds, glycogen, fats, and metabolic products especially those from pathological conditions, bacteria, vegetables, medications, anticoagulants, and drugs or alcohol
    keywords: extraction; inhibition; inhibitors; ms2; pcr; rna; rrt; samples; stool
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        item: #28 of 1349
          id: cord-000729-iq30z094
      author: Marsh, Glenn A.
       title: Cedar Virus: A Novel Henipavirus Isolated from Australian Bats
        date: 2012-08-02
       words: 6124
      flesch: 43
     summary: A morbillivirus that caused fatal disease in horses and humans Nipah virus: a recently emergent deadly paramyxovirus Paramyxoviridae: The viruses and their replication Hendra and Nipah viruses: different and dangerous Henipavirus vaccine development Fields Virology Nipah virus infection in bats (order Chiroptera) in peninsular Malaysia Antibodies to Nipah or Nipah-like viruses in bats Evidence of henipavirus infection in West African fruit bats Pteropid Bats are Confirmed as the Reservoir Hosts of Henipaviruses: A Comprehensive Experimental Study of Virus Transmission Fruit bats as reservoirs of Ebola virus Marburg virus infection detected in a common African bat Bats are natural reservoirs of SARS-like coronaviruses A previously unknown reovirus of bat origin is associated with an acute respiratory disease in humans Recombinant Nipah virus vaccines protect pigs against challenge Feline model of acute Nipah virus infection and protection with a soluble glycoprotein-based subunit vaccine A recombinant subunit vaccine formulation protects against lethal Nipah virus challenge in cats A recombinant Hendra virus G glycoprotein-based subunit vaccine protects ferrets from lethal Hendra virus challenge A neutralizing human monoclonal antibody protects african green monkeys from hendra virus challenge A neutralizing human monoclonal antibody protects against lethal disease in a new ferret model of acute Nipah virus infection Neutralization assays for differential henipavirus serology using Bio-Plex Protein Array Systems Ephrin-B2 ligand is a functional receptor for Hendra virus and Nipah virus EphrinB2 is the entry receptor for Nipah virus, an emergent deadly paramyxovirus Two key residues in ephrinB3 are critical for its use as an alternative receptor for Nipah virus Nipah virus: vaccination and passive protection studies in a hamster model Henipavirus RNA in African bats Establishment, immortalisation and characterisation of pteropid bat cell lines Tioman virus, a novel paramyxovirus isolated from fruit bats in malaysia Isolation of Nipah virus from Malaysian Island flying-foxes A novel approach for collecting samples from fruit bats for isolation of infectious agents Sensitive and broadly reactive reverse transcription-PCR assays to detect novel paramyxoviruses Cocirculation of diverse paramyxoviruses in an urban African fruit bat population Two mRNAs that differ by two nontemplated nucleotides encode the amino coterminal proteins P and V of the paramyxovirus SV5 Functional studies of host-specific ephrin-B ligands as Henipavirus receptors Chloroquine administration does not prevent Nipah virus infection and disease in ferrets Experimental hendra virus infectionin pregnant guinea-pigs and fruit Bats (Pteropus poliocephalus) Equine morbillivirus pneumonia: susceptibility of laboratory animals to the virus A golden hamster model for human acute Nipah virus infection Discovery of an ebolavirus-like filovirus in Europe Family Paramyxoviridae Antagonism of innate immunity by paramyxovirus accessory proteins The P gene of human parainfluenza virus type 1 encodes P and C proteins but not a cysteinerich V protein Genome sequencing in microfabricated high-density picolitre reactors Panmicrobial oligonucleotide array for diagnosis of infectious diseases Improved rapid amplification of cDNA ends (RACE) for mapping both the 59 and 39 terminal sequences of paramyxovirus genomes MEGA4: As a first step towards the understanding of the pathogenicity difference between CedPV and HeV, we examined the IFN responses in human HeLa cells upon virus infection.
    keywords: bats; cedpv; cell; gene; genome; henipaviruses; hev; infection; nipah; niv; protein; rna; sequence; virus
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        item: #29 of 1349
          id: cord-000736-6f8vyziv
      author: Pripuzova, Natalia
       title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens
        date: 2012-08-17
       words: 6827
      flesch: 47
     summary: The results of sensitivity testing of the real-time PCR array primer sets specific for HIV-1, HIV-2, HBV, HCV, and WNV the with FDA/CBER analytical plasma panels. Example of the experimental testing of HIV-1 specific primer set targeting gag gene (NP3/4) for its sensitivity with DNA analytical standards is shown in Figure S1 .
    keywords: array; copies; dna; hiv-1; human; pcr; plasma; primer; samples; sets; specific; virus
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        item: #30 of 1349
          id: cord-000794-l565gha4
      author: Yan, Huan
       title: Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus
        date: 2012-11-13
       words: 13433
      flesch: 47
     summary: HBV HBV genotype B virus was obtained by ultracentrifugation of plasma from an HBV chronic carrier with written consent. For HBV viral infection on HepaRG cells and PHH, ∼ 4% PEG 8000 was present during the inoculation period as previously described by Gripon et al.
    keywords: analysis; binding; cells; cross; data; days; figure; genome; hbv; hdv; hepatitis; human; infection; ntcp; pcr; peptide; pre; protein; rna; time; total; tsntcp; viral; virus
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        item: #31 of 1349
          id: cord-000804-0hlj6r10
      author: Brauburger, Kristina
       title: Forty-Five Years of Marburg Virus Research
        date: 2012-10-01
       words: 14933
      flesch: 42
     summary: Cell Host Microbe Broad-spectrum inhibition of retroviral and filoviral particle release by tetherin Tetherin-mediated restriction of filovirus budding is antagonized by the Ebola glycoprotein The Ebola virus glycoprotein and HIV-1 Vpu employ different strategies to counteract the antiviral factor tetherin The GP-protein of Marburg virus contains the region similar to the 'immunosuppressive domain' of oncogenic retrovirus P15E proteins Implication of a retrovirus-like glycoprotein peptide in the immunopathogenesis of Ebola and Marburg viruses Ectodomain shedding of the glycoprotein GP of Ebola virus Sorting of Marburg virus surface protein and virus release take place at opposite surfaces of infected polarized epithelial cells Interactions with the host cell Tsg101 is recruited by a late domain of the nucleocapsid protein to support budding of Marburg virus-like particles Phosphorylation of Marburg virus matrix protein VP40 triggers assembly of nucleocapsids with the viral envelope at the plasma membrane Establishment and application of an infectious virus-like particle system for Marburg virus VP40, the matrix protein of Marburg virus, is associated with membranes of the late endosomal compartment Interactions of Marburg virus nucleocapsid proteins The matrix protein of Marburg virus is transported to the plasma membrane along cellular membranes: exploiting the retrograde late endosomal pathway Generation of Marburg virus-like particles by co-expression of glycoprotein and matrix protein Multivesicular bodies as a platform for formation of the Marburg virus envelope Vacuolar protein sorting pathway contributes to the release of Marburg virus Oligomerization and polymerization of the filovirus matrix protein VP40 Interaction of Tsg101 with Marburg virus VP40 depends on the PPPY motif, but not the PT/SAP motif as in Viruses 2012, 4 1917 the case of Ebola virus, and Tsg101 plays a critical role in the budding of Marburg virus-like particles induced by VP40, NP, and GP Regulation of Marburg virus (MARV) budding by Nedd4.1: a different WW domain of Nedd4.1 is critical for binding to MARV and Ebola virus VP40 Conserved motifs within Ebola and Marburg virus VP40 proteins are important for stability, localization, and subsequent budding of virus-like particles Identification of amino acids in Marburg virus VP40 that are important for virus-like particle budding Marburg Virus VP40 Antagonizes Interferon Signaling in a Species-Specific Manner Marburg virus evades interferon responses by a mechanism distinct from ebola virus Global suppression of the host antiviral response by Ebolaand Marburgviruses: increased antagonism of the type I interferon response is associated with enhanced virulence The ebola virus interferon antagonist VP24 directly binds STAT1 and has a novel, pyramidal fold Filoviral immune evasion mechanisms Development and characterization of a mouse model for Marburg hemorrhagic fever Key genomic changes necessary for an in vivo lethal mouse marburgvirus variant selection process VP24 of Marburg virus influences formation of infectious particles Fold prediction of VP24 protein of Ebola and Marburg viruses using de novo fragment assembly Three of the four nucleocapsid proteins of Marburg virus, NP, VP35, and L, are sufficient to mediate replication and transcription of Marburg virus-specific monocistronic minigenomes Ultrastructural organization of recombinant Marburg virus nucleoprotein: comparison with Marburg virus inclusions Morphology of Marburg virus NP-RNA Nucleocapsid formation and RNA synthesis of Marburg virus is dependent on two coiled coil motifs in the nucleoprotein Characterization of filovirus protein-protein interactions in mammalian cells using bimolecular complementation Genus-specific recruitment of filovirus ribonucleoprotein complexes into budding particles The nucleoprotein of Marburg virus is phosphorylated The nucleoprotein of Marburg virus is target for multiple cellular kinases Phosphorylation of Marburg virus NP region II modulates viral RNA synthesis Comparison of the transcription and replication strategies of marburg virus and Ebola virus by using artificial replication systems Homo-oligomerization of Marburgvirus VP35 is essential for its function in replication and transcription Co-and posttranslational modifications and functions of Marburg virus proteins Ebola and Marburg viruses replicate in monocyte-derived dendritic cells without inducing the production of cytokines and full maturation A C-terminal basic amino acid motif of Zaire ebolavirus VP35 is essential for type I interferon antagonism and displays high identity with the RNA-binding domain of another interferon antagonist, the NS1 protein of influenza A virus Phosphorylation of VP30 Impairs Ebola Virus transcription Phosphorylation of Marburg virus VP30 at serines 40 and 42 is critical for its interaction with NP inclusions Ebola virus transcription activator VP30 is a zinc-binding protein Oligomerization of Ebola virus VP30 is essential for viral transcription and can be inhibited by a synthetic peptide Crystal structure of the C-terminal domain of Ebola virus VP30 reveals a role in transcription and nucleocapsid association The Ebola Virus VP30 is an RNA Binding Protein The Ebola virus ribonucleoprotein complex: a novel VP30-L interaction identified Ebola Virus VP30-Mediated Transcription Is Regulated by RNA Secondary Structure Formation Role of Ebola virus VP30 in transcription reinitiation Role of VP30 phosphorylation in the Ebola virus replication cycle Rescue of recombinant Marburg virus from cDNA is dependent on nucleocapsid protein VP30 Inhibition of Marburg virus protein expression and viral release by RNA interference Transcription elongation factor of respiratory syncytial virus, a nonsegmented negative-strand RNA virus Sequence comparison of five polymerases (L proteins) of unsegmented negative-strand RNA viruses: theoretical assignment of functional domains Characterization of the receptor-binding domain of Ebola glycoprotein in viral entry Comprehensive analysis of ebola virus GP1 in viral entry Structural basis for membrane fusion by enveloped viruses Covalent modifications of the ebola virus glycoprotein LSECtin interacts with filovirus glycoproteins and the spike protein of SARS coronavirus The DC-SIGN-related lectin LSECtin mediates antigen capture and pathogen binding by human myeloid cells Lentivirus vectors pseudotyped with filoviral envelope glycoproteins transduce airway epithelia from the apical surface independently of folate receptor alpha Association of the caveola vesicular system with cellular entry by filoviruses Folate receptor alpha and caveolae are not required for Ebola virus glycoprotein-mediated viral infection Differential requirements for clathrin endocytic pathway components in cellular entry by Ebola and Marburg glycoprotein pseudovirions Analysis of filovirus entry into vero e6 cells, using inhibitors of endocytosis, endosomal acidification, structural integrity, and cathepsin (B and L) activity Ebola virus enters host cells by macropinocytosis and clathrinmediated endocytosis VP24 inhibits transcription and replication of the EBOV genome Ebola virus matrix protein VP40 uses the COPII transport system for its intracellular transport Budding of Marburgvirus is associated with filopodia Electron tomography reveals the steps in filovirus budding Recombinant Marburg virus expressing EGFP allows rapid screening of virus growth and real-time visualization of virus spread Basolateral budding of Marburg virus: VP40 retargets viral glycoprotein GP to the basolateral surface Marburg virus and mononuclear phagocytes: study of interactions) Cellular immune response to Marburg virus infection in cynomolgus macaques Pathogenesis of Marburg hemorrhagic fever in cynomolgus macaques Development of a model for marburgvirus based on severe-combined immunodeficiency mice Ebola virus infection in guinea pigs: Presumable role of granulomatous inflammation in pathogenesis Marburg hemorrhagic fever: report of a case studied by immunohistochemistry and electron microscopy Filovirusinduced endothelial leakage triggered by infected monocytes/macrophages Breakdown of paraendothelial barrier function during Marburg virus infection is associated with early tyrosine phosphorylation of platelet endothelial cell adhesion molecule-1 Infection and activation of monocytes by Marburg and Ebola viruses Apoptosis induced in vitro and in vivo during infection by Ebola and Marburg viruses
    keywords: budding; cells; disease; ebola; ebola virus; ebov; entry; fever; figure; filovirus; human; infected; infection; marburg; marburg virus; marv; nucleocapsid; protein; replication; rna; role; transcription; virus; viruses; vp35; vp40
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        item: #32 of 1349
          id: cord-000822-iuglkdcp
      author: Sperschneider, Jana
       title: Predicting pseudoknotted structures across two RNA sequences
        date: 2012-12-01
       words: 5496
      flesch: 55
     summary: Single sequence structure prediction is always limited by the accuracy of the underlying folding model. The prediction results for single sequence structure prediction for each of the reference sequences with experimentally determined structures are also shown in Table 1 .
    keywords: alignment; dotknot; elements; prediction; pseudoknot; rna; sequence; structure
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        item: #33 of 1349
          id: cord-000830-jiy4cp4n
      author: Cobo, Fernando
       title: Application of Molecular Diagnostic Techniques for Viral Testing
        date: 2012-11-30
       words: 7970
      flesch: 35
     summary: An international collaborative study to establish a World Health Organization international standard for hepatitis B virus DNA nucleic acid amplification techniques The clinical implications of hepatitis B virus genotype: recent advances Hepatitis C virus RNA assays: current and emerging technologies and their clinical applications Identifying women with cervical neoplasia: Using human papillomavirus DNA testing for equivocal Papanicolaou results Declared none. Both ligated products can then serve as templates for the next reaction cycle, leading to an exponential amplification process similar to PCR amplification.
    keywords: acid; amplification; assays; detection; diagnosis; dna; laboratory; methods; nucleic; pcr; reaction; rna; target; techniques; time; virus; viruses
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        item: #34 of 1349
          id: cord-000866-dr2uow4m
      author: Picard-Jean, Frédéric
       title: The Immunosuppressive Agent Mizoribine Monophosphate Is an Inhibitor of the Human RNA Capping Enzyme
        date: 2013-01-17
       words: 7085
      flesch: 43
     summary: In silico docking of MZP on the highly conserved active site of an open conformation homology model of HCE GTase domain provides additional information on the mechanism of MZP binding to this site ( Fig. S4 and Table S1 ). The protein concentration was determined by the Bio-Rad dye binding method and stored at 280uC. The amino acids 1-219 corresponding to HCE RTase domain (HCE-T 1-219 ) and 229-597 corresponding to HCE GTase domain (HCE-G 229-597 ) were also expressed separately using the same procedure.
    keywords: activity; capping; domain; enzyme; gtase; hce; inhibition; mizoribine; mrna; mzp; protein; reaction; rna
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        item: #35 of 1349
          id: cord-000881-s90geszi
      author: Lang, Dorothy M.
       title: Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases
        date: 2012-12-25
       words: 9729
      flesch: 53
     summary: It would be interesting to explore the possibility that interactions at the surface of the protein (e.g. protein-protein contact at surface homomorph residues) may subtly affect function buried deep beneath, within the tunnel. In total, 18 well-studied viral species with solved RNA polymerase structures and four viral species with solved DNA polymerase structures were selected for analysis.
    keywords: conserved; et al; figure; homomorph; motif; polymerase; protein; residues; rna; segment; sequence; species; structure; terminal
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        item: #36 of 1349
          id: cord-000895-z5rdf0mi
      author: Belalov, Ilya S.
       title: Causes and Implications of Codon Usage Bias in RNA Viruses
        date: 2013-02-25
       words: 5459
      flesch: 39
     summary: A series of in silico shuffling algorithms were developed to account for these features and analyze the relative impact of mutational pressure components on codon usage bias in RNA viruses. The algorithms presented here provide a substantial improvement in dissecting origins of codon usage bias in RNA viruses.
    keywords: bias; codon; content; dinucleotide; enc; position; rna; usage; viruses
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        item: #37 of 1349
          id: cord-000937-8vk89i4h
      author: Law, John
       title: Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool
        date: 2013-04-17
       words: 6656
      flesch: 45
     summary: To a lesser extent (about one read per million), we also detected sequences resembling RNA viruses in our DNA libraries (Supplemental Tables S15-S28 ). This may represent alignment inaccuracies or stretches of unknown DNA viruses that resemble RNA viruses.
    keywords: dna; ends; figure; hepatitis; libraries; library; patients; plasma; read; rna; samples; sequences; target; viral; viruses
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        item: #38 of 1349
          id: cord-000979-cav9n18w
      author: Hoppe, Sebastian
       title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni
        date: 2013-05-29
       words: 10065
      flesch: 45
     summary: NCBI gene expression and hybridization array data repository Primer3 on the WWW for general users and for biologist programmers Geneious v5 Basic local alignment search tool Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes A hidden Markov model for predicting transmembrane helices in protein sequences A semi-empirical method for prediction of antigenic determinants on protein antigens New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and x-ray derived accessible sites The SWISS-MODEL Workspace: A web-based environment for protein structure homology modeling The SWISS-MODEL Repository and associated resources SWISS-MODEL: an automated protein homology-modeling server SWISS-MODEL and the Swiss-PdbViewer: A case-control study in FoodNet sites Typing of Campylobacter jejuni and Campylobacter coli isolated from live broilers and retail broiler meat by flaA-RFLP, MLST, PFGE and REP-PCR Rapid pulsed-field gel electrophoresis protocol for subtyping of Campylobacter jejuni Evaluation of three commercial latex agglutination tests for identification of Campylobacter spp Molecular Cloning: A Laboratory Manual, Third Edition Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray Immunogenic cross-reaction among outer membrane proteins of Gram-negative bacteria Microarray-based method for screening of immunogenic proteins from bacteria Proteinprotein interactions: analysis of a false positive GST pulldown result HaloTag: a novel protein labeling technology for cell imaging and protein analysis Validation of two ribosomal RNA removal methods for microbial metatranscriptomics Polyadenylic acid sequences in E. coli messenger RNA Identification of the gene for an Escherichia coli poly(A) polymerase A simple method to enrich mRNA from prokaryotic RNA Magnetic capturehybridization method for purification and probing of mRNA for neutral protease of Bacillus cereus Direct detection of recombinant gene expression by two genetically engineered yeasts in soil on the transcriptional and translational level Normalization of full-length-enriched cDNA Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq Ligation-independent cloning of PCR products (LIC-PCR) High efficiency transformation of E. coli by high voltage electroporation The Campylobacter jejuni/coli CjaA (cj0982c) gene encodes an N-glycosylated lipoprotein localized in the inner membrane Genetic diversity of the Campylobacter genes coding immunodominant proteins Immunogenicity and immunoprotection of recombinant PEB1 in Campylobacter-jejuni-infected mice The National Center for Biotechnology Information's Protein Clusters Database Characterization of Genetically Matched Isolates of Campylobacter jejuni Reveals that Mutations in Genes Involved in Flagellar Biosynthesis Alter the Organism's Virulence Potential Nutrient Acquisition and Metabolism by Campylobacter jejuni Identification of Campylobacter jejuni Genes Contributing to Acid Adaptation by Transcriptional Profiling and Genome-Wide Mutagenesis Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures The 2.0 Crystal Structure of ABC Transporter from Thermatoga maritima Toward the estimation of the absolute quality of individual protein structure models Construction and Evaluation of Normalized cDNA
    keywords: antibodies; antibody; antigenic; binding; campylobacter; cdna; epitope; immunodominant; incubation; jejuni; linear; min; pcr; proteins; reaction; rna; screening; sequence; specific
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        item: #39 of 1349
          id: cord-000981-6vloa2w3
      author: Bálint, Zoltán
       title: Double-Stranded RNA Attenuates the Barrier Function of Human Pulmonary Artery Endothelial Cells
        date: 2013-06-03
       words: 6110
      flesch: 45
     summary: Despite the obvious clinical implications associated with the presence of circulating RNA, its pathological effects on endothelial cells and the governing molecular mechanisms are still not fully elucidated. Endothelial cells express toll-like receptor 3 (TLR3)
    keywords: cells; control; dsrna; effect; endothelial; figure; hpaecs; min; permeability; serca; treatment
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        item: #40 of 1349
          id: cord-001090-qg2r691d
      author: Twin, Jimmy
       title: The Potential of Metatranscriptomics for Identifying Screening Targets for Bacterial Vaginosis
        date: 2013-09-27
       words: 3948
      flesch: 37
     summary: Overall, this library consisted of 72826 (93%) bacterial reads, 3865 (4.9%) human reads and 34 (0.04%) either plastid, fungal or viral reads (Table 1) . The metagenomics RAST server -a public resource for the automatic phylogenetic and functional analysis of metagenomes Study of inter-and intra-individual variations in the salivary microbiota Interactive metagenomic visualization in a Web browser Changes in vaginal bacterial concentrations with intravaginal metronidazole therapy for bacterial vaginosis as assessed by quantitative PCR Detection of bacterial vaginosis-related organisms by real-time PCR for Lactobacilli, Gardnerella vaginalis and Mycoplasma hominis Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR Diversity of cervicovaginal microbiota associated with female lower genital tract infections Inverse association of H 2 O 2 -producing lactobacilli and vaginal Escherichia coli colonization in women with recurrent urinary tract infections Broadrange bacterial detection and the analysis of unexplained death and critical illness Stata Statistical Software: Release 12 Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria Evidence for a commensal, symbiotic relationship between Gardnerella vaginalis and Prevotella bivia involving ammonia: potential significance for bacterial vaginosis Prevotella amnii sp.
    keywords: 16s; amnii; cdna; dna; library; prevotella; reads; rrna; study
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        item: #41 of 1349
          id: cord-001109-xs7df6a7
      author: Tapia, Karla
       title: Defective Viral Genomes Arising In Vivo Provide Critical Danger Signals for the Triggering of Lung Antiviral Immunity
        date: 2013-10-31
       words: 7179
      flesch: 43
     summary: Although full-length viral genomes were detected in both YFP + and YFP 2 CD45 2 populations sorted three days after infection, DVGs were only found in YFP + cells (Fig. 5D) , suggesting that the presence of DVGs promotes IFNb production in response to virus infection in vivo. SeV copy-back DVGs trigger a robust and sustained activation of IRF3 and NF-kB independent of type I IFN feedback To further investigate the cellular mechanisms responsible for the efficient activation of the antiviral response by SeV DVGs, we evaluated the phosphorylation of transcription factors that are critical for the expression of type I IFNs in cells infected with equivalent amounts of infectious particles of a SeV strain Cantell stock containing high levels of copy-back DVGs (SeV Cantell HD) or with SeV Cantell depleted of DVGs (SeV Cantell LD).
    keywords: cantell; cells; copy; dvgs; fig; ifn; infection; response; rna; sev; type; virus
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        item: #42 of 1349
          id: cord-001152-v6uc0ijw
      author: Girardi, Erika
       title: Identification of RNase L-Dependent, 3′-End-Modified, Viral Small RNAs in Sindbis Virus-Infected Mammalian Cells
        date: 2013-11-19
       words: 7036
      flesch: 45
     summary: Hence, we transfected siRNAs against Drosha, Dicer, or Ago2 followed by an infection with SINV and an analysis of viral small RNA accumulation. Small RNA cloning and sequencing.
    keywords: cells; fig; genome; genomic; infection; reads; rna; rnas; sequencing; sinv; small; svsrna-1; virus
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        item: #43 of 1349
          id: cord-001228-4eh22ek7
      author: Ofori, Leslie O.
       title: High-Affinity Recognition of HIV-1 Frameshift-Stimulating RNA Alters Frameshifting in Vitro and Interferes with HIV-1 Infectivity
        date: 2014-01-05
       words: 6309
      flesch: 46
     summary: All titrations started at a volume of 500 μL with the compound at 1 μM. RNA was then titrated in from a highconcentration stock (10 μM for HIV-1 FSS RNA; 40 μM for HIV-1 FSS DNA and tRNA) in 1−10 μL increments. While an RNA stem-loop structure (the “HIV-1 Frameshift Stimulating Signal”, or HIV-1 FSS) controls the frameshift efficiency and has been hypothesized as an attractive therapeutic target, developing compounds that selectively bind this RNA and interfere with HIV-1 replication has proven challenging.
    keywords: affinity; assay; binding; cells; compounds; frameshift; frameshifting; fss; gag; pol; rna; stem; virus
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        item: #44 of 1349
          id: cord-001257-t21l6i3f
      author: Kovalev, Nikolay
       title: The Expanding Functions of Cellular Helicases: The Tombusvirus RNA Replication Enhancer Co-opts the Plant eIF4AIII-Like AtRH2 and the DDX5-Like AtRH5 DEAD-Box RNA Helicases to Promote Viral Asymmetric RNA Replication
        date: 2014-04-17
       words: 10662
      flesch: 50
     summary: Yeast as a model host to explore plant virus-host interactions Cytoplasmic viral replication complexes The dependence of viral RNA replication on coopted host factors +)RNA viruses rewire cellular pathways to build replication organelles Yeast as a model host to dissect functions of viral and host factors in tombusvirus replication Host factors involved in West Nile virus replication Viral and cellular proteins involved in coronavirus replication Emerging picture of host chaperone and cyclophilin roles in RNA virus replication Hepatitis C virus replication cycle Virus factories: associations of cell organelles for viral replication and morphogenesis Virus factories: biogenesis and structural design Diverse roles of host RNA binding proteins in RNA virus replication Non-Templated Functions of Viral RNA in Picornavirus Replication Yeast as a model host to study replication and recombination of defective interfering RNA of Tomato bushy stunt virus Purification of the cucumber necrosis virus replicase from yeast cells: role of coexpressed viral RNA in stimulation of replicase activity Role of an internal and two 39-terminal RNA elements in assembly of tombusvirus replicase Specific Binding of Tombusvirus Replication Protein p33 to an Internal Replication Element in the Viral RNA Is Essential for Replication Multiple roles of viral replication proteins in plant RNA virus replication Defining the Roles of cis-Acting RNA Elements in Tombusvirus Replicase Assembly In Vitro A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA-based regulation of viral processes Tomato bushy stunt virus Co-Opts the RNA-Binding Function of a Host Metabolic Enzyme for Viral Genomic RNA Synthesis A temperature sensitive mutant of heat shock protein 70 reveals an essential role during the early steps of tombusvirus replication A key role for heat shock protein 70 in the localization and insertion of tombusvirus replication proteins to intracellular membranes In vitro assembly of the Tomato bushy stunt virus replicase requires the host Heat shock protein 70 Proteomics analysis of the tombusvirus replicase: Hsp70 molecular chaperone is associated with the replicase and enhances viral RNA replication Ubiquitin-Conjugating Enzyme Is a Component of the Tombusvirus Replicase Complex and Ubiquitinates p33 Replication Protein Translation elongation factor 1A facilitates the assembly of the tombusvirus replicase and stimulates minus-strand synthesis Translation elongation factor 1A is a component of the tombusvirus replicase complex and affects the stability of the p33 replication co-factor Synergistic Roles of Eukaryotic Translation Elongation Factors 1Bgamma and 1A in Stimulation of Tombusvirus Minus-Strand Synthesis A Co-Opted DEAD-Box RNA Helicase Enhances Tombusvirus Plus-Strand Synthesis yeast and human STRESS RESPONSE SUPPRESSOR1 and STRESS RESPONSE SUPPRESSOR2, two DEAD-box RNA helicases that attenuate Arabidopsis responses to multiple abiotic stresses SDE3 encodes an RNA helicase required for post-transcriptional gene silencing in Arabidopsis Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences Role of RNA chaperones in virus replication Similar roles for yeast Dbp2 and Arabidopsis RH20 DEAD-box RNA helicases to Ded1 helicase in tombusvirus plus-strand synthesis Dbp3p, a putative RNA helicase in Saccharomyces cerevisiae, is required for efficient pre-rRNA processing predominantly at site A3 Duplex destabilization by four ribosomal DEAD-box proteins Human eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex Yeast screens for host factors in positive-strand RNA virus replication based on a library of temperature-sensitive mutants Proteome-wide overexpression of host proteins for identification of factors affecting tombusvirus RNA replication: an inhibitory role of protein kinase C An internally located RNA hairpin enhances replication of Tomato bushy stunt virus RNAs The RNA replication enhancer element of tombusviruses contains two interchangeable hairpins that are functional during plus-strand synthesis Mechanism of stimulation of plus-strand synthesis by an RNA replication enhancer in a tombusvirus RNA chaperone activity of the tombusviral p33 replication protein facilitates initiation of RNA synthesis by the viral RdRp in vitro Use of double-stranded RNA templates by the tombusvirus replicase in vitro: Implications for the mechanism of plus-strand initiation Internal initiation by the cucumber necrosis virus RNA-dependent RNA polymerase is facilitated by promoter-like sequences Mechanism of DI RNA formation in tombusviruses: dissecting the requirement for primer extension by the tombusvirus RNA dependent RNA polymerase in vitro Partial purification and characterization of Cucumber necrosis virus and Tomato bushy stunt virus RNA-dependent RNA polymerases: similarities and differences in template usage between tombusvirus and carmovirus RNA-dependent RNA polymerases Authentic replication and recombination of Tomato bushy stunt virus RNA in a cell-free extract from yeast The p92 polymerase coding region contains an internal RNA element required at an early step in Tombusvirus genome replication Composition of plant virus RNA replicase complexes Global organization of a positive-strand RNA virus genome Yeast and human RNA helicases involved in ribosome biogenesis: current status and perspectives A genome-wide analysis of the RNA helicase gene family in Solanum lycopersicum Viral RNA replication in association with cellular membranes De novo initiation of viral RNA-dependent RNA synthesis Filling a GAP(DH) in asymmetric viral RNA synthesis Characterization of the RNA-binding domains in the replicase proteins of tomato bushy stunt virus Direct inhibition of tombusvirus plus-strand RNA synthesis by a dominant-negative mutant of a host metabolic enzyme, GAPDH, in yeast and plants Distinct DDX DEAD-box RNA helicases cooperate to modulate the HIV-1 Rev function From promoting to inhibiting: diverse roles of helicases in HIV-1 Replication Viruses and the human DEAD-box helicase DDX3: inhibition or exploitation?
    keywords: assay; atrh5; fig; helicases; host; like; p33; proteins; ren; replicase; replication; rna; synthesis; tbsv; tombusvirus; viral; yeast
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        item: #45 of 1349
          id: cord-001397-nrq4ncdf
      author: Mlera, Luwanika
       title: The role of viral persistence in flavivirus biology
        date: 2014-05-12
       words: 15612
      flesch: 33
     summary: (Appler et al., 2010; Pierson & Diamond, 2012) : WNV RNA persisted in a pantropic manner in 12% of infected mice for up to 6 months. In this study, infectious virus was recovered in the skin, and viral RNA was identified in the skin, as well as the spinal cord and brain (Appler et al., 2010) .
    keywords: animals; antibodies; cells; dengue; encephalitis; encephalitis virus; et al; flavivirus; host; ifn; infected; infection; jev; mice; mosquitoes; nile; nile virus; ns1; ns3; ns5; persistence; protein; replication; rna; role; study; tbev; tick; transmission; virus; virus infection; west; wnv
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        item: #46 of 1349
          id: cord-001453-l1r416w7
      author: Hou, Linlin
       title: Archaeal DnaG contains a conserved N-terminal RNA-binding domain and enables tailing of rRNA by the exosome
        date: 2014-11-10
       words: 8382
      flesch: 46
     summary: Genes encoding archaeal DnaG proteins are found in all genome-sequenced archaea regardless of presence or absence of an exosome (2, 44) . We conclude that the NTD of S. solfataricus DnaG is a novel, conserved archaeal RNA binding domain and its K6 and Y7 residues are important for binding of RNA.
    keywords: archaeal; binding; csl4; csl4 exosome; degradation; dnag; domain; exosome; figure; protein; rna; rrna
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        item: #47 of 1349
          id: cord-001521-l36f1gp7
      author: None
       title: Oral and Poster Manuscripts
        date: 2011-04-08
       words: 183853
      flesch: 46
     summary: The concept that swine are a mixing-vessel for the reassortment of influenza viruses and for the emergence of pandemic influenza viruses has been re-enforced by the emergence of the recent pandemic. This study was supported by Contract HHSN266200700005C from the National Institute of Allergy and Infectious Diseases, National Institutes of Pigs have been considered as hypothetical 'mixing vessels' facilitating the genesis of pandemic influenza viruses.
    keywords: age; analysis; animals; antibodies; antibody; antiviral; assay; associated; avian; b viruses; b ⁄; balb ⁄; binding; c virus; c ⁄; cases; cells; challenge; children; control; cross; culture; data; days; detection; disease; dk ⁄; dose; effect; ferrets; figure; following; gene; group; h1n1 influenza; h1n1 pandemic; h1n1 virus; h5n1 infection; h5n1 viruses; h9n2; health; high; hong; hours; human h1n1; human influenza; humans; immunity; infected; infections; influenza antigenic; influenza c; influenza epidemic; influenza infection; influenza influenza; influenza neuraminidase; influenza outbreaks; influenza pandemic; influenza patients; influenza research; influenza samples; influenza season; influenza strains; influenza surveillance; influenza transmission; influenza vaccination; influenza vaccine; influenza virus; isolates; kong ⁄; laboratory; laiv; lg ⁄; like; low; lung; mallard ⁄; mdck; method; mg ⁄; mice; model; mutation; nasal; new; non; novel; number; observed; origin influenza; oseltamivir; patients; pcr; period; pigs; population; positive; post; potential; potsdam ⁄; protection; protein; public; rate; research; resistance; respiratory; response; results; risk; rna; samples; school; seasonal; sensitivity; sequence; serum; severe; specific; specimens; studies; study; subjects; subtype influenza; sw ⁄; swine influenza; swine viruses; system; t ⁄; table; test; time; treatment; type virus; vaccines; values; virus gene; virus infection; virus isolation; virus ns1; virus replication; virus strains; virus titers; virus transmission; virus vaccine; virus ⁄; viruses; wave; years; ⁄ brisbane; ⁄ california; ⁄ genoa; ⁄ h1n1; ⁄ h3n2; ⁄ h5n1; ⁄ hk; ⁄ hok; ⁄ lee; ⁄ leningrad; ⁄ ml; ⁄ netherlands; ⁄ ns1; ⁄ panama; ⁄ pr8; ⁄ vietnam
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        item: #48 of 1349
          id: cord-001541-5d64esp4
      author: Walker, Peter J.
       title: Evolution of Genome Size and Complexity in the Rhabdoviridae
        date: 2015-02-13
       words: 9158
      flesch: 41
     summary: Despite their diversity, RNA virus genomes are ubiquitously small, averaging only 10 kb, and with a maximum size of~32 kb for some members of the order Nidovirales [3, 4] . In this study, we greatly expanded the repertoire of rhabdovirus genome sequences, which demonstrate extensive variation in genome size and complexity, allowing the assignment of seven proposed new genera.
    keywords: alternative; amino; data; evolution; expression; fig; gene; genera; genome; orfs; proteins; rhabdovirus; rna; sequence; size; transcriptional; units; viruses
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        item: #49 of 1349
          id: cord-001542-f089bs8r
      author: Lai, Kang Yiu
       title: Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus
        date: 2014-11-28
       words: 11294
      flesch: 36
     summary: implications for vaccines and therapies Proinflammatory response during Ebola virus infection of primate models: possible involvement of the tumor necrosis factor receptor superfamily Ebola virus selectively inhibits responses to interferons, but not to interleukin-1beta, in endothelial cells Inflammatory responses in Ebola virus-infected patients Human asymptomatic Ebola infection and strong inflammatory response Infection and activation of monocytes by Marburg and Ebola viruses Monocyte-derived human macrophages and peripheral blood mononuclear cells infected with ebola virus secrete MIP-1alpha and TNF-alpha and inhibit poly-ICinduced IFN-alpha in vitro Markedly elevated levels of interferon (IFN)-gamma, IFN-alpha, interleukin (IL)-2, IL-10, and tumor necrosis factor-alpha associated with fatal Ebola virus infection Pathogenesis of Ebola hemorrhagic fever in primate models: evidence that hemorrhage is not a direct effect of virus-induced cytolysis of endothelial cells Ebola virus glycoprotein toxicity is mediated by a dynamin-dependent protein-trafficking pathway Filovirus-induced endothelial leakage triggered by infected monocytes/ macrophages Ebola virus glycoproteins induce global surface protein down-modulation and loss of cell adherence Requirements for cell rounding and surface protein down-regulation by Ebola virus glycoprotein Mechanisms underlying coagulation abnormalities in ebola hemorrhagic fever: overexpression of tissue factor in primate monocytes/ macrophages is a key event Treatment of Ebola virus infection with a recombinant inhibitor of factor VIIa/tissue factor: a study in rhesus monkeys Recombinant nematode anticoagulant protein c2 and other inhibitors targeting blood coagulation factor VIIa/tissue factor Immunopathology of highly virulent pathogens: insights from Ebola virus Ebola haemorrhagic fever Pathogenesis of viral hemorrhagic fever Pathogenesis of Ebola hemorrhagic fever in cynomolgus macaques: evidence that dendritic cells are early and sustained targets of infection Molecular Basis for Ebola Virus VP35 Suppression of Human Dendritic Cell Maturation Ebola virus: the role of macrophages and dendritic cells in the pathogenesis of Ebola hemorrhagic fever The role of antigen-presenting cells in filoviral hemorrhagic fever: gaps in current knowledge Human fatal zaire ebola virus infection is associated with an aberrant innate immunity and with massive lymphocyte apoptosis Mechanisms and consequences of ebolavirus-induced lymphocyte apoptosis Ebola virus does not block apoptotic signaling pathways Characterization of host immune responses in Ebola virus infections Filoviruses and the balance of innate, adaptive, and inflammatory responses Functional CD8+ T cell responses in lethal Ebola virus infection CD8-mediated protection against Ebola virus infection is perforin dependent Induction of humoral and CD8+ T cell responses are required for protection against lethal Ebola virus infection Induction of immune responses in mice and monkeys to Ebola virus after immunization with liposome-encapsulated irradiated Ebola virus: protection in mice requires CD4(+) T cells Cutting edge: impairment of dendritic cells and adaptive immunity by Ebola and Lassa viruses Correlates of immunity to filovirus infection The Multiple Roles of sGP in Ebola Pathogenesis Ebolavirus glycoprotein GP masks both its own epitopes and the presence of cellular surface proteins Steric shielding of surface epitopes and impaired immune recognition induced by the ebola virus glycoprotein Influences of glycosylation on antigenicity, immunogenicity, and protective efficacy of ebola virus GP DNA vaccines Antibody-dependent enhancement of viral infection: molecular mechanisms and in vivo implications Infectivity-enhancing antibodies to Ebola virus glycoprotein Antibody-dependent enhancement of Ebola virus infection Epitopes required for antibody-dependent enhancement of Ebola virus infection Ebola virus can be effectively neutralized by antibody produced in natural human infection Structural basis for differential neutralization of ebolaviruses. Ethical considerations for use of unregistered interventions for Ebola viral disease Emerging targets and novel approaches to Ebola virus prophylaxis and treatment World Health Organization: potential Ebola therapies and vaccines Clinical features and pathobiology of Ebolavirus infection Ebola virus: unravelling pathogenesis to combat a deadly disease Delta-peptide is the carboxyterminal cleavage fragment of the nonstructural small glycoprotein sGP of Ebola virus The glycoproteins of Marburg and Ebola virus and their potential roles in pathogenesis Release of viral glycoproteins during Ebola virus infection The secret life of viral entry glycoproteins: moonlighting in immune evasion The pathogenesis of Ebola hemorrhagic fever Role of Ebola virus secreted glycoproteins and virus-like particles in activation of human macrophages Identification of the Ebola virus glycoprotein as the main viral determinant of vascular cell cytotoxicity and injury Shed GP of Ebola Virus Triggers Immune Activation and Increased Vascular Permeability Ebola virus glycoprotein counteracts BST-2/Tetherin restriction in a sequence-independent manner that does not require tetherin surface removal Anti-tetherin activities of HIV-1 Vpu and Ebola virus glycoprotein do not involve removal of tetherin from lipid rafts Ebolavirus Replication and Tetherin/BST-2 The nonstructural small glycoprotein sGP of Ebola virus is secreted as an antiparallel-orientated homodimer Antigenic subversion: a novel mechanism of host immune evasion by Ebola virus A novel mechanism of immune evasion mediated by Ebola virus soluble glycoprotein Distinct cellular interactions of secreted and transmembrane Ebola virus glycoproteins Ebola virus secretory glycoprotein (sGP) diminishes Fc gamma RIIIB-to-CR3 proximity on neutrophils Effects of Ebola virus glycoproteins on endothelial cell activation and barrier function Ebola virus glycoprotein GP is not cytotoxic when expressed constitutively at a moderate level Ebolavirus delta-peptide immunoadhesins inhibit marburgvirus and ebolavirus cell entry A new Ebola virus nonstructural glycoprotein expressed through RNA editing Ebola virus enters host cells by macropinocytosis and clathrin-mediated endocytosis The Ebola virus glycoprotein mediates entry via a non-classical dynamindependent
    keywords: amiodarone; antibodies; antibody; cell; ebola; ebola virus; ebov; ebov infection; entry; glycoprotein; gp1,2; host; human; infection; interferon; proteins; replication; rna; therapy; treatment; virus; virus infection; viruses
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        item: #50 of 1349
          id: cord-001655-uqw74ra0
      author: Stenglein, Mark D.
       title: Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections
        date: 2015-05-20
       words: 8113
      flesch: 45
     summary: In this case, snake arenavirus genotypes could be grouped into one or possibly more species. In all cases there were more L than S segment genotypes (Fig 4and S4 Fig).
    keywords: animals; arenavirus; fig; genome; genotypes; pcr; reads; recombination; rna; samples; segment; sequences; sequencing; snake; virus; viruses
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        item: #51 of 1349
          id: cord-001748-7e8px4vx
      author: Nobach, Daniel
       title: Shedding of Infectious Borna Disease Virus-1 in Living Bicolored White-Toothed Shrews
        date: 2015-08-27
       words: 4889
      flesch: 42
     summary: For the investigation of long lasting virus shedding BoDV-1 infected animals were sampled again after at least more than 250 days in the husbandry. Whether naturally BoDV-1 infected shrews also display subtle deficits in learning, memory and/or social behavior, especially mating, needs to be addressed in further behavioral and breeding experiments.
    keywords: animals; bodv-1; borna; disease; infection; reservoir; shedding; shrews; time; transmission; virus
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        item: #52 of 1349
          id: cord-001829-rwnbxmt4
      author: Lu, Yi-Fan
       title: IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance
        date: 2015-11-04
       words: 7169
      flesch: 40
     summary: A custom analysis pipeline identified all of the sequencing reads from IFNL3 rs4803217 G, IFNL3 rs4803217 T, and IFNL2 mRNAs. key: cord-001829-rwnbxmt4 authors: Lu, Yi-Fan; Mauger, David M.; Goldstein, David B.; Urban, Thomas J.; Weeks, Kevin M.; Bradrick, Shelton S. title: IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance date: 2015-11-04 journal: Sci Rep DOI: 10.1038/srep16037 sha: doc_id: 1829 cord_uid: rwnbxmt4 Polymorphisms near the interferon lambda 3 (IFNL3) gene strongly predict clearance of hepatitis C virus (HCV) infection.
    keywords: allele; cells; expression; fig; hcv; hepatitis; ifnl3; interferon; mrna; reporter; rs4803217; shape; snp; structure; translation; utr
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        item: #53 of 1349
          id: cord-001835-0s7ok4uw
      author: None
       title: Abstracts of the 29th Annual Symposium of The Protein Society
        date: 2015-10-01
       words: 138771
      flesch: 38
     summary: In conclusion, the analysis of hydropathic environments strongly suggests that the orientation of a residue in a three-dimensional structure is a direct consequence of its hydropathic environment, which leads us to propose a new paradigm, interaction homology, as a key factor in protein structure. In computer simulation modeling of protein structure in a solvent medium, explicit, implicit, effectivemedium, approaches are often adopted to incorporate the effects of solvation.
    keywords: acid; activation; activity; addition; affinity; amino; amyloid; analysis; antibodies; antibody; antigen; approach; assay; assembly; associated; bacterial; binding; biology; bonds; cancer; catalytic; cell; cellular; chain; changes; characterization; chemical; chemistry; coli; complex; computational; concentration; conditions; conformation; conserved; control; core; cross; crystal; crystal structure; data; department; determine; development; dimer; disease; disordered; disordered proteins; dna; docking; domain; drug; effect; energy; enzyme; essential; experiments; expression; factors; family; fluorescence; fluorescent protein; formation; forms; fragments; free; functions; gene; group; helix; human; hydrogen; hydrophobic; important; increase; inhibitors; institute; key; kinetic; level; ligand; light; like; lipid; loop; low; major; mass; mechanism; membrane protein; method; model; modification; molecular; molecules; motif; mutant; mutations; n protein; native; nature; new; nmr; non; novel; number; oligomers; order; pathways; peptide; potential; prediction; presence; present; process; processes; properties; protease; protein; protein aggregation; protein association; protein complexes; protein concentration; protein data; protein degradation; protein design; protein domain; protein dynamics; protein engineering; protein evolution; protein expression; protein families; protein folding; protein function; protein interactions; protein interface; protein kinases; protein molecules; protein production; protein sequences; protein stability; protein structure; protein surface; protein tyrosine; provide; range; ray; reaction; receptor; recognition; recombinant; region; regulation; research; residues; response; results; rna; role; self; sequence; set; shows; signal; signaling; simulations; site; size; solution; species; specific; specificity; spectroscopy; stability; state; step; structural; studies; study; substrate; subunit; surface; synthetic; system; target; target protein; tau protein; techniques; temperature; terminal; time; transcription; transfer; transition; transmembrane; type protein; understanding; unfolding; university; use; variants; virus; vitro; wild; work; yeast
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        item: #54 of 1349
          id: cord-001963-4wjvykx7
      author: Liu, Chia-Lin
       title: Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development
        date: 2016-02-26
       words: 5471
      flesch: 48
     summary: Thus, to understand the structural interactions responsible for the RNA recognition by influenza virus NP, we modeled the structure of influenza virus NP in an RNA-bound state (Fig. 8) . The influenza virus RNA synthesis machine: advances in its structure and function The mechanism by which influenza A virus nucleoprotein forms oligomers and binds RNA Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein Mutational analysis of conserved amino acids in the influenza A virus nucleoprotein The crystal structure and RNA-binding of an orthomyxovirus nucleoprotein Identification of influenza A nucleoprotein as an antiviral target Identification of amino acid residues of influenza virus nucleoprotein essential for RNA binding Learning from structure-based drug design and new antivirals targeting the ribonucleoprotein complex for the treatment of influenza Structural basis for the identification of the N-terminal domain of coronavirus nucleocapsid protein as an antiviral target Development of an anti-influenza drug screening assay targeting nucleoproteins with tryptophan fluorescence quenching Modeling the intracellular dynamics of influenza virus replication to understand the control of viral RNA synthesis Structure and sequence analysis of influenza A virus nucleoprotein Structure-based discovery of the novel antiviral properties of naproxen against the nucleoprotein of influenza A virus Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding Influenza viruses: basic biology and potential drug targets Comparison of central nervous system adverse effects of amantadine and rimantadine used as sequential prophylaxis of influenza A in elderly nursing home patients Oseltamivir, zanamivir and amantadine in the prevention of influenza: a systematic review Multidrug-resistant 2009 pandemic influenza A(H1N1) viruses maintain fitness and transmissibility in ferrets Nuclear traffic of influenza virus proteins and ribonucleoprotein complexes Oligomerization of the carboxyl terminal domain of the human coronavirus 229E nucleocapsid protein High-throughput identification of compounds targeting influenza RNA-dependent RNA polymerase activity Inhibition of influenza virus replication via small molecules that induce the formation of higher-order nucleoprotein oligomers E339…R416 salt bridge of nucleoprotein as a feasible target for influenza virus inhibitors Therapeutic roles of curcumin: lessons learned from clinical trials Correction of inner-filter effect in fluorescence excitation-emission matrix spectrometry using Raman scatter Identification of BPR3P0128 as an inhibitor of cap-snatching activities of influenza virus Crystallography & NMR system: A new software suite for macromolecular structure determination New parameters for the refinement of nucleic acidcontaining structures AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR resonance, circular dichroism spectroscopy, and fluorescence spectroscopy experiments.
    keywords: binding; cells; influenza; nps; protein; rna; viral; virus; y148
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        item: #55 of 1349
          id: cord-001964-iy6qzq58
      author: Muñoz-González, Sara
       title: Classical Swine Fever Virus vs. Classical Swine Fever Virus: The Superinfection Exclusion Phenomenon in Experimentally Infected Wild Boar
        date: 2016-02-26
       words: 6947
      flesch: 42
     summary: Samples from animal 1 (Group A: Margarita acutely infected wild boar; 10 dpi), animal 5 (Group B: Cat01 persistently infected wild boar and superinfected with CSFV Margarita strain; 13 dpi), and a Pestivirus-free wild boar (animal 1 before infection), were used to assess SIE in PBMCs (Fig 1) . Furthermore, the samples analysed from superinfected animals (Group B: CSFV Catalonia 01 persistently infected inoculated with CSFV Margarita strain) only showed the sequence corresponding to the Cat01 strain [30] (Fig 4) .
    keywords: animals; cells; csfv; fever; group; ifn; infection; margarita; rna; samples; strain; swine; virus
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        item: #56 of 1349
          id: cord-001985-iwfidoer
      author: Urayama, Syun-ichi
       title: FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance
        date: 2016-02-13
       words: 5024
      flesch: 40
     summary: This novel dsRNA targeting metagenomic method is characterized by an extremely high recovery rate of viral RNA sequences, the retrieval of terminal sequences, and uniform read coverage, which has not previously been reported in other metagenomic methods targeting RNA viruses. Microbes Environ DOI: 10.1264/jsme2.me15171 sha: doc_id: 1985 cord_uid: iwfidoer Knowledge of the distribution and diversity of RNA viruses is still limited in spite of their possible environmental and epidemiological impacts because RNA virus-specific metagenomic methods have not yet been developed.
    keywords: cdna; contigs; diatom; dsrna; flds; genome; method; reads; rna; sequences; terminal; total; viral; viruses
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        item: #57 of 1349
          id: cord-002006-pwlybr2h
      author: Liu, Yuan-yuan
       title: Specific interference shRNA-expressing plasmids inhibit Hantaan virus infection in vitro and in vivo
        date: 2016-03-14
       words: 3924
      flesch: 45
     summary: At 24 h after transfection, the cells were infected with 100 TCID 50 HTNV 76-118 (100 μL per well), and viral RNA was detected by qRT-PCR at 24 or 48 hour post-infection (hpi) to determine the interference efficiency. DMEM containing 2% FBS was used to maintain the medium after viral infection.
    keywords: cells; dpi; hantavirus; htnv; infection; psilencer; rna; rnai; shrna; virus
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        item: #58 of 1349
          id: cord-002015-s3tdllby
      author: Burton, Aaron S.
       title: The elusive quest for RNA knots
        date: 2016-02-01
       words: 3539
      flesch: 47
     summary: It also appears plausible that RNA knots, and other forms of entanglement, are not favored thermodynamically. Although RNA knots may be elusive today, it is conceivable that they were important in earlier evolutionary stages, even during the origins of life.
    keywords: dna; knots; knotted; proteins; rna; rnas; sequences; structures
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        item: #59 of 1349
          id: cord-002045-m44fic4g
      author: Horie, Masayuki
       title: An RNA-dependent RNA polymerase gene in bat genomes derived from an ancient negative-strand RNA virus
        date: 2016-05-13
       words: 4813
      flesch: 54
     summary: coronaviruses, paramyxoviruses, filoviruses, and influenza viruses Diseases and causes of death in European bats: dynamics in disease susceptibility and infection rates New adenovirus in bats CENSOR-a program for identification and elimination of repetitive elements from DNA sequences T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension Pfam: the protein families database MAFFT multiple sequence alignment software version 7: improvements in performance and usability Molecular Evolutionary Genetics Analysis version 6.0 PAML 4: phylogenetic analysis by maximum likelihood Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees A time-calibrated species-level phylogeny of bats (Chiroptera, Mammalia) Because the database search did not provide any information for the efEBLL-1 orthology, we searched for orthologous efEBLL-1 sequences in vesper bat genome sequences that were not yet deposited in the database: E. serotinus, E. nilssonii, Pipisterillus spec, Nyctalus noctula and M. daubentonii.
    keywords: acid; amino; bat; bornavirus; efebll-1; fig; proteins; rna; sequences; species; supp
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        item: #60 of 1349
          id: cord-002102-0zbp3uqf
      author: Rasche, Andrea
       title: Hepatitis E Virus Infection in Dromedaries, North and East Africa, United Arab Emirates, and Pakistan, 1983–2015
        date: 2016-07-17
       words: 1700
      flesch: 48
     summary: The global prevalence of hepatitis E virus infection and susceptibility: a systematic review New hepatitis E virus genotype in camels, the Middle East Consensus proposals for classification of the family Hepeviridae Chronic infection with camelid hepatitis E virus in a liver transplant recipient who regularly consumes camel meat and milk Antibodies against MERS coronavirus in dromedary camels MERS coronavirus neutralizing antibodies in camels Antibodies against MERS coronavirus in dromedary camels Bats worldwide carry hepatitis E virus-related viruses that form a putative novel genus within the family Hepeviridae In silico and in vitro interrogation of a widely used HEV RT-qPCR assay for detection of the species orthohepevirus A World Health Organization International Standard to harmonize assays for detection of hepatitis E virus RNA Consensus proposals for classification of the family Hepeviridae Characterization of self-assembled virus-like particles of dromedary camel hepatitis E virus generated by recombinant baculoviruses Age-related and regional differences in the prevalence of hepatitis E virus-specific antibodies in pigs in Germany Proposed reference sequences for hepatitis E virus subtypes Camel meat and meat products Wallingford (UK): CAB International We thank Monika Eschbach-Bludau, Sebastian Brünink, and Tobias Bleicker for providing excellent technical assistance. New camel HEV sequences obtained in this study are in red.
    keywords: dromedaries; hepatitis; hev; human; samples; virus
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        item: #61 of 1349
          id: cord-002179-v8lpw4r7
      author: Viktorovskaya, Olga V.
       title: Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements
        date: 2016-08-24
       words: 8043
      flesch: 41
     summary: [13] exploited a cross-linking label-free MS approach to identify DENV RNA associating proteins in cell culture by cross-linking the RNA to the proteins using short wavelength UV light and isolating DENV RNA bound proteins by anti-sense DNA affinity capture [74] . The overall down-regulation of RNA binding proteins appears to be driven by changes in cytoplasmic and mitochondrial ribosomal subunits, and proteins involved in RNA degradation and processing (S5 Fig).
    keywords: amplification; analysis; binding; cells; cross; dengue; denv; factors; fig; hnrnp; host; infection; proteins; qtux; replication; rna; virus
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        item: #62 of 1349
          id: cord-002180-gsdk5x3e
      author: Davies, Colin
       title: Expression of the NS5 (VPg) Protein of Murine Norovirus Induces a G1/S Phase Arrest
        date: 2016-08-24
       words: 4504
      flesch: 49
     summary: In this study, we show that expression of viral NS5 protein in cell culture induces an accumulation of cells in the G 0 /G This study identified that NS5 (VPg), is capable of inducing cell cycle arrest in the absence of viral replication or other viral proteins in an analogous manner to MNV-1 infection.
    keywords: cell; cycle; expression; host; ns5; phase; protein; rna; viral
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        item: #63 of 1349
          id: cord-002222-rgqwm3vb
      author: Olarte-Castillo, Ximena A.
       title: Divergent Sapovirus Strains and Infection Prevalence in Wild Carnivores in the Serengeti Ecosystem: A Long-Term Study
        date: 2016-09-23
       words: 7547
      flesch: 39
     summary: Information on sapovirus infection of wildlife is limited and is currently lacking for any free-ranging wildlife species in Africa. The likelihood of sapovirus infection decreased with increasing hyena group size, suggesting an encounter reduction effect, but was independent of socially mediated ano-genital contact, or the extent of the area over which an individual roamed.
    keywords: clan; days; hyenas; individuals; infection; likelihood; prevalence; range; samples; sapovirus; serengeti; size; species; strains; study; years
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        item: #64 of 1349
          id: cord-002238-fyztb8d9
      author: Young, D. F.
       title: Human IFIT1 Inhibits mRNA Translation of Rubulaviruses but Not Other Members of the Paramyxoviridae Family
        date: 2016-09-29
       words: 7748
      flesch: 42
     summary: However, IFN pretreatment had no discernible effect on the expression of the NP protein of PIV3 or on the expression of host cell proteins. Increasing concentrations of IFIT1 had no obvious effect on the efficiency of translation of host cell proteins, but in striking contrast, purified IFIT1 selectively inhibited the translation of the NP and M proteins of PIV5 in a concentration-dependent manner.
    keywords: a549; antiviral; cap; cells; ifit1; ifn; inhibition; mrna; paramyxoviruses; piv3; piv5; protein; translation; virus
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        item: #65 of 1349
          id: cord-002312-jyk7f8hz
      author: Branton, W. G.
       title: Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis
        date: 2016-11-28
       words: 4621
      flesch: 33
     summary: Although bacterial peptidoglycan (PGN) and RNA polymerase beta subunit immunoreactivities were observed in all patients, PGN immunodetection was correlated with demyelination and neuroinflammation in MS brains. Proteobacteria represented the chief bacterial phylum detected in human brain with restricted molecular diversity in MS brains despite the increased density of bacterial glycoproteins within demyelinating lesions.
    keywords: analysis; brain; disease; fig; human; matter; nonms; patients; pgn; rna; sequences; white
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        item: #66 of 1349
          id: cord-002320-m99amd4y
      author: Mathur, Kalika
       title: Analysis of chikungunya virus proteins reveals that non-structural proteins nsP2 and nsP3 exhibit RNA interference (RNAi) suppressor activity
        date: 2016-11-30
       words: 5683
      flesch: 48
     summary: Taken together, the current study has identified CHIKV proteins nsP2 and nsP3 to exhibit RNAi suppressor activity in the in-vitro system that was further demonstrated in its natural hosts, namely, an Aedes and mammalian cell line. RNA-based antiviral immunity Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants RNAi function, diversity, and loss in the fungal kingdom Mosquito RNAi is the major innate immune pathway controlling arbovirus infection and transmission Dicing of viral replication intermediates during silencing of latent Drosophila viruses Small silencing RNAs: an expanding universe The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster The rest is silence Dicing and slicing: the core machinery of the RNA interference pathway
    keywords: activity; binding; cell; chikv; gfp; line; motifs; nsp2; nsp3; proteins; rnai; suppressor; virus
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        item: #67 of 1349
          id: cord-002376-970934vm
      author: Mikel, Pavel
       title: Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices
        date: 2016-12-01
       words: 6588
      flesch: 39
     summary: The present article describes the process of preparation and use of such PCV– MS2 phage-like particles (MS2 PLP) – in RT-qPCR detection and quantification of enteric RNA viruses. To evaluate the usefulness of MS2 PLP in routine diagnostics different matrices known to harbor enteric RNA viruses (swab samples, liver tissue, serum, feces, and vegetables) were artificially contaminated with specific amounts of MS2 PLP.
    keywords: control; detection; extraction; ms2; ms2 plp; pcv; plp; qpcr; quantification; rna; samples; viruses
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        item: #68 of 1349
          id: cord-002398-0a3okta0
      author: Myllykoski, Matti
       title: Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase
        date: 2017-01-31
       words: 6162
      flesch: 51
     summary: In addition, a number of LigT complex structures with active-site ligands were solved, hence significantly extending the earlier results on the LigT structure, which was only available as a complex with the reaction product 2 0 -AMP In animals, 2-5As synthesized by 2 0 -5 0 -oligoadenylate synthases 2H enzyme active site structure have functions in innate immunity, whereby they specifically activate RNase L
    keywords: -amp; binding; cnpase; complex; enzyme; fig; ligand; ligt; phosphate; reaction; rna; site; structure; trna
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        item: #69 of 1349
          id: cord-002413-795wuqz5
      author: Balinsky, Corey A.
       title: IRAV (FLJ11286), an Interferon-Stimulated Gene with Antiviral Activity against Dengue Virus, Interacts with MOV10
        date: 2017-02-14
       words: 5495
      flesch: 35
     summary: A Mascot (Matrix Science, Beachwood, OH) search of the data was performed against a concatenated sequence file containing dengue virus proteins found in the UniProtKB TrEMBL database, human protein UniProtKB Swiss-Prot, and the common contaminant proteins found in the GPM.org's cRAP database, all downloaded in March 2014. MOV10 provides antiviral activity against RNA viruses by enhancing RIG-I-MAVS-independent IFN induction Host protein Moloney leukemia virus 10 (MOV10) acts as a restriction factor of influenza A virus by inhibiting the nuclear import of the viral nucleoprotein Up-frameshift protein 1 (UPF1): multitalented entertainer in RNA decay The host nonsense-mediated mRNA decay pathway restricts mammalian RNA virus replication UPF1 is crucial for the infectivity of human immunodeficiency virus type 1 progeny virions Dysregulation of TTP and HuR plays an important role in cancers Changes in cellular mRNA stability, splicing, and polyadenylation through HuR protein sequestration by a cytoplasmic RNA virus HuR displaces polypyrimidine tract binding protein to facilitate La binding to the 3= untranslated region and enhances hepatitis C virus replication Hepatitis B virus X upregulates HuR protein level to stabilize HER2 expression in hepatocellular carcinoma cells HuR and Ago2 bind the internal ribosome entry site of enterovirus 71 and promote virus translation and replication Vaccine candidates derived from a novel infectious cDNA clone of an American genotype dengue virus type 2 Epidemiologic, clinical, and virologic observations on dengue in the Kingdom of Tonga Modulation of Dengue virus infection in human cells by alpha, beta, and gamma interferons Nucleolin interacts with the dengue virus capsid protein and plays a role in formation of infectious virus particles
    keywords: a549; bodies; cells; dengue; denv; fig; gene; infection; interferon; irav; mov10; protein; replication; response; rna; role; virus
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        item: #70 of 1349
          id: cord-002423-1u44tdrj
      author: Geoghegan, Jemma L.
       title: Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families
        date: 2017-02-08
       words: 6186
      flesch: 40
     summary: Specifically, using a normalized tree topology distance metric based on the Penny and Hendy distance metric that enables comparisons between pairs of virus and host trees with different numbers of tips [14] , which we now term the 'nPH85' distance (where n = normalized), we compare phylogenies of virus families and their hosts. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies.
    keywords: data; divergence; families; host; species; transmission; trees; virus; viruses
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        item: #71 of 1349
          id: cord-002439-wesyiymn
      author: Le, My-Tra
       title: Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch
        date: 2017-02-13
       words: 12404
      flesch: 49
     summary: Structural and functional diversity of viral IRESes Molecular dynamics with coupling to an external bath McGenus: a monte carlo algorithm to predict RNA secondary structures with pseudoknots Requirement for host RNA-Silencing components and the Virus-Silencing suppressor when Second-Site mutations compensate for structural defects in the 3' Untranslated region Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA Mg(2+)-induced conformational changes in the btuB riboswitch from E. coli Structural basis for packaging the dimeric genome of moloney murine leukaemia virus Particle mesh Ewald -An n.log(N) method for Ewald sums in large systems SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments Functional complexity and regulation through RNA dynamics A guide to ions and RNA structure A smooth particle mesh ewald method Evaluation of DNA force fields in implicit solvation A ribosome-binding, 3' translational enhancer has a T-shaped structure and engages in a long-distance RNA-RNA interaction Characterization of the mechanical unfolding of RNA pseudoknots Direct observation of hierarchical folding in single riboswitch aptamers Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures Pairwise solute descreening of solute charges from a dielectric medium A simple method for 3'-labeling of RNA Two alternating structures of the HIV-1 leader RNA Unusual mechanical stability of a minimal RNA kissing complex Understanding nucleic acid-ion interactions Reversible unfolding of single RNA molecules by mechanical force DSSR: an integrated software tool for dissecting the spatial structure of RNA Callus cultures of arabidopsis Structural domains within the 3' untranslated region of turnip crinkle virus An internal tRNA-like structure regulates the life cycle of a plus-sense RNA virus Recent advances in optical tweezers Refinement of generalized born implicit solvation parameters for nucleic acids and their complexes with proteins Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme Revealing the density of encoded functions in a viral RNA Metal ions in the structure and function of RNA Comparison of turnip crinkle virus RNA-dependent RNA polymerase preparations expressed in Escherichia coli or derived from infected plants Three-state mechanism couples ligand and temperature sensing in riboswitches Probing the structural dynamics of proteins and nucleic acids with optical tweezers Ribozymes, riboswitches and beyond: regulation of gene expression without proteins RNA conformational changes in the life cycles of RNA viruses, viroids, and virusassociated RNAs 3' cap-independent translation enhancers of plant viruses Relationship between internucleotide linkage geometry and the stability of RNA Riboswitches exert genetic control through metabolite-induced conformational change A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable The 3' proximal translational enhancer of turnip crinkle virus binds to 60S ribosomal subunits Ribosome binding to a 5' translational enhancer is altered in the presence of the 3' untranslated region in cap-independent translation of turnip crinkle virus Mg(2+) shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection A cis-replication element functions in both orientations to enhance replication of turnip crinkle virus Salt contribution to RNA tertiary structure folding stability Determination of thermodynamics and kinetics of RNA reactions by force Molecular dynamics simulations of nucleic acids with a generalized born solvation model Theory and applications of the generalized born solvation model in macromolecular simulations An RNA toolbox for singlemolecule force spectroscopy studies Stretching DNA with optical tweezers Force unfolding kinetics of RNA using optical tweezers. Since the TSS is a central hub for RNA interactions within the 3'UTR and upstream sequences (Yuan et al., 2012) , it seemed possible that the widespread conformational rearrangement could be triggered by RdRp binding to, and disrupting, the TSS.
    keywords: absence; binding; et al; figure; force; h4a; h4b; pulling; rdrp; rna; simulations; tss; unfolding
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        item: #72 of 1349
          id: cord-002482-2t09zqqi
      author: Miras, Manuel
       title: Non-canonical Translation in Plant RNA Viruses
        date: 2017-04-06
       words: 13910
      flesch: 33
     summary: frameshifting mediated by a viral sequence in plant cells Aphid transmission of beet western yellows luteovirus requires the minor capsid read-through protein P74 Local and distant sequences are required for efficient readthrough of the barley yellow dwarf virus PAV coat protein gene stop codon Mechanism of cytoplasmic mRNA translation Single amino acid changes in the 6K1-CI region can promote the alternative adaptation of Prunus-and Nicotiana-propagated Plum pox virus C isolates to either host Cap-independent enhancement of translation by a plant potyvirus 5 ′ nontranslated region Blocking eIF4E-eIF4G interaction as a strategy to impair coronavirus replication A minimal RNA promoter for minusstrand RNA synthesis by the brome mosaic virus polymerase complex Long-distance kissing loop interactions between a 3 ′ proximal Y-shaped structure and apical loops of 5 ′ hairpins enhance translation of Saguaro cactus virus Aphid transmission and systemic plant infection determinants of barley yellow dwarf luteovirus-PAV are contained in the coat protein readthrough domain and 17-kDa protein In vitro and in vivo studies of the RNA conformational switch in Alfalfa mosaic virus Genome-wide RNAi screen reveals a specific sensitivity of IREScontaining RNA viruses to host translation inhibition tRNA elements mediate the assembly of an icosahedral RNA virus Norovirus translation requires an interaction between the C Terminus of the genome-linked viral protein VPg and eukaryotic translation initiation factor 4G Multifaceted regulation of translational readthrough by RNA replication elements in a tombusvirus Initiation of translation in bacteria by a structured eukaryotic IRES RNA A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated-1 ribosomal frameshifting tRNA-mRNA mimicry drives translation initiation from a viral IRES The 3 ′ untranslated region of satellite tobacco necrosis virus RNA stimulates translation in vitro The chimeric nature of the genome of pea enation mosaic virus: the independent replication of RNA 2 IRES-driven translation is stimulated separately by the FMDV 3 ′ -NCR and poly (A) sequences The elongation, termination, and recycling phases of translation in eukaryotes Control of start codon choice on a plant viral RNA encoding overlapping genes Cap-independent translation of maize Hsp101 Mechanisms and implications of programmed translational frameshifting An internal ribosome entry site located upstream of the cruciferinfecting tobamovirus coat protein (CP) gene can be used for CP synthesis in vivo Polypurine (A)-rich sequences promote crosskingdom conservation of internal ribosome entry Role of tRNA-like structures in controlling plant virus replication Transfer RNA mimicry among tymoviral genomic RNAs ranges from highly efficient to vestigial Regulation of translation initiation under biotic and abiotic stresses Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution Potyviral VPg enhances viral RNA translation and inhibits reporter mRNA translation in planta Specific requirement for translation initiation factor 4E or its isoform drives plant host susceptibility to Tobacco etch virus 5 ′ -3 ′ RNA-RNA interaction facilitates Cap-and poly(A) tail-independent translation of tomato bushy stunt virus mRNA: a potential common mechanism for Tombusviridae Analysis of a 3 ′ -translation enhancer in a tombusvirus: a dynamic model for RNA-RNA interactions of mRNA termini Untranslated regions of diverse plant viral RNAs vary greatly in translation enhancement efficiency An internal ribosome entry site directs translation of the 3 ′ -Gene from pelargonium flower break virus genomic RNA: implications for infectivity Characterization of ribosomal frameshifting in Theiler's Murine Encephalomyelitis Virus Non-canonical translation in RNA viruses Stimulation of stop codon readthrough: frequent presence of an extended 3 ′ RNA structural element A translational enhancer derived from tobacco mosaic virus is functionally equivalent to a Shine-Dalgarno sequence Protein-protein interactions required during translation Eukaryotic initiation factor eIFiso4G1 and eIFiso4G2 are isoforms exhibiting distinct functional differences in supporting translation in Arabidopsis eIF4G functionally differs from eIFiso4G in promoting internal initiation, cap-independent translation, and translation of structured mRNAs Functional analysis of the tobacco mosaic virus tRNA-like structure in cytoplasmic gene regulation The 5 ′ -leader sequence of tobacco mosaic virus RNA enhances the expression of foreign gene transcripts in vitro and in vivo The tobacco etch viral 5 ′ leader and poly (A) tail are functionally synergistic regulators of translation RNA pseudoknot domain of tobacco mosaic virus can functionally substitute for a poly (A) tail in plant and animal cells The kl-TSS translational enhancer of PEMV can bind simultaneously to ribosomes and a 5 ′ proximal hairpin The 3 ′ untranslated region of Pea enation mosaic virus contains two Tshaped, ribosome-binding, cap-independent translation enhancers A ribosome-binding, 3 ′ translational enhancer has a T-shaped structure and engages in a long-distance RNA-RNA interaction Multiple Cis-acting elements modulate programmed-1 ribosomal frameshifting in Pea enation mosaic virus The potyvirus recessive resistance gene, sbm1, identifies a novel role for translation initiation factor eIF4E in cell-to-cell trafficking A novel interaction of cap-binding protein complexes eukaryotic initiation factor (eIF) 4F and eIF(iso)4F with a region in the 3 ′ -untranslated region of satellite tobacco necrosis virus Frameshifting RNA pseudoknots: structure and mechanism The genome-linked protein VPg of vertebrate viruses-a multifaceted protein Calicivirus translation initiation requires an interaction between VPg and eIF 4 E Multiple portions of poly (A)-binding protein stimulate translation in vivo Recognition of eIF4G by rotavirus NSP3 reveals a basis for mRNA circularization The structures of eIF4E-eIF4G complexes reveal an extended interface to regulate translation initiation Base-pairing between untranslated regions facilitates translation of uncapped, nonpolyadenylated viral RNA Cofolding organizes Alfalfa mosaic virus RNA and coat protein for replication Ribosomal protein P0 promotes Potato virus A infection and functions in viral translation together with VPg and eIF (iso) 4E Formation of Potato virus A-induced RNA granules and viral translation are interrelated processes required for optimal virus accumulation Direct interaction between the rice yellow mottle virus (RYMV) VPg and the central domain of the rice eIF(iso)4G1 factor correlates with rice susceptibility and RYMV virulence On the origin of the cap-dependent initiation of translation in eukaryotes Translation of the second gene of peanut clump virus RNA 2 occurs by leaky scanning in vitro Functional analysis of individual binding activities of the scaffold protein eIF4G Sapovirus translation requires an interaction between VPg and the cap binding protein eIF4E Hsp90 interacts specifically with viral RNA and differentially regulates replication initiation of Bamboo mosaic virus and associated satellite RNA Solution structure of the porcine sapovirus VPg core reveals a stable three-helical bundle with a conserved surface patch Poly(A)-binding protein facilitates translation of an uncapped/nonpolyadenylated viral rna by binding to the 3 ′ untranslated region An unusual internal ribosomal entry site of inverted symmetry directs expression of a potato leafroll polerovirus replication-associated protein The genome-linked protein VPg of plant viruses-a protein with many partners Eukaryotic translation initiation factor 3 (eIF3) and eIF2 can promote mRNA binding to 40S subunits independently of eIF4G in yeast Context sequences of translation initiation codon in plants Structure of ratcheted ribosomes with tRNAs in hybrid states (2015) showed that viral HC-Pro and the host RNA binding protein varicose, both components of potyviral RNA granules, stimulated VPg-promoted translation of PVA. All of the above mechanisms involve the VPg stimulating RNA translation in trans, leaving open the question of how the VPg specifically recognizes only the viral RNA.
    keywords: -utr; base; binding; cap; codon; eif4e; elements; end; et al; family; genus; initiation; interaction; ires; loop; mosaic; mrna; plant; protein; ribosomal; ribosome; rna; sequence; structure; translation; virus; viruses; vpg
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        item: #73 of 1349
          id: cord-002542-f7l4ty2j
      author: Jaworski, Elizabeth
       title: Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus
        date: 2017-05-05
       words: 11801
      flesch: 44
     summary: For short-read RNAseq, we employed ‘ClickSeq’ due to its ability to sensitively and confidently detect RNA recombination events with nucleotide resolution. Our recent NGS studies of RNA recombination in FHV revealed a diverse array of RNA recombination events, suggesting that the genomic landscape of DI-RNAs is highly dynamic and likely contributes significantly to the diversity of viral genomes that form the viral quasi-species [34] .
    keywords: clickseq; data; defective; events; fhv; fig; genome; nanopore; passages; passaging; reads; recombination; recombination events; rna; rna1; rnas; sequencing; species; virus
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        item: #74 of 1349
          id: cord-002608-zn7tm1ww
      author: Sokoloski, Kevin J.
       title: Identification of Interactions between Sindbis Virus Capsid Protein and Cytoplasmic vRNA as Novel Virulence Determinants
        date: 2017-06-29
       words: 11247
      flesch: 37
     summary: These data support the identification of the C:R interaction sites as bona fide capsid: RNA interaction sites and indicate that the mutational approach is capable of reducing capsid interaction at these specific sites. However it should be noted that the direct interaction between the viral capsid protein and viral RNA has not been exhaustively characterized in the cytoplasm of infected cells, or in mature viral particles leaving our understanding of the molecular interactions between these essential components of the virus incomplete.
    keywords: analysis; binding; capsid; capsid protein; cells; data; fig; genomic rna; infection; interaction sites; mutants; mutation; particles; protein; r interaction; rna; rnas; sequence; sinv; type; virus
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        item: #75 of 1349
          id: cord-002651-9r384oxd
      author: Pauly, Matthew D.
       title: Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity
        date: 2017-08-16
       words: 8186
      flesch: 43
     summary: Mutagen-resistant variants have been a valuable tool for probing the determinants of RNA virus mutation rates and the effect of mutation rate on viral population diversity (9, 10, 22, (29) (30) (31) (32) . To this end, we identified variants within the polymerase complex of influenza virus that are able to tolerate drug-mediated increases in viral mutation rates.
    keywords: 5fu; drug; influenza; mutant; mutation; pb1; polymerase; rate; resistance; ribavirin; rna; t123a; t97i; virus
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        item: #76 of 1349
          id: cord-002673-5a1rfi6k
      author: Knibb, Wayne
       title: Regional genetic diversity for NNV grouper viruses across the Indo-Asian region – implications for selecting virus resistance in farmed groupers
        date: 2017-09-06
       words: 6692
      flesch: 39
     summary: Thus it appears unlikely there were different NNV sequences in the infections at moderate frequencies. Genbank (the National Centre for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/)) was searched in various ways for NNV sequences.
    keywords: differences; fig; fish; grouper; nnv; nucleotide; positions; region; rna; samples; sequences; species; year
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        item: #77 of 1349
          id: cord-002676-zwkl1ywk
      author: Yu, Dong-Shan
       title: The lifecycle of the Ebola virus in host cells
        date: 2017-06-15
       words: 5334
      flesch: 37
     summary: How does VP40 associate with the inner leaflet? Ebolavirus comparative genomics Neglected filoviruses The Marburg virus outbreak of 1967 and subsequent episodes A case of Ebola virus infection Clinical illness and outcomes in patients with Ebola in Sierra Leone Ebola virus: from discovery to vaccine Mechanisms underlying coagulation abnormalities in ebola hemorrhagic fever: overexpression of tissue factor in primate monocytes/macrophages is a key event Filoviruses and the balance of innate, adaptive, and inflammatory responses How Ebola and Marburg viruses battle the immune system Ebola virus: unravelling pathogenesis to combat a deadly disease Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry Nucleocapsid-like structures of Ebola virus reconstructed using electron tomography Assembly of the Ebola Virus Nucleoprotein from a Chaperoned VP35 Complex Insight into the Ebola virus nucleocapsid assembly mechanism: crystal structure of Ebola virus nucleoprotein core domain at 1.8 A resolution The Ebola virus VP35 protein inhibits activation of interferon regulatory factor 3 A C-terminal basic amino acid motif of Zaire ebolavirus VP35 is essential for type I interferon antagonism and displays high identity with the RNA-binding domain of another interferon antagonist, the NS1 protein of influenza A virus Membrane binding and bending in Ebola VP40 assembly and egress Oligomerization of Ebola virus VP40 is essential for particle morphogenesis and regulation of viral transcription Processing of the Ebola virus glycoprotein by the proprotein convertase furin Release of viral glycoproteins during Ebola virus infection CD8+ cellular immunity mediates rAd5 vaccine protection against Ebola virus infection of nonhuman primates Antigenic subversion: a novel mechanism of host immune evasion by Ebola virus Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor Ebolavirus delta-peptide immunoadhesins inhibit marburgvirus and ebolavirus cell entry GP2, from the envelope glycoprotein ectodomain Mechanistic understanding of N-glycosylation in Ebola virus glycoprotein maturation and function Comparison of N-and O-linked glycosylation patterns of ebolavirus glycoproteins Structure of the Ebola virus glycoprotein spike within the virion envelope at 11 A resolution C-type lectins DC-SIGN and L-SIGN mediate cellular entry by Ebola virus in cis and in trans DC-SIGN and DC-SIGNR bind ebola glycoproteins and enhance infection of macrophages and endothelial cells Mannose-binding lectin binds to Ebola and Marburg envelope glycoproteins, resulting in blocking of virus interaction with DC-SIGN and complement-mediated virus neutralization DC-SIGN and DC-SIGNR interact with the glycoprotein of Marburg virus and the S protein of severe acute respiratory syndrome coronavirus Modulation of virion incorporation of Ebolavirus glycoprotein: effects on attachment, cellular entry and neutralization The Tyro3 receptor kinase Axl enhances macropinocytosis of Zaire ebolavirus Tyrosine kinase receptor Axl enhances entry of Zaire ebolavirus without direct interactions with the viral glycoprotein Tyro3 family-mediated cell entry of Ebola and Marburg viruses T-cell immunoglobulin and mucin domain 1 (TIM-1) is a receptor for Zaire Ebolavirus and Lake Victoria Marburgvirus Phosphatidylserine receptors: enhancers of enveloped virus entry and infection The TIM and TAM families of phosphatidylserine receptors mediate dengue virus entry Role of the phosphatidylserine receptor TIM-1 in enveloped-virus entry Downregulation of beta1 integrins by Ebola virus glycoprotein: implication for virus entry Alpha5beta1-integrin controls ebolavirus entry by regulating endosomal cathepsins Folate receptor alpha and caveolae are not required for Ebola virus glycoprotein-mediated viral infection Lentivirus vectors pseudotyped with filoviral envelope glycoproteins transduce airway epithelia from the apical surface independently of folate receptor alpha Analysis of filovirus entry into vero e6 cells, using inhibitors of endocytosis, endosomal acidification, structural integrity, and cathepsin (B and L) activity Ebolavirus is internalized into host cells via macropinocytosis in a viral glycoprotein-dependent manner Cellular entry of ebola virus involves uptake by a macropinocytosislike mechanism and subsequent trafficking through early and late endosomes Ebola virus enters host cells by macropinocytosis and clathrinmediated endocytosis Lipid raft microdomains: a gateway for compartmentalized trafficking of Ebola and Marburg viruses The Roles of Histidines and Charged Residues as Potential Triggers of a Conformational Change in the Fusion Loop of Ebola Virus Glycoprotein Induction of Cell-Cell Fusion by Ebola Virus Glycoprotein: Low pH Is Not a Trigger Ebola sGP-the first viral glycoprotein shown to be C-mannosylated Ebolavirus glycoprotein structure and mechanism of entry Detection of cellcell fusion mediated by Ebola virus glycoproteins Functional importance of the coiled-coil of the Ebola virus glycoprotein Role of endosomal cathepsins in entry mediated by the Ebola virus glycoprotein Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway Mutational analysis of the putative fusion domain of Ebola virus glycoprotein Core structure of the envelope glycoprotein GP2 from Ebola virus at 1.9-A resolution Ebola Viral Glycoprotein Bound to Its Endosomal Receptor Niemann-Pick C1 Ebola virus entry requires the cholesterol transporter Niemann-Pick C1 Direct Visualization of Ebola Virus Fusion Triggering in the Endocytic Pathway Structure of human Niemann-Pick C1 protein VP24 of Marburg virus influences formation of infectious particles Nucleoproteins and nucleocapsids of negative-strand RNA viruses Structural perspective on the formation of ribonucleoprotein complex in negative-sense single-stranded RNA viruses Ebolavirus VP35 coats the backbone of double-stranded RNA for interferon antagonism Crystal Structure of the Marburg Virus VP35 Oligomerization Domain Assembly of the Ebola Virus Nucleoprotein from a Chaperoned VP35 Complex An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions The Ebola Virus VP30-NP Interaction Is a Regulator of Viral RNA Synthesis Effect of Ebola virus proteins GP, NP and VP35 on VP40 VLP morphology Ebola virus glycoprotein: proteolytic processing, acylation, cell tropism, and detection of neutralizing antibodies Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu Contribution of ebola virus glycoprotein, nucleoprotein, and VP24 to budding of VP40 virus-like particles The assembly of Ebola virus nucleocapsid requires virion-associated proteins 35 and 24 and posttranslational modification of nucleoprotein Ebolavirus VP24 binding to karyopherins is required for inhibition of interferon signaling Elucidation of the Cellular Interactome of Ebola Virus Nucleoprotein and Identification of Therapeutic Targets Assembly and budding of Ebolavirus Molecular architecture of the nucleoprotein C-terminal domain from the Ebola and Marburg viruses Multivesicular bodies as a platform for formation of the Marburg virus envelope
    keywords: assembly; budding; cell; ebola; ebov; entry; fusion; glycoprotein; membrane; rna; virus; vp40
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        item: #78 of 1349
          id: cord-002687-ql6zo8ka
      author: Li, Dan
       title: A potent human neutralizing antibody Fc-dependently reduces established HBV infections
        date: 2017-09-26
       words: 14964
      flesch: 48
     summary: Moreover, 2H5-A14 greatly reduced HBV infection in a treatment mouse model. HBV and HDV neutralizing assays were then performed to rank the neutralizing ability of these 16 Abs relative to that of 2H5 ( 2H5-A14 is a potent and broadly-neutralizing nAb against HBV infection that acts by blocking the binding of preS1 with the HBV receptor NTCP Competition ELISA assays showed that 2H5-A14 had almost the same peptide competition pattern as did 2H5, and mutation of G24R of preS1 did not affect 2H5-A14 binding activity, indicating that 2H5-A14 targets the same epitope as does 2H5 (Figure 2-figure supplement 4) .
    keywords: 2h5; a14; antibody; binding; cells; control; dna; et al; figure; hbsag; hbv; hdv; hepatitis; human; infection; liver; mice; mouse; neutralization; pres1; supplement; treatment; viral; virus
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        item: #79 of 1349
          id: cord-002720-lrkscs71
      author: Kurosaki, Yohei
       title: Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification
        date: 2017-10-18
       words: 4956
      flesch: 46
     summary: Zika virus: history of a newly emerging arbovirus Zika Virus Outbreak, Bahia, Brazil Zika Virus Associated with Microcephaly Possible Association Between Zika Virus Infection and Microcephaly -Brazil Association between Zika virus infection and microcephaly in Brazil Congenital Zika virus syndrome in Brazil: a case series of the first 1501 livebirths with complete investigation Probable transfusion-transmitted Zika virus in Brazil Transmission of Zika Virus Through Sexual Contact with Travelers to Areas of Ongoing Transmission -Continental United States Sexually acquired Zika virus: a systematic review Molecular evolution of Zika virus during its emergence in the 20(th) century Zika Virus Transmission from French Polynesia to Brazil Zika virus in the Americas: Early epidemiological and genetic findings Detection of Zika virus in urine Detection of Zika virus in saliva Comparison of Test Results for Zika Virus RNA in Urine, Serum, and Saliva Specimens from Persons with Travel-Associated Zika Virus Disease -Florida Persistence of Zika Virus in Body Fluids -Preliminary Report Zika Virus Testing Considerations: Lessons Learned from the First 80 Real-Time Reverse Transcription-PCR-Positive Cases Diagnosed in New York State Viral load kinetics of Zika virus in plasma, urine and saliva in a couple returning from Martinique, French West Indies Quantitative real-time PCR detection of Zika virus and evaluation with field-caught mosquitoes Genetic and serologic properties of Zika virus associated with an epidemic, Yap State, Micronesia Zika Virus: Diagnostics for an Emerging Pandemic Threat Prolonged detection of Zika virus RNA in urine samples during the ongoing Zika virus epidemic in Brazil Rapid Molecular Detection of Zika Virus in Acute-Phase Urine Samples Using the Recombinase Polymerase Amplification Assay First case of laboratory-confirmed Zika virus infection imported into Europe Cross reactivity of commercial anti-dengue immunoassays in patients with acute Zika virus infection Loop-mediated isothermal amplification of DNA Development and evaluation of a novel loop-mediated isothermal amplification method for rapid detection of severe acute respiratory syndrome coronavirus Loop-mediated isothermal amplification (LAMP): principle, features, and future prospects Deployment of a Reverse Transcription Loop-Mediated Isothermal Amplification Test for Ebola Virus Surveillance in Remote Areas in Guinea Development and Evaluation of Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) key: cord-002720-lrkscs71 authors: Kurosaki, Yohei; Martins, Danyelly Bruneska Gondim; Kimura, Mayuko; Catena, Andriu dos Santos; Borba, Maria Amélia Carlos Souto Maior; Mattos, Sandra da Silva; Abe, Haruka; Yoshikawa, Rokusuke; de Lima Filho, José Luiz; Yasuda, Jiro title: Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification date: 2017-10-18 journal: Sci Rep DOI: 10.1038/s41598-017-13836-9 sha: doc_id: 2720 cord_uid: lrkscs71 The recent outbreak of Zika virus (ZIKV) disease caused an enormous number of infections in Central and South America, and the unusual increase in the number of infants born with microcephaly associated with ZIKV infection aroused global concern.
    keywords: assay; genotype; lamp; pcr; primers; rna; samples; sequences; virus; zika; zikv
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        item: #80 of 1349
          id: cord-002746-qn34eyul
      author: Antzin-Anduetza, Irati
       title: Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication
        date: 2017-11-09
       words: 9127
      flesch: 51
     summary: HIV-1 RNA has a high percentage of adenine (A, 36%) and low percentage of cytosine (C, 18%) If this occurred, gRNA abundance would decrease due to oversplicing but the total amount of HIV-1 RNA would stay the same.
    keywords: abundance; cells; cm22; codon; cpg; dinucleotides; expression; fig; gag; grna; hiv-1; infectivity; replication; rna; sequence; type; virus
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        item: #81 of 1349
          id: cord-002763-n952re94
      author: Niu, Xiaosai
       title: Transcriptome analysis of avian reovirus-mediated changes in gene expression of normal chicken fibroblast DF-1 cells
        date: 2017-11-25
       words: 4318
      flesch: 44
     summary: The distinct effect on gene expression upon ARV infection was carefully examined. The replication of ARV was monitored by RT-qPCR analysis of ARV genes M3 and S1 effects could be seen at 18 hpi (Fig. 1b) .
    keywords: analysis; arv; avian; cells; chicken; expression; fig; gene; infection; protein; reovirus; rna; seq
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        item: #82 of 1349
          id: cord-002764-px0cz6qn
      author: Lin, Yuan
       title: Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs
        date: 2017-11-17
       words: 8395
      flesch: 42
     summary: syndrome coronavirus nucleocapsid protein modulates its multimerization, translation inhibitory activity and cellular localization Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling Phase separation of signaling molecules promotes T cell receptor signal transduction Polymer physics of intracellular phase transitions Cross-␤ polymerization of low complexity sequence domains A glass menagerie of low complexity sequences Residueby-residue view of in vitro FUS granules that bind the C-terminal domain of RNA polymerase II Sequence determinants of intracellular phase separation by complex coacervation of a disordered protein The LC domain of hnRNPA2 adopts similar conformations in hydrogel polymers, liquid-like droplets, and nuclei Phosphorylationregulated binding of RNA polymerase II to fibrous polymers of low-complexity domains The role of disordered protein regions in the assembly of decapping complexes and RNP granules Principles and properties of stress granules Eukaryotic protein domains as functional units of cellular evolution Assembly of cell regulatory systems through protein interaction domains Hydrophobic interactions of peptides with membrane interfaces Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides Hydrophobic parameters-pi of aminoacid side-chains from the partitioning of N-acetyl-amino-acid amides Handbook of Biochemistry and Molecular Biology Application of the transfer model to understand how naturally occurring osmolytes affect protein stability Principles of Polymer Chemistry Disordered regions alter protein phase separation key: cord-002764-px0cz6qn authors: Lin, Yuan; Currie, Simon L.; Rosen, Michael K. title: Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs date: 2017-11-17 journal: J Biol Chem DOI: 10.1074/jbc.m117.800466 sha: doc_id: 2764 cord_uid: px0cz6qn Liquid–liquid phase separation (LLPS) is thought to contribute to the establishment of many biomolecular condensates, eukaryotic cell structures that concentrate diverse macromolecules but lack a bounding membrane.
    keywords: binding; concentration; domains; fig; fus; idrs; interactions; liquid; llps; phase; prm; proteins; residues; rna; separation; sh3
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        item: #83 of 1349
          id: cord-002937-7xauocti
      author: Huang, Chung-Guei
       title: A pilot study on primary cultures of human respiratory tract epithelial cells to predict patients’ responses to H7N9 infection
        date: 2018-02-20
       words: 6274
      flesch: 43
     summary: Compared with H7N9 virus infections, young age (≤ 29 years) and female sex were identified as risk factors for severe H1N1pdm infection [15] . In the present study, our objectives were to discover whether viral replication and cytokine responses of NHBE cells from two donors of different ages are distinct after H7N9 and H1N1pdm virus infection, and to validate whether these changes are different after H7N9 virus infection using primary epithelial cells from the respiratory tracts of 27 donors with various patient-related characteristics.
    keywords: cells; cytokine; epithelial; h7n9; human; infection; influenza; levels; p.i; patients; rna; viral; virus
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        item: #84 of 1349
          id: cord-002990-7flusgus
      author: Kitano, Mitsutaka
       title: Selection and Characterization of Rupintrivir-Resistant Norwalk Virus Replicon Cells In Vitro
        date: 2018-04-26
       words: 7108
      flesch: 44
     summary: In contrast, while replicon cells lack many features of an authentic viral life cycle because the viral capsid protein has been replaced with a drug resistance marker, they have been widely used for the evaluation of the activities of antivirals against HuNoV (9) (10) (11) . In the present study, we isolated replicon cells with reduced susceptibility to rupintrivir after several passages in the presence of rupintrivir and identified two amino acid substitutions of alanine 105 to valine (A105V) and isoleucine 109 to valine (I109V) in the viral protease.
    keywords: a105v; cells; fig; hunov; i109v; mnv; mutations; norovirus; protease; replicon; resistance; rna; rupintrivir
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        item: #85 of 1349
          id: cord-002994-1zjrunzc
      author: Faye, Martin
       title: Full-Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus
        date: 2018-04-13
       words: 11503
      flesch: 38
     summary: Furthermore, the evolutionary rates (µ) and the highest posterior densities (HPD with 95% of confidence interval) were 1.226 × 10 Evidence of BAGV adaptation to human house-keeping genes was analyzed by calculating CAI indices using complete coding polyprotein sequences of West African BAGV isolates and BAGV sequences available from Spain, in comparison to other MBFVs such as DENV, USUV, WNV, ZIKV and YFV, NKV flaviviruses (ModV and RBV) and ISFs (CxFV and AeFV). Interestingly, CAI values of West African isolates were also significantly higher than those obtained for other MBFVs well known to infect human such as USUV (Wilcoxon Rank Sum Test, p-value < 6.796 × 10 −9 ), WNV (Wilcoxon Rank Sum Test, p-value < 2.718 × 10 −10 ), ZIKV (Wilcoxon Rank Sum Test, p-value < 1.67 × 10 −8 ) and ISFs (means CAI: 1.0015 and 1.0006 and median CAI: 1.0015 and 1.0006 for CxFV and AeFV, respectively) which showed low evidence Evidence of BAGV adaptation to human house-keeping genes was analyzed by calculating CAI indices using complete coding polyprotein sequences of West African BAGV isolates and BAGV sequences available from Spain, in comparison to other MBFVs such as DENV, USUV, WNV, ZIKV and YFV, NKV flaviviruses (ModV and RBV) and ISFs (CxFV and AeFV).
    keywords: adaptation; african; bagv; cai; codon; conserved; flaviviruses; genome; human; isolates; protein; recombination; rna; selection; sequences; sites; structural; value; virus; west
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        item: #86 of 1349
          id: cord-003006-lk2ny1wd
      author: Cantoni, Diego
       title: Ebolaviruses: New roles for old proteins
        date: 2018-05-03
       words: 6059
      flesch: 41
     summary: with massive lymphocyte apoptosis Overlapping motifs (PTAP and PPEY) within the Ebola virus VP40 protein function independently as late budding domains: involvement of host proteins TSG101 and VPS-4 Ebola virus matrix protein VP40 interaction with human cellular factors Tsg101 and Nedd4 ALIX Rescues Budding of a Double PTAP/PPEY L-Domain Deletion Mutant of Ebola VP40: A Role for ALIX in Ebola Virus Egress Inducing cell proliferation inhibition and apoptosis via silencing Dicer, Drosha, and Exportin 5 in urothelial carcinoma of the bladder Could the Ebola virus matrix protein VP40 be a drug target The natural compound silvestrol is a potent inhibitor of Ebola virus replication Productive replication of Ebola virus is regulated by the c-Abl1 tyrosine kinase The nonstructural small glycoprotein sGP of Ebola virus is secreted as an antiparallel-orientated homodimer A new Ebola virus nonstructural glycoprotein expressed through RNA editing Delta-peptide is the carboxy-terminal cleavage fragment of the nonstructural small glycoprotein sGP of Ebola virus Tyro3 family-mediated cell entry of Ebola and Marburg viruses Ebolavirus glycoprotein structure and mechanism of entry Ebola Virus Entry: A Curious and Complex Series of Events Ebolavirus is internalized into host cells via macropinocytosis in a viral glycoprotein-dependent manner Ebola Virus Enters Host Cells by Macropinocytosis and Clathrin-Mediated Endocytosis Ebola virus and severe acute respiratory syndrome coronavirus display late cell entry kinetics: evidence that transport to NPC1+ endolysosomes is a rate-defining step Ebolavirus Glycoprotein Directs Fusion through NPC1+ Endolysosomes Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic Human Adaptation of Ebola Virus during the West African Outbreak Functional Characterization of Adaptive Mutations during the West African Ebola Virus Outbreak Spontaneous mutation at amino acid 544 of the Ebola glycoprotein potentiates virus entry and selection in tissue culture Biochemical Basis for Increased Activity of Ebola Glycoprotein in the 2013-2016 Epidemic A Polymorphism within the Internal Fusion Loop of the Ebola Virus Glycoprotein Modulates Host Cell Entry The Ebola virus glycoprotein contributes to but is not sufficient for virulence in vivo Identification of the Ebola virus glycoprotein as the main viral determinant of vascular cell cytotoxicity and injury Ebola virus glycoprotein-mediated anoikis of primary human cardiac microvascular endothelial cells Ebola virus glycoprotein toxicity is mediated by a dynamin-dependent protein-trafficking pathway The ERK mitogen-activated protein kinase pathway contributes to Ebola virus glycoprotein-induced cytotoxicity Modeling of the Ebola Virus Delta Peptide Reveals a Potential Lytic Sequence Motif Ebola Virus Delta Peptide is a Viroporin Ebola virus glycoprotein GP is not cytotoxic when expressed constitutively at a moderate level Less is more: Ebola virus surface glycoprotein expression levels regulate virus production and infectivity Tetherin-mediated restriction of filovirus budding is antagonized by the Ebola glycoprotein Ebola virus glycoprotein counteracts BST-2/Tetherin restriction in a sequence-independent manner that does not require tetherin surface removal The Tetherin Antagonism of the Ebola Virus Glycoprotein Requires an Intact Receptor-Binding Domain and Can Be Blocked by GP1-Specific Antibodies Ebola Virus Glycoprotein Promotes Enhanced Viral Egress by Preventing Ebola VP40 From Associating With the Host Restriction Factor BST2/Tetherin Effects of Ebola virus glycoproteins on endothelial cell activation and barrier function Ebola Hemorrhagic Fever: Novel Biomarker Correlates of Clinical Outcome Ectodomain shedding of the glycoprotein GP of Ebola virus Shed GP of Ebola Virus Triggers Immune Activation and Increased Vascular Permeability Ebolaviruses associated with differential pathogenicity induce distinct host responses in human macrophages Ebola virus glycoprotein directly triggers T lymphocyte death despite of the lack of infection The Myeloid LSECtin Is a DAP12-Coupled Receptor That Is Crucial for Inflammatory Response Induced by Ebola Virus Glycoprotein Antigenic Subversion: A Novel Mechanism of Host Immune Evasion by Ebola Virus Structures of Ebola virus GP and sGP in complex with therapeutic antibodies GP mRNA of Ebola Virus Is Edited by the Ebola Virus Polymerase and by T7 and Vaccinia Virus Polymerases Genomic RNA Editing and Its Impact on Ebola Virus Adaptation During Serial Passages in Cell Culture and Infection of Guinea Pigs Proposal for a revised taxonomy of the family Filoviridae: Classification, names of taxa and viruses, and virus abbreviations Risks Posed by Reston, the Forgotten Ebolavirus The Pathogenesis of Ebola Virus Disease Structural characterization and membrane binding properties of the matrix protein VP40 of Ebola virus The Role of Exosomal VP40 in Ebola Virus Disease Oligomerization and polymerization of the filovirus matrix protein VP40 Structural rearrangement of ebola virus vp40 begets multiple functions in the virus life cycle A PPxY motif within the VP40 protein of Ebola virus interacts physically and functionally with a ubiquitin ligase: Implications for filovirus budding Ebola VP40 in Exosomes Can Cause Immune Cell Dysfunction Human fatal zaire ebola virus infection is associated with an aberrant innate immunity and
    keywords: binding; cell; ebola; ebolavirus; protein; replication; rna; virus; vp24; vp35; vp40
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        item: #87 of 1349
          id: cord-003044-9uqa39j9
      author: Cervera, Héctor
       title: Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host’s Transcriptome: The Tobacco Etch Potyvirus—Tobacco Case Study
        date: 2018-03-19
       words: 10888
      flesch: 39
     summary: We computed a nonparametric Spearman's correlation coefficient between viral fitness and the normalized degree of expression (z-score) for each one of the previously characterized DEGs Correlation plots between host gene expression and viral fitness for those genes that significantly vary across all viral infections (one-way ANOVA with FDR, adjusted P < 0.05), and that exhibit a significant positive (upper panel; red dots) or negative (lower panel; blue dots) trend (Spearman's correlation test, P < 0.05). This observation motivated us to identify genes whose expression significantly correlates with viral fitness; that is, systematic changes in virus fitness are associated with an increase or decrease in the expression level of a particular gene.
    keywords: correlation; data; degs; differences; et al; expression; figure; fitness; genes; genotypes; host; infection; plants; profiles; protein; response; rna; tev; virus; viruses
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        item: #88 of 1349
          id: cord-003045-r707jl16
      author: Bhuvaneshwar, Krithika
       title: viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors
        date: 2018-06-05
       words: 6547
      flesch: 48
     summary: We compared various viral detection pipeline using the several criteria (Table 1) . In this paper, we present our pipeline viGEN to not only detect and quantify read counts at the individual viral-gene level, but also detect viral variants from human RNA-seq data.
    keywords: cancer; data; gene; hepatitis; human; patients; pipeline; rna; vigen; viruses
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        item: #89 of 1349
          id: cord-003050-n25wnmq5
      author: Nibert, Max L.
       title: A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis
        date: 2018-03-07
       words: 3342
      flesch: 48
     summary: See Table S4 for a summary of abbreviations and GenBank numbers The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis Ribosomal frameshifting and transcriptional slippage: from genetic steganography and cryptography to adventitious use Expression of the rice yellow mottle virus P1 protein in vitro and in vivo and its involvement in virus spread Mutational analysis of the slippery-sequence component of a coronavirus ribosomal frameshifting signal Fast and sensitive protein alignment using DIAMOND Multiple viral infections in Agaricus bisporus-characterisation of 18 unique RNA viruses and 8 ORFans identified by deep sequencing Organelle-like membrane compartmentalization of positive-strand RNA virus replication factories Genomic Resources Development Consortium Genomic Resources Notes SOSUI: classification and secondary structure prediction system for membrane proteins ModelFinder: fast model selection for accurate phylogenetic estimates An essential fifth coding ORF in the sobemoviruses Identification of diverse mycoviruses through metatranscriptomics characterization of the viromes of five major fungal plant pathogens Ultrafast approximation for phylogenetic bootstrap IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies Virus taxonomy, ninth report of the International Committee on Taxonomy of Viruses Family Barnaviridae Identification of a subgenomic mRNA encoding the capsid protein of mushroom bacilliform virus, a single-stranded RNA mycovirus Mushroom bacilliform virus RNA: the initiation of translation at the 5´end of the genome and identification of the VPg Deduced protein sequences for the P3 (RdRp) region of P2+3 of barnaviruses (black) and sobemoviruses (gray) were aligned using MAFFT 7.3 (G-INS-i) and then subjected to maximum-likelihood phylogenetic analyses using Mod-elFinder, IQ-TREE, and UFBoot [10, 13, 14] as implemented with the Find best and apply option at https ://www.hiv.lanl.gov/conte nt/ seque nce/IQTRE E/iqtre e.html.
    keywords: barnavirus; cqabv1; mbv; orfs; region; rsbv1; sequence
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        item: #90 of 1349
          id: cord-003070-6oca1mrm
      author: Shen, Wen-Jun
       title: RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence
        date: 2018-02-28
       words: 5485
      flesch: 51
     summary: As the number of available RNA-protein binding experimental data has increased rapidly due to high-throughput sequencing methods, it is now possible to measure and understand RNA-protein interactions by computational methods. RNA-protein interactions (RPIs) have a critical influence on post-transcriptional gene regulation [1] [2]
    keywords: acid; data; interactions; method; pairs; protein; rna; rpirls; set; template
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        item: #91 of 1349
          id: cord-003104-9cx1gdze
      author: Fitzsimmons, William J.
       title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
        date: 2018-06-28
       words: 8669
      flesch: 51
     summary: Here, we present data for an alternative model whereby RNA viruses evolve high mutation rates as a byproduct of selection for increased replicative speed. A large body of theoretical and experimental work suggests that the selective pressure for higher mutation rates is due to either the physicochemical cost of maintaining a lower one or a selective advantage from an increased supply of beneficial mutations
    keywords: 3d g64s; cells; fidelity; fig; fitness; g64s; infection; mutation; passage; poliovirus; rate; rna; selection; speed; virus; viruses
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        item: #92 of 1349
          id: cord-003122-a3f4l6iu
      author: Dou, Dan
       title: Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement
        date: 2018-07-20
       words: 10292
      flesch: 26
     summary: Isolation and characterization of the signal recognition particle receptor Inefficient SRP interaction with a nascent chain triggers a mRNA quality control pathway Substratespecific translocational attenuation during ER stress defines a pre-emptive quality control pathway Solving the membrane protein folding problem X-ray structure of a protein-conducting channel Molecular code for transmembrane-helix recognition by the Sec61 translocon Polar residues and their positional context dictate the transmembrane domain interactions of influenza a neuraminidases Protein translocation across the rough endoplasmic reticulum The cotranslational maturation program for the type II membrane glycoprotein influenza neuraminidase N-linked carbohydrates act as lumenal maturation and quality control protein tags The number and location of glycans on influenza hemagglutinin determine folding and association with calnexin and calreticulin Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 A resolution Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 A resolution The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site Influenza virus M2 integral membrane protein is a homotetramer stabilized by formation of disulfide bonds Steps in maturation of influenza A virus neuraminidase Assembly of subtype 1 influenza neuraminidase is driven by both the transmembrane and head domains The influenza virus neuraminidase protein transmembrane and head domains have coevolved Influenza A viral replication is blocked by inhibition of the inositolrequiring enzyme 1 (IRE1) stress pathway Influenza induces endoplasmic reticulum stress, caspase-12-dependent apoptosis, and c-Jun N-terminal kinase-mediated transforming growth factor-beta release in lung epithelial cells Influenza a virus host shutoff disables antiviral stress-induced translation arrest Real-time RT-qPCR assay for the analysis of human influenza A virus transcription and replication dynamics Strand-specific real-time RT-PCR for distinguishing influenza vRNA, cRNA, and mRNA Translational regulation of viral secretory proteins by the 5' coding regions and a viral RNA-binding protein The signal sequence coding region promotes nuclear export of mRNA The NS1 protein from influenza virus stimulates translation initiation by enhancing ribosome recruitment to mRNAs Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens Eukaryotic translation initiation factor 4GI is a cellular target for NS1 protein, a translational activator of influenza virus Influenza virus NS1 protein stimulates translation of the M1 protein Influenza virus NS1 protein enhances the rate of translation initiation of viral mRNAs Influenza viruses cause hemolysis and fusion of cells Interaction of influenza virus hemagglutinin with target membrane lipids is a key step in virus-induced hemolysis and fusion at pH 5.2 Influenza virus hemagglutinin with multibasic cleavage site is activated by furin, a subtilisin-like endoprotease fur gene expression as a discriminating marker for small cell and nonsmall cell lung carcinomas Proteolytic activation of influenza viruses by serine proteases TMPRSS2 and HAT from human airway epithelium Proteolytic activation of the 1918 influenza virus hemagglutinin Cleavage of influenza a virus hemagglutinin in human respiratory epithelium is cell associated and sensitive to exogenous antiproteases Cleavage of influenza virus hemagglutinin by airway proteases TMPRSS2 and HAT differs in subcellular localization and susceptibility to protease inhibitors Amantadine selection of a mutant influenza virus containing an acid-stable hemagglutinin glycoprotein: evidence for virus-specific regulation of the pH of glycoprotein transport vesicles Influenza virus M2 protein ion channel activity stabilizes the native form of fowl plague virus hemagglutinin during intracellular transport Influenza and SARS-coronavirus activating proteases TMPRSS2 and HAT are expressed at multiple sites in human respiratory and gastrointestinal tracts Lipid rafts as a membrane-organizing principle Influenza virus assembly and budding Association of influenza virus proteins with membrane rafts Mutations at palmitylation sites of the influenza virus hemagglutinin affect virus formation Acylation-mediated membrane anchoring of avian influenza virus hemagglutinin is essential for fusion pore formation and virus infectivity S acylation of the hemagglutinin of influenza viruses: mass spectrometry reveals site-specific attachment of stearic acid to a transmembrane cysteine Influenza virus hemagglutinin concentrates in lipid raft microdomains for efficient viral fusion Role of transmembrane domain and cytoplasmic tail amino acid sequences of influenza a virus neuraminidase in raft association and virus budding Influenza virus M2 protein mediates ESCRT-independent membrane scission Influenza virus assembly: effect of influenza virus glycoproteins on the membrane association of M1 protein Influenza virus assembly and lipid raft microdomains: a role for the cytoplasmic tails of the spike glycoproteins Identification of the domains of the influenza A virus M1 matrix protein required for NP binding, oligomerization and incorporation into virions Membrane curvature in cell biology: an integration of molecular mechanisms Influenza virus hemagglutinin and neuraminidase, but not the matrix protein, are required for assembly and budding of plasmid-derived virus-like particles Formation of virus-like particles from human cell lines exclusively expressing influenza neuraminidase Budding capability of the influenza virus neuraminidase can be modulated by tetherin Structural analysis of the roles of influenza A virus membrane-associated proteins in assembly and morphology influenza A virus ribonucleoproteins Transport of incoming influenza virus nucleocapsids into the nucleus Nuclear import of microinjected influenza virus ribonucleoproteins Nuclear import of influenza virus RNA can be mediated by viral nucleoprotein and transport factors required for protein import The NPI-1/NPI-3 (karyopherin alpha) binding site on the influenza a virus nucleoprotein NP is a nonconventional nuclear localization signal An unconventional NLS is critical for the nuclear import of the influenza A virus nucleoprotein and ribonucleoprotein Ultrastructural analysis of the nuclear localization sequences on influenza A ribonucleoprotein complexes Colocalization of different influenza viral RNA segments in the cytoplasm before viral budding as shown by single-molecule sensitivity FISH analysis Influenza a virus assembly intermediates fuse in the cytoplasm Analysis of IAV replication and co-infection dynamics by a versatile RNA viral genome labeling method Differential use of importin-alpha isoforms governs cell tropism and host adaptation of influenza virus The RNA polymerase of influenza a virus: mechanisms of viral transcription and replication Structural insights into RNA synthesis by the influenza virus transcription-replication machine Interaction of the influenza a virus nucleocapsid protein with the viral RNA polymerase potentiates unprimed viral RNA replication Isolation and characterization of the positive-sense replicative intermediate of a negative-strand RNA virus Single-molecule FRET reveals the pre-initiation and initiation conformations of influenza virus promoter RNA Different de novo initiation strategies are used by influenza virus RNA polymerase on its cRNA and viral RNA promoters during viral RNA replication Genetic trans-complementation establishes a new model for influenza virus RNA transcription and replication Internal initiation of influenza virus replication of viral RNA and complementary RNA in vitro Structural insight into cap-snatching and RNA synthesis by influenza polymerase A unique cap(m7GpppXm)-dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription Association of the influenza A virus RNAdependent RNA polymerase with cellular RNA polymerase II RNA-free and ribonucleoproteinassociated influenza virus polymerases directly bind the serine-5-phosphorylated carboxyl-terminal domain of host RNA polymerase II Structural basis of an essential interaction between influenza polymerase and Pol II CTD The structural basis for cap binding by influenza virus polymerase subunit PB2
    keywords: binding; cell; figure; hemagglutinin; host; iavs; influenza; influenza virus; membrane; neuraminidase; nuclear; polymerase; protein; replication; rna; viral; virus; viruses
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        item: #93 of 1349
          id: cord-003130-p2h8p5bm
      author: Lindqvist, Richard
       title: Tick-Borne Flaviviruses and the Type I Interferon Response
        date: 2018-06-21
       words: 8362
      flesch: 43
     summary: Furthermore RNA-seq and mass spectrometric analysis revealed that when challenged by TBEV infection, tick cells upregulated genes involved in immunity and metabolism, whereas genes involved in cellular stress were downregulated [94] . Using gene silencing approaches, this study confirmed the antiviral effect of Ago 30 and Dcr 90 in tick cells.
    keywords: cells; disease; encephalitis; flavivirus; host; ifn; infection; interferon; lgtv; protein; replication; response; rna; tbev; tick; type; viperin; virus
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        item: #94 of 1349
          id: cord-003158-mhlqnj52
      author: Wang, Qi
       title: Adapted HCV JFH1 variant is capable of accommodating a large foreign gene insert and allows lower level HCV replication and viral production
        date: 2018-07-13
       words: 5395
      flesch: 51
     summary: Images showed that NS5A positive cells (red) were also with the blue color of X-gal staining. However, a higher titer of HCV reporter virus was produced after inserting EGFP and Rluc into NS5A C-terminus of an adaptively mutated JFH1 strain designated JFH1-AM120 (18) .
    keywords: am120; cells; egfp; gene; hcv; jfh1; lacz; ns5a; rluc; rna; virus
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        item: #95 of 1349
          id: cord-003187-qdbcdn2j
      author: Bassi, Maria Rosaria
       title: Extinction of Zika Virus and Usutu Virus by Lethal Mutagenesis Reveals Different Patterns of Sensitivity to Three Mutagenic Drugs
        date: 2018-08-27
       words: 6761
      flesch: 30
     summary: The crystal structure of Zika virus NS5 reveals conserved drug targets Crystal structure of Zika virus NS5 RNA-dependent RNA polymerase Analysis of ribonucleotide 5=-triphosphate analogs as potential inhibitors of Zika virus RNAdependent RNA polymerase using non-radioactive polymerase assays Curing of foot-and-mouth disease virus from persistently infected cells by ribavirin involves enhanced mutagenesis Mode of action of ribavirin: effect of nucleotide pool alterations on influenza virus ribonucleoprotein synthesis Persistence of West Nile virus Zika virus persistence in the central nervous system and lymph nodes of rhesus monkeys The role of viral persistence in flavivirus biology Mutagenesis-induced, large fitness variations with an invariant arenavirus consensus genomic nucleotide sequence Zika virus infection of rhesus macaques leads to viral persistence in multiple tissues Late sexual transmission of Zika virus related to persistence in the semen Sexually acquired Zika virus: a systematic review Update: interim guidance for prevention of sexual transmission of Zika virus-United States Persistent detection of Zika virus RNA in semen for six months after symptom onset in a traveller returning from Haiti to Italy, February 2016 Mosquito-borne and sexual transmission of Zika virus: recent developments and future directions Prevention and control of Zika as a mosquito-borne and sexually transmitted disease: a mathematical modeling analysis The risk of sustained sexual transmission of Zika is underestimated Zika virus infects human placental macrophages Efficacy of the broad-spectrum antiviral compound BCX4430 against Zika virus in cell culture and in a mouse model The viral polymerase inhibitor 7-deaza-2=-C-methyladenosine is a potent inhibitor of in vitro Zika virus replication and delays disease progression in a robust mouse infection model The race to find antivirals for Zika virus First evidence of simultaneous occurrence of West Nile virus and Usutu virus neuroinvasive disease in humans in Croatia during the 2013 outbreak Limited susceptibility of mice to Usutu virus (USUV) infection and induction of flavivirus cross-protective immunity A recombinant DNA vaccine protects mice deficient in the alpha/beta interferon receptor against lethal challenge with Usutu virus Emergence of Usutu virus, an African mosquito-borne Flavivirus of the Japanese encephalitis virus group Virus isolation and quantitation Isolation of fidelity variants of RNA viruses and characterization of virus mutation frequency Norovirus polymerase fidelity contributes to viral transmission in vivo A rapid and specific real-time RT-PCR assay to identify Usutu virus in human plasma, serum, and cerebrospinal fluid Coxsackievirus B3 mutator strains are attenuated in vivo
    keywords: disease; drugs; favipiravir; fig; fluorouracil; infection; mutagenesis; replication; ribavirin; rna; usuv; virus; zika; zikv
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        item: #96 of 1349
          id: cord-003254-yiqdsf9z
      author: Schlub, Timothy E
       title: A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences
        date: 2018-08-07
       words: 6314
      flesch: 40
     summary: key: cord-003254-yiqdsf9z authors: Schlub, Timothy E; Buchmann, Jan P; Holmes, Edward C title: A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences date: 2018-08-07 journal: Mol Biol Evol DOI: 10.1093/molbev/msy155 sha: doc_id: 3254 cord_uid: yiqdsf9z Overlapping genes in viruses maximize the coding capacity of their genomes and allow the generation of new genes without major increases in genome size. Despite their importance, the evolution and function of overlapping genes are often not well understood, in part due to difficulties in their detection.
    keywords: codon; frame; genes; length; method; orf; orfs; reading; sensitivity; test; virus
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        item: #97 of 1349
          id: cord-003284-hjx2d5rq
      author: Márquez-Jurado, Silvia
       title: An Alanine-to-Valine Substitution in the Residue 175 of Zika Virus NS2A Protein Affects Viral RNA Synthesis and Attenuates the Virus In Vivo
        date: 2018-10-07
       words: 9963
      flesch: 44
     summary: This DNA-lunched system ensures capping of the viral RNA and allows the recovery of infectious virus from the transfected cDNA clone without the need of an in vitro transcription step. In contrast to mock-transfected cells, increasing amounts of infectious virus were detected in the tissue culture supernatant of cells transfected with the infectious clone, with peak titers around 10 7 PFU/mL on day five ( Figure 2A ).
    keywords: bac; cdna; cells; clone; days; figure; infection; mice; mns2a; mutant; pfu; protein; rgn; rna; rzikv; vero; virus
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        item: #98 of 1349
          id: cord-003305-ya0siivm
      author: Liu, Weichi
       title: A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase
        date: 2018-11-16
       words: 8929
      flesch: 41
     summary: The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation The structure of bovine viral diarrhea virus RNA-dependent RNA polymerase and its amino-terminal domain Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5 Crystal structure of the full-length Japanese encephalitis virus NS5 reveals a conserved methyltransferase-polymerase interface Crystal structure of classical swine fever virus NS5B reveals a novel N-Terminal domain Characterization of the N-terminal domain of classical swine fever virus RNA-dependent RNA polymerase Mutational analysis of bovine viral diarrhea virus RNA-dependent RNA polymerase Site-directed mutagenesis in one day with >80% efficiency Site-directed, Ligase-Independent Mutagenesis (SLIM): a single-tube methodology approaching 100% efficiency in 4 h Processing of X-ray Diffraction Data Collected in Oscillation Mode Phaser crystallographic software Coot: model-building tools for molecular graphics PHENIX: a comprehensive Python-based system for macromolecular structure solution Crystallography & NMR system: A new software suite for macromolecular structure determination THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures Perturbation in the conserved methyltransferase-polymerase interface of flavivirus NS5 differentially affects polymerase initiation and elongation Structural and functional analysis of methylation and 5 -RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5 A novel mechanism to ensure terminal initiation by hepatitis C virus NS5B polymerase Hydrophobic and charged residues in the C-terminal arm of hepatitis C virus RNA-dependent RNA polymerase regulate initiation and elongation Characterization of soluble hepatitis C virus RNA-dependent RNA polymerase expressed in Escherichia coli Assembly, purification, and pre-steady-state kinetic analysis of active RNA-dependent RNA polymerase elongation complex Substrate complexes of hepatitis C virus RNA polymerase (HC-J4): structural evidence for nucleotide import and de-novo initiation Dali server: conservation mapping in 3D A crystal structure of the Dengue virus NS5 protein reveals a novel inter-domain interface essential for protein flexibility and virus replication Characterisation of interaction between NS3 and NS5B protein of classical swine fever virus by deletion of terminal sequences of NS5B Poliovirus RNA-dependent RNA polymerase (3Dpol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mn2+ The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent Structural insights into bunyavirus replication and its regulation by the vRNA promoter Structure of influenza A polymerase bound to the viral RNA promoter An RNA cap (nucleoside-2 -O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Structural basis for RNA replication by the hepatitis C virus polymerase Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective Coxsackievirus B3 mutator strains are attenuated in vivo Design of a genetically stable high fidelity coxsackievirus B3 polymerase that attenuates virus growth in vivo Attenuation of Foot-and-Mouth disease virus by engineered viral polymerase fidelity Structure-Function relationships underlying the replication fidelity of viral RNA-Dependent RNA polymerases Residues Arg283, Arg285, and Ile287 in the nucleotide binding pocket of bovine viral diarrhea virus NS5B RNA polymerase affect catalysis and fidelity A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity Remote site control of an active site fidelity checkpoint in a viral RNA-dependent RNA polymerase Picornaviral polymerase structure, function, and fidelity modulation Rationalizing the development of live attenuated virus vaccines Engineering attenuated virus vaccines by controlling replication fidelity
    keywords: assays; c-672; csfv; fidelity; figure; interactions; mis; misincorporation; ns5b; ntd; polymerase; rdrp; residues; rna; structure; terminal; virus
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        item: #99 of 1349
          id: cord-003382-v3w1wi5c
      author: Rahmatpanah, Farah
       title: Airway epithelial cells prime plasmacytoid dendritic cells to respond to pathogens via secretion of growth factors
        date: 2018-10-02
       words: 5552
      flesch: 51
     summary: We applied this kit to isolate RNA from PDCs cells since the numbers of cells were small. RNA isolation from PDCs Total RNA was isolated from cultured PDC cells from four individuals using FFPE RNA/DNA purification plus kit (Cat # 54300, Norgen Biotek Corp) with minor modifications.
    keywords: cells; cultured; data; dendritic; factors; ifn; influenza; pbecs; pdcs; rna; secretion; type
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        item: #100 of 1349
          id: cord-003435-ke0az7nf
      author: Schlake, Thomas
       title: mRNA as novel technology for passive immunotherapy
        date: 2018-10-17
       words: 15222
      flesch: 37
     summary: Dual targeting strategies with bispecific antibodies Diabodies: small bivalent and bispecific antibody fragments Single-chain mono-and bispecific antibody derivatives with novel biological properties and antitumour activity from a COS cell transient expression system Immunotherapeutic perspective for bispecific antibodies Antibody pharmacokinetics and pharmacodynamics Elimination mechanisms of therapeutic monoclonal antibodies Bispecific antibodies rise again Clinical use of blinatumomab for B-cell acute lymphoblastic leukemia in adults Tailoring structure-function and pharmacokinetic properties of single-chain Fv proteins by site-specific PEGylation Strategies to extend plasma half-lives of recombinant antibodies Properties, production, and applications of camelid single-domain antibody fragments Transmigration of beta amyloid specific heavy chain antibody fragments across the in vitro blood-brain barrier Protective effect of different anti-rabies virus VHH constructs against rabies disease in mice Post-exposure treatment with anti-rabies VHH and vaccine significantly improves protection of mice from lethal rabies infection A mAb recognizing a surface antigen of Mycobacterium tuberculosis enhances host survival Antibodies to a cell surface histone-like protein protect against Histoplasma capsulatum Monoclonal antibodies for prophylactic and therapeutic use against viral infections Single-chain fragment variable passive immunotherapies for neurodegenerative diseases Human respiratory syncytial virus and other viral infections in infants receiving palivizumab Bezlotoxumab (Zinplava) for prevention of recurrent Clostridium difficile infection Depletion of B cells in vivo by a chimeric mouse human monoclonal antibody to CD20 Rituximab, an anti-cd20 monoclonal antibody: history and mechanism of action Targeted therapy with the T-cell-engaging antibody blinatumomab of chemotherapy-refractory minimal residual disease in B-lineage acute lymphoblastic leukemia patients results in high response rate and prolonged leukemia-free survival Blinatumomab: a bispecific T cell engager (BiTE) antibody against CD19/CD3 for refractory acute lymphoid leukemia Alternative molecular formats and therapeutic applications for bispecific antibodies Adoptive T-cell immunotherapy T-cell therapy: options for infectious diseases Cancer regression in patients after transfer of genetically engineered lymphocytes Chimeric antigen receptor-and TCR-modified T cells enter main street and wall street Adoptive cell transfer as personalized immunotherapy for human cancer Gene therapy with human and mouse T-cell receptors mediates cancer regression and targets normal tissues expressing cognate antigen Tumor regression in patients with metastatic synovial cell sarcoma and melanoma using genetically engineered lymphocytes reactive with NY-ESO-1 T cells targeting carcinoembryonic antigen can mediate regression of metastatic colorectal cancer but induce severe transient colitis Adoptive transfer of T-cell immunity: gene transfer with MHC-restricted receptors Transgenic TCR expression: comparison of single chain with full-length receptor constructs for T-cell function Independent association of T cell receptor beta and gamma chains with CD3 in the same cell Surface expression of only gamma delta and/or alpha beta T cell receptor heterodimers by cells with four (alpha, beta, gamma, delta) functional receptor chains Alpha beta T cell receptor transfer to gamma delta T cells generates functional effector cells without mixed TCR dimers in vivo TALENmediated editing of endogenous T-cell receptors facilitates efficient reprogramming of T lymphocytes by lentiviral gene transfer Optimizing T-cell receptor gene therapy for hematologic malignancies Expression of immunoglobulin-T-cell receptor chimeric molecules as functional receptors with antibody-type specificity The T-body approach: potential for cancer immunotherapy The basic principles of chimeric antigen receptor design Specific activation and targeting of cytotoxic lymphocytes through chimeric single chains consisting of antibody-binding domains and the gamma or zeta subunits of the immunoglobulin and T-cell receptors Chimeric antigen receptors for T cell immunotherapy: current understanding and future directions Structural design of engineered costimulation determines tumor rejection kinetics and persistence of CAR T cells Chimeric antigen receptors modified T-cells for cancer therapy Adoptive T cell transfer for cancer immunotherapy in the era of synthetic biology Adoptive immunotherapy for cancer: harnessing the T cell response Chimeric antigen receptor T cells for sustained remissions in leukemia CD19 CAR-T cells of defined CD4 + :CD8 + composition in adult B cell ALL patients T cells expressing CD19 chimeric antigen receptors for acute lymphoblastic leukaemia in children and young adults: a phase 1 dose-escalation trial Chimeric antigen receptor-modified T cells for the treatment of solid tumors: defining the challenges and next steps State-of-the-art gene-based therapies: the road ahead Going viral: chimeric antigen receptor T-cell therapy for hematological malignancies Case report of a serious adverse event following the administration of T cells transduced with a chimeric antigen receptor recognizing ERBB2 Treatment of metastatic renal cell carcinoma with autologous T-lymphocytes genetically retargeted against carbonic anhydrase IX: first clinical experience Treatment of metastatic renal cell carcinoma with CAIX CAR-engineered T cells: clinical evaluation and management of on-target toxicity B-cell depletion and remissions of malignancy along with cytokineassociated toxicity in a clinical trial of anti-CD19 chimericantigen-receptor-transduced T cells Clinical development of CAR T cells-challenges and opportunities in translating innovative treatment concepts Current concepts in the diagnosis and management of cytokine release syndrome Preventing and exploiting the oncogenic potential of integrating gene vectors Gene therapy. To this end, T cells can be equipped with an additional T-cell receptor (TCR) or a chimeric antigen receptor (CAR)
    keywords: administration; antibodies; antibody; antigen; cancer; cap; cells; delivery; efficacy; encoding; expression; gene; human; immunotherapy; mice; mrna; protein; receptor; serum; studies; t cells; therapeutic; transfer; treatment; tumor; use; virus; vivo
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        item: #101 of 1349
          id: cord-003482-f1uvohf0
      author: Malmlov, Ashley
       title: Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells
        date: 2019-02-04
       words: 7514
      flesch: 51
     summary: Isolation and haemagglutination-inhibition studies on bats collected in Kenya and throughout Uganda Effect of Zika virus and Bwamba virus in the cave bat (Myotis lucifugus) Transmission studies of Hendra virus (equine morbillivirus) in the fruit bats, horses and cats Pteropid bats are confirmed as the reservoir hosts of henipaviruses: A comprehensive experimental study of virus transmission Antibody-mediated immune response in the bat, Pteropus giganteus Detection of specfic antibody responses to vaccinatin in variable flying foxes (Pteropus hypomelanus) The little brown bat, M. lucifugus, displays a highly diverse VH, DH, JH repertoire but little evidence of somatic hypermutation Tacaribe virus cases fatal infection of an ostensible reservoir host, the Jamaican fruit bat Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis) Transcriptomic signatures of tacaribe virus-infected Jamaican fruit bats Assay optimization for molecular detection of Zika virus A rhesus macaque model of Asian-lineage Zika virus infection Zika virus testing considerations: lessons learned from the first eighty real-time RT-PCR-positive cases diagnosed in New York State Detection of Zika virus in urine Long-term kinetics of Zika virus RNA and antibodies in body fluids of a vasectomized traveller returning from Martinique: a case report Persistence of Zika virus in body fluids-Preliminary report Zika virus causes testis damage and leads to male infertility in mice Zika virus infection damages the testes in mice A mouse model of Zika virus pathogenesis Zika viral infection and neutralizing human antibody response in a BLT humanized mouse model Notes from the field: Evidence of Zika virus infection in brain and placental tissues from two congenitally infected newborns and two fetal losses-Brazil Zika virus damages the human placental barrier and presents marked fetal neurotropism Pathology of congenital Zika syndrome in Brazil: a case series Zika virus infection of rhesus macaques leads to viral persistence in multiple tissues Fetal brain lesions after subcutaneous inoculation of Zika virus in a pregnant nonhuman primate Nonhuman primate models of Zika virus infection, immunity, and therapeutic development Zika viral dynamics and shedding in rhesus and cynomolgus macaques Overview of the current status of Zika virus pathogenesis and animal related research Axl mediates Zika virus entry in human glial cells and modulates innate immune responses Microglia/macrophage-specific protein Iba1 binds to fimbrin and enhances its actin-bundling activity Entry sites of Venezuelan and western equine encephalitis viruses in the mouse central nervous system following peripheral infection Detection of Zika virus in saliva Biology of Zika virus infection in human skin cells Denge virus in Mexican bats Neotropical bats that co-habit with humans function as dead-end hosts for dengue virus Detection of dengue virus neutralizing antibodies in bats from Costa Rica and Ecuador Sylvatic transmission of arboviruses among bornean orangutans Zika virus, vectors, reservoirs, amplifying hosts, and their potential to spread worldwide: what we know and what we should investigate urgently A sero-epidemiological survey for certain arboviruses (Togaviridae) in Pakistan Investigating the potential role of North American animals as hosts for Zika virus. Distribution of viral antigen in bat tissues suggests that infection in this species recapitulates human infection, which is thought to start with infection of epidermal and dermal cells with subsequent dissemination to multiple organs including salivary glands as viral RNA can be detected in human saliva [44, 45] .
    keywords: animal; bats; brain; cells; dpi; fruit; human; infection; rna; serum; study; time; tissues; urine; virus; zika; zikv
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        item: #102 of 1349
          id: cord-003505-qr6ukfti
      author: Tabraue-Chávez, Mavys
       title: A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species
        date: 2019-03-06
       words: 5671
      flesch: 45
     summary: Briefly, abasic PNA probes, PNA 1 and PNA 2 were designed in order to hybridize efficiently with the amplified single strand sense DNA, with the important particularity that the abasic positions in the PNA probes are opposing the nucleobases under interrogation. 3B , the Spin-Tube consists of: (i) a centrifuge collection tube; (ii) an internal column for the assay; (iii) a nylon membrane (pre-spotted with abasic PNA probes) immobilized onto the bottom of the column via a plastic pressure ring (iv).
    keywords: assay; biotin; detection; dna; fig; gdna; pcr; pna; probes; rna; smart; spin; tube
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        item: #103 of 1349
          id: cord-003596-6dg7i06i
      author: Xiong, Qingqing
       title: Biomedical applications of mRNA nanomedicine
        date: 2018-07-27
       words: 12815
      flesch: 30
     summary: Sci Rapidly produced SAM®vaccine against H7N9 influenza is immunogenic in mice Induction of broad-based immunity and protective efficacy by self-amplifying mRNA vaccines encoding influenza virus hemagglutinin Self-replicating replicon-RNA delivery to dendritic cells by chitosan-nanoparticles for translation in vitro and in vivo Polyethylenimine-based polyplex delivery of self-replicating RNA vaccines An RNA nanoparticle vaccine against Zika virus elicits antibody and CD8 + T cell responses in a mouse model Protective efficacy of in vitro synthesized, specific mRNA vaccines against influenza A virus infection An mRNA vaccine encoding rabies virus glycoprotein induces protection against lethal infection in mice and correlates of protection in adult and newborn pigs Safety and immunogenicity of a mRNA rabies vaccine in healthy adults: An open-label, non-randomised, prospective, first-in-human phase 1 clinical trial Type I IFN counteracts the induction of antigen-specific immune responses by lipidbased delivery of mRNA vaccines Induction of HIV-1 gag specific immune responses by cationic micelles mediated delivery of gag mRNA Preclinical and clinical demonstration of immunogenicity by mRNA vaccines against H10N8 and H7N9 influenza viruses Modified mRNA vaccines protect against Zika virus infection Vaccine mediated protection against Zika virus-induced congenital disease RNA melanoma vaccine: Induction of antitumor immunity by human glycoprotein 100 mRNA immunization Direct injection of protamine-protected mRNA: Results of a phase 1/2 vaccination trial in metastatic melanoma patients Final analysis of a phase I/IIa study with CV9103, an intradermally administered prostate cancer immunotherapy based on self-adjuvanted mRNA Lipid nanoparticle assisted mRNA delivery for potent cancer immunotherapy Intranasal mRNA nanoparticle vaccination induces prophylactic and therapeutic anti-tumor immunity Enhancement of dendritic cells transfection in vivo and of vaccination against B16F10 melanoma with mannosylated histidylated lipopolyplexes loaded with tumor antigen messenger RNA Systemic RNA delivery to dendritic cells exploits antiviral defence for cancer immunotherapy mRNA-based vaccines synergize with radiation therapy to eradicate established tumors Combination immunotherapy of MUC1 mRNA nano-vaccine and CTLA-4 blockade effectively inhibits growth of triple negative breast cancer mRNA vaccine with antigen-specific checkpoint blockade induces an enhanced immune response against established melanoma Sojourn from discovery to delivery challenges and clinics Clinical experiences with systemically administered siRNA-based therapeutics in cancer Stability of mRNA/cationic lipid lipoplexes in human and rat cerebrospinal fluid: Methods and evidence for nonviral mRNA gene delivery to the central nervous system Bax mRNA therapy using cationic liposomes for human malignant melanoma Combined effects on tumor growth and metastasis by anti-estrogenic and antiangiogenic therapies in MMTV-neu mice Systemic delivery of messenger RNA for the treatment of pancreatic cancer using polyplex nanomicelles with a cholesterol moiety Systemic messenger RNA therapy as a treatment for methylmalonic acidemia Targeted mRNA therapy for ornithine transcarbamylase deficiency Hopx and the cardiomyocyte parentage Therapeutic efficacy in a hemophilia B model using a biosynthetic mRNA liver depot system Systemic delivery of factor IX messenger RNA for protein replacement therapy Treatment of neurological disorders by introducing mRNA in vivo using polyplex nanomicelles Messenger RNA-based therapeutics for the treatment of apoptosis-associated diseases Transcript-activated collagen matrix as sustained mRNA delivery system for bone regeneration Chemically modified RNA induces osteogenesis of stem cells and human tissue explants as well as accelerates bone healing in rats Translation of angiotensin-converting enzyme 2 upon liver-and lungtargeted delivery of optimized chemically modified mRNA Therapeutic genome editing: Prospects and challenges Genome editing with engineered zinc finger nucleases Small CRISPR RNAs guide antiviral defense in prokaryotes The CRISPR craze Multiplex genome engineering using CRISPR/Cas systems The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA carbonate apatite-cationic liposome conjugates Systemic activation of antigen-presenting cells via RNA-loaded nanoparticles Optimization of lipid nanoparticle formulations for mRNA delivery in vivo with fractional factorial and definitive screening designs Reprogramming human fibroblasts to pluripotency using modified mRNA Delivery materials for siRNA therapeutics Optimization of lipid nanoparticle formulations for mRNA delivery in vivo with fractional factorial and definitive screening designs An orthogonal array optimization of lipid-like nanoparticles for mRNA delivery in vivo Dual-functional lipid-like nanoparticles for delivery of mRNA and MRI contrast agents Bioinspired alkenyl amino alcohol ionizable lipid materials for highly potent in vivo mRNA delivery Boosting intracellular delivery of lipid nanoparticleencapsulated mRNA Chapter 2-Studying lipids involved in the endosomal pathway Lipid nanoparticles for targeted siRNA delivery-going from bench to bedside Lipid nanoparticle systems for enabling gene therapies Polycation gene delivery systems: Escape from endosomes to cytosol Dual-responsive polyplexes with enhanced disassembly and endosomal escape for efficient delivery of siRNA A welldefined coil-comb polycationic brush with star polymers as side chains for gene delivery Enhanced intranasal delivery of mRNA vaccine by overcoming the nasal epithelial barrier via intra-and paracellular pathways Self-aggregating 1.8 kDa polyethylenimines with dissolution switch at endosomal acidic pH are delivery carriers for plasmid DNA, mRNA, siRNA and exon-skipping oligonucleotides Poly-β amino ester-containing microparticles enhance the activity of nonviral genetic vaccines Dual-responsive nanoparticles based on oxidized pullulan and a disulfide-containing poly(β-amino ester) for efficient delivery of genes and chemotherapeutic agents targeting hepatoma Degradable terpolymers with alkyl side chains demonstrate enhanced gene delivery potency and nanoparticle stability Polymer-lipid nanoparticles for systemic delivery of mRNA to the lungs Polymer vectors via controlled/ living radical polymerization for gene delivery PEGylation improves nanoparticle formation and transfection efficiency of messenger RNA Multifunctional triblock copolymers for intracellular messenger RNA delivery Reductive decationizable block copolymers for stimuliresponsive mRNA delivery Dendrimer-RNA nanoparticles generate protective immunity against lethal Ebola, H1N1 influenza, and Toxoplasma gondii challenges with a single dose Chitosans for delivery of nucleic acids Chitosan/hyaluronic acid nanoparticles: Rational design revisited for RNA delivery Protamine enhancement of RNA uptake by cultured chick cells Toll-like receptor-dependent activation of several human blood cell types by protaminecondensed mRNA RNActive® technology: Generation and testing of stable and immunogenic mRNA vaccines Self-adjuvanted mRNA vaccination in advanced prostate cancer patients: A first-in-man phase I/IIa study A targeted and stable polymeric nanoformulation enhances systemic delivery of mRNA to tumors Biodegradable dendronized polymers for efficient mRNA delivery Differentially charged hollow core/shell lipid-polymer-lipid hybrid nanoparticles for small interfering RNA delivery Ultra-small lipid-polymer hybrid nanoparticles for tumorpenetrating drug delivery Cell membrane-derived nanomaterials for biomedical applications Multifunctional envelope-type siRNA delivery nanoparticle platform for prostate cancer therapy Tumor microenvironment-responsive multistaged nanoplatform for systemic RNAi and cancer therapy Restoration of tumor suppression in vivo by systemic delivery of chemically-modified PTEN mRNA nanoparticles Systemic delivery of modified mRNA encoding herpes simplex virus 1 thymidine kinase for targeted cancer gene therapy In vitro and in vivo mRNA delivery using lipid-enveloped pHresponsive polymer nanoparticles Selfassembled inorganic/organic hybrid nanoparticles with multi-functionalized surfaces for active targeting drug delivery Drastic effect of nanoapatite particles on liposome-mediated mRNA delivery to mammalian cells
    keywords: applications; cancer; cap; cas9; cells; delivery; dna; editing; encoding; expression; gene; human; ivt; lipid; mrna; nanoparticles; protein; stability; study; system; therapy; transfection; translation; virus; vivo
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        item: #104 of 1349
          id: cord-003597-zj3w9ptj
      author: Altman, Matthew C.
       title: Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children
        date: 2019-04-08
       words: 13566
      flesch: 37
     summary: By using systems-scale network analysis, we identify repertoires of cellular transcriptional pathways that lead to and underlie distinct patterns of asthma exacerbation. Several additional immune pathways have been linked to asthma exacerbations, generally through targeted investigations 9 .
    keywords: analysis; asthma; blood; cell; cold; data; events; exacerbation; expression; fdr; fig; genes; modules; nasal; network; pathways; response; samples; study; type; virus
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        item: #105 of 1349
          id: cord-003676-kr4o8hoc
      author: Tan, Chee Wah
       title: Serological evidence and experimental infection of cynomolgus macaques with pteropine orthoreovirus reveal monkeys as potential hosts for transmission to humans
        date: 2019-05-28
       words: 3953
      flesch: 47
     summary: We experimentally infected three seronegative, wild-caught monkeys with PRV3M. We demonstrated that monkeys were susceptible to PRV3M infection, but the infection was subclinical. PRV infections in humans vary from asymptomatic or mild flu-like to severe respiratory diseases.
    keywords: animals; bat; bats; human; infection; monkeys; prv; prv3; rna; transmission; virus
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        item: #106 of 1349
          id: cord-003707-fbe47bgi
      author: Russo, Alice G
       title: Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes
        date: 2019-06-18
       words: 9015
      flesch: 45
     summary: I. scapularis NIRVS are enriched in bunya- and orthomyxo-like sequences, reflecting that ticks are a dominant host for these virus groups. Unlike in mosquitoes, I. scapularis NIRVS are more commonly derived from the non-structural region (replicase) of negative-sense viruses, as opposed to structural regions (e.g. glycoprotein).
    keywords: aegypti; et al; fig; genome; like; nirvs; pirna; rna; scapularis; sequences; table; tick; viruses
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        item: #107 of 1349
          id: cord-003711-l3brhmzq
      author: Munnur, Deeksha
       title: Reversible ADP-ribosylation of RNA
        date: 2019-06-20
       words: 6863
      flesch: 46
     summary: We expressed and purified full length PARP10 and tested it for RNA modification activity. For this, we analysed RNA ADP-ribosylation catalysed by PARP10 catalytic domain in the excess presence of adenosine mono-phosphate (AMP) or 5 -phosphoadenosine 3 phosphate (PAP) as potential competitors and we observed no significant change in RNA modification in presence of nucleotide analogue in excess (Supplementary Figure S1D) .
    keywords: activity; adp; catalytic; dna; domain; figure; modification; oligo; parp10; protein; ribosylation; rna; trpt1
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        item: #108 of 1349
          id: cord-003792-v48xeqdz
      author: Izquierdo-Suzán, Mónica
       title: Natural Vertical Transmission of Zika Virus in Larval Aedes aegypti Populations, Morelos, Mexico
        date: 2019-08-17
       words: 4025
      flesch: 36
     summary: Vertical transmission of Zika virus in Ae. aegypti mosquitoes has been evaluated under laboratory conditions by searching for the presence of Zika virus RNA in several organs from the offspring of infected mosquitoes, demonstrating the presence of viral RNA in the guts and salivary glands of the offspring (12) . Only a few studies have addressed the natural vertical transmission of Zika virus in wild mosquito populations; most of these have been carried out in Brazil, where Zika virus RNA has been detected in male Ae. aegypti mosquitoes and in adult Ae. albopictus mosquitoes raised from field-collected eggs (26, 27) .
    keywords: aedes; aegypti; isolate; larvae; mosquitoes; rna; transmission; virus; zika; zika virus
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        item: #109 of 1349
          id: cord-003898-y6zpvw84
      author: Tan, Kai Sen
       title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications
        date: 2019-08-27
       words: 7697
      flesch: 39
     summary: Hence, production of factors such as STAT1 [28] by the hNECs is also crucial in ensuring appropriate regulation of IFNγ-mediated expression of influenza response genes to modulate inflammation and to minimize damage. At later time points, the number of gene expression changes increased substantially, with upregulation of 704 and 1080 genes, and downregulation of 217 and 758 genes at 24 and 48 hpi, respectively.
    keywords: analysis; cells; changes; epithelium; expression; genes; hnecs; hpi; infection; influenza; nasal; responses; rnaseq; time; virus
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        item: #110 of 1349
          id: cord-004274-cot05vx7
      author: Jackson, Nicholas A. C.
       title: The promise of mRNA vaccines: a biotech and industrial perspective
        date: 2020-02-04
       words: 4261
      flesch: 25
     summary: key: cord-004274-cot05vx7 authors: Jackson, Nicholas A. C.; Kester, Kent E.; Casimiro, Danilo; Gurunathan, Sanjay; DeRosa, Frank title: The promise of mRNA vaccines: a biotech and industrial perspective date: 2020-02-04 journal: NPJ Vaccines DOI: 10.1038/s41541-020-0159-8 sha: doc_id: 4274 cord_uid: cot05vx7 mRNA technologies have the potential to transform areas of medicine, including the prophylaxis of infectious diseases. Assuming that mRNA vaccines will be proven clinically efficacious and safe, one of the central advantages hinges on rapidity of manufacture.
    keywords: cap; clinical; delivery; development; expression; human; mrna; novel; phase; self; translation; vaccines
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        item: #111 of 1349
          id: cord-004280-c470nlie
      author: Coleman, Kristen K.
       title: Airborne Influenza A Virus Exposure in an Elementary School
        date: 2020-02-05
       words: 4124
      flesch: 33
     summary: Our study represents the first identification and quantification of airborne influenza virus in an elementary school, and the results suggest that airborne IAV has the potential to circulate in schools during influenza season, in large enough doses known to cause infection. Although airborne influenza virus has been detected in select indoor settings 37, 38, 44, [61]
    keywords: air; densities; iav; influenza; particles; rna; school; student; transmission; virus
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        item: #112 of 1349
          id: cord-004507-ezuyjcxs
      author: Tomazatos, Alexandru
       title: Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes (Natrix natrix)
        date: 2020-02-21
       words: 6329
      flesch: 43
     summary: Putative functions of LEAV proteins were assigned by comparison to sequences in Genbank, using BLASTx. A new fusogenic orthoreovirus species Whole genome characterization of a chelonian orthoreovirus strain identifies significant genetic diversity and may classify reptile orthoreoviruses into distinct species Ecological Partitioning between Dice Snakes (Natrix tessellata) and Grass Snakes (Natrix natrix) in Southern Croatia Cimodo virus belongs to a novel lineage of reoviruses isolated from African mosquitoes A Newly Isolated Reovirus Has the Simplest Genomic and Structural Organization of Any Reovirus A survey of antibody to 10 arboviruses (Koongol group, Mapputta group and ungrouped) isolated in Queensland A new orbivirus isolated from mosquitoes in North-Western Australia shows antigenic and genetic similarity to corriparta virus but does not replicate in vertebrate cells Genetic characterization of Tribeč virus and Kemerovo virus, two tick-transmitted human-pathogenic Orbiviruses Vector competence is strongly affected by a small deletion or point mutations in bluetongue virus Genetic and phylogenetic analysis of the core proteins VP1, VP3, VP4, VP6 and VP7 of epizootic haemorrhagic disease virus (EHDV) RNA segment 9 exists as a duplex concatemer in an Australian strain of epizootic haemorrhagic disease virus (EHDV): Genetic analysis and evidence for the presence of concatemers as a normal feature of orbivirus replication Complete characterisation of the American grass carp reovirus genome (genus Aquareovirus: Family Reoviridae) reveals an evolutionary link between aquareoviruses and coltiviruses Genomic concatemerization/deletion in rotaviruses: A new mechanism for generating rapid genetic change of potential epidemiological importance Genomic rearrangement in genome segment 12 of rice dwarf phytoreovirus A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene Crystal structure of the top domain of African horse sickness virus VP7: Comparisons with bluetongue virus VP7 RGD tripeptide of bluetongue virus VP7 protein is responsible for core attachment to Culicoides cells Characterization of Orungo virus, an orbivirus from Uganda and Nigeria Orungo Virus: Transmission Studies with Aedes Albopictus and Aedes Aegypti (Diptera: Culicidae)1 Replication of Eubenangee virus in Culicoides nubeculosus (Mg.) and Culicoides variipennis (Coq.)
    keywords: analysis; culicoides; figure; genome; genus; host; leav; novel; orbivirus; protein; reassortment; rna; sbov; snakes; species; table; virus; viruses
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        item: #113 of 1349
          id: cord-004509-jkzqmkz6
      author: Thirion, Laurence
       title: Lyophilized Matrix Containing Ready-to-Use Primers and Probe Solution for Standardization of Real-Time PCR and RT-qPCR Diagnostics in Virology
        date: 2020-01-30
       words: 4401
      flesch: 40
     summary: The corresponding volume of P&P solution was dispensed in 2-mL glass vials (WHEATON ® , Dominique Dutscher, Brumath, France). Glass vials containing P&P solution to perform 8 to 96 reactions can be prepared using the protocols presented in Table 2 .
    keywords: assays; chikv; liquid; lyoph; p&p; pcr; results; rna
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        item: #114 of 1349
          id: cord-004534-jqm1hxps
      author: None
       title: Abstract
        date: 2009-06-09
       words: 139178
      flesch: 39
     summary: This simple model illustrates how differential detergent selectivity for faces and strong constraints coming from purely environmental features could influence transmembrane helix packing, membrane protein structure and assembly. Imaging of mobile stable lipid rafts in the live cell plasma membrane M. Brameshuber 1 , J. Weghuber 1 , V. Ruprecht 1 , H. Stockinger 2 , G. J. Schuetz 1 1 Johannes Kepler University Linz, Austria, 2 Medical University of Vienna, Austria The organization of the cellular plasma membrane at a nanoscopic length scale is believed to affect the association of distinct sets of membrane proteins for the regulation of multiple signaling pathways.
    keywords: acid; actin; activation; activity; addition; affinity; afm; aggregates; aggregation; amyloid; analysis; applications; approach; assembly; atomic; atp; behavior; bilayer; binding; biological; biology; biophysics; brain; calcium; cancer; cell; cell membrane; cell surface; center; chain; changes; channel; characterization; charge; chemical; chemistry; cholesterol; combination; complex; complexes; concentration; conditions; confocal; conformational; constant; contrast; control; correlation; cross; current; data; decrease; delivery; density; department; design; detection; development; diffusion; disease; distribution; dna; domain; drug; dynamics; effect; electron; emission; energy; environment; enzyme; excitation; experiments; expression; fibrils; field; flow; fluorescence; fluorescence microscopy; fluorescent protein; force; force microscopy; formation; france; free; fret; function; gene; genova; germany; group; growth; helix; human; imaging; increase; influence; institute; intensity; interaction; intracellular; italy; key; kinetics; laser; length; level; lifetime; ligand; light; lipid; lipid membranes; liposomes; living; measurements; mechanism; membrane; membrane protein; membrane surface; method; microscopy; model; model membrane; molecular; molecules; muscle; mutant; nanoparticles; neuronal; neurons; new; non; novel; number; order; parameters; particles; peptide; phase; physical; physics; plasma membrane; pore; potential; presence; present; probe; process; processes; properties; protein; protein complexes; protein dynamics; protein interactions; protein structure; range; rate; ray; reaction; receptor; region; release; report; research; residues; resolution; response; results; rna; role; sample; scanning; scattering; sciences; second; self; sequence; signal; simulations; site; size; solvent; species; specific; spectroscopy; stability; state; step; structure; studies; study; surface; system; target; techniques; temperature; terminal; time; transfer; transition; transmembrane; transport; treatment; type; understanding; unfolding; university; use; vesicles; virus; vitro; vivo; water; work
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        item: #115 of 1349
          id: cord-004584-bcw90f5b
      author: None
       title: Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary
        date: 2011-08-06
       words: 106959
      flesch: 38
     summary: to that of cell proteins (amide II band at *1550 cm -1 ) Membrane proteins and peptides are acting in an environment rich in other proteins or peptides.
    keywords: acid; actin; activation; activity; affinity; aggregation; amino; amyloid; analysis; applications; approach; assembly; associated; atomic; bilayer; binding; biological; cancer; cell; cell membrane; cell surface; chain; changes; channel; charge; chemical; cholesterol; complex; complexes; composition; compounds; concentration; conditions; conformational; control; correlation; data; delivery; detection; development; diffusion; distribution; dna; domain; drug; dynamics; effect; electron; energy; environment; enzyme; experiments; expression; fast; field; fluorescence; force; formation; free; function; fusion; gene; group; human; hydrophobic; imaging; increase; influence; institute; interaction; key; kinetics; laser; level; ligand; light; lipid; lipid membranes; liposomes; living; magnetic; major; measurements; mechanism; membrane; membrane binding; membrane interaction; membrane protein; membrane structure; membrane surface; method; microscopy; model; model membrane; molecular; molecules; nanoparticles; native; network; new; nmr; non; novel; number; order; organization; parameters; peptide; phase; plasma membrane; potential; presence; processes; properties; protein; protein complex; protein dynamics; protein interactions; protein structure; proton; range; rate; ray; reaction; receptor; region; regulation; research; residues; resolution; response; results; role; scattering; self; signal; simulations; sites; size; species; specific; spectra; spectroscopy; stability; state; structure; studies; study; substrate; surface; system; techniques; temperature; terminal; time; transfer; transition; transport; type; understanding; university; use; vesicles; vitro; vivo; water; work
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        item: #116 of 1349
          id: cord-004656-n4h295e5
      author: Olson, Ann Louise
       title: Developmental Regulation of Angiotensinogen Gene Expression in Sheep
        date: 1990
       words: 2419
      flesch: 49
     summary: Ontogeny of the renin-angiotensin-aldosterone system in the fetal and newborn lamb Neurohormonal regulation of renal function during development Factors influencing plasma renin and angiotensin I1 in the conscious ewe and its foetus Plasma renin levels in the normal and anephric fetus at birth Angiotensinogen gene is expressed and differentially regulated in multiple tissues of the rat Peach MJ 1988 Fetal expression of the angiotensinogen gene The influence of mating management on fertility in ewes following progesterone PMS treatment Developmental aspects of the fetal renal response to exogenous arginine vasopressin Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease Localization of preangiotensinogen messenger RNA sequences in the rat brain Number and evolutionary conservation of alpha and beta-tubulin and cytoplasmic beta and gamma-actin genes using specific cloned cDNA probes Measurement of prothrombin mRNA during gestation and early neonatal development Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter Boedtker H 1977 RNA molecular weight determinations by gel electrophoresis under denaturating conditions, a critical re-examination The Iowa State University Press Induction of rat liver angiotensinogen mRNA following acute inflammation Tissue-specific regulation of angiotensinogen mRNA accumulation by dexamethasone Regulation of liver angiotensinogen mRNA by glucocorticoids and thyroxine Sodium balance effects on renin, angiotensinogen, and atrial natriuretic polypeptide mRNA levels Sodium regulation of angiotensinogen mRNA expression in rat kidney cortex and medulla Tissue distribution of rat angiotensinogen mRNA and structural analysis of its heterogeneity Regional distribution of angiotensinogen messenger RNA in rat adrenal and kidney Intrarenal localization of angiotensinogen mRNA by RNA-DNA dot-blot hybridization Angiotensinogen mRNA is expressed in both rat renal cortex and medulla A comparative study of the distribution of renin and angiotensinogen messenger ribonucleic acids in rat and mouse tissues Angiotensinogen gene expression in extrahepatic rat tissues: application of a solution hybridization assay Regional localization of virus in the central nervous system of mice persistently infected with murine coronavirus JHM Among the fetal and newborn sheep, it appeared that the highest level of liver angiotensinogen mRNA was expressed in the nearterm fetuses.
    keywords: angiotensinogen; expression; kidney; liver; mrna; rat; sheep
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        item: #117 of 1349
          id: cord-004719-3stcx0dd
      author: Mushegian, A. R.
       title: Cell-to-cell movement of plant viruses: Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems
        date: 1993
       words: 6347
      flesch: 38
     summary: Also, as binding of movement proteins to RNA is thought not to be sequence-specific [14, 17] , it could be anticipated that the majority of movement protein will bind to cellular RNAs, which in the case of TMV infection are in excess over virus RNAs at the time when 30 kD protein is transiently expressed [18] . All the proteins containing the conserved motifs shown in Fig. 1 should be considered a single vast, and highly diverged superfamily of plant virus movement proteins.
    keywords: acid; amino; cell; mosaic; movement; movement proteins; plant; proteins; rna; sequence; virus; viruses
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        item: #118 of 1349
          id: cord-004827-bnf3mvaf
      author: Desselberger, U.
       title: Report on an ICTV-sponsored symposium on Virus Evolution
        date: 2005-01-13
       words: 2768
      flesch: 43
     summary: The viruses and their replication Molecular evidence of HIV-1 transmission in a criminal case The nonclonal and transitory nature of HIV in vivo Don't forget about viruses Topological organization of picornaviral genomes: Statistical prediction of RNA structural signals New real-time reverse transcriptase-initiated PCR assay with single-copy sensitivity for human immunodeficiency virus type 1 RNA in plasma Reproducible nonlinear population dynamics and critical points during replicative competitions of RNA virus quasispecies Retroids in Archaea: phylogeny and lateral origins The structure of a thermophilic archaeal virus shows a double stranded DNA viral capsid that spans all domains of life Generation of coronavirus spike deletion variants by high-frequency recombination at regions of predicted RNA secondary structure Evolutionary history of Cucumber mosaic virus deduced by phylogenetic analyses Plant RNA virus evolution Synchronous loss of quasispecies memory in parallel viral lineages: a deterministic feature of viral quasispecies Lethal mutagenesis of the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) New Haven CT 30. A new model for coronavirus transcription Genetic diversity in RNA virus quasispecies is controlled by host-virus interaction Unique and conserved features of genome and proteome of SARS-coronavirus, an early split off from the coronavirus group 2 lineage Of statistics and genomes VP1 of infectious bursal disease virus is an RNA dependent RNA polymerase The 3C-like proteinase of an invertebrate nidovirus links coronavirus and potyvirus homologs On finding all suboptimal foldings of an RNA molecule Prediction of RNA secondary structure by energy minimization Parc d'Innovation, Boulevard Sébastian Brandt, 67400 Illkirch, France.
    keywords: cell; evolution; genome; hiv; quasispecies; recombination; rna; structure; virus; viruses
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        item: #119 of 1349
          id: cord-004848-2cfphi88
      author: Carter, M. J.
       title: Transcription of feline calicivirus RNA
        date: 1990
       words: 3361
      flesch: 56
     summary: [10] employing oligo-dT as primer for the reverse transcription of 2 gg of virus RNA. We have used this to probe FCV-infected cells for the synthesis of virus specific RNA and confirm and extend the observations of Neill and Mengeling.
    keywords: end; fcv; genome; rna; rnas; sense; sequence; virus
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        item: #120 of 1349
          id: cord-004851-h9ppa064
      author: Plagemann, P. G. W.
       title: Hepatitis C virus
        date: 1991
       words: 6839
      flesch: 45
     summary: It also has become apparent that HepCV RNA becomes detectable by polymerase chain reaction (PCR) procedures much sooner after infection than anti-HepCV antibodies and that HepCV RNA might be detectable in the absence of detectable levels of serum antibodies. HepCV RNA was detectable in serum of two experimentMly infected chimpanzees 3 days p.i.
    keywords: amino; antibodies; genome; hepatitis; hepcv; non; pestiviruses; protein; rna; sequence; virus
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        item: #121 of 1349
          id: cord-004879-pgyzluwp
      author: None
       title: Programmed cell death
        date: 1994
       words: 81833
      flesch: 47
     summary: 8cl-2(z is a mitochondrial or perinuclear-associated oncoprotein that prolongs the life span of a variety of cell types by interfering with programmed cell death. Single and repetitive uptake and release of CPZ were measured in each cell type after individual exposure or exposure in any combination of cell types: In 2 hour competitive uptake studies fibreblasts reached 1.7 and 2.6 times the concentrations of C6-and ROC-cells, :respectively.
    keywords: acid; activation; activity; addition; adult; amino; analysis; animals; antibodies; binding; brain; calcium; cdna; cell lines; cells; changes; cloned; complex; concentrations; conditions; contrast; control; cultures; current; data; days; decrease; development; different; differentiation; dna; domain; early; effects; end; enzyme; epithelial; experiments; expression; extracts; factor; family; fold; form; formation; function; fusion; gene; gene expression; growth; homology; hormone; human; increase; induction; infected; inhibition; institut; interaction; intracellular; kda; kinase; levels; major; mammalian; mechanisms; medium; membrane; mice; molecular; mouse; mrna; muscle; mutant; nerve; neuronal; neurons; new; non; nuclear; nucleus; number; order; pathway; phosphorylation; play; positive; potential; presence; present; process; production; promoter; properties; protein; protein expression; rat; rate; rats; reaction; receptor; recombinant; recombination; region; regulation; release; replication; response; results; rna; role; sequence; signal; sites; species; specific; stage; stimulation; structure; studies; study; subunit; surface; synthesis; system; t cells; target; terminal; time; tissue; tnf; transcription; treatment; tumor; type; university; virus; vitro; vivo; yeast
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        item: #122 of 1349
          id: cord-005010-xg2bv9gy
      author: Dayer, Mohammad Reza
       title: Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus
        date: 2015-01-30
       words: 4252
      flesch: 40
     summary: The lower RMSF of CCHFV nucleoprotein complex with negative sense RNA compared to its complex with positive sense RNA indicates lower flexibility and therefore more stable conformation of the former complex. The preferential packaging of the negative sense RNA by CCHFV nucleoprotein in viral assembly seems to be assisted by specific structure recognition characteristics which differentiates between negative sense RNA and positive sense one.
    keywords: binding; cchfv; fever; nucleoprotein; rna; sense; sense rna; structure; virus
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        item: #123 of 1349
          id: cord-005060-n901y2d4
      author: ZHANG, Feiyun
       title: Complete Nucleotide Sequence of Ryegrass Mottle Virus : A New Species of the Genus Sobemovirus
        date: 2001
       words: 2606
      flesch: 53
     summary: Sobemovirus genome appears to encode a serine protease related to cysteine proteases of picornaviruses Genus sobemovirus Signals for ribosomal frameshifting in the rous sarcoma virus gag-pol region Characterization of ribosomal frameshift in HIV-1 gag-pol expression The putative replicase of the cocksfoot mottle sobemovirus is translated as a part of the polyprotein by -1 ribosomal frameshift Sequence and organization of barley yellow dwarf virus genomic RNA Luteovirus gene expression genome characterization of rice yellow mottle virus RNA Nucleotide sequence of the bean strain of southern bean mosaic virus Identification of four conserved motifs among the RNA-dependent polymerases encoding elements Messenger RNA for the coat protein of southern bean mosaic virus Nucleotide sequence of RNA from the sobemovirus found in infected cocksfoot shows a luteovirus-like arrangement of the putative replicase and protease genes Translation of southern bean mosaic virus RNA in wheat embryo and rabbit reticulocyte extracts Complementarity between the 5'-and 3'-terminal sequences of rice stripe virus RNAs Identification of genes encoding for the cocksfoot mottle virus proteins Cocksfoot mottle virus in Japan Ryegrass mottle virus, a new virus from Lolium multiflorum in Japan Nucleotide sequence of RNA 1, the largest genomic segment of rice stripe virus, the prototype of the tenuivirus The genome-linked protein (VPg) of southern bean mosaic virus is encoded by the ORF2 Guidelines to the demarcation of virus species Sequence and organization of southern bean mosaic virus genomic RNA Evolution of RNA viruses Analysis of the in vitro translation products of RGMoV RNA suggests that the 68 kDa protein may represent a fusion protein of ORF 2-ORF 3 produced by frameshifting.
    keywords: amino; kda; orf; protein; rgmov; rna; sequence; virus
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        item: #124 of 1349
          id: cord-005147-mvoq9vln
      author: None
       title: Autorenregister
        date: 2017-02-23
       words: 86765
      flesch: 41
     summary: While a long list of gene mutations have so far been described to be responsible for the disease phenotype, little is known about the underlying neuronal mechanisms. WD pathogenesis, however, can not only be explained by gene coding mutations since phenotypes exhibit strong variations despite the same exonic DNA makeup in the gene.
    keywords: activity; addition; age; allele; analysis; approach; array; association; autosomal; blood; brain; breast; cancer; candidate; carriers; cases; cause; cell; children; chromosome; clones; coding; cohort; complex; conclusion; controls; data; delay; deletion; development; diagnosis; different; disability; disease; disease genes; disorders; dna; dominant; effect; exome; exome sequencing; exon; expression; factors; families; family; features; female; findings; function; gene; gene expression; generation; genetic; genome; genomic; germany; germline; growth; heterozygous; homozygous; human; identification; individuals; institute; levels; loci; loss; low; methods; methylation; mice; missense; model; molecular; mouse; mrna; mutations; negative; new; ngs; non; normal; novel; novo; number; onset; p =; panel; parents; pathways; patients; pcr; phenotype; potential; present; protein; receptor; recessive; regions; report; results; risk; rna; role; samples; sequence; sequencing; sites; skin; specific; spectrum; splice; splicing; studies; study; syndrome; system; target; testing; time; tissue; transcription; treatment; tumor; variants; wes; years
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        item: #125 of 1349
          id: cord-005281-wy0zk9p8
      author: Blinov, V. M.
       title: Viral component of the human genome
        date: 2017-05-09
       words: 6592
      flesch: 37
     summary: The reverse process, i.e., the acquisition of host genes or shorter sequences by viruses, is also possible, although viral genomes obviously have a lower abso-lute capacity for storing the acquired material. However, these relations are in fact two-sided and involve modifications of both the virus and host genomes.
    keywords: cells; dna; elements; genes; genome; host; host genome; human; insertions; retroviruses; rna; sequences; virus; viruses
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        item: #126 of 1349
          id: cord-005377-36io7zsm
      author: Sidoti, Francesca
       title: Alternative Molecular Tests for Virological Diagnosis
        date: 2012-04-09
       words: 5999
      flesch: 30
     summary: A virus (H1N1) by real-time nucleic acid sequence-based amplification Development and validation of a commercial real time NASBA assay for the rapid confirmation of influenza AH5N1 virus in clinical samples Clinical evaluation of NucliSens magnetic extraction and Nu-cliSens analytical specific reagents for the real-time detection of respiratory syncytial virus (RSV) in pediatric respiratory specimens A one-tube quantitative HIV-1 RNA NASBA nucleic acid amplification assay using electrochemiluminiscent (ECL) labelled probes Quantitation of human immunodeficiency virus type 1 RNA in different biological compartments Single rapid realtime monitored isothermal RNA amplification assay for quantification of human immunodeficiency virus type 1 isolates from groups M, N, and O Evaluation of the persistence of infectious human norovirus on food surfaces by using real time nucleic acid sequence-based amplification Diagnosis of human metapneumovirus infection in immunosuppressed lung transplant recipients and children evaluated for pertussis Real time NASBA detection of SARSassociated coronavirus and comparison with real-time reverse transcription-PCR Evaluation of real time nucleic acid based amplification for detection of Chikungunya virus in clinical sample Nucleic acid sequencebased amplification assays for rapid detection of West Nile and St. Louis encephalitis viruses Real time nucleic acid sequence-based amplification assay for detection of hepatitis A virus Characterization of the quantitative HCV NASBA assay Evaluation of a new NASBA assay for the detection of hepatitis C virus based on the NucliSens basic kit reagents Detection of rhinoviruses by tissue culture and two independent amplification techniques, nucleic acid sequence-based amplification and reverse transcription-PCR, in children with acute respiratory infections during a winter season A sensitive and robust method for measles RNA detection Comparative detection of rabies RNA by NASBA, real-time PCR and conventional PCR Rapid and simple method for the purification of nucleic acids Comparison of five methods for extraction of Legionella pneumophila from respiratory specimens Evaluation of NucliSens easyMAG for automated nucleic acid extraction from various clinical specimens Development and evaluation of nucleic acid sequence based amplification (NASBA) for diagnosis of enterovirus infections using the NucliSens Ò Basic Kit Development of a novel one-tube isothermal reverse transcription thermophilic helicase-dependent amplification platform for rapid RNA detection Helicase dependent OnChip-amplification and its use in multiplex pathogen detection Bacteriophage T4 gene 32 protein: modulation of protein-nucleic acid and protein-protein association by structural domains Snapshot of the genome of the pseudo-T-even bacteriophage RB49 Escherichia coli helicase II (uvrD) protein can completely unwind fully duplex linear and nicked circular DNA Characterization of a thermostable UvrD helicase and its participation in helicase-dependent amplification Colorimetric detection of Helicobacter pylori DNA using isothermal helicase-dependent amplification and gold nanoparticle probes Improving isothermal DNA amplification speed for the rapid detection of Mycobacterium tuberculosis An oligomeric form of E. coli UvrD is required for optimal helicase activity Helicase-dependent isothermal DNA amplification Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements Bacteriophage T7: minimal requirements for the replication of a duplex DNA molecule Characterization of the helicase and primase activities of the 63-kDa component of the bacteriophage T7 gene 4 protein Cloning and expression of gene 4 of bacteriophage T7 and creation and analysis of T7 mutants lacking the 4A primase/ helicase or the 4B helicase DNA replication DNA-dependent nucleoside 5 0 -triphosphatase activity of the gene 4 protein of bacteriophage T7 Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7 Isothermal DNA amplification in vitro: the helicase-dependent amplification system Nucleic acid assay system for tier II labs and moderately complex clinics to detect HIV in low-resource settings A rapid and simple isothermal nucleic acid amplification test for detection of herpes simplex virus types 1 and 2 Detection of Helicobacter pylori by enzyme-linked immunosorbent assay of thermophilic helicase-dependent isothermal DNA amplification Helicase-dependent amplification: use in OnChip amplification and potential for point-of-care diagnostics Real-time PCR array chip with capillary-driven sample loading and reactor sealing for point-ofcare applications An integrated disposable device for DNA extraction and helicase dependent amplification Real-time electrochemical monitoring of isothermal helicase-dependent amplification of nucleic acids The first HDA system for isothermal DNA amplification was developed by using E. coli UvrD DNA helicase (*82 kDa) along with a DNA polymerase, and two accessory proteins (SSBs): T4 gene 32 or RB 49 gene 32 proteins [78, 79] .
    keywords: amplification; detection; dna; helicase; isothermal; lamp; loop; method; nasba; nucleic; reaction; rna; time; virus
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        item: #127 of 1349
          id: cord-005378-u2bbgn8k
      author: Yun, Sang-Im
       title: Overview: Replication of porcine reproductive and respiratory syndrome virus
        date: 2013-12-19
       words: 6592
      flesch: 19
     summary: Autocatalytic processing of these precursors generates at least 14 nonstructural proteins (NSPs) (Ziebuhr et al., 2000; Fang and Snijder, 2010) : 10 encoded in ORF1a (NSP1α, NSP1β, NSP2 to NSP6, NSP7α, NSP7β, and NSP8) and 4 encoded in ORF1b (NSP9 to NSP12) (Snijder et al., 1992 (Snijder et al., , 1994 den Boon et al., 1995; van Dinten et al., 1996; This proteolytic processing is mediated by four viral proteases residing in NSP1α, NSP1β, NSP2, and NSP4 (den Boon et al., 1995; Snijder et al., 1996; van Aken et al., 2006b) .
    keywords: arterivirus; domain; et al; genome; porcine; protease; protein; prrsv; replication; rna; snijder; snijder et; syndrome; syndrome virus; synthesis; van; virus
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        item: #128 of 1349
          id: cord-005392-0pgcfk6b
      author: Sidoti, Francesca
       title: Development of a Quantitative Real-Time Nucleic Acid Sequence-Based Amplification Assay with an Internal Control Using Molecular Beacon Probes for Selective and Sensitive Detection of Human Rhinovirus Serotypes
        date: 2011-07-05
       words: 3623
      flesch: 34
     summary: We described a simple method to accurately quantify RNA target by computing the time to positivity (TTP) values for HRV RNA. Titrations of IC RNA (between 10 and 10 6 copies) and HRV RNA were performed to determine the optimal amount of internal control to generate the greatest dynamic range for the assay without interference with the detection of HRV RNA (data not shown).
    keywords: amplification; assay; detection; hrv; nasba; reaction; rna; time
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        item: #129 of 1349
          id: cord-005654-n9u2em10
      author: Campbell, David A.
       title: Apparent discontinuous transcription of Trypanosoma brucei variant surface antigen genes
        date: 1984
       words: 4261
      flesch: 52
     summary: To enable nucleotide sequence analysis of the mini-exon repeat, recombinant plasmids containing individual repeats were generated. As the mini-exon should include an RsaI site, nucleotide sequence analysis in the vicinity of this site was performed on one of the plasmids (pMEP.1).
    keywords: exon; fig; gene; medrna; mini; repeat; rna; sequence; site; vsg
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        item: #130 of 1349
          id: cord-005865-7lohh5ty
      author: Pipper, Juergen
       title: Catching bird flu in a droplet
        date: 2007-09-23
       words: 4176
      flesch: 45
     summary: At present, we are working on the implementation of a second optical channel for an internal control that allows the user to check on the SPE of the RNA as well as for possible PCR inhibition. QuantiTect SYBR Green RT-PCR Kit (Qiagen) (8.7, 50, 480), SuperScript III Platinum SYBR Green One-Step qRT-PCR Kit (Invitrogen) (8.4, 60, 180) and LightCycler RNA Master SYBR Green I Kit (Roche) (8.5, 61, 240).
    keywords: droplet; h5n1; influenza; particles; pcr; rna; sample; time
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        item: #131 of 1349
          id: cord-006049-sw1hki4r
      author: Keefe, Anthony D.
       title: Aptamers as therapeutics
        date: 2010
       words: 9812
      flesch: 32
     summary: Antisoma website A randomized, repeat-dose, pharmacodynamic and safety study of an antidotecontrolled factor IXa inhibitor Phase 1b randomized study of antidote-controlled modulation of factor IXa activity in patients with stable coronary artery disease Crystal structure of von Willebrand factor (VWF) A1 domain in complex with aptamer ARC1172, an inhibitor of VWF-platelet binding First-in-human evaluation of anti von Willebrand factor therapeutic aptamer ARC1779 in healthy volunteers Phase I clinical evaluation of ARC1779, a von Willebrand factor-specific aptamer that was driven to bind the A1 domain of the target by toggling between different target forms during SELEX Effect of NU172 and bivalirudin on ecarin clotting time in human plasma and whole blood Drusen associated with aging and age-related macular degeneration contain proteins common to extracellular deposits associated with atherosclerosis, elastosis, amyloidosis, and dense deposit disease Discovery of a PDGF-specific aptamer that is currently undergoing clinical evaluation as part of a combination therapy for AMD Podocytes produce homeostatic chemokine stromal cell-derived factor-1/CXCL12, which contributes to glomerulosclerosis, podocyte loss and albuminuria in a mouse model of type 2 diabetes Anti-Ccl2 Spiegelmer permits 75% dose reduction of cyclophosphamide to control diffuse proliferative lupus nephritis and pneumonitis in MRL-Fas(lpr) mice Physicochemical stability of NOX-E36, a 40mer l-RNA (Spiegelmer) for therapeutic applications Late onset of Ccl2 blockade with the Spiegelmer mNOX-E36-3′PEG prevents glomerulosclerosis and improves glomerular filtration rate in db/db mice Automated RNA selection Automated selection of anti-protein aptamers Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer Micromagnetic selection of aptamers in microfluidic channels Generation of highly specific aptamers via micromagnetic selection The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamerbased proteomics array RNA-mediated metal-metal bond formation in the synthesis of hexagonal palladium nanoparticles RNA-catalysed carbon-carbon bond formation Selection of RNA amide synthases Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes In silico selection of RNA aptamers Cell-specific aptamers for targeted therapies Identification of liver cancerspecific aptamers using whole live cells A tenascin-C aptamer identified by tumor cell SELEX: systematic evolution of ligands by exponential enrichment An early example of cell SELEX in which selection was performed against a monolayer of living tumour-derived cells with the target identification occurring once SELEX was complete Technical and biological issues relevant to cell typing with aptamers Directed evolution of gold nanoparticle delivery to cells Using aptamers evolved from cell-SELEX to engineer a molecular delivery platform Combinatorial selection of high affinity RNA ligands to live African trypanosomes In vivo selection of tumor-targeting RNA motifs A novel antidote-controlled anticoagulant reduces thrombin generation and inflammation and improves cardiac function in cardiopulmonary bypass surgery Assembling OX40 aptamers on a molecular scaffold to create a receptor-activating aptamer Bivalent aptamers deliver the punch Aptamers and aptamer targeted delivery An autonomous molecular computer for logical control of gene expression Escort aptamers: a delivery service for diagnosis and therapy Overview of prostate-specific membrane antigen The clinical role of prostate-specific membrane antigen (PSMA) Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen An aptamer-doxorubicin physical conjugate as a novel targeted drug-delivery platform Molecular assembly of an aptamer-drug conjugate for targeted drug delivery to tumor cells Phototoxic aptamers selectively enter and kill epithelial cancer cells Gelonin analogs with engineered cysteine residues form antibody immunoconjugates with unique properties Aptamer:toxin conjugates that specifically target prostate tumor cells RNA interference: antiviral defense and genetic tool On the delivery of small interfering RNAs into mammalian cells Harnessing in vivo siRNA delivery for drug discovery and therapeutic development Aptamer mediated siRNA delivery Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras First demonstration of antitumour activity in a mouse xenograft model with the systemic delivery of an aptamer-targeted siRNA conjugate Demonstration of activity in vivo for a HIV-specific siRNA conjugated to a gp120-specific aptamer that enables the targeting of infected cells Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of Dicer substrate siRNAs into HIV infected cells Nanoparticle-aptamer bioconjugates: a new approach for targeting prostate cancer cells Targeted delivery of cisplatin to prostate cancer cells by aptamer functionalized Pt(IV) prodrug-PLGA-PEG nanoparticles Precise engineering of targeted nanoparticles by using self-assembled biointegrated block copolymers Reversible cell-specific drug delivery with aptamer-functionalized liposomes CELL-SELEX: novel perspectives of aptamer-based therapeutics RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase Selection and design of high-affinity RNA ligands for HIV-1 Rev High-affinity RNA ligands to basic fibroblast growth factor inhibit receptor binding Isolation of virus-neutralizing RNAs from a large pool of random sequences Isolation of highaffinity RNA ligands to HIV-1 integrase from a random pool Nuclease-resistant nucleic acid ligands to vascular permeability factor/vascular endothelial growth factor High-affinity oligonucleotide ligands to human IgE inhibit binding to Fc epsilon receptor I Calcium-dependent oligonucleotide antagonists specific for l-selectin Isolation of a nucleaseresistant decoy RNA that can protect human acetylcholine receptors from myasthenic antibodies Isolation and characterization of 2′-fluoro-,2′-amino-, and 2′-fluoro-/amino-modified RNA ligands to human IFN-γ that inhibit receptor binding Potent 2′-amino-, and 2′-fluoro-2′-deoxyribonucleotide RNA inhibitors of keratinocyte growth factor In vivo imaging of inflammation using an aptamer inhibitor of human neutrophil elastase Oligonucleotide inhibitors of P-selectin-dependent neutrophil-platelet adhesion In vitro selection of RNA molecules that displace cocaine from the membrane-bound nicotinic acetylcholine receptor High-affinity aptamers selectively inhibit human nonpancreatic secretory phospholipase A2 (hnps-PLA2) RNA molecules that bind to and inhibit the active site of a tyrosine phosphatase Selection of a RNA aptamer that binds to human activated protein C and inhibits its protease function Cutting edge: novel RNA ligands able to bind CD4 antigen and inhibit CD4 + T lymphocyte function Selection and characterization of an RNA decoy for transcription factor NF-κB Cytoplasmic RNA modulators of an inside-out signal-transduction cascade Controlling small guanine-nucleotideexchange factor function through cytoplasmic RNA intramers Nucleic acid ligands to integrins Targeted inhibition of αvβ3 integrin with an RNA aptamer impairs endothelial cell growth and survival Tenascin-C aptamers are generated using tumor cells and purified protein Optimizing aptamer activity for gene therapy applications using expression cassette SELEX Generation of RNA aptamers to the G-protein-coupled receptor for neurotensin, NTS-1 Structure/function analysis of an RNA aptamer for hepatitis C virus NS3 protease Neutralization of infectivity of diverse R5 clinical isolates of human immunodeficiency virus type 1 by gp120-binding 2′F-RNA aptamers Multivalent RNA aptamers that inhibit CTLA-4 and enhance tumor immunity Discriminatory aptamer reveals serum response element transcription regulated by cytohesin-2 Identification of potent and selective RNA antagonists of the IFN-γ-inducible CXCL10 chemokine Neutralizing aptamers from wholecell SELEX inhibit the RET receptor tyrosine kinase DNA aptamers that bind to MUC1 tumour marker: design and characterization of MUC1-binding single-stranded DNA aptamers A nuclease-resistant RNA aptamer specifically inhibits angiopoietin-1-mediated Tie2 activation and function Anti-bovine prion protein RNA aptamer containing tandem GGA repeat interacts both with recombinant bovine prion protein and its beta isoform with high affinity Antimetastatic potential of PAI-1-specific RNA aptamers Aptamers selected against the unglycosylated EGFRvIII ectodomain and delivered intracellularly reduce membrane-bound EGFRvIII and induce apoptosis Affinity capture onto magnetic beads is also amenable to miniaturization 91, 92 , and using picomolar amounts of targets aptamers with dissociation constants as low as 25 nm were selected.
    keywords: activity; affinity; aptamers; cancer; cells; delivery; dna; drug; factor; human; oligonucleotides; peg; protein; receptor; rna; selection; selex; sirna; specific; target; therapeutic; vivo
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        item: #132 of 1349
          id: cord-006068-w3if1hns
      author: Marshak-Rothstein, Ann
       title: Toll-like receptors in systemic autoimmune disease
        date: 2006
       words: 10136
      flesch: 33
     summary: Importantly, IFNα markedly upregulates the expression of TLR7 and the TLR adaptor protein MyD88 (myeloid differentiation primary-response gene 88) in both human B cells 41 and mouse B cells (A.M.R. and T. Behrens, unpublished observations) and can also increase the response of B cells to TLR9 ligands 42 . The optimal motif for stimulation of mouse cells is GACGTT, and GTCGTT is the optimal motif for stimulation of human cells 108 .
    keywords: activation; antibodies; autoimmune; cells; complexes; disease; dna; immune; ligands; lupus; mice; receptor; rna; sle; tlr7; tlr9; toll
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        item: #133 of 1349
          id: cord-006129-5rog0s98
      author: Hemida, Maged Gomaa
       title: Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases: Expectations and Limitations
        date: 2012-08-16
       words: 7449
      flesch: 39
     summary: [12] We will discuss the roles and therapeutic potential of cellular as well as viral miRNAs (if any) in the pathogenesis and treatment of different viral diseases. HPyVs are able to encode viral miRNAs for their own benefit.
    keywords: cellular; diseases; expression; gene; host; human; immune; infection; micrornas; mirnas; replication; target; targeting; virus; viruses
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        item: #134 of 1349
          id: cord-006331-s2qf98lj
      author: Spiridonova, V. A.
       title: Molecular recognition elements: DNA/RNA-aptamers to proteins
        date: 2010-05-23
       words: 7145
      flesch: 57
     summary: Now convincing evidence exists that aptamers are a new effective group of therapeutics, which may represent The scheme illustrating the SELEX method for preparation of DNA and RNA aptamers. The range of disso ciation constants characterizing binding of DNA and RNA aptamers to their protein targets varies from nanomolar to subnanomolar levels.
    keywords: activity; aptamer; binding; cells; complex; control; dna; hiv; human; library; molecules; protein; rna; rounds; selection; thrombin
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        item: #135 of 1349
          id: cord-006452-mmdk2xom
      author: Chen, Jing
       title: Nucleic Acid-Based Therapeutics for Pulmonary Diseases
        date: 2018-10-18
       words: 6615
      flesch: 28
     summary: One of the most challenging intracellular barriers for nucleic acids delivery is their tendency to remain entrapped in endosomes. The susceptibility of nucleic acids to degradation and the complex structure of lungs retard the effective pulmonary delivery of nucleic acid drug.
    keywords: acids; administration; cancer; cells; delivery; diseases; drug; gene; lung; nucleic; patients; pulmonary; sirna; target; therapeutic; therapy; tumor
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        item: #136 of 1349
          id: cord-006826-vnmg0zid
      author: Rayaprolu, Vamseedhar
       title: Length of encapsidated cargo impacts stability and structure of in vitro assembled alphavirus core-like particles
        date: 2017-12-06
       words: 6546
      flesch: 52
     summary: In our previous work we used a 27mer oligo to drive RRV CP assembly into CLPs With HBV, CP protein missing the arginine-rich domain can self-assemble but when this domain is present either nucleic acid or phosphorylation of the CP is necessary, implying that electrostatic repulsion between argininerich domains must be neutralized before assembly can occur, ( [45, 46] , personal communication M Comos Garcia and W Gelbart).
    keywords: 27mer; 48hp; assembly; capsid; cargo; clps; figure; interactions; length; structure; virus
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        item: #137 of 1349
          id: cord-006935-wzz5t3sv
      author: Gorbalenya, Alexander E.
       title: Viral cysteine proteinases
        date: 1996
       words: 8126
      flesch: 60
     summary: RNA virus proteinases mediate their liberation from giant multidomain precursors in which they tend to occupy conserved positions. The essential nature of the enzymes When tested, the majority of (+)RNA viral cysteine proteinases appeared to be essential for viral growth.
    keywords: 3cl; activity; cysteine; pr °; proteinases; residues; rna; site; viral; virus; viruses
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        item: #138 of 1349
          id: cord-006951-tj22dh5o
      author: Li, Siyu
       title: The effect of RNA stiffness on the self-assembly of virus particles
        date: 2018-01-31
       words: 4914
      flesch: 57
     summary: In all previous theoretical and simulation studies related to the impact of RNA topology on virus assembly, the focus has been on the importance of the degree of branching, ignoring the impact of base-pairing on the RNA Kuhn length and linear charge density. These experiments emphasize the impact of RNA structure on the assembly of viral shells, as RNA1 of BMV has a more compact structure than that of CCMV
    keywords: branched; capsid; kuhn; length; linear; number; rna
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        item: #139 of 1349
          id: cord-006960-9pho3hk6
      author: Prakash, R.
       title: Droplet Microfluidic Chip Based Nucleic Acid Amplification and Real-Time Detection of Influenza Viruses
        date: 2013-12-27
       words: 6281
      flesch: 46
     summary: Single surface droplet actuation methodologies for transport, mixing and cycling of PCR samples and reagents.-Dispensing, mixing and subsequent manipulations of PCR sample and reagent droplets were achieved using two popular electro-actuation methods, namely Droplet dielectrophoresis (D-DEP) 16, 17 and/or, Electrowetting (EW). In this investigation, we have leveraged electro-actuation based Droplet microfluidics (DMF), where electric field effects are utilized for dispensing and subsequent handling of droplets, as the method of choice for handling PCR samples and reagents.
    keywords: amplification; chip; detection; droplet; electrode; figure; influenza; micro; pcr; reaction; rna; sample; temperature
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        item: #140 of 1349
          id: cord-007009-4wbvdg1r
      author: Takahashi, Toru
       title: The First Identification and Retrospective Study of Severe Fever With Thrombocytopenia Syndrome in Japan
        date: 2014-03-15
       words: 4691
      flesch: 44
     summary: SFTSV RNA was present, with high copy numbers, in the right axillary and cervical lymph node sections (Supplementary Table 3 ). Consistent with immunohistochemical analysis results, low copy numbers (100-1000 copies) of SFTSV RNA were also detected in the bone marrow, the spleen, the liver, and the adrenal glands.
    keywords: cells; fever; figure; japan; lymph; nodes; patients; rna; serum; sftsv; syndrome; thrombocytopenia; virus
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        item: #141 of 1349
          id: cord-007041-rloey02j
      author: Harel, Noam
       title: Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations
        date: 2019-12-16
       words: 7128
      flesch: 45
     summary: In microbes, such diversity is generated in particular by high mutation rates, which may generate both nucleotide substitutions as well as point insertions or deletions (indels) (1) . We devised a method called AssociVar that detects the real variants in the data, based on the following properties: (a) the method searches for the strongest non-random associations, (b) the method takes into account that pairs of proximal positions (i.e. up to 15 bases apart) that have high associations between them are likely false positives induced by the MinION machine itself, (c) in order to make the different positions comparable, the method normalizes the distribution of chi square scores per position, essentially searching for outliers from all the associations of a given po-sition, (d) the method also takes into account that because proximal positions are highly associated, a position next to a real mutation may be associated with other real mutations due to transitivity.
    keywords: associvar; data; errors; frequency; genome; illumina; minion; mutations; positions; rna; sequencing; variants
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        item: #142 of 1349
          id: cord-007066-zn10rnrm
      author: Park, Noh Jin
       title: Characterization of RNA in Saliva
        date: 2006-06-01
       words: 4651
      flesch: 55
     summary: In this study, we analyzed the integrity, sources, and stability of salivary RNA. Methods: We measured the integrity of salivary RNA with reverse transcription followed by PCR (RT-PCR) or RT-quantitative PCR (RT-qPCR).
    keywords: -actin; fig; human; mrna; pcr; rna; saliva; salivary
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        item: #143 of 1349
          id: cord-007181-qpahuqld
      author: YOGO, Yoshiaki
       title: Polyadenylate in the Virion RNA of Mouse Hepatitis Virus
        date: 1977-10-17
       words: 2061
      flesch: 53
     summary: MH virion RNA can bind to a poly(U)-fiberglass filter, indicating that MH virion RNA contains poly(A). These results suggest that MH virion RNA contains poly(A).
    keywords: poly(a; rna; virion; virus
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        item: #144 of 1349
          id: cord-007208-wnkjdg6y
      author: Li, Sheng-Hsiang
       title: Demonstration of a Glycoprotein Derived From the Ceacam10 Gene in Mouse Seminal Vesicle Secretions(1)
        date: 2005-09-01
       words: 5646
      flesch: 52
     summary: The role of the seminal vesicles, coagulating glands and prostate glands on the fertility and fecundity of mice Effects of seminal vesicle removal on fertility and uterine sperm motility in the house mouse The androgendependent mouse seminal vesicle secretory protein IV: characterization and complementary deoxyribonucleic acid cloning A novel heat-labile phospholipid-binding protein, SVS VII, in mouse seminal vesicle as a sperm motility enhancer Developmental profile of a caltrin-like protease inhibitor, P12, in mouse seminal vesicle and characterization of its binding sites on sperm surface Seminal vesicle autoantigen, a novel phospholipid-binding protein secreted from luminal epithelium of mouse seminal vesicle, exhibits the ability to suppress mouse sperm motility A seminal vesicle autoantigen of mouse is able to suppress sperm capacitation-related events stimulated by serum albumin The cea10 gene encodes a secreted member of the murine carcinoembryonic antigen family and is expressed in the placenta, gastrointestinal tract and bone marrow Enzymatic deglycosylation of asparagine-linked glycans: purification, properties, and specificity of oligosaccharide-cleaving enzymes from Flavobacterium meningosepticum Measurement of protein using bicinchoninic acid Various forms of mouse lactoferrins: purification and characterization Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Molecular Cloning. 5PW column (Waters, Milford, MA); Vydac 218TP54 C 18 column (Separations Group, Hesperia, CA); AminoLink coupling gel, bicinchoninic protein assay kit (Pierce, Rockford, IL); testosterone propionate, nitroblue tetrazolium, 5-bromo-4-chloro-3-indolyl phosphate (BCIP), PMSF, periodic acid Schiff reagent, and silanated glass slides (Sigma Chemical Co., St Louis, MO); cDNA integrity kit, alkaline phosphataseconjugated streptavidin, and biotin-conjugated goat anti-rabbit immunoglobulin G (IgG; Kirkegaard & Perry Laboratories, Gaithersburg, MD); rhodamine-conjugated goat anti-rabbit IgG (Zymed Laboratories, San Francisco, CA); Nuclear Fast Red (Vector Laboratories, Burlingame, CA); enhanced chemiluminescent substrate and [␣- 32 A) Fractionation of soluble mouse SVS proteins by ion exchange chromatography on a DEAE-Sephacel column.
    keywords: ceacam10; column; fig; mice; min; motility; mouse; peak; protein; rna; solution; sperm; vesicle
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        item: #145 of 1349
          id: cord-007236-8hiymqyb
      author: Sun, Ji-Min
       title: Inhibition of hepatitis C virus replication by Monascus pigment derivatives that interfere with viral RNA polymerase activity and the mevalonate biosynthesis pathway
        date: 2011-11-09
       words: 4995
      flesch: 38
     summary: The 65 kDa HCV NS5B protein has RNA-dependent RNA polymerase (RdRp) activity and is a key player in HCV RNA replication. The production of geranylgeranyl lipids and cholesterol through the mevalonate pathway is important for HCV RNA replication.
    keywords: aads; activity; cells; derivatives; hcv; hepatitis; inhibitors; mevalonate; mop; ns5b; replication; rna; virus
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        item: #146 of 1349
          id: cord-007382-5kb16qb7
      author: Hartmann, G.
       title: Nucleic Acid Immunity
        date: 2016-12-15
       words: 16190
      flesch: 33
     summary: The involvement of SAMHD1 in innate immunity was initially proposed based on its mouse ortholog Mg11 which is IFN-inducible in macrophages and dendritic cells (Li et al., 2000) , hence the alternative name dendritic cell-derived IFN-γ-induced protein. TLR7 and TLR8 are preferentially activated by polyU or by G-and U-rich sequences (Diebold et al., 2004; Heil et al., 2004; Hornung et al., 2005; Judge et al., 2005) .
    keywords: acid; activation; activity; cells; cgas; cpg; dna; dnase; et al; foreign; function; human; ifn; immune; immunity; interferon; mda5; nucleic; pkr; protein; receptors; rig; rna; rnai; samhd1; sensing; signaling; tlr9; type; viral; virus
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        item: #147 of 1349
          id: cord-007463-8g0zklzy
      author: Pocock, D.H.
       title: Characterisation of rotavirus isolates from sub-clinically infected calves by genome profile analysis
        date: 2002-11-13
       words: 1939
      flesch: 37
     summary: Asymptomatic rotavirus infections in day care centers Development of immunity to porcine rotavirus in piglets protected from disease by bovine colostrum Variation in virulence of bovine rotaviruses Neonatal calf diarrhoea: identification of a reoviruslike (rotavirus) agent in faeces by immunofluorescence and immune electron microscopy Comparative virulence of different bovine rotavirus isolates Asymptomatic endemic rotavirus infections in the newborn A rapid and sensitive method for analysing the genome profiles of field isolates of rotavirus Rotavirus infections in calves in dairy herds Quantitation of the relatedness of Reovirus serotypes 1,2 and 3 at the gene level Rapid diagnosis of rotavirus infection by direct detection of viral nucleic acid in silver-stained polyacrylamide gels Comparison of human and animal rotaviruses by gel electropboresis of viral RNA Distinctive ribonueleic acid patterns of human rotavirus subgroups 1 and 2 Cleavage of structural proteins during the assembly of the head of bacteriophage T 4 Longitudinal survey of rotavirus infection in calves Molecular characterization of rotaviruses with distinct group antigens The epidemiology of enteric virus infections of calves Evaluation of ELISA and electron microscopy for the detection of coronavirus and rotavirus in bovine faeces Comparison of the genomes of simian, bovine and human rotaviruses by gel electrophoresis and detection of genomic variation among bovine isolates Rotavirus infection in lambs: studies on passive protection Comparison of atypical rotaviruses from calves, piglets, lambs and man key: cord-007463-8g0zklzy authors: Pocock, D.H. title: Characterisation of rotavirus isolates from sub-clinically infected calves by genome profile analysis date: 2002-11-13 journal: Vet Microbiol DOI: 10.1016/0378-1135(87)90095-2 sha: doc_id: 7463 cord_uid: 8g0zklzy Rotaviruses isolated from 43 sub-clinically infected calves from a single farm were analysed by genome profile analysis.
    keywords: calves; genome; profiles; rna; rotavirus
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        item: #148 of 1349
          id: cord-007474-ckqghr3b
      author: Johnson, Michael E.
       title: Development of specific nucleic acid probes for the differentiation of porcine rotavirus serotypes
        date: 2002-11-13
       words: 6492
      flesch: 42
     summary: key: cord-007474-ckqghr3b authors: Johnson, Michael E.; Paul, Prem S.; Gorziglia, Mario; Rosenbusch, Ricardo title: Development of specific nucleic acid probes for the differentiation of porcine rotavirus serotypes date: 2002-11-13 journal: Vet Microbiol DOI: 10.1016/0378-1135(90)90180-4 sha: doc_id: 7474 cord_uid: ckqghr3b A dot blot hybridization assay is described for the detection and differentiation of porcine rotavirus serotypes. OSU and Gottfried strains have been designated as the prototype strains for porcine rotavirus serotypes 1 and 2 (Bohl et al., 1984) .
    keywords: conditions; et al; gene; gottfried; hybridization; osu; porcine; rna; rotavirus; serotype; stringency
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        item: #149 of 1349
          id: cord-007621-rapinodd
      author: Vidovic, Maria
       title: Induction and regulation of class II major histocompatibility complex mRNA expression in astrocytes by interferon-γ and tumor necrosis factor-α
        date: 2002-11-13
       words: 6691
      flesch: 45
     summary: Furthermore, astrocyte class II mRNA expression was inhibited when cycloheximide (CHX) was added together with IFN-γ or IFN-γ/TNF-α, and when CHX was added up to 4 h after treatment with IFN-γ or IFN-γ/TNF-α. These results indicate that astrocyte class II mRNA expression is mediated by newly synthesized proteins induced by IFN-γ and/or IFN-γ/TNF-α.
    keywords: astrocytes; cells; class; class ii; et al; expression; ifn; mhc; mrna; tnf
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        item: #150 of 1349
          id: cord-007689-0vpp3xdl
      author: Schlee, M.
       title: Beyond Double-Stranded RNA-Type I IFN Induction by 3pRNA and Other Viral Nucleic Acids
        date: 2007
       words: 7770
      flesch: 38
     summary: With notable exceptions such as the Picornavirus family (see below), viral RNA-dependent RNA polymerases (RdRp) initiate polymerase activity de novo, without a specific primer (Kao et al. 2001) . Both activated PKR and OAS were found to block translation of viral RNA by distinct mechanisms.
    keywords: cells; dsrna; et al; ifn; induction; interferon; protein; receptor; response; rig; rna; tlr3; type; virus
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        item: #151 of 1349
          id: cord-007714-n3omlvfl
      author: Brown, J. W. S.
       title: The Role of the Plant Nucleolus in Pre-mRNA Processing
        date: 2008
       words: 7263
      flesch: 34
     summary: More than 90% of the aberrant transcripts found in plant nucleoli are putative NMD substrates based on NMD determinants in plants (Kim et al., unpublished; Kertész et al. 2006) . The localisation by fluorescence microscopy and in situ hybridisation of nucleolar proteins, rRNA gene regions and snoRNA species to sub-domains within plant nucleoli have been correlated with early and late events in rRNA processing (Beven et al. 1996; Brown and Shaw 1998) .
    keywords: assembly; bodies; cell; et al; export; functions; mrna; nuclear; nucleolus; plant; pre; processing; proteins; ribosomal; rna; rrna
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        item: #152 of 1349
          id: cord-007819-51h2jrsy
      author: Schommer, Susan K.
       title: Use of a PRRSV Infectious Clone to Evaluate in Vitro Quasispecies Evolution
        date: 2006
       words: 1393
      flesch: 42
     summary: key: cord-007819-51h2jrsy authors: Schommer, Susan K.; Kleiboeker, Steven B. title: Use of a PRRSV Infectious Clone to Evaluate in Vitro Quasispecies Evolution date: 2006 journal: The Nidoviruses DOI: 10.1007/978-0-387-33012-9_78 sha: doc_id: 7819 cord_uid: 51h2jrsy nan hallmark of RNA viruses. This diversity is considered to be an important mechanism of virus persistence and pathogenesis in many virus systems and provides a mechanism to rapidly respond to changes in the host environment.
    keywords: clone; infectious; syndrome; virus
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        item: #153 of 1349
          id: cord-007890-bie1veti
      author: None
       title: ECC-4 Abstracts
        date: 2002-04-16
       words: 86133
      flesch: 45
     summary: On the whole, E. coli showed an elevated sensitivity rate ( !/90% of tested strains) to nitrofurantoin, gentamicin, amikacin, and 2nd-and 3rd-generation cephalosporins, while only amoxicillin and piperacillin had a mean resistance rate !/30 % for M41L, D67N, K103N, M184V, L210W, T215YF, and for L10I, M36I, L63P, A71VT, L90M for P Inhibitors (PI).
    keywords: acid; activity; acute; administration; aeruginosa; agar; agents; aim; amoxicillin; analysis; antibiotic; antimicrobial; associated; aureus; b b; bacteria; beta; blood; candida; care; cases; cells; children; chronic; ciprofloxacin; clinical; coli; combination; concentrations; conclusion; control; cultures; data; days; department; diagnosis; disease; dna; dose; drug; effect; efficacy; erythromycin; esbl; fever; following; france; general; gentamicin; gram; group; haart; hcv; health; hepatitis; high; hiv; hospital; human; ifn; imipenem; incidence; infected; infection; influenza; institute; isolates; l b; laboratory; level; linezolid; mean; medical; medicine; methods; microbiology; mics; months; mrsa; nccls; negative; new; non; nosocomial; number; oral; patients; pcr; penicillin; period; plasma; pneumoniae; positive; presence; present; prevalence; pts; purpose; rate; resistance; results; risk; rna; samples; school; sensitivity; serum; spain; species; specific; spp; staphylococcus; strains; streptococcus; study; susceptibility; system; teicoplanin; tested; therapy; time; tissue; total; tract; treatment; university; urinary; urine; use; vancomycin; virus; vitro; years
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        item: #154 of 1349
          id: cord-007920-mh3tesdc
      author: Dhar, Arun K.
       title: Genomic Organization, Biology, and Diagnosis of Taura Syndrome Virus and Yellowhead Virus of Penaeid Shrimp
        date: 2004-11-11
       words: 19363
      flesch: 41
     summary: Observation of the pathognomonic acute-phase lesion in cuticular epithelium (Fig. 3A ) by light microscopy is sufficient to make a definitive diagnosis of TSV infection Hasson et al., 1995 Hasson et al., , 1997 Hasson et al., , 1999a Lightner, 1995 Lightner, , 1996a These are valuable references for researchers interested in shrimp viruses.
    keywords: acute; cowley et; detection; disease; et al; fig; gav; gene; genome; hasson et; infected; infection; lightner et; monodon; pcr; penaeid; penaeus; phase; protein; region; rna; sequence; shrimp; spann et; specific; syndrome; taura; tsv; vannamei; virus; viruses; yellowhead; yhv
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        item: #155 of 1349
          id: cord-008407-jbp8bxjz
      author: Derdeyn, Cynthia A.
       title: Characterization of defective-interfering RNAs of rubella virusgenerated during serial undiluted passage
        date: 1995-01-10
       words: 6730
      flesch: 50
     summary: 5A and 5C, after 5 to 10 serial passages of each of these stocks, except for the synovial explant persistent infection supernatants (Fig. 5C, lanes 4 and 5) , a DI RNA species similar in size to the large P12 DI RNA was generated. Thus, the prevalence of the large DI RNA species during serial passage is probably due to its having a selective advantage over other DI RNA species.
    keywords: di rna; genome; large; p12; rna; rnas; rub; site; species; start
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        item: #156 of 1349
          id: cord-008426-ktn8c0zx
      author: Othman, Yasmin
       title: Nucleotide sequence of the bean strain of southern bean mosaic virus()
        date: 1995-01-10
       words: 5397
      flesch: 45
     summary: However, the absence of a clear helicase domain in SBMV sequences is consistent with the observation that no such viral-encoded function has been identified in viruses with a compact (<5 kb) genome (Gorbalenya and Koonin, 1989) . The 5' terminus of SBMV RNA has a covalently linked protein (VPg) (Ghosh et al., 1979) of molecular weight between 10 (SBMV-C) and 12 kDa (SBMV-B) (Mang et al., 1982) , which is essential for infectivity (Veerisetty and Sehgal, 1980) .
    keywords: bean; fig; mosaic; orf; protein; rna; rymv; sbmv; sequence; virus
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        item: #157 of 1349
          id: cord-008541-0u2fatbg
      author: Bujarski, Jozef J.
       title: Molecular Studies of Genetic RNA–RNA Recombination in Brome Mosaic Virus
        date: 2008-02-28
       words: 6380
      flesch: 46
     summary: Studies described in this chapter summarize the molecular approaches used to increase the frequency of recombination among BMV RNA segments and, more importantly, to target the sites of crossovers to specific BMV RNA regions. Studies described below summarize molecular approaches used to increase the frequency of recombination among BMV RNA segments and, more importantly, to target the sites of crossovers to specific BMV RNA regions.
    keywords: bmv; dm4; et al; mutants; recombination; region; rna; rna3; rnal; sequence
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        item: #158 of 1349
          id: cord-008556-oetrdm8g
      author: Kozak, Marilyn
       title: Regulation of Protein Synthesis in Virus-Infected Animal Cells
        date: 2008-03-01
       words: 23992
      flesch: 40
     summary: On the regulation of protein synthesis in vaccinia virus infected cells A joint product of the genes gag and pol of avian sarcoma virus: A possible precursor of reverse transcriptase Post-translational regulation of the 54K cellular tumor antigen in normal and transformed cells The influence of the host cell on the inhibition of virus protein synthesis in cells doubly infected with VSV and mengovirus Sequence studies of several alphavirus genomic RNAs in the region containing the start of the subgenomic RNA Characterization of a ts mutant of vaccinia virus 25,422-426. The replication of picornaviruses Expression from an internal AUG codon of herpes simplex thymidine kinase gene inserted in a retrovirus vector The number of ribosomes on SV40 late 16s mRNA is determined in part by the nucleotide sequence of its leader Complete nucleotide sequence of alfalfa mosaic virus RNA 3 Sequence analysis of hepatitis A virus cDNA coding for capsid proteins and RNA polymerase Direct mapping of adeno-associated virus capsid proteins B and C: A possible ACG initiation codon Structure of the FMDV translation initiation site and of the structural proteins UAG readthrough during TMV RNA translation: Isolation and sequence of two tRNAsTyr with suppressor activity from tobacco plants The molecular basis for differential translation of TMV RNA in tobacco and wheat germ Measles virus P gene codes for two proteins Inhibition of HeLa cell protein synthesis during adenovirus infection Regulatory mutants of polyoma virus defective in DNA replication and the synthesis of early proteins Solubilization of a protein synthesis inhibitor from vaccinia virions Codon selection in yeast Translational interference a t overlapping reading frames in prokaryotic mRNA Effect of the tripartite leader on synthesis of a nonviral protein in an adenovirus 5 recombinant Poliovirus mutant that does not selectively inhibit host cell protein synthesis Two small RNAs encoded by Epstein-Barr virus can functionally substitute for the virus-associated RNAs in the lytic growth of adenovirus 5 Construction and analysis of additional adenovirus substitution mutants confirm the complementation of VAI RNA function by two small RNAs encoded by Epstein-Barr virus Structural requirements of adenovirus VAI RNA for its translation enhancement function Differential inhibition of host cell RNA synthesis in several picornavirus-infected cell lines Effect of viral infection on host protein synthesis and mRNA association with the cytoplasmic cytoskeletal structure Intermolecular duplexes formed from polyadenylated vaccinia virus RNA
    keywords: adenovirus; aug; binding; cap; cells; codon; et al; gene; host; host mrnas; host protein; host translation; infection; influenza; inhibition; initiation; late; mechanism; mrnas; poliovirus; protein; protein synthesis; reovirus; ribosomes; sequence; shutoff; site; synthesis; translation; upstream; vaccinia; viral; virus; virus mrnas
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        item: #159 of 1349
          id: cord-008575-bbpmlo3c
      author: Lawton, Jeffrey A
       title: Mechanism of genome transcription in segmented dsRNA viruses
        date: 2004-01-07
       words: 15902
      flesch: 33
     summary: In Virology Structure of L-A virus: A specialized compartment for the transcription and replication of double-stranded RNA Intracellular RNA synthesis directed by temperature sensitive mutants of simian rotavirus SA11 Rescue of infectivity by sequential in vitro transcapsidation of rotavirus core particles with inner capsid and outer capsid proteins Template-dependent, in vitro replication of rotavirus RNA Rotavirus open cores catalyze 5'-capping and methylation of enogenous RNA: evidence that VP3 is a methyl transferase Fungal virus capsids, cytoplasmic compartments for the replication of double-stranded RNA, formed as icosahedral shells of asymmetric Gag dimers Ribonucleic acid polymerase activity associated with purified calf rotavirus Activation of rotavirus RNA polymerase by calcium chelation Specimen preparation methods for electron crystallography of soluble proteins Nucleotide sequence of bovine rotavirus gene 1 and expression of the gene product in baculovirus Characterization of virus-like particles produced by the expression of rotavirus capsid proteins in insect cells Isolation of genomeenzyme complex from cytoplasmic polyhedrosis virus of silkworm Bombyx mori Early steps in reovirus infection are associated with dramatic changes in supramolecular structure and protein conformation: Analysis of virions and subviral particles by cryoelectron microscopy and image reconstruction Internal structures containing transcriptase-related proteins in top component particles of mammalian orthoreovirus Microbiol Virus taxonomy--the classification and nomenclature of viruses Trypsin-induced structural transformation in aquareovirus Structure of mammalian orthoreovirus particles Characterization of an ATPase activity in reovirus cores and its genetic association with core-shell protein kl Core protein ~2 is a second determinant of nucleoside triphosphatase activities by reovirus cores In vitro transcription of the double-stranded RNA bacteriophage ¢p6 is influenced by purine NTPs and calcium In vitro assembly of infectious nucleocapsids of bacteriphage ~6: Formation of a recombinant double-stranded RNA virus RNA polymerase activity associated with bacteriophage ~6 nucleocapsid Rotavirus VP1 alone specifically binds to the 3' end of viral mRNA, but the interaction is not sufficient to initiate minus-strand synthesis RNA-binding and capping activities of proteins in rotavirus open cores cis-Acting signals that promote genome replication in rotavirus mRNA Rotavirus RNA polymerase requires the core shell protein to synthesize the double-stranded RNA genome Cytoplasmic polyhedrosis viruses A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase Characterization of rotavirus guanylyltransferase activity associated with polypeptide VP3 Effect of nucleotide analogues on rotavirus transcription and replication Identification of four conserved motifs among the RNA-dependent polymerase encoding elements Structure of rotavirus Molecular basis of rotavirus replication: Structure-function correlations Three-dimensional structure of rotavirus Localization of VP4 neutralization sites in rotavirus by three-dimensional cryo-electron microscopy Three-dimensional structure of single-shelled BTV Visualization of ordered genomic RNA and localization of transcriptional complexes in rotavirus Stoichiometric packaging of the three genomic segments of double-stranded RNA bacteriophage ~6 Capping and methylation of mRNA by purified recombinant VP4 protein of bluetongue virus Bluetongue virus core protein VP4 has nucleoside triphosphate phosphohydrolase activity Studies on the mechanism of the antiviral activity of ribavirin against reovirus Structure of the reovirus core at 3.6A Transcription and replication of bacteriophage (p6 RNA Novel circular forms of mengovirus-specific double-stranded RNA detected by electron microscopy Interconversion of linear and circular forms of double-stranded RNA of encephalomyocarditis virus Reoviruses and the interferon system Role of the inner protein capsid on in vitro human rotavirus transcription Structure of Broadhaven virus by cryoelectron microscopy:
    keywords: capsid; capsid layer; core; dsrna; dsrna viruses; et al; genome; genome transcription; mrna; particle; polymerase; protein; rotavirus; segments; structure; studies; transcription; transcripts; viruses; vp2; vp2 capsid
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        item: #160 of 1349
          id: cord-008588-4eu9v5d3
      author: Chastain, Michael
       title: Structural Elements in RNA
        date: 2008-02-29
       words: 13702
      flesch: 52
     summary: The division of RNA structure into building blocks consisting of secondary or tertiary interactions makes it easier to describe RNA structures. Finally, the division of RNA structure into building blocks consisting of secondary or tertiary interactions makes it easier to describe RNA structures.
    keywords: base; bulge; dna; form; helix; hydrogen; interactions; junction; loop; nucleotides; protein; regions; rna; rna structure; structure; tertiary
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        item: #161 of 1349
          id: cord-008613-tysyq6o4
      author: Thomas, Sheila M.
       title: Two mRNAs that differ by two nontemplated nucleotides encode the amino coterminal proteins P and V of the paramyxovirus SV5
        date: 1988-09-09
       words: 8438
      flesch: 43
     summary: The SV5 P gene has been shown to encode both the P protein (Mr = 44,000), and protein V (Mr = 24,000) by the arrest of translation in vitro of both P and V using a cDNA clone derived from SV5-specific mRNAs (Paterson et al., 1984) . and is part of the transcriptase complex (Buetti and Choppin, 1977) , while protein V is found in infected cells and is of unknown function (Peluso et al., 1977) .
    keywords: amino; cdna; dna; et al; figure; frame; gene; mrna; nucleotides; protein; reading; region; residues; sequence; sv5; virus
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        item: #162 of 1349
          id: cord-009376-a35a92gh
      author: Lovatt, Archie
       title: Applications of quantitative PCR in the biosafety and genetic stability assessment of biotechnology products
        date: 2002-01-07
       words: 9218
      flesch: 45
     summary: The development and validation of PCR assays to meet the requirements of regulatory authorities is a key element in the production and marketing of final products. Further studies Quantitation of DNArRNA using real time PCR detection Inverted Alu repeats unstable in yeast are excluded from the human genome High throughput detection of retrovirus-associated reverse transcriptase using an improved Fluorescent Product Enhanced Reverse Ž Transcriptase Assay F-PERT and its comparison to conventional detection methods Pharmaceutical perspectives of nonviral gene therapy Zoonoses and haemorrhagic fever Elimination of background signals in a modified polymerase chain reaction-based reverse transcriptase assay The role of deer as a possible reservoir host of Potosi virus recognised arbovirus in the United States Simultaneous screening for HBV DNA and HCV RNA genomes in blood donations using a novel TaqMan PCR Rapid reverse transcription-PCR detection of hepatitis C virus RNA in serum using TaqMan fluorogenic detection system Development of a real-time PCR procedure including an internal control for the measurement of HCMV viral load Different real-time PCR formats compared for the quantitative detection of human cytomegalovirus DNA Human exposure to bovine polyomavirus: a zoonosis? Target selection and optimisation of amplification reactions Ultra-sensitive retro-v irus detection by a reverse transcriptase assay based on product enhancement Critical factors for successful PCR.
    keywords: acid; assay; cell; control; copy; detection; dna; extraction; nucleic; number; pcr; rna; sample; target; test; time; virus; viruses
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        item: #163 of 1349
          id: cord-009662-ntjngiem
      author: Moulton, Jon D.
       title: Using Morpholinos to Control Gene Expression
        date: 2007-01-15
       words: 11640
      flesch: 43
     summary: Because a Morpholino concentration of 10 µM might cause nonspecific effects due to interaction with nontarget genes, functional assays should be performed using a range of Morpholino concentrations. However, although antisense activity can be achieved at Morpholino concentrations that do not produce detectable fluorescence, proof-of-delivery experiments do require detectable fluorescence.
    keywords: activity; antisense; blocking; cells; concentration; control; delivery; et al; exon; knockdown; morpholino; mrna; oligo; protein; sequence; splice; target; targeting; translation
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        item: #164 of 1349
          id: cord-009943-fzynh14x
      author: Ai‐Nakib, W.
       title: Detection of Human Rhinoviruses and Their Molecular Relationship Using cDNA Probes
        date: 2005-12-11
       words: 2881
      flesch: 51
     summary: We have, therefore, developed an alternative approach to rhinovirus detection: that of viral RNA detection using cDNA:RNA hybridization procedures. We hope to pursue further studies on the direct detection of rhinovirus RNA using cDNA:RNA hybridization procedures and to develop in time an appropriate clinical assay.
    keywords: cdna; detection; hybridization; rhinoviruses; rna
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        item: #165 of 1349
          id: cord-010045-eqzs01au
      author: Britton, P.
       title: Sequence of the nucleoprotein gene from a virulent British field isolate of transmissible gastroenteritis virus and its expression in Saccharomyces cerevisiae
        date: 2006-10-27
       words: 6194
      flesch: 49
     summary: The nucleoprotein gene was expressed in yeast cells under the control of two types of yeast promoters: the constitutive PGK promoter, and the inducible GAL1 promoter. Yeast cells containing recombinant plasmids, with the nucleoprotein gene in the correct orientation, produced a polypeptide of M, 47000, identical to the viral product, that reacted with a specific monoclonal antibody.
    keywords: cdna; cells; expression; fragment; gene; mrna; nucleoprotein; plasmid; promoter; reading; sequence; species; tgev; tgev nucleoprotein; virus; yeast
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        item: #166 of 1349
          id: cord-010092-uftc8inx
      author: None
       title: Abstract of 29th Regional Congress of the ISBT
        date: 2019-06-07
       words: 233543
      flesch: 50
     summary: One central question is the need of individual NAT screening (ID) versus minipool NAT screening (MP) approaches to identify all relevant viremias in blood donors. 3A-S02-03 Background: The screening of blood donors and returning travelers from active transmission areas have highlighted the importance of diagnosis of acute arboviral infections.
    keywords: abo blood; addition; aims; allele; alloimmunization; analysis; anemia; anti; antibodies; antibody; antigen; apheresis; approach; assay; available; average; background; bacterial; bleeding; blood bank; blood cells; blood center; blood chimerism; blood collection; blood components; blood count; blood culture; blood demand; blood donation; blood donors; blood establishments; blood flow; blood group; blood grouping; blood loss; blood management; blood plasma; blood platelet; blood pressure; blood processing; blood products; blood results; blood safety; blood samples; blood services; blood supply; blood system; blood test; blood transfusion; blood type; blood units; blood volume; care; cases; cause; cell donors; cell transfusion; clinical; concentrates; concentration; conclusions; confirmed; content; control; cord blood; countries; criteria; cross; current; data; day; days; deferral; detection; difference; disease; dna; donations; donor samples; effect; events; evidence; exon; expression; factors; female; ferritin; flow; following; frequency; gel; gene; genotyping; group system; groups; hbv; hcv; health; hemoglobin; hev; history; hiv; hla; hospital; hospital blood; human; identification; igg; impact; incidence; increase; individuals; infection; information; international; iron; laboratory; levels; life; low; major; mean; median; medical; methods; min; ml blood; model; molecular; months; n =; national; need; negative; new; non; number; order; overall; p =; patients; pcr; pcs; period; phenotype; plasma; plasma donors; plasma transfusion; platelet; platelet donors; platelet transfusion; population; positive; post; potential; practice; presence; present; prevalence; procedure; process; production; quality; quality blood; range; rate; rbc blood; rbc transfusion; rbcs; reactive; red; reduced; repeat donors; research; results; rhd; rhd blood; risk; routine; screening; selection; sequencing; serum; significant; specific; staff; standard; status; storage; studies; study; summary; surgery; systems; tested; testing; tests; therapy; time donors; total; transfusion medicine; transfusion reactions; transfusion safety; transfusion service; transfusion therapy; transfusions; treated; treatment; typing; use; value; variant; versus; weak; women; years
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        item: #167 of 1349
          id: cord-010120-mqvm9zn4
      author: Dinman, Jonathan D.
       title: Ribosomal frameshifting in yeast viruses
        date: 2004-01-29
       words: 6742
      flesch: 56
     summary: Loss of the ability of a HIS3-marked TyZ cDNA clone to transpose into the yeast genome paralleled the increase in +1 ribosomal frameshifting in polyamine-starved spe2 cells.3 Taken together, these findings support the hypothesis that the efficiency of ribosomal frameshifting is critical for viral propagation, and that agents which affect ribosomal frameshifting efficiency may have antiviral a c True mof mutants, by virtue of their effect upon -1 ribosomal frameshifting efficiency, should not be capable of propagating M,, i.e. they should have Mak-phenotypes (MAK = MAintenance of Killer; for review, see reference 58).
    keywords: efficiency; frameshifting; gene; mrna; mutants; ribosomal; site; slippery; stem; trna; yeast
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        item: #168 of 1349
          id: cord-010161-bcuec2fz
      author: Matson, David O.
       title: IV, 6. Calicivirus RNA recombination
        date: 2004-09-14
       words: 3338
      flesch: 37
     summary: It is clear that such clades are related to differences in capsid gene sequences; sequence differences are less marked in the RNA polymerase gene: when RNA polymerase region sequences are analyzed in phylogenetic analyses, statistically significant differences similar to those observed among capsid gene sequences do not occur . Models for RNA virus recombination have utilized two terminologies to describe the degree that features of the donor and acceptor templates are shared: homologous, aberrant homologous, and non-homologous types (Lai and Cavanagh, 1997) or sequence similarity-essential, similarity-assisted, and similarity-nonessential (Nagy and Simon, 1997) .
    keywords: capsid; cvs; recombination; rna; sequence; strains
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        item: #169 of 1349
          id: cord-010188-884d196k
      author: Schlesinger, Sondra
       title: Alphaviruses — vectors for the expression of heterologous genes
        date: 2004-08-26
       words: 3051
      flesch: 42
     summary: Trends Biotechnol DOI: 10.1016/0167-7799(93)90070-p sha: doc_id: 10188 cord_uid: 884d196k DNA viruses and retroviruses are well established as vectors for the expression of heterologous genes, but there is increasing interest in the possibilities of using RNA viruses, which do not replicate through a DNA intermediate, for this purpose. This article summarizes some of the general properties of RNA viruses and concentrates on one class of RNA viruses — the alphaviruses — and their potential as expression vectors.
    keywords: cells; genes; proteins; rna; vector; virus; viruses
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        item: #170 of 1349
          id: cord-010273-0c56x9f5
      author: Simmonds, Peter
       title: Virology of hepatitis C virus
        date: 2001-10-10
       words: 7904
      flesch: 30
     summary: Homology of the predominant genotype with the prototype American strain Detection of three types of hepatitis C virus in blood donors: Investigation of type-specific differences in serological reactivity and rate of alanine aminotransferase abnormalities Identification of hepatitis C viruses with a nonconserved sequence of the 5' untranslated region Sequence analysis of the 5' noncoding region of hepatitis C virus At least five related, but distinct, hepatitis C viral genotypes exist Typing of hepatitis C virus isolates and new subtypes using a line probe assay Sequence analysis of the 5' untranslated region in isolates of at least four genotypes of hepatitis C virus in the Netherlands Use of the 5' non-coding region for genotyping hepatitis C virus Genotypes of hepatitis C virus in Italian patients with chronic hepatitis C Heterogeneity of hepatitis C virus genotypes in France Genotypic analysis of hepatitis C virus in American patients Hepatitis C virus infection in Egyptian volunteer blood donors in Riyadh Risk factors associated with a high seroprevalence of hepatitis C virus infection in Egyptian blood donors High HCV prevalence in Egyptian blood donors Sequence variability in the 5' non coding region of hepatitis C virus: Identification of a new virus type and restrictions on sequence diversity Geographical distribution of hepatitis C virus genotypes in blood donors: An international collaborative survey New genotype of hepatitis C virus in South-Africa Typing of hepatitis C virus (HCV) genomes by restriction fragment length polymorphisms Distribution of plural HCV types in Japan Clinical backgrounds of the patients having different types of hepatitis C virus genomes Genomic typing of hepatitis C viruses present in China HCV genotypes in China HCV genotypes in different countries Differences in the hepatitis C virus genotypes in different countries Prevalence, genotypes, and an isolate (HC-C2) of hepatitis C virus in Chinese patients with liver disease Imported hepatitis C virus genotypes in Japanese hemophiliacs Genotypic subtyping of hepatitis C virus Survey of major genotypes and subtypes of hepatitis C virus using restriction fragment length polymorphism of sequences amplified from the 5' non-coding region A new type of hepatitis C virus in patients in Thailand Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups Prediction of response to interferon treatment of chronic hepatitis C HCV genotypes in chronic hepatitis C and response to interferon Detection of hepatitis C virus by polymerase chain reaction and response to interferon-alpha therapy: hepatitis C virus isolates and PCR primers for specific detection Application of six hepatitis C virus genotyping systems to sera from chronic hepatitis C patients in the United States Use of NS-4 peptides to identify typespecific antibody to hepatitis C virus genotypes 1, 2, 3, 4, 5 and 6 Characterization of hypervariable regions in the putative envelope protein of hepatitis C virus Evidence for immune selection of hepatitis C virus (HCV) putative envelope glycoprotein variants:
    keywords: c virus; cell; cleavage; genome; genotypes; hcv; hepatitis; infection; patients; proteins; region; replication; rna; sequence; virus
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        item: #171 of 1349
          id: cord-010374-z9ygudv6
      author: Siddell, S.G.
       title: Coronaviridae1
        date: 2008-07-24
       words: 1542
      flesch: 45
     summary: The replicative structures from which they are produced have not been char acterized, but it has been demonstrated that the negative-stranded template from which murine hepatitis virus mRNAs are copied is of genome length. For murine hepatitis virus, the mRNA function of each of the subgenomic viral RNAs has been demonstrated in vitro, and the mRNAs encod ing each of the virion proteins, or its precur sors, have been identified ( fig. 1 ).
    keywords: coronaviruses; infection; protein; rna; virus
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        item: #172 of 1349
          id: cord-010680-lc1onm53
      author: Patel, Ami
       title: In Vivo Delivery of Nucleic Acid-Encoded Monoclonal Antibodies
        date: 2020-03-10
       words: 13069
      flesch: 37
     summary: The original studies surrounding in vivo antibody gene delivery focused primarily on gene delivery using recombinant viral vectors such as AAV and adenovirus (Ad), which were advanced clinically, building on work in the traditional gene therapy-based field. Understanding the safety of gene delivery platforms is paramount for in vivo antibody gene delivery to progress.
    keywords: aav; administration; antibodies; antibody; delivery; development; dmab; dna; expression; gene; human; mab; mabs; mice; mrna; pdna; plasmid; potential; studies; study; synthetic; therapy; vectors; virus; vivo
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        item: #173 of 1349
          id: cord-010762-c01wgg4v
      author: Wu, Jiqin
       title: A conformation-based intra-molecular initiation factor identified in the flavivirus RNA-dependent RNA polymerase
        date: 2020-05-01
       words: 9106
      flesch: 46
     summary: Moreover, the RdRP fidelity and initiation enhancement offered by the pesitvirus NS5B NTD and flavivirus NS5 MTase, respectively, is likely not an improvement of a specific function relative to the corresponding RdRP ancestors, but a balance between gaining an extra module and maintaining the levels of key enzymatic properties for the RdRPs. Large-scale protein conformational changes are amazing events in biological systems, albeit associated with very different characteristics. https://doi.org/10.1371/journal.ppat.1008484.g008 MTase as RdRP initiation factor in NS5 understandings of the conformational diversity and conservation in flavivirus NS5, highlighting the important role of the MTase module, a natural fusion partner of the NS5 RdRP module, in the initiation phase of RNA synthesis.
    keywords: conformation; denv2; denv2 ns5; fig; flavivirus; initiation; interactions; interface; jev; mode; mtase; ns5; polymerase; protein; rdrp; rna; structure; virus
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        item: #174 of 1349
          id: cord-010977-fwz7chzf
      author: Myserlis, Pavlos
       title: Translational Genomics in Neurocritical Care: a Review
        date: 2020-02-20
       words: 12007
      flesch: 21
     summary: Given that diseases common to the neurocritical care population so rarely afford access to brain tissue for pathologic or genomic analysis antemortem, model system genomic studies offer an important adjunct for translational research. As such, many model system studies start with RNA, examining how the genome responds to perturbation through the transcriptome.
    keywords: animal; approach; brain; care; disease; expression; gene; genome; genomic; hemorrhage; human; injury; mechanisms; models; patients; research; risk; sequencing; stroke; studies; study; systems; tbi; translational; variants
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        item: #175 of 1349
          id: cord-011794-ejoufvvj
      author: Binder, Florian
       title: Isolation and characterization of new Puumala orthohantavirus strains from Germany
        date: 2020-04-23
       words: 5994
      flesch: 47
     summary: Phylogenetic analysis of the concatenated S, M and L segment coding sequences grouped the novel isolates together with Astrup prototype strain in sister relationship to PUUV sequences from France (Fig. 4a) . Moreover, the hybrid-capture-based enrichment of PUUV sequences allows a rapid determination of the complete genome and underlines the value of this workflow for hantavirus surveillance and molecular evolution studies [35] .
    keywords: antibodies; bank; cells; germany; hantavirus; isolates; isolation; monoclonal; novel; osnabrück; puuv; rna; strain; v29; veroe6; virus; vole
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        item: #176 of 1349
          id: cord-011803-9122f1zc
      author: Zhao, Yang
       title: The RNA quality control pathway nonsense-mediated mRNA decay targets cellular and viral RNAs to restrict KSHV
        date: 2020-07-03
       words: 8417
      flesch: 43
     summary: In addition, by RNA FISH-FLOW we observed a~4-fold increase in PAN RNA expressing lytic cells 24 h post-induction (Fig. 3c) . Furthermore, we observed~2-fold increase in PAN RNA expressing lytic cells by RNA FISH-FLOW ( Fig.
    keywords: 3′utr; bcbl1; cells; data; expression; fig; gene; increase; kshv; lytic; mrna; orf50; reactivation; rna; rta; supplementary; trex; upf1
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        item: #177 of 1349
          id: cord-012032-zolowuhj
      author: Yu, Peifa
       title: 2’-Fluoro-2’-deoxycytidine inhibits murine norovirus replication and synergizes MPA, ribavirin and T705
        date: 2020-08-08
       words: 3511
      flesch: 39
     summary: The combination of 2’-FdC with mycophenolic acid, ribavirin or favipiravir (T705) exerts synergistic antiviral effects. Human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and murine The 50% cytotoxic concentration (CC 50 ) (n = 16) and 50% inhibitory concentration (IC 50 ) (n = 4-6) against viral replication were calculated using GraphPad Prism 5 software.
    keywords: 2'-fdc; cells; expression; fig; mnv; norovirus; replication; ribavirin; rna; treatment
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        item: #178 of 1349
          id: cord-012420-llh22iq2
      author: Stott, Robert J.
       title: Distinct Molecular Mechanisms of Host Immune Response Modulation by Arenavirus NP and Z Proteins
        date: 2020-07-21
       words: 12026
      flesch: 34
     summary: Viruses Inhibition of Innate Immune Responses Is Key to Pathogenesis by Arenaviruses Persistent virus infection inhibits type I interferon production by plasmacytoid dendritic cells to facilitate opportunistic infections Lassa virus infection of human dendritic cells and macrophages is productive but fails to activate cells Hemorrhagic Fever-Causing Arenaviruses: Lethal Pathogens and Potent Immune Suppressors Human dendritic cells infected with the nonpathogenic Mopeia virus induce stronger T-cell responses than those infected with Lassa virus Non-Pathogenic Mopeia Virus Induces More Robust Activation of Plasmacytoid Dendritic Cells than Lassa Virus Intrinsic immunity: A front-line defense against viral attack HIV-1 and interferons: Who's interfering with whom? Resistance of Transmitted Founder HIV-1 to IFITM-Mediated Restriction Characterization of the alpha interferon-induced postentry block to HIV-1 infection in primary human macrophages and T cells Thus, this host protein acts as a positive regulator of the late stages of virus infection by enhancing the processes of viral release and virus production [180] .
    keywords: activity; arenavirus; binding; cells; host; ifn1; infection; interferon; junv; lassa; lasv; lcmv; pathogenic; protein; replication; response; rig; rna; viral; virus; viruses
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        item: #179 of 1349
          id: cord-012484-c9ajmbw2
      author: Wahlund, Martina
       title: The Feasibility of Host Transcriptome Profiling as a Diagnostic Tool for Microbial Etiology in Childhood Cancer Patients with Febrile Neutropenia
        date: 2020-07-26
       words: 5091
      flesch: 41
     summary: Guideline for the management of fever and neutropenia in children with cancer and hematopoietic stem-cell transplantation recipients: 2017 update A prospective multicenter study of microbiologically defined infections in pediatric cancer patients with fever and neutropenia: Swiss Pediatric Oncology Group 2003 fever and neutropenia study Respiratory viruses, a common microbiological finding in neutropenic children with fever A prospective study on the epidemiology of febrile episodes during chemotherapy-induced neutropenia in children with cancer or after hemopoietic stem cell transplantation Respiratory viral infections and coinfections in children with cancer, fever and neutropenia: Clinical outcome of infections caused by different respiratory viruses Nasopharyngeal detection of respiratory viruses in febrile neutropenic children Clinical utility of PCR for common viruses in acute respiratory illness Frequent respiratory viral infections in children with febrile neutropenia-A prospective follow-up study Principles of intracellular viral recognition Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans Gene expression profiles in febrile children with defined viral and bacterial infection Diagnostic test accuracy of a 2-transcript host RNA signature for discriminating bacterial vs viral infection in febrile children Association of RNA biosignatures with bacterial infections in febrile infants aged 60 days or younger Integrative omics to detect bacteremia in patients with febrile neutropenia Quantitative relationships between circulating leukocytes and infection in patients with acute leukemia Febrile neutropenia in paediatric oncology Acute respiratory infections in children and adolescents with acute lymphoblastic leukemia Frequency and clinical outcome of respiratory viral infections and mixed viral-bacterial infections in children with cancer, fever and neutropenia Rhinovirus detection in symptomatic and asymptomatic children: Value of host transcriptome analysis Host gene expression in nose and blood for the diagnosis of viral respiratory infection A 2-transcript host cell signature distinguishes viral from bacterial diarrhea and it is influenced by the severity of symptoms Host-based peripheral blood gene expression analysis for diagnosis of infectious diseases A qPCR expression assay of IFI44L gene differentiates viral from bacterial infections in febrile children To investigate if there were any group-specific pathways that were activated, a new pathway analysis was performed on group-specific genes (viral, n = 75, unknown n = 265, and co-infection n = 149, Figure 2A ) and only few genes clustered into any pathway in samples with viral infection etiology, while the resulting top canonical pathways for samples with unknown and co-infection etiology were identical (data not shown).
    keywords: bacterial; children; episodes; etiology; expression; gene; infection; rna; samples
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        item: #180 of 1349
          id: cord-012552-porty653
      author: Tan, Kun
       title: The role of the NMD factor UPF3B in olfactory sensory neurons
        date: 2020-08-10
       words: 11550
      flesch: 43
     summary: Identification of UPF3B-regulated genes and NMD target genes in the olfactory system. Gene expression values were log normalized and regressed by mitochondrial expression ('percent.mt') and cell cycle gene expession ('S.Score' and 'G2M.Score') using the SCTransform function.
    keywords: analysis; cell; clusters; decay; development; et al; expression; figure; file; genes; mice; mosns; mrnas; nonsense; olfactory; olfr; seq; sub; translation; upf3b
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        item: #181 of 1349
          id: cord-012784-c74jr4ga
      author: Zhang, Le-le
       title: Identification of nagilactone E as a protein synthesis inhibitor with anticancer activity
        date: 2020-02-11
       words: 4894
      flesch: 44
     summary: NLE treatment inhibited the proliferation of lung cancer cells via G2 phase cell cycle arrest mediated by the downregulation of Cyclin B1 [6] . Compared with the body weights of mice in the control group, NLE treatment did not have an obvious effect on mouse body weight (Fig. 1c) .
    keywords: a549; analysis; assay; cancer; cells; expression; fig; genes; nle; protein; rna; synthesis; treatment
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        item: #182 of 1349
          id: cord-012909-o6t2srim
      author: Chaudhari, Jayeshbhai
       title: Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain
        date: 2020-07-28
       words: 9329
      flesch: 38
     summary: A portion of freshly isolated PBMCs were used for measurement of T cell responses while the rest of PBMCs were cryopreserved for future analysis. Briefly two replicates of 250,000 PBMCs or ILN cells freshly collected from each pig were plated into two wells of a 96-well plate with PVDF membrane that were coated with anti-porcine IFN-γ antibody.
    keywords: activation; apoptosis; cells; con90; expression; figure; genes; ifn; iln; infection; pigs; porcine; prrsv; rna; study; syndrome; tissue; usa; viral; virus
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        item: #183 of 1349
          id: cord-013171-wgn529rc
      author: Zhong, Yi
       title: STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of the nerve growth factor receptor signaling pathway
        date: 2020-09-16
       words: 6773
      flesch: 43
     summary: 1D , there was a correlation between STAU1 OE cells and control cells; there was also a significant correlation between the biological replicates. Distribution of reads reflected the relative location of genes and the relative read abundance, which further demonstrated differential expression in control cells and STAU1 OE cells.
    keywords: analysis; binding; cells; expression; factor; fig; genes; growth; hela; overexpression; pathway; protein; receptor; response; rna; role; seq; signaling; stau1
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        item: #184 of 1349
          id: cord-013176-6ckuya1w
      author: Ninfali, Paolino
       title: Antiviral Properties of Flavonoids and Delivery Strategies
        date: 2020-08-21
       words: 8135
      flesch: 29
     summary: Front Antiviral Phytochemicals: An Overview Flavonoids: Promising natural compounds against viral infections Antiviral effects of phytochemicals from medicinal plants: Applications and drug delivery strategies Antiviral activity of Disticella elongata (Vahl) Urb. Concerning the combination of flavonoids in an antiviral cocktail, each phytochemical may be used initially at a concentration of about 0.5 g/day with the aim of reaching an intake of 3 g/day of antiviral flavonoids.
    keywords: activity; anti; bioavailability; cells; delivery; drugs; effects; flavonoids; hcv; influenza; inhibition; phytochemicals; protein; quercetin; replication; rna; virus
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        item: #185 of 1349
          id: cord-013177-whd0znan
      author: Han, Zhenzhi
       title: The Husavirus Posa-Like Viruses in China, and a New Group of Picornavirales
        date: 2020-09-07
       words: 5051
      flesch: 41
     summary: With the development of deep transcriptome sequencing, more novel unclassified RNA virus genomes have been identified, redefining the proposed evolutionary progress of the virosphere [4, 5] . Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture The evolutionary history of vertebrate RNA viruses Redefining the invertebrate RNA virosphere Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness Virome heterogeneity and connectivity in waterfowl and shorebird communities Using Metagenomics to Characterize an Expanding Virosphere A Highly Divergent Picornavirus in a Marine Mammal A novel genus in the order Picornavirales detected in human stool The Fecal Virome of Pigs on a High-Density Farm Identification of a novel Picornavirales virus distantly related to posavirus in swine feces Complex virome in feces from Amerindian children in isolated Amazonian villages Highly diverse posaviruses in swine faeces are aquatic in origin Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China Detection and complete genome characteristics of Posavirus 1 from pigs in China Virome comparisons in wild-diseased and healthy captive giant pandas Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing Type 2 Poliovirus Detection after Global Withdrawal of Trivalent Oral Vaccine Faecal Virome Analysis of Wild Animals from Brazil Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica).
    keywords: china; genome; genomic; husavirus; length; picornavirales; posa; samples; sequences; strains; viruses
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        item: #186 of 1349
          id: cord-013243-1hj5clsw
      author: Brewer, Gary
       title: Editorial for “Methods to characterize virus small RNAs and RNA structures”
        date: 2020-10-16
       words: 577
      flesch: 31
     summary: [12; Contreras paper] directly probes the accessibility of unpaired regions within RNA structure by using an antisense platform that has been engineered to express GFP only when hybridized to the appropriate RNA target. Methods for detection and study of virus derived small RNAs produced from the intramolecular base-pairing region of the picornavirus genome A cytoplasmic RNA virus generates functional viral small RNAs and regulates viral IRES activity in mammalian cells Functional analyses of mammalian virus 5'UTR-derived, small RNAs that regulate virus translation HuR and Ago2 bind the internal ribosomal entry site of enterovirus 71 and promote virus replication In vitro production of synthetic viral RNAs and their delivery into mammalian cells and the application of viral RNAs in the study of innate interferon responses From current knowledge to best practice: A primer on Viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants Potential functional pathways of plant RNA virus-derived small RNAs in a vector insect Molecular characterization and RSV Co-infection of Nicotiana benthamiana with three distinct begomoviruses Integrated approaches to reveal Mechanisms by which RNA viruses reprogram the cellular environment Mapping the RNA structural landscape of viral genomes Viral RNA structure analysis using DMS-MaPseq Antisense probing of dynamic RNA structures CLIP for studying protein-RNA interactions that regulate virus replication These include construction of bicistronic IRES-luciferase reporters, protein-RNA interaction assays, knockdown of RNA-binding proteins using RNA interference, and assessing effects of vsRNAs and host RNA-binding proteins on viral protein synthesis and replication.
    keywords: rna; rnas; virus
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        item: #187 of 1349
          id: cord-013280-kczj24se
      author: Yang, Bo
       title: Molecular Mechanisms of Immune Escape for Foot-and-Mouth Disease Virus
        date: 2020-09-04
       words: 11333
      flesch: 41
     summary: Recently, new mechanisms and functions of FMDV proteins inhibiting innate immunity have been discovered. This review summrized the molecular mechanisms of immune evasion caused by FMDV proteins.
    keywords: cells; disease; disease virus; expression; fmdv; foot; host; ifn; immune; infection; mouth; mouth disease; pathway; protein; replication; response; virus
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        item: #188 of 1349
          id: cord-013412-gj443yei
      author: Lebedeva, Natalya Sh.
       title: The Application of Porphyrins and Their Analogues for Inactivation of Viruses
        date: 2020-09-23
       words: 13472
      flesch: 42
     summary: There are several different types of photosensitized oxidation which may be important in biological systems Photodynamic efficiency: From molecular photochemistry to cell death Singlet oxygen-mediated damage to proteins and its consequences Effect of irradiation spectral range on porphyrin-Protein complexes Sewage bacteriophage inactivation by cationic porphyrins: Influence of light parameters Photodynamic inactivation of bacteriophage MS2: The A-protein is the target of virus inactivation TMPyP functionalised chitosan membrane for efficient sunlight driven water disinfection Oxidation of virus proteins during UV254 and singlet oxygen mediated inactivation Photodynamic inactivation of mammalian viruses and bacteriophages Photo-oxidation of proteins and its role in cataractogenesis Oxidative modification of cytochrome c by singlet oxygen. The most serious human diseases caused by RNA viruses are Ebola hemorrhagic fever, SARS, COVID-19, rabies, influenza, hepatitis C and E, West Nile fever, poliomyelitis, measles, etc.
    keywords: activity; analogues; binding; cell; complex; complexes; dna; figure; formation; gp120; inactivation; oxidation; p&a; porphyrins; protein; rna; tmpyp4; type; virus; viruses
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        item: #189 of 1349
          id: cord-013784-zhgjmt2j
      author: Tang, Min
       title: Three-dimensional bioprinted glioblastoma microenvironments model cellular dependencies and immune interactions
        date: 2020-06-04
       words: 13724
      flesch: 40
     summary: e Gene set enrichment analysis (GSEA) of the glioblastoma tissue vs cell culture signature as defined in d when applied to RNA-seq data comparing the 3D tetra-culture system with sphere cell culture. Data was derived from Miller et al. 36 g GSEA of the glioblastoma tissue vs cell culture signature as defined in f when applied to RNA-seq data comparing the 3D tetraculture system with sphere cell culture.
    keywords: 3d tetra; analysis; bars; brain; cancer; cell; cell culture; culture; culture model; expression; fig; gene; glioblastoma; gscs; human; macrophages; model; rna; signature; sphere; sphere culture; system; test; tetra; tissue; tri; tumor
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        item: #190 of 1349
          id: cord-013854-wadpugbj
      author: Fratter, Carl
       title: EMQN best practice guidelines for genetic testing in dystrophinopathies
        date: 2020-05-18
       words: 12726
      flesch: 32
     summary: Eur J Hum Genet DOI: 10.1038/s41431-020-0643-7 sha: doc_id: 13854 cord_uid: wadpugbj Dystrophinopathies are X-linked diseases, including Duchenne muscular dystrophy and Becker muscular dystrophy, due to DMD gene variants. Finally, atypical findings (such as non-contiguous deletions and dual DMD variants), implications for personalised medicine and clinical trials and incidental findings (identification of DMD gene variants in patients where a clinical diagnosis of dystrophinopathy has not been considered or suspected) are discussed.
    keywords: analysis; carrier; cases; deletions; diagnosis; dmd; dmd gene; duplications; dystrophinopathy; dystrophy; exon; gene; guidelines; muscle; muscular; pathogenic; sequencing; testing; variant
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        item: #191 of 1349
          id: cord-014397-7b88ycv8
      author: Gavora, JS
       title: Resistance of livestock to viruses: mechanisms and strategies for genetic engineering
        date: 1996-12-15
       words: 11586
      flesch: 35
     summary: The transgenic birds that expressed only the viral envelope coding region of the recombinant genome were shown to be resistant to the corresponding subgroup of the avian leukosis virus (Salter and Crittenden, 1989; Gavora et al, 1995a) , due to a blockage of virus receptors by the viral envelope proteins. and 1 Erythrocyte P antigen: cellular receptor for B 19 parvovirus Resistance to parvovirus B19 infection due to lack of virus receptor (erythrocyte P antigen)
    keywords: avian; cells; disease; et al; gene; genome; host; infection; livestock; mechanisms; plants; protein; receptor; replication; resistance; resistance mechanisms; rna; strategies; virus; viruses
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        item: #192 of 1349
          id: cord-014462-11ggaqf1
      author: None
       title: Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh
        date: 2011-04-21
       words: 35463
      flesch: 47
     summary: The following virus isolates have been used in the analysis: GTPV-Uttarkashi, P60, vaccine virus; GTPV Mukteswar, P10, Challenge virus; GTPV (Akola), GTPV Bareilly/00, GTPV Ladakh/01 and GTPV Sambalpur/82, field isolates and SPPV Srinagar, P40; SPPV Ranipet, P50; SPPV-RF, P50, vaccine viruses and SPPV Makdhoom/07, SPPV CIRG/08, SPPV Pune/08, SPPV Bareilly, SPPV 183/03 and SPPV 125/02, field isolates. Present paper discusses about virus disease of quarantine importance affecting ornamental and fruit plants such as Chrysanthimum, Dahlia, Dianthus, Rosabengalensis, Cattleya, Cymbidium, Dendrobium, Lilium, Citrus, Vitis etc.
    keywords: acid; analysis; animals; antibodies; antigen; assay; cases; cells; cloned; control; crop; curl; dengue; detection; development; disease; dna; elisa; expression; field; food; gene; host; india; infection; isolates; leaf; management; methods; molecular; mosaic; mosaic virus; nucleotide; pathogens; patients; pcr; plant; positive; present; primers; production; protein; region; resistance; response; results; rna; samples; sequence; specific; study; symptoms; time; tomato; total; vaccine; vector; viral; virus; virus infection; viruses; world; yellow
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        item: #193 of 1349
          id: cord-014685-ihh30q6f
      author: None
       title: Posters P788 - P999
        date: 2005-09-21
       words: 38408
      flesch: 42
     summary: 12 physical property parameters of protein structure were chosen to construct a 12-dimension physical property space. These systems have proven to be also valuable as membrane mimetic structures, as promising matrices for controlled-release and delivery of proteins, vitamins and small drugs in pharmacological applications, and they offer a 3D lipid matrix for successful crystallization of membrane proteins which do not easily crystallize in bulk solution.
    keywords: activity; aggregation; analysis; beta; binding; cells; changes; complex; complexes; concentration; conformational; data; delivery; dna; domain; drug; dynamics; effect; energy; experiments; folding; function; human; institute; interaction; light; lipid; loop; mechanism; membrane; membrane protein; method; model; molecular; native; new; nmr; order; peptide; phase; potential; presence; process; properties; protein; protein structure; region; residues; results; rna; rst; sequence; signi; site; solution; speci; stability; state; step; structure; studies; study; surface; system; temperature; terminal; time; transition; transport; type; unfolding; university; uorescence; water; work
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        item: #194 of 1349
          id: cord-014908-jys1y0k9
      author: Yadav, Rakesh
       title: Trends and Perspectives of Biosensors for Food and Environmental Virology
        date: 2010-05-19
       words: 5123
      flesch: 21
     summary: A color-shifting glycopolythiophene sensor that contains sialic acid as the receptor and a fluorescent polymer as the transducer has been reported for virus detection at the zeptomole level (Leclerc 1999; Baek et al. 2000) . Genosensor on gold films with enzymatic electrochemical detection of a SARS virus sequence Design and synthesis of novel glycopolythiophene assemblies for colorimetric detection of Influenza virus and E. coli Evaluation of viral extraction methods on a broad range of ready-to-eat foods with conventional and real-time RT-PCR for Norovirus GII detection A biosensor for Dengue virus detection:
    keywords: acid; aptamers; biosensor; detection; dna; et al; food; hepatitis; pcr; rna; sample; sensors; virion; virus; viruses
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        item: #195 of 1349
          id: cord-015237-8cxfa8wf
      author: None
       title: Structure Watch
        date: 2005
       words: 274
      flesch: 50
     summary: As an abundant eukaryotic RNAbinding protein, PTB1 is implicated in various aspects of RNA metabolism, but how it functions in these processes is not well understood. Structure of PTB bound to RNA: specific binding and implications for splicing regulation
    keywords: rna
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        item: #196 of 1349
          id: cord-015376-z739ifu5
      author: Savarino, Andrea
       title: Potential therapies for coronaviruses
        date: 2006-08-31
       words: 6367
      flesch: 46
     summary: A review providing the immunological grounds for a potential use of chloroquine in the clinical management of SARS Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine This article describes the first experiments showing an anti-SARS-CoV effect of chloroquine Chloroquine is a potent inhibitor of SARS coronavirus infection and spread This research article provides the mechanisms of SARS-CoV inhibition by chloroquine Using siRNA in prophylactic and therapeutic regimens against SARS coronavirus in Rhesus macaque The coronavirus replicase Binding site-based classification of coronaviral papain-like proteases Virus-encoded proteinases and proteolytic processing in the Nidovirales Intracellular localization and protein interactions of the gene 1 protein p28 during mouse hepatitis virus replication Identification and characterization of severe acute respiratory syndrome coronavirus replicase proteins Viral RNA replication in association with cellular membranes Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs Dissection study on the severe acute respiratory syndrome 3C-like protease reveals the critical role of the extra domain in dimerization of the enzyme: defining the extra domain as a new target for design of highly specific protease inhibitors A novel auto-cleavage assay for studying mutational effects of the active site of severe acute respiratory syndrome coronavirus 3C-like protease Medical treatment of viral pneumonia including SARS in immunocompetent adult Treatment of severe acute respiratory syndrome with lopinavir/ritonavir: a multicentre retrospective matched cohort study Role of lopinavir/ritonavir in the treatment of SARS: initial virological and clinical findings HIV protease inhibitor nelfinavir inhibits replication of SARS-associated coronavirus In vitro susceptibility of 10 clinical isolates of SARS coronavirus to selected antiviral compounds Severe acute respiratory syndrome-related coronavirus is inhibited by IFN-α Expanding the frontiers of existing antiviral drugs: possible effects of HIV-1 protease inhibitors against SARS and avian influenza This paper reviews the information available on the use of HIV-1 protease inhibitors against SARS-CoV and provides the results of a molecular docking study Identifying inhibitors of the SARS coronavirus proteinase This bioinformatic analysis of drug/enzyme docking provides interesting insights on the use of HIV-1 protease inhibitors as lead compounds for development of 3Clpro inhibitors Old drugs as lead compounds for a new disease?
    keywords: 3clpro; chloroquine; compounds; coronavirus; cov; drug; effects; inhibitors; protease; replication; rna; sars; use
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        item: #197 of 1349
          id: cord-015394-uj7fe5y6
      author: None
       title: Scientific Abstracts
        date: 2008-12-23
       words: 242809
      flesch: 48
     summary: The highest level of -tubulin acetylation (2.5-fold) was observed with Vinblastine at 10-fold IC 50 after 48 h. Exposure to Microtubule interacting agents and TSA resulted in increased cell surface expression of Ep-CAM in a time and dose dependent manner. Finally, we elucidated a link between the RA and TGF-pathways by assessing the impact of RA treatment of TGF-3 expression, demonstrating that TGF-3 template decreased to levels comparable to myometrial cell expression (0.84±0.12 fold).
    keywords: acid; activation; activity; addition; administration; adult; aea; age; aim; analysis; animals; anova; anti; antibodies; antibody; apoptosis; arteries; artery; assay; associated; association; background; baseline; binding; birth; blood; blood cells; blot; bmi; body; brain; cancer; cancer cells; cases; cells; center; cervix; cesarean; changes; clinical; collagen; concentrations; conclusions; conditions; contractions; contrast; contribute; control; control cells; control group; correlation; cortisol; crf; culture; cycle; cytokines; data; day; days; decidua; decrease; delivery; design; development; differences; differentiation; disease; dna; dose; effect; elisa; endometriosis; endometrium; endothelial; eoc cells; epithelial; estradiol; estrogen; evidence; explants; exposure; expression; expression levels; factor; fat; female; fetal; fetuses; findings; flow; fluid; fold; following; free; function; gene; gestation; glucose; gnrh; group; growth; gynecology; hcg; high; hormone; hospital; hours; human; hypertension; hypothesis; hypoxia; il-6; il-8; immune; immunohistochemistry; implantation; increase; induction; infection; inflammation; inhibitor; insulin; introduction; invasion; iugr; ivf; kinase; labor; leptin; levels; lps; male; maternal; mean; mechanisms; media; medical; medicine; medium; membranes; menstrual; methods; mice; min; model; mouse; mrna expression; mrna levels; muscle cells; myometrial; n=6; neonatal; new; non; normal; novel; nuclear; number; obesity; objective; obstetrics; offspring; onset; oocytes; outcome; ovarian; oxygen; p<0.001; p<0.05; pathway; patients; pattern; pcos; pcr; period; phase; phosphorylation; placental; placental cells; plasma; play; population; positive; post; potential; preeclampsia; pregnancies; pregnancy; pregnant; presence; present; pressure; preterm; primary; production; progesterone; proliferation; protein expression; protein levels; proteins; range; rate; rats; receptor; receptor expression; reduced; regulation; relative; release; reproductive; response; restriction; results; risk; role; samples; secretion; sections; serum; sheep; signaling; smooth; specific; staining; stress; studies; study; study group; subjects; syndrome; system; t cells; term; test; time; tissue; tnf; total; treatment; trimester; trophoblast cells; tumor; type; university; usa; uterine; uterus; vascular; vegf; vehicle; vitro; vivo; weeks; weight; western; women; years
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        item: #198 of 1349
          id: cord-015527-ph576eji
      author: Mostajo, Nelly F
       title: A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
        date: 2019-09-30
       words: 8399
      flesch: 48
     summary: Other ncRNAs are currently unknown from bat genomes or not well documented. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 RNA-Seq gene expression estimation with read mapping uncertainty Rfam: an RNA family database Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families Non-coding RNA analysis using the Rfam database Infernal 1.0: inference of RNA alignments Infernal 1.1: 100-fold faster RNA homology searches RALEE--RNA Alignment editor in Emacs RNAmmer: consistent and rapid annotation of ribosomal RNA genes tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence Matching of Soulmates: coevolution of snoRNAs and their targets Characterisation of novel microRNAs in the Black flying fox (Pteropus alecto) by deep sequencing LNCipedia 5: towards a reference set of human long non-coding RNAs MITOS: Improved de novo metazoan mitochondrial genome annotation A comprehensive study of de novo genome assemblers: current challenges and future prospective Genome-wide signatures of convergent evolution in echolocating mammals A high-resolution map of human evolutionary constraint using 29 mammals Comparative analysis of bat genomes provides insight into the evolution of flight and immunity The genomes of two bat species with long constant frequency echolocation calls Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii Exploring the genome and transcriptome of the cave nectar bat Eonycteris spelaea with PacBio long-read sequencing The Egyptian rousette genome reveals unexpected features of bat antiviral immunity Reference sequence (RefSeq) database at [NCBI: current status, taxonomic expansion, and functional annotation sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis)
    keywords: annotated; annotations; assembly; bat; bats; coding; data; gene; genome; mirnas; ncrnas; rna; seq; set; species; table
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        item: #199 of 1349
          id: cord-015606-h9bbvpzd
      author: Highfield, P.E.
       title: Translation of infectious bronchitis virus RNA
        date: 2006-03-27
       words: 1126
      flesch: 61
     summary: Both of these peptides were also present in the products found in the wheat germ system when it was stimulated by IBV virion RNA, but neither was found in the virus particle. It is clear from these results that IBV virion RNA can be translated into characterisable products, one of which is probably a virus structural protein.
    keywords: ibv; rna; system
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        item: #200 of 1349
          id: cord-015642-p46abodr
      author: Backofen, Rolf
       title: Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures
        date: 2013
       words: 4204
      flesch: 60
     summary: Alg 2d meets 4g: G-quadruplexes in rna secondary structure prediction Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure The equilibrium partition function and base pair binding probabilities for RNA secondary structure RNA structure and the mechanisms of alternative splicing The secondary structure of RNA under tension Topology and prediction of RNA pseudoknots A practical guide to single-molecule FRET From sequences to shapes and back: a case study in RNA secondary structures Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches The ends of a large RNA molecule are necessarily close This work was supported in part by the Deutsche Forschungsgemeinschaft proj. Spatial distance can be approximated by the graph-distance in RNA secondary structure.
    keywords: base; distance; graph; rna; structure
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        item: #201 of 1349
          id: cord-015673-rz74sh32
      author: Lamers, Anne E.
       title: RNA Interference Mechanisms and Therapeutic Applications
        date: 2006
       words: 2959
      flesch: 44
     summary: The choice of RNA polymerase promoters appears to be critical for the effective production of shRNA. An ancient process for defense against viral infections and transposons, and in higher developed organisms an endogenous process that regulates gene expression, triggered by double-stranded RNA (dsRNA) was recently revealed (for reviews see Carrington and Ambros, 2003; Hammond et al., 2001; Sharp, 2001) .
    keywords: et al; gene; rna; rnai; sequence; silencing
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        item: #202 of 1349
          id: cord-015850-ef6svn8f
      author: Saitou, Naruya
       title: Eukaryote Genomes
        date: 2013-08-22
       words: 7442
      flesch: 48
     summary: The complete nucleotide sequence of the tobacco mitochondrial genome: Comparative analysis of mitochondrial genomes in higher plants and multipartite organization Widespread horizontal transfer of mitochondrial genes in fl owering plants Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin Small, repetitive DNAs contribute signifi cantly to the expanded mitochondrial genome of cucumber The complete nucleotide sequence of the tobacco chloroplast genome: Its gene organization and expression Changes in the structure of DNA molecules and the amount of DNA per plastid during chloroplast development in maize Pattern of organization of human mitochondrial pseudogenes in the nuclear genome Why genes in pieces? Introns. As for plants, Kaplinsky [ 62 ] ) compared genome sequences of Arabidopsis, grape rice, and Brachypodium and found >100 times more abundant CNSs from monocots than dicots.
    keywords: dna; duplication; eukaryotes; evolution; genes; genome; human; introns; junk; number; plants; protein; rna; sequence; size; species; type
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        item: #203 of 1349
          id: cord-015871-1tuf4zxi
      author: Ergonul, Onder
       title: Treatment of Crimean-Congo Hemorrhagic Fever
        date: 2007
       words: 8244
      flesch: 41
     summary: However hemorrhagic fever virus infections can be approached by the following different therapeutic strategies [6] : (i) administration of high-titered neutralizing antibodies and/or (ii) treatment with antiviral drugs. During the last decade, the potential of RNA interference as a therapeutic agent against virus infection has been discussed.
    keywords: antibody; cases; cchf; congo; crimean; effect; fever; human; infection; interferon; patients; plasma; platelet; ribavirin; rna; therapy; treatment; virus; viruses
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        item: #204 of 1349
          id: cord-015933-x5cq4k4x
      author: Verbrugh, H.A.
       title: 1 Micro-organismen, de mens en het ontstaan van infectieziekten: algemene principes
        date: 2011
       words: 19366
      flesch: 44
     summary: Afhankelijk van de mate van sensibilisatie van de gastheer kunnen de huidreacties achterwege blijven, pas na enkele weken optreden, of optreden direct na een hernieuwd contact met de parasiet. De productie van kopieën van het virale genoom ten behoeve van nieuwe infectieuze partikels vindt bij DNA- virussen nagenoeg altijd plaats in de celkern (uitzondering vormen Poxviridae, waaronder variola, de verwekker van menselijke pokken) maar bij RNA-virussen bijna altijd in het cytoplasma (uitzondering: Orthomyxoviridae, waaronder influenzavirus).
    keywords: aan; aan de; aantal; afhankelijk; alle; alleen; als; andere; antimicrobiële; antistoffen; bacteriën; behandeling; belang; belangrijkste; bepaalde; bij; bij de; bij een; bij het; bijv; bijvoorbeeld; binnen; cellen; dan; dat; dergelijke; deze; die; dit; dna; door; door het; een; eerste; effect; eigenschappen; eiwitten; figuur; fungi; gastheer; gastheercel; geen; genetische; genoemd; gevolg; goed; groot; hebben; heeft; het; het micro; hiv; huid; hun; infecties; infectieziekten; kan; komen; kunnen; levende; lichaam; maar; maken; meer; meestal; mens; micro; middelen; mogelijk; moleculen; naar; niet; nieuwe; nog; omdat; onder; ontstaan; ook; op de; op een; op het; organismen; pathogene; patiënt; personen; plaats; replicatie; resistentie; rna; rol; schade; sommige; soms; soort; soorten; specifieke; steeds; tabel; tegen; terwijl; tijd; tot; tussen; uit; vaak; van; van de; van deze; van een; van het; van infectieziekten; van micro; veel; vele; verschillende; virale; virussen; voor; voor de; voor het; vooral; vormen; waarbij; waardoor; weer; weerstand; wel; wijze; worden; wordt; zeer; zich; zijn; zijn het; zijn van; zijn voor; zoals
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        item: #205 of 1349
          id: cord-016095-jop2rx61
      author: Vignais, Pierre V.
       title: Challenges for Experimentation on Living Beings at the Dawn of the 21(st) Century
        date: 2010-06-08
       words: 42858
      flesch: 42
     summary: Nevertheless, research on such cells is mandatory if we wish to move on to a regenerative medicine that aims to be a new frontier in the art of healing. In Man, such cells could be directed by differentiation towards stable cell lines creating well-defined tissues and organs (liver, muscle…) that could be used in regenerative medicine.
    keywords: animal; atp; beings; biology; case; cells; century; chapter; cloning; dna; domain; enzyme; example; experiments; fact; figure; gene; genome; human; information; life; living; means; medicine; messenger; metabolic; method; molecular; molecules; neurons; non; order; plant; present; progress; proteins; research; rise; rnas; science; sequence; species; stem; stem cells; study; subject; synthesis; techniques; technology; time; type; use; way; years
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        item: #206 of 1349
          id: cord-016108-jlono0x7
      author: Marthaler, Douglas
       title: Next-Generation Sequencing for Porcine Coronaviruses
        date: 2015-09-10
       words: 1440
      flesch: 51
     summary: However, achieving viral genomes directly from samples can be diffi cult since the total RNA, including mRNA from host cells and bacteria, is also sequenced [ 11 -13 ] . De novo assembly for viral genomes.
    keywords: assembly; genome; reads; reference
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        item: #207 of 1349
          id: cord-016144-280kwlev
      author: Maan, Sushila
       title: Novel Molecular Diagnostics and Therapeutic Tools for Livestock Diseases
        date: 2018-04-26
       words: 6527
      flesch: 39
     summary: In multiplex PCR the design of various primer pairs is crucial so that they complementarily anneal to specific DNA sequences at more or less similar temperatures, i.e. annealing temperature should be the same for different primer pairs used in combination. This is to avoid false positive results from contaminating DNA from previous PCR reactions (Raoult et al. 2000) .
    keywords: amplification; detection; diagnosis; disease; dna; et al; method; nucleic; pathogens; pcr; primer; rna; sequencing; target; virus
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        item: #208 of 1349
          id: cord-016179-4i1n9j4x
      author: Chen, Yi-Ning
       title: Real-Time Reverse Transcription-Polymerase Chain Reaction for Detection and Quantitation of Turkey Coronavirus RNA in Feces and Intestine Tissues
        date: 2015-09-10
       words: 2085
      flesch: 54
     summary: In step 2, TCoV RNA was extracted from feces using QIAamp viral RNA mini kit or intestine tissues using RNAeasy mini kit. In this chapter, the protocol for one-step real-time RT-PCR to detect, differentiate, and quantitative TCoV RNA in the feces and intestinal tissue is presented.
    keywords: pcr; rna; tcov; time; turkey
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        item: #209 of 1349
          id: cord-016209-6p9btua0
      author: Merl, S.
       title: Targeting Viral Heart Disease by RNA Interference
        date: 2008
       words: 7176
      flesch: 25
     summary: Merl and Wessely 2007; Yuan et al. 2005) , the capsid protein VP2 (Merl and Wessely 2007) , the viral protease 2A (Merl et al. 2005; Yuan et al. 2005) , the viral protease 3C (Merl and Wessely 2007) and the RNA dependent RNA polymerase 3D (Ahn et al. 2005; Kim et al. 2007; Merl and Wessely 2007; Schubert et al. 2005; Werk et al. 2005; Yuan et al. 2005) . Of note, siRNAs targeting the 5′ as well as 3′ UTR had no substantial effect on viral cytopathogenicity and replication (Kim et al. 2007;
    keywords: antiviral; cells; et al; expression; gene; interference; interfering; replication; rna; rnai; rnas; silencing; sirna; target; targeting; virus
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        item: #210 of 1349
          id: cord-016261-jms7hrmp
      author: Liu, Chunmei
       title: Profiling and Searching for RNA Pseudoknot Structures in Genomes
        date: 2005
       words: 4334
      flesch: 49
     summary: Applications to protein modeling Prediction of RNA Pseudoknots-Comparative Study of Genetic Algorithms RNA pseudoknot prediction in energy based models RNAMotif, an RNA secondary structure definition and search algorithm Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in E. coli tmRNA 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics The language of RNA: a formal grammar that includes pseudoknots A Dynamic Programming Algorithm for RNA Structure Prediction Including Pseudoknots An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots Stochastic Context-Free Grammars for tRNA Modeling An expanding universes of noncoding RNAs Tree adjoining grammars for RNA structure prediction The 7SK small nuclear RNA inhibits the Cdk9/cyclin T1 kinase to control transcription Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots RNA Pseudoknot Modeling Using Intersections of Stochastic Context Free Grammars with Applications to Database Search Small subunit ribosomal RNA modeling using stochastic context-free grammars Stochastic Modeling of Pseudoknot Structures: A Grammatical Approach Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids RNA sequence analysis using covariance models Ribonuclease P: unity and diversity in a tRNA processing ribozyme Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles Characterization of the RNA components of a Putative Molecular Switch in the 3' Untranslated Region of the Murine Coronavirus Genome Rfam: an RNA family database RSEARCH:
    keywords: components; model; pseudoknot; rna; sequence; stems; structures
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        item: #211 of 1349
          id: cord-016293-pyb00pt5
      author: Newell-McGloughlin, Martina
       title: The flowering of the age of Biotechnology 1990–2000
        date: 2006
       words: 22413
      flesch: 45
     summary: These DNA chips have broad commercial applications and are now used in many areas of basic and clinical research including the detection of drug resistance mutations in infectious organisms, direct DNA sequence comparison of large segments of the human genome, the monitoring of multiple human genes for disease associated mutations, the quantitative and parallel measurement of mRNA expression for thousands of human genes, and the physical and genetic mapping of genomes. Of course for such a radical approach certain basal level criteria needed to be established for selecting disease candidates for human gene therapy.
    keywords: animal; biology; biotechnology; cancer; cells; company; data; development; disease; dna; drug; expression; food; gene; gene therapy; genome; human; influenza; information; level; molecular; nih; number; plant; production; products; project; protein; research; rna; scientists; sequence; sequencing; stem cells; studies; system; techniques; technology; therapy; time; transfer; transgenic; university; use; virus; year
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        item: #212 of 1349
          id: cord-016309-6mw8okmt
      author: Bule, Mohammed
       title: Antivirals: Past, Present and Future
        date: 2019-06-06
       words: 8230
      flesch: 27
     summary: Therefore, the major concern in antiviral drug development is the identification of specific targets with increased selectivity and reduced side effects, which limit the therapeutic use of antiviral drugs in comparison to antibacterial agents (Dal Pozzo and Thiry 2014) . Antiviral drugs not just penetrate to disrupt the virus’ cellular divisions but also have a negative impact on normal physiological pathways in the host.
    keywords: activity; acyclovir; agents; antiviral; cats; compounds; diseases; dna; drug; et al; feline; herpes; infection; replication; rna; treatment; virus; viruses; vitro
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        item: #213 of 1349
          id: cord-016313-n4ewq0pt
      author: Baranyi, Lajos
       title: Advances in Lentiviral Vector-based Cell Therapy with Mesenchymal Stem Cells
        date: 2012-09-27
       words: 20593
      flesch: 29
     summary: However, much more needs to be known about the normal differentiation and functioning of the airway's basal cells and the differentiation and lineages of stem cells to have more ef fi cient treatment options both for gene therapy and for stem cell therapy [ 207 ] . Alas, the dif fi culties in research are faithfully re fl ected in the confusion in the nomenclature used for describing and classifying stem cells, including the classes of stem cells of mesodermal origin.
    keywords: alpha; beta; bone; cell therapy; ciency; cient; delivery; differentiation; disease; ef fi; endothelial; expression; fi c; fi cient; gene; gene therapy; human; lentiviral; mesenchymal; mesenchymal stem; mice; model; mscs; novel; potential; protein; signi; signi fi; speci; speci fi; stem cells; therapy; tissue; transduction; transfer; transplantation; use; vector; virus; vivo
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        item: #214 of 1349
          id: cord-016343-wc3i54fc
      author: Frese, Michael
       title: Interferon-Induced Effector Proteins and Hepatitis C Virus Replication
        date: 2008
       words: 10118
      flesch: 31
     summary: 1b infection Interferon action: RNA cleavage pattern of a (2 -5 )oligoadenylate-dependent endonuclease Regulation of interferon regulatory factor-3 by the hepatitis C virus serine protease Human MxA protein inhibits tick-borne Thogoto virus but not Dhori virus Interferon-alpha inhibits hepatitis C virus subgenomic RNA replication by an MxA-independent pathway Interferon-gamma inhibits replication of subgenomic and genomic hepatitis C virus RNAs Hepatitis C virus RNA replication is resistant to tumour necrosis factor-alpha Kissing-loop interaction in the 3 end of the hepatitis C virus genome essential for RNA replication Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection Control of PKR protein kinase by hepatitis C virus nonstructural 5A protein: molecular mechanisms of kinase regulation Impact of protein kinase PKR in cell biology: from antiviral to antiproliferative action Human RNA-specific adenosine deaminase ADAR1 transcripts possess alternative exon 1 structures that initiate from different promoters, one constitutively active and the other interferon inducible Cell growth regulatory and antiviral effects of the P69 isozyme of 2-5 (A) synthetase TRAF family proteins link PKR with NF-kappa B activation Evaluation of IFN-alpha bioavailability by MxA mRNA in HCV patients involvement of both nitric oxide and oxygen radicals Nitric oxide inhibits the replication cycle of severe acute respiratory syndrome coronavirus Hepatitis C virus subgenomic replicons in the human embryonic kidney 293 cell line Essential role for the dsRNA-dependent protein kinase PKR in innate immunity to viral infection Novel insights into hepatitis C virus replication and persistence Clonal expansion of hypermutated measles virus in an SSPE brain DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection Secondary structure determination of the conserved 98-base sequence at the 3 terminus of hepatitis C virus genome RNA Efficient initiation of HCV RNA replication in cell culture Role of IFN-induced indoleamine 2,3 dioxygenase and inducible nitric oxide synthase in the replication of human cytomegalovirus in retinal pigment epithelial cells The nonstructural 5A protein of hepatitis C virus genotype 1b does not contain an interferon sensitivitydetermining region Interferons and indoleamine 2,3-dioxygenase: role in antimicrobial and antitumor effects
    keywords: cells; et al; expression; gene; hcv; hepatitis; human; ifn; ifns; interferon; mice; mxa; patients; pkr; protein; replication; response; rna; type; virus
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        item: #215 of 1349
          id: cord-016419-v1f6dx3e
      author: Gupta, Varsha
       title: Production of Recombinant Pharmaceutical Proteins
        date: 2016-10-23
       words: 9655
      flesch: 48
     summary: The gene is transcribed under the control of powerful polyhedron promoter with high yields (~30 % of total cell protein). Any kind of impairment in protein production, such as production of mutated protein, or misfolded protein, leads to disruption of the pathway controlled by that protein.
    keywords: blood; cell; coli; expression; factor; form; gene; glycosylation; growth; hormone; host; human; insulin; mammalian; modifi; production; promoter; protein; recombinant; scale; system
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        item: #216 of 1349
          id: cord-016499-5iqpl23p
      author: Mackay, Ian M.
       title: Rhinoviruses
        date: 2014-02-27
       words: 23417
      flesch: 34
     summary: ARIs linked to HRV infections are associated with excessive and perhaps inappropriate antibiotic prescribing and with significant direct and indirect healthcare expenditure. ARIs linked to HRV infections are associated with excessive and perhaps inappropriate antibiotic prescribing [ 4 ] and with signifi cant direct and indirect healthcare expenditure [ 5 , 6 ] .
    keywords: acute; adults; airway; antiviral; ari; asthma; cells; children; cold; culture; defi; detection; disease; exacerbations; host; hrsv; hrv; hrv infection; hrvs; human; identifi; ifn; illness; infection; infl; nasal; pcr; receptor; response; rhinovirus; rna; role; species; studies; study; symptoms; time; tract; type; viruses
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        item: #217 of 1349
          id: cord-016538-4og05fuo
      author: Dolja, V. V.
       title: Biotechnology Applications of Grapevine Viruses
        date: 2017-03-30
       words: 6279
      flesch: 33
     summary: The application of plant virus vectors is of potential interest to the worldwide, multibillion dollar, grape and wine industries. The major applications of plant virus vectors are epitomized by Tobacco mosaic virus (TMV), Tobacco rattle virus (TRV), and Potato virus X (PVX) (Kumagai et al. 1995; Ratcliff et al. 2001; Burton et al. 2000) , which are the most widely used in protein expression and functional genomics.
    keywords: et al; expression; gene; grapevine; host; infection; plant; rna; vector; vigs; virus; viruses
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        item: #218 of 1349
          id: cord-016652-x8t3lf1x
      author: Matthews, David
       title: Viruses and the Nucleolus
        date: 2011-05-23
       words: 6640
      flesch: 12
     summary: Although many RNA virus proteins have been shown to localise to the nucleolus, most attention has focused on viral capsid proteins. These advances have provided fundamental insights as to how and why the nucleolus is targeted by many different viruses both to usurp normal functioning and to recruit nucleolar proteins to facilitate virus replication.
    keywords: cell; et al; herpes; human; infection; localization; nuclear; nucleocapsid; nucleolar; nucleolus; nucleus; protein; replication; rna; virus; viruses
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        item: #219 of 1349
          id: cord-016755-ye37z5h9
      author: Li, Jiandong
       title: The Discovery Process of SFTS in China
        date: 2019-10-12
       words: 2313
      flesch: 49
     summary: On the other hand, 10 out of 186 ticks (5.4%) of the species Haemaphysalis longicornis collected from domestic animals in the same areas were positive for SFTS virus RNA. The virus was named as SFTS virus.
    keywords: fever; patients; rna; serum; sfts; viral; virus
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        item: #220 of 1349
          id: cord-016796-g4kqqpy1
      author: Bramhachari, Pallaval Veera
       title: Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges
        date: 2019-11-05
       words: 5647
      flesch: 24
     summary: Immunofluorescence assay is extensively used for rapid identification of virus infections through detection of virus antigen or virus-specific antibodies in clinical specimens. AuNP-based detection techniques were reported by various groups of clinically relevant viruses with a unique focus on applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats were recently developed (Draz and Shafiee 2018).
    keywords: antibodies; assay; detection; diagnosis; human; infections; influenza; pcr; rna; sensitivity; time; virus; viruses; zikv
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        item: #221 of 1349
          id: cord-016808-gy8d8285
      author: Agol, Vadim I.
       title: The Origin and Evolution of Viruses
        date: 2008
       words: 3257
      flesch: 39
     summary: The frequency of mutations in DNA viruses may be several orders of magnitude lower than in RNA viruses, whose replicative enzyme, the RNA-dependent RNA polymerase, lacks proof-reading activity. On the other hand, a very significant proportion of the cellular genetic material has evolutionary relatedness to the genetic composition of the ancient world of RNA viruses.
    keywords: dna; genome; host; mutations; rna; viruses
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        item: #222 of 1349
          id: cord-017167-8cdbcrh7
      author: Ahola, Tero
       title: Functions of Chikungunya Virus Nonstructural Proteins
        date: 2016-12-03
       words: 10506
      flesch: 39
     summary: Reaction in alphavirus mRNA capping: formation of a covalent complex of nonstructural protein nsP1 with 7-methyl-GMP Sequence analysis reveals a conserved extension in the capping enzyme of the alphavirus supergroup, and a homologous domain in nodaviruses Critical residues of Semliki Forest virus RNA capping enzyme involved in methyltransferase and guanylyltransferase-like activities Semliki Forest virus mRNA capping enzyme requires association with anionic membrane phospholipids for activity Evasion of the innate immune response: the Old World alphavirus nsP2 protein induces rapid degradation of Rpb1, a catalytic subunit of RNA polymerase II An in vitro assay to study chikungunya virus RNA synthesis and the mode of action of inhibitors Development of Sindbis viruses encoding nsP2/GFP chimeric proteins and their application for studying nsP2 functioning Interferon-stimulated poly(ADP-Ribose) polymerases are potent inhibitors of cellular translation and virus replication A unique role for the host ESCRT proteins in replication of Tomato bushy stunt virus Semliki forest virus-induced endoplasmic reticulum stress accelerates apoptotic death of mammalian cells Computer-aided identification, design and synthesis of a novel series of compounds with selective antiviral activity against chikungunya virus Expression of the zinc-finger antiviral protein inhibits alphavirus replication Mapping of chikungunya virus interactions with host proteins identified nsP2 as a highly connected viral component Semliki Forest virus nonstructural protein 2 is involved in suppression of the type I interferon response Comparative analysis of the genome sequences and replication profiles of chikungunya virus isolates within the East, Central and South African (ECSA) lineage Arbovirus high fidelity variant loses fitness in mosquitoes and mice Tracking and elucidating alphavirus-host protein interactions Host factors associated with the Sindbis virus RNA-dependent RNA polymerase: role for G3BP1 and G3BP2 in virus replication Heat shock protein 90 positively regulates Chikungunya virus replication by stabilizing viral non-structural protein nsP2 during infection Functional cross-talk between distant domains of chikungunya virus non-structural protein 2 is decisive for its RNA-modulating activity Design and validation of novel chikungunya virus protease inhibitors Sindbis virus RNA polymerase is degraded by the N-end rule pathway Conventional and unconventional mechanisms for capping viral mRNA Mutations in the chikungunya virus non-structural proteins cause resistance to favipiravir (T-705), a broad-spectrum antiviral The viral capping enzyme nsP1: a novel target for the inhibition of chikungunya virus infection Modification of Asn374 of nsP1 suppresses a Sindbis virus nsP4 minus-strand polymerase mutant Macrodomain-containing proteins: regulating new intracellular functions of mono(ADP-ribosyl)ation Selection of RNA replicons capable of persistent noncytopathic replication in mammalian cells Random insertion mutagenesis of sindbis virus nonstructural protein 2 and selection of variants incapable of downregulating cellular transcription Roles of nonstructural protein nsP2 and alpha/beta interferons in determining the outcome of Sindbis virus infection Formation of nsP3-specific protein complexes during Sindbis virus replication Functional Sindbis virus replicative complexes are formed at the plasma membrane Chikungunya virus nonstructural protein 2 inhibits type I/II interferonstimulated JAK-STAT signaling Chikungunya virus nsP3 blocks stress granule assembly by recruitment of G3BP into cytoplasmic foci The C-terminal domain of chikungunya virus nsP2 independently governs viral RNA replication, cytopathicity, and inhibition of interferon signaling Chikungunya virus nsP2-mediated host shut-off disables the unfolded protein response Sindbis virus nonstructural protein nsP2 is cytotoxic and inhibits cellular transcription The Old World and New World alphaviruses use different virus-specific proteins for induction of transcriptional shutoff PKR-dependent and -independent mechanisms are involved in translational shutoff during Sindbis virus infection Inhibition of transcription and translation in Sindbis virus-infected cells Ability of minus strands and modified plus strands to act as templates in Semliki Forest virus RNA replication Thiazolidone derivatives as inhibitors of chikungunya virus BST-2/tetherin-mediated restriction of chikungunya (CHIKV) VLP budding is counteracted by CHIKV non-structural protein 1 (nsP1) Chikungunya virus-induced autophagy delays caspase-dependent cell death Species-specific impact of the autophagy machinery on chikungunya virus infection Functions of alphavirus nonstructural proteins in RNA replication Template RNA length determines the size of replication complex spherules for Semliki Forest virus NTPase and 5′-RNA triphosphatase activities of chikungunya virus nsP2 protein New World and Old World alphaviruses have evolved to exploit different components of stress granules, FXR and G3BP proteins, for assembly of viral replication complexes Three-dimensional analysis of a viral RNA replication complex reveals a virus-induced mini-organelle Chikungunya triggers an autophagic process which promotes viral replication Construction of an infectious chikungunya virus cDNA clone and stable insertion of mCherry reporter genes at two different sites The effects of palmitoylation on membrane association of Semliki forest virus RNA capping enzyme Membrane binding mechanism of an RNA virus-capping enzyme Polypeptide requirements for assembly of functional Sindbis virus replication complexes: a model for the temporal regulation of minus-and plus-strand RNA synthesis Viral macro domains reverse protein ADP-ribosylation Identification of the amino acid sequence in Sindbis virus nsP4 that binds to the promoter for the synthesis of the subgenomic RNA A phenotypic assay to identify chikungunya virus inhibitors targeting the nonstructural protein nsP2 Molecular determinants of substrate specificity for Semliki Forest virus nonstructural protease Macromolecular assembly-driven processing of the 2/3 cleavage site in the alphavirus replicase polyprotein Presentation overrides specificity: probing the plasticity of alphaviral proteolytic activity through mutational analysis The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket Role for conserved residues of Sindbis virus nonstructural protein 2 methyltransferase-like domain in regulation of minus-strand synthesis and development of cytopathic infection Ribosomal protein S6 associates with alphavirus nonstructural protein 2 and mediates expression from alphavirus messages SH3 domain-mediated recruitment of host cell amphiphysins by alphavirus nsP3 promotes viral RNA replication RIG-I and MDA-5 detection of viral RNA-dependent RNA polymerase activity restricts positive-strand RNA virus replication The C-terminal repeat domains of nsP3 from the Old World alphaviruses bind directly to G3BP Expression and biochemical characterization of nsP2 cysteine protease of chikungunya virus Architecture and biogenesis of plus-strand RNA virus replication factories Nuclear localization of Semliki Forest virus-specific nonstructural protein nsP2 Inhibitors of alphavirus entry and replication identified with a stable Chikungunya replicon cell line and virus-based assays Differential unfolded protein response during Chikungunya and Sindbis virus infection: CHIKV nsP4 suppresses eIF2alpha phosphorylation Chikungunya virus nsP3 & nsP4 interacts with HSP-90 to promote virus replication: Similar to other alphaviruses, CHIKV nsPs not only perform virus RNA replication but are also crucial for other activities essential for virus infection and pathogenesis.
    keywords: alphavirus; cells; chikungunya; chikv; domain; et al; host; infection; nsp1; nsp2; nsp3; nsp4; nsps; protein; replication; rna; strand; terminal; virus
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        item: #223 of 1349
          id: cord-017181-ywz6w2po
      author: Maus, Carsten
       title: Component-Based Modelling of RNA Structure Folding
        date: 2008
       words: 5368
      flesch: 48
     summary: RNA structures are hierarchically organised (see figure 2 ). To allow RNA structures to escape from local energy minima and refold to more stable structures, the base pair dissociation time will be randomised, which leads to very short bonding times in some cases although the activation energy needed for opening the base pair is quite large.
    keywords: base; folding; level; macro; model; pair; ribosome; rna; simulation; structure; time
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        item: #224 of 1349
          id: cord-017297-q3qtgrfc
      author: Rajagopal, Vaishnavi
       title: Viral Helicases
        date: 2008-11-01
       words: 11566
      flesch: 39
     summary: Proteins carrying a conserved D-E-A-D sequence, also referred to as the DEAD-box proteins, are predominantly RNA helicases (Koonin 1991; Koonin 1992; Linder and Daugeron 2000; Cordin et al. 2006) , while proteins carrying variant of the DEAD sequence like DEAH/DEXH are usually DNA helicases (Subramanya et al. 1996; Linder 2000; Linder and Daugeron 2000) . Allosteric effects of single-stranded and duplex DNA The origin DNA-binding and single-stranded DNA-binding domains of simian virus 40 large T antigen are distinct Role of single-stranded DNA binding activity of T antigen in simian virus 40 DNA replication Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing Structure of DNA helicase RepA in complex with sulfate at 1.95 A resolution implicates structural changes to an open form Structure of the Dengue virus
    keywords: acid; bacteriophage; binding; dna; dna helicase; domain; enzyme; et al; helicase; hepatitis; hydrolysis; mechanism; motif; ns3; ntp; protein; replication; rna; structure; translocation; unwinding; virus
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        item: #225 of 1349
          id: cord-017732-1pwa6zsk
      author: Miller, W. Allen
       title: Ribosomal Frameshifting in Decoding Plant Viral RNAs
        date: 2009-07-21
       words: 10644
      flesch: 45
     summary: RNA viruses have evolved to compress maximal protein-coding capacity and regulatory signals for RNA replication, localization, encapsidation, and gene expression into minimal sequence space (Belshaw et al., 2007; Holmes, 2003) . Viruses in the Closteroviridae family of positive sense RNA viruses have the largest genomic RNA of any plant virus, ranging from 12 to 20 kb.
    keywords: base; codon; downstream; et al; fig; frameshifting; loop; orf; protein; pseudoknot; rdrp; ribosomal; rna; sequence; site; stem; structure; virus; viruses
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        item: #226 of 1349
          id: cord-017764-h1w9gbxk
      author: Meanwell, Nicholas A.
       title: The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex
        date: 2018-06-08
       words: 9282
      flesch: 31
     summary: Hepatitis C viruses NS5A -from obscurity to new target for HCV therapy Targeting the NS5A protein of HCV: an emerging option Small molecule inhibitors of the hepatitis C virus-encoded NS5A protein NS5A: a new target for antiviral drugs in the treatment of hepatitis C virus infection HCV NS5A replication complex inhibitors Modeling shows that the NS5A inhibitor daclatasvir has two modes of action and yields a shorter estimate of the hepatitis C virus half-life Kinetic analyses reveal potent and early blockade of hepatitis C virus assembly by NS5A inhibitors Multiple ascending dose study of BMS-790052, a nonstructural protein 5A replication complex inhibitor, in patients infected with hepatitis C virus genotype 1 Interaction between hepatitis C virus and host cell factors HCVpro: hepatitis C virus protein interaction database Understanding the biological context of NS5A-host interactions in HCV infection: a network-based approach Affinity capture and identification of host cell factors associated with hepatitis C virus (+) strand subgenomic RNA The Discovery and Development of Daclatasvir: An Inhibitor of the Identification and comparative analysis of hepatitis C virus-host cell protein interactions Host cell kinases and the hepatitis C virus lifecycle Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA Direct binding of ledipasvir to HCV NS5A: mechanism of resistance to an HCV antiviral agent Resensitizing daclatasvir-resistance hepatitis C variants by allosteric modulation of NS5A Synergistic activity of combined NS5A inhibitors Asymmetric binding to NS5A by daclatasvir (BMS-790052) and analogs suggests two novel modes of HCV inhibition Resistance patterns associated with HCV NS5A inhibitors provide limited insight into drug binding A refined model of the HCV NS5A protein bound to daclatasvir explains drug-resistant mutations and activity against divergent genotypes A comprehensive computational analysis for the binding modes of hepatitis C virus NS5A inhibitors: the question of symmetry Overall structural model of NS5A protein from hepatitis C virus and modulation by mutations conferring resistance of virus replication to cyclosporin A Mechanisms of hepatitis C viral resistance to direct acting antivirals From structure to function: new insights into hepatitis C virus RNA replication Inhibition and avoidance of mRNA degradation by RNA viruses Attacked from all sides: RNA decay in antiviral defense Small molecules targeting hepatitis C virus-encoded NS5A cause subcellular redistribution of their target: insights into compound modes of action The effect of NS5A inhibitors on NS5A phosphorylation, polyprotein processing and localization Daclatasvir-like inhibitors of NS5A block early biogenesis of hepatitis C virus-induced membranous replication factories, independent of RNA replication Daclatasvir prevents hepatitis C virus infectivity by blocking transfer of the viral genome to assembly sites The hepatitis C virus NS5A inhibitor (BMS-790052) alters the subcellular localization of the NS5A non-structural viral protein Cyclophilin and NS5A inhibitors, but not other anti-hepatitis C virus (HCV) agents, preclude HCV-mediated formation of double-membrane-vesicle viral factories Practical and efficient strategy for evaluating oral absolute bioavailability with an intravenous microdose of a stable isotopically-labeled drug using a selected reaction monitoring mass spectrometry assay Daclatasvir: a review of its use in adult patients with chronic hepatitis C virus infection Daclatasvir: a review of preclinical and clinical pharmacokinetics Daclatasvir: a review in chronic hepatitis C Contribution of a mutational bias in hepatitis C virus replication to the genetic barrier in the development of drug resistance Antiviral resistance and the future landscape of hepatitis C virus infection therapy Importance of HCV genotype 1 subtypes for drug resistance and response to therapy Genotypic and phenotypic analysis of variants resistant to hepatitis C virus nonstructural protein 5A replication complex inhibitor BMS-790052 in humans: in vitro and in vivo correlations Hepatitis C virus RNA elimination and development of resistance in replicon cells treated with BMS-790052 Hepatitis C viral dynamics in vivo and the antiviral efficacy of interferon-α therapy New kinetic models for the hepatitis C virus Modeling HCV kinetics under therapy using PK and PD information Treatment of hepatitis C virus infection with interferon and small molecule direct antivirals: viral kinetics and modeling Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rate The Discovery and Development of Daclatasvir: An Inhibitor of the Mathematical modeling of HCV infection: what can it teach us in the era of direct-acting antiviral agents? The efficacy and safety of dual oral therapy with daclatasvir and asunaprevir for genotype 1b in Japanese real-life settings The practical management of chronic hepatitis C infection in Japan -dual therapy of daclatasvir + asunaprevir The Discovery and Development of Daclatasvir: An Inhibitor of the Daclatasvir for the treatment of hepatitis C virus infection Efficacy and safety of daclatasvir in hepatitis C: an overview Discovery and preclinical characterization of the cyclopropylindolobenzazepine BMS-791325, a potent allosteric inhibitor of the hepatitis C virus NS5B polymerase UNITY-1 Study Group (2013) Fixed-dose combination therapy with daclatasvir, asunaprevir, and beclabuvir for noncirrhotic patients with HCV genotype 1 infection Daclatasvir in combination with asunaprevir and beclabuvir for hepatitis C virus genotype 1 infection with compensated cirrhosis A randomized trial of daclatasvir in combination with asunaprevir and beclabuvir in patients with chronic hepatitis C virus genotype 4 infection Daclatasvir/asunaprevir/ beclabuvir fixed-dose combination in Japanese patients with HCV genotype 1 infection Daclatasvir/asunaprevir/beclabuvir, all-oral, fixed-dose combination for patients with chronic hepatitis C virus genotype 1 Beclabuvir in combination with asunaprevir and daclatasvir for hepatitis C virus genotype 1 infection: a systematic review and meta-analysis Daclatasvir with sofosbuvir and ribavirin for hepatitis C virus infection with advanced cirrhosis or post-liver transplantation recurrence Daclatasvir plus sofosbuvir for HCV in patients coinfected with HIV-1 All-oral 12-week treatment with daclatasvir plus sofosbuvir in patients with hepatitis C virus genotype 3 infection: ALLY-3 phase III study Daclatasvir plus sofobuvir, with and without ribavirin, achieved high sustained virological response rates in patients with HCV infection and advanced liver disease in a real-world cohort Long-term follow-up of clinical trial patients treated for chronic HCV infection with daclatasvir-based regimens Current therapy for chronic hepatitis C: the role of direct-acting antivirals Short-duration treatment for chronic hepatitis C virus with daclatasvir, asunaprevir, beclabuvir and sofosbuvir (FOURward study)
    keywords: activity; c virus; daclatasvir; discovery; genotype; gt-1a; hcv; hepatitis c; infection; inhibitors; ns5a; patients; protein; replication; replicon; rna; virus
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        item: #227 of 1349
          id: cord-017968-17d37a2z
      author: Lewinski, Martin
       title: Systems Approaches to Map In Vivo RNA–Protein Interactions in Arabidopsis thaliana
        date: 2018-08-30
       words: 6573
      flesch: 38
     summary: Arabidopsis chloroplast RNA binding proteins CP31A and CP29A associate with large transcript pools and confer cold stress tolerance by influencing multiple chloroplast RNA processing steps The RNA-binding protein repertoire of embryonic stem cells Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues Genome-wide identification, biochemical characterization, and expression analyses of the YTH domain-containing RNA-binding protein family in Arabidopsis and Rice The cardiomyocyte RNA-binding proteome: links to intermediary metabolism and heart disease HITS-CLIP yields genome-wide insights into brain alternative RNA processing A glycine-rich RNA-binding protein affects gibberellin biosynthesis in Arabidopsis ) atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes RBP45 and RBP47, two oligouridylatespecific hnRNP-like proteins interacting with poly(A)+ RNA in nuclei of plant cells A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin Gene expression regulatory networks in Trypanosoma brucei: insights into the role of the mRNA-binding proteome The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains The RNA-binding protein repertoire of Arabidopsis thaliana Conserved mRNA-binding proteomes in eukaryotic organisms GraphProt: modeling binding preferences of RNAbinding proteins Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7 Global analysis of yeast mRNPs SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export Comprehensive identification of mRNA-binding proteins of Leishmania donovani by interactome capture Pseudomonas HopU1 affects interaction of plant immune receptor mRNAs to the RNA-binding protein GRP7 Three types of nuclear genes encoding chloroplast RNAbinding proteins (cp29, cp31 and cp33) are present in Arabidopsis thaliana: presence of cp31 in chloroplasts and its homologue in nuclei/cytoplasms Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions Role for LSM genes in the regulation of circadian rhythms A member of the Whirly family is a multifunctional RNA-and DNA-binding protein that is essential for chloroplast biogenesis A putative RNA-binding protein positively regulates salicylic acid-mediated immunity in Arabidopsis In planta determination of the mRNA-binding proteome of Arabidopsis etiolated seedlings Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis Arabidopsis RNA-binding protein UBA2a relocalizes into nuclear speckles in response to abscisic acid PEPPER, a novel K-homology domain gene, regulates vegetative and gynoecium development in Arabidopsis Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L Slave to the rhythm Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes The RNA-recognition motif in chloroplasts A circadian clock-regulated toggle switch explains AtGRP7 and AtGRP8 oscillations in Arabidopsis thaliana
    keywords: arabidopsis; atgrp7; binding; chloroplast; cross; et al; mrna; proteins; rbps; rna; splicing; sr45; thaliana; transcripts; vivo
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        item: #228 of 1349
          id: cord-018017-c8myq6bi
      author: Iversen, Patrick L.
       title: The Threat from Viruses
        date: 2018-09-30
       words: 11576
      flesch: 47
     summary: Antisense oligonucleotide-based therapy for HIV-1 infection from laboratory to clinical trials Oligodeoxynucleotide phosphoramidates and phosphorothioates as inhibitors of human immunodeficiency virus A tribute to Sheik Humarr Khan and all the healthcare workers in West Africa who have sacrificed in the fight against Ebola virus disease: mae we hush Inhibition of Norovirus replication by Morpholino oligomers targeting the 5'-end of the genome Marine viruses: truth or dare Cancer virus Oseltamivir-resistant 2009 pandemic influenza A (H1N1) virus infection in two summer campers receiving prophylaxis-North Carolina Approved antiviral drugs of the past 50 years The Eradicatio of smallpox: Edward Jenner and the first and only eradication of a human infectious disease Oseltamivir resistance during treatment of influenza A (H5N1) infection In vitro resistance and in vivo efficacy of antisense oligomer against West Nile virus Outbreak of antiviral drug-resistant influenza A in long-term care facility The perpetual challenge of infectious disease Clonal integration of a polyomavirus in human Merkel cell carcinoma Morpholino oligomers targeting the PB1 and NP genes enhance survival of mice infected with highly pathogenic influenza A H7N7 virus Inhibition of multiple subtypes of influenza a virus in cell cultures with morpholino oligomers Safety and pharmacokinetic profiles of phosphorodiamidate morpholino oligomers with activity against Ebola virus and Marburg virus: results of two single ascending dose studies Cytomegalovirus infection and atherosclerosis in candidate of coronary artery bypass graft Inhibition of dengue virus translation and RNA synthesis by a morpholino oligomer targeted to the terminal 3′ stem-loop structure Pharmacokinetics of an antisense phosphorothioate oligodeoxynucleotide against rev from human immunodeficiency virus type 1 in the adult male rat following single injections and continuous infusion Phase 2a study of the CCR5 monoclonal antibody PRO 140 administered intravenously to HIV-infected adults Anti-HIV-1 activity of weekly or biweekly treatment with subcutaneous PRO 140, a CCR5 monoclonal antibody Oseltamivir for influenza in adults and children: systemic review of clinical study reports and summary of regulatory comments Passive immunity in prevention and treatment of infectious diseases Viral diversity and clonal evolution from unphased genomic data Ecology of viruses in soils: past, present and future perspectives Inhibition of dengue virus serotypes 1 to 4 in cell culture with Morpholino oligomers Inhibition of respiratory Syncitial virus infections in cell cultures and in mice with morpholino oligomers Dissemination, divergence and establishment of H7N9 influenza viruses in China Health impact of globalization: towards global governance Inhibition of influenza A H3N8 virus infections in mice by morpholino oligomers Isolation and characterization of a new Vesivirus from rabbits Phosphorothioate analogs of oligodeoxyribonucleotides: inhibitors of replication and cytopathic effects of human immunodeficiency virus Endogenous retroviruses: with us and against us The value of neuraminidase inhibitors for the prevention and treatment of seasonal influenza: a systematic review of systematic reviews Antisense morpholino oligomers directed against the 5'-end of the genome inhibit coronavirus proliferation and growth Inhibition, escape and attenuation of SARS coronavirus treated with antisense morpholino oligomers Inactivating mutations in an SH2 domain-encoding gene in X-linked lymphoproliferative syndrome Inhibition of alphavirus infection in cell culture and in mice with antisense morpholino oliogmers Immunological disorders and malignancies in five young brothers Spillover animal infections and the next human pandemic Deposition rates of viruses and bacteria above the atmospheric boundary layer A prospective monitoring study of cytomegalovirus infection in nonimmunosuppressed critical heart surgery patients Inhibition of acquired immunodeficiency syndrome virus by oligonucleotide methylphosphonates Lymphocytic Choriomeningitis virus infection in FVB mouse produces hemorrhagic disease Ancient Athenian plague proves to be typhoid Inhibition of Measles virus infection in cell cultures by peptide-conjugated Morpholino oligomers Vesivirus viremia and Seroprevalence in humans Virus specific antiviral therapy for controlling severe and fatal outbreaks of feline Calicivirus infection Chimpanzee adenovirus vaccine generates acute and durable protective immunity against ebolavirus challenge Inhibition of Vesivirus infetions in mammalian tissue culture with antisense morpholino oligomers Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxynucleotide Inhibition of multiple species of picornavirus using a morpholino oligomer targeting highly conserved IRES sequence Increased risk of hepatocellular carcinoma in male hepatiis B surface antigen carriers with chronic hepatitis who have detectable aflatoxin metabolite M1 Viruses in the sea Chemical modifications to phosphorodiamidate Morpholino oligomer antisense molecules targeting VP24 modify their efficacy against Ebola virus infection Use of ChAd3-EBO-Z Ebola virus vaccine in Malian adults with MVA-BN-Filo: a phase I, single-blind, randomized trial, a phase 1b, open label and double blind, doseescallation trial, and a nested, randomized, double-blind, placebo-controlled trial Inhibition of foot-and-mouth disease virus in cell cultures with antisense morpholino oligomers Antiviral activity of morpholino oligomers designed to block various aspects of Equine arteritis virus amplification in cell culture PCR for detection of oseltamivir resistance mutation in influenza A(H7N9) virus IgG antibodies to dengue enhanced for FcγRIIIA binding determine disease severity Gene-specific countermeasures against Ebola virus based on antisense phosphorodiamidate morpholino oligomers Advanced antisense therapies for postexposure protection against lethal filovirus infections Single component AVI-7537 antisense compound provides greater protection than double component AVI-6002 against Lethal Ebola virus infection in Rhesus Monkeys Isolation of an arenavirus closely related to Lassa virus from Mastomys natalensis in south-east Inhibition of coxsackievirus b3 in cell cultures and in mice by Peptide-conjugated morpholino oligomers targeting the internal ribosomal entry site Inhibition of Rous sarcoma virus replication and transformation by a specific oligodeoxynucleotide Characteristic chromosomal abnormalities in biopsies and lymphoid-cell lines from patients with Burkitt and non-Burkitt lymphomas Effect of early and late GB virus C viremia on survival of HIV-infected individuals: a meta-analysis Suppression of porcine reproductive and respiratory syndrome virus replication by morpholino antisense oligomers West Nile virus genome cyclization and RNA replication require two pairs of long-distance RNA interactions The focus has been on viral infections because they rely on host ribosomes to produce their proteins, recent emerging infections have been from single-stranded RNA genome viruses, and replication of RNA viruses is error prone.
    keywords: antisense; antiviral; cell; disease; dna; ebv; et al; genome; hiv; host; human; infected; infections; influenza; inhibition; life; lymphoma; morpholino; oligomers; outbreak; percent; population; rna; studies; table; virus; viruses; years
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        item: #229 of 1349
          id: cord-018164-h5k1zsyg
      author: Taylor, Milton W.
       title: What Is a Virus?
        date: 2014-07-22
       words: 4774
      flesch: 58
     summary: The discovery of the Mimivirus has given rise to the discussion as to whether this is an ancestor of other viruses or is the result of genes breaking away from the host and becoming independent. The ability to undergo self-assembly makes it easy to reconstruct viruses in the test tube, and has been done for polio and other viruses.
    keywords: acid; cell; dna; host; infection; protein; rna; spread; virus; viruses
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        item: #230 of 1349
          id: cord-018437-yjvwa1ot
      author: Mitchell, Michael
       title: Taxonomy
        date: 2013-08-26
       words: 9285
      flesch: 42
     summary: Structure-function relations The DNA sequence of human herpesvirus-6: structure, coding content, and genome evolution Processing of genome 5′ termini as a strategy of negative-strand RNA viruses to avoid RIG-Idependent interferon induction Respiratory syncytial virus and parainfl uenza virus Infl uenza virus, Chap 42 Global and regional distribution of HIV-1 genetic subtypes and recombinants in Parainfl uenza viruses Gene mapping of the putative structural region of the hepatitis C virus genome by in vitro processing analysis Evolutionary history and phylogeography of human viruses What does virus evolution tell us about virus origins? Nucleotide sequence and genome organization of human parvovirus B19 isolated from the serum of a child during aplastic crisis CXCR4 as a functional coreceptor for human immunodeficiency virus type 1 infection of primary macrophages The genome length of human parainfl uenza virus type 2 follows the rule of six, and recombinant viruses recovered from non-poly-hexameric-length antigenomic cDNAs contain a biased distribution of correcting mutations Respiratory syncytial virus nonstructural proteins decrease levels of multiple members of the cellular interferon pathways Infl uenza virus evolution, host adaptation, and pandemic formation Mechanisms and enzymes involved in SARS coronavirus genome expression
    keywords: classifi; dna; envelope; family; genes; genome; host; human; proteins; reading; rna; sequence; species; type; uenza; viral; virions; virus; viruses
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        item: #231 of 1349
          id: cord-018564-3igg5s57
      author: Schomburg, Dietmar
       title: RNA helicase 3.6.4.13
        date: 2013
       words: 12353
      flesch: 50
     summary: [1] ; <10> the enzyme plays an important role in viral replication [4] ; <10> multifunctional enzyme showing protease, helicase, and NTPase activities [4] ; <16> multifunctional enzyme showing protease, helicase, and NTPase activities, the enzyme has a function in RNA replication complex assembly besides its function in RNA synthesis/capping, the enzyme activity is located in the C-terminal nucleoside triphosphatase/helicase domain of the BMV 1a protein RNA replication factor [5] ; <20> substrate specificity, bifunctional enzyme, NS3 is an RNA-stimulated nucleoside triphosphatase NTPase/RNA helicase and a 5-RNA triphosphatase RTPase, overview, the full-length NS3 with or without NS2B cofactor domain exhibits a catalytically more efficient RNA helicase activity than the N-terminally-truncated NS3 helicase domain, suggesting that the protease domain enhances RNA helicase activity [2] ; <12> the multifunctional enzyme shows RNAdependent NTPase and helicase activities, no activity with ADP and AMP [1] ; <19> nonstructural protein 3 (NS3) possesses three enzyme activities that are likely to be essential for virus replication: a serine protease located in the N-terminus and NTPase as well as helicase activities located in the C-terminus [35] ; <11> NS3 includes a protease and a helicase that are essential to virus replication and to RNA capping [29] ; <8> the enzyme is unable to unwind duplex DNA [ Specific activity (U/mg) 0.00000001 <5> (<5> about, wild-type enzyme, RNA helicase activity [43] )
    keywords: activities; activity; atpase; binding; domain; enzyme; helicase; mutant; ns3; protein; replication; rna; rna helicase; type; unwinding; virus
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        item: #232 of 1349
          id: cord-018724-ss8x2g3b
      author: Stobbe, Anthony
       title: Plant Virus Diversity and Evolution
        date: 2016-06-22
       words: 7457
      flesch: 36
     summary: Recombination between genomic RNAs of two cucumoviruses under conditions of minimal selection pressure Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology Seeking agricultures ancient roots Crop pests and pathogens move polewards in a warming world Multihost experimental evolution of a plant RNA virus reveals local adaptation and host-specific mutations Concerning a contagium vivum fluidum as cause of the spot disease of tobacco leaves Integration of multiple repeats of geminiviral DNA into nuclear genome of tobacco during evolution The RNA world hypothesis: the worst hypothesis of early evolution of life (except for all the others) Role of recombination in the evolution of natural populations of Cucumber mosaic virus, a tripartite RNA plant virus High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution Frequent homologous recombination events between molecules of one RNA component in a multipartite RNA virus Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives A real-time RT-PCR assay for quantifying the fitness of tobacco etch virus in competition experiments Rice genomes recorded ancient pararetrovirus activities: virus genealogy and multiple origins of endogenization during rice speciation Suppression of viral RNA recombination by a host exoribonuclease Widespread endogenization of genome sequences of non-retroviral RNA viruses into plant genomes Wild plants and viruses: underinvestigated ecosystems Environmentally dependent host-pathogen and vector-pathogen interactions in the Barley yellow dwarf virus pathosystem An RNA proofreading machine regulates replication fidelity and diversity A map of the diversity of RNA3 recombinants appearing in plants infected with Cucumber mosaic virus and Tomato aspermy virus Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus Tomato yellow leaf curl virus Experimental evolution of plant RNA viruses Molecular ecology and emergence of tropical plant viruses Insect vectors as drivers of plant virus emergence The major role of viruses in cellular evolution: facts and hypotheses Recombination every day: abundant recombination in a virus during a single multi-cellular host infection Founder effect, plant host, and recombination shape the emergence populations of begomoviruses that cause tomato yellow leaf curl disease in the Mediterranean basis Variation and evolution of plant virus populations Time--the emerging dimension of plant virus studies Molecular evolution of plant RNA viruses Mixed infections of Pepino mosaic virus strains modulate the evolutionary dynamics of this emergent virus Plant feeding by insect vectors can affect ife cycle, population genetics and evolution of plant viruses Citrus tristeza virus: evolution of complex and varied genotypic groups Plant virus ecology: ingredients, interactions and environmental influences Virus variation in relation to resistance-breaking in plants Origin and evolution of viruses Consequences of interspecies hybridization and virus infection on the growth and fecundity of three threatened coastal Lepidium (Brassicaceae) species from New Zealand Plant viruses alter insect behavior to enhance their spread Plant virus ecology and epidemiology: historical perspectives, recent progress and future prospects Paleovirology: inferring viral evolution from host genome sequence data Impacts of biodiversity on the emergence and transmission of infectious diseases Virus world as an evolutionary network of viruses and capsidless selfish elements Origins and evolution of viruses of eukaryotes: the ultimate modularity Plant viruses of the Almagaviridae family evolved via recombination between virusese with double-stranded and negative-strand RNA genomes Variation in phytopathogenic viruses Previously unknown and highly divergent viruses populate the oceans Environmental nutrient supply alters prevalence and weakens competitive interactions among coinfecting viruses Effect of host species on the distribution of mutational fitness effects for an RNA virus Comparative molecular epidemiology provides new insights into Zucchini yellow mosaic virus occurrence in France Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome Genetic bottlenecks reduce population variation in an experimental RNA virus population Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes Plasmodesmata: the intercellular organelles of green plants Virus infection in remnant native bunchgrasses from invaded California grasslands A virus responds instantly to the presence of the vector on the host and forms transmission morphs Current impact and future directions of high throughput sequencing in plant virus diagnostics Transmission mechanisms shape pathogen effects on host-vector interactions: evidence from plant viruses Infection of host plants by Cucumber mosaic virus increases the susceptibility of Myzus persicae aphis to the parasitoid Virus infection influences host plant interactions with non-vector herbivores and predators Pathogen population genetics, evolutionary potential, and durable resistance Molecular evolution of Pepino mosaic virus during long-term passaging in different hosts and its impact on virus evolution New insights into the mechanisms of RNA recombination Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies Possible emergence of new geminiviruses by frequent recombination Long-term evolution of the Luteoviridae: time scale and mode of virus speciation Effect of biodiversity changes in disease risk: exploring disease emergence in a plant-virus system Fixation of emerging interviral recombinants in Cucumber mosaic virus populations Mapping viral functional domains for genetic diversity in plants Environment determines fidelity for an RNA virus replicase Mutation and recombination frequencies reveal a biological contrast within strains of Cucumber mosaic virus Community ecology of plant viruses. Recent efforts have expanded our knowledge of the true diversity of plant viruses by studying those viruses that infect wild, undomesticated plants.
    keywords: diversity; et al; evolution; host; mosaic; new; plant; recombination; rna; roossinck; species; variation; vector; viruses; wild
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        item: #233 of 1349
          id: cord-018798-yzxy9ogf
      author: Jain, Pradeep Kumar
       title: RNAi for Resistance Against Biotic Stresses in Crop Plants
        date: 2018-07-10
       words: 12574
      flesch: 34
     summary: An ample number of studies in insect orders of Coleoptera, Diptera, Lepidoptera, Hemiptera, and others comprising of several insect pests have shown that RNAi targeting insect genes can affect growth and development of insects, often leading to insect death (Tables 4.3 and 4.4). If the transcripts of target genes are prevalently expressed in tissues outside the gut cells, the systemic RNAi has to occur for spreading of silencing signal.
    keywords: aphid; control; delivery; development; dsrna; effect; elegans; et al; expression; feeding; gene; host; insect; interference; nematodes; pathway; pest; plants; protein; resistance; rnai; root; silencing; sirnas; species; specific; studies; target; transgenic; uptake
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        item: #234 of 1349
          id: cord-018804-wj35q88f
      author: Lázaro, Ester
       title: Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity
        date: 2007
       words: 8515
      flesch: 43
     summary: Finally, the heterogeneity of RNA virus populations makes it also difficult to eradicate diseases with antiviral drugs, due to the emergence of drug-resistant mutants [10] , a problem that will be treated in more detail in the next sections. Analysis of RNA virus populations, either at the phenotypic or genotypic level showed that these populations have a structure similar to the molecular quasi-species described theoretically
    keywords: error; fitness; genomes; host; mutations; number; population; rate; rna; rna viruses; sequence; viruses
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        item: #235 of 1349
          id: cord-018944-du42ho11
      author: Shin, Jeong Hwan
       title: Nucleic Acid Extraction and Enrichment
        date: 2018-11-10
       words: 6858
      flesch: 38
     summary: Philadelphia: F.A. Davis Molecular cloning: A laboratory manual Comparison of different methods of isolation of DNA of commonly encountered Candida species and its quantitation by using a real-time PCR-based assay Correlates of quantitative measurement of BK polyomavirus (BKV) DNA with clinical course of BKV infection in renal transplant patients A solid-phase extraction procedure for DNA purification Detection of microorganisms in vessel wall specimens of the abdominal aorta: development of a PCR assay in the absence of a gold standard Current nucleic acid extraction methods and their implications to point-of-care diagnostics RNA purification and analysis; Sample preparation, extraction, chromatography The effect of metal ions on the activity and thermostability of the extracellular proteinase from a thermophilic Bacillus, strain EA.1 Comparison of commercial DNA extraction kits for extraction of bacterial genomic DNA from whole-blood samples Evaluation of LightCycler PCR for implementation of laboratory diagnosis of herpes simplex virus infections Diagnosis of herpes simplex virus infections in the clinical laboratory by LightCycler PCR Comparison of the Roche LightCycler vanA/vanB detection assay and culture for detection of vancomycin-resistant enterococci from perianal swabs Automated extraction of viral-pathogen RNA and DNA for high-throughput quantitative real-time PCR Comparison of automated nucleic acid extraction methods with manual extraction Monitoring transplant patients for human cytomegalovirus: diagnostic update Comparison of methods for extraction of viral DNA from cellular specimens Comparison of the NucliSENS easyMAG and Qiagen BioRobot 9604 nucleic acid extraction systems for detection of RNA and DNA respiratory viruses in nasopharyngeal aspirate samples Evaluation of NucliSENS easyMAG for automated nucleic acid extraction from various clinical specimens Comparison of two highly automated DNA extraction systems for quantifying Epstein-Barr virus in whole blood Severe acute respiratory syndrome (SARS) Laboratory diagnosis of SARS Multicenter comparison of nucleic acid extraction methods for detection of severe acute respiratory syndrome coronavirus RNA in stool specimens Improved amplification of microbial DNA from blood cultures by removal of the PCR inhibitor sodium polyanetholesulfonate A simple and sensitive method to extract bacterial, yeast and fungal DNA from blood culture material Hydrogen peroxide improves the efficiency of a peripheral blood PCR assay for diagnosis of human brucellosis Serum is the preferred clinical specimen for diagnosis of human brucellosis by PCR Comparison of seven commercial DNA extraction kits for the recovery of Brucella DNA from spiked human serum samples using real-time PCR Real-time PCR of the 16S-rRNA gene in the diagnosis of neonatal bacteraemia Molecular detection and identification of Candida and Aspergillus spp. The method for the nucleic acid extraction can be divided into manual or automated, and this is an important point in the classification of nucleic acid extraction methods.
    keywords: acid; blood; detection; dna; extraction; kits; method; nucleic; pcr; rna; specimens; time
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        item: #236 of 1349
          id: cord-019051-gtruu1op
      author: Weber, Olaf
       title: The role of viruses in the etiology and pathogenesis of common cold
        date: 2009-11-10
       words: 12336
      flesch: 41
     summary: Indeed, approximately 80% of asthma exacerbations in children [26] and about 70% in adults [27] are associated with respiratory virus infections, and the vast majority of these are RV infections [28] . The epidemiology of acute respiratory tract infection in young children Risk of respiratory syncytial virus infection for infants from low-income families in relationship to age, sex, ethnic group and maternal antibody level Respiratory syncytial virus Differential production of inflammatory cytokines in primary infection with human metapneumovirus and with other common respiratory viruses of infancy Effectiveness of drug therapies to treat or prevent respiratory syncytial virus infection-related morbidity Genetic susceptibility to RSV disease Bronchoalveolar lavage cytokine profiles in acute asthma and acute bronchiolitis Human infant respiratory syncytial virus (RSV)-specific type 1 and 2 cytokine responses ex vivo during primary RSV infection Type 1 and type 2 cytokine imbalance in acute respiratory syncytial virus bronchiolitis Priming immunization determines T helper cytokine mRNA expression patterns in lungs of mice challenged with respiratory syncytial virus Respiratory syncytial virus deficient in soluble G protein induced an increased proinflammatory response in human lung epithelial cells The cysteinerich region of respiratory syncytial virus attachment protein inhibits innate immunity elicited by the virus and endotoxin Pattern recognition receptors TLR4 and CD14 mediate response to respiratory syncytial virus Severe respiratory syncytial virus disease in Alaska native children Palivizumab in the prophylaxis of respiratory syncytial virus infection Respiratory syncytial virus disease mechanisms implicated by human, animal model, and In vitro data facilitate vaccine strategies and new therapeutics Experimental respiratory syncytial virus infection of four species of primates Respiratory syncytial virus infects the bonnet monkey, Macaca radiata The pathogenesis of respiratory syncytial virus infection in cotton rats Enhancement of respiratory syncytial virus pulmonary pathology in cotton rats by prior intramuscular inoculation of formalin-inactivated virus Mechanism of antibody-mediated viral clearance in immunotherapy of respiratory syncytial virus infection of cotton rats Primary respiratory syncytial virus infection in mice Respiratory syncytial virus infection in mice Intracellular IFN-gamma expression in natural killer cells precedes lung CD8 + T cell recruitment during respiratory syncytial virus infection Immune-mediated disease pathogenesis in respiratory syncytial virus infection Chinchilla and murine models of upper respiratory tract infections with respiratory syncytial virus Evaluation of severe disease induced by aerosol inoculation of calves with bovine respiratory syncytial virus Complete sequence of the RNA genome of pneumonia virus of mice (PVM) Parainfluenza viruses Parainfluenza viruses Myxoviruses: Parainfluenza International Committee on Taxonomy of Viruses The role of viral glycoproteins in adsorption, penetration, and pathogenicity of viruses New frontiers opened by the exploration of host cell receptors Acquisition of serum antibodies to specific glycoproteins of parainfluenza virus 3 in children ) secretory immunological response in infants and children to parainfluenza virus types 1 and 2 Brief report: Parainfluenza virus type 3 infections:
    keywords: adenovirus; cause; cell; children; cold; coronavirus; disease; human; infection; influenza; pathogenesis; protein; response; rna; role; rsv; symptoms; tract; virus; viruses
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        item: #237 of 1349
          id: cord-019076-4qu9j953
      author: Ulferts, Rachel
       title: Expression and Functions of SARS Coronavirus Replicative Proteins
        date: 2009-07-22
       words: 10055
      flesch: 40
     summary: Xu et al. 2009 ). The molecular mechanisms of the dephosphorylation reaction have not been elucidated but are thought to differ from other phosphatases as there is no sequence and/or structural similarity between the respective enzymes (Allen et al. 2003; Egloff et al. 2006) .
    keywords: activity; binding; conserved; coronavirus; cov; domain; et al; genome; mhv; processing; protein; replicase; replication; residues; rna; sars; structure; syndrome; synthesis; terminal
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        item: #238 of 1349
          id: cord-020010-q58x6xb0
      author: None
       title: 19th ICAR Abstracts:
        date: 2006-03-13
       words: 46881
      flesch: 40
     summary: Although anti-inflammatory agents are not very active in vitro, it is thought that they might be efficacious in reducing any deleterious inflammatory response associated with virus infections such as SARS infections in humans. Although only BTCRB and BDCRB were inhibitors of the ATPase activity, two other compounds, dBDCRB and Cl4RB, inhibited virus replication in a plaque-reduction assay, thus indicating that those have a different mode of action.
    keywords: acid; action; activity; agents; animals; antiviral; assay; cdv; cells; combination; compounds; concentrations; containing; control; culture; days; department; derivatives; development; disease; dna; dose; drug; effect; efficacy; gene; hcv; hiv; human; infection; influenza; influenza virus; inhibited; inhibition; inhibitors; institute; mice; model; molecular; mutations; new; novel; nucleoside; polymerase; potent; potential; presence; present; properties; protein; reduction; replication; research; resistance; results; rna; specific; strain; structure; studies; study; synthesis; system; target; tested; therapeutic; therapy; treatment; type; university; usa; virus; virus infection; virus replication; viruses; vitro; vivo
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        item: #239 of 1349
          id: cord-020235-stcrozdw
      author: None
       title: Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981
        date: 2012-03-15
       words: 13511
      flesch: 54
     summary: 2. the number of virus producing cells is not cor related with the appe arance of slgM or sIgG. 3. virus yields seem to be influenced by the cell cycle: the number of chick emb ryo fibro blasts producing plaques in infectious center assays is increased after synchro nisa tion of the cells before infection. Recent studies on protein kinases from a number of tumor viruses have raised the possibility that the phosphorylation of cell proteins is involved in the processes leading to cell transformation.
    keywords: acid; activity; analysis; antibodies; antigen; cells; cultures; disease; dna; fragments; genome; glycoproteins; hsv; human; infection; influenza; inst; mice; particles; positive; protein; restriction; results; rna; sera; sites; specific; strains; test; type; univ; virus; viruses
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        item: #240 of 1349
          id: cord-020969-lh2ergpm
      author: STRAUSS, JAMES H.
       title: Gene Therapy
        date: 2012-07-27
       words: 11796
      flesch: 49
     summary: Recombination has been used to insert foreign genes and to delete virus genes involved in lytic growth or toxicity. In principle, any virus can be used as a vector, and systems that use a very wide spectrum of virus vectors have been described.
    keywords: approach; cells; dna; expression; gene; gene therapy; genome; interest; protein; results; rna; therapy; trials; vaccinia; vectors; virus; virus vectors; viruses
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        item: #241 of 1349
          id: cord-021115-2fkghukw
      author: Guo, Yun
       title: Molecular dynamics simulation of RNA pseudoknot unfolding pathway
        date: 2013-03-12
       words: 3272
      flesch: 54
     summary: The statistical mechanics of RNA folding Predicting secondary structural folding kinetics for nucleic RNA folding: Models and perspectives Exposing the kinetic traps in RNA folding Predicting loop-helix tertiary structural contacts in RNA pseudoknots Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity Predicting structures and stabilities for H-type pseudoknots with interhelix loops Atomistic analysis of pseudoknotted RNA unfolding RNA and protein folding: common themes and variations Structure and assembly of group I introns Characterization of the structure and dynamics of the HDV ribozyme in different stages along the reaction path RNA folding, conformational statistics, folding kinetics, and ion electrostatics How RNA folds RNA folding energy landscapes A molecular switch underlies a human telomerase disease Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an RNA pseudoknot Viral RNA pseudoknots: Versatile motifs in gene expression and replication Ribosomal pausing during translation of an RNA pseudoknot Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting The 9-A solution: How mRNA pseudoknots promote efficient programmed-1 ribosomal frameshifting RNA structures with diverse functions A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting Predicting ribosomal frameshifting efficiency The stimulatory RNA of the Visna-Maedi retrovirus ribosomal frameshifting signal is an unusual pseudoknot with an interstem element A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated −1 ribosomal frameshifting Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of −1 ribosomal frameshifting A mutant RNA pseudoknot that promotes ribosomal frameshifting in mouse mammary tumor virus RNA pseudoknots: folding and finding Conformation of a Nonframeshifting RNA pseudoknot from mouse mammary tumor virus Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin NAMD2: greater scalability for parallel molecular dynamics Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach Comparison in structural stability between chain A and B of CLC-ec1 exchanger by using MD simulation CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes DNA polymorphism: A comparison of force fields for nucleic acids RNA stability under different combinations of amber force fields and solvation models Salt contribution to RNA tertiary structure folding stability Predicting ion binding properties for RNA tertiary structures RNA helix stability in mixed Na + /Mg 2+ solution A dynamic programming algorithm for RNA structure prediction including pseudoknots Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information Computer prediction of RNA structure: Methods in enzymology Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure Thermodynamics of stabilization of RNA pseudoknots by cobalt(III) hexaammine The structural features of MMTV RNA pseudoknot in different ion concentration, the unfolding process of RNA pseudoknot, and two hairpin helices that constituted the RNA pseudoknot were studied with all atom molecular dynamics simulation method in this paper.
    keywords: base; helix; process; pseudoknot; rna; unfolding
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        item: #242 of 1349
          id: cord-021481-tvs1pnib
      author: Singh, Gatikrushna
       title: Cellular RNA Helicases Support Early and Late Events in Retroviral Replication
        date: 2018-08-17
       words: 6057
      flesch: 33
     summary: Current understanding of RNA helicase activities in retroviruses has been propelled by results of genome-wide screens. A key to interpreting RNA helicase activity in reverse transcription of retroviral RNA has been the determination of stoichiometry in virions and cognate viral RNA structure, as determined for DHX9 Boeras et al., 2016) .
    keywords: activity; binding; dhx9; et al; export; helicase; hiv; protein; replication; rev; rna; rnp; transcription; translation; virus
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        item: #243 of 1349
          id: cord-021568-tdfn6up8
      author: STRAUSS, JAMES H.
       title: Subviral Agents
        date: 2012-07-27
       words: 10945
      flesch: 56
     summary: DIs of many RNA viruses have been the best studied. Some satellites of RNA plant viruses encode only a nonstructural protein required for RNA replication, and the RNA is encapsidated by the capsid protein of the helper virus.
    keywords: cases; cjd; disease; fig; hdv; infected; infection; prion; protein; prp; prp sc; replication; rna; rnas; virus
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        item: #244 of 1349
          id: cord-022084-hap7flng
      author: ARRUDA, EURICO
       title: Respiratory Tract Viral Infections
        date: 2009-05-15
       words: 19198
      flesch: 38
     summary: Although a HMPV vaccine is not available at this time, the demonstration that hamsters, ferrets, and African green monkeys are susceptible to infection by HMPV, and that hamsters vaccinated with serotype A The epidemiology of acute respiratory tract infection in young children: Comparison of findings from several developing countries Report of a workshop on respiratory viral infections: Epidemiology, diagnosis, treatment and prevention Acute respiratory viral infections in ambulatory children of urban northeast Brazil Longitudinal studies of infectious diseases and physical growth of infants in Huascar, an underprivileged peri-urban community in At the edge of Development: Health Crises in a Transitional Society Epidemiology of acute respiratory infections in children of developing countries Pan American Health Organization: Acute respiratory infections in the Americas The magnitude of mortality from acute respiratory infections in children under 5 years in developing countries Acute lower respiratory tract infections in hospitalized patients with diarrhea in Dhaka Day-care center attendance and hospitalization for lower respiratory tract illness Viral respiratory infections in young children attending day care in urban Northeast Brazil Epidemiology and seasonality of respiratory tract virus infections in the tropics The cultural context of breastfeeding: Perspectives on the recent decline in breast-feeding in Northeast and Northcentral Brazil Reduced mortality among children in Southern India receiving a small weekly dose of vitamin A Search for a solution: Blending oral rehydration therapy (ORT) and popular medicine Pathogenesis of respiratory infections due to influenza virus: Implications for developing countries Respiratory viruses predisposing to bacterial infections: Role of neuraminidase Influenza: Emergence and control Orthomyxoviridae: The viruses and their replication Influenza virus Viral vaccines for the prevention of childhood pneumonia in developing nations: Priorities and prospects The effect of influenza on hospitalizations, outpatient visits, and courses of antibiotics in children Etiology of acute respiratory infections in children in tropical southern India A community-based study of acute respiratory tract infection in Thai children Etiology of acute lower respiratory tract infection in children from Alabang, Metro Manilla Outbreak of influenza type A (H1N1) in Iporanga Antigenic and genomic relation between human influenza viruses that circulated in Argentina in the period 1995-1999 and the corresponding vaccine components Regional perspectives on influenza surveillance in Africa H5N1 influenza: A protean pandemic threat Influenza type A and B infections in hospitalized pediatric patients Influenza viruses, cell enzymes, and pathogenicity Detection of influenza virus by centrifugal inoculation of MDCK cells and staining with monoclonal antibodies Rapid detection and simultaneous subtype differentiation of influenza A viruses by real time PCR Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 Rational design of potent sialidase-based inhibitors of influenza virus replication Efficacy and safety of the neuraminidase inhibitor zanamivir in the treatment of influenzavirus infections Resistant influenza 31 Up to 50% of influenza virus infections in adults are subclinical.
    keywords: acute; adults; age; cause; cell; children; clinical; cov; days; detection; disease; hcov; hmpv; hrv; human; illness; infants; infections; influenza; patients; pcr; rna; rsv; sars; studies; tract; tropical; vaccine; virus; viruses; years
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        item: #245 of 1349
          id: cord-022128-r8el8nqm
      author: Domingo, Esteban
       title: Molecular basis of genetic variation of viruses: error-prone replication
        date: 2019-11-08
       words: 17674
      flesch: 30
     summary: Mechanisms and Consequences Structure-function relationships underlying the replication fidelity of viral RNAdependent RNA polymerases Phage as agents of lateral gene transfer Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective Mutations and A/I hypermutations in measles virus persistent infections Evolution of sex in RNA viruses Viral RNAdirected RNA polymerases use diverse mechanisms to promote recombination between RNA molecules Insertion/deletion frequencies match those of point mutations in the hypervariable regions of the simian immunodeficiency virus surface envelope gene Arbovirus high fidelity variant loses fitness in mosquitoes and mice Genetic variation in retroviruses Variation in RNA virus mutation rates across host cells Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection The vaccinia virus DNA polymerase and its processivity factor Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations Improvement of phi29 DNA polymerase amplification performance by fusion of DNA binding motifs Linking RNA sequence, structure, and function on massively parallel highthroughput sequences Defective interfering influenza virus RNAs: time to reevaluate their clinical potential as broad-spectrum antivirals? Virus entry into error catastrophe as a new antiviral strategy Viral Quasispecies Nucleotide sequence heterogeneity of an RNA phage population Genetic variability and antigenic diversity of foot-and-mouth disease virus Quasispecies: the concept and the word Quasispecies and RNA Virus Evolution: Principles and Consequences Evolution of footand-mouth disease virus Viral quasispecies: dynamics, interactions and pathogenesis A constant rate of spontaneous mutation in DNA-based microbes Mutation rates among RNA viruses Detenction of truncated virus particles in a persistent RNA virus infection in vivo Evolvability is a selectable trait High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing Error catastrophe and antiviral strategy Sequence space and quasispecies distribution Adaptive value of high mutation rates of RNA viruses: separating causes from consequences Multiple molecular pathways for fitness recovery of an RNA virus debilitated by operation of Muller's ratchet RT-PCR amplification and cloning of large viral sequences Adaptation of mRNA structure to control protein folding A comparison of viral RNA-dependent RNA polymerases Structural insights into replication initiation and elongation processes by the FMDV RNA-dependent RNA polymerase Random mutagenesis using error-prone DNA polymerases Specialized DNA polymerases, cellular survival, and the genesis of mutations DNA Repair and Mutagenesis Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection Extremely high mutation rate of a hammerhead viroid RNA recombination in vivo in the absence of viral replication Comparative analysis of the molecular mechanisms of recombination in hepatitis C virus DNA replication-a matter of fidelity Evolutionary transition toward defective RNAs that are infectious by complementation Information dynamics in carcinogenesis and tumor growth Evolution of circulating wild poliovirus and of vaccine-derived poliovirus in an immunodeficient patient: a unifying model In-depth, longitudinal analysis of viral quasispecies from an individual triply infected with late-stage human immunodeficiency virus type 1, using a multiple PCR primer approach Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution Molecular Basis of Virus Evolution Functional and genetic plasticities of the poliovirus genome: quasi-infectious RNAs modified in the 5'-untranslated region yield a variety of pseudorevertants Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces? Mutation frequencies measured by subjecting virus to a specific selective agent (e.g., mutants that escape the neutralizing activity of a monoclonal antibody or mutants that escape inhibition by a drug) span a broad range of values (10 À 3 to 10 À 8 ) for DNA and RNA viruses (Smith and Inglis, 1987; Sarisky et al., 2000; Domingo et al., 2001) (Table 2 .1).
    keywords: acid; amino; cells; chapter; dna; error; et al; evolution; fidelity; forms; frequency; genome; mechanisms; mutant; mutation; mutation rates; nucleotide; polymerase; rates; reassortment; recombination; repair; replication; rna; rna viruses; selection; sequence; site; template; type; variation; viral; virus; viruses
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        item: #246 of 1349
          id: cord-022196-1tionxun
      author: FENNER, FRANK
       title: The Nature and Classification of Animal Viruses
        date: 2013-11-17
       words: 9589
      flesch: 42
     summary: In viruses whose genome consists of single-stranded nucleic acid, the viral nucleic acid is either the positive strand (in RNA viruses, equivalent to messenger RNA) or the negative (complementary) strand. The diameters of the nucleocapsids of several viruses have been measured, but in only a few cases is the length or the pitch of the helix known.
    keywords: acid; animal; capsomers; classification; dna; envelope; genome; genus; protein; rna; type; units; virion; viruses
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        item: #247 of 1349
          id: cord-022262-ck2lhojz
      author: Gromeier, Matthias
       title: Genetics, Pathogenesis and Evolution of Picornaviruses
        date: 2007-09-02
       words: 28053
      flesch: 39
     summary: With this experiment, reverse genetics of RNA viruses was born as the RNA genome was now amenable to manipulations developed for DNA. As is discussed in Chapter 7, this phenomenon has profound biological consequences for RNA viruses.
    keywords: capsid; cell; cleavage; conserved; disease; et al; evolution; expression; figure; gene; genome; host; human; ires; new; picornaviruses; poliovirus; poliovirus rna; polyprotein; proteins; pr~; receptor; recombination; region; replication; rna; rna viruses; sequence; strand; structure; synthesis; translation; type; viruses; vpg; wimmer et
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        item: #248 of 1349
          id: cord-022290-p0l1kv6n
      author: Bergmann, Ernst M.
       title: Proteolytic Enzymes of the Viruses of the Family Picornaviridae
        date: 2007-05-09
       words: 9466
      flesch: 48
     summary: The crystal structures of 3C proteinases have allowed one to deduce a structural model for an intramolecular cleavage of 3C at its own amino-terminus (Matthews et al., 1994; Bergmann et al., 1997) . Refined crystal structures of 3C proteinases have now been published for the enzymes from hepatitis A virus (HAV), poliovirus (PV), and human rhinovirus (HRV) (Matthews et al., 1994; Bergmann et al., 1997; Mosimann et al., 1997) .
    keywords: binding; chymotrypsin; cleavage; et al; hav; poliovirus; polyprotein; proteinases; residues; rna; site; virus; viruses
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        item: #249 of 1349
          id: cord-022336-zqnczjpp
      author: Robertson, Hugh D.
       title: Virus Origins: Conjoined RNA Genomes as Precursors to DNA Genomes
        date: 2007-09-02
       words: 6166
      flesch: 38
     summary: While other cases in which RNA viruses acquire altered RNAs from each other or even from host sources by RNA recombination have been cited above, the delta agent is the only known case where a coding sequence thought to be cellular in origin has entered a functional association with a replicating virus-like element at the level of RNA only, with no DNA involvement, so that the translation-level expression of the protein has survived and the replicating ele, ment remains functional. A replication cycle for viroids and other small infectious RNAs Longer-than-unit-length viroid minus strands are present in RNA from infected plants An ultraviolet-sensitive RNA structural element in a viroid-like domain of the hepatitis delta virus The brotherhood of circular RNA pathogens: viroids, circular satellites, and the delta agent A cellular homolog of hepatitis delta antigen: implications for viral replication and evolution Changes in locations of crossover sites over time in de novo generated RNA recombinants In vivo restoration of biologically active 3' ends of virus-associated RNAs by nonhomologous RNA recombination and replacement of a terminal motif Involvement of a stem-loop structure in the location of junction sites in viral RNA recombination RNA enzymes Structure and replication of the genome of the hepatitis delta virus Nonhomologous RNA recombination in a cell-free system: evidence for a transesterification mechanism guided by secondary structure Recent advances in pestivirus research Split genes and RNA splicing A model for the involvement of viroids in RNA splicing Viroids and Viroid Diseases Are viroids escaped introns? Circular RNAs: relics of precellular evolution? Genetic recombination of poliovirus in a cell-free system A mutation in the putative RNA polymerase gene inhibits nonhomologous, but not homologous, genetic recombination in an RNA virus Genetic exchange by recombination or reassortment is infrequent in natural populations of a tripartite RNA plant virus A recombinational event in the history of luteoviruses probably induced by base-pairing between the genomes of two distinct viruses The RNA world The exon theory of genes Evidence for intron capture: an unusual path for the evolution of proteins Recombination between viral RNA and transgenic plant transcripts Nucleotide sequence and secondary structure of potato spindle tuber viroid Heterogeneity and evolution rates of delta virus RNA sequences Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the hemagglutinin gene of an influenza virus The mechanism of RNA recombination in poliovirus The hepatitis delta virus possesses a circular RNA Substitution rates in hepatitis delta virus RNA recombination in animal and plant viruses Genetic recombination in RNA viruses
    keywords: delta; dna; protein; recombination; replication; rna; rnas; template; viroid; virus
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        item: #250 of 1349
          id: cord-022348-w7z97wir
      author: Sola, Monica
       title: Drift and Conservatism in RNA Virus Evolution: Are They Adapting or Merely Changing?
        date: 2007-09-02
       words: 10898
      flesch: 50
     summary: Muller's ratchet decreases fitness of a DNA-based microbe Increased immune response elicited by DNA vaccination with a synthetic gp120 sequence with optimized codon usage The phylogeny of The Canterbury Tales Isolation of new ribozymes from a large pool of random sequences Forced evolution of a regulatory RNA helix in the HIV-1 genome Role of the first and third extracellular domains of CXCR-4 in human immunodeficiency virus coreceptor activity Molecular Mechanisms of Immune Responses in Insects Nucleotide composition as a driving force in the evolution of retroviruses Unusually high frequency of Epstein-Barr virus genetic variants in Papua New Guinea that can escape cytotoxic T-cell recognition: implications for virus evolution Role of host immune response in selection of equine infectous anemia virus variants Fitness of RNA virus decreased by Muller's ratchet Evolution of sex and the molecular clock in RNA viruses HIV and T-cell expansion in splenic white pulps is accompanied by infiltration of HIV-specific cytotoxic T-lymphocytes Antigenic stimulation by BCG as an in vivo driving force for SIV replication and dissemination Genetic bottlenecks and population passages cause profound fitness differences in RNA viruses Nucleotide sequences of three Nodavirus RNA2's: the messengers for their coat protein precursors Primary and secondary structure of black beetle virus RNA2, the genomic messenger for BBV coat protein precursor HLA-A11 epitope loss isolates of Epstein-Barr virus from a highly Al1+ population T cell responses and virus evolution: loss of HLA All-restricted CTL epitopes in Epstein-Barr virus isolates from highly All-positive populations by selective mutation of anchor residues RNA virus quasispecies populations can suppress vastly superior mutant progeny The genome sequence of herpes simplex virus type 2 RNA viral mutations and fitness for survival Basic concepts in RNA virus evolution Origins and evolutionary relationships of retroviruses Rates of spontaneous mutations among RNA viruses Rapid fitness losses in mammalian RNA virus clones due to Muller's ratchet High viral load and CD4 lymphopenia in rhesus and cynomolgus macaques infected by a chimeric primate lentivirus constructed using the env, rev, tat, and vpu genes from HIV-1 Lai The viral quasispecies Sequence space and quasispecies distribution Structurally complex and highly active RNA ligases derived from random RNA sequences Does the VP1 gene of foot-and-mouth disease virus behave as a molecular clock? key: cord-022348-w7z97wir authors: Sola, Monica; Wain-Hobson, Simon title: Drift and Conservatism in RNA Virus Evolution: Are They Adapting or Merely Changing? date: 2007-09-02 journal: Origin and Evolution of Viruses DOI: 10.1016/b978-012220360-2/50007-6 sha: doc_id: 22348 cord_uid: w7z97wir This chapter argues that the vast majority of genetic changes or mutations fixed by RNA viruses are essentially neutral or nearly neutral in character.
    keywords: acid; amino; et al; evolution; example; figure; fitness; genomes; hiv; human; immunodeficiency; mutations; number; proteins; rna; selection; sequence; substitutions; variation; virus; viruses; vivo
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        item: #251 of 1349
          id: cord-022888-dnsdg04n
      author: None
       title: Poster Sessions
        date: 2009-08-19
       words: 189173
      flesch: 41
     summary: Our aim is to describe how B cell lymphoma cells respond to TGF-b compared to normal peripheral B cells, to create an overview of the different signaling pathways involved, and to characterize the mechanisms behind the loss of sensitivity to TGF-b. Methods: Proliferation assays were performed on 11 different B-cell lymphoma cell lines and normal peripheral B cells to screen for TGF-b-induced effects. Using a CD3 and CD28 activation model system -TLR4 presence on CD4+ cells is found in mouse T cells, human T cells and Jurkat cell lines.
    keywords: + cells; ability; absence; activity; addition; analysis; antibodies; antibody; antigen; apoptosis; apoptotic; assay; associated; autoimmune; b cells; b t; binding; blood; bone; c mice; cancer cells; capacity; cd4; cd8 +; cd8 cells; cd8 t; cell activation; cell activity; cell culture; cell cycle; cell death; cell development; cell differentiation; cell epitopes; cell function; cell level; cell lines; cell membrane; cell population; cell proliferation; cell receptor; cell responses; cell subsets; cell surface; cell tolerance; cell types; cells cells; changes; chronic; class; clinical; colitis; complex; conclusion; contrast; control; control cells; cross; ctl; cytokine; cytokine production; cytometry; cytotoxic t; data; day; days; dcs; deficient; delta t; dendritic; disease; dna; early; effector cells; effector t; effects; elisa; expansion; experiments; expression; expression levels; factor; family; findings; flow; following; formation; function; gamma; gd cells; gd t; gene; gene expression; group; high; hiv; hla; host; human; ifn; ifng; igg; il-10; il-2; il-4; il-6; immune; immunity; increase; independent; induction; infected; infection; inflammation; inflammatory; inhibition; inkt; interaction; intracellular; levels; lps; macrophages; major; marrow cells; mast cells; mechanisms; membrane; memory t; methods; mhc; mice; model; molecules; monocytes; mouse; mouse t; mrna; murine; negative; neutrophils; new; nkt cells; non; normal; novel; number; objectives; pathway; patients; pcr; peptide; peripheral; plasma cells; play; positive; potential; presence; presentation; primary; production; promoter; protein; protein expression; receptors; regulation; regulatory; release; results; role; secretion; serum; signaling; skin; sle; specific; spleen; stem cells; stimulation; studies; study; surface expression; system; t cells; t em; t h; t helper; t lymphocytes; target cells; tcr; test; th1 cells; time; tissue; tlr; tnf; tolerance; transcription; treatment; tumor cells; type; university; vaccination; vaccine; vg9vd2 t; virus; vitro; vivo; work
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        item: #252 of 1349
          id: cord-022889-lv6fy6e6
      author: Dávalos, Alberto
       title: Literature review of baseline information on non‐coding RNA (ncRNA) to support the risk assessment of ncRNA‐based genetically modified plants for food and feed
        date: 2019-08-07
       words: 96106
      flesch: 44
     summary: In a later observational study, Lukasik et al. evaluated plant miRNAs miR-166a, miR-156a, miR-157a, miR-172a and miR-168a and reported the presence of plant miRNAs in human (n=6) breast milk, both in whole milk and exosomes . This HEN1-dependent 2'-Omethylation on the 3' terminal ribose is a Mg2+ dependent methylation mechanism that will ultimately stabilize miRNAs (Abe et al., 2010; Molnar et al., 2007; Yu et al., 2005; Yang et al., 2006) .The
    keywords: activity; administration; animals; authors; barriers; biological; blood; bodies; breast; cells; cellular; conclusions; conditions; context; contract; degradation; delivery; dietary; document; dsrna; effects; efsa; et al; european food; exogenous; exosomes; expression; food safety; function; gene; human; immune; information; issues; juliano et; key; levels; literature; mammalian; mice; milk; molecules; mouse; mrna; naked; ncrnas; non; oligonucleotides; oral; output; pathway; plant mirnas; plant ncrna; plant rna; plants; plasma; position; prejudice; presence; present; principle; procedure; proteins; publication; review; rice; rights; rnai; role; safety authority; samples; search; section; serum; silencing; sirna; small; specific; srnas; stability; studies; study; subject; synthetic; system; target; task; tender; tender procedure; tissue; total; transparency; transparency principle; uptake; view; vivo; words; zhang et
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        item: #253 of 1349
          id: cord-022940-atbjwpo5
      author: None
       title: Poster Sessions
        date: 2016-09-07
       words: 241687
      flesch: 44
     summary: Among used cancer cell lines, ERICD was highly expressed and ARID3A had lower expression in U-2OS (osteosarcoma), A-172 (glioblastoma) and A549 (lung cancer). Clear cell renal cell cancer (ccRCC) with metastases has pour prognosis: 5-year survival is about 9%.
    keywords: a549 cells; acid; activation; activities; activity; activity levels; acute; addition; administration; affinity; agents; aim; albumin; allele; alterations; alternative; amino; analysis; analysis results; animals; ankara; anti; antibodies; antibody; anticancer; antioxidant; apoptosis; applications; approach; assay; association; bacteria; beta; binding; biology; blood; body; bone; brain; breast cancer; cancer cells; cancer group; cancer patients; cancer stem; cancer treatment; cancers; cause; cell cycle; cell death; cell growth; cell lines; cell proliferation; cell survival; cell viability; changes; characterization; chemical; cholesterol; chronic; clinical; coli; colorectal; combination; comparison; complex; complexes; compounds; concentrations; conclusion; conditions; content; control cells; control group; control study; controls; correlation; culture; curcumin; current; cytotoxic; damage; data; day; days; decrease; department; detection; determination; development; diabetes; differences; differentiation; discussion; disease; dna; domain; dose; drug; effects; elevated; elisa; energy; enzyme; enzyme activity; ethanol; experimental; expression analysis; expression levels; expressions; extract; factor; faculty; family; fat; findings; flow; fluorescence; fold; food; formation; free; function; gene expression; genes; genetic; genome; genotype; glucose; glutathione; group; growth; gsh; health; hours; human; immune; increase; inflammation; inflammatory; inhibition; inhibitors; injury; institute; insulin; interaction; intracellular; introduction; invasion; investigation; ischemia; kinase; laboratory; lead; levels; light; like; lipid; liver; low; lung; male; manner; markers; mass; materials; matrix; mcf-7; mda; mda levels; mean; mechanisms; medical; medicine; medium; membrane; metabolism; methods; methylation; mice; microscopy; migration; mirnas; mitochondrial; model; modified; molecular; molecules; mrna; muscle; mutant; mutations; n =; nanoparticles; negative; non; normal; novel; number; obese; obesity; oil; order; oxidative; oxygen; p =; p-02.08.5; parameters; pathway; patients; pcr; peptide; phase; plant; plasma; play; point; polymorphisms; population; potential; presence; present; process; processes; production; products; profile; progression; promoter; properties; prostate; prostate cancer; protective; protein; protein expression; protein levels; purpose; radical; range; rate; rats; reaction; receptor; recombinant; region; regulation; related; relationship; research; resistance; response; results; risk; role; samples; science; scientific; screening; sequence; serum; serum levels; signaling; site; size; sod; species; specific; stability; stage; status; stem cells; strain; stress; structure; studies; study; study group; subjects; surface; survival; synthesis; system; target; technique; temperature; test; tested; therapeutic; therapy; time; tissue; tnf; total; transcription; treatment; treatment group; tumor; tumor cells; turkey; type; university; use; values; vitamin; vitro; water; weight; western; wild; women; work; years
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        item: #254 of 1349
          id: cord-023017-k6edtg58
      author: None
       title: AASLD Abstracts (pp. 282A–382A)
        date: 2006-02-10
       words: 65964
      flesch: 47
     summary: The aim of the present study was to investigate if the same inhibition takes place in livers cells of patients with chronic hepatitis C. From February 2001 to April 2002, all patients with chronic hepatitis C referred to the outpatient liver clinic of the University Hospital Basel were asked for their permission to use part of the liver biopsy for this study. Increased T cell activation with Eta may also suggest that TNFA suppress T cell function and may contribute to refractoriness to INF therapy in HCV patients.
    keywords: -no; activation; activity; addition; age; alpha; alt; analysis; anti; biopsies; biopsy; blood; cases; cd8; cells; chronic; chronic hcv; chronic hepatitis; cirrhosis; combination; conclusions; control; core; culture; data; days; dcs; different; disease; dose; effect; expression; factors; fibrosis; gene; genotype; group; hcc; hcv; hcv genotype; hcv infection; hcv patients; hcv rna; hepatic; hepatitis; hepatocytes; hsc; human; ifn; infection; interferon; levels; liver; mean; meld; methods; mice; months; negative; non; ns3; patients; pcr; population; positive; protein; rats; rejection; relationships; response; results; ribavirin; risk; role; serum; specific; steatosis; stem; studies; study; subjects; survival; system; t cells; therapy; time; total; transplantation; treated; treatment; virus; weeks; years
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        item: #255 of 1349
          id: cord-023120-jcgf2401
      author: None
       title: Animal virus genetics
        date: 2004-06-18
       words: 17827
      flesch: 65
     summary: i f f e r e n t endogenous r e t r o e t e c t the virus during purification.
    keywords: c e; c r; c t; cells; dna; e l; e n; e s; h e; l l; l s; l y; n c; n s; n t; o l; o n; p t; r e; r l; r n; r u; rna; s c; s t; t e; t h; t l; t o; t r; t t; t u; u s; virus
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        item: #256 of 1349
          id: cord-023208-w99gc5nx
      author: None
       title: Poster Presentation Abstracts
        date: 2006-09-01
       words: 71178
      flesch: 41
     summary: Peptide structures can be approached by spectroscopy and NMR techniques but data from these approaches too frequently diverge. To increase the stability and the therapeutic efficacy of peptide sequences from myelin oligodendrocyte protein (MOG) that act as multiple sclerosis (MS) antigens, we grafted them onto a framework of a particularly stable class of peptides, the cyclotides.
    keywords: acid; activation; activity; affinity; aggregation; aim; alpha; amino; amino acid; analogues; analysis; approach; arg; assay; beta; binding; blood; bond; cancer; cell; chain; chemical; chemistry; complex; complexes; compounds; concentration; conformational; conjugates; cyclic; data; derivatives; design; development; disulfide; dna; domain; effect; enzyme; epitope; fmoc; fragment; gly; group; growth; hplc; human; inhibitors; integrin; interaction; ligands; mechanism; membrane; method; mice; model; molecular; molecules; native; new; nmr; non; novel; opioid; order; patients; peptide; peptide analogues; peptide chain; peptide synthesis; phase; phase peptide; phe; position; potential; prepared; presence; products; proline; properties; protein; reaction; receptor; residues; results; role; sequence; site; solution; specific; spectroscopy; stability; strategy; structure; studies; study; surface; synthetic; system; target; terminal; therapeutic; treatment; tumor; turn; type; tyr; use; vivo; water; work
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        item: #257 of 1349
          id: cord-023346-8sqbqjm1
      author: None
       title: MONDAY: POSTERS
        date: 2005-06-08
       words: 130150
      flesch: 50
     summary: The Polish Blood Transfusion Act of 22nd August 1997, in force since January 1st 1999, has been supplemented by 8 Decrees: 1. procedures for external BTS audits; 2. requirements for donor selection; 3. requirements and procedures for organization and safe management of blood transfusion in hospitals; 4. requirements for implementing of national and regional donor registers; 5. employment criteria for BTS personnel; 6. training requirements for hospital personnel involved in blood and blood product administration; 7. national, uniform price list for blood and blood products; 8. organization requirements for setting up of a National Committee for Blood and Blood Transfusion. Introduction: TRALI is a life threatening adverse reaction of blood transfusion.
    keywords: aim; analysis; anti; antibodies; antibody; antigens; apheresis; assay; associated; background; blood banking; blood banks; blood cells; blood center; blood collection; blood components; blood donation; blood donors; blood establishments; blood group; blood loss; blood plasma; blood pressure; blood products; blood safety; blood samples; blood service; blood supply; blood system; blood transfusion; blood units; blood volume; cases; clinical; complications; concentrates; conclusion; control; cord blood; count; data; day; days; detection; disease; dna; donations; effect; events; factor; ffp; following; frequency; general; groups; hbsag; hbv; hcv; health; high; hla; hospital; hospital blood; identification; important; increase; infections; information; introduction; iron; laboratory; level; low; major; management; mean; medical; methods; national; negative; new; non; number; order; patients; pcr; period; plasma; platelet; platelet transfusion; population; positive; post; practice; presence; present; procedure; process; quality; range; rbc; rbc transfusion; rbcs; red; results; rhd; risk; routine; screening; serum; specific; standard; storage; studies; study; surgery; system; table; test; tested; testing; therapy; time blood; total; transfusion medicine; transfusion reactions; transfusion service; transfusion therapy; transfusions; treatment; type; use; weak; women; years
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        item: #258 of 1349
          id: cord-023354-f2ciho6o
      author: None
       title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS
        date: 2005-06-08
       words: 130154
      flesch: 50
     summary: The Polish Blood Transfusion Act of 22nd August 1997, in force since January 1st 1999, has been supplemented by 8 Decrees: 1. procedures for external BTS audits; 2. requirements for donor selection; 3. requirements and procedures for organization and safe management of blood transfusion in hospitals; 4. requirements for implementing of national and regional donor registers; 5. employment criteria for BTS personnel; 6. training requirements for hospital personnel involved in blood and blood product administration; 7. national, uniform price list for blood and blood products; 8. organization requirements for setting up of a National Committee for Blood and Blood Transfusion. Introduction: TRALI is a life threatening adverse reaction of blood transfusion.
    keywords: aim; analysis; anti; antibodies; antibody; antigens; apheresis; assay; associated; background; blood banking; blood banks; blood cells; blood center; blood collection; blood components; blood donation; blood donors; blood establishments; blood group; blood loss; blood plasma; blood pressure; blood products; blood safety; blood samples; blood service; blood supply; blood system; blood transfusion; blood units; blood volume; cases; clinical; complications; concentrates; conclusion; control; cord blood; count; data; day; days; detection; disease; dna; donations; effect; events; factor; ffp; following; frequency; general; groups; hbsag; hbv; hcv; health; high; hla; hospital; hospital blood; identification; important; increase; infections; information; introduction; iron; laboratory; level; low; major; management; mean; medical; methods; national; negative; new; non; number; order; patients; pcr; period; plasma; platelet; platelet transfusion; population; positive; post; practice; presence; present; procedure; process; quality; range; rbc; rbc transfusion; rbcs; red; results; rhd; risk; routine; screening; serum; specific; standard; storage; studies; study; surgery; system; table; test; tested; testing; therapy; time blood; total; transfusion medicine; transfusion reactions; transfusion service; transfusion therapy; transfusions; treatment; type; use; weak; women; years
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        item: #259 of 1349
          id: cord-023364-ut56gczm
      author: None
       title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS
        date: 2005-06-08
       words: 130157
      flesch: 50
     summary: The Polish Blood Transfusion Act of 22nd August 1997, in force since January 1st 1999, has been supplemented by 8 Decrees: 1. procedures for external BTS audits; 2. requirements for donor selection; 3. requirements and procedures for organization and safe management of blood transfusion in hospitals; 4. requirements for implementing of national and regional donor registers; 5. employment criteria for BTS personnel; 6. training requirements for hospital personnel involved in blood and blood product administration; 7. national, uniform price list for blood and blood products; 8. organization requirements for setting up of a National Committee for Blood and Blood Transfusion. Introduction: TRALI is a life threatening adverse reaction of blood transfusion.
    keywords: aim; analysis; anti; antibodies; antibody; antigens; apheresis; assay; associated; background; blood banking; blood banks; blood cells; blood center; blood collection; blood components; blood donation; blood donors; blood establishments; blood group; blood loss; blood plasma; blood pressure; blood products; blood safety; blood samples; blood service; blood supply; blood system; blood transfusion; blood units; blood volume; cases; clinical; complications; concentrates; conclusion; control; cord blood; count; data; day; days; detection; disease; dna; donations; effect; events; factor; ffp; following; frequency; general; groups; hbsag; hbv; hcv; health; high; hla; hospital; hospital blood; identification; important; increase; infections; information; introduction; iron; laboratory; level; low; major; management; mean; medical; methods; national; negative; new; non; number; order; patients; pcr; period; plasma; platelet; platelet transfusion; population; positive; post; practice; presence; present; procedure; process; quality; range; rbc; rbc transfusion; rbcs; red; results; rhd; risk; routine; screening; serum; specific; standard; storage; studies; study; surgery; system; table; test; tested; testing; therapy; time blood; total; transfusion medicine; transfusion reactions; transfusion service; transfusion therapy; transfusions; treatment; type; use; weak; women; years
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        item: #260 of 1349
          id: cord-023608-w2g7v7g1
      author: None
       title: ISAR News
        date: 2017-10-20
       words: 6063
      flesch: 45
     summary: Infection with ZIKV, which can result in congenital deformities in newborn babies when the mothers are infected during pregnancy as well as Guillain-Barré syndrome in otherwise healthy adults, has brought intense international focus on this emerging threat with calls for urgent development of antiviral drugs. Each award Dengue fever disease is caused by the four serotypes of dengue virus (DENV 1-4) and is mostly transmitted by the urban dwelling Aedes aegypti mosquito.
    keywords: antiviral; dengue; development; drug; icar; isar; meeting; research; rna; society; support; vaccine; virus; viruses; women; year
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        item: #261 of 1349
          id: cord-023705-3q9yr6np
      author: FENNER, FRANK
       title: Viral Replication
        date: 2014-06-27
       words: 8336
      flesch: 48
     summary: The eclipse period ranges from 5 to 15 hours for the various DNA viruses and from 3 to 10 hours for RNA viruses (see Table 4 -2). 4 -3 (for DNA viruses) and Fig. 4 -5 (for RNA viruses).
    keywords: cell; dna; fig; genome; membrane; mrna; polymerase; proteins; replication; rna; sense; synthesis; transcription; virion; viruses
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        item: #262 of 1349
          id: cord-023724-5at0rhqk
      author: Cann, Alan J.
       title: Infection
        date: 2015-07-24
       words: 14985
      flesch: 44
     summary: The former strategy relies on two approaches: public and personal hygiene, which perhaps plays the major role in preventing virus infection (e.g., provision of clean drinking water and disposal of sewage; good medical practice such as the sterilization of surgical instruments) and vaccination, which makes use of the immune system to combat virus infections. A common misconception is that virus infection inevitably results in disease.
    keywords: cell; dna; expression; gene; host; ifn; ifns; infection; mechanisms; plant; proteins; replication; resistance; response; result; rna; system; vaccines; virus; virus infection; virus replication; viruses
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        item: #263 of 1349
          id: cord-023726-2fduzqyb
      author: STRAUSS, JAMES H.
       title: The Structure of Viruses
        date: 2012-07-27
       words: 10619
      flesch: 54
     summary: The two families of enveloped DNA viruses that we consider here, the poxviruses and the herpesviruses, contain large genomes and complicated virus structures. The structure of most enveloped viruses is not as rigorously constrained as that of icosahedral virus particles.
    keywords: assembly; budding; cell; enveloped; fig; form; glycoproteins; membrane; nucleocapsid; protein; rna; structure; symmetry; virion; viruses
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        item: #264 of 1349
          id: cord-023766-qx0qdjmt
      author: Nirwan, Sonam
       title: Rhinovirus RNA Polymerase: Structure, Function, and Inhibitors
        date: 2018-11-02
       words: 10494
      flesch: 43
     summary: The RNA synthesis of rhinovirus is carried out by RNA-dependent RNA polymerase, also known as 3D(Pol). De novo synthesis of RNA by the dengue virus RNA-dependent RNA polymerase exhibits temperature dependence at the initiation but not elongation phase Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus Two groups of rhinoviruses revealed by a panel of antiviral compounds present sequence divergence and differential pathogenicity Crystal structure of complete rhinovirus RNA polymerase suggests front loading of protein primer Poliovirus RNA-dependent RNA polymerase (3Dpol) is sufficient for template switching in vivo Remote site control of an active site fidelity checkpoint in a viral RNAdependent RNA polymerase Site size of cooperative single-stranded RNA binding by poliovirus RNA-dependent RNA polymerase Identification and properties of the RNAdependent RNA polymerase of hepatitis C virus Crystal structures of the RNA-dependent RNA polymerase genotype 2a of hepatitis C virus reveal two conformations and suggest mechanisms of inhibition by nonnucleoside inhibitors In vitro tests to evaluate immunotoxicity: a preliminary study Action of 3-methylquercetin on poliovirus RNA replication Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA-and DNAdependent RNA and DNA polymerases Nucleic acid polymerases use a general acid for nucleotidyl transfer Viral polymerases.
    keywords: activity; enzyme; et al; hrv; hrv16; initiation; motif; nucleotide; polymerase; primer; protein; replication; rna; rna polymerase; site; strand; synthesis; template; virus
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        item: #265 of 1349
          id: cord-023770-ymxapsv6
      author: None
       title: Closteroviridae
        date: 2011-11-23
       words: 3664
      flesch: 48
     summary: The natural and experimental host ranges of individual virus species are usually restricted, except for a few members of the genus Crinivirus. No serological relationships reported among different virus species of the genus.
    keywords: family; genome; genus; kda; members; protein; size; species; virus
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        item: #266 of 1349
          id: cord-023865-6rafp3x3
      author: Surjit, Milan
       title: The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential
        date: 2009-07-22
       words: 9217
      flesch: 36
     summary: Another study done by Wang et al. (2005) has attempted to use plasmid DNA expressing S, M, and N proteins as an efficient vaccine candidate. A bound to the amino-terminal domain of HIV-1 capsid Effects of a SARS-associated coronavirus vaccine in monkeys The nucleocapsid protein of SARS-CoV induces transcription of hfgl2 prothrombinase gene dependent on C/EBP alpha Activation of AP-1 signal transduction pathway by SARS coronavirus nucleocapsid protein Analysis of multimerization of the SARS coronavirus nucleocapsid protein Characterization of monoclonal antibody against SARS coronavirus nucleocapsid antigen and development of an antigen capture ELISA Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent Chronological evolution of IgM, IgA, IgG and neutralisation antibodies after infection with SARS-associated coronavirus Structure of the N-terminal RNA-binding domain of the SARS CoV nucleocapsid protein Generation and characterization of DNA vaccines targeting the nucleocapsid protein of severe acute respiratory syndrome coronavirus Severe acute respiratory syndrome coronavirus open reading frame (ORF) 3b, ORF 6, and nucleocapsid proteins function as interferon antagonists Mass spectrometric characterization of proteins from the SARS Virus: a preliminary report Characterization of F-actin bundling activity of Tetrahymena elongation factor 1 alpha investigated with rabbit skeletal muscle actin Extremely low exposure of a community to severe acute respiratory syndrome coronavirus: false seropositivity due to use of bacterially derived antigens Sumoylation of the nucleocapsid protein of severe acute respiratory syndrome coronavirus Detection of the nucleocapsid protein of severe acute respiratory syndrome coronavirus in serum: comparison with results of other viral markers SARS patients-derived human recombinant antibodies to S and M proteins efficiently neutralize SARS-coronavirus infectivity Activation of NF-kappaB by the full-length nucleocapsid protein of the SARS coronavirus The C-terminal portion of the nucleocapsid protein demonstrates SARS-CoV antigenicity High-yield expression of recombinant SARS coronavirus nucleocapsid protein in methylotrophic yeast Pichia pastoris Immunofluorescence assay for detection of the nucleocapsid antigen of the severe acute respiratory syndrome (SARS)-associated coronavirus in cells derived from throat wash samples of patients with SARS Immunological characterizations of the nucleocapsid protein based SARS vaccine candidates Nucleocapsid protein of SARS coronavirus tightly binds to human cyclophilin A In vitro biochemical and thermodynamic characterization of nucleocapsid protein of SARS The nucleocapsid protein of SARS coronavirus has a high binding affinity to the human cellular heterogeneous nuclear ribonucleoprotein A1 Carboxyl terminus of severe acute respiratory syndrome coronavirus nucleocapsid protein: self-association analysis and nucleic acid binding characterization Lung pathology of fatal severe acute respiratory syndrome Nucleophosmin/B23 is a target of CDK2/cyclin E in centrosome duplication Protective humoral responses to severe acute respiratory syndrome-associated coronavirus: implications for the design of an effective protein-based vaccine Expression of SARS-coronavirus nucleocapsid protein in Escherichia coli and Lactococcus lactis for serodiagnosis and mucosal vaccination Use of the COOH portion of the nucleocapsid protein in an antigen-capturing enzymelinked immunosorbent assay for specific and sensitive detection of severe acute respiratory syndrome coronavirus Smad3 is key to TGF-beta-mediated epithelial-to-mesenchymal transition, fibrosis, tumor suppression and metastasis Characterization of a novel coronavirus associated with severe acute respiratory syndrome Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells Recombinant nucleocapsid protein-based IgG enzyme-linked immunosorbent assay for the serological diagnosis of SARS Characterization and application of monoclonal antibodies against N protein of SARScoronavirus Antigenic characterization of severe acute respiratory syndrome-coronavirus nucleocapsid protein expressed in insect cells: The effect of phosphorlation on immunoreactivity and specificity Inhibition of beta interferon induction by severe acute respiratory syndrome coronavirus suggests a two-step model for activation of interferon regulatory factor 3 Antigenic cross-reactivity between the nucleocapsid protein of severe acute respiratory syndrome (SARS) coronavirus and polyclonal antisera of antigenic group I animal coronaviruses: implication for SARS diagnosis The nucleocapsid protein of the SARS coronavirus is capable of self-association through a C-terminal 209 amino acid interaction domain The SARS coronavirus nucleocapsid protein induces actin reorganization and apoptosis in COS-1 cells in the absence of growth factors The severe acute respiratory syndrome coronavirus nucleocapsid protein is phosphorylated and localizes in the cytoplasm by 14-3-3-mediated translocation The nucleocapsid protein of severe acute respiratory syndrome-coronavirus inhibits the activity of cyclin-cyclin-dependent kinase complex and blocks S phase progression in mammalian cells Nuclear/nucleolar localization properties of C-terminal nucleocapsid protein of SARS coronavirus Specific phosphorylation of nucleophosmin on Thr(199) by cyclin-dependent kinase 2-cyclin E and its role in centrosome duplication Direct sequencing of SARScoronavirus S and
    keywords: activity; binding; cells; coronavirus; cov; et al; infection; interaction; nucleocapsid; protein; rna; sars; specific; syndrome
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        item: #267 of 1349
          id: cord-024282-t5wl0bih
      author: Mao, Shunfu
       title: BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance
        date: 2020-02-01
       words: 3458
      flesch: 53
     summary: How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult task. We can formulate the problem of assembly parameter tuning as follows.
    keywords: assembly; datasets; parameters; reference; rna
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        item: #268 of 1349
          id: cord-025181-eg108wcd
      author: Zheng, Zhihang
       title: Establishment of Murine Infection Models with Biological Clones of Dengue Viruses Derived from a Single Clinical Viral Isolate
        date: 2020-05-25
       words: 5990
      flesch: 50
     summary: Our research here provides two kinds of dengue virus infection mouse models, which reproduce both severe and self-limited manifestations of human diseases, expanding the current choice of dengue viral infection small animal models. As type I/II interferon deficient mice are more susceptible to dengue virus infection, we determined the in vivo infectivity of these two viruses in type I and type II IFN receptors double knock-out AG6 mice.
    keywords: cells; dengue; denv-2; ifn; infection; mice; pfu; type; viral; virus; viruses
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        item: #269 of 1349
          id: cord-025948-6dsx7pey
      author: Maitra, Arindam
       title: Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility
        date: 2020-06-04
       words: 7221
      flesch: 48
     summary: Viral RNA sequences obtained from two samples S11 and S12 shared all mutations except a V32L mutation at ORF8 harboured by S11 and not by S12. The sequencing reads obtained in shotgun RNA-Seq experiment were mapped to reference viral sequence, variants detected and consensus sequence for each sample built using Dragen RNA pathogen detection software (version 9) in BaseSpace (Illumina Inc, USA).
    keywords: binding; chain; clade; cov-2; d614; genome; india; mirnas; mutations; protein; rna; samples; sars; sequences
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        item: #270 of 1349
          id: cord-026641-eemp6b5j
      author: Kabiljo, Julijan
       title: From threat to cure: understanding of virus-induced cell death leads to highly immunogenic oncolytic influenza viruses
        date: 2020-06-11
       words: 6705
      flesch: 28
     summary: A virus replication in vitro through induction of toll-like receptor 3 dependent apoptosis Regulated necrosis: the expanding network of non-apoptotic cell death pathways Radiotherapy as a backbone for novel concepts in cancer immunotherapy Intratumoral activation of the necroptotic pathway components RIPK1 and RIPK3 potentiates antitumor immunity ZBP1/DAI is an innate sensor of influenza virus triggering the NLRP3 inflammasome and programmed cell death pathways Cellular inhibitor of apoptosis protein cIAP2 protects against pulmonary tissue necrosis during influenza virus infection to promote host survival Pathology of natural infections by H5N1 highly pathogenic avian influenza virus in mute (Cygnus olor) and whooper (Cygnus cygnus) swans Genomic analysis of increased host immune and cell death responses induced by 1918 influenza virus Highly pathogenic avian influenza H5N1 virus delays apoptotic responses via activation of STAT3 H5N1 influenza virus-induced mediators upregulate RIG-I in uninfected cells by paracrine effects contributing to amplified cytokine cascades H5N1 virus activates signaling pathways in human endothelial cells resulting in a specific imbalanced inflammatory response Pandemic H1N1 influenza A viruses suppress immunogenic RIPK3-driven dendritic cell death The NS1 protein of influenza Influenza virus is an enveloped, negative-strand RNA virus with no reverse transcriptase or DNA integration activity 28 .
    keywords: activation; apoptosis; cancer; cell; death; immunogenic; infection; influenza; ns1; oncolytic; protein; rna; tumor; virus; viruses
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        item: #271 of 1349
          id: cord-027865-p1epjn51
      author: Sterchi, Diane L.
       title: Molecular pathology
        date: 2020-06-22
       words: 13239
      flesch: 50
     summary: Moreover, PCR allows great flexibility in the choice of probe sequences by the use of appropriate primers. FISH probes have been developed for the majority of recurrent chromosomal aberrations found in hematological malignancies (Table 21 .4).
    keywords: acid; cells; chromosome; detection; dna; fish; gene; hybridization; ish; methods; minutes; molecular; non; nucleic; probe; rna; sequences; signals; situ; slides; solution; target; tissue; use
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        item: #272 of 1349
          id: cord-027975-77544sed
      author: Tars, Kaspars
       title: ssRNA Phages: Life Cycle, Structure and Applications
        date: 2020-06-30
       words: 11668
      flesch: 46
     summary: The lysis function of RNA bacteriophage Qb is mediated by the maturation (A2) protein Effect of the sequences upstream from the ribosome-binding site on the yield of protein from the cloned gene for phage MS2 coat protein Genome structure of caulobacter phage phiCb5 Bacterial microcompartments Nucleotide sequence of a ssRNA phage from Acinetobacter: kinship to coliphages Bacteriophage MS2 as a tool for targeted delivery in solid tumor chemotherapy Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ Dual-surfacemodified bacteriophage MS2 as an ideal scaffold for a viral capsid-based drug delivery system Recombinant RNA phage Q beta capsid particles synthesized and self-assembled in Escherichia coli Formation of capsid-like structures as a result of expression of coat protein gene of RNA phage fr Stages in phage R17 infection. Development of a Mimotope vaccine targeting the Staphylococcus aureus quorum sensing pathway Role of the coat protein-RNA interaction in the life cycle of bacteriophage MS2 Subunit fusion confers tolerance to peptide insertions in a virus coat protein Immunogenic display of diverse peptides on virus-like particles of RNA phage MS2 The capsid of the small RNA phage PRR1 is stabilized by metal ions Encapsidation of heterologous RNAs by bacteriophage MS2 coat protein The structure of bacteriophage phiCb5 reveals a role of the RNA genome and metal ions in particle stability and assembly T cells control the generation of nanomolar-affinity anti-glycan antibodies The true story and advantages of RNA phage capsids as Nanotools Molecular characterization of the plant virus genus Ourmiavirus and evidence of interkingdom reassortment of viral genome segments as its possible route of origin Glycan-targeted viruslike nanoparticles for photodynamic therapy Direct evidence for packaging signal-mediated assembly of bacteriophage MS2 Crystal structure of the read-through domain from bacteriophage Qbeta A1 protein Diversity of pili-specific bacteriophages: genome sequence of IncM plasmid-dependent RNA phage M Crystal structure of the bacteriophage qbeta coat protein in complex with the RNA operator of the replicase gene Crystal structure of the maturation protein from bacteriophage Qbeta Protein-RNA interactions in the single-stranded RNA bacteriophages Observations on the adsorption of Caulobacter bacteriophages containing ribonucleic acid Redefining the invertebrate RNA virosphere New type of infectious complex of E. coli RNA phage Structure of AP205 coat protein reveals circular permutation in ssRNA bacteriophages Secondary structure of bacteriophage MS2.
    keywords: bacteriophage; binding; cell; dimers; et al; gene; genome; interactions; ms2; particles; phages; pili; pp7; protein; rna; ssrna; structure; surface; virus; vlps
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        item: #273 of 1349
          id: cord-029779-9b6zs1sb
      author: Casey, Sophie
       title: Temporally Altered miRNA Expression in a Piglet Model of Hypoxic Ischemic Brain Injury
        date: 2020-07-27
       words: 11398
      flesch: 47
     summary: ng t erm neurodevelopmental outcome -a systematic review The human miRNA repertoire of different blood compounds Selection of reference genes is critical for miRNA expression analysis in human cardiac tissue. Dharap et al. noted that multiple miRNAs exhibit rapid temporal alterations in their expression levels after an ischemic insult in the adult rat [26] , while Ziu et al. have reported that a hypoxic insult causes temporal alterations in miRNA expression in vitro
    keywords: analysis; blood; brain; cells; controls; expression; fig; hie; human; hypoxic; inhibition; injury; ischemic; mir-128; mir-181a; mir-374a; mirnas; samples; study; time
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        item: #274 of 1349
          id: cord-030028-s6sxi8uj
      author: Rubio, Luis
       title: Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution
        date: 2020-07-17
       words: 14694
      flesch: 22
     summary: IF acknowledges financial support from the Spanish Ministerio de Economia y Competitividad, through the Severo Ochoa Programme for Centers of Excellence in R&D 2016-2019 (SEV-2015-0533). Detection and quantitation of two cucurbit criniviruses in mixed infection by real-time RT-PCR Mutations associated with resistancebreaking isolates of Beet necrotic yellow vein virus and their allelic discrimination using TaqMan technology Advances in plant virus evolution: translating evolutionary insights into better disease management Codon usage bias amongst plant viruses Virus adaptation by manipulation of host's gene expression Ecogenomic survey of plant viruses infecting tobacco by next generation sequencing Simultaneous detection and identification of Pepino mosaic virus (PepMV) isolates by multiplex one-step RT-PCR Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants Analysis of genetic bottlenecks during horizontal transmission of Cucumber mosaic virus Multiplex RT-PCR detection of three common viruses infecting orchids Rapid generation of genetic heterogeneity in progenies from individual cDNA clones of peach latent mosaic viroid in its natural host Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers Control methods of virus diseases in the Mediterranean basin Simultaneous detection of six RNA plant viruses affecting tomato crops using a single digoxigenin-labelled polyprobe Development of a molecular assay for the detection of Cucumber mosaic virus and the discrimination of its subgroups I and II Detection of five seedborne legume viruses in one sensitive multiplex polymerase chain reaction test Single-step multiplex RT-PCR for simultaneous and colourimetric detection of six RNA viruses in olive trees Real-time RT-PCR high-resolution melting curve analysis and multiplex RT-PCR to detect and differentiate grapevine leafroll-associated virus 3 variant groups I, II, III and VI Estimation of the effective number of founders that initiate an infection after aphid transmission of a multipartite plant virus Localizing viruses in their insect vectors Third generation sequencing: technology and its potential impact on evolutionary biodiversity research Microarrays for rapid identification of plant viruses Methods in virus diagnostics: from ELISA to next generation sequencing Real time portable genome sequencing for global food security Epidemiology and control of tomato mosaic virus Nanopore sequencing as a surveillance tool for plant pathogens in plant and insect tissues Multiple virus resistance at a high frequency using a single transgene construct DNA microarray: parallel detection of potato viruses Design, synthesis, and functional analysis of highly specific artificial small RNAs with antiviral activity in plants Fast-forward generation of effective artificial small RNAs for enhanced antiviral defense in plants Multi-targeting of viral RNAs with synthetic trans-acting small interfering RNAs enhances plant antiviral resistance A real-time RT-PCR assay for quantifying the fitness of Tobacco etch virus in competition experiments Diagnosis of plant diseases using the Nanopore sequencing platform Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission A phylogenetic survey of recombination frequency in plant RNA viruses Antibody array in a multiwell plate format for the sensitive and multiplexed detection of important plant pathogens Multiple virus resistance using artificial trans-acting siRNAs Next-generation diagnostics with CRISPR Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses The promiscuous evolutionary history of the family Bromoviridae NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian vineyards Lethal mutagenesis of an RNA plant virus via lethal defection Contribution of uneven distribution of genomic RNA variants of citrus tristeza virus (CTV) within the plant to changes in the viral population following aphid transmission A multiplex reverse transcription PCR assay for simultaneous detection of five tobacco viruses in tobacco plants Induction of silencing in plants by high-pressure spraying of in vitro-synthesized small RNAs Recombination profiles between Tomato yellow leaf curl virus and Tomato yellow leaf curl Sardinia virus in laboratory and field conditions: evolutionary and taxonomic implications Emergence and Phylodynamics of Citrus tristeza virus in Sicily, Italy Molecular detection of papaya meleira virus in the latex of carica papaya by RT-PCR Characterization of RNA-mediated resistance to tomato spotted wilt virus in transgenic tobacco plants Dominant resistance against plant viruses Detection, discrimination and absolute quantitation of Tomato spotted wilt virus isolates using real time RT-PCR with TaqMan ® MGB probes Transmission of Tomato spotted wilt virus isolates able and unable to overcome tomato or pepper resistance by its vector Frankliniella occidentalis Increase in Zucchini yellow mosaic virus symptom severity in tolerant zucchini cultivars is related to a point mutation in P3 protein and is associated with a loss of relative fitness on susceptible plants Differentiation of Cucumber mosaic virus isolates by hybridization to Rubio et al. genome move systemically and protect cucurbits against ZYMV Entomopathogenic viruses and bacteria for insect-pest control, in Integrated Pest Management: Current concepts and ecological perspective Nonparametric estimation from incomplete observations Plant virology and next generation sequencing: experiences with a potyvirus Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control Polycistronic artificial miRNA-mediated resistance to Wheat dwarf virus in barley is highly efficient at low temperature Current trends in diagnostics of viral infections of unknown etiology Lateral flow assays Population structure and genetic diversity within California Citrus tristeza virus (CTV) isolates The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses MEGA X: molecular evolutionary genetics analysis across computing platforms Multiple artificial microRNAs targeting conserved motifs of the replicase gene confer robust transgenic resistance to negative-sense singlestranded RNA plant virus Tempo and mode of plant RNA virus escape from RNA interferencemediated resistance Improving the effectiveness of artificial microRNA (amiR)-mediated resistance against Turnip mosaic virus by combining two amiRs or by targeting highly conserved viral genomic regions Viruses of cucurbit crops in the Mediterranean region: an ever-changing picture Phylogenetic and recombination analysis of tomato spotted wilt virus Simultaneous detection of three lilyinfecting viruses using a multiplex Luminex bead array Genetic diversity and biological variation among California isolates of Cucumber mosaic virus Molecular evolution of a viral non-coding sequence under the selective Virus Variability: Diagnosis and Control pressure of amiRNA-mediated silencing Development of a one-step immunocapture real-time TaqMan RT-PCR assay for the broad spectrum detection of Pepino mosaic virus Effectiveness of chemo-and thermotherapeutic treatments on Pepino mosaic virus in tomato seed MicroRNA-mediated gene silencing in plant defense and viral counter-defense Development of real-time and conventional RT-PCR assays for the detection of potato yellow vein virus (PYVV)
    keywords: analysis; citrus; control; detection; disease; dna; et al; hybridization; isolates; mosaic; multiplex; new; nucleotide; pcr; plant; plant viruses; primers; probes; recombination; resistance; rna; sequence; sequencing; species; techniques; time; tomato; variants; virus; viruses
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        item: #275 of 1349
          id: cord-030654-8yxa1r1c
      author: Zhang, Changhui
       title: Structural basis for the multimerization of nonstructural protein nsp9 from SARS-CoV-2
        date: 2020-08-20
       words: 4293
      flesch: 54
     summary: This homotetrameric structure comprised two significant styles of dimeric conformation that were found in nsp9 structures published in the last decade [19, 21] . Initially, 2 nmol DNA was incubated with different concentrations of nsp9 protein (in the native), in a solution containing 10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (pH 8.0), 50 mM KCl, 1 mM ethylenediaminetetraacetic acid (EDTA), 0.05% Triton-X-100, and 5% glycerol, for 30 min at 4°C.
    keywords: coronavirus; cov-2; fig; interface; nsp9; protein; residues; rna; sars; structure
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        item: #276 of 1349
          id: cord-031907-ilhr3iu5
      author: None
       title: ISEV2020 Abstract Book
        date: 2020-07-15
       words: 201435
      flesch: 40
     summary: Normal pancreas cells (hTERT-HPNE and HPDE-H6c7) were co-cultured with cancer cell EVs for 24-48 hours. Before EV isolation cells were kept for 24 h either under normoxia or hypoxia (1% oxygen).
    keywords: ability; activation; activity; ad evs; addition; aim; analysis; analysis methods; anti; approach; assay; associated; bacterial evs; biological; biomarkers; blood; blood cells; blood evs; blot; bone; brain; breast; breast cancer; cancer cells; cancer evs; cancer introduction; cancer patients; cd63; cd81; cd9; cell communication; cell culture; cell evs; cell exosomes; cell function; cell lines; cell proliferation; cell surface; cell types; cells; cells introduction; changes; characterization; chromatography; composition; concentration; conclusion; conditions; content; control; control evs; cultured; current; cytometry; data; delivery; density; detection; development; diagnosis; differential; disease; distribution; dna; drug; effect; electron; endothelial; enrichment; epithelial; ev analysis; ev cargo; ev evs; ev isolation; ev markers; ev numbers; ev preparations; ev production; ev protein; ev release; ev research; ev rna; ev samples; ev subpopulations; ev surface; ev treatment; ev uptake; evs; exclusion; exosomal; exosomes; experiments; expression; expression analysis; extracellular; factors; findings; flow; fluorescent; fluorescent evs; fold; formation; fractions; free; function; funding; gene; group; growth; host cells; human; human evs; imaging; immune; increase; inflammation; inflammatory; introduction; isolated; isolation methods; key; large; levels; lipid; lung; macrophages; mass; mechanisms; media; medium; membrane; membrane vesicles; mesenchymal; metastasis; methods; mice; microscopy; migration; milk evs; mirna; model; molecular; molecules; mouse; msc evs; mscs; nanoparticle; national; neuronal; neurons; new; non; normal; novel; nta; number; particles; pathway; patients; plasma evs; plasma samples; platelet; platform; play; positive; positive evs; post; potential; presence; present; primary; process; production; profile; profiling; progression; proliferation; properties; prostate; prostate cancer; protein; protein cargo; protein expression; protein markers; proteomic; purification; purity; range; recipient cells; research; resistance; response; results; rna; rnas; role; samples; sec; secretion; sequencing; serum; sevs; signalling; single; size; small evs; specific; specific evs; spectrometry; stem cells; stromal cells; studies; study; summary; surface; system; target cells; targets; tau; techniques; tested; therapeutic; therapy; time; tissue; total; total evs; tracking; transfer; transmission; treatment; tumour cells; ultracentrifugation; university; uptake; urinary evs; urine; usa; usa introduction; use; vesicles; vesicles introduction; vitro; vivo; work
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        item: #277 of 1349
          id: cord-033692-txfuuu7d
      author: Lim, Byeonghwi
       title: Integrated time-serial transcriptome networks reveal common innate and tissue-specific adaptive immune responses to PRRSV infection
        date: 2020-10-13
       words: 7941
      flesch: 38
     summary: The remaining pigs were humanely euthanised without virus infection as an uninfected control (0 dpi) group. Dynamic changes in these significant gene subsets at 3 dpi may represent biological signals associated with general and early immunological mechanisms in response to virus infection.
    keywords: dpi; expression; figure; genes; group; immune; infection; lung; porcine; prrsv; responses; rna; signalling; syndrome; time; tissues; virus
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        item: #278 of 1349
          id: cord-034648-vfqth54o
      author: None
       title: WITHDRAWN
        date: 2020-10-12
       words: 2009
      flesch: 51
     summary: The expression of SEPT12 was further examined in 15 embryos, 9 were enriched (>90%) for trophectoderm cells (TE) and 6 enriched (>80%) for inner cell mass cells (ICM). Additionally, novel RNA sequencing data from 18 samples of human cumulus cells was generated.
    keywords: cells; culture; expression; invasion; migration; rna; sept12
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        item: #279 of 1349
          id: cord-035067-ic843wr9
      author: de Almeida, Joana Ferro Machado
       title: COVID-19 and the gastrointestinal tract: what do we already know?
        date: 2020-11-05
       words: 5454
      flesch: 50
     summary: SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues ACE-2 expression in the small airway epithelia of smokers and COPD Patients: Implications for COVID-19 COVID-19 and diabetes: Knowledge in progress Association of angiotensin-converting enzyme inhibitor or angiotensin receptor blocker use with covid-19 diagnosis and mortality Association of renin-angiotensin system inhibitors with severity or risk of death in patients with hypertension hospitalized for coronavirus disease 2019 (COVID-19) infection in Wuhan, China Emerging WuHan (COVID-19) coronavirus: glycan shield and structure prediction of spike glycoprotein and its interaction with human CD26 Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms Gastrointestinal symptoms of 95 cases with SARS-CoV-2 infection Clinical characteristics of COVID-19 patients with digestive symptoms in Hubei, China Enteric involvement in hospitalised patients with COVID-19 outside Wuhan Prevalence and characteristics of gastrointestinal symptoms in patients with SARS-CoV-2 infection in the United States: a multicenter cohort study Gastrointestinal symptoms and COVID-19: case-control study from the United States High prevalence of concurrent gastrointestinal manifestations in patients with SARS-CoV-2: early experience from California Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan Effect of gastrointestinal symptoms on patients infected with COVID-19 Gastrointestinal manifestations of SARS-CoV-2 infection and virus load in fecal samples from the Hong Kong cohort and systematic review and meta-analysis Imaging and clinical features of patients with 2019 novel coronavirus SARS-CoV-2: a systematic review and meta-analysis COVID-19 patients' clinical characteristics, discharge rate, and fatality rate of meta-analysis Gastrointestinal infection could be new focus for coronavirus diagnosis Individual variation of the SARS-CoV2 receptor ACE2 gene expression and regulation Those infected may be asymptomatic, present typical symptoms (fever, dry cough and dyspnea), gastrointestinal symptoms (diarrhea, nausea, vomiting and abdominal pain) and viral RNA in stools.
    keywords: cov-2; covid-19; disease; patients; sars; studies; study; symptoms; viral; virus
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        item: #280 of 1349
          id: cord-035110-5lkzhjfh
      author: Zhu, Le
       title: Isolation and characterization of exosomes for cancer research
        date: 2020-11-10
       words: 14696
      flesch: 25
     summary: Mounting evidence has proven that specific cellular components derived from the original tumor cells accumulate in exosomes and that exosomes can then mediate functional responses via interactions with target tumor cells and by re-programming various types of cancer cells Notably, exosome-mediated stromal communication with cancer cells can influence treatment responses.
    keywords: biomarker; breast; cancer; cancer cells; carcinoma; cells; development; exosomal; exosomes; extracellular; immune; isolation; metastasis; non; patients; plasma; potential; progression; proteins; resistance; rna; serum; studies; techniques; therapy; treatment; tumor; tumor cells; vesicles
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        item: #281 of 1349
          id: cord-048198-zjufx4fo
      author: Pasternak, Alexander O.
       title: Sequence requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA synthesis
        date: 2001-12-17
       words: 7620
      flesch: 48
     summary: Various models have been put forward to explain the cotranscriptional fusion of non-contiguous parts of the nidovirus genome during sg RNA synthesis ( Figure 1B and C). The EAV genomic RNA contains several sequences that match the leader TRS precisely, but nevertheless are not used for sg RNA synthesis (den Boon et al., 1996; Pasternak et al., 2000) .
    keywords: body; body trs; leader; leader trs; mutants; rna; strand; synthesis; trs
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        item: #282 of 1349
          id: cord-048204-6lvn10f4
      author: Shi, Stephanie T.
       title: Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus
        date: 2000-09-01
       words: 7672
      flesch: 49
     summary: Since hnRNP A1 protein is involved in a variety of important cellular functions, including RNA splicing, transport, turnover and translation, it is conceivable that other redundant gene products may substitute for the function of hnRNP A1 in CB3 cells. Retroviral insertions downstream of the heterogeneous nuclear ribonucleoprotein A1 gene in erythroleukemia cells: evidence that A1 is not essential for cell growth Speci®c binding of polypyrimidine tract binding protein and hnRNP A1 to HIV-1 CRS elements Primary structure of the heterogeneous nuclear ribonucleoprotein A2, B1 and C2 proteins: a diversity of RNA binding proteins is generated by small peptide inserts cDNA cloning of human hnRNP protein A1 reveals the existence of multiple mRNA isoforms Regulation of alternative splicing in vivo by overexpression of antagonistic splicing factors In vitro replication of mouse hepatitis virus strain A59 Identi®cation and characterization of a host protein required for ef®cient template selection in viral RNA replication ) hnRNP proteins and the biogenesis of mRNA Antigenic relationships of murine coronaviruses: analysis using monoclonal antibodies to JHM (MHV-4) virus Nuclear import of hnRNP A1 is mediated by a novel cellular cofactor related to karyopherin-b Three different cellular proteins bind to the complementary sites on the 5¢-end positive-and 3¢-end negative-strands of mouse hepatitis virus RNA Four proteins processed from the replicase gene polyprotein of mouse hepatitis virus colocalize in the cell periphery and adjacent to sites of virion assembly Association of heterogeneous nuclear ribonucleoprotein A1 and C proteins with reiterated AUUUA sequences Modulation of AUUUA response element binding by heterogeneous nuclear ribonucleoprotein A1 in human T lymphocytes.
    keywords: cells; dbt; figure; hnrnp; hnrnp a1; mhv; protein; replication; rna; transcription
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        item: #283 of 1349
          id: cord-048222-1pq6dkl5
      author: Imbeaud, Sandrine
       title: Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces
        date: 2005-03-30
       words: 7009
      flesch: 41
     summary: The relevance of the RNA quality metrics for assessment of gene expression differences was tested by Q-PCR, revealing a significant decline of the relative expression of genes in RNA samples of disparate quality, while samples of similar, even poor integrity were found highly comparable. It requires only a very small amount of RNA sample (as low as 200 pg), the use of a size standard during electrophoresis allows the estimation of sizes of RNA bands and the measurement appears relatively unaffected by contaminants.
    keywords: degfact; degradation; expression; figure; integrity; mean; quality; rin; rna; samples
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        item: #284 of 1349
          id: cord-048322-5eqdrd52
      author: Aigner, Achim
       title: Delivery Systems for the Direct Application of siRNAs to Induce RNA Interference (RNAi) In Vivo
        date: 2006-05-18
       words: 7344
      flesch: 28
     summary: Molecular Vision Antitumor activity of small interfering RNA/cationic liposome complex in mouse models of cancer Small interfering RNA-mediated functional silencing of vasopressin V 2 receptors in the mouse kidney Therapeutic EphA2 gene targeting in vivo using neutral liposomal small interfering RNA delivery siRNA-induced caveolin-1 knockdown in mice increases lung vascular permeability via the junctional pathway Cationic liposome-mediated delivery of siRNAs in adult mice Efficient delivery of small interfering RNA for inhibition of IL-12p40 expression in vivo Small interfering RNAs directed against beta-catenin inhibit the in vitro and in vivo growth of colon cancer cells Gene silencing by systemic delivery of synthetic siRNAs in adult mice Intravesical administration of small interfering RNA targeting PLK-1 successfully prevents the growth of bladder cancer In vitro and in vivo suppression of GJB2 expression by RNA interference Blockage of the macrophage migration inhibitory factor expression by short interference RNA inhibited the rejection of an allogeneic tracheal graft Widespread lipoplex-mediated gene transfer to vascular endothelial cells and hemangioblasts in the vertebrate embryo Systemic delivery of Raf-siRNA using cationic cardiolipin liposomes silences Raf-1 expression and inhibits tumor growth in xenograft model of human prostate cancer Novel cationic cardiolipin analogue-based liposome for efficient DNA and small interfering RNA delivery in vitro and in vivo An efficient intrathecal delivery of small interfering RNA to the spinal cord and peripheral neurons Comparison of antisense oligonucleotides and siR-NAs in cell culture and in vivo An siRNA-based microbicide protects mice from lethal herpes simplex virus 2 infection Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs Potent and persistent in vivo anti-HBV activity of chemically modified siR-NAs Inhibition of gene expression in mice muscle by in vivo electrically mediated siRNA delivery Small interfering RNA targeting Raf-1 inhibits tumor growth in vitro and in vivo A small interfering RNA targeting vascular endothelial growth factor as cancer therapeutics Atelocollagenmediated synthetic small interfering RNA delivery for effective gene silencing in vitro and in vivo Efficient delivery of small interfering RNA to bone-metastatic tumors by using atelocollagen in vivo Rad51 siRNA delivered by HVJ envelope vector enhances the anti-cancer effect of cisplatin Antibody mediated in vivo delivery of small interfering RNAs via cell-surface receptors Silencing heat shock factor 1 by small interfering RNA abrogates heat shock-induced cardioprotection against ischemiareperfusion injury in mice Reconstituted influenza virus envelopes as an efficient carrier system for cellular delivery of small-interfering RNAs A statistical sampling algorithm for RNA secondary structure prediction Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents.
    keywords: cancer; cells; complex; delivery; dna; expression; gene; growth; molecules; pei; silencing; sirnas; small; targeting; tumor; vitro; vivo
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        item: #285 of 1349
          id: cord-048327-xgwbl8em
      author: Henderson, Clark M.
       title: Antisense-induced ribosomal frameshifting
        date: 2006-08-18
       words: 4342
      flesch: 37
     summary: Similarly, for +1 frameshift sites, the identity of the codons in the P-and A-sites of the ribosome is critical for efficient frameshifting. However, visual examination of upstream codons does not reveal an obvious À1 or +1 frameshift site.
    keywords: antisense; antizyme; codon; frameshifting; pseudoknot; ribosomal; shift site; site; uga
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        item: #286 of 1349
          id: cord-048471-7jszm1nd
      author: Salim, Omar
       title: Functional Analysis of the 5′ Genomic Sequence of a Bovine Norovirus
        date: 2008-05-14
       words: 5667
      flesch: 44
     summary: To date, it has not been possible to explain the difference in the predicted and observed sizes for the JV N-term, and the addition of the 14 amino acid V5 epitope within JV N-term does not account for this apparent large shift in molecular weight. It cannot be ruled out, however, that the wild type JV N-term aberrantly co-migrates with the 39 kDa JV 2C protein in SDS-PAGE.
    keywords: cells; initiation; ires; kda; protein; rna; term; translation; virus
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        item: #287 of 1349
          id: cord-048478-ftlb5b95
      author: Mroczek, Seweryn
       title: Apoptotic signals induce specific degradation of ribosomal RNA in yeast
        date: 2008-04-01
       words: 9819
      flesch: 35
     summary: Nevertheless, a similar approach had been used to demonstrate that DNA damage in apoptotic yeast cells was an enzymatic process (30) . Cytochrome c release and mitochondria involvement in programmed cell death induced by acetic acid in Saccharomyces cerevisiae Production of reactive oxygen species and loss of viability in yeast mitochondrial mutants: protective effect of Bcl-xL Application of inhibitors and uncouplers for a study of oxidative phosphorylation Effects of the inhibitors azide, dicyclohexylcarbodiimide, and aurovertin on nucleotide binding to the three F1-ATPase catalytic sites measured using specific tryptophan probes The mitochondrial F0F1-ATPase proton pump is required for function of the proapoptotic protein Bax in yeast and mammalian cells Translational control in stress and apoptosis Translational control by the ER transmembrane kinase/ribonuclease IRE1 under ER stress Ribosome inactivating proteins and apoptosis Rearrangement of nuclear ribonucleoprotein (RNP)-containing structures during apoptosis and transcriptional arrest Lsm proteins are required for normal processing and stability of ribosomal RNAs Yeast programmed cell death: an intricate puzzle The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response Role of mitochondria in the pheromone-and amiodarone-induced programmed death of yeast Saccharomyces cerevisiae has distinct adaptive responses to both hydrogen peroxide and menadione Mitochondrial function is required for resistance to oxidative stress in the yeast Saccharomyces cerevisiae The role of respiration, reactive oxygen species and oxidative stress in mother cell-specific ageing of yeast strains defective in the RAS signalling pathway Starvation for an essential amino acid induces apoptosis and oxidative stress in yeast Cells depleted of mitochondrial DNA (rho0) yield insight into physiological mechanisms Physiological regulation of yeast cell death in multicellular colonies is triggered by ammonia Defects in N-glycosylation induce apoptosis in yeast
    keywords: 25s; acid; apoptosis; apoptotic; cells; cleavage; death; degradation; dna; figure; response; ros; rrna; specific; stress; yeast
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        item: #288 of 1349
          id: cord-048485-b8xb1f12
      author: Hulst, Marcel
       title: Early transcriptional response in the jejunum of germ-free piglets after oral infection with virulent rotavirus
        date: 2008-06-04
       words: 6320
      flesch: 41
     summary: The rotavirus enterotoxin NSP4 mobilizes intracellular calcium in human intestinal cells by stimulating phospholipase C-mediated inositol 1, 4, 5-trisphosphate production Rotaviruses and their replication Transmission of F4 + E coli in groups of early weaned piglets Molecular cloning of spermidine/spermine N1-acetyltransferase from the periimplantation porcine uterus by messenger ribonucleic acid differential display: temporal and conceptus-modulated gene expression Twists and turns in the development and maintenance of the mammalian small intestine epithelium Il-6 and its soluble receptor orchestrate a temporal switch in the pattern of leukocyte recruitment seen during acute inflammation Inactivation of the RNase activity of glycoprotein E rns of classical swine fever virus results in a cytopathogenic virus Increased thioredoxin-1 inhibits SSAT expression in MCF-7 human breast cancer cells Inclusion of linseed and linseed expeller meal in piglet diets affects intestinal gene expression profiles Regulatory role for a novel human thioredoxin peroxidase in NF-kappaB activation Rotavirus infection reduces sucrase-isomaltase expression in human intestinal epithelial cells by perturbing protein targeting and organization of microvillar cytoskeleton Txr1: a transcriptional regulator of thrombospondin-1 that modulates cellular sensitivity to taxanes Role of the enteric nervous system in the fluid and electrolyte secretion of rotavirus diarrhea Pathogenesis of rotavirus diarrhea Mechanisms of CD47-induced caspase-independent cell death in normal and leukemic cells: link between phosphatidylserine exposure and cytoskeleton organization Interplay between IFN-gamma and IL-6 signaling governs neutrophil trafficking and apoptosis during acute inflammation State University of Utrecht 33. It is tempting to link up-regulation of MS4A2 directly to NSP4induced enhancement of Ca 2+ permeability of the plasma and ER membranes in intestinal epithelial cells [29, 40] .
    keywords: analysis; cells; expression; genes; hpi; ifn; infection; intestinal; mrna; piglets; regulation; response; rna; rotavirus
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        item: #289 of 1349
          id: cord-102336-ex3zlq38
      author: De Wijngaert, Brent
       title: Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase
        date: 2020-04-14
       words: 2286
      flesch: 52
     summary: Much of our understanding of mitochondrial DNA transcription comes from studies of yeast (S. cerevisiae) and human mtRNAPs (2, 3, 5) . Insights into transcription: structure and function of singlesubunit DNA-dependent RNA polymerases Maintenance and Expression of Mammalian Mitochondrial DNA Structural basis of mitochondrial transcription Mechanism of bacterial transcription initiation: RNA polymerase -promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis Mechanism of transcription initiation by the yeast mitochondrial RNA polymerase Structural Basis of Mitochondrial Transcription Initiation The thumb subdomain of yeast mitochondrial RNA polymerase is involved in processivity, transcript fidelity and mitochondrial transcription factor binding Crystal structure of the transcription factor sc-mtTFB offers insights into mitochondrial transcription Transcription factor-dependent DNA bending governs promoter recognition by the mitochondrial RNA polymerase Mutations in the yeast mitochondrial RNA polymerase specificity factor, Mtf1, verify an essential role in promoter utilization Structure of a transcribing T7 RNA polymerase initiation complex Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism Movies S1 -S3 Movie S1.
    keywords: dna; fig; mtf1; rna; transcription
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        item: #290 of 1349
          id: cord-102412-cnlvyey4
      author: Tekman, Mehmet
       title: A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework
        date: 2020-08-28
       words: 6425
      flesch: 46
     summary: The rst wave of software utilities to deal with the analysis of single cell datasets were statistical packages, aimed at tackling the issue of dropout events during sequencing, which would manifest as a high prevalence of zero-entries in over 80% of the featurecount matrix. The continuing rise in single cell technologies has led to previously unprecedented levels of analysis into cell heterogeneity within tissue samples, providing new insights into developmental and differentiation pathways for a wide range of disciplines.
    keywords: 10x; analysis; cell; data; datasets; erent; galaxy; processing; scrna; seq; sequencing; tools; training; user; work
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        item: #291 of 1349
          id: cord-102547-nxut8ov1
      author: Grädel, C.
       title: Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing
        date: 2020-06-09
       words: 6510
      flesch: 48
     summary: More than 98% of basecalled RNA reads (9,065 reads) were taxonomically classified using BLASTN against NCBI's nucleotide (nt) database. We used a chloroform/bead pre-treatment in DRS samples for enrichment of viral capsid and although it might be efficient in enriching viral reads, it could also reduce the overall amount of RNA extracted.
    keywords: drs; enterovirus; genome; illumina; miseq; nanopore; preprint; reads; rna; samples; sequences; sequencing
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        item: #292 of 1349
          id: cord-102766-n6mpdhyu
      author: Alam, Md. Nafis Ul
       title: Short k-mer Abundance Profiles Yield Robust Machine Learning Features and Accurate Classifiers for RNA Viruses
        date: 2020-06-25
       words: 3202
      flesch: 47
     summary: It has been 90 demonstrated that RNA-Seq data can be a very promising avenue for improving knowledge on 91 RNA viruses when leveraged by tactful algorithms Viral metagenomics Third generation sequencing: technology and its potential impact on 602 evolutionary biodiversity research Virus taxonomy: the database of the International Committee on 606 Nucleic Acids Research Accelerated Profile HMM Searches BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-610 seq Data Bridger: a new framework for de novo transcriptome assembly using 612 RNA-seq data Shannon: An Information-Optimal de Novo RNA-Seq Assembler rnaSPAdes: <em>a de novo</em> transcriptome assembler and 616 its application to RNA-Seq data IDBA-tran: a more robust de novo de Bruijn graph assembler for 621 transcriptomes with uneven expression levels SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq 623 reads De novo assembly and analysis of RNA-seq data Full-length transcriptome assembly from RNA-Seq data without a 627 reference genome Oases: robust de novo RNA-seq assembly across the dynamic range 629 of expression levels S1 Fig.
    keywords: data; feature; genomes; learning; machine; models; rna; sequence; viruses
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        item: #293 of 1349
          id: cord-102866-40s64455
      author: Bhadra, Sanchita
       title: One enzyme reverse transcription qPCR using Taq DNA polymerase
        date: 2020-05-30
       words: 2867
      flesch: 43
     summary: We report optimized buffer and salt compositions that promote the reverse transcriptase activity of Taq DNA polymerase, and thereby allow it to be used as the sole enzyme in TaqMan RT-qPCR reactions. The buffer was supplemented with 0.4 mM deoxyribonucleotides (dNTP), 402 nM each of forward and reverse PCR primer pairs, 102 nM of the TaqMan probe, and 2.5 units of Taq DNA polymerase from indicated commercial vendors.
    keywords: dna; polymerase; qpcr; rna; taq
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        item: #294 of 1349
          id: cord-102892-nt1zoktv
      author: Sweeney, Blake A.
       title: R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types
        date: 2020-09-11
       words: 3368
      flesch: 40
     summary: 150 Comprehensive 2D structure template library 151 We compiled a library of 3,632 templates aggregating RNA 2D structure layouts from different 152 sources (Table 1) While the majority of the 3,632 templates were integrated from the existing sources (Table 1) , 164 103 templates have been manually curated specifically for this project, as described below (also 165 see Supplementary Table 1) . As new 2D structure templates are 318 introduced, the pipeline can be extended to cover new RNA types, including structured viral 319 RNAs.
    keywords: diagrams; models; r2dt; rna; sequence; structure; templates
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        item: #295 of 1349
          id: cord-102898-eyyd7ent
      author: Rizvi, Vaseef A.
       title: Translation regulation of Japanese encephalitis virus revealed by ribosome profiling
        date: 2020-07-17
       words: 3049
      flesch: 36
     summary: Together, our study sheds light on distinct mechanisms that modulate JEV translation with likely consequences for viral pathogenesis. However, these sites do not represent commonly associated Studies on RNA viruses have suggested adaptations in codon usage of viral genes to the host translation [30] .
    keywords: codon; jev; protein; region; ribosome; site; start; translation; trna; usage; virus
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        item: #296 of 1349
          id: cord-102931-vxkbctiz
      author: Mao, Kai
       title: Induction of RNA interference by C. elegans mitochondrial dysfunction via the DRH-1/RIG-I homologue RNA helicase and the EOL-1/RNA decapping enzyme
        date: 2020-06-06
       words: 8685
      flesch: 37
     summary: If the unique strand transcriptional architecture of the Caenorhabditis mitochondrial genome is linked with production of dsRNA from the mitochondria, and if the release of mitochondrial RNA into the cytosol in mitochondrial mutants is the trigger for the formation of EOL-1 foci, we would expect a suppression of EOL-1 focus formation by shutting down mitochondrial RNA biogenesis. Therefore, the formation EOL-1 foci required the biogenesis of mitochondrial RNA.
    keywords: antiviral; caenorhabditis; drh-1; elegans; et al; figure; genes; hsp-6(mg585; interference; mutant; mutations; pathway; response; rnai; silencing; transgene
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        item: #297 of 1349
          id: cord-102934-7e2mqooe
      author: Dogra, N.
       title: exRNA Signatures in Extracellular Vesicles and their Tumor-Lineage from Prostate Cancer
        date: 2020-09-30
       words: 5830
      flesch: 43
     summary: We interrogated the key satellite alteration in tumor-derived EVs and found that resection of tumor prostate cancer tissue leads to differential expression of novel RNA biomarkers, ROS, P53 pathways, inflammatory/cytokines, major oncogenes, and tumor suppressors in the EV nanosatellites. In order to examine the overall genomic landscape of cancer RNA in the EVs, we leveraged three different data sets for generating a cumulative group of most significant gene-sets in cancer and their manifestation in the EVs.
    keywords: cancer; evs; fig; medrxiv; patients; preprint; prostate; rna; serum; tissue; tumor; urine
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        item: #298 of 1349
          id: cord-102967-dx0tg077
      author: Mahajan, Lakshmi S.
       title: Mapping RNA dependent RNA polymerase activity and immune gene expression using PRO-seq
        date: 2020-06-16
       words: 2855
      flesch: 51
     summary: While PRO-seq is highly specific for nascent, biotin-labeled RNAs, it is also possible that DAV PRO-seq reads may have derived from the mature DAV RNA genome that contaminated the sample in small frequencies. Precision Run-On sequencing (PRO-seq) is a nuclear run-on based nascent RNA sequencing method, widely used to map eukaryotic RNA polymerases by using labeled nucleotide analogues.
    keywords: dav; genome; pro; rdrp; reads; rna; seq
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        item: #299 of 1349
          id: cord-102968-mhawyect
      author: Desirò, Daniel
       title: SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structural RNAs
        date: 2018-09-23
       words: 4046
      flesch: 50
     summary: For example, long-range RNA-RNA interactions (LRIs) play an important role in the life cycle of RNA viruses. Conclusion We applied our tool on two experimentally validated influenza A virus and hepatitis C virus interactions and we were able to predict potential double mutants for in vitro validation experiments.
    keywords: hepatitis; interactions; range; rna; sequence; sim; tool; virus
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        item: #300 of 1349
          id: cord-103015-3dxwbmd2
      author: Shengjuler, Djoshkun
       title: The RNA-binding site of poliovirus 3C protein doubles as a phosphoinositide-binding domain
        date: 2017-08-04
       words: 7102
      flesch: 59
     summary: The outcome is a new structural class of PIP-367 binding proteins with the capacity for multivalent binding to any mono-, bis-or tris-phosphorylated PIP, but with a unique conformational state determined by the nature of the 369 bound PIP. This approach was validated by using the PLC-δ1 PH domain 115 as a positive control, which showed PI(4,5)P2 binding specificity, as expected ( Figure S1 )
    keywords: binding; et al; figure; membrane; pi(4,5)p2; pi4p; pip; protein; residues; rna; structure
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        item: #301 of 1349
          id: cord-103163-0rreoh4o
      author: Smith, Sydni Caet
       title: Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage
        date: 2020-10-22
       words: 8989
      flesch: 40
     summary: The rsT3D I S4 RNA profiles were more consistent among lineages than those of the M1 and L1 segments and were similar to those of rsT1L S4, with non-canonical RNA segments just slightly larger than the full-length segment and at ~0.15 kb detected in several passages (Fig. 4) . Non-canonical reovirus segments feature large deletions.
    keywords: cells; dvgs; fig; length; passage; products; recombination; reovirus; rna; rotavirus; rst1l; rst3d; segments; sequence; sites; viruses
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        item: #302 of 1349
          id: cord-103377-j1mmx7k7
      author: Karasik, Agnes
       title: Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences
        date: 2020-09-11
       words: 11800
      flesch: 49
     summary: However, given the short time frame of RNase L activation, detection of cryptic peptides in RNase L activated cells has proven to be difficult (data not shown). We did not observe this trend in RNase L KO cells, showing that RNase L activation is required for the process.
    keywords: activation; analysis; cells; cleavage; codons; data; density; et al; figure; footprints; fragments; frame; mrna; orf; ribosome; rnase; rnase l; start; translation
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        item: #303 of 1349
          id: cord-103430-x6zzuu7v
      author: Contu, Lara
       title: Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay
        date: 2020-10-12
       words: 8307
      flesch: 46
     summary: Among the many identified cellular interactors of SFV proteins, the enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD) was striking, reflecting the virus’ hijacking of the translation machinery and indicating viral countermeasures for escaping NMD by inhibiting NMD at later time points during the infectious cycle. b, Flowchart outlining the experimental approach to transiently express N-7 terminally FLAG-tagged (yellow rectangle) SFV proteins in mammalian cells in order to construct a SFV-host protein-protein 8 interactome.
    keywords: capsid; cells; figure; host; infection; interactors; nsp2; nsp3; proteins; rna; sfv; translation; viral; virus
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        item: #304 of 1349
          id: cord-103511-31njndob
      author: Broggi, Achille
       title: Type III interferons disrupt the lung epithelial barrier upon viral recognition
        date: 2020-05-05
       words: 3898
      flesch: 50
     summary: Although different viruses vary in their virulence and pathogenic potential, 235 the most severe cases of lung RNA viral infections share similar features that suggest an immune 236 pathological etiology. The EpCAMcells were sorted for immune cells as follows: aMac were gated as CD45 + Ly6g -CD11c hi Siglec-F + , monocytes and monocyte-derived cells (Mo) were gated as CD45 + Ly6g -Siglec-F -Ly6C
    keywords: cells; fig; ifn; infections; lung; mice; poly; production; rna
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        item: #305 of 1349
          id: cord-103638-n5kpvsvg
      author: Nguyen, Long T.
       title: Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection
        date: 2020-04-14
       words: 5390
      flesch: 48
     summary: key: cord-103638-n5kpvsvg authors: Nguyen, Long T.; Smith, Brianna M.; Jain, Piyush K. title: Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection date: 2020-04-14 journal: bioRxiv DOI: 10.1101/2020.04.13.036079 sha: doc_id: 103638 cord_uid: n5kpvsvg The CRISPR/Cas12a RNA-guided complexes have a tremendous potential for nucleic acid detection due to its ability to indiscriminately cleave ssDNA once bound to a target DNA. In order to measure the collateral or trans-cleavage activity of Cas12a, we employed a FRET-based reporter used in DETECTR, 1 composed of a fluorophore (FAM) and a quencher (3IABkFQ) connected by a 5-nucleotide sequence (TTATT), which displays increased fluorescence upon cleavage.
    keywords: activity; cleavage; crrna; detection; dna; fig; lbcas12a; supplementary; trans
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        item: #306 of 1349
          id: cord-103735-nil1vv6h
      author: Alfano, Niccolo
       title: Non-invasive surveys of mammalian viruses using environmental DNA
        date: 2020-03-29
       words: 5837
      flesch: 49
     summary: Viral contigs were confirmed by PCR and Sanger sequencing for samples L7, L17, L25 and L37 (Suppl. Of the 11 water filtrate samples tested, two samples from Mongolia (WM3 and WM20) (18.2%) had viral contigs with 100% identity to the Equid herpesvirus 1 and 3 (EHV-1 and EHV-3).
    keywords: capture; contigs; dna; fig; identity; leeches; pcr; reads; rna; samples; sediment; sequences; suppl; viruses; water; wildlife
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        item: #307 of 1349
          id: cord-103739-mmkrwj8t
      author: Snijder, Eric J.
       title: A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis
        date: 2020-03-24
       words: 3813
      flesch: 35
     summary: However, it is not clear that DMVs always play the primary role 421 in virus replication that we demonstrate here for CoV. For picornaviruses, for example, virus- were freeze-substituted in a Leica AFS2 system with 0.1% (wt/vol) uranyl acetate as 576 previously described [71] , with the only modification that acetone was replaced by ethanol 577 from the last washing step before Lowycril infiltration onwards. The comprehensive analysis presented here demonstrates that viruses across different CoV 371 genera induce essentially the same type of membrane structures.
    keywords: autoradiography; coronavirus; cov; dmss; dmvs; membrane; replication; rna; virus
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        item: #308 of 1349
          id: cord-103787-qhftb6d7
      author: Garcia, Elizabeth P.
       title: Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics
        date: 2005-10-31
       words: 7379
      flesch: 42
     summary: PCR primers are designed for each target so that the amplicon length serves as a unique identifier for each particular target. Second, because detection does not require probe hydrolysis, all restrictions related to the probe design (probe length and composition, distance to PCR primers) do not influence primer selection.
    keywords: amplification; analysis; expression; gene; multiplex; pcr; primers; reaction; rna; samples; sars; sequence; star; time
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        item: #309 of 1349
          id: cord-103807-x4hrwhkz
      author: Prokop, J. W.
       title: Viral Induced Genetics Revealed by Multi-Dimensional Precision Medicine Transcriptional Workflow
        date: 2020-04-06
       words: 6849
      flesch: 43
     summary: Using a combination of PAXgene tubes with ribosomal reduced RNAseq, we present here a dissection of both cellular and acellular RNA signatures of PICU MODS patients, suggesting utility for transcriptomics in precision medicine. The definition for MODS was taken from the original definition (56) in which among other criteria, MODS patients were clinically identified with two or more organs in failure.
    keywords: april; day; day0; elevation; fig; funder; genes; license; medrxiv; mods; organ; patient; perpetuity; preprint; rnaseq; samples; version
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        item: #310 of 1349
          id: cord-103823-3rchp9yy
      author: Taufer, Michela
       title: RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology
        date: 2008-11-30
       words: 10174
      flesch: 47
     summary: Mechanisms and enzymes involved in SARS coronavirus genome expression Stem-loop structures in prokaryotic genomes An atypical RNA pseudoknot simulator and an upstream attenuation signal for À1 ribosomal frameshifting of SARS coronavirus A pseudoknot in the 3 0 non-core region of the glmS ribozyme enhances self-cleavage activity Simultaneous solution of the RNA folding, alignment, and protosequence problems Computer prediction of RNA structure Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide A dynamic programming algorithm for RNA structure prediction including pseudoknots Design, implementation, and evaluation of a practical pseudoknot folding algorithm based on thermodynamics ILM: a web server for predicting RNA secondary structures with pseudoknots HotKnots: heuristic prediction of RNA secondary structures including pseudoknots PseudoBase: a database with RNA pseudoknots Palindromes in SARS and other coronaviruses CompPknots: a framework for parallel prediction and comparison of RNA secondary structures with pseudoknots An algorithm for comparing multiple RNA secondary structures Comparing multiple RNA secondary structures using tree comparisons Predictor@Home: a protein structure prediction supercomputer based on global computing Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide distributed computing Vienna RNA secondary structure server RNA secondary structure prediction using stochastic context-free grammars and evolutionary history CONTRAfold: RNA secondary structure prediction without physics-based models Exploring the space of RNA secondary structure motifs using suffix arrays Identification of consensus RNA secondary structures using suffix arrays Comparison of the predicted and observed secondary structure of T4 phage lysozyme Depth annotation of RNA folds for secondary structure motif search RNA motif search using the structure to string str 2 method Nonrandom clusters of palindromes in herpesvirus genomes NuPack: a software suite for the analysis and design of nucleic acids Distributed computing in practice: the Condor experience BOINC: a system for public-resource computing and storage PseudoViewer2: visualization of RNA pseudoknots of any type Identification of common molecular subsequences A general method applicable to the search for similarities in the amino acid sequences of two proteins An approach to selecting putative RNA motifs using MDL principle Nodamura virus from Japan: a new and unusual arbovirus resistant to diethyl ether and chloroform A small RNA virus with a divided genome from Heteronychus arator (F.) Previously, grid technology was applied successfully to protein structure prediction [17, 18] and similar achievements are expected for RNA secondary structure prediction.
    keywords: algorithm; computing; fig; motifs; nucleotides; pknots; prediction; pseudoknots; replication; rna; rnavlab; segments; sequences; structures; virus
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        item: #311 of 1349
          id: cord-103853-ar09nzmw
      author: Wayment-Steele, Hannah K.
       title: RNA secondary structure packages ranked and improved by high-throughput experiments
        date: 2020-05-31
       words: 4331
      flesch: 35
     summary: key: cord-103853-ar09nzmw authors: Wayment-Steele, Hannah K.; Kladwang, Wipapat; Das, Rhiju title: RNA secondary structure packages ranked and improved by high-throughput experiments date: 2020-05-31 journal: bioRxiv DOI: 10.1101/2020.05.29.124511 sha: doc_id: 103853 cord_uid: ar09nzmw The computer-aided study and design of RNA molecules is increasingly prevalent across a range of disciplines, yet little is known about the accuracy of commonly used structure prediction packages in real-world tasks. As more sources of structural data continue to be made available in higher quantity, resolution, and scope, the EternaBench and EternaFold frameworks will allow for the usage of these datasets in continually assessing and improving RNA structure prediction.
    keywords: chemical; contrafold; data; datasets; figure; mapping; packages; prediction; rna; structure
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        item: #312 of 1349
          id: cord-103899-6tqm99g1
      author: Mirzaei, Rasoul
       title: The emerging role of microRNAs in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection
        date: 2020-11-13
       words: 9770
      flesch: 42
     summary: [121] Global Trends in Epidemiology of Coronavirus Disease 2019 (COVID-19) Virus against virus: a potential treatment for 2019-nCov (SARS-CoV-2) and other RNA viruses A realistic two-strain model for MERS-CoV infection uncovers the high risk for epidemic propagation Development of genetic diagnostic methods for novel coronavirus 2019 (nCoV-2019) in Japan How miRNAs can protect humans from coronaviruses COVID-19 Overview of the current promising approaches for the development of an effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine Clinical features of patients infected with 2019 novel coronavirus in Coronavirus disease 2019 (COVID-19): Immunological approaches and emerging pharmacologic treatments A novel coronavirus outbreak of global health concern Bacterial co-infections with SARS-CoV-2 COVID-19, SARS and MERS: are they closely related? Coronavirus disease (COVID-19) pandemic Exosome and exosomal microRNA: trafficking, sorting, and function Role of microRNAs in Staphylococcus aureus infection: Potential biomarkers and mechanism Role of microRNAs in the immune system, inflammation and cancer MicroRNAs and the immune response to respiratory virus infections Host Immune Response and Immunobiology of Human SARS-CoV-2 Infection The human immune system against Staphylococcus epidermidis Prevalence of atlE, ica, mecA, and mupA Genes in Staphylococcus epidermidis Isolates T cell-mediated immune response to respiratory coronaviruses Structural, glycosylation and antigenic variation between 2019 novel coronavirus (2019-nCoV) and SARS coronavirus (SARS-CoV) T cell responses to whole SARS coronavirus in humans Profile of specific antibodies to the SARS-associated coronavirus Recent Advances in the Vaccine Development Against Middle East Respiratory Syndrome-Coronavirus Vaccine-elicited CD8+ T cells protect against respiratory syncytial virus strain A2-line19F-induced pathogenesis in BALB/c mice Interferon interplay helps tissue cells to cope with SARS-coronavirus infection CD8+ T cells and macrophages regulate pathogenesis in a mouse model of Middle East respiratory syndrome Dysregulation of immune response in patients with COVID-19 in Immunopathology of SARS-CoV-2 infection: immune cells and mediators, prognostic factors, and immune-therapeutic implications A contemporary review on pathogenesis and immunity of COVID-19 infection In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Elevated exhaustion levels and reduced functional diversity of T cells in peripheral blood may predict severe progression in COVID-19 patients Pathological findings of COVID-19 associated with acute respiratory distress syndrome Cytokine storm induced by SARS-CoV-2 Interferon-mediated immunopathological events are associated with atypical innate and adaptive immune responses in patients with severe acute respiratory syndrome COVID-19: consider cytokine storm syndromes and immunosuppression Pattern recognition receptors and inflammation Activation of airway epithelial cells by toll-like receptor agonists NF-κB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses Advances in microRNAs: implications for immunity and inflammatory diseases Expression and function of micro RNAs in immune cells during normal or disease state Integrating microRNAs into a system biology approach to acute lung injury miR-146a is critical for endotoxin-induced tolerance , regulates murine macrophage inflammatory responses Co-ordinated role of TLR3, RIG-I and MDA5 in the innate response to rhinovirus in bronchial epithelium Retinoic acidinducible gene I-inducible miR-23b inhibits infections by minor group rhinoviruses through downregulation of the very low density lipoprotein receptor MicroRNAs: small RNAs with big effects MicroRNAs and immunity: novel players in the regulation of normal immune function and inflammation, Seminars in cancer biology Skare, miR-181a is an intrinsic modulator of T cell sensitivity and selection Expression profiling of human immune cell subsets identifies miRNA-mRNA regulatory relationships correlated with cell type specific expression An emerging player in the adaptive immune response: microRNA-146a is a modulator of IL-2 expression and activation-induced cell death in T lymphocytes MicroRNA miR-155 affects antiviral effector and effector Memory CD8 T cell differentiation Micro-RNA 155 is required for optimal CD8+ T cell responses to acute viral and intracellular bacterial challenges Rosas-Taraco, microRNAs in viral acute respiratory infections: immune regulation, biomarkers, therapy, and vaccines A recently identified rhinovirus genotype is associated with severe respiratory-tract infection in children in Germany Structure of a human common cold virus and functional relationship to other picornaviruses Rhinovirus and dsRNA induce RIG-I-like receptors and expression of interferon β
    keywords: cells; coronavirus; cov-2; covid-19; expression; host; human; infection; mers; micrornas; mirnas; proteins; replication; responses; rsv; sars; study; target; virus
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        item: #313 of 1349
          id: cord-103914-ppgx7mci
      author: Maughan, Elizabeth F.
       title: Cell-intrinsic differences between human airway epithelial cells from children and adults
        date: 2020-04-20
       words: 8208
      flesch: 38
     summary: The differentiated cell types in this slow-turnover tissue are replenished by airway basal cells, which act as multipotent progenitors (Rock et al., 2010; Teixeira et al., 2013) . However, the majority of differentially expressed genes do not have previously described roles in airway basal cells.
    keywords: adult; age; airway; analysis; basal; cells; children; culture; differences; epithelium; et al; expression; figure; genes; human; lung; medium; paediatric; rna; samples
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        item: #314 of 1349
          id: cord-103925-i73ymrov
      author: Hill, Chris H.
       title: Structural and molecular basis for protein-stimulated ribosomal frameshifting in Theiler’s murine encephalomyelitis virus
        date: 2020-08-11
       words: 11567
      flesch: 45
     summary: Cardioviruses are genetically diverse and cause common enteric infections in South Asian children Phylogenetic analysis of the species Theilovirus: emerging murine and human pathogens Facets of Theiler's Murine Encephalomyelitis Virus-Induced Diseases: An Update A detailed kinetic analysis of the in vitro synthesis and processing of encephalomyocarditis virus products Proteolytic processing of picornaviral polyprotein Cell-specific proteins regulate viral RNA translation and virus-induced disease However, 2A protein sequences are highly divergent within cardioviruses, and the TMEV protein shares only ~ 27 % pairwise amino acid sequence identity with its EMCV orthologue.
    keywords: analysis; binding; cells; data; emcv; figure; frameshifting; genome; loop; prf; protein; reads; ribosomal; ribosome; rna; sequence; site; tmev; translation; virus
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        item: #315 of 1349
          id: cord-104162-fe51v2pt
      author: Zhang, Chiyu
       title: Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy
        date: 2020-11-02
       words: 3746
      flesch: 42
     summary: [22] were primarily concerned with the statistical significance of RNA folding, rather than with distinguishing the relative contributions of base composition and base order. Just as a local arrangement of words conveys specific meaning to a text, so base order better reflects local evolutionary pressures.
    keywords: base; composition; folding; genome; order; regions; rna; sars; structure
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        item: #316 of 1349
          id: cord-104186-fyw1xfgi
      author: Cui, Y
       title: Mof4-1 is an allele of the UPF1/IFS2 gene which affects both mRNA turnover and -1 ribosomal frameshifting efficiency.
        date: 1996-10-15
       words: 7868
      flesch: 49
     summary: key: cord-104186-fyw1xfgi authors: Cui, Y; Dinman, J D; Peltz, S W title: Mof4-1 is an allele of the UPF1/IFS2 gene which affects both mRNA turnover and -1 ribosomal frameshifting efficiency. The 1.9% of -1 ribosomal frameshifting efficiency determines the stoichiometry of Gag to Gag-pol protein.
    keywords: allele; cells; figure; frameshifting; gene; mof4; mrna; nonsense; ribosomal; strain
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        item: #317 of 1349
          id: cord-122092-gdyt02er
      author: Fatehi, Farzad
       title: Comparing antiviral strategies against COVID-19 via multi-scale within host modelling
        date: 2020-10-18
       words: 10084
      flesch: 51
     summary: medRxiv The architecture of SARS-CoV-2 transcriptome Mathematical modeling of triphasic viral dynamics in patients with HBeAg-positive chronic hepatitis B showing response to 24-week clevudine therapy Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): the epidemic and the challenges The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported confirmed cases: estimation and application Droplet expulsion from the respiratory tract In silico single cell dynamics of hepatitis B virus infection and clearance Viral and cellular mRNA translation in coronavirusinfected cells Modeling within-host dynamics of influenza virus infection including immune responses Comparative study of the effects of heptameric slippery site composition on -1 frameshifting among different eukaryotic systems A contemporary view of coronavirus transcription Kinetics of SARS-CoV-2 specific IgM and IgG responses in COVID-19 patients How can viral dynamics models inform endpoint measures in clinical trials of therapies for acute viral infections Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys Fields Virology Exhaled droplets due to talking and coughing Epidemiologic features and clinical course of patients infected with SARS-CoV-2 in Singapore Binding mechanism of remdesivir to SARS-CoV-2 RNA dependent RNA polymerase SARS-CoV-2 viral load in upper respiratory specimens of infected patients Exact stochastic simulation of coupled chemical reactions Coronaviruses: an overview of their replication and pathogenesis Control of translation initiation: a model-based analysis from limited experimental data Viral and cellular mRNA translation in coronavirusinfected cells A structural view of SARS-CoV-2 RNA replication machinery: RNA synthesis, proofreading and final capping The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling Emerging coronaviruses: genome structure, replication, and pathogenesis Dynamics of coronavirus replication-transcription complexes Our stochastic model of viral infection dynamics within an infected host cell tracks the different viral and cellular components required for formation of progeny virus.
    keywords: cells; fig; infection; load; model; rate; rna; rtc; sars; therapy; time; treatment
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        item: #318 of 1349
          id: cord-146406-85usg3uh
      author: Morelli, Marco J.
       title: Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing
        date: 2011-01-27
       words: 4376
      flesch: 39
     summary: Curr Top Nucleotide 612 sequence heterogeneity of an RNA phage population Rates of spontaneous mutation among RNA viruses Mutation rates among RNA viruses Infidelity of SARS--CoV Nsp14--exonuclease mutant virus 620 replication is revealed by complete genome sequencing Viral population 628 estimation using pyrosequencing Statistical distributions The quasispecies nature and 632 biological implications of the hepatitis C virus The structure and function of a foot--and--mouth disease virus--636 oligosaccharide receptor complex DNA bar coding and pyrosequencing to identify rare HIV 641 drug resistance mutations Is the quasispecies concept relevant to 646 RNA viruses Statistical analysis of the DNA 648 sequence of human chromosome 22 Efficient 652 infection of cells in culture by type O foot--and--mouth disease virus requires 653 binding to cell surface heparan sulfate Low--abundance HIV drug--659 resistant viral variants in treatment--experienced persons correlate with 660 historical antiretroviral use Sequence space coverage, 662 entropy of genomes and the potential to detect non--human DNA in human 663 samples From RNA to 665 quasispecies: a DNA polymerase with proofreading activity is highly 666 recommended for accurate assessment of viral diversity Ultra--deep pyrosequencing of 671 hepatitis B virus quasispecies from nucleoside and nucleotide reverse--672 transcriptase inhibitor (NRTI)--treated patients and NRTI--naive patients Cross--talk between orientation--dependent 676 recognition determinants of a complex control RNA element, the enterovirus 677 oriR Simple methods for estimating the numbers 679 of synonymous and nonsynonymous nucleotide substitutions Increased fidelity reduces poliovirus 682 fitness and virulence under selective pressure in mice Massively 685 parallel pyrosequencing highlights minority variants in the HIV--1 env 686 quasispecies deriving from lymphomonocyte sub--populations Tissue culture adaptation of foot--and--mouth disease virus 690 selects viruses that bind to heparin and are attenuated in cattle Deciphering human 696 immunodeficiency virus type 1 transmission and early envelope 697 diversification by single--genome amplification and sequencing Spontaneous mutation rate 700 of measles virus: direct estimation based on mutations conferring 701 monoclonal antibody resistance The 3' end 703 of the foot--and--mouth disease virus genome establishes two distinct long--704 range RNA--RNA interactions with the 5' end region Low--abundance 710 drug--resistant viral variants in chronically HIV--infected, antiretroviral 711 treatment--naive patients significantly impact treatment outcomes Use of massively parallel ultradeep pyrosequencing to 715 characterize the genetic diversity of hepatitis B virus in drug--resistant and 716 drug--naive patients and to detect minor variants in reverse transcriptase and 717 hepatitis B S antigen The relationship between mutation frequency and replication strategy 720 in positive--sense single--stranded RNA viruses 724 Quantitative deep sequencing reveals dynamic HIV--1 escape and large 725 population shifts during CCR5 antagonist therapy in vivo 731 Characterization of mutation spectra with ultra--deep pyrosequencing: 732 application to HIV--1 drug resistance key: cord-146406-85usg3uh authors: Morelli, Marco J.; Wright, Caroline F.; Th'ebaud, Gael; Knowles, Nick J.; Herzyk, Pawel; Paton, David J.; Haydon, Daniel T.; King, Donald P. title: Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing date: 2011-01-27 journal: nan DOI: nan sha: doc_id: 146406 cord_uid: 85usg3uh The sequence diversity of viral populations within individual hosts is the starting material for selection and subsequent evolution of RNA viruses such as foot-and-mouth disease virus (FMDV).
    keywords: foot; genome; inoculum; number; reads; rna; sequencing; sites; virus
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        item: #319 of 1349
          id: cord-184744-oyc2djxk
      author: Parvez, Md Sorwer Alam
       title: Virtual Screening of Plant Metabolites against Main protease, RNA-dependent RNA polymerase and Spike protein of SARS-CoV-2: Therapeutics option of COVID-19
        date: 2020-05-22
       words: 3659
      flesch: 41
     summary: Drug discoveries & therapeutics Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases Quantitative structure-activity relationship and molecular docking revealed a potency of anti-hepatitis C virus drugs against human corona viruses From SARS to MERS, thrusting coronaviruses into the spotlight Homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross-species transmission from snake to human Structure of SARS coronavirus spike receptor-binding domain complexed with receptor Substrate specificity profiling and identification of a new class of inhibitor for the major protease of the SARS coronavirus Design of wide-spectrum inhibitors targeting coronavirus main proteases Antiviral drugs specific for coronaviruses in preclinical development. Hence, extensive in silico studies were performed to identify potential drug candidates, for example, Prulifloxacin, Bictegravir, Nelfinavir, and Tegobuvi, were identified as repurposing candidates against COVID-19 by looking for drugs with high binding capacity with SARS-CoV main protease [28] .
    keywords: cov-2; covid-19; drug; inhibitors; kcal; protease; protein; rna; sars; spike
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        item: #320 of 1349
          id: cord-243806-26n22jbx
      author: Vandelli, Andrea
       title: Structural analysis of SARS-CoV-2 and prediction of the human interactome
        date: 2020-03-30
       words: 5262
      flesch: 39
     summary: A significant overlap exists with the list of protein interactions reported by Gordon et al. 58 , and among the candidate partners we identified AKAP8L, involved as a DEAD/H-box RNA helicase binding protein involved in HIV infection 59 . in StatPearls Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor Furin cleavage of the SARS coronavirus spike glycoprotein enhances cell-cell fusion but does not affect virion entry Isolation and Characterization of 2019-nCoV-like Coronavirus from Malayan Pangolins Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV Identification of sialic acid-binding function for the Middle East respiratory syndrome coronavirus spike glycoprotein The Structure and Functions of Coronavirus Genomic 3' and 5' Ends A high-throughput approach to profile RNA structure A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs RNA structure drives interaction with proteins An Integrative Study of Protein-RNA Condensates Identifies Scaffolding RNAs and Reveals Players in Fragile X-Associated Tremor/Ataxia Syndrome Phase separation drives X-chromosome inactivation: a hypothesis Identification of a Coronavirus Transcription Enhancer catRAPID omics: a web server for large-scale prediction of protein-RNA interactions Quantitative predictions of protein interactions with long noncoding RNAs Predicting protein associations with long noncoding RNAs RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data Cloaked similarity between HIV-1 and SARS-CoV suggests an anti-SARS strategy Inhibition of furin-mediated cleavage activation of HIV-1 glycoprotein gp160 Differential downregulation of ACE2 by the spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus NL63 Conserved structural RNA domains in regions coding for cleavage site motifs in hemagglutinin genes of influenza viruses Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China ViennaRNA Package 2.0 The EMBL-EBI search and sequence analysis tools APIs in 2019 RNA-Seq methods for transcriptome analysis The proximal origin of SARS-CoV-2 A pneumonia outbreak associated with a new coronavirus of probable bat origin T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension Distinct Roles for Sialoside and Protein Receptors in Coronavirus Infection Silico evidence for two receptors based strategy of SARS-CoV-2 Host cell proteins interacting with the 3' end of TGEV coronavirus genome influence virus replication Structural determinants and mechanism of HIV-1 genome packaging An Overview of Their Replication and Pathogenesis Protein aggregation, structural disorder and RNA-binding ability: a new approach for physico-chemical and gene ontology classification of multiple datasets UniProt: a worldwide hub of protein knowledge SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems omiXcore: a web server for prediction of protein interactions with large RNA Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2 RNA-RNA and RNAprotein interactions in coronavirus replication and transcription Insights into RNA biology from an atlas of mammalian mRNA-binding proteins HIV Gag polyprotein: processing and early viral particle assembly The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function Viral interactions with the Notch pathway What retroviruses teach us about the involvement of c-Myc in leukemias and lymphomas The architecture of SARS-CoV-2 transcriptome. bioRxiv
    keywords: binding; coronavirus; cov-2; fig; host; human; interactions; protein; region; rna; sars; spike; structure
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        item: #321 of 1349
          id: cord-252268-o63ep08b
      author: Carolan, Louise A.
       title: TaqMan real time RT-PCR assays for detecting ferret innate and adaptive immune responses
        date: 2014-09-01
       words: 6668
      flesch: 40
     summary: We also assessed TNF␣ expression using previously published TaqMan primers and probe (Nakata et al., 2009 ) and SYBR Green primers Rowe et al., 2010) with our samples and the profiles were consistent with those obtained with the TaqMan assay designed in this study (data not shown). The gene stability of housekeeping genes was calculated using geNorm in qbase+ Version 2.5 (Biogazelle) (Vandesompele et al., 2002) .
    keywords: cells; cytokine; efficiency; et al; expression; ferret; fig; genes; influenza; pcr; rna; taqman; time; virus
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        item: #322 of 1349
          id: cord-252433-0e9lonq4
      author: Cullen, Bryan R.
       title: Viral RNAs: Lessons from the Enemy
        date: 2009-02-20
       words: 3564
      flesch: 48
     summary: Although IRES elements were first discovered in RNA viruses, a subset of cellular mRNAs are now known to also contain IRESs. The RRE contains a single, high-affinity Rev-binding site and also functions as a scaffold for the multimerization of Rev on viral mRNAs.
    keywords: cells; cellular; mrnas; rev; translation; viruses
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        item: #323 of 1349
          id: cord-252466-usrpodjx
      author: Yun, Nadezhda E.
       title: Pathogenesis of Lassa Fever
        date: 2012-10-09
       words: 5673
      flesch: 36
     summary: Selection of optimally effective plasma for treatment by passive immunization Detection of Lassa virus antinucleoprotein immunoglobulin G (IgG) and IgM antibodies by a simple recombinant immunoblot assay for field use Baculovirus expression of the glycoprotein gene of Lassa virus and characterization of the recombinant protein Identification of Lassa fever virus infection with recombinant nucleocapsid protein antigen Antibodies to Lassa virus Z protein and nucleoprotein co-occur in human sera from Lassa fever endemic regions Antigenic relatedness between arenaviruses defined at the epitope level by monoclonal antibodies Epitope mapping of the Lassa virus nucleoprotein using monoclonal anti-nucleocapsid antibodies Characteristics of monoclonal antibodies against Lassa virus Early and strong immune responses are associated with control of viral replication and recovery in Lassa virus-infected cynomolgus monkeys Characterization of human CD4+ T-cell clones recognizing conserved and variable epitopes of the Lassa virus nucleoprotein Old and New World arenaviruses share a highly conserved epitope in the fusion domain of the glycoprotein 2, which is recognized by Lassa virusspecific human CD4+ T-cell clones Lassa virus lethality for inbred mice Biology and pathogenesis of lymphocytic choriomeningitis virus infection Pathogenesis of Lassa virus infection in guinea pigs Endemic Lassa fever in Liberia. A study of 23 hospital cases An outbreak of Lassa fever on the Jos Plateau Surveillance of Lassa fever in missionaries stationed in West Africa Imported Lassa fever in Germany: molecular characterization of a new Lassa virus strain Circumstances and Consequences of Cross-Species Transmission; Childs Detection of Lassa virus Lassa Fever Fact Sheet Casecontrol study of Mastomys natalensis and humans in Lassa virus-infected households in Sierra Leone Review of cases of nosocomial Lassa fever in Nigeria: the high price of poor medical practice No evidence for increased risk of Lassa fever infection in hospital staff Effect of environmental factors on aerosolinduced lassa virus infection Experimental studies of arenaviral hemorrhagic fevers Lassa virus isolation from Mastomys natalensis rodents during an epidemic in Sierra Leone Comparative pathology of Lassa virus infection in monkeys, guinea pigs, and Mastomys natalensis A case-control study of the clinical diagnosis and course of Lassa fever Pathologic and virologic study of fatal Lassa fever in man Acute sensorineural deafness in Lassa fever Clinical virology of Lassa fever in hospitalized patients Early diagnosis of Lassa fever by reverse transcription-PCR Evaluation of the polymerase chain reaction for diagnosis of Lassa virus infection T celldependence of Lassa fever pathogenesis The pathology of Lassa fever: A tribute to the late Dr Lassa virus hepatitis: a study of fatal Lassa fever in humans The pathology of human Lassa fever Hematologic dysfunction in Lassa fever Monitoring of clinical and laboratory data in two cases of imported Lassa fever Low levels of interleukin-8 and interferon-inducible protein-10 in serum are associated with fatal infections in acute Lassa fever Lassa and Mopeia virus replication in human monocytes/macrophages and in endothelial cells: Different effects on IL-8 and TNF-α gene expression Cutting edge: impairment of dendritic cells and adaptive immunity by Ebola and Lassa viruses Lassa virus infection of human dendritic cells and macrophages is productive but fails to activate cells Human dendritic cells infected with the nonpathogenic Mopeia virus induce stronger T-cell responses than those infected with Lassa virus Endemic Lassa fever in Liberia.
    keywords: animals; cells; disease; fever; human; infection; lassa; lasv; necrosis; patients; protein; replication; rna; virus
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        item: #324 of 1349
          id: cord-252485-cxi3cr15
      author: Yoshida, Asuka
       title: IFN-β-inducing, unusual viral RNA species produced by paramyxovirus infection accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner
        date: 2015-08-04
       words: 7105
      flesch: 38
     summary: The SG-like structures have been suggested to serve as the sites at which the RLRs encounter viral RNA and subsequently activate the IFN signaling pathways in infections by RNA viruses (Onomoto et al., 2012; Yoo et al., 2014) . In spite of the large number of studies conducted in this field, it remains unknown what kinds of viral RNA species are recognized by RLRs and where the sites of recognition are in real infections by RNA viruses.
    keywords: cells; et al; figure; granules; ifn; protein; rig; rna; sev; virus; viruses
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        item: #325 of 1349
          id: cord-252871-qfrpuy3t
      author: Nasir, Arshan
       title: Investigating the Concept and Origin of Viruses
        date: 2020-11-03
       words: 5157
      flesch: 39
     summary: First, the subset of virus genes for which reliable homologs can be found is extremely small [48] . We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution.
    keywords: cells; evolution; genes; genomes; origin; protein; rna; virion; viruses
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        item: #326 of 1349
          id: cord-253024-b393ea2u
      author: Fu, Kaisong
       title: Evidence for variable rates of recombination in the MHV genome
        date: 1992-07-31
       words: 8467
      flesch: 40
     summary: To assist in precisely defining the location of these mutations and examining the mechanism for MHV RNA recombination within the S glycoprotein gene, a panel of revertants were obtained from six of the RNA+ mutants (Table 1) . If MHV RNA recombination is mediated by freely segregating RNA segments that are generated by transcriptional pausing during RNA synthesis, preferred sites of recombination may also exist in AU-rich regions and/or in regions of secondary structure in the MHV genome (Baric et al., 1987) .
    keywords: a/.; coronavirus; et al; frequency; gene; genome; glycoprotein; group; mhv; mutants; polymerase; recombination; rna; virus; viruses
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        item: #327 of 1349
          id: cord-253115-ekgdsv4f
      author: Mehta, Meenu
       title: Oligonucleotide therapy: An emerging focus area for drug delivery in chronic inflammatory respiratory diseases
        date: 2019-08-01
       words: 7331
      flesch: 32
     summary: III: effects of chitosan-glutamate and carbomer on epithelial tight junctions in vitro Respiratory syncytial virus infection in Fischer 344 rats is attenuated by short interfering RNA against the RSV-NS1 gene Inhibition of respiratory syncytial virus infection with intranasal siRNA nanoparticles targeting the viral NS1 gene Pulmonary delivery of chitosan-DNA nanoparticles enhances the immunogenicity of a DNA vaccine encoding HLA-A*0201-restricted T-cell epitopes of Mycobacterium tuberculosis Naked siLNA-mediated gene silencing of lung bronchoepithelium EGFP expression after intravenous administration Chitosan Related Compositions and Methods for Delivery of Nucleic Acids and Oligonucleotides into a Cell Nasal delivery of chitosan-DNA plasmid expressing epitopes of respiratory syncytial virus (RSV) induces protective CTL responses in BALB/c mice Intranasal IFNgamma gene transfer protects BALB/c mice against respiratory syncytial virus infection Chitosan-DNA nanoparticles as gene carriers: synthesis, characterization and transfection efficiency Dendritic cell targeted chitosan nanoparticles for nasal DNA immunization against SARS CoV nucleocapsid protein Biodegradable polymeric nanocarriers for pulmonary drug delivery Poly(lactic acid)-poly(ethylene glycol) nanoparticles as new carriers for the delivery of plasmid DNA Design and gene delivery activity of modified polyethylenimines Characterization of commercially available and synthesized polyethylenimines for gene delivery PLGA-PEI nanoparticles for gene delivery to pulmonary epithelium Poly(amidoamine) dendrimer nanocarriers and their aerosol formulations for siRNA delivery to the lung epithelium Application of dendrimers for the treatment of infectious diseases Dendrimer nanocarriers for transport modulation across models of the pulmonary epithelium Synthesis and influenza virus inhibitory activities of carbosilane dendrimers peripherally functionalized with hemagglutinin-binding Peptide Dendrimer-inspired nanomaterials for the in vivo delivery of siRNA to lung vasculature Nanocarriers as pulmonary drug delivery systems to treat and to diagnose respiratory and non respiratory diseases In vitro/in vivo investigation on the potential of Pluronic(R) mixed micelles for pulmonary drug delivery Microencapsulated chitosan nanoparticles for lung protein delivery Sustained delivery by leucinemodified chitosan spray-dried respirable powders Attenuation of fibrosis in vitro and in vivo with SPARC siRNA Self-assembled micelle interfering RNA for effective and safe targeting of dysregulated genes in pulmonary fibrosis Characterization of polymeric micelles for pulmonary delivery of beclomethasone dipropionate Use of oligonucleotide microarrays for rapid detection and serotyping of acute respiratory disease-associated adenoviruses Use of an oligonucleotide array for laboratory diagnosis of bacteria responsible for acute upper respiratory infections A review of antisense therapeutic interventions for molecular biological targets in asthma Silencing of microRNAs in vivo with antagomirs Cellular uptake and intracellular trafficking of oligonucleotides Mepolizumab for severe eosinophilic asthma (DREAM): a multicentre, double-blind, placebo-controlled trial Infusion-related and hypersensitivity reactions of monoclonal antibodies used to treat colorectal cancer-identification, prevention, and management A randomised, open-label, parallel group phase 2 study of antisense oligonucleotide therapy in acromegaly An overview of the clinical application of antisense oligonucleotides for RNA-targeting therapies FDA-approved oligonucleotide therapies in 2017 Antisense technologies. Particles with 1-100 nm size range are termed as nanoparticles which have been newly employed in targeted drug delivery [38] .
    keywords: antisense; cancer; cells; chitosan; delivery; diseases; dna; drug; gene; liposomes; lung; nanoparticles; oligonucleotides; potential; sirna; targeting; therapy; treatment
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        item: #328 of 1349
          id: cord-253282-zwl0safn
      author: Plant, Ewan P.
       title: Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production
        date: 2013-01-18
       words: 5023
      flesch: 52
     summary: In an effort to further our understanding of how the SARS frameshift signal functions we performed deletion and mutagenesis studies an analyzed the effects on frameshifting efficiency, RNA structure and viral RNA production. The observed effects in vivo should therefore reflect changes related to RNA structure within the frameshifting signal, rather than changes in the function of the encoded proteins.
    keywords: coronavirus; efficiency; frameshifting; genomic; loop; pseudoknot; rna; sequence; stem; structure
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        item: #329 of 1349
          id: cord-253307-4bpdfgau
      author: Sanz, Miguel A.
       title: Inhibition of host protein synthesis by Sindbis virus: correlation with viral RNA replication and release of nuclear proteins to the cytoplasm
        date: 2014-11-19
       words: 10217
      flesch: 40
     summary: Changes in cellular mRNA stability, splicing, and polyadenylation through HuR protein sequestration by a cytoplasmic RNA virus The leader protein of cardioviruses inhibits stress granule assembly Semliki Forest virus nonstructural protein 2 is involved in suppression of the type I interferon response Generation of bovine respiratory syncytial virus (BRSV) from cDNA: BRSV NS2 is not essential for virus replication in tissue culture, and the human RSV leader region acts as a functional BRSV genome promoter Heterogeneous nuclear ribonuclear protein K interacts with Sindbis virus nonstructural proteins and viral subgenomic mRNA Hijacking the translation apparatus by RNA viruses Molecular bases for the action and selectivity of nucleoside antibiotics RNA nuclear export is blocked by poliovirus 2A protease and is concomitant with nucleoporin cleavage The multifaceted poliovirus 2A protease: regulation of gene expression by picornavirus proteases Dephosphorylation of HuR protein during alphavirus infection is associated with HuR relocalization to the cytoplasm Modification of Asn374 of nsP1 suppresses a Sindbis virus nsP4 minus-strand polymerase mutant Comparison of the effects of Sindbis virus and Sindbis virus replicons on host cell protein synthesis and cytopathogenicity in BHK cells Selection of RNA replicons capable of persistent noncytopathic replication in mammalian cells Random insertion mutagenesis of Sindbis virus nonstructural protein 2 and selection of variants incapable of downregulating cellular transcription Chikungunya virus nsP3 blocks stress granule assembly by recruitment of G3BP into cytoplasmic foci Requirements for eIF4A and eIF2 during translation of Sindbis virus subgenomic mRNA in vertebrate and invertebrate host cells Sindbis virus nonstructural protein nsP2 is cytotoxic and inhibits cellular transcription The 3′ untranslated region of Sindbis virus represses deadenylation of viral transcripts in mosquito and Mammalian cells Sindbis virus-induced inhibition of protein synthesis is partially reversed by medium containing an elevated potassium concentration Na+ and K+ concentrations and the regulation of protein synthesis in Sindbis virus-infected chick cells RNA helicase activity of Semliki Forest virus replicase protein NSP2 PKR-dependent and -independent mechanisms are involved in translational shutoff during Sindbis virus infection Inhibition of transcription and translation in Sindbis virus-infected cells Alphaviruses. However, individual expression of nsP1, nsP2, nsP3 or nsP1‐4 does not block cellular protein synthesis in BHK cells.
    keywords: anti; bhk; cells; et al; fig; nsp1; nsp2; nuclear; protein; replication; rna; sinv; synthesis; translation; virus
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        item: #330 of 1349
          id: cord-253466-7gpije5d
      author: Netherton, Christopher
       title: A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication
        date: 2007-08-31
       words: 26447
      flesch: 32
     summary: Ultrastructural studies and sequential development of virus isolated from normal and tumor tissue Acidic C terminus of vaccinia virus DNAbinding protein interacts with ribonucleotide reductase Formation of DNA replication structures in herpes virus-infected cells requires a viral DNA binding protein Comparison of the intranuclear distributions of herpes simplex virus proteins involved in various viral functions Origin-independent plasmid replication occurs in vaccinia virus cytoplasmic factories and requires all five known poxvirus replication factors MHC I-dependent antigen presentation is inhibited by poliovirus protein 3A Autophagy in innate and adaptive immunity Poliovirus 3A protein limits interleukin-6 (IL-6), IL-8, and beta interferon secretion during viral infection Inhibition of cellular protein secretion by poliovirus proteins 2B and 3A Inhibition of endoplasmic reticulum-to-Golgi traffic by poliovirus protein 3A: These initially appear close to the nuclear envelope, possibly at sites where the genome first enters the nucleus following capsid disassembly at nuclear pores (Everett and Murray, 2005) , and are then seen throughout the nucleus (Everett et al., 2004) .
    keywords: asfv; assembly; bodies; capsid; cells; complex; contain; cytoplasmic; dna; dna replication; early; electron; et al; expression; factories; factory; fever; formation; gene; genome; golgi; herpes; host; inclusions; infection; localization; membrane; nuclear; nucleus; poliovirus; polymerase; protein; replicase; replication; replication complex; rna; role; sites; structures; swine; type; vaccinia; vaccinia virus; vesicles; viral; virus; virus factories; virus replication; viruses
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        item: #331 of 1349
          id: cord-253480-qchrw337
      author: Pu, Jieying
       title: Antiviral activity of Carbenoxolone disodium against dengue virus infection
        date: 2016-12-23
       words: 5320
      flesch: 49
     summary: Here, we found that the production of infectious DENV particles was significantly decreased by CBX treatment in DENV‐permissive cells, while the viral RNA and viral protein synthesis were not affected. Furthermore, DENV RNA from progeny virions in the supernatants was significantly decreased by CBX treatment in a dose‐dependent manner.
    keywords: cbx; cells; dengue; denv; denv-2; infection; titer; treatment; virus
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        item: #332 of 1349
          id: cord-253501-hkxlq3os
      author: Anang, Saumya
       title: Recent Advances Towards the Development of a Potent Antiviral Against the Hepatitis E Virus
        date: 2018-06-28
       words: 4428
      flesch: 30
     summary: In vivo evidence for ribavirin-induced mutagenesis of the hepatitis E virus genome Mutagenic effects of ribavirin on hepatitis E virus-viral extinction versus selection of fitness-enhancing mutations Ribavirin at the era of novel direct antiviral agents for the treatment of hepatitis C virus infection: relevance of pharmacological monitoring Three-month pegylated interferon-alpha-2a therapy for chronic hepatitis E virus infection in a haemodialysis patient P61 Pegylated interferon and ribavarin combination therapy achieves hepatitis E virus clearance in chronic hepatitis E virus/human immunodeficiency virus co-infection Treatment of chronic hepatitis E in liver transplant recipients with pegylated interferon alpha-2b Chronic hepatitis E virus infection: successful virologic response to pegylated interferon-alpha therapy Antiviral activities of different interferon types and subtypes against hepatitis E virus replication Disparity of basal and therapeutically activated interferon signalling in constraining hepatitis E virus infection Hepatitis E virus inhibits type I interferon induction by ORF1 products Suppression of interferon-a signaling by hepatitis E virus The hepatitis E virus ORF3 protein modulates epidermal growth factor receptor trafficking, STAT3 translocation, and the acute-phase response Neuropsychiatric adverse effects of interferon-alpha: recognition and management Pegylated interferon-alpha for treating chronic hepatitis E virus infection after liver transplantation Antiviral strategies for hepatitis E virus Calcineurin inhibitors stimulate and mycophenolic acid inhibits replication of hepatitis E virus Cross talk between nucleotide synthesis pathways with cellular immunity in constraining hepatitis E virus replication Nucleoside analogue 2'-C-methylcytidine inhibits hepatitis E virus replication but antagonizes Molecular virology of hepatitis E virus Transfusiontransmitted hepatitis E in a patient with myelodysplastic syndromes A case of transfusion-transmitted hepatitis E caused by blood from a donor infected with hepatitis E virus via zoonotic food-borne route Fetal and neonatal health consequences of vertically transmitted hepatitis E virus infection Seroprevalence and mother-to-infant transmission of hepatitis E virus among pregnant women in the United Arab Emirates Hepatitis E in pregnancy Clinical course and duration of viremia in vertically transmitted hepatitis E virus (HEV) infection in babies born to HEVinfected mothers Expanding host range and cross-species infection of hepatitis E virus Hepatitis E virus and chronic hepatitis in organ-transplant recipients Hepatitis E-induced severe myositis Hepatitis E virus infection in HIV-infected persons Hepatitis E virus infection as a cause of graft hepatitis in liver transplant recipients Chronic hepatitis e in heart transplant recipients Chronic hepatitis E infection in a persistently immunosuppressed patient unable to be eliminated after ribavirin therapy Incidence and severity of viral hepatitis in pregnancy Outcome of hepatitis E virus infection in Indian pregnant women admitted to a tertiary care hospital HEV-associated cryoglobulinaemia and extrahepatic manifestations of hepatitis E Hepatitis E virus infection and acute non-traumatic neurological injury: A prospective multicentre study Rash and arthralgia caused by hepatitis E Extrahepatic replication and infection of hepatitis E virus in neuronal-derived cells The global burden of hepatitis E virus genotypes 1 and 2 in 2005
    keywords: antiviral; chronic; hepatitis; hev; host; infection; polymerase; protein; replication; ribavirin; rna; virus
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        item: #333 of 1349
          id: cord-253539-0kcujnfa
      author: Agranovsky, A. A.
       title: Principles of Molecular Organization, Expression, and Evolution of Closteroviruses: Over The Barriers
        date: 1996-12-31
       words: 10730
      flesch: 50
     summary: The genome of the Ukrainian strain of B W (BW-U) consists of 15,480 nucleotides (nt), is 5'-capped and contains no 3'-poly(A) (Karasev et al., 1989; Among plant RNA viruses, CTV has the largest undivided genome (1 9,296 nt for the Florida T36 isolate), exceeding that of B W by about 4 kb (Karasev et al., 199413, 1995; Pappu ~t al., 1994) .
    keywords: agranovsky et; b w; byv; closteroviruses; ctv; domains; et al; fig; gene; genomes; hel; kda; kda protein; orfs; particles; plant; protein; rna; sequence; viruses
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        item: #334 of 1349
          id: cord-253616-7jyui5ca
      author: Lai, Zheng-Zong
       title: Harringtonine Inhibits Zika Virus Infection through Multiple Mechanisms
        date: 2020-09-07
       words: 4986
      flesch: 43
     summary: Substantial research on screening antiviral agents against ZIKV and preventing ZIKV infection are globally underway, but Food and Drug Administration (FDA)-approved treatments are not available yet. Results of IFA assay also showed that harringtonine treatment inhibited ZIKV infection in a dose-dependent manner ( Figure 1E ,F).
    keywords: assay; cells; figure; harringtonine; infection; rna; treatment; vero; virus; zikv
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        item: #335 of 1349
          id: cord-253862-jl1zhg13
      author: Khalaf, Khalil
       title: SARS-CoV-2: Pathogenesis, and Advancements in Diagnostics and Treatment
        date: 2020-10-06
       words: 14633
      flesch: 37
     summary: A cohort study Interleukin-1 blockade with high-dose anakinra in patients with COVID-19, acute respiratory distress syndrome, and hyperinflammation: a retrospective cohort study Use of convalescent plasma therapy in SARS patients in Hong Kong Treatment with convalescent plasma for influenza A (H5N1) infection Challenges of convalescent plasma infusion therapy in Middle East respiratory coronavirus infection: a single centre experience Effectiveness of convalescent plasma therapy in severe COVID-19 patients Treatment of 5 critically Ill patients with COVID-19 with convalescent plasma Safety update: COVID-19 convalescent plasma in 20,000 hospitalized patients Severe acute respiratory syndrome coronavirus viroporin 3A activates the NLRP3 inflammasome The deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China Biology of IL-38 and its role in disease IL-37 is a fundamental inhibitor of innate immunity Induction of pro-inflammatory cytokines (IL-1 and IL-6) and lung inflammation by COVID-19 (CoV-19 or SARS-CoV-2): anti-inflammatory strategies Baricitinib as potential treatment for 2019-nCoV acute respiratory disease Use of baricitinib in patients with moderate and severe COVID-19 Evaluation of human monoclonal antibody 80R for immunoprophylaxis of severe acute respiratory syndrome by an animal study, epitope mapping, and analysis of spike variants Human monoclonal antibody as prophylaxis for SARS coronavirus infection in ferrets Human monoclonal antibody combination against SARS coronavirus: synergy and coverage of escape mutants Neutralizing epitopes of the SARS-CoV S-protein cluster independent of repertoire, antigen structure or mAb technology Monoclonal antibodies targeting the HR2 domain and the region immediately upstream of the HR2 of the S protein neutralize in vitro infection of severe acute respiratory syndrome coronavirus Neutralizing human monoclonal antibodies to severe acute respiratory syndrome coronavirus: target, mechanism of action, therapeutic potential Perspectives on monoclonal antibody therapy as potential therapeutic intervention for Coronavirus disease-19 (COVID-19) Similar to SARS, infected patients presented with a variety of clinical courses, from mild upper respiratory symptoms to fulminant pneumonia and multi-organ system failure.
    keywords: acute; antibodies; antibody; antiviral; cells; coronavirus; cov-2; covid-19; disease; et al; group; host; human; infection; novel; patients; protein; receptor; respiratory; rna; sars; study; syndrome; treatment; trial; use
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        item: #336 of 1349
          id: cord-254070-v9gabn1a
      author: Bordería, Antonio V.
       title: Fidelity Variants and RNA Quasispecies
        date: 2015-10-25
       words: 7019
      flesch: 37
     summary: The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses Structure-function relationships of the viral RNA-dependent RNA polymerase: fidelity, replication speed, and initiation mechanism determined by a residue in the ribose-binding pocket Rationalizing the development of live attenuated virus vaccines High mutation frequencies among Escherichia coli and Salmonella pathogens Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site Fidelity Variants of RNA Dependent RNA Polymerases Uncover an Indirect Fidelity variants of RNA dependent RNA polymerases uncover an indirect, mutagenic activity of amiloride compounds Vaccine-derived mutation in motif D of poliovirus RNA-dependent RNA polymerase lowers nucleotide incorporation fidelity I. A comparison of the deoxyribonucleic acid polymerases of mutator, antimutator, and wild type strains of bacteriophage T4 Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase Crystal structure of Norwalk virus polymerase reveals the carboxyl terminus in the active site cleft Structure-function relationships among RNA-dependent RNA polymerases Substrate complexes of hepatitis C virus RNA polymerase (HC-J4): structural evidence for nucleotide import and de-novo initiation The structure of a birnavirus polymerase reveals a distinct active site topology A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity Increased fidelity reduces poliovirus fitness and virulence under selective pressure in mice DNA polymerization in the absence of exonucleolytic proofreading: in vivo and in vitro studies Alphavirus mutator variants present host-specific defects and attenuation in mammalian and insect models A study of the virulence in mice of high copying fidelity variants of human enterovirus 71 Ribavirin-resistant mutants of human enterovirus 71 express a high replication fidelity phenotype during growth in cell culture
    keywords: et al; fidelity; g64s; mutation; mutator; nucleotide; poliovirus; polymerase; rdrp; rna; structure; type; variants; virus
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        item: #337 of 1349
          id: cord-254100-u6x5zd4i
      author: Taliansky, M.E.
       title: Involvement of the Plant Nucleolus in Virus and Viroid Infections: Parallels with Animal Pathosystems
        date: 2010-10-15
       words: 13999
      flesch: 28
     summary: Therefore, the main emphasis of this review will be on what is known about the different aspects of interactions between plant virus proteins and the nucleolus, of which the functional significance in control of virus movement and interference with host antiviral defense has started to appear only recently. The most common technique for studying the nucleolar targeting of plant virus proteins is based on the confocal microscopy localization of the proteins which have been tagged with a fluorescent fusion protein (such as green fluorescent protein, GFP).
    keywords: cbs; cell; et al; fibrillarin; functions; host; infection; interaction; localization; movement; nia; nucleolar; nucleolus; nucleus; orf3; plant; protein; replication; rna; role; silencing; translation; viral; virus; viruses; vpg
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        item: #338 of 1349
          id: cord-254192-86ksgl5t
      author: Li, Liang
       title: IFN-Lambda 3 Mediates Antiviral Protection Against Porcine Epidemic Diarrhea Virus by Inducing a Distinct Antiviral Transcript Profile in Porcine Intestinal Epithelia
        date: 2019-10-17
       words: 7276
      flesch: 42
     summary: The IFN family is categorized into three different types: type I IFN (IFN-α/β), type II IFN (IFN-γ), and type III IFN (IFN-λ). Mice with type I IFN or III IFN receptor knockout experience more severe viral intestinal infections, but Ifnl −/− mice show higher viral loads and more serious clinical symptoms than IFNAR −/− mice (17, 18) .
    keywords: antiviral; cells; expression; genes; ifn; ifns; iii; infection; pedv; porcine; signaling; type
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        item: #339 of 1349
          id: cord-254210-3mi2aop5
      author: Haddad, Rodrigo
       title: Silencing of HTLV-1 gag and env genes by small interfering RNAs in HEK 293 cells
        date: 2011-01-26
       words: 4505
      flesch: 45
     summary: When env gene expression was analyzed, the results showed a significant reduction (p < 0.05) of gene expression by 64% or 75% in cells co-transfected with siRNAs Env2 or Env3 and pEGFP-Env, respec-tively, compared to siRNA Scr Env co-transfected cells (Fig. 3B) . Significant reduction (*p < 0.05) of gene expression was obtained in cells co-transfected with siRNAs Env2 or Env3 and pEGFP-Env compared to siRNA Scr Env co-transfected cells.
    keywords: cells; env; expression; fluorescence; gag; gene; htlv-1; pegfp; sirna; virus
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        item: #340 of 1349
          id: cord-254250-l0v602x9
      author: Hooper, Chantelle
       title: A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh
        date: 2020-10-02
       words: 6445
      flesch: 44
     summary: Global scale of freshwater prawn farming A review on the diseases of freshwater prawns with special focus on white tail disease of Macrobrachium rosenbergii Current status and prospects of farming the giant river prawn Macrobrachium rosenbergii (De Man) in Bangladesh Shrimp Research Station Mass larval mortality in a giant freshwater prawn Macrobrachium rosenbergii hatchery: An attempt to detect microbes in the berried and larvae Fishing for prawn larvae in Bangladesh: An important coastal livelihood causing negative effects on the environment Distinctive histopathology of Spiroplasma eriocheiris infection in the giant river prawn Macrobrachium rosenbergii A viral disease associated with mortalities in hatchery-reared postlarvae of the giant freshwater prawn Macrobrachium rosenbergii Extra small virus-like particles (XSV) and nodavirus associated with whitish muscle disease in the giant freshwater prawn, Macrobrachium rosenbergii White tail disease of the giant freshwater prawn Macrobrachium rosenbergii in Thailand Experimental transmission and tissue tropism of Macrobrachium rosenbergii nodavirus (MrNV) and its associated extra small virus (XSV) RT-PCR amplification and sequence analysis of extra small virus associated with white tail disease of Macrobrachium rosenbergii (de Man) cultured in Taiwan Macrobrachium rosenbergii nodavirus infection in a giant freshwater prawn hatchery in Indonesia Isolation and Characterization of a Novel Dicistrovirus Associated with Moralities of the Great Freshwater Prawn, Macrobrachium rosenbergii Infectious hypodermal and haematopoietic necrosis virus (IHHNV) infections in giant freshwater prawn, Macrobrachium rosenbergii Description of a Natural Infection with Decapod Iridescent Virus 1 in Farmed Giant Freshwater Prawn, Macrobrachium rosenbergii Parvo-like virus in the hepatopancreas of freshwater prawns Macrobrachium rosenbergii cultivated in Thailand Tolerance of Macrobrachium rosenbergii to white spot syndrome virus Clearance of white spot syndrome virus (WSSV) and immunological changes in experimentally WSSV-injected Macrobrachium rosenbergii In experimental challenge with infectious clones of Macrobrachium rosenbergii nodavirus (MrNV) and extra small virus (XSV), MrNV alone can cause mortality in freshwater prawn (Macrobrachium rosenbergii) Characterization and pathogenicity studies of Vibrio parahaemolyticus isolated from diseased freshwater prawn A Wrapper Tool around Cutadapt and FastQC to Consistently Apply Quality and Adapter Trimming to FastQ Files A Quality Control Tool for High Throughput Sequence Data Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads Accurate de novo assembly of RNA virus genomes Fast and sensitive protein alignment using DIAMOND MEGAN Community Edition-Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data Fast and accurate short read alignment with Burrows-Wheeler transform Genome Project Data Processing The Sequence Alignment/Map format and SAMtools Integrative genomics viewer Evaluating next-generation sequencing alignment data Prokka: Rapid prokaryotic genome annotation GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Furthermore, RNA viruses can only be visualised indirectly in histology sections (normally associated with damaged host cells and nuclei).
    keywords: bangladesh; disease; genome; hatcheries; hatchery; larvae; macrobrachium; mortalities; mrgv; prawn; protein; rna; rosenbergii; virus
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        item: #341 of 1349
          id: cord-254592-wa5il5go
      author: Brierley, Liam
       title: Tissue tropism and transmission ecology predict virulence of human RNA viruses
        date: 2019-11-26
       words: 5889
      flesch: 31
     summary: Six-rank system of classifying human RNA virus virulence with available data (specifically, severity rating from main text, fatalities in vulnerable individuals and healthy adults, and severe strains), along with example viruses and number of viruses fitting each exclusive rank's criteria. The emergence of previously unseen viruses means that the set of known human viruses continually could not be assigned a disease severity rating and were excluded from all analyses (hepatitis delta virus, which is reliant on hepatitis B virus coinfection, and primate T-lymphotropic virus 3, which may be associated with chronic disease like other T-lymphotropic viruses but has not been known in humans long enough for cohort observations).
    keywords: data; disease; forest; human; models; risk; tissue; transmission; tropism; virulence; viruses
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        item: #342 of 1349
          id: cord-254596-wsmnlnlk
      author: Grädel, Carole
       title: Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing
        date: 2020-07-31
       words: 6917
      flesch: 45
     summary: key: cord-254596-wsmnlnlk authors: Grädel, Carole; Terrazos Miani, Miguel A.; Baumann, Christian; Barbani, Maria Teresa; Neuenschwander, Stefan; Leib, Stephen L.; Suter-Riniker, Franziska; Ramette, Alban title: Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing date: 2020-07-31 journal: Viruses DOI: 10.3390/v12080841 sha: doc_id: 254596 cord_uid: wsmnlnlk Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. More than 98% of basecalled RNA reads (9065 reads) were taxonomically classified using BLASTN against the NCBI's nucleotide (nt) database.
    keywords: cdna; drs; enterovirus; genome; illumina; min; nanopore; reads; rna; samples; sequences; sequencing; total
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        item: #343 of 1349
          id: cord-254713-ghcwfcx2
      author: Razanajatovo, Norosoa H
       title: Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar
        date: 2015-03-12
       words: 4165
      flesch: 44
     summary: Some authors have reported the detection of bat CoVs from mainland Africa Thus, further molecular epidemiology studies would be required to fully understand the dispersal potential of CoVs amongst Malagasy bats species.
    keywords: bats; coronaviruses; covs; human; madagascar; malagasy; min; species; study
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        item: #344 of 1349
          id: cord-254747-vox5xsgd
      author: Deng, Xufang
       title: An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses
        date: 2018-04-01
       words: 5743
      flesch: 43
     summary: In line with this prediction, we and others reported a specific, punctate, perinuclear localization of CoV nsp15 during viral infection (Heusipp et al., 1997; Shi et al., 1999; Deng et al., 2017; Athmer et al., 2017) , while ectopically expressed nsp15 was distributed throughout the cytoplasm (Cao and Zhang, 2012) . It was first discovered that the EndoU activity of nsp15 mediates the evasion of host recognition of viral dsRNA by infecting primary macrophages with EndoU-deficient CoVs (Deng et al., 2017; Kindler et al., 2017) .
    keywords: activity; cov; dsrna; endou; et al; ifn; nsp15; protein; replication; rna; virus
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        item: #345 of 1349
          id: cord-254895-ym0jsir5
      author: Eisenächer, Katharina
       title: The role of viral nucleic acid recognition in dendritic cells for innate and adaptive antiviral immunity
        date: 2008-01-18
       words: 9107
      flesch: 31
     summary: TLR7 does not seem to play an essential role in the innate immune response to RNA virus infection in vivo. (Xu et al., 2005) and CARD adapter inducing IFN-b (CARDIF) (Meylan et al., 2005) , respectively.
    keywords: antiviral; cells; et al; ifn; immune; infection; response; rig; rna; signaling; tlr9; type; viral; virus; viruses
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        item: #346 of 1349
          id: cord-254903-g9ropt9c
      author: Xu, Xiaofeng
       title: Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data
        date: 2020-09-16
       words: 3282
      flesch: 56
     summary: MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the origin and evolution of RNA viruses. In the present study, we conclude: (1) the high-quality, well-curated and full-length Yunnan2016 genome (MT080097, MT080098, MT080099 and MT080100) should be included in the NCBI RefSeq database for future studies on MGTV, JMTV, KITV and GXTV; (2) To the best of our knowledge, this is the first study in which 5′ and 3′ sRNAs were used to generate full-length genome sequences of, but not limited to, RNA viruses; (3) it is feasible to use the sRNA-seq based method for the detection of viruses in pooled two and even possible one small ticks; (4) MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the The workflow to generate a full-length genome using 5′ and 3′ sRNAs can be seen in the Additional file 1.
    keywords: data; genome; mgtv; seq; srna; ticks; virus; viruses
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        item: #347 of 1349
          id: cord-254916-y1rw9q11
      author: Ogando, Natacha S.
       title: SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology
        date: 2020-06-22
       words: 8596
      flesch: 42
     summary: The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade The proteolytic regulation of virus cell entry by furin and other proprotein convertases A pneumonia outbreak associated with a new coronavirus of probable bat origin Host cell entry of middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein Furin cleavage of the SARS coronavirus spike glycoprotein enhances cell-cell fusion but does not affect virion entry Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein Cathepsin L functionally cleaves the severe acute respiratory syndrome coronavirus class I fusion protein upstream of rather than adjacent to the fusion peptide Coronavirus cell entry occurs through the endo-/ lysosomal pathway in a proteolysis-dependent manner SARS coronavirus, but not human coronavirus NL63, utilizes cathepsin L to infect ACE2-expressing cells Identification of a common deletion in the spike protein of SARS-CoV-2 Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site A hypervariable region within the 3' cis-acting element of the murine coronavirus genome is nonessential for RNA synthesis but affects pathogenesis A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro SARS-CoV-2 sensitive to type I interferon pretreatment Isolation, sequence, infectivity and replication kinetics of SARS-CoV-2 Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells Apical entry and release of severe acute respiratory syndromeassociated coronavirus in polarized Calu-3 lung epithelial cells Exogenous ACE2 expression allows refractory cell lines to support severe acute respiratory syndrome coronavirus replication SARS-Associated coronavirus replication in cell lines Discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replicationspecific multiplex reverse transcription-PCR Studies on the mechanism of the priming effect of interferon on interferon production by cell cultures exposed to poly(rI)-poly(rC) Regulation of the interferon system: evidence that Vero cells have a genetic defect in interferon production A novel coronavirus from patients with pneumonia in China The FDAapproved gold drug auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway Sars coronavirus 7a protein blocks cell cycle progression at G0/G1 phase via the cyclin D3/pRb pathway The ORF7b protein of severe acute respiratory syndrome coronavirus (SARS-CoV) is expressed in virus-infected cells and incorporated into SARS-CoV particles The SARS-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors The 8ab protein of SARS-CoV is a luminal ER membrane-associated protein and induces the activation of ATF6 SARS-Coronavirus open reading Frame-8b triggers intracellular stress pathways and activates NLRP3 inflammasomes Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China Severe acute respiratory syndrome (SARS) A new coronavirus associated with human respiratory disease in China Fast gapped-read alignment with Bowtie 2 Proteolytic processing of the replicase ORF1a protein of equine arteritis virus Production and characterization of monoclonal antibodies against the nucleocapsid protein of SARS-CoV Monoclonal antibodies to double-stranded RNA as probes of RNA structure in crude nucleic acid extracts Localization of mouse hepatitis virus nonstructural proteins and RNA synthesis indicates a role for late endosomes in viral replication Debio 025, a cyclophilin binding molecule, is highly efficient in clearing hepatitis C virus (HCV) replicon-containing cells when used alone or in combination with specifically targeted antiviral therapy for HCV (STAT-C) inhibitors The intracellular sites of early replication and budding of SARScoronavirus Sars-Coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum Double-Stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negativestrand RNA viruses Ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex Infectious bronchitis virus generates spherules from zippered endoplasmic reticulum membranes The porcine deltacoronavirus replication organelle comprises Double-Membrane vesicles and Zippered endoplasmic reticulum with Double-Membrane spherules Replication of coronavirus MHV-A59 in sac-cells: determination of the first site of budding of progeny virions Ultrastructural characterization of SARS coronavirus Coronavirus susceptibility to the antiviral Remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine Chloroquine is a potent inhibitor of SARS coronavirus infection and spread Human coronavirus
    keywords: acute; cells; cleavage; coronavirus; cov-2; fig; genome; human; plaque; protein; reads; replication; rna; sars; site; syndrome; synthesis; vero; viruses
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        item: #348 of 1349
          id: cord-254963-cnvxlv6h
      author: Paskey, Adrian C.
       title: Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples
        date: 2019-02-26
       words: 6211
      flesch: 40
     summary: This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. For the guano samples, these consisted of an aliquot of each of the TruSeq RNA Access libraries from the step prior to virus enrichment.
    keywords: detection; enrichment; genome; probes; reads; rna; samples; sequencing; target; viral; virus; viruses
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        item: #349 of 1349
          id: cord-255090-2gpsu1y4
      author: Lv, Ke
       title: Transient inhibition of foot-and-mouth disease virus replication by siRNAs silencing VP1 protein coding region
        date: 2009-06-30
       words: 6476
      flesch: 44
     summary: To identify efficacious small interfering RNAs (siRNAs) to inhibit the replication of FMDV, candidate siRNAs corresponding to FMDV VP1 gene were designed and synthesized in vitro using T7 RNA polymerase. The recombinant plasmids pVP1-EGFP-N1 containing the whole length of VP1 gene sequence and p3C-EGFP-N1 containing 3C gene sequence were constructed as follows.
    keywords: cells; egfp; fmdv; gene; primer; rna; rnai; sirnas; viral; virus; vp1
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        item: #350 of 1349
          id: cord-255252-md0avnqg
      author: Tang, Julian W.
       title: Quantitative temporal‐spatial distribution of severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) in post‐mortem tissues
        date: 2007-07-02
       words: 5319
      flesch: 64
     summary: Persistent infection of SARS coronavirus in colonic cells in vitro Coronaviral hypothetical and structural proteins were found in the intestinal surface enterocytes and pneumocytes of severe acute respiratory syndrome (SARS) SARS-associated viral hepatitis caused by a novel coronavirus: Report of three cases Viral shedding patterns of coronavirus in patients with probable severe acute respiratory syndrome ACE2 gene polymorphisms do not affect outcome of severe acute respiratory syndrome Detection of severe acute respiratory syndrome-associated coronavirus in pneumocytes of the lung Angiotensin-converting enzyme 2 is an essential regulator of heart function The clinical pathology of severe acute respiratory syndrome (SARS): A report from China Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: Implications for pathogenesis and virus transmission pathways Fatal severe acute respiratory syndrome is associated with multiorgan involvement by coronavirus Lung pathology of severe acute respiratory syndrome (SARS): This implies that SARS-CoV RNA remains detectable in the body tissue of SARS patients for a long period after death, though infectious SARS-CoV was only cultured from the lung and bowel tissue (Table II) .
    keywords: cov; gapdh; load; ratio; rna; sars
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        item: #351 of 1349
          id: cord-255495-xnoppq3y
      author: Elrashdy, Fatma
       title: On the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity
        date: 2020-07-09
       words: 7538
      flesch: 35
     summary: Disaster Medicine and Public Health Preparedness MERS-coronavirus replication induces severe in vitro cytopathology and is strongly inhibited by cyclosporin A or interferon-a treatment Possible vertical transmission of SARS-CoV-2 from an infected mother to her newborn Eleven faces of coronavirus disease Ultrastructural evidence for direct renal infection with SARS-CoV-2 Vaginal delivery in SARS-CoV-2 infected pregnant women in Northern Italy: A retrospective analysis Spread and dynamics of the COVID-19 epidemic in Italy: Effects of emergency containment measures The role of extracellular vesicles as allies of HIV, HCV and SARS viruses Expanding our understanding of the role polyprotein conformation plays in the coronavirus life cycle Modern uses of electron microscopy for detection of viruses Ultrastructural characterization of SARS coronavirus Pathology and pathogenesis of severe acute respiratory syndrome Respiratory viral infection in lung transplantation induces exosomes that trigger chronic rejection Donorderived exosomes with lung self-antigens in human lung allograft rejection The role of extracellular vesicles in COVID-19 virus infection Recurrence of positive SARS-CoV-2 in patients recovered from COVID-19 Retest positive for SARS-CoV-2 RNA of recovered patients with COVID-19: A very interesting case was recently reported, where a 78-year-old woman that was ready to be discharged after the three consecutive PCR tests on her nasopharyngeal swab samples indicated that she was SARS-CoV-2 negative, her conditions were significantly improved, and CT examination showed absorption of pulmonary exudation, but suddenly she fell into the cardiac arrest and died (Yao et al., 2020) .
    keywords: cells; coronavirus; cov-2; covid-19; dmvs; et al; infection; membrane; particles; patients; pcr; replication; rna; sars; vesicles; virus
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        item: #352 of 1349
          id: cord-255499-31xmue1g
      author: Bujarski, J.J.
       title: Recombination
        date: 2008-07-30
       words: 4858
      flesch: 37
     summary: The involvement of host cell genes in RNA virus recombination has begun to get elucidated in several RNA viruses. Biochemically, the processes of DNA and RNA recombination are different reflecting the specifics of DNA versus RNA replication as well as their use inside the cell.
    keywords: dna; events; phage; recombination; replication; rna; rnas; strand; template; virus; viruses
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        item: #353 of 1349
          id: cord-255545-nycdhdsd
      author: Schoenike, Barry
       title: Quantitative sense-specific determination of murine coronavirus RNA by reverse transcription polymerase chain reaction
        date: 1999-03-10
       words: 6182
      flesch: 37
     summary: A striking change in the expected relative or absolute abundance of viral RNA of a given sense may provide clues as to the mode of viral replication in vitro or of viral pathogenesis in vivo. However, in many experiments, particularly with samples obtained in vivo, viral RNA may not be of sufficiently high concentration to allow detection by this technique.
    keywords: assay; pcr; primers; reaction; rna; rnas; sense; sequences; templates; viral
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        item: #354 of 1349
          id: cord-255576-738khdwv
      author: Van Duyne, Rachel
       title: Localization and Sub-Cellular Shuttling of HTLV-1 Tax with the miRNA Machinery
        date: 2012-07-10
       words: 9857
      flesch: 50
     summary: Interestingly, in Tax expressing cells, Drosha is almost exclusively found in the nucleus at specific foci colocalizing with Tax ( Figures 2B, C) . Here we question whether the remaining Drosha is functional in Tax expressing cells.
    keywords: binding; cells; control; drosha; expression; htlv-1; human; infected; infection; levels; mirna; pathway; protein; rna; tax; virus
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        item: #355 of 1349
          id: cord-255607-dbexsugq
      author: Wu, Yang
       title: Porcine Epidemic Diarrhea Virus nsp15 Antagonizes Interferon Signaling by RNA Degradation of TBK1 and IRF3
        date: 2020-05-31
       words: 6424
      flesch: 39
     summary: Briefly, nuclease reactions contained 4 µg of purified wild-type PEDV nsp15 protein, PEDV nsp15 mutant protein, or GST tag protein as control, and 6 µg TBK1 or IRF3 RNA transcribed and purified in vitro. The number below the red residue indicates its corresponding position at PEDV nsp15 protein, respectively.
    keywords: activity; cells; expression; ifn; infection; interferon; irf3; nsp15; pedv; porcine; proteins; rna; tbk1; type; virus
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        item: #356 of 1349
          id: cord-255619-5h3l6nh6
      author: Kuo, Shu-Ming
       title: Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity
        date: 2013-03-23
       words: 6332
      flesch: 47
     summary: 1D and E are representative, we included all the strains in Fig. 1B and constructed their Bayesian trees (Fig. S2) according to the two segments of N-terminal and C-terminal amino acid sequences of IBV N protein (Fig. 1C) . IBV N protein may be vulnerable to alteration under immunological pressure.
    keywords: binding; fig; ibv; ibvs; n protein; ntd; protein; recombination; rna; selection; strains
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        item: #357 of 1349
          id: cord-255738-r8zfdsix
      author: Ge, Feng
       title: Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening
        date: 2007-03-30
       words: 5115
      flesch: 41
     summary: This SARS-associated replicon cell line is based on the use of SARS replicon cDNAs generated by reverse genetic techniques. Thus, these data indicate that although replicon cells may express sufficient GFP-BlaR to survive blasticidin selection, the amount of GFP BlaR protein was insufficient to be detected by flow cytometry.
    keywords: cells; coronavirus; cov; et al; expression; gene; line; replicon; replicon rna; rna; sars
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        item: #358 of 1349
          id: cord-255795-su7f5ges
      author: Yelin, Idan
       title: Evaluation of COVID-19 RT-qPCR test in multi-sample pools
        date: 2020-03-27
       words: 2270
      flesch: 51
     summary: Pooling clinical RNA samples, we tested previously confirmed positive samples alone and combined with an increasing number of previously confirmed negative samples and found that positive samples can still be well observed in pools of up to 32 samples, and possibly even 64 with additional PCR cycles. Detection of positive samples diluted in even up to 64 samples may also be attainable, though may require additional amplification cycles.
    keywords: license; pooling; preprint; rna; samples
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        item: #359 of 1349
          id: cord-255883-mz6nyisw
      author: Asif, Muhammad
       title: COVID-19 and therapy with essential oils having antiviral, anti-inflammatory, and immunomodulatory properties
        date: 2020-08-14
       words: 5302
      flesch: 35
     summary: After the emergence of shreds of preliminary scientific evidences about anti-SARC-CoV-2 potentials of essential oils and their active components, various essential oils selling and extraction companies claimed about efficacy of their essential oils bearing products against COVID-19. MicrobiologyOpen 6:e00459 Safety of essential oils Relaxant effects of the essential oil of Eucalyptus tereticornis and its main constituent 1,8-cineole on guinea-pig tracheal smooth muscle Menthol: effects on nasal sensation of airflow and the drive to breathe SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective Structurally related monoterpenes p-cymene, carvacrol and thymol isolated from essential oil from leaves of Lippia sidoides Cham.
    keywords: cells; cov-2; covid-19; effects; eos; et al; eucalyptus; oils; sarc; sars; study; virus
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        item: #360 of 1349
          id: cord-256036-gd53s4dv
      author: Sandmann, Lisa
       title: Barriers of hepatitis C virus interspecies transmission
        date: 2013-01-01
       words: 7905
      flesch: 23
     summary: The role of transferrin receptor in Hepatitis C virus entry Hepatitis C virus induces interferon-lambda and interferonstimulated genes in primary liver cultures Expression of human CD81 in transgenic mice does not confer susceptibility to hepatitis C virus infection Determinants of hepatitis C translational initiation in vitro, in cultured cells and mice Telaprevir with peginterferon and ribavirin for chronic HCV genotype 1 infection The tight junction proteins claudin-1, -6, and -9 are entry cofactors for hepatitis C virus Hepatitis C virus replication in mice with chimeric human livers Biochemical and morphological properties of hepatitis C virus particles and determination of their lipidome The human liver-uPA-SCID mouse: a model for the evaluation of antiviral compounds against HBV and HCV The human liver-uPA-SCID mouse: a model for the evaluation of antiviral compounds against HBV and HCV Morphological and biochemical characterization of a human liver in a uPA-SCID mouse chimera Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus Species-specific regions of occludin required by hepatitis C virus for cell entry Identification of host genes involved in hepatitis C virus replication by small interfering RNA technology Association between hepatitis C virus and very-lowdensity lipoprotein (VLDL)/LDL analyzed in iodixanol density gradients Hepatitis C virus NS4B protein targets STING and abrogates RIG-I-mediated type-I interferon-dependent innate immunity Sustained viral response in a hepatitis C virus-infected chimpanzee via a combination of direct-acting antiviral agents Convergent evolution of escape from hepaciviral antagonism in primates The contributions of hepatitis B virus and hepatitis C virus infections to cirrhosis and primary liver cancer worldwide Binding of hepatitis C virus to CD81 Hepatitis C virus host cell entry Human occludin is a hepatitis C virus entry factor required for infection of mouse cells Persistent hepatitis C virus infection in microscale primary human hepatocyte cultures Hepatitis C virus glycoproteins interact with DC-SIGN and DC-SIGNR Boceprevir for untreated chronic HCV genotype 1 infection Immunity in hepatitis C infection Transgenic mice and the pathogenesis of poliomyelitis Cellular cofactors affecting hepatitis C virus infection and replication Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment Human pluripotent stem cell-derived hepatocytes support complete replication of hepatitis C virus Identification of the Niemann-Pick C1-like 1 cholesterol absorption receptor as a new hepatitis C virus entry factor The human scavenger receptor class B type I is a novel candidate receptor for the hepatitis C virus Molecular and serologic analysis in the transmission of the GB hepatitis agents The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of scandentia to other eutherian orders Interferon-stimulated genes and their antiviral effector functions A diverse range of gene products are effectors of the type I interferon antiviral response Modeling hepatitis C virus infection using human induced pluripotent stem cells Current animal models: transgenic animal models for the study of measles pathogenesis Memory CD8 þ T cells are required for protection from persistent hepatitis C virus infection Humanized mice in translational biomedical research Isolation of novel virus-like sequences associated with human hepatitis Lack of susceptibility of Chacma baboons (Papio ursinus orientalis) to hepatitis C virus infection Identification of human kinases involved in hepatitis C virus replication by small interference RNA library screening A functional genomic screen identifies cellular cofactors of hepatitis C virus replication Hepatic Niemann-Pick C1-like 1 regulates biliary cholesterol concentration and is a target of ezetimibe Kinases required in hepatitis C virus entry and replication highlighted by small interference RNA screening Replication of a hepatitis C virus replicon clone in mouse cells Identification of a lipid kinase as a host factor involved in hepatitis C virus RNA replication INX-08189, a phosphoramidate prodrug of 6-O-methyl-2 0 -C-methyl guanosine, is a potent inhibitor of hepatitis C virus replication with excellent pharmacokinetic and pharmacodynamic properties Disruption of Erk-dependent type I interferon Lack of susceptibility of various primates and woodchucks to hepatitis C virus Niemann-Pick C1 Like 1 protein is critical for intestinal cholesterol absorption Pathogenesis of hepatitis C virus infection in Tupaia belangeri Expression of paramyxovirus V proteins promotes replication and spread of hepatitis C virus in cultures of primary human fetal liver cells Assembly of infectious hepatitis C virus particles Roles for endocytic trafficking and phosphatidylinositol 4-kinase III alpha in hepatitis C virus replication Intrinsic immunity: a front-line defense against viral attack Human liver chimeric mice provide a model for hepatitis B and C virus infection and treatment Adaptation of hepatitis C virus to mouse CD81 permits infection of mouse cells in the absence of human entry factors Efficient initiation of HCV RNA replication in cell culture Highly permissive cell lines for hepatitis C virus genomic and subgenomic RNA replication Class III phosphatidylinositol 4-kinase alpha and beta are novel host factor regulators of hepatitis C virus replication Nonstructural 3/4A protease of hepatitis C virus activates epithelial growth factor-induced signal transduction by cleavage of the T-cell protein tyrosine phosphatase Host range studies of GB virus-B hepatitis agent, the closest relative of hepatitis C virus, in New World monkeys and chimpanzees Serology-enabled discovery of genetically diverse hepaciviruses in a new host miR-122, a mammalian liverspecific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1 Replication of hepatitis C virus (HCV) RNA in mouse embryonic fibroblasts: protein kinase R (PKR)-dependent and PKR-independent mechanisms for controlling HCV RNA replication and mediating interferon activities Humanized mice with ectopic artificial liver tissues Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome Debio 025, a cyclophilin binding molecule, is highly efficient in clearing hepatitis C virus (HCV) replicon-containing cells when used alone or in combination with specifically targeted antiviral therapy for HCV (STAT-C) inhibitors RNA interference and single particle tracking analysis of hepatitis C virus endocytosis L-SIGN (CD209L) and DC-SIGN (CD209) mediate transinfection of liver cells by hepatitis C virus New horizons for studying human hepatotropic infections Studies on the transmission of human viral hepatitis to marmoset monkeys.
    keywords: c virus; cd81; cells; entry; et al; hcv; hepatitis; host; human; infection; liver; mice; mouse; receptor; replication; rna; species; virus
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        item: #361 of 1349
          id: cord-256325-q70rky3r
      author: Stewart, Cameron R.
       title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease
        date: 2017-07-04
       words: 8331
      flesch: 28
     summary: Collectively, these data suggest that let-7 miRNAs inhibit HeV by suppressing host proteins required for virus infection. Central to this work was the development of a recombinant HeV expressing the renilla luciferase construct, which allowed for high throughput and rapid measurement of virus infection (Marsh et al. 2013 ).
    keywords: cell; disease; et al; fibrillarin; genes; henipavirus; hev; host; human; ifn; infection; niv; nuclear; proteins; rna; translation; virus; viruses
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        item: #362 of 1349
          id: cord-256370-cz88t29n
      author: Jansen van Vuren, Petrus
       title: Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa
        date: 2016-02-29
       words: 5541
      flesch: 43
     summary: 1 63.0 54.3 53.9 63.1 63.8 63.3 63.6 64.7 MAHLV replicated efficiently in Vero cell culture, with the inoculum containing a high dose of virus (10 5 TCID 50 /mL) leading to rapid monolayer destruction after inoculation, with a peak in virus RNA (measured by real-time RT-PCR) by day 7, followed by a decrease on day 13. The ectoparasite pool homogenate used for virus isolation was used as DNA source for phylogenetic confirmation of species.
    keywords: acid; amino; bat; bats; cells; culture; isolation; mahlv; orthoreovirus; protein; sequence; species; vero; virus; viruses
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        item: #363 of 1349
          id: cord-256444-grw5s2pf
      author: Lai, Michael M.C.
       title: The Molecular Biology of Coronaviruses
        date: 1997-12-31
       words: 35274
      flesch: 43
     summary: This phenomenon is reminiscent of the RNA reassortment that occurs in RNA viruses with segmented RNA genomes. This structure places coronavirus in a unique position among RNA viruses because it takes on the characteristics of positive-, negative-and double-strand RNA viruses in morphology.
    keywords: binding; cells; coronavirus; coronavirus rna; di rna; different; end; et al; fusion; gene; genomic rna; hepatitis virus; ibv; infection; leader rna; mhv; mouse; mrna; murine; n protein; orf; protein; receptor; recombination; rna; rna recombination; rna replication; rna sequence; rna synthesis; rna transcription; rnas; s protein; sequence; site; strand rna; subgenomic; tgev; transcription; viral; virus; virus rna
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        item: #364 of 1349
          id: cord-256508-ce59ovan
      author: Asselah, Tarik
       title: COVID-19: discovery, diagnostics and drug development
        date: 2020-10-08
       words: 9235
      flesch: 42
     summary: If RT-qPCR-based molecular assays for detecting SARS CoV-2 in respiratory specimens remain the current reference standard for diagnosis, point-of care technologies, and serologic immunoassays have also rapidly emerged [57] Indeed, antibodies to this protein are frequently detected in COVID-19 patient [64]
    keywords: antibodies; cell; coronavirus; cov-2; covid-19; disease; drug; human; immune; infection; liver; patients; remdesivir; samples; sars; study; testing; tests; treatment; virus
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        item: #365 of 1349
          id: cord-256510-orr2roxz
      author: de Castro, Isabel Fernández
       title: Virus factories: biogenesis and structural design
        date: 2012-10-04
       words: 5194
      flesch: 31
     summary: A revealed by fluorescence resonance energy transfer Emerging viruses: the Bunyaviridae Virion assembly factories in the nucleus of polyomavirus-infected cells Endogenous viruses: insights into viral evolution and impact on host biology Novel replication complex architecture in rubella replicon-transfected cells The unique architecture of Bunyamwera virus factories around the Golgi complex Three-dimensional structure of Rubella virus factories Functional Sindbis virus replicative complexes are formed at the plasma membrane Viral life cycles captured in three-dimensions with electron microscopy tomography Implication of mitochondria in the replication of Nodamura virus in larvae of the Lepidoptera, Galleria mellonella (L.) and in suckling mice /p33, a member of a new class of multifunctional and multicompartmental cellular proteins, is involved in inflammation and infection Ultrastructural characterization of SARS coronavirus A superhighway to virus infection Cellular factors in plant virus movement: at the leading edge of macromolecular trafficking in plants Intracellular transport of viruses and their components: utilizing the cytoskeleton and membrane highways Oligomeric structures of poliovirus polymerase are important for function Viral reorganization of the secretory pathway generates distinct organelles for RNA replication Breaking the diffraction barrier: super-resolution imaging of cells The Rubella virus capsid protein inhibits mitochondrial import Mitochondrial p32 is a critical mediator of ARF-induced apoptosis Electron tomography of the supramolecular structure of virus-infected cells Visualizing HIV-1 assembly Essential role of cyclophilin A for hepatitis C virus replication and virus production and possible link to polyprotein cleavage kinetics Coxsackievirus infection induces autophagy-like vesicles and megaphagosomes in pancreatic acinar cells in vivo SARScoronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum Ultrastructural characterization of arterivirus replication structures: reshaping the endoplasmic reticulum to accommodate viral RNA synthesis Three-dimensional analysis of a viral RNA replication complex reveals a virus-induced miniorganelle Aggresomes, inclusion bodies and protein aggregation The virophage as a unique parasite of the giant mimivirus Visualizing flock house virus infection in Drosophila cells with correlated fluorescence and electron microscopy Rubella virus replication and links to teratogenicity The tobacco mosaic virus 126-kilodalton protein, a constituent of the virus replication complex, alone or within the complex aligns with and traffics along microfilaments Synaptic vesicle-like lipidome of human cytomegalovirus virions reveals a role for SNARE machinery in virion egress Visualization and functional analysis of RNA-dependent RNA polymerase lattices Wrapping things up about virus RNA replication Rubella virus replication complexes are virus modified lysosomes Review: properties and assembly mechanisms of ND10, PML bodies, or PODs Modification of intracellular membrane structures for virus replication The N-terminal conserved domain of rubella virus capsid interacts with the C-terminal region of cellular p32 and overexpression of p32 enhances the viral infectivity Vaccinia-like cytoplasmic replication of the giant mimivirus Global genomics and proteomics approaches to identify host factors as targets to induce resistance against Tomato bushy stunt virus The dependence of viral RNA replication on co-opted host factors Virus factories, double membrane vesicles and viroplasm generated in animal cells Cellular pathways for viral transport through plasmodesmata Virus factories: associations of cell organelles for viral replication and morphogenesis The host Pex 19p plays a role in peroxisomal localization of tombusvirus replication proteins Three-dimensional visualization of gammaherpesvirus life cycle in host cells by electron tomography Modulation of membrane traffic between endoplasmic reticulum, ERGIC and Golgi to generate compartments for the replication of bacteria and viruses In vitro assembly of the Tomato bushy stunt virus replicase requires the host Heat shock protein 70 Detection and subcellular localization of the Turnip Yellow Mosaic Virus 66K replication protein in infected cells Oligomeric interaction of hepatitis C virus NS5B is critical for catalytic activity of RNAdependent RNA polymerase Viral interactions with the cytoskeleton: a hitchhiker's guide to the cell Redefining viruses: lessons from Mimivirus Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment Endoplasmic reticulum-Golgi intermediate compartment membranes and vimentin filaments participate in vaccinia virus assembly Specific, sensitive, high-resolution detection of protein molecules in eukaryotic cells using metal-tagging transmission electron microscopy Migration of mitochondria to viral assembly sites in African swine fever virus-infected cells Assembly of vaccinia virus: the second wrapping cisterna is derived from the trans-Golgi network Intracellular transport of plant viruses: finding the door out of the cell A positive-strand RNA virus replication complex parallels form and function of retrovirus capsids Enzymatic and nonenzymatic functions of viral RNA-dependent RNA polymerases within oligomeric arrays Phosphatidylinositol 3-kinase-, actin-, and microtubuledependent transport of Semliki Forest Virus replication complexes from the plasma membrane to modified lysosomes Electron microscopy of high-pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution Vaccinia virus DNA replication occurs in ER-enclosed cytoplasmic mini-nuclei Intracellular membrane traffic at high resolution Recent advances in the molecular and cellular biology of bunyaviruses Cyclophilin B is a functional regulator of hepatitis C virus RNA polymerase Composition and threedimensional architecture of the dengue virus replication and assembly sites Aggresomes and autophagy generate sites for virus replication Cryo-electron microscopy of the giant Mimivirus Distinct DNA exit and packaging portals in the virus Acanthamoeba polyphaga mimivirus A tyrosine-based motif in the cytoplasmic domain of the alphavirus envelope protein is essential for budding Our gratitude to Drs Isabelle Jupin, Cynthia Goldsmith, Karla Kirkegaard, Lindsay Whitton, Yael Mutsafi, Abraham Minsky, Juan Fontana and José Jesús Fernández for providing images and to Catherine Mark for editorial assistance. Since the early reviews on virus factories and replication organelles (Mackenzie, 2005; Novoa et al., 2005; Wileman, 2006) , there has been considerable progress in their characterization, as shown in several excellent, recently published reviews that cover different aspects of the cell biology of viral replication (Den Boon and Ahlquist 2010; Nagy and Pogany, 2011; Netherton and Wileman, 2011) .
    keywords: assembly; cell; et al; factories; factory; fig; membranes; mitochondria; replication; rna; virus; viruses
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        item: #366 of 1349
          id: cord-256561-fnh2do4z
      author: Barik, Sailen
       title: Therapy of Respiratory Viral Infections with Intranasal siRNAs
        date: 2014-09-23
       words: 2612
      flesch: 50
     summary: Here, we provide an example of tested functional siRNA sequences based on the L polymerase gene of RSV ( Table 1 ). Together, the small but representative datasets cover multiple viruses, modifi ed and unmodifi ed siRNA.
    keywords: intranasal; modifi; rsv; sirna; strand; virus
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        item: #367 of 1349
          id: cord-256615-gvq8uyfk
      author: Rosenberg, Ronald
       title: Detecting the emergence of novel, zoonotic viruses pathogenic to humans
        date: 2014-11-22
       words: 6694
      flesch: 42
     summary: Understanding how such adaptability works could focus our attention on those virus families or species with the greatest chance of infecting humans but how this knowledge could be used more specifically to identify potential threats to humans among animal viruses, as has recently been proposed Because all scientists worked in a single unit connections between human virus isolates and those from animals or vectors were readily made.
    keywords: animal; arboviruses; discovery; disease; human; novel; number; pathogens; rna; species; surveillance; transmission; viruses
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        item: #368 of 1349
          id: cord-256918-mauzesor
      author: Domingo, Esteban
       title: Quasispecies and the implications for virus persistence and escape
        date: 1998-07-15
       words: 2095
      flesch: 28
     summary: Crisis in infectious disease RNA virus evolution and the control of viral disease Biological significance of viral quasispecies Complications of RNA heterogeneity for the engineering of virus vaccines and antiviral agents RNA virus mutations and fitness for survival Nucleotide sequence heterogeneity of an RNA phage population Quasispecies: the concept and the word Viral quasispecies and the problem of vaccine-escape and drug-resistant mutants RNA virus quasispecies: significance for viral disease and epidemiology Self-organisation of matter and the evolution of biological macromolecules On the nature of viral quasispecies A Principle of Natural Self-Organisation How Escherichia coli can bias the results of molecular cloning: preferential selection of defective genomes of hepatitis C virus during the cloning procedure Canyon rim residues, including antigenic determinants, modulate serotype-specific binding of poliovirus to mutants of the poliovirus receptor Rapid evolution of RNA genomes RNA virus populations as quasispecies Efficient infection of cells in culture by type O foot-and-mouth disease virus requires binding to cell surface heparan sulfate Resistance to antimicrobial drugs-a worldwide calamity Emerging Infections. Mutations associated with drug resistance in virus from patients undergoing no drug therapy Rapid viral quasispecies evolution: implications for vaccine and drug strategies Quasispecies evolution of a hypervariable region of the feline calicivirus capsid gene in cell culture and in persistently infected cats Evolution of mouse hepatitis virus: detection and characterization of spike deletion variants during persistent infection Tissue culture adaptation of foot-and-mouth disease virus selects viruses that bind to heparin and are attenuated in cattle Structural and mechanistic relationships between nucleic acid polymerases Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase From the double-helix to novel approaches to the sequencing of large genomes The author is indebted to John Holland and his colleagues for many years of collaboration and helpful discussions, and to may colleagues and students from the laboratory for contributions to RNA virus quasispecies.
    keywords: genomes; quasispecies; rna; virus; viruses
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        item: #369 of 1349
          id: cord-256940-yuja99jg
      author: Wei, Bo
       title: Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports
        date: 2020-07-20
       words: 2000
      flesch: 50
     summary: Molecular docking-based virtual screening of all approved drugs showed that DNVr has the best binding energy to inhibit the main protease of SARS-CoV-2 14 . Herein, we present four COVID-19 cases who had positive nucleic acid results for about two months.
    keywords: cov-2; covid-19; results; rna; sars
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        item: #370 of 1349
          id: cord-257456-15bm9psj
      author: Arumugam, Arunkumar
       title: A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings
        date: 2020-09-24
       words: 5296
      flesch: 55
     summary: As a reference, we can detect five copies of SARS-CoV-2, positive control plasmid (CDC) per PCR reaction using primer targeting N2. Our findings in this paper with COVID-19 clinical samples suggest that it is possible to eliminate the RNA extraction step in COVID-19 testing without a significant drop in assay sensitivity for samples from symptomatic patients.
    keywords: cov-2; covid-19; extraction; pcr; rna; samples; sars; time
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        item: #371 of 1349
          id: cord-257569-36qx1sy9
      author: Hanada, Kousuke
       title: A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes
        date: 2004-06-17
       words: 3461
      flesch: 36
     summary: To estimate the degree of variation in mutation rates of RNA viruses and to understand the source of such variation, we studied the synonymous substitution rate because synonymous substitution is exempt from functional constraints at the protein level, and its rate reflects the mutation rate to a great extent. We estimated the synonymous substitution rates for a total of 49 different species of RNA viruses, and we found that the rates had tremendous variation by 5 orders of magnitude (from 1.3 × 10(−7) to 6.2 × 10(−2) /synonymous site/year).
    keywords: infection; rates; rna; rna viruses; substitution; transmission; viruses
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        item: #372 of 1349
          id: cord-257652-ndt8f812
      author: Zhang, Yong-Zhen
       title: The diversity, evolution and origins of vertebrate RNA viruses
        date: 2018-08-13
       words: 4250
      flesch: 33
     summary: Although we know a great deal more about the diversity and evolution of RNA viruses than we did before the start of this millennium, it is also apparent that we are only just starting to scratch the surface of their true biodiversity and evolution of vertebrate RNA viruses. A successful application of meta-transcriptomics to pathogen discovery from both arthropods and vertebrates, and documented the first evidence of hepcivirus in sharks Evolution of hantaviruses: co-speciation with reservoir hosts for more than 100 MYR Interspecies transmission and emergence of novel viruseslessons from bats and birds Cross-species transmission in the speciation of the currently known murinae-associated hantaviruses Migration of Norway rats resulted in the worldwide distribution of Seoul hantavirus today Extensive diversity of coronaviruses in bats from China Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families Reveals that 'host-jumping' plays an important role in shaping virus macroevolution Endogenous nonretroviral RNA virus elements in mammalian genomes Filoviruses are ancient and integrated into mammalian genomes A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors Backbone of RNA viruses uncovered This study was supported by the National Natural Science Foundation of China (Grants 81861138003, 81672057) and the Special National Project on Research and Development of Key Biosafety Technologies (2016YFC1201900, 2016YFC1200101).
    keywords: diversity; evolution; fish; hosts; rna; vertebrate; viruses
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        item: #373 of 1349
          id: cord-257693-rnchfjbe
      author: Wang, Yeming
       title: Factors Associated With Prolonged Viral Shedding in Patients With Avian Influenza A(H7N9) Virus Infection
        date: 2018-04-10
       words: 3997
      flesch: 35
     summary: Notes Human infection with a novel avian-origin influenza A (H7N9) virus Epidemiology of avian influenza A H7N9 virus in human beings across five epidemics in mainland China, 2013-17: an epidemiological study of laboratory-confirmed case series Sudden increase in human infection with avian influenza A(H7N9) virus in China Update: increase in human infections with novel Asian lineage avian influenza A(H7N9) viruses during the fifth epidemic -China Epidemiology of human infections with highly pathogenic avian influenza A(H7N9) virus in Guangdong Preliminary epidemiology of human infections with highly pathogenic avian influenza A(H7N9) virus, China Novel influenza A viruses and pandemic threats Pathogenesis of influenza-induced acute respiratory distress syndrome Influenza virus-induced lung injury: pathogenesis and implications for treatment Viral loads and duration of viral shedding in adult patients hospitalized with influenza Toronto Invasive Bacterial Diseases Network. Outcomes from pandemic influenza A H1N1 infection in recipients of solid-organ transplants: a multicentre cohort study Effectiveness of oseltamivir on disease progression and viral RNA shedding in patients with mild pandemic 2009 influenza A H1N1: opportunistic retrospective study of medical charts in China Treatment with neuraminidase inhibitors for critically ill patients with influenza A (H1N1)pdm09 Impact of neuraminidase inhibitor treatment on outcomes of public health importance during the 2009-2010 influenza A(H1N1) pandemic: a systematic review and meta-analysis in hospitalized patients Effectiveness of neuraminidase inhibitors in reducing mortality in patients admitted to hospital with influenza A H1N1pdm09 virus infection: a meta-analysis of individual participant data Determinants of antiviral effectiveness in influenza virus A subtype H5N1 Systematic review of influenza A(H1N1)pdm09 virus shedding: duration is affected by severity, but not age Benefit of early initiation of neuraminidase inhibitor treatment to hospitalized patients with avian influenza A (H7N9) virus Adjuvant Corticosteroid Treatment in Adults With Influenza A (H7N9) Viral Pneumonia Clinical findings in 111 cases of influenza A (H7N9) virus infection Use of corticosteroids in acute lung injury and acute respiratory distress syndrome: a systematic review and meta-analysis Corticosteroid therapy for critically ill patients with the middle east respiratory syndrome Fatal outcome of human influenza A (H5N1) is associated with high viral load and hypercytokinemia H5N1 infection of the respiratory tract and beyond: a molecular pathology study The role of adjuvant immunomodulatory agents for treatment of severe influenza Effects of early corticosteroid treatment on plasma SARS-associated Coronavirus RNA concentrations in adult patients Association between adverse clinical outcome in human disease caused by novel influenza A H7N9 virus and sustained viral shedding and emergence of antiviral resistance Human infection with highly pathogenic avian influenza A(H7N9) virus, China Bivir Study Group.
    keywords: a(h7n9; days; influenza; nai; oseltamivir; patients; rna; shedding; treatment
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        item: #374 of 1349
          id: cord-258035-2tk7maqk
      author: DeFilippis, Victor
       title: Functional genomics in virology and antiviral drug discovery
        date: 2003-10-31
       words: 4774
      flesch: 35
     summary: A special case of virus modulation of host cell gene expression in which functional genomics will reveal novel targets and treatments is viral oncogenesis. In addition, non-hypothesisdriven global gene expression profiling can reveal host cell genes that promote viral growth.
    keywords: cell; dna; expression; gene; host; microarrays; replication; rna; sirna; targets; virus; viruses
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        item: #375 of 1349
          id: cord-258172-p54j4zzo
      author: Barker, Harlan
       title: Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2
        date: 2020-10-28
       words: 8473
      flesch: 43
     summary: In lung, ACE2 expressing cells are generally uncommon with no cell type having a ratio of ACE2-expressing cells greater than 2.6%. [27] , whereas Sims and colleagues demonstrated ACE2 expression on the luminal surface of ciliated cells in freshly excised human nasal and tracheobronchial tissue
    keywords: ace2; analysis; angiotensin; binding; cells; cov-2; covid-19; data; expression; gene; human; lung; mrna; receptor; sars; tissues
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        item: #376 of 1349
          id: cord-258286-lodjcj8c
      author: Zhang, Xuming
       title: Expression of Interferon-γ by a Coronavirus Defective-Interfering RNA Vector and Its Effect on Viral Replication, Spread, and Pathogenicity
        date: 1997-07-07
       words: 5890
      flesch: 46
     summary: Correlation between IFN resistance and cally elucidate the mechanism of pathogenesis of MHV viral pathogenicity has also been documented for meaat the molecular level. (B) Neutralization assay of IFN-g. Both UV-irradiated supernatants (IFN-g and CAT) were incubated with 1 mg/ml of a hamster anti-IFN-g neutralizing monoclonal antibody for 2 hr at room temperature prior to being used for pretreatment of cells.
    keywords: antiviral; cells; ifn; infection; jhm; mhv; rna; virus
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        item: #377 of 1349
          id: cord-258547-47cyyetb
      author: Asasi, Keramat
       title: Changes of several acute phase factors in broiler chickens in response to infectious bronchitis virus infection
        date: 2013-08-01
       words: 3595
      flesch: 44
     summary: A preliminary investigation of using acute-phase variables to assess diseases in chickens LNA probe-based real-time RT-PCR for the detection of infectious bronchitis virus from the oviduct of unvaccinated and vaccinated laying hens Evaluation of serum sialic acid as an inflammation marker in cattle with traumatic reticulo peritonitis Recent advances and future prospects for the use of acute phase proteins as markers of disease in animals The time is right for acute phase protein assays Acute-phase proteins and other systemic responses to inflammation Acute phase reaction and acute phase proteins The toxicity of purified fumonisin B 1 in broiler chicks Comparison of the effects of infection with Salmonella enteritidis, in combination with an induced molt, on serum levels of the acute phase protein α1-acid glycoprotein in hens Serum levels of mannan-binding lectin (MBL) in chickens prior to and during experimental infection with avian infectious bronchitis virus (IBV) Avian Cytokines and Chemokines Lipid associated sialic acid test for the detection of human cancer Changes in the protein profile in birds with experimental acute fowl typhoid The acute phase response in Japanese quail (Coturnix coturnix japonica) Evaluation of goose serum amyloid Inflammatory reaction in infected chicks following IBV inoculation causes the release and elevation of pro-inflammatory cytokine concentrations.
    keywords: acute; infected; lbsa; phase; serum; tsa
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        item: #378 of 1349
          id: cord-258595-bk35vxlr
      author: Westhaus, Sandra
       title: Detection of SARS-CoV-2 in raw and treated wastewater in Germany – Suitability for COVID-19 surveillance and potential transmission risks
        date: 2020-08-18
       words: 4968
      flesch: 45
     summary: For the content of the dry residues, a defined volume of wastewater sample was dried at 105°C for 24 h (DIN 38409-1 (1987-01)), and the residue was weighed by a Sartorius A 120 S balance. In this study, wastewater samples were analysed with two different PCRs targeting SARS-CoV-2 RdRP and M-gene.
    keywords: cases; cov-2; covid-19; gene; qpcr; rna; samples; sars; studies; wastewater
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        item: #379 of 1349
          id: cord-258678-0atfsivf
      author: Liu, Hong Yan
       title: A Universal Protein Tag for Delivery of SiRNA-Aptamer Chimeras
        date: 2013-11-07
       words: 4800
      flesch: 40
     summary: Unfortunately, these conventional siRNA nanocarriers are unsuitable for chimera delivery, and, in fact, reverse the signature property of chimera, simple formulation for regulatory approval and clinical translation 15, 16 . Although positively charged nanocarriers promote siRNA cell entry, it is well known that they are also quickly cleared by the RES, increase non-specific binding with cells and cytotoxicity 35 .
    keywords: aptamer; binding; cells; chimera; delivery; dsrbd; gfp; protein; silencing; sirna; specific; tag; targeting
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        item: #380 of 1349
          id: cord-258696-01wj76es
      author: Decaro, Nicola
       title: Experimental infection of dogs with a novel strain of canine coronavirus causing systemic disease and lymphopenia
        date: 2008-04-30
       words: 3449
      flesch: 55
     summary: The thermal profile consisted of activation of iTaq DNA polymerase at 95 8C for 10 min, followed by 45 cycles of denaturation at 95 8C for 15 s, annealing at 48 8C (type II-specific assay) for 30 s and extension at 60 8C for 1 min. Plasma samples from inoculated dogs were tested in parallel by virus neutralisation (VN) and ELISA tests (Pratelli et al., 2002) . key: cord-258696-01wj76es authors: Decaro, Nicola; Campolo, Marco; Lorusso, Alessio; Desario, Costantina; Mari, Viviana; Colaianni, Maria Loredana; Elia, Gabriella; Martella, Vito; Buonavoglia, Canio title: Experimental infection of dogs with a novel strain of canine coronavirus causing systemic disease and lymphopenia date: 2008-04-30 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2007.10.008 sha: doc_id: 258696 cord_uid: 01wj76es A pantropic canine coronavirus (CCoV) strain (CB/05) has been recently associated to a fatal outbreak of systemic disease in young dogs.
    keywords: ccov; days; dogs; p.i; rna
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        item: #381 of 1349
          id: cord-259152-pwvcwlh8
      author: Ji, Wei
       title: Cross‐species transmission of the newly identified coronavirus 2019‐nCoV
        date: 2020-02-19
       words: 1695
      flesch: 44
     summary: To investigate possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019‐nCoV sequence. The availability of viral RNA sequence has made it All authors contributed equally to this work.
    keywords: 2019; analysis; coronavirus; ncov; recombination
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        item: #382 of 1349
          id: cord-259233-smmhhroe
      author: de Armas‐Rillo, Laura
       title: Membrane dynamics associated with viral infection
        date: 2016-01-28
       words: 7119
      flesch: 35
     summary: ASFVs are thought to reorganize cell membranes through viral proteins that contain a KDE motif, inducing the redistribution of ERassociated proteins [88] and the viral p54 protein. Modification of intracellular membrane structures for virus replication Viruses and endosome membrane dynamics When autophagy meets viruses: a double-edged sword with functions in defense and offense Viral infection: moving through complex and dynamic cell-membrane structures How to get out: ssRNA enveloped viruses and membrane fission Neutrophil granules and secretory vesicles in inflammation A guide to viral inclusions, membrane rearrangements, factories, and viroplasm produced during virus replication.
    keywords: assembly; autophagy; budding; cell; complex; escrt; figure; formation; infection; membrane; proteins; replication; rna; vesicles; virus; viruses
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        item: #383 of 1349
          id: cord-259246-azt5sr9w
      author: Peng, Qi
       title: Structural basis of SARS-CoV-2 polymerase inhibition by Favipiravir
        date: 2020-10-19
       words: 3229
      flesch: 46
     summary: Besides, the cyanogroup in the ribose ring may cause steric clash with polymerase residues during elongation, resulting in aberrant termination of RNA synthesis 29,31 . Due to the key roles of polymerase complex for viral replication, it has long been thought of as a promising antiviral drug target 25 .
    keywords: complex; favipiravir; fig; polymerase; residues; rna; sars; structure; template
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        item: #384 of 1349
          id: cord-259311-ccx61owl
      author: Kapitula, D. S.
       title: Performance & Quality Evaluation of Marketed COVID-19 RNA Detection Kits
        date: 2020-05-01
       words: 3189
      flesch: 47
     summary: In conclusion, Jade Biomedical (Suzhou) Co, Ltd has identified the Best Total Solution (BTS) for COVID-19 RNA testing, which involves using Tiangen or Qiagen RNA extraction and BGI qPCR kits. Notably, the initial failure in quality virus testing kits distributed by US CDC is viewed as a critical mistake in the management of the crises by the US government resulting in compromised ability to test and trace the earlier infected population clusters before they spread to wider populations through community contacts.
    keywords: china; covid-19; detection; kits; performance; rna; table; testing; virus
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        item: #385 of 1349
          id: cord-259500-ndjbrtrv
      author: Satyanarayana, Tatineni
       title: Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli
        date: 2003-09-01
       words: 6484
      flesch: 48
     summary: Reverse genetics, the ability to produce specific mutations followed by examination of phenotype, revolutionized the study of RNA viruses. Yet it is possible that slippery sequences serve as a survival mechanism for large RNA viruses.
    keywords: cdna; clar; coli; fig; frameshift; rna; virus
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        item: #386 of 1349
          id: cord-259593-shrd1s7r
      author: Qin, Zhao-ling
       title: siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA
        date: 2007-06-27
       words: 4617
      flesch: 45
     summary: The results showed that the M protein is mainly located in the Golgi apparatus, and that the specific siRNAs corresponding to SCoV M gene specifically degraded M mRNA, significantly inhibiting M protein expression. The changes of SCoV M gene expression in siRNA co-transfected cells, normalized to GAPDH and relative to its expression in mock-transfected cells, were calculated for each sample.
    keywords: cells; coronavirus; egfp; expression; fluorescence; gene; protein; sars; scov; sirna
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        item: #387 of 1349
          id: cord-259603-bh198xgl
      author: Snijder, E.J.
       title: The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing
        date: 2016-09-14
       words: 24307
      flesch: 38
     summary: Whereas the poor replication fidelity generally restricts RNA virus genome sizes, it has been postulated that nidovirus genome expansion was enabled by the acquisition of specific replicative functions that counter the error rate of the RNA polymerase (Deng et al., 2014; Eckerle et al., 2010; Snijder et al., 2003) (discussed in more detail later). A recent structural study of the arterivirus nsp10-helicase (Deng et al., 2014) will be discussed in more detail later.
    keywords: activity; binding; bouvet et; chen et; complex; conserved; coronavirus; cov; covs; domain; et al; exon; fig; genome; helicase; interactions; lehmann et; mrna; mtase; nidovirus; nsp10; nsp8; protein; rdrp; replicase; replication; residues; rna; rna synthesis; role; sars; site; structure; studies; synthesis
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        item: #388 of 1349
          id: cord-259671-7de21oaq
      author: Madhugiri, Ramakanth
       title: RNA structure analysis of alphacoronavirus terminal genome regions
        date: 2014-12-19
       words: 11177
      flesch: 34
     summary: Despite major progress in the characterization of proteins and cis-acting RNA elements involved in coronavirus RNA synthesis, the molecular mechanisms that mediate specific steps of coronavirus RNA replication and transcription are far from being understood. A conserved RNA pseudoknot in a putative molecular switch domain of the 3 -untranslated region of coronaviruses is only marginally stable Leader switching occurs during the rescue of defective RNAs by heterologous strains of the coronavirus infectious bronchitis virus Dodecamer structure of severe acute respiratory syndrome coronavirus nonstructural protein nsp10 Dependence of coronavirus RNA replication on an NH2-terminal partial nonstructural protein 1 in cis Severe acute respiratory syndrome coronavirus nsp1 facilitates efficient propagation in cells through a specific translational shutoff of host mRNA The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent Genome organization and reverse genetic analysis of a type I feline coronavirus A mobile genetic element with unknown function found in distantly related viruses Infectious RNA transcribed in vitro from a cDNA copy of the human coronavirus genome cloned in vaccinia virus Suppression of host gene expression by nsp1 proteins of group 2 bat coronaviruses Expression and functions of SARS coronavirus replicative proteins Discontinuous subgenomic RNA synthesis in arteriviruses is guided by an RNA hairpin structure located in the genomic leader region Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome The leader RNA of coronavirus mouse hepatitis virus contains an enhancer-like element for subgenomic mRNA transcription Severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp1 and rational design of an attenuated strain Evolution of virus and defective-interfering RNAs in BHK cells persistently infected with Sindbis virus LocARNA-P: accurate boundary prediction and improved detection of structural RNAs Analysis of a hypervariable region in the 3 non-coding end of the infectious bronchitis virus genome A phylogenetically conserved hairpin-type 3 untranslated region pseudoknot functions in coronavirus RNA replication Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia Reselection of a genomic upstream open reading frame in mouse hepatitis coronavirus 5 -untranslatedregion mutants Common RNA replication signals exist among group 2 coronaviruses: evidence for in vivo recombination between animal and human coronavirus molecules Regulation of coronaviral poly(A) tail length during infection Bovine coronavirus 5 -proximal genomic acceptor hotspot for discontinuous transcription is 65 nucleotides wide Nonstructural proteins 7 and 8 of feline coronavirus form a 2:1 heterotrimer that exhibits primer-independent RNA polymerase activity Mouse hepatitis virus stem-loop 4 functions as a spacer element required to drive subgenomic RNA synthesis Strategy for systematic assembly of large RNA and DNA genomes: transmissible gastroenteritis virus model Reverse genetics with a full-length infectious cDNA of severe acute respiratory syndrome coronavirus Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer Coronavirus leader RNA regulates and initiates subgenomic mRNA transcription both in trans and in cis Coronavirus replicative proteins Characterization of a human coronavirus (strain 229E) 3C-like proteinase activity
    keywords: base; cis; conserved; coronavirus; elements; et al; genome; interactions; loop; mhv; protein; region; replication; rna; sequence; stem; structure; utr
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        item: #389 of 1349
          id: cord-259710-qrht9tq3
      author: Burimuah, Vitus
       title: Molecular-based cross-species evaluation of bovine coronavirus infection in cattle, sheep and goats in Ghana
        date: 2020-10-27
       words: 3543
      flesch: 54
     summary: Substantial economic toll can be exerted by BCoV infection when a large herd are infected, resulting in drastic reduction in milk yield [12, 13] . Despite the health and economic significance of BCoV in livestock, only limited studies have been conducted to evaluate BCoV infection in livestock in Ghana to date.
    keywords: bcov; bovine; cattle; coronavirus; ghana; goats; infection; rna; study
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        item: #390 of 1349
          id: cord-259916-gr6v098c
      author: Wang, Hongliang
       title: Mechanisms of Cellular Membrane Reorganization to Support Hepatitis C Virus Replication
        date: 2016-05-20
       words: 6205
      flesch: 28
     summary: In addition, as DRMs are important platforms for cellular membrane trafficking and signal transduction [27, 28] , it is conceivable that this property of HCV replication membranes may also regulate signal transduction and membrane trafficking at viral replication sites. These findings suggest a model in which PI4P recruits LTPs such as OSBP and FAPP2 to HCV replication organelles, which in turn result in the trafficking of cholesterol and glycosphingolipids to HCV replication membranes.
    keywords: dmvs; formation; hcv; hepatitis; membrane; ns5a; protein; replication; rna; viral; virus
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        item: #391 of 1349
          id: cord-259927-xh9cw9ao
      author: Papadopoulos, Nikolaos G.
       title: Promising approaches for the treatment and prevention of viral respiratory illnesses
        date: 2017-07-21
       words: 7351
      flesch: 24
     summary: A viruses Hemagglutinin-stem nanoparticles generate heterosubtypic influenza protection Self-assembling influenza nanoparticle vaccines elicit broadly neutralizing H1N1 antibodies Layer-by-layer nanoparticle vaccines carrying the G protein CX3C motif protect against RSV infection and disease Eleven years of Inflexal V-a virosomal adjuvanted influenza vaccine Human papillomavirus and HPV vaccines: a review AS01 malaria vaccine with or without a booster dose in infants and children in Africa: final results of a phase 3, individually randomised, controlled trial M2e-based universal influenza A vaccine Virus-like particles as a highly efficient vaccine platform: diversity of targets and production systems and advances in clinical development Comparison of a novel microcrystalline tyrosine adjuvant with aluminium hydroxide for enhancing vaccination against seasonal influenza Matrix M H5N1 vaccine induces cross-H5 clade humoral immune responses in a randomized clinical trial and provides protection from highly pathogenic influenza challenge in ferrets Safety and immunogenicity of a recombinant M2e-flagellin influenza vaccine (STF2.4xM2e) in healthy adults Chitosan-a versatile semi-synthetic polymer in biomedical applications Genetic immunization is a simple method for eliciting an immune response Development of an intradermal DNA vaccine delivery strategy to achieve single-dose immunity against respiratory syncytial virus Modified mRNA vaccines protect against Zika virus infection DNA and RNA-based vaccines: principles, progress and prospects Replicon RNA viral vectors as vaccines Transforming growth factor-beta promotes rhinovirus replication in bronchial epithelial cells by suppressing the innate immune response Efficacy and safety of high-dose influenza vaccine in elderly adults: a systematic review and meta-analysis Effectiveness of MF59-adjuvanted seasonal influenza vaccine in the elderly: a systematic review and meta-analysis A systematic review and meta-analysis of cross-reactivity of antibodies induced by oil-in-water emulsion adjuvanted influenza H5N1 virus monovalent vaccines Preclinical pharmacokinetics of MHAA4549A, a human monoclonal antibody to influenza A virus, and the prediction of its efficacious clinical dose for the treatment of patients hospitalized with influenza A Efficacy and safety of treatment with an anti-m2e monoclonal antibody in experimental human influenza Safety and upper respiratory pharmacokinetics of the hemagglutinin stalk-binding antibody VIS410 support treatment and prophylaxis based on population modeling of seasonal influenza A outbreaks Priming by a novel universal influenza vaccine (Multimeric-001)-a gateway for improving immune response in the elderly population A highly potent extended half-life antibody as a potential RSV vaccine surrogate for all infants Safety and immunogenicity of a Sf9 insect cell-derived respiratory syncytial virus fusion protein nanoparticle vaccine Immunogenicity and safety of a respiratory syncytial virus fusion protein (RSV F) nanoparticle vaccine in older adults Evaluation of the immunogenicity and safety of different doses and formulations of a broad spectrum influenza vaccine (FLU-v) developed by SEEK: study protocol for a single-center, randomized, double-blind and placebo-controlled clinical phase IIb trial Caparr os-Wanderley W. Synthetic Influenza vaccine (FLU-v) stimulates cell mediated immunity in a double-blind, randomised, placebo-controlled phase I trial A synthetic influenza virus vaccine induces a cellular immune response that correlates with reduction in symptomatology and virus shedding in a randomized phase Ib live-virus challenge in humans A T cell-inducing influenza vaccine for the elderly: safety and immunogenicity of MVA-NP1M1 in adults aged over 50 years A Phase IIA study to assess the safety and efficacy of a new influenza candidate vaccine MVA-NP1M1 in healthy adults-Flu002 Clinical Study Report Evaluating the immunogenicity and safety of a BiondVax-developed universal influenza vaccine (Multimeric-001) either as a standalone vaccine or as a primer to H5N1 influenza vaccine Back to the future: immunization with M-001 prior to trivalent influenza vaccine in 2011/12 enhanced protective immune responses against 2014/15 epidemic strain Safety and immunogenicity of multimeric-001-a novel universal influenza vaccine Implication of respiratory syncytial virus (RSV) F transgene sequence heterogeneity observed in Phase 1 evaluation of MEDI-534, a live attenuated parainfluenza type 3 vectored RSV vaccine Phase-I study MEDI-534, of a live, attenuated intranasal vaccine against respiratory syncytial virus and parainfluenza-3 virus in seropositive children A randomized, blinded, controlled, dose-ranging study of a respiratory syncytial virus recombinant fusion (F) nanoparticle vaccine in healthy women of childbearing age Efficacy of motavizumab for the prevention of respiratory syncytial virus disease in healthy Native American infants: a phase 3 randomised double-blind placebo-controlled trial Motavizumab for prophylaxis of respiratory syncytial virus in high-risk children: a noninferiority trial Trivalency of a nanobody specific for the human respiratory syncytial virus fusion glycoprotein drastically enhances virus neutralization and impacts escape mutant selection Efficacy, safety, and pharmacokinetics of a new 10% liquid intravenous immunoglobulin containing high titer neutralizing antibody to RSV and other respiratory viruses in subjects with primary immunodeficiency disease Treatment with novel RSV Ig RI-002 controls viral replication and reduces pulmonary damage in immunocompromised Sigmodon hispidus Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection Highly conserved protective epitopes on influenza B viruses Human antibodies reveal a protective epitope that is highly conserved among human and nonhuman influenza A viruses Tackling influenza with broadly neutralizing antibodies Influenza virus vaccine based on the conserved hemagglutinin stalk domain Chimeric hemagglutinin influenza virus vaccine constructs elicit broadly protective stalk-specific antibodies Chimeric hemagglutinin constructs induce broad protection against influenza B virus challenge in the mouse model Epitope specificity plays a critical role in regulating antibody-dependent cell-mediated cytotoxicity against influenza A virus Influenza vaccine research funded by the European Commission FP7-Health-2013-Innovation-1 project Antibodies to watch in 2017 Protective efficacy and immunogenicity of an adenoviral vector vaccine encoding the codon-optimized F protein of respiratory syncytial virus Immunogenicity of RSV F DNA vaccine in BALB/c Mice RSV fusion (F) protein DNA vaccine provides partial protection against viral infection Chimeric virus-like particles containing a conserved region of the G protein in combination with a single peptide of the M2 protein confer protection against respiratory syncytial virus infection Baculovirus-expressed virus-like particle vaccine in combination with DNA encoding the fusion protein confers protection against respiratory syncytial virus Co-immunization with virus-like particle and DNA vaccines induces protection against respiratory syncytial virus infection and bronchiolitis Respiratory syncytial virus: infection, detection, and new options for prevention and treatment Immunogenicity and efficacy of codon optimized DNA vaccines encoding the F-protein of respiratory syncytial virus Mucosal vaccines against respiratory syncytial virus Prevention of colds by vaccination against a rhinovirus: a report by the scientific committee on common cold vaccines Challenges in developing a cross-serotype rhinovirus vaccine Misdirected antibody responses against an N-terminal epitope on human rhinovirus VP1 as explanation for recurrent RV infections Wide-scale prevention through immunization appears to be within reach for respiratory syncytial virus and promising for influenza virus, whereas additional effort is needed in regard to rhinovirus, as well as other respiratory tract viruses.
    keywords: antiviral; asthma; human; ifv; immune; infection; influenza; novel; patients; prevention; rhinovirus; rna; rsv; safety; tract; treatment; trial; vaccine; virus; viruses
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        item: #392 of 1349
          id: cord-260042-cs0wp99n
      author: Khan, Samiullah
       title: Genes involved in mitochondrial biogenesis and function may not show synchronised responses to mitochondria in shell gland of laying chickens under infectious bronchitis virus challenge
        date: 2019-04-01
       words: 6940
      flesch: 41
     summary: Similarly, increases in mitochondrial DNA (mtDNA) have been observed during myogenesis in rats [17] and in brown adipocytes of various mammals in response to low temperature [18] . Infectious bronchitis virus; mtDNA: mitochondrial DNA; Na + -K
    keywords: cells; challenge; dna; egg; expression; formation; genes; gland; ibv; oviduct; rna; shell; time; tissue; virus
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        item: #393 of 1349
          id: cord-260168-rb7j94dh
      author: Gu, Jiang
       title: H5N1 infection of the respiratory tract and beyond: a molecular pathology study
        date: 2007-09-27
       words: 6314
      flesch: 46
     summary: Our comprehensive investigation of the tissue tropism of H5N1 infl uenza virus, based on two adult autopsies and one fetal autopsy, focuses on the localisation of viral genomic sequences and antigens. In cultures of human tracheobronchial epithelial cells, H5N1 infl uenza viruses have been reported to infect mainly ciliated cells, which express mainly avian infl uenza virus receptors (α-2,3-linked sialic acids), although a limited number of non-ciliated cells (<20% of all infected cells) have also been reported to be infected.
    keywords: cells; gure; h5n1; human; hybridisation; infl; patient; pcr; rna; situ; uenza; virus
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        item: #394 of 1349
          id: cord-260225-bc1hr0fr
      author: Sirpilla, Olivia
       title: SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes
        date: 2020-07-20
       words: 8938
      flesch: 32
     summary: Superfamily 1 Helicase Has RNA and DNA Duplex-Unwinding Activities with 5′-to-3′ Polarity Structure-Function Analysis of Severe Acute Respiratory Syndrome Coronavirus RNA Cap Guanine-N7-Methyltransferase Functional Screen Reveals SARS Coronavirus Nonstructural Protein Nsp14 as a Novel Cap N7 Methyltransferase Characterization of the Guanine-N7 Methyltransferase Activity of Coronavirus Nsp14 on Nucleotide GTP The Cellular RNA Helicase DDX1 Interacts with Coronavirus Nonstructural Protein 14 and Enhances Viral Replication Crystal Structure and Mechanistic Determinants of SARS Coronavirus Nonstructural Protein 15 Define an Endoribonuclease Family Crystal Structure of a Monomeric Form of Severe Acute Respiratory Syndrome Coronavirus Endonuclease Nsp15 Suggests a Role for Hexamerization as an Allosteric Switch Structural and Biochemical Characterization of Endoribonuclease Nsp15 Encoded by Middle East Respiratory Syndrome Coronavirus Binding of the Methyl Donor S-Adenosyl-l-Methionine to Middle East Respiratory Syndrome Coronavirus 2′-O-Methyltransferase nsp16 Promotes Recruitment of the Allosteric Activator nsp10 Coronavirus Nonstructural Protein 16 Is Group 2 Bat Coronaviruses A Two-Pronged Strategy to Suppress Host Protein Synthesis by SARS Coronavirus Nsp1 Protein Severe Acute Respiratory Syndrome Coronavirus Protein Nsp1 Is a Novel Eukaryotic Translation Inhibitor That Represses Multiple Steps of Translation Initiation Severe Acute Respiratory Syndrome Coronavirus Evades Antiviral Signaling: Role of Nsp1 and Rational Design of an Attenuated Strain Unique SARS-CoV Protein Nsp1: Bioinformatics, Biochemistry and Potential Effects on Virulence Coronavirus Nonstructural Protein 1: Common and Distinct Functions in the Regulation of Host and Viral Gene Expression Protein Structure and Sequence Reanalysis of 2019-NCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1
    keywords: blast; cells; coronavirus; cov-2; decay; figure; human; immune; information; interaction; mrna; nonsense; nucleocapsid; protein; replication; respiratory; rna; sars; sequences; structure; syndrome
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        item: #395 of 1349
          id: cord-260250-t48y27wg
      author: Decaro, Nicola
       title: Quantitation of canine coronavirus RNA in the faeces of dogs by TaqMan RT-PCR
        date: 2004-05-07
       words: 3332
      flesch: 39
     summary: The CCoV fluorogenic RT-PCR assay, which targeted the ORF5 (M gene), was more sensitive than a conventional RT-PCR assay targeting the same gene, showing a detection limit of 10 copies of CCoV standard RNA, and was linear from 10 to 10(8) copies, allowing quantitation of samples with a wide range of CCoV RNA loads. Several RT-PCR based methods have been developed for detecting CCoV RNA in the faeces of dogs, but none of these were designed to be quantitative (Bandai et al., 1999; Naylor et al., 2001; Pratelli et al., 1999 Pratelli et al., , 2002c .
    keywords: assay; ccov; et al; fluorogenic; pcr; rna
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        item: #396 of 1349
          id: cord-260345-ugd8kkor
      author: Giles, Ian G.
       title: A compendium of reviews in biochemistry and molecular biology published in the first half of 1992
        date: 1992-12-31
       words: 5346
      flesch: 43
     summary: Biomembrane 24, 99-110. anion channel; contact sites; selective channels; brain mitochondria; lot] channci; conductance; protein; Ca*'; mitoplasts;CatiOllS. L. and Herzfeld J. (1992) NMR studies of retinal proteins. position effect variegation; Drarophila; protein.
    keywords: acid; amino; analysis; binding; brain; cells; channel; delta; dna; expression; factor; gamma; gene; growth; heat; human; lipid; liver; membrane; messenger; muscle; plasma; protein; rat; receptor; regulation; review; rna; sequence; shock; system
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        item: #397 of 1349
          id: cord-260422-z22t57ju
      author: Godet, Julien
       title: Comparative nucleic acid chaperone properties of the nucleocapsid protein NCp7 and Tat protein of HIV-1
        date: 2012-06-26
       words: 9194
      flesch: 29
     summary: Later, a similar chaperone activity was shown for the HIV-1 NC protein (Darlix et al., 1990; De Rocquigny et al., 1992; Barat et al., 1993; Dib-Hajj et al., 1993; Lapadat-Tapolsky et al., 1993) . In sharp contrast to NCp7, multimerization of Gag or Gag-related proteins dramatically compromises reverse transcription since the cooperative binding and the slow dissociation rate of the multimerized Gag proteins impaired RT processivity (Wu et al., 2010) .
    keywords: acid; activity; annealing; binding; chaperone; dna; et al; gag; human; ncp7; nucleic; primer; protein; rna; strand; tat; transcription; trna; virus
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        item: #398 of 1349
          id: cord-260452-js4nr4d8
      author: Yu, Junyang
       title: Activation and Role of NACHT, LRR, and PYD Domains-Containing Protein 3 Inflammasome in RNA Viral Infection
        date: 2017-10-31
       words: 4114
      flesch: 16
     summary: Viral RNA (vRNA) moleculeinduced NLRP3 inflammasome activation also comes about by post-translational priming, but involving the RIP1/caspase 8/RIP3 signaling pathway (29, 45) , which may ultimately result in the deubiquitination of NLRP3 protein by BRCC3 (46, 47) . Among the other viral proteins involved in NLRP3 inflammasome activation are IAV PB1-F2 (a small protein encoded by an alternate + 1 open reading frame in the viral PB1 gene) (7) and EV71 3D protein (an RNA-dependent RNA polymerase) (34) .
    keywords: activation; cells; iav; infection; inflammasome; nlrp3; protein; response; rna; virus
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        item: #399 of 1349
          id: cord-260647-7bjhobg7
      author: Coudray-Meunier, Coralie
       title: A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System
        date: 2016-01-29
       words: 5584
      flesch: 39
     summary: This information is available on line on the web site of the Institut de Veille Sanitaire (IVS) at http://www. invs.sante.fr/content/download/6498/42945/version/2/file/fiche_info_patient.pdf for HAV samples and on the web site of the NRC at www.cnr-ve.org for enteric virus samples. Sensitive and quantitative detection of human enteric viruses is typically achieved through quantitative RT-PCR (RT-qPCR).
    keywords: array; assays; detection; dpcr; qpcr; rna; samples; time; viruses
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        item: #400 of 1349
          id: cord-260695-qwepi0we
      author: Postler, Thomas S.
       title: Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection
        date: 2017-11-01
       words: 6331
      flesch: 45
     summary: Specific examples include influenza A virus (IAV), hepatitis C virus, severe acute respiratory syndrome-related coronavirus, adenovirus, herpes simplex virus 1 (HSV-1), human cytomegalovirus, and HIV-1 (Carnero et al., 2016; Chang et al., 2011; Hu et al., 2016; Ouyang et al., 2015; Peng et al., 2010 Peng et al., , 2014 Trypsteen et al., 2016; Winterling et al., 2014; Zhang et al., 2016; Zhao et al., 2016) . In this report, we describe a meta-analysis of two independent RNA-seq studies of HIV-1-infected cells and show that, unexpectedly, only three lncRNAs are differentially expressed in both of these datasets (Chang et al., 2011; Mohammadi et al., 2013) .
    keywords: cells; data; et al; expression; fig; human; infection; jurkat; levels; linc00173; lnc173; lncrnas; rna; transcripts
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        item: #401 of 1349
          id: cord-260705-huyyw5z6
      author: Moshe, Adi
       title: Virus-Induced Aggregates in Infected Cells
        date: 2012-10-17
       words: 5070
      flesch: 35
     summary: The role of aggregation in the context of a specific virus is often poorly understood, especially in the case of plant viruses. The same statement could be applied for virus-induced aggregation even though analogy between virus aggregates, JUNQ and/or IPOD has not been demonstrated.
    keywords: aggregates; bodies; cells; factories; infection; nuclear; plant; proteins; replication; rna; virus; viruses
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        item: #402 of 1349
          id: cord-260708-l9w5jhsw
      author: Lasecka, Lidia
       title: The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses
        date: 2013-12-11
       words: 10711
      flesch: 38
     summary: This genus includes a number of human and livestock pathogens, as well as a collection of other viruses about which little is known, not even the host in which they naturally circulate. Region 1, based on sequence similarity with other viruses, appears to be responsible for capsnatching endonuclease activity [52, 136, 189] ; however, this needs to be confirmed experimentally.
    keywords: binding; cchfv; cells; congo; conserved; crimean; domain; fever; fever virus; hemorrhagic; human; isg15; nairoviruses; protein; replication; rna; sequence; ubiquitin; virus
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        item: #403 of 1349
          id: cord-260782-1lm8tzbc
      author: Giles, Julia
       title: Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus)
        date: 2018-07-14
       words: 6576
      flesch: 37
     summary: Multifocal dense aggregates of glial cells (glial nodules) involving both grey or white matter were present in 5/12 (41.7%) infected possums (possums 5, 7, 8, 12, 16) and 1/4 (25%) control possum. The rN protein had previously been shown to be recognised by sera from WPDV infected possums by enzyme-linked immunosorbent assay and Western blot (Giles et al., 2018) .
    keywords: control; disease; et al; infected; infection; levels; perrott; possums; rna; tissues; virus; wpdv
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        item: #404 of 1349
          id: cord-261110-cnj0e0s9
      author: Debarnot, Claire
       title: Crystallization and diffraction analysis of the SARS coronavirus nsp10–nsp16 complex
        date: 2011-02-25
       words: 2688
      flesch: 60
     summary: This positive RNA virus encodes a large replicase polyprotein made up of 16 gene products (nsp1–16), amongst which two methyltransferases, nsp14 and nsp16, are involved in viral mRNA cap formation. The crystal structure of nsp16 is unknown.
    keywords: complex; cov; nsp10; protein; rna; sars
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        item: #405 of 1349
          id: cord-261160-g92zhv19
      author: Rowland, Raymond R.R
       title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero
        date: 2003-10-30
       words: 6389
      flesch: 42
     summary: A unique aspect of this study was the thorough analysis of virus replication in pig tissues during asymptomatic infection (Roman numeral III, Fig. 2 ). key: cord-261160-g92zhv19 authors: Rowland, Raymond R.R; Lawson, Steven; Rossow, Kurt; Benfield, David A title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date: 2003-10-30 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2003.07.006 sha: doc_id: 261160 cord_uid: g92zhv19 The ability of porcine reproductive and respiratory syndrome virus (PRRSV) to establish a persistent infection is the principal contributing factor to the world-wide spread of the disease.
    keywords: days; infection; pigs; porcine; positive; prrsv; replication; syndrome; virus
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        item: #406 of 1349
          id: cord-261279-6mef38eo
      author: Chu, Daniel K W
       title: Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia
        date: 2020-01-31
       words: 2999
      flesch: 49
     summary: Interestingly, several bat coronaviruses that are genetically similar to human SARS coronavirus were detected in horseshoe bats. This virus is genetically similar to SARS coronavirus and bat SARS-like coronaviruses.
    keywords: assays; coronavirus; human; ncov; patients; rna; samples; sars
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        item: #407 of 1349
          id: cord-261417-4pf5nsw2
      author: Harwig, Alex
       title: The Battle of RNA Synthesis: Virus versus Host
        date: 2017-10-21
       words: 7878
      flesch: 47
     summary: For this reason, RNA viruses have evolved capping mechanisms that are different from capping during cellular transcription. Genetic conflicts: The usual suspects and beyond Paleovirology-Modern consequences of ancient viruses Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors Evolutionary genomics of nucleo-cytoplasmic large DNA viruses Viral-encoded enzymes that target host chromatin functions Retroviral micrornas Mechanisms of HIV-1 control Virus meets host microrna: The destroyer, the booster, the hijacker DNA-binding specificities of human transcription factors Sensing of RNA viruses: A review of innate immune receptors involved in recognizing RNA virus invasion Rna function.
    keywords: binding; dna; elongation; end; figure; host; initiation; mrna; polymerase; promoter; protein; rna; rnapii; synthesis; transcription; virus; viruses
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        item: #408 of 1349
          id: cord-261532-q923xxn2
      author: Chen, Huihui
       title: The essential adaptors of innate immune signaling
        date: 2012-09-21
       words: 7451
      flesch: 34
     summary: On the other hand, RNA virus infection triggers STING activation through STING-MAVS interaction on MAVS-resident MAM or peroxisomal (Pex) membrane; activated STING then dissociates with MAVS and recruits STAT6 and TBK1, leading to STAT6 activation. Then JAKs further phosphorylate STAT6 at the receptor: activated STAT6 dimerizes through SH2 domain and translocates into nucleus to function as a transcriptional factor, regulating IL-4/IL-13-dependent signaling such as Th2 differentiation, immunoglobulin E (IgE) and chemokine production and mucus generation.
    keywords: activation; adaptor; cells; domain; et al; expression; immune; myd88; protein; rig; signaling; stat6; sting; type; virus
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        item: #409 of 1349
          id: cord-261735-03hvi4el
      author: Rodrigues, R.
       title: Development of a one step real time RT-PCR assay to detect and quantify Dugbe virus
        date: 2011-06-14
       words: 2642
      flesch: 52
     summary: Hazara virus, a new agent isolated from Ixodes redikorzevi ticks from the Kaghan Valley, W. Pakistan Structure and morphogenesis of Dugbe virus (Bunyaviridae Nairovirus) studied by immunogold electron microscopy of ultrathin cryosection Pathogenesis of Dugbe virus infection in wild-type and interferon-deficient mice Dugbe nairovirus S segment: correction of published sequence and comparison of five isolates Investigation of tick-borne viruses as pathogens of humans in South Africa and evidence of Dugbe virus infection in a patient with prolonged thrombocytopenia Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays Supplement to the catalogue of Arthropod-borne viruses Kupe virus, a new virus in the family bunyaviridae, genus nairovirus Dugbe virus: a tick-borne arbovirus from Nigeria Nairobi sheep disease Bunyaviridae Seroprevalence of five arboviruses in Zebu cattle in the Central African Republic Dugbe nairovirus M RNA:nucleotide sequence and coding strategy Large RNA segment of Dugbe nairovirus encodes the putative RNA polymerase Differential activation profiles of Crimean-Congo hemorrhagic fever virus versus Dugbe virus infected antigen presenting cells Tickborne arbovirus surveillance in marquet livestock Epidemiologic and clinical features of Crimean-Congo hemorrhagic fever in southern Africa CLUSTALW: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice Ticks of Domestic Animals in Africa: A Guide to Identification of Species Detection of an arbovirus in an invertebrate and a vertebrate host using the polymerase chain reaction Expression of the nucleocapsid protein of Dugbe virus and antigenic crossreactions with other nairoviruses This work was partly funded by IRBA and Fondation Mérieux. Dugbe virus (DUGV), a member of the genus Nairovirus of the Bunyaviridae family, was first isolated in 1964 from the Amblyomma variegatum tick in Nigeria (Causey, 1970) .
    keywords: assay; dugv; pcr; rna; virus
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        item: #410 of 1349
          id: cord-262076-b5u5hp2r
      author: Liu, Ying Poi
       title: Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron
        date: 2008-03-16
       words: 6911
      flesch: 46
     summary: We therefore selected the 19-nt inhibitors for the construction of antiviral miRNA polycistrons. HIV-1 sequences are blue, mature wild-type miRNA sequences are red, pre-miRNA sequences are black, Watson-Crick base pairs are shown with dashes and GU wobbles with dots.
    keywords: antiviral; cells; construct; expression; figure; hairpin; inhibition; ldr9; luciferase; mirna; shrna
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        item: #411 of 1349
          id: cord-262282-9xh51cd1
      author: Serwer, Philip
       title: Optimizing Anti-Viral Vaccine Responses: Input from a Non-Specialist
        date: 2020-05-15
       words: 4324
      flesch: 54
     summary: (1) Although phage uptake into human cells occurs, no evidence exists that phages replicate in human cells Pathogen homolog RNA phage vaccines, on the other hand, would have an a priori and reasonable projection (not certainty) of safety.
    keywords: antibody; objective; option; phage; sars; strategy; type; vaccine; virus; viruses
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        item: #412 of 1349
          id: cord-262318-qpztmdnw
      author: Guo, Jingxu
       title: In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors
        date: 2020-07-16
       words: 6366
      flesch: 47
     summary: Studies have indicated that norovirus 3CL proteases have a preferential order of processing the polyprotein, for example, the Southampton virus 3CL pro has a preference for cleavage at LQ-GP and LQ-GK, but it can also cleave at ME-GK, FE-AP and LE-GG (Hussey et al., 2011) . A further 10 compounds were found to bind in the central cavity of this putative tetrameric form of the enzyme. Expression and purification of SV3CP was conducted using the method described by Hussey et al., (2011) .
    keywords: 3cl; crystal; et al; fig; fragment; j01; norovirus; protease; protein; rna; screening; site; structure; sv3cp
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        item: #413 of 1349
          id: cord-262347-ejhz9rra
      author: Kappes, Matthew A.
       title: PRRSV structure, replication and recombination: Origin of phenotype and genotype diversity
        date: 2015-03-07
       words: 10173
      flesch: 21
     summary: PRRSV replication closely ties three key features: rearrangement of host membranes to establish viral replication complexes (RC), synthesis and expression of gRNA, transcription of sgRNA for the efficient expression of structural proteins, at the same time as the unique ability to produce aberrant PRRSV sgRNAs known as heteroclites (Yuan et al., 2000 (Yuan et al., , 2004 . DI RNAs are generated through nonhomologous recombination between viral genomes resulting in random internal deletions but still encode the replication elements essential for generation of defective progeny virus including the genes encoding for the polymerase, essential replicase proteins, and capsid protein(s) (Yuan et al., 2000) .
    keywords: arterivirus; body; et al; genome; isolates; porcine; protein; prrsv; rdrp; recombination; region; replication; rna; sequence; sgrna; strains; syndrome; syndrome virus; synthesis; transcription; trs; type; virus
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        item: #414 of 1349
          id: cord-262511-96xp1v0r
      author: Khabar, Khalid S. A.
       title: Rapid transit in the immune cells: the role of mRNA turnover regulation
        date: 2007-03-30
       words: 6568
      flesch: 35
     summary: As cities cope with the rapid entry of people by using rapid transit systems, post-transcriptional control of immune system helps in rapid activation of immune cells by mechanisms that involve rapid translocation of mRNA stabilization proteins such as HuR to effector cellular compartments and/or temporal inactivation, e.g., by phosphorylation or proteolysis of RNA decay proteins such as TTP or KSRP. With the coordinated kinetics model, stabilizing RNA-binding proteins such as HuR can occur initially following immune cell activation, allowing rapid and early response of cytokine production.
    keywords: activation; cell; expression; hur; mrna; p38; protein; regulation; response; stabilization; tnf-; transcriptional; ttp
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        item: #415 of 1349
          id: cord-262592-0rdiosxd
      author: Cuevas, José M.
       title: Human norovirus hyper-mutation revealed by ultra-deep sequencing
        date: 2016-04-17
       words: 5847
      flesch: 44
     summary: To more directly test for hyper-mutation, we performed transfection assays in which the production of mutations was restricted to a single cell infection cycle. Two of the samples showing hyper-mutation belonged to newborns, whereas the other two belonged to adults, with no significant association between age and hyper-mutation at this low sample size (Fisher's exact test, P = 0.547).
    keywords: base; et al; hyper; mutation; pcr; reads; region; rna; virus
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        item: #416 of 1349
          id: cord-262609-cssgzvus
      author: Sivakumaran, K
       title: RNA sequence and secondary structural determinants in a minimal viral promoter that directs replicase recognition and initiation of genomic plus-strand RNA synthesis
        date: 1999-12-03
       words: 10589
      flesch: 47
     summary: RNA1 (U57305), cowpea chlorotic mottle virus RNA1 (M65139), cowpea chlorotic mottle virus RNA2 (M28817), cowpea chlorotic mottle virus RNA3 (M28818), cowpea mosaic virus RNA B (X00206), cowpea mosaic virus RNA M (X00729), cucumber mosaic virus RNA1 (D12537 D01199), cucumber mosaic virus RNA2 (D12538 D01200), cucumber mosaic virus RNA3 (D10539), cymbidium mosaic virus (U62963), grapevine virus A (X75433), olive latent virus 1 (X85989), olive latent virus 2 RNA1 (X94346), olive latent virus 2 RNA2 (X94347), olive latent virus 2 RNA3 (X76993), olive latent virus 2 RNA4 (X77115), papaya mosaic virus (D13957 D00580), peanut clump virus RNA1 (X78602), peanut clump virus RNA2 (L07269), peanut mottle virus (AF023848), pepper mottle virus (M96425), potato mop-top virus RNA3 (D16193), potato virus X (D00344), potato virus Y (A08776), raspberry bushy dwarf virus RNA1 (S51557), ryegrass mosaic virus (AF035818), soil-borne wheat mosaic virus RNA1 (L07937), soil-borne wheat mosaic virus RNA2 (L07938), soybean mosaic virus (S42280), sweet clover necrotic mosaic virus (S46028), tobacco mosaic virus (D13438) Subgenomic RNA promoters dictate the mode of recognition by bromoviral RNA-dependent RNA polymerases Minimal templates directing accurate initiation of subgenomic RNA synthesis in vitro by the brome mosaic virus RNA-dependent RNA polymerase Mechanistic analysis of RNA synthesis by RNA-dependent RNA polymerase from two promoters reveals similarities to DNA-dependent RNA polymerase Bromovirus RNA replication and transcription Near identity of 3 H RNA secondary structure in bromoviruses and cucumber mosaic virus Infectious in vitro transcripts from cowpea chlorotic mottle virus cDNA clones and exchange of individual components with brome mosaic virus Sequence of cowpea chlorotic mottle virus RNAs 2 and 3 and evidence of a recombination event during bromovirus evolution Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16S RNA. II. interactions Exchangeable proton NMR without base-line distortion, using strongpulse sequences Sequence comparison of ®ve polymerases (L proteins) of unsegmented negative-strand RNA viruses: theoretical assignment of functional domains The requirement for a stem-loop structure in brome mosaic virus replication supports a new model for viral positive-strand RNA initiation Absorbence melting curves of RNA Puri®cation and characterization of brome mosaic virus RNA-dependent RNA polymerase The nucleotide sequence and genome organization of the RNA2 and RNA3 segments in broad bean mottle virus Aura virus is a new world representative of Sindbis-like viruses Isolation of an RNAdirected RNA polymerase-speci®c cDNA clone from tomato Coronavirus subgenomic minus-strand RNAs and potential for mRNA replicons Structure of the Ockelbo virus genome and its relationship to other Sindbis viruses Sequence-speci®c recognition of a subgenomic promoter by a viral RNA polymerase Moieties in an RNA promoter speci®cally recognized by a viral RNA-dependent RNA polymerase Use of DNA, RNA and chimeric templates by a viral RNA-dependent RNA polymerase RNAmediated trans-activation of transcription from a viral RNA Initiation of genomic positive strand synthesis from DNA and RNA templates by a viral RNA-dependent RNA polymerase Requirement of a 3 H -terminal stem-loop in in vivo transcription by an RNA dependent RNA polymerase Coronavirus transcription: subgenomic mouse hepatitis virus replicative intermediates function in RNA synthesis Spatial requirements for promoter recognition by a viral RNA-dependent RNA polymerase A brome mosaic virus intergenic RNA3 replication signal functions with viral replication protein 1a to dramatically stabilize RNA in vivo RNA synthesis by the brome mosaic virus RNA-dependent RNA polymerase: transition from initiation to elongation Characterization of RNA products associated with or aborted by a viral RNA-dependent RNA polymerase Initiation of (À)-strand RNA synthesis catalyzed by the BMV RNA-dependent RNA polymerase: synthesis of oligonucleotides RNA structure prediction Identi®cation of poliovirus polypeptide p63 as a soluble RNAdependent RNA polymerase RNA structure and NMR spectroscopy Antisense globin RNA in mouse erythroid tissues: structure, origin, and possible function Transcription elongation and termination are competitive kinetic processes Characterization of bacteriophage
    keywords: b2(à)26; bmv; figure; genomic; initiation; mosaic; replicase; rna; rna synthesis; rnas; strand; strand rna; structure; synthesis; virus
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        item: #417 of 1349
          id: cord-262753-jld1ygxt
      author: Neidermyer, William J.
       title: Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells
        date: 2019-06-21
       words: 9262
      flesch: 40
     summary: Collectively, these studies suggest additional mechanisms may contribute to the shut-off of host cell protein synthesis. An RNA polymerase in the virion L protein requirement for in vitro RNA synthesis by vesicular stomatitis virus Transcriptional activity and mutational analysis of recombinant vesicular stomatitis virus RNA polymerase Amino acid residues within conserved domain VI of the vesicular stomatitis virus large polymerase protein essential for mRNA cap methyltransferase activity A single amino acid change in the L-polymerase protein of vesicular stomatitis virus completely abolishes viral mRNA cap methylation A unique strategy for mRNA cap methylation used by vesicular stomatitis virus Unconventional mechanism of mRNA capping by the RNA-dependent RNA polymerase of vesicular stomatitis virus A conserved motif in region v of the large polymerase proteins of nonsegmented negative-sense RNA viruses that is essential for mRNA capping Rebinding of transcriptase components (L and NS proteins) to the nucleocapsid template of vesicular stomatitis virus Location of the binding domains for the RNA polymerase L and the ribonucleocapsid template within different halves of the NS phosphoprotein of vesicular stomatitis virus Structure of the vesicular stomatitis virus nucleoprotein-RNA complex Structure of the vesicular stomatitis virus nucleocapsid in complex with the nucleocapsid-binding domain of the small polymerase cofactor Molecular architecture of the vesicular stomatitis virus RNA polymerase Critical phosphoprotein elements that regulate polymerase architecture and function in vesicular stomatitis virus Synthesis of poly(A) in vitro by purified virions of vesicular stomatitis virus In vitro synthesis of RNA that contains polyadenylate by virion-associated RNA polymerase of vesicular stomatitis virus Site on the vesicular stomatitis virus genome specifying polyadenylation and the end of the L gene mRNA Aberrant polyadenylation by a vesicular stomatitis virus mutant is due to an altered L protein cis-Acting signals involved in termination of vesicular stomatitis virus mRNA synthesis include the conserved AUAC and the U7 signal for polyadenylation Translational control of protein synthesis after infection by vesicular stomatitis virus Vesicular stomatitis virus mRNA and inhibition of translation of cellular mRNA-is there a P function in vesicular stomatitis virus? Effect of intracellular vesicular stomatitis virus mRNA concentration on the inhibition of host cell protein synthesis Complete intergenic and flanking gene sequences from the genome of vesicular stomatitis virus Complete sequences of the ribosome recognition sites in vesicular stomatitis virus
    keywords: associated; association; cells; cellular; eif4e; fig; gene; host; hpi; infection; mrnas; polysome; protein; reads; stomatitis; synthesis; translation; virus; vsv
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        item: #418 of 1349
          id: cord-262776-6k7tcgfs
      author: Burnouf, Thierry
       title: Assessment of the viral safety of antivenoms fractionated from equine plasma
        date: 2004-09-30
       words: 8214
      flesch: 39
     summary: For instance, equipment for bulk in process virus inactivation, such as the acid pH incubation or the caprylic acid treatment, should ideally be fully enclosed. The duration of the first stage should be such that the majority of virus inactivation (as found during the viral validation studies) has occurred.
    keywords: acid; antivenoms; blood; disease; enveloped; equine; horses; human; igg; inactivation; manufacturing; plasma; production; products; safety; treatment; virus; viruses
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        item: #419 of 1349
          id: cord-262841-nr42rs8f
      author: Li, Lanjuan
       title: SARS-coronavirus replicates in mononuclear cells of peripheral blood (PBMCs) from SARS patients
        date: 2003-12-31
       words: 2129
      flesch: 50
     summary: SARS-coronavirus replicates in mononuclear cells of peripheral blood (PBMCs) from SARS patients It has been confirmed that the pathogen for severe acute respiratory syndrome (SARS) is a novel coronavirus termed SARS-coronavirus (SARS-CoV). Study design: Peripheral blood mononuclear cells collected from SARS cases infected by the same infectious source were tested for both negative-stranded RNA (minus-RNA, “replicative intermediates”) and positive-stranded RNA (genomic RNA) of SARS-CoV during the course of hospitalization by reverse transcription-polymerase chain reaction (RT-PCR).
    keywords: cov; minus; pbmcs; rna; sars
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        item: #420 of 1349
          id: cord-262844-qeheeqe3
      author: Xia, Xuhua
       title: Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense
        date: 2020-04-14
       words: 3310
      flesch: 36
     summary: Second, many experimental studies (Burns et al., 2009; Ficarelli et al., 2020; Odon et al., 2019; Trus et al., 2019; Tulloch et al., 2014) Fifth, the cellular receptor for SARS-CoV-2 entry into the cell is ACE2 (angiotensin I converting enzyme 2) (Zhou et al., 2020) . ZAP inhibits viral replication and mediates viral genome degradation (Ficarelli et al., 2020; Ficarelli et al., 2019; Meagher et al., 2019; Takata et al., 2017) .
    keywords: coronavirus; cpg; et al; genomes; rna; sars; zap
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        item: #421 of 1349
          id: cord-262923-kgzbd6w3
      author: Koo, Bonhan
       title: CRISPR/dCas9-mediated biosensor for detection of tick-borne diseases
        date: 2018-11-10
       words: 3653
      flesch: 41
     summary: Over the past decade, biosensors combined with electrical, electrochemical, and optical techniques have been developed to improve detection sensitivity [10] . First, CRISPR/dCas9-mediated biosensor enhances detection sensitivity through triple-targeting (primer, target strand, and dCas9).
    keywords: biosensor; crispr; dcas9; detection; dna; rna; sensitivity; sfts; target
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        item: #422 of 1349
          id: cord-263033-4790dhc5
      author: Laptev, I. G.
       title: Posttranscriptional modification of messenger RNAs in eukaryotes
        date: 2015-12-11
       words: 6798
      flesch: 53
     summary: Regions distant from the mRNA ends may contain N6 methyladenosine (m 6 A), 5 methylcytidine (m 5 C), pseudouridine (Ψ), and inosine (I), which were believed to play only a minor role because their pro portion in cell RNA is extremely low as compared with the standard nucleotides. In addition to RNA methylation, demethylation occurs as an opposite process.
    keywords: adenosine; cells; editing; fto; human; method; methylation; modification; mrna; nsun2; proteins; pseudouridine; rna; rnas; sequencing; sites
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        item: #423 of 1349
          id: cord-263157-8jin6oru
      author: Martínez, Miguel Angel
       title: Progress in the Therapeutic Applications of siRNAs Against HIV-1
        date: 2008-10-13
       words: 9242
      flesch: 34
     summary: This review highlights the evidence showing that RNAi provides a robust method for specifically inhibiting the expression of targeted HIV-1 genes, and its promise as a novel and broadly applicable approach to antiviral therapy. Soon after the demonstration that synthetic siRNAs were able to induce the RNAi mechanism in mammalian cells (15) , several studies reported that HIV-1 gene expression and replication ex vivo could be inhibited by virus-specific synthetic siR-NAs (16 - 22) or expressed siRNAs (16, 18) that were targeted to early or late phases of virus replication.
    keywords: cells; expression; gene; human; infection; interference; replication; rna; rnai; sequence; shrna; silencing; sirnas; target; therapy; virus; vivo
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        item: #424 of 1349
          id: cord-263239-andje0wu
      author: Dorobantu, Cristina M.
       title: Modulation of the Host Lipid Landscape to Promote RNA Virus Replication: The Picornavirus Encephalomyocarditis Virus Converges on the Pathway Used by Hepatitis C Virus
        date: 2015-09-25
       words: 9046
      flesch: 40
     summary: EMCV and HCV converged to recruit a common lipid-modifying pathway in building replication sites Several lines of evidence suggest that the picornavirus EMCV and the distantly related flavivirus HCV have evolved to exploit common host components in assisting virus RNA replication. To rule out a possible involvement of PI4KB in establishing the elevated PI4P levels observed in EMCV infected cells, we treated cells with the PI4KB inhibitor BF738735 (Compound 1)
    keywords: 3ab; al-9; cells; cholesterol; emcv; fig; golgi; host; infection; membrane; osbp; pi4ka; pi4p; protein; replication; rna; ros; virus
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        item: #425 of 1349
          id: cord-263302-z5uhrta5
      author: Zhang, Xuming
       title: Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription
        date: 2000-12-05
       words: 8057
      flesch: 52
     summary: Three intergenic regions of coronavirus mouse hepatitis virus strain A59 genome RNA contain a common nucleotide sequence that is homologous to the 3Ј-end of the viral mRNA leader sequence Analysis of a recombinant mouse hepatitis virus expressing a foreign gene reveals a novel aspect of coronavirus transcription TGEV coronavirus ORF4 encodes a membrane protein that is incorporated into virions Replication and plaque formation of mouse hepatitis virus (MHV-2) in mouse cell line DBT culture Characterization of an internal ribosome entry site within mRNA5 of murine hepatitis virus Cellular factors in the transcription and replication of viral RNA genomes: a parallel to DNA-dependent RNA transcription Characterization of leader RNA sequences on the virion and mRNAs of mouse hepatitis virus-a cytoplasmic RNA virus The molecular biology of coronaviruses Mouse hepatitis virus A59: Our findings thus support the notion that base-pairing between the leader (or antileader) and the IG is not the sole mechanism in subgenomic RNA transcription.
    keywords: cat; fig; ig5; leader; mrna5; pcr; primer; rna; sequence; subgenomic; transcription
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        item: #426 of 1349
          id: cord-263315-g7os15m1
      author: Martins-da-Silva, Andrea
       title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response
        date: 2018-01-18
       words: 7015
      flesch: 41
     summary: When mRNA levels changed at 12 or 24 h post transfection (either by up-or down-regulation), we detected a corresponding change in secreted protein levels 12 or 24 h after the mRNA level changes. Based on the data presented in Figure 3A , we observed that in the majority of the molecules (six out of seven) there was a correlated change of secreted protein levels 12 h to 24 h after changes in mRNA levels.
    keywords: antiviral; cells; change; dsrna; expression; factor; fold; infection; insect; interferon; levels; ll5; mrna; non; protein; response; secretion; transfection; virus
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        item: #427 of 1349
          id: cord-263334-wwkdum94
      author: Li, Chen
       title: Cellular DDX3 regulates Japanese encephalitis virus replication by interacting with viral un-translated regions
        date: 2014-01-20
       words: 7751
      flesch: 44
     summary: 23 Discovery of the first small molecule inhibitor of human DDX3 specifically designed to target the RNA binding site: towards the next generation HIV-1 inhibitors Recent advances in flavivirus antiviral drug discovery and vaccine development DEAD-box proteins: the driving forces behind RNA metabolism Human DEAD-box protein 3 has multiple functions in gene regulation and cell cycle control and is a prime target for viral manipulation Candidate tumor suppressor DDX3 RNA helicase specifically represses cap-dependent translation by acting as an eIF4E inhibitory protein Recent advances in Japanese encephalitis A complex RNA motif defined by three discontinuous 5-nucleotide-long strands is essential for Flavivirus RNA replication DEAD-box protein DDX3 associates with eIF4F to promote translation of selected mRNAs The DEADbox helicase DDX3X is a critical component of the TANK-binding kinase 1-dependent innate immune response Analysis of virion-incorporated host proteins required for Herpes simplex virus type 1 Infection through a RNA interference screen Meanwhile, we also found that endogenous DDX3 colocalized with JEV RNA in the cytoplasm (Fig. 6B) , implying that DDX3 might be involved in JEV RNA replication.
    keywords: anti; antibody; bhk-21; cells; ddx3; et al; fig; helicase; infected; jev; ns3; ns5; protein; replication; rna; virus
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        item: #428 of 1349
          id: cord-263357-krvei97r
      author: Holmes, Kathryn V.
       title: The New Age of Virus Discovery: Genomic Analysis of a Novel Human Betacoronavirus Isolated from a Fatal Case of Pneumonia
        date: 2013-01-08
       words: 2080
      flesch: 37
     summary: The discovery of severe acute respiratory syndrome-CoV (SARS-CoV) as the cause of the SARS pandemic of 2002 to 2003 demonstrated the epidemic potential of this large family of RNA viruses and emphasized their importance in human respiratory diseases. Results of standard diagnostic tests of his clinical samples for known respiratory viruses were all negative, which prompted testing of infected cell culture supernatants using a pan-coronavirus reverse transcription-PCR (RT-PCR) assay to amplify a short, highly conserved region of the RNA-dependent RNA polymerase gene.
    keywords: coronavirus; emc; hcov; human; rna; virus
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        item: #429 of 1349
          id: cord-263433-oldy0gta
      author: Barriocanal, Marina
       title: Long Non-Coding RNA BST2/BISPR is Induced by IFN and Regulates the Expression of the Antiviral Factor Tetherin
        date: 2015-01-09
       words: 8780
      flesch: 42
     summary: The proteomics identifications (PRIDE) database and associated tools: status in 2013 Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes Quantification of different human alpha interferon subtypes and pegylated interferon activities by measuring MxA promoter activation Influenza A virus lacking the NS1 gene replicates in interferon-deficient systems Inhibition of vesicular stomatitis virus infection in epithelial cells by alpha interferon-induced soluble secreted proteins An abundance of bidirectional promoters in the human genome Complex Loci in human and mouse genomes Identification of a member of the interferon regulatory factor family that binds to the interferonstimulated response element and activates expression of interferon-induced genes Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data Transcription factor binding and modified histones in human bidirectional promoters Systematic analysis of headto-head gene organization: evolutionary conservation and potential biological relevance Bidirectional gene organization: a common architectural feature of the human genome Expression of the murine RanBP1 and Htf9-c genes is regulated from a shared bidirectional promoter during cell cycle progression Divergent transcription is associated with promoters of transcriptional regulators Functional consequences of bidirectional promoters Induced ncR-NAs allosterically modify RNA-binding proteins in cis to inhibit transcription Antisense expression increases gene expression variability and locus interdependency Tetherin inhibits HIV-1 release by directly tethering virions to cells BST-2/tetherin: structural biology, viral antagonism, and immunobiology of a potent host antiviral factor Intrinsic cellular defenses against human immunodeficiency viruses BST-2 expression in human hepatocytes is inducible by all three types of interferons and restricts production of hepatitis C virus Mechanism of HIV-1 virion entrapment by tetherin BST2/Tetherin inhibits hepatitis C virus production in human hepatoma cells Vpu binds directly to tetherin and displaces it from nascent virions Influenza virus partially counteracts restriction imposed by tetherin/BST-2 Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu Interferoninduced cell membrane proteins, IFITM3 and tetherin, inhibit vesicular stomatitis virus infection via distinct mechanisms Regulation of hepatic innate immunity by hepatitis C virus Interferon type I gene expression in chronic hepatitis C Interferon signaling and treatment outcome in chronic hepatitis C Intrahepatic gene expression during chronic hepatitis C virus infection in chimpanzees Hepatitis C virus controls interferon production through PKR activation Hepatitis C virus blocks interferon effector function by inducing protein kinase R phosphorylation Interferon-induced ISG15 pathway: an ongoing virus-host battle The antiviral activities of ISG15 Positive regulation of interferon regulatory factor 3 activation by Herc5 via ISG15 modification The interferon stimulated gene 15 functions as a proviral factor for the hepatitis C virus and as a regulator of the IFN response IFN-stimulated gene 15 functions as a critical antiviral molecule against influenza, herpes, and Sindbis viruses ISG15, a ubiquitin-like interferon-stimulated gene, promotes hepatitis C virus production in vitro: implications for chronic infection and response to treatment Negative feedback regulation of RIG-Imediated antiviral signaling by interferon-induced ISG15 conjugation The antiviral protein viperin inhibits hepatitis C virus replication via interaction with nonstructural protein 5A Regulation of Interferon-stimulated gene BST2 by a lncRNA transcribed from a shared bidirectional promoter Barriocanal contributed to the writing of the manuscript; Victor Segura was in charge of all the bioinformatic analyses; and Puri Fortes conceived the project and the required experiments, provided the budget, interpreted the data, and wrote the manuscript. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus Cutting edge: influence of Tmevpg1, a long intergenic noncoding RNA, on the expression of Ifng by Th1 cells An integrated encyclopedia of DNA elements in the human genome The rise of regulatory RNA Human cancer long non-coding RNA transcriptomes Specific expression of long noncoding RNAs in the mouse brain Landscape of transcription in human cells Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a Control of alternative splicing through siRNA-mediated transcriptional gene silencing Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA Long noncoding RNAs: fresh perspectives into the RNA world Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities Comparison of approaches for rational siRNA design leading to a new efficient and transparent method Production of infectious hepatitis C virus in tissue culture from a cloned viral genome Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair Induction and evasion of type I interferon responses by influenza viruses
    keywords: analysis; bispr; cells; coding; expression; figure; genes; hcv; ifn; interferon; levels; lncbst2; lncisg15; lncrnas; non; response; rna; virus
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        item: #430 of 1349
          id: cord-263468-996kl9jz
      author: Cattaneo, Roberto
       title: Biased hypermutation and other genetic changes in defective measles viruses in human brain infections
        date: 1988-10-21
       words: 7647
      flesch: 41
     summary: Expression of defective measles virus genes in brain tissues of patients with subacute sclerosing panencephalitis Restriction of measles virus gene expression in measles inclusion body encephalitis The transcription complex of vesicular stomatitis virus Matrix genes of measles virus and of canine distemper virus: cloning, nucleotide sequences, and deduced amino acid sequences Identification of a nonproductive, cell-associated form of measles virus by its resistance to inhibition by recombinant human interferon Defective translation of measles virus matrix protein in subacute sclerosing panencephalitis Accumulated measles virus mutations in a case of subacute sclerosing panencephalitis: interrupted matrix protein reading frame and transcription alteration Altered transcription from a defective measles virus genome derived from a diseased human brain Altered ratios of measles virus transcripts in diseased human brains Multiple viral mutations rather than host factors cause defective measles virus gene expression in a subacute scierosing panencephalitis ceil line Fluorographic detection of radioactivity in polyacrylamide gels with the water-soluble fluor, sodium salycilate Ribosomal initiation from an ACG codon in the Sendai virus P/C mRNA Nucleotide sequence of the gene encoding the matrix protein of a recent measles virus isolate Nucleotide sequence heterogeneity of an RNA phage population Measles virus nucleic acid sequences in human brain Studies on an attenuated measles virus vaccine: techniques for assay of effects of vaccination Extensive editing of cytochrome c oxidase From the sequence analysis presented in Figure 3 , it is immediately evident that mutations in this gene are more abundant than in other M genes and that U to C transitions account for a large majority of mutations.
    keywords: brain; case; et al; figure; gene; measles; mutations; protein; rna; sequence; virus; viruses
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        item: #431 of 1349
          id: cord-263580-zxnmylkw
      author: Pyle, Anna Marie
       title: RNA helicases and remodeling proteins
        date: 2011-08-20
       words: 2654
      flesch: 45
     summary: The conformational state and stability of RNA are controlled by RNA remodeling proteins, which are ubiquitous motor proteins in the cell. Here, we review advances in our understanding of the structure and function of three major structural families of RNA remodeling proteins, the hexameric ring proteins, the processive monomeric RNA translocase/helicases, and the functionally diverse DEAD-box remodeling proteins.
    keywords: atp; box; helicases; hydrolysis; proteins; rna; unwinding
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        item: #432 of 1349
          id: cord-263645-wupre5uj
      author: Morgan, Brittany S
       title: Insights into the development of chemical probes for RNA
        date: 2018-09-19
       words: 7113
      flesch: 31
     summary: We discuss the applicability of current tools to identify and evaluate RNA-targeted chemical probes, suggest criteria to assess the quality of RNA chemical probes and targets, and propose areas where new tools are particularly needed. A virus RNA promoter for up-regulating the translation of Antiamyloidogenic Secretase, a Disintegrin and Metalloproteinase 10 (ADAM10), by binding to the G-quadruplex-forming sequence in the 5 untranslated region (UTR) of its mRNA Studying a drug-like, RNA-focused small molecule library identifies compounds that inhibit RNA toxicity in Myotonic Dystrophy Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways Chemical correction of pre-mRNA splicing defects associated with sequestration of muscleblind-like 1 protein by expanded r(CAG)-containing transcripts Structure-based design of an RNA-binding p-terphenylene scaffold that inhibits HIV-1 Rev protein function Targeting RNA-protein interactions within the Human Immunodeficiency Virus Type 1 lifecycle A small molecule that represses translation of G-quadruplex-containing mRNA Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones Development of small molecules with a noncanonical binding mode to HIV-1 Trans Activation Response (TAR) RNA
    keywords: binding; cell; chemical; discovery; library; ligands; molecules; probes; protein; rna; rnas; screening; structure; target; targeting
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        item: #433 of 1349
          id: cord-263699-gosqpg3k
      author: Martínez, José L.
       title: Role of the Guanine Nucleotide Exchange Factor GBF1 in the Replication of RNA Viruses
        date: 2020-06-24
       words: 12360
      flesch: 36
     summary: GBF1 has been shown not only to facilitate the intracellular traffic of different viral and cellular elements during infection, but also to modulate the replication of viral RNA, the formation and maturation of viral replication complexes, and the processing of viral proteins through mechanisms that do not depend on its canonical role in intracellular transport. Besides its role in regulating the transport of viral proteins to the plasma membrane, it has been shown that GBF1 interacts specifically with the protein M2 [74] .
    keywords: activity; arf1; bfa; copi; factor; gbf1; golgi; membrane; proteins; replication; rna; rna replication; role; transport; vesicle; virus; virus replication; viruses
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        item: #434 of 1349
          id: cord-263987-ff6kor0c
      author: Holmes, Ian H.
       title: Solving the master equation for Indels
        date: 2017-05-12
       words: 7132
      flesch: 39
     summary: Parameterizing sequence alignment with an explicit evolutionary model Multiple genome rearrangement and breakpoint phylogeny Analytical expression of the purine/pyrimidine codon probability after and before random mutations Analytical solutions of the dinucleotide probability after and before random mutations RNA secondary structure prediction using stochastic context-free grammars and evolutionary history Evolution probabilities and phylogenetic distance of dinucleotides Genome evolution by transformation, expansion and contraction (GETEC) An evolutionary model for maximum likelihood alignment of DNA sequences An introduction to probability theory and its applications Evolutionary HMMs: a Bayesian approach to multiple alignment Using guide trees to construct multiple-sequence evolutionary HMMs Accurate reconstruction of insertion-deletion histories by statistical phylogenetics A note on probabilistic models over strings: the linear algebra approach Statistical alignment based on fragment insertion and deletion models Evolutionary inference via the poisson indel process Inching toward reality: an improved likelihood model of sequence evolution Models of sequence evolution for DNA sequences containing gaps Evolutionary models for insertions and deletions in a probabilistic modeling framework Probabilistic phylogenetic inference with insertions and deletions A probabilistic model for the evolution of RNA structure Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures A probabilistic model for sequence alignment with context-sensitive indels Sequence alignments and pair hidden Markov models using evolutionary history Joint Bayesian estimation of alignment and phylogeny BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny Incorporating indel information into phylogeny estimation for rapidly emerging pathogens Phylogenetic automata, pruning, and multiple alignment Hand Align: Bayesian multiple sequence alignment, phylogeny, and ancestral reconstruction A long indel model for evolutionary sequence alignment An improved model for statistical alignment Chain Monte Carlo Expectation Maximization algorithm for statistical analysis of DNA sequence evolution with neighbor-dependent substitution rates Accurate estimation of substitution rates with neighbor-dependent models in a phylogenetic context Patterns of insertion and deletion in mammalian genomes Exhaustive matching of the entire protein sequence database Pattern and rate of indel evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes For indel models, this latent information must be extended to include hidden site boundaries [56] .
    keywords: alignment; distributions; evolution; finite; gap; indel; length; matrix; models; probability; sequence; state; time
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        item: #435 of 1349
          id: cord-264051-ps0x2es1
      author: Li, Wei
       title: Human Identical Sequences of SARS-CoV-2 Promote Clinical Progression of COVID-19 by Upregulating Hyaluronan via NamiRNA-Enhancer Network
        date: 2020-11-05
       words: 8954
      flesch: 43
     summary: Such discrepancies may be owing to the binding of hyaluronan and its ligand CD44, which can induce the death of activated T cells (McKallip et al., 2002) . Noteworthily, as the antiviral immunity guardian, T cells are reduced significantly in COVID-19 patients (Diao et al., 2020) , which is negatively correlated with survival rates.
    keywords: cov-2; covid-19; et al; expression; g t; gene; hek293 t; host; human; hyaluronan; level; patients; rna; sars; t c; t cells; t t; virus
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        item: #436 of 1349
          id: cord-264159-e9071tyv
      author: Lin, Weikang Nicholas
       title: The Role of Single-Cell Technology in the Study and Control of Infectious Diseases
        date: 2020-06-10
       words: 13350
      flesch: 31
     summary: COVID-19 Coronavirus Pandemic Trade Set to Plunge as COVID-19 Pandemic Upends Global Economy Microbiology by numbers History of the discovery of the malaria parasites and their vectors The use of single-cell RNA-Seq to understand virus-host interactions Breaking the population barrier by single cell analysis: One host against one pathogen Single-cell analysis and stochastic modelling unveil large cell-to-cell variability in influenza A virus infection Extreme heterogeneity of influenza virus infection in single cells High-Throughput Single-Cell Kinetics of Virus Infections in the Presence of Defective Interfering Particles Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity Single-Cell Analysis of RNA Virus Infection Identifies Multiple Genetically Diverse Viral Genomes within Single Infectious Units Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses Phenotypic variation of Salmonella in host tissues delays eradication by antimicrobial chemotherapy Single-Cell Analysis of the Impact of Host Cell Heterogeneity on Infection with Foot-and-Mouth Disease Virus Nile Virus-Inclusive Single-Cell RNA Sequencing Reveals Heterogeneity in the Type One area of virology that has benefited from the enhanced resolution of single-cell technologies is the study of variation in infection across single cells and the reasons for such variation.
    keywords: analysis; antibodies; antibody; antigen; cell; cytometry; data; disease; expression; flow; heterogeneity; host; human; infection; pathogen; responses; rna; scrna; seq; sequencing; studies; study; technologies; throughput; vaccine; virus
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        item: #437 of 1349
          id: cord-264488-989t9ld1
      author: Park, Il-Hyun
       title: Inhibition of hepatitis B virus replication by ligand-mediated activation of RNase L
        date: 2014-02-06
       words: 5333
      flesch: 46
     summary: Because p2-5A is a unique and specific activator for RNase L, these results strongly indicated that the observed inhibition of HBV was the result of RNase L activation. RNase L activation requires 2-5A, which is synthesized by OAS.
    keywords: antiviral; cells; dna; expression; hbv; poly(i; replication; rnase
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        item: #438 of 1349
          id: cord-264678-wt0lvhfl
      author: Wu, Tzong-Yuan
       title: IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico
        date: 2009-05-27
       words: 5336
      flesch: 54
     summary: However, IRES element secondary structure prediction is more complicated than other RNA structures due to three different IRES types that are all related with eIF4 and 40S ribosome subunit but diverse RNA structures. IRSS searches IRES elements by structure comparison that contains neighbor regions for structure prediction and avoids short consensus primary sequences problem to improve IRES structures prediction.
    keywords: elements; figure; ires; irss; prediction; rna; search; structure; system; virus
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        item: #439 of 1349
          id: cord-264746-gfn312aa
      author: Muse, Spencer
       title: GENOMICS AND BIOINFORMATICS
        date: 2012-03-29
       words: 10983
      flesch: 54
     summary: In addition to providing storage and retrieval of gene sequences, several of these databases also offer advanced sequence analysis methods and powerful visualization tools. However, if two or more such distantly related organisms have gene sequences that are nearly identical, a strong argument can be made that the gene is critical in both organisms and that the same function has been maintained throughout evolutionary history.
    keywords: alignment; data; database; dna; expression; figure; gene; genome; genomic; human; levels; nucleotides; number; protein; rna; sequence
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        item: #440 of 1349
          id: cord-264884-ydkigome
      author: Villarreal, Luis P.
       title: The Widespread Evolutionary Significance of Viruses
        date: 2008-07-05
       words: 23160
      flesch: 41
     summary: key: cord-264884-ydkigome authors: Villarreal, Luis P. title: The Widespread Evolutionary Significance of Viruses date: 2008-07-05 journal: Origin and Evolution of Viruses DOI: 10.1016/b978-0-12-374153-0.00021-7 sha: doc_id: 264884 cord_uid: ydkigome In the last 30 years, the study of virus evolution has undergone a transformation. Originally concerned with disease and its emergence, virus evolution had not been well integrated into the general study of evolution.
    keywords: complex; disease; diversity; dna; dna viruses; et al; eukaryotic; evolution; example; genes; genomes; host; host evolution; human; infection; infl; life; like; mhv; mouse; origin; persistence; phage; populations; quasispecies; recombination; replication; rna; role; specifi; tness; type; uenza; viral; virus; virus evolution; viruses
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        item: #441 of 1349
          id: cord-264944-7xj27r98
      author: Koopmans, Marion
       title: Optimization of extraction and PCR amplification of RNA extracts from paraffin-embedded tissue in different fixatives
        date: 1993-07-31
       words: 5186
      flesch: 46
     summary: In the work reported here we used paraffin-embedded torovirus-infected cell pellets to compare the effect of different fixatives and RNA extraction methods on RT-PCR amplification of tissue extracts. Dewaxing of tissue sections had no effect on the yield and quality of RNA extractions, and further purification of the extracts using gel filtration did not improve the results.
    keywords: actin; amplification; extraction; method; pcr; primers; results; rna; torovirus
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        item: #442 of 1349
          id: cord-265095-lf5j4ic7
      author: Ten Dam, Edwin B.
       title: RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs
        date: 1990
       words: 5156
      flesch: 59
     summary: key: cord-265095-lf5j4ic7 authors: Ten Dam, Edwin B.; Pleij, Cornelius W. A.; Bosch, Leendert title: RNA pseudoknots: The characteristics of RNA pseudoknots and their prediction and detection have been reviewed (12, 14) .
    keywords: downstream; hairpin; nucleotides; pseudoknot; rna; rnas; sequence
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        item: #443 of 1349
          id: cord-265139-x7g3jcjm
      author: Zaiou, Mohamed
       title: The Emerging Role and Promise of Circular RNAs in Obesity and Related Metabolic Disorders
        date: 2020-06-16
       words: 8185
      flesch: 34
     summary: This assumption was based on the observation that treatment of differentiated primary mouse subcutaneous adipocytes with soluble tumor necrosis factor (TNF)-α led to significant reduction in circRNAs expression [80] . In this study, thousands of adipose circRNAs were identified to be regulated during adipogenesis.
    keywords: adipogenesis; adipose; circrnas; diseases; expression; function; human; inflammation; insulin; metabolic; obesity; potential; protein; role; studies; tissue
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        item: #444 of 1349
          id: cord-265173-70wyecwj
      author: Trujillo-Uscanga, Adrian
       title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication
        date: 2020-08-27
       words: 5702
      flesch: 41
     summary: Protein p53 (p53), a 393 amino acid protein expressed from the TP53 gene (Saha, Kar, & Sa, 2015) , also known as the guardian of the genome that functions as a DNA sequence-specific transcriptional regulator. Even though it is well known that all the members of the Caliciviridae family induce apoptosis, the role of p53 in this pathway or in other stages of viral replication has not been studied; therefore, the aim of this work was to determine if p53 host cell protein has a role in the replicative cycle of FCV, one of the best models to study the replication of this family.
    keywords: cells; fcv; fig; infected; p53; protein; replication; rna; viral; virus; vp1
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        item: #445 of 1349
          id: cord-265381-ppjohov8
      author: Pillai-Nair, Neeta
       title: Cis-acting Regulatory Elements in the Potato Virus X 3′ Non-translated Region Differentially Affect Minus-strand and Plus-strand RNA Accumulation
        date: 2003-02-21
       words: 10068
      flesch: 48
     summary: Multiple sequence elements important for PVX RNA accumulation reside within the 3 0 NTR The importance of elements in the upstream region of the PVX 3 0 NTR for RNA accumulation in protoplasts was analyzed by directed deletions using exonuclease III ( Figure 5(A) ). Sequence elements in the stem of SL2 are important for minus and/or plus-strand RNA accumulation The importance of the predicted structure SL2 to PVX RNA accumulation was examined by creating mutants SL2-A, SL2-B, SL2-C and SL2-D ( Figure 7 (A)).
    keywords: accumulation; elements; figure; minus; ntr; plus; pvx; rna; rna accumulation; sequence; sl2; sl3; strand rna; structure; virus
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        item: #446 of 1349
          id: cord-265410-khwzdi79
      author: Bartlett, Stuart
       title: Defining Lyfe in the Universe: From Three Privileged Functions to Four Pillars
        date: 2020-04-16
       words: 9440
      flesch: 42
     summary: In blue and green are hypothetical alien origins of life (lyfe); these and the trajectories that resulted in Earth life converge at a point in parameter space that universal narratives seek to describe. The two designations are distinguished as follows: • Life represents life as we know it; it uses the specific disequilibria and classes of components of earthly life.
    keywords: chemical; definition; earth; emergence; evolution; example; functions; information; learning; life; living; lyfe; origins; pillars; rna; system; world
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        item: #447 of 1349
          id: cord-265461-hj2b1wc4
      author: Decroly, Etienne
       title: Biochemical principles and inhibitors to interfere with viral capping pathways
        date: 2017-05-18
       words: 5105
      flesch: 40
     summary: -O methylations of viral RNA cap In vitro reconstitution of SARS-coronavirus mRNA cap methylation Unconventional mechanism of mRNA capping by the RNA-dependent RNA polymerase of vesicular stomatitis virus Reaction in alphavirus mRNA capping: formation of a covalent complex of nonstructural protein nsP1 with 7-methyl-GMP Characterization of the AdoMet-dependent guanylyltransferase activity that is associated with the N terminus of bamboo mosaic virus replicase mRNA capping by Venezuelan equine encephalitis virus nsP1: functional characterization and implications for antiviral research The first demonstration of actual transfer of the m7G cap onto acceptor RNA using a Togaviridae enzyme The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit Structural insight into cap-snatching and RNA synthesis by influenza polymerase A landmark paper of the crystal structure of the 3 subunit influenza polymerase presenting how RNA synthesis and RNA cap-snatching are physically coupled and coordinated Bunyaviridae RNA polymerases (L-protein) have an N-terminal, influenza-like endonuclease domain, essential for viral cap-dependent transcription Comparative structural and functional analysis of bunyavirus and arenavirus cap-snatching endonucleases Structural, enzymatic, and evolutionary perspective of the ambisense RNA virus endonucleases, examined comparatively to that of the influenza virus. Novel class of anti-chikungunya compounds is presented, together with the assays described in Ref Histidine-mediated RNA transfer to GDP for unique mRNA capping by vesicular stomatitis virus RNA polymerase Structure of the L protein of vesicular stomatitis virus from electron cryomicroscopy First long awaited high resolution structure (according to Cryo-EM standards) of a L protein from a NNS virus, uncovering how RdRp and capping enzymes are spatially organized and putatively co-ordinated HIV integrase inhibitors: 20-year landmark and challenges The structural basis for cap binding by influenza virus polymerase subunit PB2 Molecular basis of mRNA cap recognition by influenza B polymerase PB2 subunit The influenza virus polymerase complex: an update on its structure, functions, and significance for antiviral drug design Quantitative analysis of influenza virus RNP interaction with RNA cap structures and comparison to human cap binding protein eIF4E Discovery of a novel, first-in-class, orally bioavailable azaindole inhibitor (VX-787) of influenza PB2 Binding of the methyl donor S-adenosyl-L-methionine to middle east respiratory syndrome coronavirus 2 0 -Omethyltransferase nsp16 promotes recruitment of the allosteric activator nsp10 Metabolism and antiviral activity of ribavirin Ribavirin for the treatment of chronic hepatitis C virus infection: a review of the proposed mechanisms of action A structural basis for the inhibition of the NS5 dengue virus mRNA 2 0
    keywords: binding; capping; enzymes; inhibitors; mrna; mtase; protein; rna; structure; viral; virus; viruses
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        item: #448 of 1349
          id: cord-265508-t1nfyzf5
      author: Boursnell, M.E.G.
       title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B
        date: 1984-08-31
       words: 2134
      flesch: 51
     summary: RNA sequence data from this region might also enable us to predict the properties and thus aid the identification of possible polypeptides coded for by mRNA B. key: cord-265508-t1nfyzf5 authors: Boursnell, M.E.G.; Brown, T.D.K. title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B date: 1984-08-31 journal: Gene DOI: 10.1016/0378-1119(84)90169-0 sha: doc_id: 265508 cord_uid: t1nfyzf5 Abstract DNA sequencing of genomic cDNA clones of avian infectious bronchitis virus (IBV) has been carried out.
    keywords: ibv; mrna; rna; sequence
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        item: #449 of 1349
          id: cord-265855-zf52vl11
      author: Mayor-Ibarguren, Ander
       title: A Hypothesis for the Possible Role of Zinc in the Immunological Pathways Related to COVID-19 Infection
        date: 2020-07-10
       words: 5330
      flesch: 38
     summary: However, although plasma zinc concentration moderately correlates to habitual intake, the test also has limited specificity because zinc levels are depressed during inflammatory disease states or pregnancy and increase with acute catabolic states (42) . In severe infectious diseases, CRP levels can reach 100-200 mg/L, with a much greater decrease in zinc levels (40-60%) (43) .
    keywords: activation; covid-19; deficiency; disease; il-6; infection; levels; plasma; protein; response; rna; sars; treatment; zinc
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        item: #450 of 1349
          id: cord-265895-ck7eto16
      author: Baric, Ralph S.
       title: Analysis of intracellular small RNAs of mouse hepatitis virus: evidence for discontinuous transcription
        date: 1987-02-28
       words: 4521
      flesch: 54
     summary: Preparation of MHV intracellular RNA RNA was extracted from infected cells by the phenol/ chloroform method between 5 and 7 hr postinfection (70% CPE) (Baric et al., 1983) . Computing stability of MHV RNA secondary structure Predictions for regions of secondary structure in MHV RNA were made using the Zucker RNA folding program through Bionet (Zucker and Stiegler, 1981) .
    keywords: a/.; fig; leader; mhv; nucleotides; rna; rnas; species
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        item: #451 of 1349
          id: cord-266127-phv08xe2
      author: Mukhopadhyay, Urbi
       title: Biphasic regulation of RNA interference during rotavirus infection by modulation of Argonaute2
        date: 2019-08-26
       words: 7658
      flesch: 33
     summary: Furthermore, sensitivity of RV protein expression to shRNA-mediated RNAi in infection scenario was analysed. The proviral significance of AGO2 degradation was further confirmed when ectopic overexpression of AGO2 significantly reduced RV infection.
    keywords: ago2; anti; antiviral; cells; et al; expression; figure; infection; ma104; nsp1; protein; rnai; rotavirus; sa11
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        item: #452 of 1349
          id: cord-266464-wuf3s8m0
      author: Kim, So Yeon
       title: Viral RNA in Blood as Indicator of Severe Outcome in Middle East Respiratory Syndrome Coronavirus Infection
        date: 2016-10-17
       words: 1812
      flesch: 42
     summary: Blood viral RNA has been detected in a few case reports of MERS-CoV fatalities (8) (9) (10) . Our data of 42 specimens from cross-sectional time points focusing on early viremia showed that blood viral RNA was present in a subpopulation of patients and that these patients had significantly poorer prognoses, as demonstrated by the need for more frequent mechanical ventilation and the increased risk for death.
    keywords: blood; cov; mers; patients; rna; specimens
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        item: #453 of 1349
          id: cord-266520-n439dwcx
      author: Levanova, Alesia A.
       title: Enzymatically synthesized 2'-fluoro-modified Dicer-substrate siRNA swarms against herpes simplex virus demonstrate enhanced antiviral efficacy and low cytotoxicity
        date: 2020-08-13
       words: 3639
      flesch: 39
     summary: Therefore, to produce siRNA swarms for the cellular experiments we used 2'-F-dATP, 2'-F-dCTP, or 2'-F-dUTP, but not their mixture. We have previously reported a novel enzymatic approach to synthetize large pools of siRNA molecules, which we refer to as siRNA swarms.
    keywords: 2'-f; antiviral; et al; fig; sirna; swarms; ul29
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        item: #454 of 1349
          id: cord-266521-vovas81d
      author: Yokobayashi, Yohei
       title: Aptamer-based and aptazyme-based riboswitches in mammalian cells
        date: 2019-06-22
       words: 3235
      flesch: 35
     summary: DNA polymerase In vitro selection of RNA molecules that bind specific ligands Controlling gene expression in living cells through small molecule-RNA interactions Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression Synthetic RNA-based switches for mammalian gene expression control Exogenous control of mammalian gene expression through modulation of RNA self-cleavage Identification of inhibitors of ribozyme self-cleavage in mammalian cells via high-throughput screening of chemical libraries Controlling mammalian gene expression by allosteric hepatitis delta virus ribozymes Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems Conditional control of mammalian gene expression by tetracycline-dependent hammerhead ribozymes A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression Highly motif-and organism-dependent effects of naturally occurring hammerhead ribozyme sequences on gene expression This work surveyed a panel of ribozymes in various cellular and genetic contexts and showed that ribozyme activity is highly context dependent. Protein-based engineered transcription factors (TFs), such as Tet-ON and Tet-OFF systems derived from a bacterial TF, are among the most widely used tools to control mammalian gene expression in response to small molecule triggers [1] .
    keywords: cells; control; expression; gene; mammalian; riboswitches; ribozyme; rna
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        item: #455 of 1349
          id: cord-266585-jfjrk9gy
      author: Fang, Shouguo
       title: An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells
        date: 2007-02-05
       words: 7179
      flesch: 49
     summary: In vitro assembly of full-length coronavirus clones, generation of full-length transcripts in vitro using a bacteriophage DNA-dependent RNA polymerase, and recovery of infectious viruses by introduction of the in vitro-synthesized transcripts into cells, first used by Yount et al. (2000) , are a rapid and reliable approach to construct infectious clones from large RNA viruses. key: cord-266585-jfjrk9gy authors: Fang, Shouguo; Chen, Bo; Tay, Felicia P.L.; Ng, Beng Sern; Liu, Ding Xing title: An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date: 2007-02-05 journal: Virology DOI: 10.1016/j.virol.2006.08.020 sha: doc_id: 266585 cord_uid: jfjrk9gy Genetic manipulation of the RNA genomes by reverse genetics is a powerful tool to study the molecular biology and pathogenesis of RNA viruses.
    keywords: cells; fig; ibv; length; mutant; mutation; rna; transcripts; vero; virus
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        item: #456 of 1349
          id: cord-266634-bww62vx8
      author: Gopinath, M.
       title: Evidence for N(7) guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus
        date: 2015-10-07
       words: 2307
      flesch: 50
     summary: In the present work, we present evidence for N 7 guanine methyl transferase activity of RPV L protein and further demonstrate that this activity is localized to aa 1717-2183 of L protein indicating the modular nature of the RdRP. Sequence alignment of RPV L protein with 2 0 -O-methyl transferase from other species revealed the conservation of KDKE tetrad suggesting the presence of this motif in domain III of RPV L protein (Fig. 1a) .
    keywords: cap; methyl; mrna; protein; transferase
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        item: #457 of 1349
          id: cord-266921-x9q7dwc4
      author: Worrall, Jonathan AR
       title: Information available at cut rates: structure and mechanism of ribonucleases
        date: 2006-12-26
       words: 4617
      flesch: 41
     summary: The apparent wanton destruction of RNA by ribonucleases poses several questions: how do cells maintain folded RNA structures, such as tRNA and ribosomes, in the presence of all these keen ribonucleases? The crystal structure of the RNase E catalytic domain has been solved in complex with RNA substrate at 2.85 Å (Figure 1a )
    keywords: coli; crystal; exosome; figure; fold; mechanism; processing; ribonucleases; rnase; site; structure
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        item: #458 of 1349
          id: cord-266960-kyx6xhvj
      author: Temple, Mark D.
       title: Real-time audio and visual display of the Coronavirus genome
        date: 2020-10-02
       words: 6781
      flesch: 52
     summary: This paper demonstrates that sonification of RNA sequence data may also be useful to understand how the genome functions. During this time a large body of evidence has arisen regarding RNA sequence homology to other SARS like virus strains
    keywords: audio; data; display; genome; reading; region; rna; sequence; sonification; transcription; translation
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        item: #459 of 1349
          id: cord-266985-9qwttt2y
      author: Gale, P.
       title: Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose–response models as a case study
        date: 2014-11-04
       words: 8073
      flesch: 33
     summary: Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection Human Microbiome Project Protective HLA molecules determine infection outcome in hepatitis C virus infection by preferential preservation of peptides from conserved viral proteins Consistent change in the B-C loop of VP2 observed in foot-and-mouth disease virus from persistently infected cattle: implications for association with persistence The carbohydrate moiety and high molecular weight carrier of histo-blood group antigens are both required for norovirus-receptor recognition Rotavirus cell entry Genetic basis of host resistance to norovirus infection Quasispecies theory and the behaviour of RNA viruses Role of cell culture for virus detection in the age of technology The Society for Applied Microbiology Human susceptibility and resistance to Norwalk virus infection Heterotrophic humoral and cellular immune responses following Norwalk virus infection Severe acute respiratory syndrome coronavirus protein nsp1 is a novel eukaryotic translation inhibitor that represses multiple steps of translation initiation An expanded protein-protein interaction network in Bacillus subtilis reveals a group of hubs: exploration by an integrative approach Mucin dynamics and enteric pathogens Filoviruses require endosomal cysteine proteases for entry but exhibit distinct protease preferences A risk assessment model for Campylobacter in broiler meat Central to understanding virus replication in step 4 is the application of proteomics to determine protein-protein contacts in situ in the infected cell and thus how the individual virus proteins associate with host cell proteins and hence work together.
    keywords: binding; cell; data; dose; et al; host; human; infection; nov; omics; pathogen; proteins; rna; step; virus; viruses
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        item: #460 of 1349
          id: cord-267027-diwm1940
      author: Le, Shu-Yun
       title: Conserved tertiary structure elements in the 5′ untranslated region of human enteroviruses and rhinoviruses
        date: 1992-12-31
       words: 4364
      flesch: 49
     summary: key: cord-267027-diwm1940 authors: Le, Shu-Yun; Chen, Jih-H.; Sonenberg, Nahum; Maizel, Jacob V. title: Conserved tertiary structure elements in the 5′ untranslated region of human enteroviruses and rhinoviruses date: 1992-12-31 journal: Virology DOI: 10.1016/0042-6822(92)90261-m sha: doc_id: 267027 cord_uid: diwm1940 Abstract A combination of comparative sequence analysis and thermodynamic methods reveals the conservation of tertiary structure elements in the 5′ untranslated region (UTR) of human enteroviruses and rhinoviruses. Conserved tertiary structure elements in the 5' UTR of human enteroviruses and rhinoviruses Figures 2-4 show the common tertiary structures in the 5' UTR of PV2L, HRV89, and CB4, respectively.
    keywords: a/.; human; poliovirus; pseudoknot; rna; sequence; structure
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        item: #461 of 1349
          id: cord-267036-llngs3v5
      author: Lai, Ming‐Chih
       title: Functional interplay between viral and cellular SR proteins in control of post‐transcriptional gene regulation
        date: 2009-02-10
       words: 4469
      flesch: 42
     summary: Viral SR proteins. Phosphorylation of the RS domain can modulate the biological function of viral SR proteins, which may in turn impact on viral gene expression or other activities (Fig. 2) .
    keywords: expression; mrna; phosphorylation; proteins; rna; splicing
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        item: #462 of 1349
          id: cord-267115-6jqdi417
      author: Giobbe, Giovanni Giuseppe
       title: SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids
        date: 2020-06-24
       words: 8091
      flesch: 38
     summary: Here we show the novel derivation of fetal gastric organoids from 8-21 post-conception week (PCW) fetuses, and from pediatric biopsies, to be used as an in vitro model for SARS-CoV-2 gastric infection. While R-spondin 1,Wnt-3A and Noggin withdrawal led to more differentiated morphology, CHIR99021 (GSK-3 inhibitor) proved to be essential in the formation of fetal gastric organoids starting from single cells (Fig. 2a) .
    keywords: analysis; cells; cov-2; data; degs; expression; fig; gastric; human; infection; organoids; pcw; pediatric; rna; samples; sars; stages; virus
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        item: #463 of 1349
          id: cord-267124-8efdzlc0
      author: Wichmann, Dominic
       title: Autopsy Findings and Venous Thromboembolism in Patients With COVID-19: A Prospective Cohort Study
        date: 2020-05-06
       words: 4071
      flesch: 45
     summary: retrospective study Multiple roles of the coagulation protease cascade during virus infection Diagnosis, prevention, and treatment of thromboembolic complications in COVID-19: report of the National Institute for Public Health of the Netherlands Coagulation disorders in coronavirus infected patients: COVID-19, SARS-CoV-1, MERS-CoV and lessons from the past SARS-CoV-2 and viral sepsis: observations and hypotheses German recommendations for critically ill patients with COVID-19 The stimulation of thrombosis by hypoxia Histopathologic changes and SARS-CoV-2 immunostaining in the lung of a patient with COVID-19 Pulmonary pathology of early-phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer Effectiveness of convalescent plasma therapy in severe COVID-19 patients The characteristics of 50 hospitalized COVID-19 patients with and without ARDS Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Anticoagulant treatment is associated with decreased mortality in severe coronavirus disease 2019 patients with coagulopathy COVID-19 and thrombotic or thromboembolic disease: implications for prevention, antithrombotic therapy, and follow-up Current Author Addresses Dr. Becker: Department of Pulmonology and Internal Intensive Care, Asklepios Hospital Barmbek Dr. de Weerth: Department of Internal Medicine, Agaplesion Diakonie Hospital Author Contributions: Conception and design: D Provision of study materials or patients Standard weights for men and women (adopted from Molina and DiMaio [13, 14]), respectively, are as follows (the dependence of standard organ weights on body weight was not considered here): brain, 1401 g and 1233 g; heart, 331 g and 245 g; lung (right), 445 g and 340 g; lung (left), 395 g and 299 g; liver, 1561 g and 1288 g; kidney (right), 129 g and 108 g Figure 1 . To our knowledge, only 3 case reports have been published about COVID-19 patients who have undergone complete autopsy (7, 8) .
    keywords: autopsy; cases; cov-2; covid-19; death; findings; lung; patients; sars
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        item: #464 of 1349
          id: cord-267326-355q6k6k
      author: Gu, Xiaoqiong
       title: Geospatial distribution of viromes in tropical freshwater ecosystems
        date: 2018-06-15
       words: 8436
      flesch: 35
     summary: Viral communities in different reservoirs in terms of land use impact were compared and the majority of viral communities were largely conserved and stable at the family level with Myoviridae, Siphoviridae and Podoviridae as the main family level, and small differences observed in Dicistroviridae and other families (Fig. 2B) . Bacteriophage observations and evolution The marine viromes of four oceanic regions The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes Globally mobile populations and the spread of emerging pathogens Prevalence and genetic diversity of waterborne pathogenic viruses in surface waters of tropical urban catchments Prevalence and genotypes of human noroviruses in tropical urban surface waters and clinical samples in Singapore Identification of viral pathogen diversity in sewage sludge by metagenome analysis Genomic analysis of uncultured marine viral communities The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments Oxygen minimum zones harbour novel viral communities with low diversity Spatial and temporal variability across life's hierarchies in the terrestrial Antarctic Human and bovine viruses in the Milwaukee River watershed: hydrologically relevant representation and relations with environmental variables Metagenomic analysis of coastal RNA virus communities Human norovirus transmission and evolution in a changing world Bacteria-phage interactions in natural environments Functional metagenomic profiling of nine biomes Metagenomic analysis of RNA viruses in a fresh water lake Zoonotic hepatitis E virus: classification, animal reservoirs and transmission routes Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara Global consequences of land use A latitudinal diversity gradient in planktonic marine bacteria Cyclovirus CyCV-VN species distribution is not limited to Vietnam and extends to Viral metagenomics analysis of planktonic viruses in East Lake Diarrhea and enteric emerging viruses in HIV-infected patients Bacteriophages: update on application as models for viruses in water Unbiased detection of respiratory viruses by use of RNA sequencing-based metagenomics: a systematic comparison to a commercial PCR panel Enteric viruses and diarrhea in HIV-infected patients Ecology drives the worldwide distribution of human diseases Novoalign.
    keywords: areas; community; contigs; diversity; et al; human; land; metagenomics; pathogens; qpcr; reads; reservoirs; singapore; study; tributaries; virome; viruses; water
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        item: #465 of 1349
          id: cord-267377-wyhsxj6g
      author: Edwards, Michael C.
       title: Coat protein expression strategy of oat blue dwarf virus()
        date: 2014-01-14
       words: 4710
      flesch: 42
     summary: Thus, we propose the consensus sequence at the predicted cleavage site associated with minor CP expression in marafiviruses is LXG[G/A]. The locations of major CP (Maj. CP), minor CP (Min. CP), genomic (gRNA), and subgenomic RNA (sgRNA), on the blots are shown.
    keywords: cleavage; initiation; major; minor; mutant; obdv; protoplasts; sequence; sgrna
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        item: #466 of 1349
          id: cord-267475-6f4h3cck
      author: Kozak, Marilyn
       title: Pushing the limits of the scanning mechanism for initiation of translation
        date: 2002-10-16
       words: 24556
      flesch: 32
     summary: The upstream AUG codons often create small ORFs (upORFs) which are indeed translated, as shown by detecting the encoded peptide (Hackett et al., 1986; Raney et al., 2000; Wang and Wessler, 2001) or by fusing a reporter gene to the upORF (Abastado et al., 1991; Donzé et al., 1995; Liu et al., 1999; Steel et al., 1996; Tanaka et al., 2001; Xu et al., 2001) . The position effect, indicative of scanning, is seen when a mutation creates an AUG codon upstream from the normal start codon and translation shifts to the upstream site (Bergenhem et al., 1992; Cai et al., 1992; Gross et al., 1998; Harington et al., 1994; Liu et al., 1999; Lock et al., 1991; Mével-Ninio et al., 1996; Muralidhar et al., 1994; Wada et al., 1995) .
    keywords: alternative; aug; aug codon; aug start; cases; cells; codon; context; control; downstream; et al; expression; factor; fig; frame; gene; human; initiation; internal; isoforms; kozak; leader; leaky; leaky scanning; mechanism; mrna; position; production; promoter; protein; reading; region; regulation; ribosomes; scanning; sequence; site; splicing; start; start codon; structure; transcripts; translation; translation initiation; uporf; upstream; virus
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        item: #467 of 1349
          id: cord-267532-5rnqd9mb
      author: Zhang, Xuming
       title: Expression of Hemagglutinin/Esterase by a Mouse Hepatitis Virus Coronavirus Defective–Interfering RNA Alters Viral Pathogenesis
        date: 1998-03-01
       words: 7005
      flesch: 48
     summary: To assess the function of HE protein, we were interested in determining if the expression of a functional HE gene derived from JHM virus by the DI RNA vector could influence the pathogenesis of A59 virus (Fig. 1 ). These data demonstrate that the expression of the JHM virus HE gene by the DI RNA vector substantially alters the pathogenesis of A59 virus infection.
    keywords: a59; cat; cns; expression; infection; mice; p.i; protein; rna; virus
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        item: #468 of 1349
          id: cord-267533-nmgtan4e
      author: Hu, Zhigang
       title: Delayed hospital admission and high-dose corticosteroids potentially prolong SARS-CoV-2 RNA detection duration of patients with COVID-19
        date: 2020-10-29
       words: 3608
      flesch: 39
     summary: By shrinking down to zero coefficient weights, LASSO regression analysis has the ability to eliminate exposures that are non-related to the outcome [9, 11] . In the first step of our study, we identified the independent risk factors of long-term positive SARS-CoV-2 RNA detection by using LASSO logistic regression analysis and SARS-CoV-2 RNA detection duration by using LASSO Cox regression analysis.
    keywords: covid-19; detection; duration; patients; rna; rna detection; sars
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        item: #469 of 1349
          id: cord-267588-ruuzr6l1
      author: Garnett, Lauren
       title: Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages
        date: 2020-08-08
       words: 3099
      flesch: 40
     summary: key: cord-267588-ruuzr6l1 authors: Garnett, Lauren; Bello, Alexander; Tran, Kaylie N.; Audet, Jonathan; Leung, Anders; Schiffman, Zachary; Griffin, Bryan D.; Tailor, Nikesh; Kobasa, Darwyn; Strong, James E. title: Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages date: 2020-08-08 journal: J Virol Methods DOI: 10.1016/j.jviromet.2020.113947 sha: doc_id: 267588 cord_uid: ruuzr6l1 On March 11, 2020, the World Health Organization (WHO) assessed COVID-19, caused by SARS-CoV-2, as a pandemic. To tackle this issue, we evaluated the utility of different swabs and transport mediums for the molecular detection of SARS-CoV-2.
    keywords: cov-2; detection; sars; swabs; testing; transport; virus
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        item: #470 of 1349
          id: cord-267867-q52nvn0n
      author: Chevalier, Christophe
       title: Inhibition of Hepatitis C Virus Infection in Cell Culture by Small Interfering RNAs
        date: 2016-12-14
       words: 8023
      flesch: 37
     summary: The siRNAs si240-1a and si244 proved to be the most efficient inhibitors of HCV RNA replication with inhibition doses 50 of 19 ng (0.64 nmol/l) and 33 ng (1.11 nmol/l), respectively, and all siRNAs exhibited inhibition doses 50 within the 19-141 ng range. These results correlated well with inhibition levels of reporter SEAP activity, and confirmed that HCV RNA replication is strongly inhibited, if not abolished, in cells treated with 2 μg of the three most efficient siRNAs (si240-1a, si244, and si313).
    keywords: cells; figure; genotype; hcv; hepatitis; ntat2aneo; ntr; replication; replicon; rna; si240; sirnas; viral; virus
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        item: #471 of 1349
          id: cord-268071-ow2aijmj
      author: Pachetti, Maria
       title: Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant
        date: 2020-04-22
       words: 4460
      flesch: 48
     summary: Viruses with RdRp mutation have a median of 3 point mutations [range: 2–5], otherwise they have a median of 1 mutation Interestingly, viral genomes present in North American patients carrying RdRp mutation (14%) do not carry any of the European specific mutations.
    keywords: cov-2; drug; genomes; mutation; number; patients; positions; rdrp; rna; sars
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        item: #472 of 1349
          id: cord-268122-74nj66vb
      author: Xie, Na
       title: NAD(+) metabolism: pathophysiologic mechanisms and therapeutic potential
        date: 2020-10-07
       words: 32145
      flesch: 32
     summary: Alzheimer disease Nicotinamide restores cognition in Alzheimer's disease transgenic mice via a mechanism involving sirtuin inhibition and selective reduction of Thr231-phosphotau Nicotinamide mononucleotide adenylyltransferase uses its NAD(+) substrate-binding site to chaperone phosphorylated Tau Parkinson's disease psychosis: presentation, diagnosis and management Decreased sirtuin deacetylase activity in LRRK2 G2019S iPSCderived dopaminergic neurons Mitochondrial metabolism regulates microtubule acetylome and autophagy trough sirtuin-2: impact for Parkinson's disease The NAD+ precursor nicotinamide riboside rescues mitochondrial defects and neuronal loss in iPSC and fly models of Parkinson's disease Enhancing NAD(+) salvage metabolism is neuroprotective in a PINK1 model of Parkinson's disease Parp mutations protect against mitochondrial dysfunction and neurodegeneration in a PARKIN model of Parkinson's disease Phenothiazine normalizes the NADH/ NAD(+) ratio, maintains mitochondrial integrity and protects the nigrostriatal dopamine system in a chronic rotenone model of Parkinson's disease A novel treatment target for Parkinson's disease c-Jun N-terminal kinase (JNK)-mediated phosphorylation of SARM1 regulates NAD(+) cleavage activity to inhibit mitochondrial respiration SARM1 and TRAF6 bind to and stabilize PINK1 on depolarized mitochondria High doses of nicotinamide prevent oxidative mitochondrial dysfunction in a cellular model and improve motor deficit in a Drosophila model of Parkinson's disease Implications of NAD metabolism in pathophysiology and therapeutics for neurodegenerative diseases Clinical features of Huntington's disease Huntington's disease-update on treatments Huntington's disease: a clinical review The neuropsychology of Huntington's disease PGC-1α, sirtuins and PARPs in Huntington's disease and other neurodegenerative conditions: NAD+ to rule them all trans-(-)-ε-Viniferin increases mitochondrial sirtuin 3 (SIRT3), activates AMP-activated protein kinase (AMPK), and protects cells in models of Huntington disease Thermoregulatory and metabolic defects in Huntington's disease transgenic mice implicate PGC-1alpha in Huntington's disease neurodegeneration Impaired PGC-1alpha function in muscle in Huntington's disease PGC-1α rescues Huntington's disease proteotoxicity by preventing oxidative stress and promoting TFEB function Nicotinamide improves motor deficits and upregulates PGC-1α and BDNF gene expression in a mouse model of Huntington's disease Inhibition of mTOR induces autophagy and reduces toxicity of polyglutamine expansions in fly and mouse models of Huntington disease The kynurenine pathway modulates neurodegeneration in a Drosophila model of Huntington's disease Kynurenine pathway measurements in Huntington's disease striatum: evidence for reduced formation of kynurenic acid Antioxidant alternatives in the treatment of amyotrophic lateral sclerosis: a comprehensive review Evaluation of the NAD(+) biosynthetic pathway in ALS patients and effect of modulating NAD(+) levels in hSOD1-linked ALS mouse models ALS genes in the genomic era and their implications for FTD Is SOD1 loss of function involved in amyotrophic lateral sclerosis Oxidative stress in neurodegenerative diseases Mutations in Cu/Zn superoxide dismutase gene are associated with familial amyotrophic lateral sclerosis Differential effects of mutant SOD1 on protein structure of skeletal muscle and spinal cord of familial amyotrophic lateral sclerosis: role of chaperone network The genetics and neuropathology of amyotrophic lateral sclerosis Astrocytes expressing ALS-linked mutated SOD1 release factors selectively toxic to motor neurons Increased glutathione biosynthesis by Nrf2 activation in astrocytes prevents p75NTR-dependent motor neuron apoptosis A role for astrocytes in motor neuron loss in amyotrophic lateral sclerosis Enhancing NAD+ salvage pathway reverts the toxicity of primary astrocytes expressing amyotrophic lateral sclerosis-linked mutant superoxide dismutase 1 and~90 μM for mitochondrial NAD + , respectively.
    keywords: acid; activation; activity; aging; als; biosynthesis; cancer; cd38; cells; clock; cycle; damage; disease; dna; enzymes; expression; fatty; function; gene; glucose; homeostasis; human; inflammation; inhibition; injury; insulin; levels; liver; metabolism; mice; mitochondrial; nad +; nadph; nampt; nicotinamide; nmn; oxidative; parps; pathway; production; protein; redox; regulation; repair; response; rna; role; ros; salvage; signaling; sirt1; sirtuins; stress; tissue; transcription
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        item: #473 of 1349
          id: cord-268139-tgpsu4qz
      author: Brockway, Sarah M.
       title: Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication
        date: 2005-09-30
       words: 10196
      flesch: 49
     summary: Intracellular localization of mutant nsp1 proteins. The clarified media supernatants from cells transfected with VUSB1, VUSB2, VUSB3, VUSB4, or VUSB7 RNA were capable of infecting DBT-9 cells, indicating that they contained nsp1 mutant viruses.
    keywords: cells; fig; gene; icwt; kda; mhv; mutant; nsp1; nsp1dc; nsp2; protein; replication; rna; synthesis; viral; virus; viruses
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        item: #474 of 1349
          id: cord-268206-ino9srb6
      author: Hamed, Manal A.
       title: An overview on COVID-19: reality and expectation
        date: 2020-06-01
       words: 6090
      flesch: 35
     summary: However, there is no clear evidence that the BCG vaccine protects people against infection with COVID-19 virus. In a study involving patients with pandemic influenza (H1N1) and SARS virus, treatment of severe infection with convalescent plasma was associated with reduced respiratory viral load, serum cytokine response, and mortality (Cheng et al. 2005; Hung et al. 2011) .
    keywords: angiotensin; chloroquine; coronavirus; cov-2; covid-19; disease; enzyme; et al; infection; novel; obesity; patients; protein; sars; treatment
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        item: #475 of 1349
          id: cord-268337-o6lo55o8
      author: Lloyd, Richard E.
       title: Translational control by viral proteinases
        date: 2005-11-21
       words: 9429
      flesch: 38
     summary: The major apoptotic pathway activated and suppressed by poliovirus Foot-and-mouth disease virus 3C protease induces cleavage of translation initiation factors eIF4A and eIF4G within infected cells Picornavirus IRESes and the poly(A) Translational repression by a novel partner of human poly(A) binding protein, Paip2 Foot-and-mouth disease virus leader proteinase: purification of the lb form and determination of its cleavage site on eIF-4 gamma Loss of a phosphorylated form of transcription factor CREB/ATF in poliovirus-infected cells Structural basis of ligand recognition by PABC, a highly specific peptide-binding domain found in poly(A)-binding protein and a HECT ubiquitin ligase Structure and function of the C-terminal PABC domain of human poly(A)-binding protein Calicivirus 3C-like proteinase inhibits cellular translation by cleavage of poly(A)-binding protein Efficient cleavage of ribosome-associated poly(A)-binding protein by enterovirus 3C protease Cleavage of poly(A)-binding protein by poliovirus 3C protease inhibits host cell translation: a novel mechanism for host translation shutoff Mapping of functional domains in eukaryotic protein synthesis initiation factor 4G (eIF4G) with picornaviral proteases -implications for cap-dependent and cap-independent translational initiation Mapping the cleavage site in protein synthesis initiation factor-eIF-4G of the 2A proteases from human Coxsackievirus and rhinovirus Isolation and structural characterization of cap-binding proteins from poliovirus-infected HeLa cells Purification of two picornaviral 2A proteinases -interaction with eIF-4G and influence on in vitro translation Homeostasis in mRNA initiation: wheat germ poly(A)-binding protein lowers the activation energy barrier to initiation complex formation Capdependent translation initiation in eukaryotes is regulated by a molecular mimic of eIF4G Eukaryotic translation initiation factor 4G is targeted for proteolytic cleavage by caspase 3 during inhibition of translation in apoptotic cells A cellular protein that binds to the 5 -noncoding region of poliovirus RNA: implications for internal translation initiation La autoantigen enhances and corrects aberrant translation of poliovirus RNA in reticulocyte lysate Cap-dependent and cap-independent translation in eukaryotic systems Messenger RNA turnover in eukaryotes: pathways and enzymes Messenger RNA poly(A) tail, a 3 enhancer of translational initiation An internal ribosome entry segment promotes translation of the simian immunodeficiency virus genomic RNA In vitro cleavage of eIF4GI but not eIF4GII by HIV-1 protease and its effects on translation in the rabbit reticulocyte lysate system The C-terminal domain of eukaryotic protein synthesis initiation factor (eIF) 4G is sufficient to support cap-independent translation in the absence of eIF4E Dominant negative mutants of mammalian translation initiation factor eIF-4A define a critical role for eIF-4F in cap-dependent and cap-independent initiation of translation Functional dissection of eukaryotic initiation factor 4F: the 4A subunit and the central domain of the 4G subunit are sufficient to mediate internal entry of 43S preinitiation complexes Haemoglobin synthesis and polysomes in intact reticulocytes A cell cycle-dependent protein serves as a template-specific translation initiation factor Cell-specific proteins regulate viral RNA translation and virus-induced disease Dual function of the messenger RNA cap structure in poly(A)-tail-promoted translation in yeast Starting the protein synthesis machine: eukaryotic translation initiation Poly(A)-tail-promoted translation in yeast: implications for translational control Characterization of a novel RNA-binding region of eIF4GI critical for ribosomal scanning Lack of direct correlation between p220 cleavage and the shut-off of host translation after poliovirus infection ATP-dependent unwinding of messenger RNA structure by eukaryotic initiation factors Caspases are not involved in the cleavage of translation initiation factor eIF4GI during picornavirus infection eIF4A: the godfather of the DEAD box helicases Variability in apoptotic response to poliovirus infection Paip1 interacts with poly(A) binding protein through two independent binding motifs Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F Infection of HeLa cells with poliovirus results in modification of a complex that binds to the rRNA promoter The poly(A)-binding protein is required for poly(A) shortening and 60S ribosomal subunit dependent translation initiation Eukaryotic translation initiation: there are (at least) two sides to every story Translation initiation and viral tricks Nuclear entry of poliovirus protease-polymerase precursor 3CD: implications for host cell transcription shut-off
    keywords: binding; cap; cells; cleavage; eif4; eif4gi; et al; infection; initiation; mrna; pabp; pro; protein; translation
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        item: #476 of 1349
          id: cord-268467-btfz6ye8
      author: Schreiber, Steven S.
       title: Sequence analysis of the nucleocapsid protein gene of human coronavirus 229E
        date: 1989-03-31
       words: 5049
      flesch: 51
     summary: RNAGenetits Characterization of leader RNA sequences on the virion and mRNAs of mouse hepatitis virus, a cytoplasmic virus Mouse hepatitis virus A59: The mRNAs of coronaviruses contain a stretch of leader sequence which is derived from the 5'-end of the viral genome and exhibits homologywith the intergenic consensus sequence Budzilowicz et al., 1985) .
    keywords: a/.; coronaviruses; hcv-229e; human; leader; mrna; nucleocapsid; protein; rna; sequence; virus
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        item: #477 of 1349
          id: cord-268565-2sg1tlrg
      author: Clarke, David K.
       title: Recombinant vesicular stomatitis virus as an HIV-1 vaccine vector
        date: 2006-09-15
       words: 8297
      flesch: 28
     summary: Sequential transcription of the genes of vesicular stomatitis virus Ability of the matrix protein of vesicular stomatitis virus to suppress beta interferon gene expression is genetically correlated with the inhibition of host RNA and protein synthesis Role of the nucleocapsid protein in regulating vesicular stomatitis virus RNA synthesis Order of transcription of genes of vesicular stomatitis virus Phenotypic consequences of rearranging the P, M, and G genes of vesicular stomatitis virus Multiplication in and transmission by Aedes aegypti of vesicular stomatitis virus Chandipura: a new Arbovirus isolated in India from patients with febrile illness Vesicular stomatitis virus matrix protein inhibits host cell-directed transcription of target genes in vivo Interaction of VSV leader RNA and nucleocapsid protein may control VSV genome replication N protein of vesicular stomatitis virus selectively encapsidates leader RNA in vitro Characterization of vesicular stomatitis virus recombinants that express and incorporate high levels of hepatitis C virus glycoproteins A newly recognized vesiculovirus, Calchaqui virus, and subtypes of Melao and Maguari viruses from Argentina, with serologic evidence for infections of humans and horses Role of the membrane (M) protein in endogenous inhibition of in vitro transcription by vesicular stomatitis virus Comparative immunogenicity in rhesus monkeys of DNA plasmid, recombinant vaccinia virus, and replication-defective adenovirus vectors expressing a human immunodeficiency virus type 1 gag gene The matrix (M) protein of vesicular stomatitis virus regulates transcription Basic amino acid residues at the carboxy-terminal eleven amino acid region of the phosphoprotein (P) are required for transcription but not for replication of vesicular stomatitis virus genome RNA Isolation of Chandipura virus from sandflies in Aurangabad RNA virus mutations and fitness for survival Immunogenicity of attenuated vesicular stomatitis virus vectors expressing HIV type 1 Env and SIV Gag proteins: comparison of intranasal and intramuscular vaccination routes Priming with plasmid DNAs expressing interleukin-12 and simian immunodeficiency virus gag enhances the immunogenicity and efficacy of an experimental AIDS vaccine based on recombinant vesicular stomatitis virus Both NS and L proteins are required for in vitro RNA synthesis by vesicular stomatitis virus Generation of hepatitis C virus-like particles by use of a recombinant vesicular stomatitis virus vector VSV disrupts the Rae1/mrnp41 mRNA nuclear export pathway Human infection with the virus of vesicular stomatitis during an epizootic Avian influenza (H5N1) viruses isolated from humans in Asia in 2004 exhibit increased virulence in mammals Monkey neurovirulence test for live mumps vaccine The budding mechanism of spikeless vesicular stomatitis virus particles Neuropathological and immunofluorescence studies of experimental vesicular stomatitis virus encephalitis in mice Neurovirulence tests of type 3 oral poliovirus vaccine manufactured by Lederle Laboratories Recombinant vesicular stomatitis virus vectors expressing herpes simplex virus type 2 gD elicit robust CD4+ Th1 immune responses and are protective in mouse and guinea pig models of vaginal challenge Comparative studies on the viruses of vesicular stomatitis and equine encephalomyelitis Cytoplasmic domain requirement for incorporation of a foreign envelope protein into vesicular stomatitis virus An optimized vaccine vector based on recombinant vesicular stomatitis virus gives high-level, long-term protection against Yersinia pestis challenge Phosphorylation within the amino-terminal acidic domain I of the phosphoprotein of vesicular stomatitis virus is required for transcription but not for replication Cell-free synthesis and assembly of vesicular stomatitis virus nucleocapsids The earliest events in vesicular stomatitis virus infection of the murine olfactory neuroepithelium and entry of the central nervous system Genetic characteristics of conditional lethal mutants of vesicular stomatitis virus induced by 5-fluorouracil, 5-azacytidine, and ethyl methane sulfonate The genetics of vesiculoviruses Highly effective control of an AIDS virus challenge in macaques by using vesicular stomatitis virus and modified vaccinia virus Ankara vaccine vectors in a single-boost protocol A vesicular stomatitis virus recombinant expressing granulocyte-macrophage colony-stimulating factor induces enhanced T-cell responses and is highly attenuated for replication in animals Experimental transmission of Chandipura virus by mosquitoes Viral replication in olfactory receptor neurons and entry into the olfactory bulb and brain Intranasal vaccination with a recombinant vesicular stomatitis virus expressing cottontail rabbit papillomavirus L1 protein provides complete protection against papillomavirus-induced disease Cell surface expression of fusogenic vesicular stomatitis virus G protein from cloned cDNA Vaccination with a recombinant vesicular stomatitis virus expressing an influenza virus hemagglutinin provides complete protection from influenza virus challenge Attenuated vesicular stomatitis viruses as vaccine vectors The membrane-proximal stem region of vesicular stomatitis virus G protein confers efficient virus assembly Rhabdoviridae: the viruses and their replication Glycoprotein exchange vectors based on vesicular stomatitis virus allow effective boosting and generation of neutralizing antibodies to a primary isolate of human immunodeficiency virus type 1 An effective AIDS vaccine based on live attenuated vesicular stomatitis virus recombinants Neurological manifestations of avian influenza viruses in mammals The mumps virus neurovirulence safety test in rhesus monkeys: a comparison of mumps virus strains Influence of host factors on neuroinvasiveness of vesicular stomatitis virus: C. C. Thomas Growth and transovarial transmission of Chandipura virus (Rhabdoviridae: Vesiculovirus) in Phlebotomus papatasi Ecologic studies of vesicular stomatitis virus.
    keywords: attenuation; cell; expression; gene; genome; protein; replication; responses; rna; rvsv; stomatitis; transcription; vaccine; vectors; virus
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        item: #478 of 1349
          id: cord-268718-tt07cwrf
      author: Tan, Heng Wee
       title: Angiotensin‐converting enzyme 2: The old door for new severe acute respiratory syndrome coronavirus 2 infection
        date: 2020-06-30
       words: 6373
      flesch: 41
     summary: So far, three CoVs (HCoV-NL63, SARS-CoV, and SARS-CoV-2) have shown to utilize human ACE2 receptor. The known and suspected hosts of human coronaviruses that utilized human ACE2 receptors (HCoV-NL63, SARS-CoV, and SARS-CoV-2) are shown.
    keywords: ace2; coronavirus; cov; cov-2; covid-19; covs; enzyme; expression; host; human; patients; protein; receptor; sars; spike
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        item: #479 of 1349
          id: cord-268763-s16n7f17
      author: Williams, J. G.
       title: Identification of Three Endotypes in Pediatric Acute Respiratory Distress Syndrome by Nasal Transcriptomic Profiling
        date: 2020-05-02
       words: 4792
      flesch: 41
     summary: https://doi.org/10.1101/2020.04.28.20083451 doi: medRxiv preprint Group B had decreased and Group C had increased representation of genes related to ciliary function microtubule motor activity. Analysis of the 15 specimens processed and analyzed by standard techniques identified the same processes as differentiating Groups A, B, and C. Mortality appeared to be higher in group B (25%) and C subjects (28.6%) compared to A subject (5%, p=0.1).
    keywords: author; funder; license; medrxiv; pards; peer; preprint; review; specimens
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        item: #480 of 1349
          id: cord-268970-uz7q6z2f
      author: Ott, Isabel M.
       title: Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices
        date: 2020-08-04
       words: 2794
      flesch: 48
     summary: Prior work from saliva samples, however, has indicated that some buffers optimized for host nucleic acid stabilization may actually inhibit viral RNA detection, 4-6 particularly in extraction-free PCR workflows. To explore the viability of broadly deploying affordable saliva-based surveillance approaches 8 , we characterized SARS-CoV-2 RNA stability and virus infectivity from saliva samples stored in widely available, sterile, nuclease-free laboratory plastic (polypropylene) tubes.
    keywords: cov-2; preprint; rna; saliva; sars; testing
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        item: #481 of 1349
          id: cord-269011-230p8rsf
      author: de Haan, Cornelis A.M.
       title: Molecular Interactions in the Assembly of Coronaviruses
        date: 2005-08-31
       words: 22995
      flesch: 36
     summary: MHV M proteins carry a well-conserved SS(X)TTXXP sequence at their extreme amino terminus. As the expression of these enzymes varies in cells, conservation of the SS(X)TTXXP motif in MHV M protein may serve to increase opportunities for the protein to become glycosylated in different cell types.
    keywords: amino; assembly; binding; budding; cells; coronavirus; domain; envelope; et al; fusion; golgi; haan et; hepatitis; interaction; membrane; membrane protein; mhv; mouse; n protein; nucleocapsid; particles; protein; receptor; rna; s protein; sequence; spike; spike protein; terminal; tgev; virions; viruses
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        item: #482 of 1349
          id: cord-269150-d1sgnxc0
      author: Tan, Yong Wah
       title: Binding of the 5′-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription
        date: 2012-02-22
       words: 6997
      flesch: 41
     summary: Western blot analysis also noted a reduction in the expression of viral structural genes, between 50% and 90% reduction for S and N proteins, with a reduction between 40% and 80% of MADP1 protein ( Figure 5B ). key: cord-269150-d1sgnxc0 authors: Tan, Yong Wah; Hong, Wanjin; Liu, Ding Xiang title: Binding of the 5′-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription date: 2012-02-22 journal: Nucleic Acids Res DOI: 10.1093/nar/gks165 sha: doc_id: 269150 cord_uid: d1sgnxc0 Coronaviruses RNA synthesis occurs in the cytoplasm and is regulated by host cell proteins.
    keywords: -utr; binding; cells; coronavirus; figure; flag; ibv; interaction; madp1; protein; replication; rna; sars; stem
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        item: #483 of 1349
          id: cord-269193-a647hwu9
      author: Lin, Debby A.
       title: Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses
        date: 1991-05-31
       words: 2955
      flesch: 46
     summary: Nick-translated DNAs of plasmids pD21-39, pD50-40, pD43-22, pD68-30, pD22-39, pD26-16, and pD12a-35 hybridized to RNAs 1, 2, 3, 4, 5, 6, and 7, respectively in a Northern blot analysis of Dhori virus RNA (Fig. 1) 35, contains a small insert of segment 1 as well as an belonging to the group that hybridized to RNA seginsert for segment 7 (unpublished results). The sequence of the third largest segment of Thogoto/SiAr/l26/72 virus was recently determined (Staunton et al., 1989) unique in having a net negative charge unlike the net positive charge of the corresponding A, B, and C virus proteins.
    keywords: dhori; influenza; protein; rna; sequence; virus
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        item: #484 of 1349
          id: cord-269194-b1wlr3t7
      author: Engstrom-Melnyk, Julia
       title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology
        date: 2015-12-31
       words: 12555
      flesch: 22
     summary: Determining a patient's HIV viral load is indicated prior to entry into care, at the initiation of ART, at 2-8 weeks after ART initiation, and then typically every 3-4 months while on treatment: (1) to establish a baseline level of HIV viral load; (2) to establish viral response to the therapy to assess the virologic efficacy of ART; and (3) to monitor for abnormalities that may be associated with antiretroviral drugs (DHHS HIV, 2014) . (A) HIV viral loads will fluctuate as patients are on treatment, and, in most instances, will remain 'undetectable' (at or below dotted line); viral 'blips' are not uncommon and will result in transient 'detectable' and even quantifiable results (above the dashed line).
    keywords: assays; chronic; clinical; cmv; disease; et al; fda; hcv; hiv; infection; laboratory; load; molecular; patients; pcr; results; rna; testing; tests; therapy; time; time pcr; transplant; treatment; virus
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        item: #485 of 1349
          id: cord-269294-vx7xr80t
      author: Kwong, Ann D.
       title: Viral and cellular RNA helicases as antiviral targets
        date: 2005-09-23
       words: 6386
      flesch: 50
     summary: This is illustrated by an overlay of the structures for HCV RNA helicase 10 (red; three domains) and PcrA DNA helicase 11 (cyan; four domains) in FIG. The successful results of the HSV helicase inhibitors were not made public until several years after many companies had started screening for HCV helicase inhibitors.
    keywords: domain; g g; hcv; helicase; hepatitis; inhibitors; rna; s g; s s; viral; virus
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        item: #486 of 1349
          id: cord-269466-9hnal9ad
      author: Agbeci, Maxime
       title: Contribution of Host Intracellular Transport Machineries to Intercellular Movement of Turnip Mosaic Virus
        date: 2013-10-03
       words: 7192
      flesch: 42
     summary: In addition, CP and cylindrical inclusion (CI) protein are required for virus intercellular movement [34] [35] [36] and are associated with PD [37, 38] . In this study, we used a novel dual gene cassette construct that differentiated primary infected cells from cells infected after virus intercellular movement to show that the early as well as the late secretory pathway, but not endocytosis, was important for TuMV transport.
    keywords: cells; fig; fluorescence; intercellular; movement; myosin; pathway; plant; protein; red; replication; rna; secretory; transport; tumv; virus
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        item: #487 of 1349
          id: cord-269496-tnw7sxlh
      author: Sen Gupta, Parth Sarthi
       title: Binding mechanism and structural insights into the identified protein target of COVID-19 and importin-α with in-vitro effective drug ivermectin
        date: 2020-10-28
       words: 4918
      flesch: 42
     summary: But the exact mechanism and the specific target which Ivermectin inhibits were not known. Importin-a targeting compound Ivermectin inhibits by binding to the NLS-binding site of Importin-a, precluding Importin-a/b1 heterodimer formation and subsequently its combination with coronavirus followed by transportation from the cytoplasm to the nucleus through the nuclear pore complex (Atkinson et al., 2018; King et al., 2020; Shechter et al., 2017; Wagstaff et al., 2011; Yang et al., 2020) .
    keywords: complex; et al; figure; helicase; importin; ivermectin; protein; rdrp; rna; sars; targets
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        item: #488 of 1349
          id: cord-269720-o81j3d1j
      author: Page, Kevin W.
       title: Sequence analysis of the leader RNA of two porcine coronaviruses: Transmissible gastroenteritis virus and porcine respiratory coronavirus
        date: 1990
       words: 3559
      flesch: 51
     summary: An oligonucleotide, oligo 58, was synthesised that was complementary to the 5' end of the TGEV and PRCV leader RNA sequences (Fig. 1) . In this paper we describe the elucidation of the leader RNA sequences from the porcine coronaviruses TGEV and PRCV, the first leader sequence to be described from the TGEV serogroup of coronaviruses.
    keywords: leader; leader rna; mrna; prcv; rna; sequence; species; tgev
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        item: #489 of 1349
          id: cord-269726-z0frgm7s
      author: Gidari, Anna
       title: Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature
        date: 2020-10-10
       words: 6714
      flesch: 47
     summary: Long-term effects of COVID-19 in a patient on maintenance dialysis Glucocorticoid-induced relapse of COVID-19 in a patient with sarcoidosis Reevaluation of retested nucleic acid-positive cases in recovered COVID-19 patients: Report from a designated transfer hospital in Chongqing Recurrence of positive SARS-CoV-2 RNA in COVID-19: a case report Clinical recurrences of COVID-19 symptoms after recovery: viral relapse, reinfection or inflammatory rebound? Positive SARS-CoV-2 RNA recurs repeatedly in a case recovered from COVID-19: dynamic results from 108 days of follow-up Persistent SARS-COV-2 RNA positivity in a patient for 92 days after disease onset: a case report Positive conversion of COVID-19 after two consecutive negative RT-PCR results: a role of low-dose CT Recurrent presence of SARS-CoV-2 RNA in a 33-year-old man Repositive cases of nucleic acid tests in discharged patients with COVID-19: a follow-up study Positive SARS-Cov-2 test in a woman with COVID-19 at 22 days after hospital discharge: a case report Low humoral immune response and ineffective clearance of SARS-Cov-2 in a COVID-19 patient with CLL during a 69-day follow-up Recurrent positive nucleic acid detection in a recovered COVID-19 patient: a case report and literature review Successful recovery of recurrence of positive SARS-CoV-2 RNA in COVID-19 patient with systemic lupus erythematosus: a case report and review Clinical characteristics of severe acute respiratory syndrome coronavirus 2 reactivation Absent immune response to SARS-CoV-2 in a 3-month recurrence of coronavirus disease 2019 (COVID-19) case Recurrence of SARS-CoV-2 infection with a more severe case after mild COVID-19, reversion of RT-qPCR for positive and late antibody response: case report Repeated COVID-19 relapse during post-discharge surveillance with viral shedding lasting for 67 days in a recovered patient infected with SARS-CoV-2 COVID-19 infection recurrence presenting with meningoencephalitis Post discharge positive re-tests in COVID-19: common but clinically non-significant Progressive CT findings and positive RT-PCR again of recovered and discharged patients with COVID-19 Changes in RT-PCR test results and symptoms during the menstrual cycle of female individuals infected with SARS-CoV-2: report of two cases Incidence, clinical course and risk factor for recurrent PCR positivity in discharged COVID-19 patients in Guangzhou, China: a prospective cohort study COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing The treatment and follow-up of 'recurrence' with discharged COVID-19 patients: data from Guizhou Recurrent recurrence of positive SARS-CoV-2 RNA in a COVID-19 patient Recurrence or relapse of COVID-19 in older patients: a description of three cases Recurrent pneumonia in a patient with new coronavirus infection after discharge from hospital for insufficient antibody production: a case report A case presentation for positive SARS-CoV-2 RNA recurrence in a patient with a history of type 2 diabetes that had recovered from severe COVID-19 Clinical features of discharged COVID-19 patients with an extended SARS-CoV-2 RNA positive signal in respiratory samples The dilemma of COVID-19 recurrence after clinical recovery Persistent positivity and fluctuations of SARS-CoV-2 RNA in clinically-recovered COVID-19 patients Probable causes and risk factors for positive SARS-CoV-2 test in recovered patients: evidence from Brunei Darussalam Epidemiological characteristics of COVID-19 patients in convalescence period Chest CT study of fifteen COVID-19 patients with positive RT-PCR retest results after discharge Rate of re-positive RT-PCR test among patients recovered from COVID-19 Discontinuation of antiviral drugs may be the reason for recovered COVID-19 patients testing positive again Changes in serum virus-specific IgM/IgG antibody in asymptomatic and discharged patients with reoccurring positive COVID-19 nucleic acid test (RPNAT) Chest CT and clinical follow-up of discharged patients with COVID-19 in Wenzhou City A cluster of the Corona Virus Disease 2019 caused by incubation period transmission in Wuxi Re-positive coronavirus disease 2019 PCR test: could it be a reinfection? Diagnostic testing and screening for SARS-CoV-2 Growth kinetics of SARS-coronavirus in Vero E6 cells Detection and isolation of SARS-CoV-2 in serum, urine, and stool specimens of COVID-19 patients from the Republic of Korea Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement Positive result of Sars-Cov-2 in faeces and sputum from discharged patient with COVID-19 in Yiwu Song S Recurrence of positive SARS-CoV-2 viral RNA in recovered COVID-19 patients during medical isolation observation Positive RT-PCR test results in discharged COVID-19 patients: reinfection or residual Coronavirus disease (COVID-19) in a paucisymptomatic patient: Epidemiological and clinical challenge in settings with limited community transmission Seven discharged patients turning positive again for SARS-CoV-2 on quantitative RT-PCR Serial CT features in discharged COVID-19 patients with positive RT-PCR re-test A case series of recurrent viral RNA positivity in recovered COVID-19 Chinese patients The clinical features and outcomes of discharged coronavirus disease 2019 patients: a prospective cohort study Re-infection by COVID-19: a real threat for the future management of pandemia? Letter to the Editor: Three cases of re-detectable positive SARS-CoV-2 RNA in recovered COVID-19 Microbiol Infect Dis patients with antibodies Two cases of COVID-19 with positive salivary and negative pharyngeal or respiratory swabs at hospital discharge: a rising concern Persistent viral RNA positivity during recovery period of a patient with SARS-CoV-2 infection Recurrent PCR positivity after hospital discharge of people with coronavirus disease 2019 (COVID-19) Rehospitalization of a recovered coronavirus disease 19 (COVID-19) child with positive nucleic acid detection
    keywords: assay; cases; cov-2; covid-19; nasopharyngeal; patients; pcr; positive; recurrence; rna; sars; swab
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        item: #490 of 1349
          id: cord-269766-arjoemla
      author: Dutescu, R. Michael
       title: Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs
        date: 2020-09-08
       words: 2144
      flesch: 51
     summary: In our study, despite high levels of viral RNA in tears, we were unable to confirm the presence of viral conjunctivitis in patients with proven SARS-CoV AQ : 7 infection. Therefore, clinicians and patients are advised to stay in quarantine if COVID-19 is suspected, even if they had initially tested negative.
    keywords: cov-2; patients; rna; sars; study; tear
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        item: #491 of 1349
          id: cord-269771-hffxb7bm
      author: Cheung, Ka Shing
       title: Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis
        date: 2020-04-03
       words: 4805
      flesch: 38
     summary: We previously reported the high prevalence of enteric symptoms in patients with SARS and demonstrated acute viral replication in the small intestinal mucosa of SARS patients. The sewage concentrates of two hospitals receiving SARS patients in Beijing were also found to have SARS-CoV RNA detected at that time.
    keywords: clinical; coronavirus; covid-19; gastrointestinal; patients; rna; sars; stool; symptoms; viral
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        item: #492 of 1349
          id: cord-269866-3tpyj04y
      author: Liu, D. X.
       title: Identification of two new polypeptides encoded by mRNA5 of the coronavirus infectious bronchitis virus
        date: 1992-01-31
       words: 3168
      flesch: 44
     summary: Thus both the 5a and 5b ORFs are expressed in infected cells. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera.
    keywords: cells; mrna; orfs; virus
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        item: #493 of 1349
          id: cord-269975-1ebmq7t8
      author: Duplantier, Allen J.
       title: Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges
        date: 2020-05-27
       words: 12977
      flesch: 23
     summary: infection Protection against filovirus diseases by a novel broad-spectrum nucleoside analogue BCX4430 BioCryst Pharmaceuticals BioCryst announces study results for BCX4430 in a non-human primate model of Ebola Virus infection BioCryst Pharmaceuticals BioCryst announces positive study results for BCX4430 delayed treatment of Ebola virus infection in a non-human primate model Successful treatment of advanced Ebola virus infection with T-705 (favipiravir) in a small animal model Intracellular conversion and in vivo dose response of favipiravir (T-705) in rodents infected with Ebola virus Synthesis of [(18)F] favipiravir and biodistribution in C3H/HeN mice as assessed by positron emission tomography Efficacy of favipiravir (T-705) in nonhuman primates infected with Ebola virus or Marburg virus Post-exposure efficacy of oral T-705 (Favipiravir) against inhalational Ebola virus infection in a mouse model Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys FDA-approved selective estrogen receptor modulators inhibit Ebola virus infection Singledose pharmacokinetic study of clomiphene citrate isomers in anovular patients with polycystic ovary disease A screen of approved drugs and molecular probes identifies therapeutics with anti-Ebola virus activity Categorization and prioritization of drugs for consideration for testing or use in patients infected with Ebola Addressing therapeutic options for Ebola virus infection in current and future outbreaks A rapid screening assay identifies monotherapy with interferon-ss and combination therapies with nucleoside analogs as effective inhibitors of Ebola virus Evaluation of immune globulin and recombinant interferon-alpha2b for treatment of experimental Ebola virus infections Interferon-beta therapy prolongs survival in rhesus macaque models of Ebola and Marburg hemorrhagic fever Postexposure protection of non-human primates against a lethal Ebola virus challenge with RNA interference: a proof-ofconcept study Lipid nanoparticle siRNA treatment of Ebola-virus-Makona-infected nonhuman primates Discovery and early development of AVI-7537 and AVI-7288 for the treatment of Ebola virus and Marburg virus infections Advanced antisense therapies for postexposure protection against lethal filovirus infections A single phosphorodiamidate morpholino oligomer targeting VP24 protects rhesus monkeys against lethal Ebola virus infection A potent Lassa virus antiviral targets an arenavirus virulence determinant Favipiravir (T-705), a novel viral RNA polymerase inhibitor Lassa virus infection of rhesus monkeys: pathogenesis and treatment with ribavirin Usefulness of monitoring ribavirin plasma concentrations to improve treatment response in patients with chronic hepatitis C Stampidine prevents mortality in an experimental mouse model of viral hemorrhagic fever caused by Lassa virus Zidampidine, an aryl phosphate derivative of AZT: in vivo pharmacokinetics, metabolism, toxicity, and anti-viral efficacy against hemorrhagic fever caused by Lassa virus Use of favipiravir to treat Lassa virus infection in macaques GuthrieW.I.P. Organization, N4-hydroxycytidine and derivatives and anti-viral uses related thereto Efficacy of a ML336 derivative against Venezuelan and eastern equine encephalitis viruses Development of (E)-2-((1,4-dimethylpiperazin-2-ylidene)amino)-5-nitro-N-phenylbenzamide, ML336: Monoclonal and cocktail antibody therapies approved by the Food and Drug Administration for countering anthrax and under development for treatment of Ebola virus infection are discussed.
    keywords: agents; animal; antibodies; antibody; biothreat; burkholderia; cell; combination; development; disease; drug; ebola; efficacy; fever; host; human; infection; inhibitors; model; pathogens; protein; pseudomallei; replication; resistance; screening; studies; target; therapy; treatment; virus; viruses
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        item: #494 of 1349
          id: cord-270143-muxrxvyo
      author: Markotter, Wanda
       title: Paramyxo- and Coronaviruses in Rwandan Bats
        date: 2019-07-02
       words: 4903
      flesch: 43
     summary: Host gene sequences were subsequently compared to bat sequences available in the public domain (on the NCBI GenBank and BOLD databases), results were interpreted and compared with the respective morphological field identifications. In addition to morphological identification of bat species, we also did molecular confirmation of species identities, contributing to the known genetic database available for African bat species.
    keywords: africa; assay; bats; coronaviruses; host; paramyxoviruses; rna; rwanda; samples; sequences; species; usa; viruses
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        item: #495 of 1349
          id: cord-270243-moxleyjg
      author: Cholleti, Harindranath
       title: Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique
        date: 2018-05-28
       words: 3246
      flesch: 44
     summary: Parasit Vectors Discovery of novel viruses in mosquitoes from the Zambezi valley of Mozambique Quality control and preprocessing of metagenomic datasets Fast gapped-read alignment with Bowtie 2 Evolution and ecology of influenza A viruses Johnston atoll, and lake chad viruses are novel members of the family orthomyxoviridae Arboviruses isolated from ARGAS TICKS IN Egypt: quaranfil, Chenuda, and Nyamanini Isolation of Nyamanini and Quaranfil viruses from Argas (Persicargas) arboreus ticks in Nigeria Identification and comparison of two viruses isolated from ticks of the genus Ornithodoros Cyclic avian mass mortality in the northeastern USA is associated with a novel orthomyxovirus Cygnet River virus, a novel orthomyxovirus from ducks Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. Many of these viral sequences showed very low sequence identity The contigs aligning to the amino acid positions of the closest relative and its identity to known viruses, indicating that they most likely correspond to novel viruses.
    keywords: family; identity; protein; reads; rhipicephalus; rna; sequences; study; ticks; viruses
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        item: #496 of 1349
          id: cord-270473-5tok4mqk
      author: Nanda, S. K.
       title: Mitochondrial HSP70, HSP40, and HSP60 bind to the 3′ untranslated region of the Murine hepatitis virus genome
        date: 2003-09-19
       words: 7111
      flesch: 44
     summary: The finding that antibodies to HSP40 and HSP60 only supershifted a relatively small portion of RNA-protein complex 1 suggests that for these two chaperones, only a small fraction of these molecules participated in the formation of MHV RNA-protein complexes. MHV RNA-protein complexes (4, 6, 8) or with primers for the abundant mRNA for GAPDH (5, 7, 9) .
    keywords: aconitase; anti; antibody; binding; complex; fig; hsp40; kda; mhv; mitochondrial; mthsp70; protein; rna
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        item: #497 of 1349
          id: cord-270550-if748w2n
      author: Bailey, Adam L.
       title: SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis
        date: 2020-11-05
       words: 5824
      flesch: 40
     summary: Figure 1 : ACE2 is expressed in the human heart and in stem cell derived cardiomyocytes. After infection with SARS-CoV-2, engineered tissues display typical features of myocarditis, including cardiomyocyte cell death, impaired cardiac contractility, and innate immune cell activation.
    keywords: ace2; cardiomyocytes; cell; cms; cov-2; expression; fig; hpsc; human; infected; infection; mock; sars; tissues
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        item: #498 of 1349
          id: cord-270594-62xotol3
      author: He, Lei
       title: Identification and characterization of vp7 gene in Bombyx mori cytoplasmic polyhedrosis virus
        date: 2017-09-05
       words: 4463
      flesch: 48
     summary: To prepare polyclonal antibody against VP7 proteins of BmCPV, the cDNA with primers listed in Table 1 was amplified with PCR. VP7 recombinant protein was purified from the transfected cells.
    keywords: antibody; bmcpv; bmn; cells; expression; fig; gene; genome; proteins; segments; silkworm; virus; vp7
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        item: #499 of 1349
          id: cord-270604-u62437dh
      author: Cuthill, Jennifer Hoyal
       title: A SIMPLE MODEL EXPLAINS THE DYNAMICS OF PREFERENTIAL HOST SWITCHING AMONG MAMMAL RNA VIRUSES
        date: 2013-02-19
       words: 7444
      flesch: 33
     summary: Specifically, host switch distance (HSD) was estimated, for each virus, as the average phylogenetic distance between each pair (i, j) of host species of that virus: where d ij is the midbranch distance between two host species i and j, and n is the number of host species. For all three host phylogenies, ABC selected a relatively low value for the parameter β, indicating a strong effect of host phylogenetic distance (HSD) on the probability of a successful host switch.
    keywords: distance; host; model; parameter; primates; probability; rna; species; switching; virus; viruses
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        item: #500 of 1349
          id: cord-270670-cubh9jxc
      author: Domingo, E.
       title: Viruses as Quasispecies: Biological Implications
        date: 2006
       words: 10501
      flesch: 29
     summary: Despite all cellular organisms being highly polymorphic genetically (in that distinct alleles from a gene are represented among individuals of one biological species), the level of heterogeneity of RNA virus populations confers a much greater adaptability than the levels of polymorphism estimated for cells. The units of selection Lethal mutagenesis of HIV by mutagenic ribonucleoside analogs Lethal mutagenesis of HIV with mutagenic nucleoside analogs Hepatitis C virus RNA-dependent RNA polymerase (NS5B) as a mediator of the antiviral activity of ribavirin Foot-and-mouth disease virus Interferon alfa-2b alone or in combination with ribavirin as initial treatment for chronic hepatitis C. Hepatitis Interventional Therapy Group Clonal interference and the evolution of RNA viruses A mutation in tomato aspermy cucumovirus that abolishes cell-to-cell movement is maintained to high levels in the viral RNA population by complementation Pol gene quasispecies of human immunodeficiency virus: mutations associated with drug resistance in virus from patients undergoing no drug therapy Contributions of vesicular stomatitis virus to the understanding of RNA virus evolution Negative effect of genetic bottlenecks on the adaptability of vesicular stomatitis virus Size of genetic bottlenecks leading to virus fitness loss is determined by mean initial population fitness Exponential fitness gains of RNA virus populations are limited by bottleneck effects Density-dependent selection in vesicular stomatitis virus
    keywords: cell; error; et al; evolution; fitness; genomes; memory; mutant; mutations; number; population; quasispecies; replication; rna; spectra; spectrum; virus; viruses; volume
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        item: #501 of 1349
          id: cord-270892-ycc3csyh
      author: Rollinger, Judith M.
       title: The human rhinovirus: human‐pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery
        date: 2010-12-13
       words: 19699
      flesch: 35
     summary: if by hand How contagious are common respiratory tract infections? Environmental contamination with rhinovirus and transfer to fingers of healthy individuals by daily life activity Aerosol transmission of rhinovirus colds Hand-to-hand transmission of rhinovirus colds Transmission of experimental rhinovirus infection by contaminated surfaces Interruption of experimental rhinovirus transmission Virucidal activity and cytotoxicity of the liposomal formulation of povidone-iodine Virucidal hand treatments for prevention of rhinovirus infection Localization of human rhinovirus replication in the upper respiratory tract by in situ hybridization Experimental rhinovirus infection in volunteers Detection of rhinovirus RNA in lower airway cells during experimentally induced infection Relationship of upper and lower airway cytokines to outcome of experimental rhinovirus infection Histopathologic examination and enumeration of polymorphonuclear leukocytes in the nasal mucosa during experimental rhinovirus colds Sites of rhinovirus recovery after point inoculation of the upper airway Incubation periods of experimental rhinovirus infection and illness Quantitative and qualitative analysis of rhinovirus infection in bronchial tissues Rhinoviruses infect the lower airways Incidence and characteristics of viral community-acquired pneumonia in adults Etiology of community-acquired pneumonia in 254 hospitalized children Improved diagnosis of the etiology of community-acquired pneumonia with real-time polymerase chain reaction Etiology of community-acquired pneumonia in hospitalized school-age children: Evidence for high prevalence of viral infections Association between interleukin-8 concentration in nasal secretions and severity of symptoms of experimental rhinovirus colds Symptom profile of common colds in schoolaged children The microbial etiology and antimicrobial therapy of adults with acute community-acquired sinusitis: A fifteen-year experience at the University of Virginia and review of other selected studies Bacterial coinfections in children with viral wheezing Amplified rhinovirus colds in atopic subjects Experimental rhinovirus 16 infection potentiates histamine release after antigen bronchoprovocation in allergic subjects Lower airways inflammation during rhinovirus colds in normal and in asthmatic subjects The effects of rhinovirus infections on allergic airway responses Rhinovirus upper respiratory infection increases airway hyperreactivity and late asthmatic reactions An experimental model of rhinovirus induced chronic obstructive pulmonary disease exacerbations: A pilot study Rhinovirus-induced lower respiratory illness is increased in asthma and related to virus load and Th1/2 cytokine and IL-10 production The economic burden of non-influenzarelated viral respiratory tract infection in the United States Rhinovirus chemotherapy Excessive antibiotic use for acute respiratory infections in the United States Influenza virus and rhinovirus-related otitis media: Potential for antiviral intervention The viruses and their replication Analysis of the structure of a common cold virus, human rhinovirus 14, refined at a resolution of 3.0 A The refined structure of human rhinovirus 16 at 2.15 A resolution: Implications for the viral life cycle Crystal structure of human rhinovirus serotype 1A (HRV1A) 1. Effect of shape on binding of steroids to carrier proteins Investigation on QSAR and binding mode of a new class of human rhinovirus-14 inhibitors by CoMFA and docking experiments Synthesis and structure-activity studies of some disubstituted phenylisoxazoles against human picornavirus CoMFA analysis of the interactions of antipicornavirus compounds in the binding pocket of human rhinovirus-14 dihydro-2-oxazolyl)phenoxy]alkyl]-3-methylisoxazoles: Inhibitors of picornavirus uncoating Understanding human rhinovirus infections in terms of QSAR Site-directed mutagenesis suggests close functional relationship between a human rhinovirus 3C cysteine protease and cellular trypsin-like serine proteases The picornaviral 3C proteinases: Cysteine nucleophiles in serine proteinase folds Substituted benzamide inhibitors of human rhinovirus 3C protease: Structure-based design, synthesis, and biological evaluation Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors.
    keywords: activity; agents; antiviral; binding; capsid; cells; cold; compounds; discovery; drug; echinacea; effect; efficacy; fig; group; hrv; human; infection; inhibitors; protease; protein; receptor; replication; results; rhinovirus; rhinovirus infection; rna; serotypes; structure; studies; study; synthesis; table; treatment
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        item: #502 of 1349
          id: cord-270940-acwkh6ed
      author: Kallio-Kokko, Hannimari
       title: Viral zoonoses in Europe
        date: 2005-06-29
       words: 14707
      flesch: 41
     summary: key: cord-270940-acwkh6ed authors: Kallio-Kokko, Hannimari; Uzcategui, Nathalie; Vapalahti, Olli; Vaheri, Antti title: Viral zoonoses in Europe date: 2005-06-29 journal: FEMS Microbiol Rev DOI: 10.1016/j.femsre.2005.04.012 sha: doc_id: 270940 cord_uid: acwkh6ed A number of new virus infections have emerged or re-emerged during the past 15 years. During the past 15 years a number of new virus infections have emerged or re-emerged.
    keywords: antibodies; avian; cases; congo; crimean; detection; disease; encephalitis; europe; fever; fever virus; fig; genome; hantavirus; human; infections; influenza; kda; new; patients; protein; rabies; rna; segment; species; table; tick; virus; viruses; years
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        item: #503 of 1349
          id: cord-271091-ffn59sgf
      author: Galao, Rui P
       title: Saccharomyces cerevisiae: a versatile eukaryotic system in virology
        date: 2007-10-10
       words: 6551
      flesch: 35
     summary: The strategy to use yeast cells for vaccination could also be used to elicit protective immune responses against human pathogenic yeasts. The amino terminal deletion mutants of hepatitis C virus nonstructural protein NS5A function as transcriptional activators in yeast Hepatitis C virus nonstructural protein 5A contains potential transcriptional activator domains Characterization of the nuclear localization signal and subcellular distribution of hepatitis C virus nonstructural protein NS5A Hepatitis C virus nonstructural region 5A protein is a potent transcriptional activator The hepatitis C virus core protein interacts with NS5A and activates its caspase-mediated proteolytic cleavage Use of an in vitro model and yeast two-hybrid system to investigate the pathogenesis of hepatitis C Cleavage of hepatitis C virus nonstructural protein 5A by a caspase-like protease(s) in mammalian cells Hepatitis C virus core protein: an update on its molecular biology, cellular functions and clinical implications The core protein of hepatitis C virus is imported into the nucleus by transport receptor Kap123p but inhibits Kap121p-dependent nuclear import of yeast AP1-like transcription factor in yeast cells Differential subcellular localization of hepatitis C virus core gene products.
    keywords: cell; cerevisiae; drug; factors; gene; hcv; hepatitis; host; protein; replication; rna; studies; virus; viruses; yeast
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        item: #504 of 1349
          id: cord-271127-l9bxqtqs
      author: Renault, Sylvaine
       title: Commensal and mutualistic relationships of reoviruses with their parasitoid wasp hosts
        date: 2005-02-28
       words: 6793
      flesch: 46
     summary: DpRV-1 virions were isolated from 2 g of frozen parasitized D. pulchellus (Rabouille et al., 1994a) and purified by the Freon procedure (Chen and Ramig, 1992) . Several properties of DpRV-1 virions and its biological relationship with the wasp and lepidopteran pupal host show that this virus is very unusual and requires further study.
    keywords: dpav-4; dprv-1; et al; fig; host; parasitoid; pulchellus; pupae; rna; virions; viruses; wasp
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        item: #505 of 1349
          id: cord-271130-6s79q1c1
      author: Filoni, Claudia
       title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi)
        date: 2017-11-17
       words: 6586
      flesch: 42
     summary: The outcomes of FeLV infection in domestic cats vary according to host susceptibility, virus strain, and infectious challenge dose. We previously reported on FeLV infections in jaguarundis.
    keywords: animals; antibodies; cats; feline; felv; infection; jaguarundis; leukemia; loads; pcr; proviral; rna; time; virus; wild
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        item: #506 of 1349
          id: cord-271188-ewlxy5po
      author: Liu, Wei
       title: Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival
        date: 2020-04-20
       words: 4264
      flesch: 35
     summary: Thus, limiting iron represents a promising adjuvant strategy in treating viral infection through oral uptake or venous injection of iron chelators, or through the manipulation of the key iron regulators. The first strategy is to deplete iron directly by iron chelators which have strong and selective affinity with iron ions [47, 48] .
    keywords: cells; chelators; coronavirus; cov; cov-2; covs; human; infection; iron; protein; replication; rna; sars
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        item: #507 of 1349
          id: cord-271241-w1q46y63
      author: Ruggiero, Emanuela
       title: Viral G-quadruplexes: New frontiers in virus pathogenesis and antiviral therapy
        date: 2020-05-18
       words: 8942
      flesch: 39
     summary: In this chapter, we present the state of the art on the structural and functional characterization of viral G4s in RNA viruses, DNA viruses and retroviruses. 51 HCV was also used as the reference RNA virus to develop a fluorescence light-up probe, a thioflavine T derivative (ThT-NE), for the direct visualization of the native HCV RNA genome in living cells.
    keywords: activity; antiviral; cells; dna; ebna1; g4s; genome; hcv; host; human; ligands; ltr; quadruplex; replication; rna; viral; virus; viruses
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        item: #508 of 1349
          id: cord-271419-v6dfel3l
      author: Adachi, Shun
       title: Commentary: Origin and evolution of pathogenic coronaviruses
        date: 2020-04-21
       words: 1213
      flesch: 44
     summary: The type of adaptation phenomena in virus evolution is testable either in clinical medicine or in vitro evolution system. Since RNA viruses are easy to mutate and coronaviruses have high potentials for recombination, we can easily see the track of mutations and evolutions of the viruses, especially for SARS-CoV and MERS-CoV. RNA recombination by RNA-dependent RNA polymerase with a low fidelity is widely observed and is supposed to shape current viruses by rearranging their genomes or disseminating functional modules (6) .
    keywords: coronaviruses; cov; sars; viruses
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        item: #509 of 1349
          id: cord-271434-30nh2gc7
      author: Tian, Fei
       title: A fully automated centrifugal microfluidic system for sample-to-answer viral nucleic acid testing
        date: 2020-07-27
       words: 4324
      flesch: 44
     summary: We envisioned that this microfluidic system free of aerosol contamination may facilitate viral nucleic acid detection outside the diagnostic laboratory, promoting diagnosis efficiency of infectious diseases and preventing onward transmission. In another work, a multifunctional microfluidic device pre-loaded with wax-sealed reagents was designed for extraction and amplification of viral nucleic acids in a point-of-care format [33] .
    keywords: chamber; detection; disc; lamp; nucleic; reaction; rna; sample; sars
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        item: #510 of 1349
          id: cord-271504-t3y1w9ef
      author: Luo, Zichao
       title: Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community
        date: 2020-06-16
       words: 14501
      flesch: 38
     summary: Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol New small-molecule drug design strategies for fighting resistant influenza A Characteristics of arbidol-resistant mutants of influenza virus: implications for the mechanism of anti-influenza action of arbidol Mechanism of inhibition of enveloped virus membrane fusion by the antiviral drug arbidol Membranotropic effects of arbidol, a broad antiviral molecule, on phospholipid model membranes Clinical characteristics and therapeutic procedure for four cases with 2019 novel coronavirus pneumonia receiving combined Chinese and Western medicine treatment Discovering drugs to treat coronavirus disease 2019 (COVID-19) Effects of chloroquine on viral infections: an old drug against today's diseases Effect of weak bases on the intralysosomal pH in mouse peritoneal macrophages Mechanisms of action of hydroxychloroquine and chloroquine: implications for rheumatology Chloroquine inhibits autophagic flux by decreasing autophagosomelysosome fusion New insights into the antiviral effects of chloroquine Anti-HIV effects of chloroquine: inhibition of viral particle glycosylation and synergism with protease inhibitors Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro Chloroquine is a potent inhibitor of SARS coronavirus infection and spread In vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro Breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies Chloroquine and hydroxychloroquine as available weapons to fight COVID-19 In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Effects of chronic exposure to hydroxychloroquine or chloroquine on inner retinal structures Animal toxicity and pharmacokinetics of hydroxychloroquine sulfate Retroviral proteases and their roles in virion maturation Host cell proteases: critical determinants of coronavirus tropism and pathogenesis Influenza and SARS-coronavirus activating proteases TMPRSS2 and HAT are expressed at multiple sites in human respiratory and gastrointestinal tracts Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases Virusencoded proteinases and proteolytic processing in the Nidovirales The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide Simultaneous treatment of human bronchial epithelial cells with serine and cysteine protease inhibitors prevents severe acute respiratory syndrome coronavirus entry Protease inhibitors targeting coronavirus and filovirus entry Efficacy of camostat mesilate compared with famotidine for treatment of functional dyspepsia: is camostat mesilate effective? Camostat mesilate attenuates pancreatic fibrosis via inhibition of monocytes and pancreatic stellate cells activity Recent research by Hoffmann et al. showed a promising in vitro inhibitory effect of this serine protease inhibitor in SARS-CoV and 2019-nCoV on human lung cells, showing potential as a viable option for COVID-19 treatment [113] .
    keywords: amplification; antibodies; antiviral; cells; china; chloroquine; coronavirus; covid-19; crispr; detection; disease; dna; drug; genome; host; infection; lamp; mers; ncov; novel; nucleic; patients; pcr; potential; protease; protein; rna; sars; syndrome; therapeutic; treatment
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        item: #511 of 1349
          id: cord-271526-14nfqusv
      author: Molenkamp, Richard
       title: Identification of a Specific Interaction between the Coronavirus Mouse Hepatitis Virus A59 Nucleocapsid Protein and Packaging Signal
        date: 1997-12-08
       words: 5569
      flesch: 50
     summary: We observed specific interaction In order to serve as template DNA, pPs290 was linearbetween in vitro transcripts containing the Ps and N proized with BamHI, extracted with phenol/chloroform, and tein isolated from infected cells, but also with N protein precipitated with ethanol. If the N protein is indeed part of the complex, binding to N of a N-specific antibody should result in the formation of a large complex composed of Ps290 RNA, N protein, and N-specific antibody.
    keywords: cells; encapsidation; fig; interaction; lysate; mhv; nucleocapsid; protein; ps290; rna; virus
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        item: #512 of 1349
          id: cord-271648-m2c5bvuj
      author: Ashour, Hossam M.
       title: Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks
        date: 2020-03-04
       words: 7550
      flesch: 53
     summary: Implications for virus origins and receptor binding Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Efficient activation of the severe acute respiratory syndrome coronavirus spike protein by the transmembrane protease TMPRSS2 Host cell proteases: Critical determinants of coronavirus tropism and pathogenesis Elastase-mediated activation of the severe acute respiratory syndrome coronavirus spike protein at discrete sites within the S2 domain Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade Protease-mediated enhancement of severe acute respiratory syndrome coronavirus infection Identification of a broad-spectrum antiviral small molecule against severe acute respiratory syndrome coronavirus and Ebola, Hendra, and Nipah viruses by using a novel high-throughput screening assay Functional analysis of potential cleavage sites in the MERS-coronavirus spike protein Generation and characterization of human monoclonal neutralizing antibodies with distinct binding and sequence features against SARS coronavirus using XenoMouse Identification of human neutralizing antibodies against MERS-CoV and their role in virus adaptive evolution Identification of an antigenic determinant on the S2 domain of the severe acute respiratory syndrome coronavirus spike glycoprotein capable of inducing neutralizing antibodies Human monoclonal antibodies against highly conserved HR1 and HR2 domains of the SARS-CoV spike protein are more broadly neutralizing Fully human monoclonal antibody directed to proteolytic cleavage site in severe acute respiratory syndrome (SARS) That sort of adaptation required a set of amino acid changes in the RBD of S protein of SARS viruses that were circulating in bats [65] .
    keywords: china; coronavirus; cov; cov-2; covs; human; mers; outbreak; protein; sars; syndrome; viruses
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        item: #513 of 1349
          id: cord-271701-tx0lqgff
      author: te Velthuis, Aartjan J.W.
       title: The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension
        date: 2011-10-29
       words: 7431
      flesch: 46
     summary: Given the absence of classical RdRp A and C motifs in the nsp8 sequence (12), we screened an alignment of CoV nsp8 sequences for conserved D/ExD/E motifs. Mutagenesis of nsp8 was performed to identify residues that may contribute to the catalytic centre of the nsp(7+8) polymerase, while differently tagged nsp8 recombinant proteins were constructed to explain some striking differences with previous observations.
    keywords: activity; binding; complex; cov; figure; nsp(7; nsp7; nsp8; polymerase; protein; rdrp; rna; sars; terminal
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        item: #514 of 1349
          id: cord-271781-cfv0ta10
      author: Patel, Kishan P.
       title: Transmission of SARS-CoV-2: an update of current literature
        date: 2020-07-07
       words: 4478
      flesch: 39
     summary: Environmental contamination through airflow may perpetuate viral transmission through infectious droplets [25] . A study analyzing COVID-19 patients from three hospitals in China demonstrated higher positive rates of viral RNA in bronchoalveolar lavage fluid, sputum, and
    keywords: coronavirus; cov-2; covid-19; patients; rna; sars; study; transmission
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        item: #515 of 1349
          id: cord-271972-qhr6iir6
      author: Gaglia, Marta Maria
       title: Viruses and the cellular RNA decay machinery
        date: 2010-05-06
       words: 6598
      flesch: 38
     summary: 32 How do RNA viruses avoid Xrn1-mediated degradation? 76 dsRNA is most often found upon infection with RNA viruses that produce dsRNA intermediates during genome replication, although dsDNA viruses can also produce dsRNA due to annealing of complementary RNAs transcribed from opposite strands of the genome.
    keywords: cells; complex; decay; degradation; figure; lsm; mrna; protein; replication; rna; rnase; translation; viruses
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        item: #516 of 1349
          id: cord-272050-0u62j7nj
      author: Okamoto, Kimiyuki
       title: cis-Preferential requirement of a − 1 frameshift product p88 for the replication of Red clover necrotic mosaic virus RNA1
        date: 2008-05-25
       words: 5409
      flesch: 38
     summary: cis-Acting RNA elements also play essential roles in viral RNA replication. Both p27 and p88 are required for viral RNA replication.
    keywords: cis; p27; p88; pubrc1; replication; rna; rna1; translation; virus
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        item: #517 of 1349
          id: cord-272268-8vrcwwll
      author: Kedersha, Nancy
       title: Chapter 4 Regulation of Translation by Stress Granules and Processing Bodies
        date: 2009-10-27
       words: 8608
      flesch: 34
     summary: The deacetylase HDAC6 is a novel critical component of stress granules involved in the stress response Disruption of microtubules inhibits cytoplasmic ribonucleoprotein stress granule formation Interaction with 14-3-3 adaptors regulates the sorting of hMex-3B RNA-binding protein to distinct classes of RNA granules hnRNP A1 relocalization to the stress granules reflects a role in the stress response Formation of stress granules inhibits apoptosis by suppressing stress-responsive MAPK pathways Codependent functions of RSK2 and the apoptosis-promoting factor TIA-1 in stress granule assembly and cell survival An essential function of the SRC-3 coactivator in suppression of cytokine mRNA translation and inflammatory response Microtubuledependent association of AKAP350A and CCAR1 with RNA stress granules Sequestration of TRAF2 into stress granules interrupts tumor necrosis factor signaling under stress conditions Tdrd3 is a novel stress granule-associated protein interacting with the Fragile-X syndrome protein FMRP TDRD3, a novel tudor domain-containing protein, localizes to cytoplasmic stress granules Hsp90 regulates the function of argonaute 2 and its recruitment to stress granules and P-bodies Translation initiation factor eIF4G-1 binds to eIF3 through the eIF3e subunit Recycling of eukaryotic posttermination ribosomal complexes Inhibition of cytoplasmic mRNA stress granule formation by a viral proteinase How viruses avoid stress Importance of eIF2alpha phosphorylation and stress granule assembly in alphavirus translation regulation Reovirus induces and benefits from an integrated cellular stress response Interaction of TIA-1/TIAR with West Nile and dengue virus products in infected cells interferes with stress granule formation and processing body assembly Sendai virus trailer RNA binds TIAR, a cellular protein involved in virus-induced apoptosis Mouse hepatitis coronavirus replication induces host translational shutoff and mRNA decay, with concomitant formation of stress granules and processing bodies Interactions between brome mosaic virus RNAs and cytoplasmic processing bodies Antiviral protein APOBEC3G localizes to ribonucleoprotein complexes found in P bodies and stress granules A micrococcal nuclease homologue in RNAi effector complexes Inosine-containing dsRNA binds a stress-granule-like complex and downregulates gene expression in trans LINE-1 ORF1 protein localizes in stress granules with other RNA-binding proteins, including components of RNAi RISC Retrotransposons revisited: the restraint and rehabilitation of parasites Fragile X syndrome: loss of local mRNA regulation alters synaptic development and function Fragile X mental retardation protein shifts between polyribosomes and stress granules after neuronal injury by arsenite stress or in vivo hippocampal electrode insertion Cells lacking the fragile X mental retardation protein (FMRP) have normal RISC activity but exhibit altered stress granule assembly Activation of the integrated stress response during T helper cell differentiation A RING-type ubiquitin ligase family member required to repress follicular helper T cells and autoimmunity MK2-induced tristetraprolin:14-3-3 complexes prevent stress granule association and ARE-mRNA decay Prolonged translation arrest in reperfused hippocampal cornu Ammonis 1 is mediated by stress granules Persistent redistribution of poly-adenylated mRNAs correlates with translation arrest and cell death following global brain ischemia and reperfusion Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules The anti-HIV-1 editing enzyme APOBEC3G binds HIV-1 RNA and messenger RNAs that shuttle between polysomes and stress granules Human retroviral host restriction factors APOBEC3G and APOBEC3F localize to mRNA processing bodies Ataxin-2 interacts with the DEAD/H-box RNA helicase DDX6 and interferes with P-bodies and stress granules Post-translational arginylation of calreticulin: a new isospecies of calreticulin component of stress granules Distinct structural features of caprin-1 mediate its interaction with G3BP-1 and its induction of phosphorylation of eukaryotic translation initiation factor 2alpha, entry to cytoplasmic stress granules, and selective interaction with a subset of mRNAs Identification of FUSE-binding proteins as interacting partners of TIA proteins The cold-inducible RNAbinding protein migrates from the nucleus to cytoplasmic stress granules by a methylationdependent mechanism and acts as a translational repressor The eIF4G-homolog p97 can activate translation independent of caspase cleavage MBNL1 associates with YB-1 in cytoplasmic stress granules The DEAD-box RNA helicase DDX3 associates with export messenger ribonucleoproteins as well as tip-associated protein and participates in translational control Recruitment of the RNA helicase RHAU to stress granules via a unique RNA-binding domain A functional link between Disrupted-In-Schizophrenia 1 and the eukaryotic translation initiation factor 3 The enhancer of decapping proteins, Edc1p and Edc2p, bind RNA and stimulate the activity of the decapping enzyme Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping A role for the eIF4E-binding protein 4E-T in P-body formation and mRNA decay Regulation of stress granule dynamics by Grb7 and FAK signalling pathway Trapping of messenger RNA by Fragile X Mental Retardation protein into cytoplasmic granules induces translation repression The multifunctional FUS, EWS and TAF15 proto-oncoproteins show cell type-specific expression patterns and involvement in cell spreading and stress response Functional dissection of the human TNRC6 (GW182-related) family of proteins Ge-1 is a central component of the mammalian cytoplasmic mRNA processing body Nuclear RNA export factor 7 is localized in processing bodies and neuronal RNA granules through interactions with shuttling hnRNPs hnRNP K interacts with RNA binding motif protein 42 and functions in the maintenance of cellular ATP level during stress conditions Human hnRNP Q re-localizes to cytoplasmic granules upon PMA, thapsigargin, arsenite and heat-shock treatments Stress granule assembly is mediated by prion-like aggregation of TIA-1 HuR binding to cytoplasmic mRNA is perturbed by heat shock Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs Intracellular localization of human inositol 1,3,4,5,6-pentakisphosphate 2-kinase Localization of the developmental timing regulator Lin28 to mRNP complexes, P-bodies and stress granules The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci Identification of novel argonaute-associated proteins Neural RNA-binding protein Musashi1 inhibits translation initiation by competing with eIF4G for PABP Inhibition of G(1) to S phase progression by a novel zinc finger protein P58(TFL) at P-bodies Identification of PatL1, a human homolog to yeast P body component Pat1 Selective localization of PCBP2 to cytoplasmic processing bodies Identification of the junctional plaque protein plakophilin 3 in cytoplasmic particles containing RNA-binding proteins and the recruitment of plakophilins 1 and 3 to stress granules Polysome-bound endonuclease PMR1 is targeted to stress granules via stress-specific binding to TIA-1 Dendritic localization of the translational repressor Pumilio 2 and its contribution to dendritic stress granules RNA-associated protein 55 (RAP55) localizes to mRNA processing bodies and stress granules Rpp 20 interacts with SMN and is re-distributed into SMN granules in response to stress The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs Sam68 functions in nuclear export and translation of HIV-1 RNA SGNP: an essential Stress Granule/Nucleolar Protein potentially involved in 5.8s rRNA processing/transport Mammalian Smaug is a translational repressor that forms cytoplasmic foci similar to stress granules Staufen recruitment into stress granules does not affect early mRNA transport in oligodendrocytes Mammalian Staufen 1 is recruited to stress granules and impairs their assembly Survival motor neuron protein facilitates assembly of stress granules Probing the mRNA processing body using protein macroarrays and autoantigenomics ZBP1 regulates mRNA stability during cellular stress A PKR-like eukaryotic initiation factor 2alpha kinase from zebrafish contains Z-DNA binding domains instead of dsRNA binding domains RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2a to the assembly of mammalian stress granules Cytoplasmic heat shock granules are formed from precursor particles and are associated with a specific set of mRNAs Plant stress granules and mRNA processing bodies are distinct from heat stress granules Mammalian stress granules: highly dynamic sites of mRNA triage during stress induced translational arrest TIA-1 is a translational silencer that selectively regulates the expression of TNF-alpha Visibly stressed: the role of eIF2, TIA-1, and stress granules in protein translation Stressful initiations Evidence that ternary complex (eIF2-GTP-tRNA(i)(Met))-deficient preinitiation complexes are core constituents of mammalian stress granules Mammalian stress granules represent sites of accumulation of stalled translation initiation complexes The RasGAPassociated endoribonuclease G3BP assembles stress granules Rasputin, more promiscuous than ever: a review of G3BP MK2-induced tristetraprolin: 14-3-3 complexes prevent stress granule association and ARE-mRNA decay Inhibition of eukaryotic translation initiation by the marine natural product pateamine A RNAmediated sequestration of the RNA helicase eIF4A by pateamine A inhibits translation initiation Eukaryotic initiation factor 2alpha-independent pathway of stress granule induction by the natural product pateamine A Inhibition of ribosome recruitment induces stress granule formation independently of eukaryotic initiation factor 2alpha phosphorylation An antiviral response directed by PKR phosphorylation of the RNA helicase A Decapping and decay of messenger RNA occur in cytoplasmic processing bodies Cytoplasmic foci are sites of mRNA decay in human cells P bodies: at the crossroads of post-transcriptional pathways P bodies and the control of mRNA translation and degradation The highways and byways of mRNA decay The control of mRNA decapping and P-body formation Perk is essential for translational regulation and cell survival during the unfolded protein response Signal integration via PKR The exonjunction-complex-component metastatic lymph node 51 functions in stress-granule assembly Distinctive properties of the 5'-untranslated region of human hsp70 mRNA Mammalian stress granules and processing bodies Translational control is required for the unfolded protein response and in vivo glucose homeostasis Metazoan stress granule assembly is mediated by P-eIF2 {alpha}-dependent and -independent mechanisms Heme-regulated inhibitor (HRI) kinase-mediated phosphorylation of eukaryotic translation initiation factor 2 (eIF2) inhibits translation, induces stress granule formation, and mediates survival upon arsenite exposure Stress-dependent relocalization of translationally primed mRNPs to cytoplasmic granules that are kinetically and spatially distinct from P-bodies Accumulation of polyadenylated mRNA, Pab1p, eIF4E, and eIF4G with P-bodies in Saccharomyces cerevisiae P bodies promote stress granule assembly in Saccharomyces cerevisiae Robust heat shock induces eIF2{alpha}-phosphorylation-independent assembly of stress granules containing eIF3 and 40S ribosomal subunits in budding yeast, Saccharomyces cerevisiae Stress granules and processing bodies are dynamically linked sites of mRNP remodeling Subnuclear organelles: new insights into form and function The translational regulator CPEB1 provides a link between dcp1 bodies and stress granules Dynamic shuttling of TIA-1 accompanies the recruitment of mRNA to mammalian stress granules A functional RNAi screen links O-GlcNAc modification of ribosomal proteins to stress granule and processing body assembly Dynein motor contributes to stress granule dynamics in primary neurons
    keywords: assembly; binding; bodies; cells; eif2a; formation; granules; initiation; mrna; pbs; proteins; response; sgs; stress; tia-1; translation; virus
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        item: #518 of 1349
          id: cord-272378-umvi0veu
      author: Subramanian, Subbaya
       title: Special Issue: MicroRNA Regulation in Health and Disease
        date: 2019-06-15
       words: 2128
      flesch: 38
     summary: Further, it has been shown that a number of nuclear receptors are involved in the transcriptional regulation of miRNA expression, including the small heterodimer partner (SHP) and farnesoid X receptor (FXR). In their article, Yuan et al. postulate that the altered nutrient composition and miRNA expression in colorectal cancer (CRC) microenvironment selectively exerts pressure on the surrounding microbiota, leading to alterations in its composition [11] .
    keywords: disease; expression; gene; mirna; rnas
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        item: #519 of 1349
          id: cord-272573-wxqly479
      author: Maia Chagas, Andre
       title: Leveraging open hardware to alleviate the burden of COVID-19 on global health systems
        date: 2020-04-24
       words: 5088
      flesch: 48
     summary: Most of the technology discussed above is classed as a medical device when used in a diagnostic or clinical setting; a challenge faced by only a small number of existing open hardware devices and therefore in need of further research. [Internet Return on investment for open source scientific hardware development How poorer countries are scrambling to prevent a coronavirus disaster 3D printing and milling a real-time PCR device for infectious disease diagnostics A Customized Bolus Produced Using a 3-Dimensional Printer for Radiotherapy A low-cost and small USV platform for water quality monitoring A Portable 3D Printer System for the Diagnosis and Treatment of Multidrug-Resistant Bacteria A versatile and low-cost open source pipetting robot for automation of toxicological and ecotoxicological bioassays Smart Citizen Kit and Station: An open environmental monitoring system for citizen participation and scientific experimentation PlasmoTron: an open-source platform for automated culture of malaria parasites Open(G)PIAS: An Open-Source Solution for the Construction of a High-Precision Acoustic Startle Response Setup for Tinnitus Screening and Threshold Estimation in Rodents Open-source automated external defibrillator RSG Safety-EN Standards & Approvals European standards for medical supplies freely available.
    keywords: community; coronavirus; cov-2; covid-19; detection; example; fosh; hardware; masks; rna; sars; source; testing; use; ventilators
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        item: #520 of 1349
          id: cord-272576-ez731lif
      author: Wada, Yoshiko
       title: Directional and reoccurring sequence change in zoonotic RNA virus genomes visualized by time-series word count
        date: 2016-11-03
       words: 5673
      flesch: 43
     summary: A viruses reveals a mutational bias on the viral genomes Oligonucleotide motifs that disappear during the evolution of influenza in humans increase IFN-α secretion by plasmacytoid endritic cells Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM) -characterization of horizontally transferred genes with emphasis on the E. coli O157 genome Informatics for unveiling hidden genome signatures Prediction of directional changes of influenza A virus genome sequences with emphasis on pandemic H1N1/09 as a model case Novel bioinformatics strategies for prediction of directional sequence changes in influenza virus genomes and for surveillance of potentially hazardous strains Novel Swine-Origin Influenza A (H1N1) Virus Investigation Team. Directional change in MERS virus genomes.
    keywords: changes; human; influenza; mers; sequences; strains; subtypes; time; viruses
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        item: #521 of 1349
          id: cord-272579-aenuyht0
      author: Emmett, Stevan R.
       title: The Cell Cycle and Virus Infection
        date: 2005
       words: 6470
      flesch: 56
     summary: Increasingly we have found that proteomic approaches allow the rapid analysis of a whole plethora of cell cycle proteins that may be affected by virus infection. The supernatant is removed, and the cells are processed for flow cytometry to detect either incorporated BrdU or cell cycle marker proteins.
    keywords: cell; cell cycle; cycle; dna; gel; min; replication; rna; virus; viruses
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        item: #522 of 1349
          id: cord-272666-3uidpr79
      author: Doyle, Nicole
       title: Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing
        date: 2018-09-06
       words: 7506
      flesch: 48
     summary: As the role in membrane rearrangements for nsp3 and 4 is well-established for several nidoviruses and considering that nsp6 may also play some role, here we investigated the role that these three nsps play in the formation of IBV membrane rearrangements. A Key Role for Nonstructural Protein 3 in the Remodeling of Intracellular Membranes Open Reading Frame 1a-Encoded Subunits of the Arterivirus Replicase Induce Endoplasmic Reticulum-Derived Double-Membrane Vesicles Which Carry the Viral Replication Complex Non-structural proteins 2 and 3 interact to modify host cell membranes during the formation of the arterivirus replication complex Evolving the largest RNA virus genome Membrane rearrangements mediated by coronavirus nonstructural proteins 3 and 4.
    keywords: beaur; cells; expression; formation; ibv; m41; membrane; nsp3; nsp4; nsp6; proteins; rearrangements; replication; virus
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        item: #523 of 1349
          id: cord-272702-7uc4ozjy
      author: Graham, T. G. W.
       title: Inexpensive, versatile and open-source methods for SARS-CoV-2 detection
        date: 2020-09-18
       words: 8080
      flesch: 51
     summary: It is conceivable that sample degradation contributed to the observed reduction in sensitivity, as RNA samples were frozen after being assayed with TaqPath, stored at -80°C for 1 week, and thawed for testing with BEARmix. . Probe mixture (Integrated DNA Technologies, Cat. #10006606), RNA sample, and water to a final volume of 20 µl.
    keywords: addition; amplification; cov-2; fig; min; qpcr; rna; samples; sars; swab
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        item: #524 of 1349
          id: cord-272729-nbgdmavr
      author: Kim, Youngnam
       title: Ribavirin efficiently suppresses porcine nidovirus replication
        date: 2012-10-27
       words: 6673
      flesch: 37
     summary: Our results demonstrated that ribavirin treatment dose-dependently inhibited the replication of both nidoviruses. N protein staining revealed that the number of cells expressing viral antigen, as quantified by N protein staining results, was also reduced during ribavirin treatment, resulting in a maximum of ∼80% inhibition in response to 50 M and 200 M for PRRSV and PEDV, respectively ( Fig.
    keywords: cells; infection; nidovirus; pam; pedv; porcine; prrsv; replication; ribavirin; rna; virus
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        item: #525 of 1349
          id: cord-272871-gu9ptt9y
      author: White, K.Andrew
       title: Defective RNAs of clover yellow mosaic virus encode nonstructural/coat protein fusion products
        date: 1991-08-31
       words: 4704
      flesch: 54
     summary: First-strand synthesis of cDNA was primed with oligonucleotide CY-11 complementary to the 3' terminus of CYMV RNA (5'GAGAGTCGAClrl-TTATACACCCAAAAGTCTACGGG). In vitro translation was also carried out on 0.25 pg of CYMV RNA extracted from virions and on 0.25 pg of brome mosaic virus (BMV) RNA.
    keywords: coat; cymv; fig; grna; kb rnas; protein; rnas
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        item: #526 of 1349
          id: cord-273019-hbpfz8rt
      author: Glingston, R. Sahaya
       title: Organelle dynamics and viral infections: at cross roads
        date: 2018-06-25
       words: 9525
      flesch: 30
     summary: Current review briefly summarizes our knowledge of the various cell organelles/compartments following virus infection. caspase-independent cell death Lysosomal cell death at a glance A zinc finger protein Tsip1 controls cucumber mosaic virus infection by interacting with the replication complex on vacuolar membranes of the tobacco plant Visualization of assembly intermediates and budding vacuoles of Singapore grouper iridovirus in grouper embryonic cells Involvement of the vacuolar H(þ)-ATPase in animal virus entry Membrane and protein interactions of a soluble form of the semliki forest virus fusion protein The entry of reovirus into L cells is dependent on vacuolar proton-ATPase activity Cellular v-ATPase is required for virion assembly compartment formation in human cytomegalovirus infection Endocytosis via caveolae Endocytosis of simian virus 40 into the endoplasmic reticulum Cellular entry of ebola virus involves uptake by a macropinocytosis-like mechanism and subsequent trafficking through early and late endosomes Membrane dynamics associated with viral infection Biogenesis of the semliki forest virus RNA replication complex Fusion of SV40-induced endocytotic vacuoles with the nuclear membrane Interaction of endocytotic vacuoles with the inner nuclear membrane in simian virus 40 entry into CV-1 cell nucleus ESCRT complexes and the biogenesis of multivesicular bodies Involvement of vacuolar protein sorting pathway in ebola virus release independent of TSG101 interaction Identification of alpha-taxilin as an essential factor for the life cycle of hepatitis B virus Divergent roles of autophagy in virus infection
    keywords: cells; complex; degradation; expression; formation; golgi; hepatitis; host; human; infection; lipid; membrane; nuclear; nucleus; order; organelles; protein; replication; rna; virus; viruses
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        item: #527 of 1349
          id: cord-273326-gmw8gl2r
      author: Saiz, Juan-Carlos
       title: Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus
        date: 2018-08-24
       words: 7153
      flesch: 28
     summary: Front Pathogenic exploitation of Fc activity Pathogenesis of flavivirus infections: Using and abusing the host cell Role of host cell factors in flavivirus infection: Implications for pathogenesis and development of antiviral drugs Broad-spectrum agents for flaviviral infections: Dengue, zika and beyond Targeting host factors to treat West Nile and dengue viral infections Zika virus replicons for drug discovery Establishment and application of flavivirus replicons Probing molecular insights into Zika virus (-)host interactions Zika virus cell tropism in the developing human brain and inhibition by azithromycin Genetic ablation of axl does not protect human neural progenitor cells and cerebral organoids from Zika virus infection Axl mediates Zika virus entry in human glial cells and modulates innate immune responses Axl is not an indispensable factor for Zika virus infection in mice Axl-mediated productive infection of human endothelial cells by Zika virus Curcumin inhibits zika and chikungunya virus infection by inhibiting cell binding Polysulfonate suramin inhibits Zika virus infection Suramin inhibits Zika virus replication by interfering with virus attachment and release of infectious particles Molecular mechanisms of flavivirus membrane fusion Acid-dependent viral entry Screening bioactives reveals nanchangmycin as a broad spectrum antiviral active against Zika virus Lipids and flaviviruses, present and future perspectives for the control of dengue, zika, and West Nile viruses Arbidol (umifenovir): A broad-spectrum antiviral drug that inhibits medically important arthropod-borne flaviviruses Infection by Zika viruses requires the transmembrane protein AXL, endocytosis and low pH 25-hydroxycholesterol protects host against Zika virus infection and its associated microcephaly in a mouse model A screen of FDA-approved drugs for inhibitors of Zika virus infection Obatoclax, saliphenylhalamide and gemcitabine inhibit Zika virus infection in vitro and differentially affect cellular signaling, transcription and metabolism Obatoclax inhibits alphavirus membrane fusion by neutralizing the acidic environment of endocytic compartments Evaluation of anti-Zika virus activities of broad-spectrum antivirals and NIH clinical collection compounds using a cell-based, high-throughput screen assay Chloroquine, an endocytosis blocking agent, inhibits Zika virus infection in different cell models Antiviral activities of selected antimalarials against dengue virus type 2 and Zika virus Inhibition of autophagy limits vertical transmission of Zika virus in pregnant mice FDA-approved drug, prevents Zika virus infection and its associated congenital microcephaly in mice Repurposing of the anti-malaria drug chloroquine for Zika virus treatment and prophylaxis -(arylmethylimino)ethyl)-7-chloroquinolin-4-amine derivatives, synthesized by thermal and ultrasonic means, are endowed with anti-Zika virus activity (trifluoromethyl)quinoline analogs show improved anti-Zika virus activity, compared to mefloquine The antimalarial drug amodiaquine possesses anti-Zika virus activities Identification of small-molecule inhibitors of Zika virus infection and induced neural cell death via a drug repurposing screen Niclosamide rescues microcephaly in a humanized in vivo model of zika infection using human induced neural stem cells Antiviral effects of ferric ammonium citrate Inhibition of Zika virus replication by silvestrol Antiviral activity of N-(4-hydroxyphenyl) retinamide (4-HPR) against Zika virus Interferon-induced spermidine-spermine acetyltransferase and polyamine depletion restrict zika and chikungunya viruses Inhibition of polyamine biosynthesis is a broad-spectrum strategy against rna viruses The composition of West Nile virus lipid envelope unveils a role of sphingolipid metabolism in flavivirus biogenesis Direct activation of adenosine monophosphate-activated protein kinase (AMPK) by PF-06409577 inhibits flavivirus infection through modification of host cell lipid metabolism Suppression of Zika virus infection and replication in endothelial cells and astrocytes by PKA inhibitor PKI 14-22 Zika virus targets human STAT2 to inhibit type I interferon signaling Ribavirin-Current status of a broad spectrum antiviral agent Broad-spectrum antiviral activity of the imp dehydrogenase inhibitor VX-497: A comparison with ribavirin and demonstration of antiviral additivity with alpha interferon Rna virus error catastrophe: Direct molecular test by using ribavirin Extinction of hepatitis c virus by ribavirin in hepatoma cells involves lethal mutagenesis Efficacy of the broad-spectrum antiviral compound BCX4430 against Zika virus in cell culture and in a mouse model In vitro susceptibility of geographically and temporally distinct Zika viruses to favipiravir and ribavirin Ribavirin inhibits Zika virus (zikv) replication in vitro and suppresses viremia in zikv-infected stat1-deficient mice Favipiravir and ribavirin inhibit replication of Asian and African strains of Zika virus in different cell models an impdh inhibitor, suppresses replication of Zika virus and other emerging viral pathogens A sensitive virus yield assay for evaluation of antivirals against Zika virus Inhibition of pyrimidine biosynthesis pathway suppresses viral growth through innate immunity Discovery of a broad-spectrum antiviral compound that inhibits pyrimidine biosynthesis and establishes a type 1 interferon-independent antiviral state High-content screening in HPSC-neural progenitors identifies drug candidates that inhibit Zika virus infection in fetal-like organoids and adult brain The Brazilian Zika virus strain causes birth defects in experimental models Zika virus impairs growth in human neurospheres and brain organoids Zika virus disrupts neural progenitor development and leads to microcephaly in mice N-methyl-D-aspartate (NMDA) receptor blockade prevents neuronal death induced by Zika virus infection Ebselen alleviates testicular pathology in mice with Zika virus infection and prevents its sexual transmission Zika virus infectious cell culture system and the in vitro prophylactic effect of interferons Type iii interferons produced by human placental trophoblasts confer protection against Zika virus infection Gestational stage and IFN-lambda signaling regulate ZIKV infection in utero The IFITMs inhibit Zika virus replication
    keywords: activity; antiviral; cell; drug; flavivirus; host; human; infection; inhibitor; inhibits; mice; protein; replication; rna; virus; zika; zika virus; zikv; zikv infection
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        item: #528 of 1349
          id: cord-273366-xd84f8ct
      author: Brownsword, Matthew J.
       title: Infectious Bronchitis Virus Regulates Cellular Stress Granule Signaling
        date: 2020-05-14
       words: 8918
      flesch: 43
     summary: When IBV infected cells were treated with sodium arsenite, there was also a significant increase in the level of phosphorylated eIF2α when compared to IBV infected untreated cells. When IBV infected cells were treated with sodium arsenite, there was also a significant increase in the level of phosphorylated eIF2α when compared to IBV infected untreated cells.
    keywords: anti; cells; eif2α; g3bp1; ibv; infected; infection; replication; rna; stress; translation; virus
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        item: #529 of 1349
          id: cord-273367-gl266pvt
      author: Gunawardana, M.
       title: Longitudinal COVID-19 Surveillance and Characterization in the Workplace with Public Health and Diagnostic Endpoints
        date: 2020-07-28
       words: 5742
      flesch: 53
     summary: Related exploratory study goals include: characterizing the rate of SARS-CoV-2 459 acquisition in employee and household members; quantifying antibody-specific responses in 460 blood at baseline (previously exposed) and while on study (to capture asymptomatic/pre-461 symptomatic, newly infected); characterizing viral shedding parameters in saliva and stool 462 Clinical SARS-CoV-2 RNA test kits that have received Emergency Use Authorization 464 (EUA) by the FDA and are processed in a laboratory certified according to the Clinical 465 Laboratory Improvement Amendments (CLIA). Study participants (27 employees and 27 household members) consented to provide frequent nasal or oral swab samples that were analyzed by RT-qPCR for SARS-CoV-2 RNA using CDC protocols.
    keywords: author; copyright holder; funder; license; medrxiv; medrxiv preprint; peer; peer review; preprint; version
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        item: #530 of 1349
          id: cord-273379-w8vy5rl8
      author: Mizutani, Tetsuya
       title: Nascent Synthesis of Leader Sequence-Containing Subgenomic mRNAs in Coronavirus Genome-Length Replicative Intermediate RNA
        date: 2000-09-30
       words: 4080
      flesch: 43
     summary: In contrast, alphaviruses, which produce a subgenomic mRNA that corresponds to the 3Ј-region of viral genome, produce three RF RNAs after RNase A treatment of alphavirus RI RNA; with this virus, genome RNA and subgenomic RNA elongate on a genome-length negativestrand RNA in its RI RNA (19) . Accordingly, if the negative-strand genome-length MHV RNA is a template for subgenomic mRNA synthesis, then all the subgenomic mRNAs are likely to be elongating in a genome-length RI RNA.
    keywords: gel; genome; length; mrna; rna; subgenomic
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        item: #531 of 1349
          id: cord-273487-nfgjz6f9
      author: Xu, Zaikun
       title: The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles
        date: 2012-11-10
       words: 5384
      flesch: 50
     summary: Loss of DDX56 helicase activity did not affect expression of WNV capsid protein (Fig. 4A ) nor its secretion from infected cells in the form of virus particles (Fig. 5A ). Arrowheads indicate colocalization between capsid, DDX56 proteins and the nucleolar resident protein nucleolin.
    keywords: box; capsid; cells; ddx56; dead; helicase; myc; protein; rnai; virus; wnv
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        item: #532 of 1349
          id: cord-273609-whm2ce4u
      author: Li, Qingdi Quentin
       title: Evaluation of reference genes for real-time quantitative PCR studies in Candida glabrata following azole treatment
        date: 2012-06-29
       words: 8182
      flesch: 42
     summary: Adding the third gene to the most stable two reference genes, RDN18 and The fold change shown in the table represents the difference in reference gene expression between azole-treated and untreated C. glabrata without normalization to an internal control gene. key: cord-273609-whm2ce4u authors: Li, Qingdi Quentin; Skinner, Jeff; Bennett, John E title: Evaluation of reference genes for real-time quantitative PCR studies in Candida glabrata following azole treatment date: 2012-06-29 journal: BMC Mol Biol DOI: 10.1186/1471-2199-13-22 sha: doc_id: 273609 cord_uid: whm2ce4u BACKGROUND: The selection of stable and suitable reference genes for real-time quantitative PCR (RT-qPCR) is a crucial prerequisite for reliable gene expression analysis under different experimental conditions.
    keywords: act1; expression; gene expression; genes; glabrata; pcr; rdn5.8; reference; reference genes; rna; target; transcription
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        item: #533 of 1349
          id: cord-273711-bxijla09
      author: Zhao, Zhixun
       title: RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells
        date: 2012-02-17
       words: 4185
      flesch: 46
     summary: Transfection of the siRNA expression cassettes into BHK-21 cells BHK-21 cells were seeded in six-well plates and cultured at 37°C and 5% CO2 overnight. To determine transfection efficiency, we monitored GFP fluorescence intensity of transfected cells using fluorescent microscope analysis.
    keywords: cells; expression; gene; gfp; gtpv; orf095; pcr; protein; rna; sirna; virus
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        item: #534 of 1349
          id: cord-273723-srfypn7j
      author: Omar, Sarah
       title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis
        date: 2020-07-30
       words: 2935
      flesch: 40
     summary: Only one of the nine reviewed studies had looked at COVID-19 patients with mild disease in an outpatient setting; it found viral RNA to be detectable in symptomatic patients for a mean duration of 25.2 days. key: cord-273723-srfypn7j authors: Omar, Sarah; Bartz, Christoph; Becker, Sabine; Basenach, Silke; Pfeifer, Sandra; Trapp, Corinna; Hamm, Hildegard; Schlichting, Hans Christoph; Friederichs, Magdalena; Koch, Ulrich; Jestrabek, Christian; Hilger, Ernst; Vogt, Manfred; Jahn, Klaus; Chen, Simiao; Bärnighausen, Till; Zanger, Philipp title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis date: 2020-07-30 journal: Euro Surveill DOI: 10.2807/1560-7917.es.2020.25.30.2001292 sha: doc_id: 273723 cord_uid: srfypn7j We analysed consecutive RT-qPCR results of 537 symptomatic coronavirus disease (COVID-19) patients in home quarantine.
    keywords: cov-2; covid-19; patients; qpcr; rna
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        item: #535 of 1349
          id: cord-273910-fna7s9te
      author: Bochud, Pierre-Yves
       title: Innate immunogenetics: a tool for exploring new frontiers of host defence
        date: 2007-07-20
       words: 7069
      flesch: 27
     summary: Similarly, polymorphism of cytokines and cytokine receptor genes, which are key eff ector molecules, have also been associated with altered susceptibility to invasive pathogens. The development of the Human Genome Project in 1990 propelled the scientifi c community into a new era, allowing genetic mapping and the development of large-scale gene identifi cation that has greatly facilitated the study of gene polymorphisms.
    keywords: association; diff; disease; domain; gene; host; human; infection; infl; innate; mutations; polymorphisms; proteins; receptor; specifi; studies; susceptibility; tlrs; toll
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        item: #536 of 1349
          id: cord-274049-3gw65kpu
      author: Zhang, Han
       title: CRISPR Editing in Biological and Biomedical Investigation
        date: 2017-05-31
       words: 6629
      flesch: 30
     summary: CRISPR/Casmediated genome engineering Multiple gene repression in cyanobacteria using CRISPRi Genome editing using CRISPR-Cas9 to create the HPFH genotype in HSPCs: An approach for treating sickle cell disease and beta-thalassemia Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system TG2 and NF-kappaB signaling coordinates the survival of mantle cell lymphoma cells via IL6-mediated autophagy Hedgehog inhibitors selectively target cell migration and adhesion of mantle cell lymphoma in bone marrow microenvironment CRISPR-Cas9 technology and its application in haematological disorders Tampering with cancer chemoresistance by targeting the TGM2-IL6-autophagy regulatory network Painting a specific chromosome with CRISPR/Cas9 for live-cell imaging High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells Generation of gene-target dogs using CRISPR/Cas9 system This work is supported by R01 (R01CA181319) and R21 (R21CA202212) given to NM. Of the three types of CRISPR systems, the type II CRISPR nuclease system is the simplest for genome editing technology, which requires only a Cas9 protein and two RNAs: CRISPR RNAs (crRNA) and transactivating crRNAs (tracrRNA)
    keywords: cas9; cells; crispr; dna; editing; et al; gene; genome; human; mouse; mutations; rna; sgrna; system; target; vivo
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        item: #537 of 1349
          id: cord-274080-884x48on
      author: Rumlová, Michaela
       title: In vitro methods for testing antiviral drugs
        date: 2018-06-30
       words: 18015
      flesch: 26
     summary: Virus-encoded methyltransferases have been identified and characterized in flaviviruses such as Zika virus Coutard et al., 2017; Duan et al., 2017; Munjal et al., 2017; Zhao et al., 2017) , West Nile virus, and dengue virus (Dong et al., 2012) ; rhabdoviruses such as vesicular stomatitis virus (VSV) (Rahmeh et al., 2009 ); coronaviruses such as SARS (Wang et al., 2015b) ; and roniviruses (Zeng et al., 2016) . Alternatively, cleavage products may be monitored by analysis of proteolytic products by mass spectrometric methods (Hu et al., 2015; Joshi et al., 2017; Lathia et al., 2011; Rumlová et al., 2003) , analytical HPLC (Teruya et al., 2016) , or electrochemical methods based on the difference in penetration of substrate and cleavage products through the membrane of a polyionselective sensor (Gemene and Meyerhoff, 2011; Han et al., 1996) .
    keywords: activity; assay; assembly; binding; capsid; cell; coronavirus; dna; drug; entry; envelope; et al; fluorescence; fusion; genome; hbv; hcv; helicase; hepatitis; host; human; infection; influenza; inhibitors; integrase; kinase; membrane; method; particles; polymerase; protease; protein; replication; rna; screening; specific; target; transcription; type; uncoating; viral; virus; viruses
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        item: #538 of 1349
          id: cord-274097-11hvriqy
      author: Katz, Louis M.
       title: Is SARS‐CoV‐2 transfusion transmitted?
        date: 2020-06-16
       words: 2026
      flesch: 42
     summary: Vigorous attempts are needed to isolate the virus from donated blood and/or demonstrate its infectivity in animal models and/or tissue culture when RNA-positive donors are identified. lkatz@mvrbc.org 1 Mississippi Valley Regional Blood Center, Davenport, IA Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Detection of SARS-CoV-2 in different types of clinical specimens Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes Severe acute respiratory syndrome coronavirus 2 RNA detected in blood donations Post-donation COVID-19 identification in blood donors Updated information for blood establishments regarding the novel coronavirus outbreak.
    keywords: blood; coronavirus; cov-2; donors; rna; sars
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        item: #539 of 1349
          id: cord-274110-nyyunoha
      author: Orlinger, Klaus K.
       title: An inactivated West Nile Virus vaccine derived from a chemically synthesized cDNA system
        date: 2010-04-26
       words: 5129
      flesch: 44
     summary: West Nile and dengue viruses Flaviviridae: the viruses and their replication Functional cDNA clones of the Flaviviridae: strategies and applications A stable full-length yellow fever virus cDNA clone and the role of conserved RNA elements in flavivirus replication Infectious cDNA clones of Langat tick-borne flavivirus that differ from their parent in peripheral neurovirulence Identification of a major determinant of mouse neurovirulence of dengue virus type 2 using stably cloned genomic-length cDNA Characterization of infectious Murray Valley encephalitis virus derived from a stably cloned genome-length cDNA Synthesis and characterization of an infectious dengue virus type-2 RNA genome (New Guinea C strain) Completion of Kunjin virus RNA sequence and recovery of an infectious RNA transcribed from stably cloned full-length cDNA Construction of infectious cDNA clones for dengue 2 virus: strain 16681 and its attenuated vaccine derivative, strain PDK-53 Infectious RNA transcribed from stably cloned full-length cDNA of dengue type 4 virus Molecular and functional analyses of Kunjin virus infectious cDNA clones demonstrate the essential roles for NS2A in virus assembly and for a nonconservative residue in NS3 in RNA replication Infectious cDNA clones of tick-borne encephalitis virus European subtype prototypic strain Neudoerfl and high virulence strain Hypr Infectious clone construction of dengue virus type 2, strain Jamaican 1409, and characterization of a conditional E6 mutation Infectious cDNA clone of attenuated Langat tick-borne flavivirus (strain E5) and a 3 deletion mutant constructed from it exhibit decreased neuroinvasiveness in immunodeficient mice Infectious RNA transcripts from fulllength dengue virus type 2 cDNA clones made in yeast Construction of a full length infectious clone for dengue-1 virus Western Pacific, 74 strain Transcription of infectious yellow fever RNA from full-length cDNA templates produced by in vitro ligation Infectious cDNA clone of the epidemic west nile virus from New York City Infectious Japanese encephalitis virus RNA can be synthesized from in vitro-ligated cDNA templates An infectious clone of the West Nile flavivirus A new strategy in design of +RNA virus infectious clones enabling their stable propagation in E. coli Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template Synthetic viruses: a new opportunity to understand and prevent viral disease Functional analysis of the tick-borne encephalitis virus cyclization elements indicates major differences between mosquito-borne and tick-borne flaviviruses Proteolytic activation of tick-borne encephalitis virus by furin Kunjin virus replicons: an RNAbased, non-cytopathic viral vector system for protein production, vaccine and gene therapy applications Preclinical and clinical development of YFV 17D-based chimeric vaccines against dengue, West Nile and Japanese encephalitis viruses The test-tube synthesis of a chemical called poliovirus Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides Characterization of the reconstructed 1918 Spanish influenza pandemic virus Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice Rates of spontaneous mutation Viral quasispecies Addressing biosecurity concerns related to the synthesis of select agents. RNA viruses replicate their genome with an error prone mechanism (for reviews see [33] ), resulting in a multitude of distinct but related nucleic acids forming a quasispecies [34] .
    keywords: cdna; cells; genome; mice; rna; sequence; synthesis; type; vero; virus; viruses; wnv; wnvsyn
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        item: #540 of 1349
          id: cord-274353-tzlcpx7q
      author: McDermott, Amy
       title: Inner Workings: Molecular biologists offer “wartime service” in the effort to test for COVID-19
        date: 2020-05-05
       words: 1989
      flesch: 41
     summary: Institutions with medical centers, such as the University of Washington, have the advantage of large clinical labs and some certified medical laboratory scientists onsite, meaning they can, in fact, legally and appropriately pivot into COVID-19 testing centers. Even so, the urgency of the pandemic has spurred some states to relax legal restrictions on who can perform COVID-19 testing.
    keywords: centers; covid-19; laboratory; researchers; testing; university
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        item: #541 of 1349
          id: cord-274401-pjyvg53w
      author: Hrkach, Jeff
       title: From micro to nano: evolution and impact of drug delivery in treating disease
        date: 2020-05-08
       words: 2059
      flesch: 34
     summary: The developments of many of today's most innovative therapeutics are utilizing nanoparticle drug delivery systems, and for our scope, we will focus on RNA nanomedicines. key: cord-274401-pjyvg53w authors: Hrkach, Jeff; Langer, Robert title: From micro to nano: evolution and impact of drug delivery in treating disease date: 2020-05-08 journal: Drug Deliv Transl Res DOI: 10.1007/s13346-020-00769-6 sha: doc_id: 274401 cord_uid: pjyvg53w Over the past 50 years, drug delivery breakthroughs have enabled the approval of several important medicines.
    keywords: cancer; delivery; drug; medicines; mrna; release
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        item: #542 of 1349
          id: cord-274463-0nvw2egm
      author: Sánchez-Navarro, Jesús A.
       title: Plant tissue distribution and chemical inactivation of six carnation viruses
        date: 2006-12-11
       words: 2940
      flesch: 42
     summary: Studies on the diagnosis of hop stunt viroid in fruit trees: Identification of new hosts and application of a nucleic acid extraction procedure based on non-organic solvents Plant Viruses Online: Descriptions and Lists from the VIDE Database Molecular variability of twenty-one geographically distinct isolates of Carnation mottle virus (CarMV) and phylogenetic relationships within the tombusviridae family Chemical degradation of Tobacco mosaic virus followed by infectivity assay, reverse transcription-polymerase chain reaction and gel electrophoresis Influence of the plant growing conditions on the translocation routes and systemic infection of Carnation mottle virus in Chenopodium quinoa plants Detection of Melon necrotic spot virus in water samples and melon plants by molecular methods Saponaria vaccaria 'Pink Beauty', a new test plant for Carnation mottle virus Simultaneous detection of six stone fruit viruses by non-isotopic molecular hybridization using a unique riboprobe or 'polyprobe Productivity of virus-tested carnation clones and the rate of re-infection with virus Transmission, movement and inactivation of Cymbidium mosaic and Odontoglossum ringspot viruses Effectiveness of commercial disinfectants for inactivating hepatitis a virus on agri-food surfaces Beitra¨ge zur kenntnis ver vektorlosen u¨bertragung pflanzenpathogener viren Plant viruses in German rivers and lakes Detection of Petunia asteroid mosaic, Carnation ringspot and Tobacco necrosis viruses in ditches and drainage canals in a grapevine-growing area in west Germany Evaluation of various species demarcation criteria in attempts to classify ten new tombusvirus isolates Inactivation of respiratory syncytial virus by detergents and disinfectants Nucleotides and the covalent structure of nucleic acids Cell culture and PCR determination of poliovirus inactivation by disinfectants Efficient expression of foreign proteins in roots from tobravirus vectors Detection of plant RNA viruses by non-isotopic dot-blot hybridisation Non-radioactive molecular hybridisation detection of Carnation mottle virus in infected carnations and its comparison to serological and biological techniques Comparative analysis of ELISA, non-radioactive molecular hybridisation and PCR for the detection of Prunus necrotic ringspot virus in herbaceous and Prunus hosts Simultaneous detection of five carnation viruses by non-isotopic molecular hybridisation Interruption of rotavirus spread through chemical disinfection Immunological detection and mutational analysis of the RNA2-encoded nematode transmission proteins of Pea early browning virus Specific detection and quantification of Plum pox virus by real-time fluorescent reverse transcription-PCR A comparison of the virucidal properties of chlorine, chlorine dioxide, bromine chloride, and iodine Laboratory-scale inactivation of African swine fever virus and swine vesicular disease virus in pig slurry Roles of the 35S promoter and multiple overlapping domains in the pathogenicity of the pararetrovirus Cauliflower mosaic virus Inactivation of bacterial and viral indicators in secondary sewage effluents, using chlorine and ozone Study on the resistance of severe acute respiratory syndrome-associated coronavirus Isometric plant viruses in ditches and streams in agricultural areas: recovery of previously found viruses and identification of hitherto unrecorded carmo-and tombusviruses including Grapevine Algerian latent virus CarMV is distributed world wide (Can˜izares et al., 2001) and is the most difficult virus among carnation viruses to eliminate by thermotherapy or meristem culture (Hollings et al., 1972) and rapidly propagates after its introduction into virus-free crops (Zandvoort, 1973; Hollings et al., 1972) .
    keywords: carnation; plants; tissue; viral; virus; viruses
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        item: #543 of 1349
          id: cord-274536-fv7mltj7
      author: Tong, Yongqing
       title: Necessity for detection of SARS-CoV-2 RNA in multiple types of specimens for the discharge of the patients with COVID-19
        date: 2020-11-02
       words: 3129
      flesch: 47
     summary: In addition to the 5 cases, another 1 case (P8 at Table 2 ) was only detected ORF1ab gene RNA from nasopharynx swab and N gene RNA from oropharyngeal swab in the quarantine time, this patient did not meet the criteria of viral carrier. All of the 6 patients showed positive viral RNA for at least one gene in nasopharyngeal swab, 2 patients had both ORF1ab and N gene positive, another 3 patients only showed ORF1ab positive and 2 patients showed N gene positive.
    keywords: cov-2; patients; rna; sars; specimens; swab
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        item: #544 of 1349
          id: cord-274567-xd37wxxf
      author: Monpoeho, S.
       title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid
        date: 2002-07-13
       words: 3286
      flesch: 42
     summary: The variability observed with 50 copies of EV RNA standard was acceptable, and the detection limit of the RT-PCR is therefore 50 copies of EV RNA standard per reaction. Only duration of hospitalization showed a statistically significant decrease from 2.7 days for patients with negative PCR results to 1.8 days for patients with positive PCR results (P=0.042).
    keywords: amplification; csf; culture; meningitis; pcr; rna
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        item: #545 of 1349
          id: cord-274569-jh0dyyz7
      author: Alenquer, Marta
       title: Exosome Biogenesis, Regulation, and Function in Viral Infection
        date: 2015-09-17
       words: 7877
      flesch: 38
     summary: Importantly for the context of this review, cells infected with viruses were shown to release exosomes containing viral proteins and RNAs [43] [44] It is now well established that tumor cells secrete exosomes
    keywords: cells; endosomes; exosomes; human; membrane; mvbs; pathway; proteins; rab11; rabs; recycling; release; rna; vesicles; virus; viruses
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        item: #546 of 1349
          id: cord-274663-zyzgk2z3
      author: Chang, Stewart T.
       title: Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4(+) T Cell Line
        date: 2011-09-20
       words: 7009
      flesch: 43
     summary: Microarray data on gene modulation by HIV-1 in immune cells: 2000 -2006 Molecular biology of human immunodeficiency virus type 1 Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays Functional genomics analyses of differential macaque peripheral blood mononuclear cell infections by human immunodeficiency virus-1 and simian immunodeficiency virus Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(ϩ)-T-cell lines Transcriptional profiling in pathogenic and nonpathogenic SIV infections reveals significant distinctions in kinetics and tissue compartmentalization A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling BCL11B is a general transcriptional repressor of the HIV-1 long terminal repeat in T lymphocytes through recruitment of the NuRD complex HIV-1 down-regulates the expression of CD1d via Nef Gene set enrichment analysis: a knowledgebased approach for interpreting genome-wide expression profiles RNA and disease hnRNP A1 controls HIV-1 mRNA splicing through cooperative binding to intron and exon splicing silencers in the context of a conserved secondary structure Role of cellular RNA processing factors in human immunodeficiency virus type 1 mRNA metabolism, replication, and infectivity The multiple roles of TDP-43 in pre-mRNA processing and gene expression regulation Cloning and characterization of a novel cellular protein, TDP-43, that binds to human immunodeficiency virus type 1 TAR DNA sequence motifs TDP-43: multiple targets, multiple disease mechanisms? Using NGS, we detected small but significant changes in host gene expression affecting T cell function that coincided with the initiation of viral RNA production at 12 h postinfection (hpi).
    keywords: activation; cell; changes; data; expression; fig; genes; hiv; host; hpi; infected; infection; rna; virus
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        item: #547 of 1349
          id: cord-274773-3jhka8wl
      author: Zhang, Jialin
       title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge
        date: 2019-09-30
       words: 3958
      flesch: 44
     summary: Therefore, fast and effective preventive measures are essential for the prevention and control of PDCoV. Currently, implementing vaccines remain the most effective means of disease control; however, there are no commercial vaccines available for PDCoV. Due to their immature immune system, neonatal piglets are highly susceptible to viral infection during their first few weeks of life. Immunized sows can transfer antibodies against enteroviruses (e.g. PEDV, TGEV and porcine rotavirus) to neonatal piglets through their colostrum and milk.
    keywords: antibodies; challenge; igg; milk; pdcov; piglets; serum; sows; vaccine
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        item: #548 of 1349
          id: cord-274785-9jgg8ukr
      author: Zhang, Qiang
       title: Viral Regulation of RNA Granules in Infected Cells
        date: 2019-04-29
       words: 7401
      flesch: 28
     summary: RNA viruses modulate stress response pathway at different levels of SG formation (Table 1) : One is to regulate eIF2a phosphorylation, and the other is to regulate the process of SG nucleation. It seems that a portion of RNA viruses encode RNA binding proteins to antagonize the activity of PKR.
    keywords: assembly; bodies; cells; et al; formation; granules; host; infection; mrna; pkr; protein; replication; rna; stress; translation; virus; viruses
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        item: #549 of 1349
          id: cord-275225-fvq8hezk
      author: Hornyák, Ákos
       title: Detection of subgenomic mRNA of feline coronavirus by real-time polymerase chain reaction based on primer-probe energy transfer (P-sg-QPCR)
        date: 2012-02-18
       words: 7145
      flesch: 42
     summary: The prevalence of types I and II feline coronavirus infections in cats Morphologic features and development of granulomatous vasculitis in feline infectious peritonitis Correlation of genomic detection of feline coronavirus with various diagnostic assays for feline infectious peritonitis Prevalence and genetic pattern of feline coronaviruses in urban cat populations Feline coronavirus serotypes 1 and 2: seroprevalence and association with disease in Switzerland FCoV shedding pattern of privately owned cats under field conditions Experimental studies with three new strains of feline infectious peritonitis virus: FIPV-UCD2, FIPV-UCD3, and FIPV-UCD4 Virologic and immunologic aspects of feline infectious peritonitis virus infection Development of a novel quantitative real-time RT-PCR assay for the simultaneous detection of all serotypes of foot-and-mouth disease virus Quantitative multiplex assay for simultaneous detection and identification of Indiana and New Jersey serotypes of vesicular stomatitis virus A simple method of estimating fifty percent endpoints Acquisition of macrophage tropism during the pathogenesis of feline infectious peritonitis is determined by mutations in the feline coronavirus spike protein A mRNA PCR for the diagnosis of feline infectious peritonitis Isolation and identification of feline peritoneal macrophages for in vitro studies of coronavirus-macrophage interactions Taxonomic proposal of the Coronavirus Study Group to the ICTV Executive Committee Natural history of a recurrent feline coronavirus infection and the role of cellular immunity in survival and disease Evaluation of real-time RT-PCR for the quantification of FCoV shedding in the faeces of domestic cats SYBR Green real-time reverse transcription-polymerase chain reaction assay for the generic detection of coronaviruses Patterns of feline coronavirus infection and faecal shedding from cats in multiple-cat environments Zwischenmolekulare Energiewanderung und Fluoreszenz Discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replication-specific multiplex reverse transcription-PCR Development of a real-time PCR assay based on primer-probe energy transfer for the detection of swine vesicular disease virus The molecular genetics of feline coronaviruses: comparative sequence analysis of the ORF7a/7b transcription unit of different biotypes Persistence and evolution of feline coronavirus in a closed cat-breeding colony Feline coronavirus type II strains 79-1683 and 79-1146 originate from a double recombination between feline coronavirus type I and canine coronavirus Characterization of monoclonal antibodies against feline infectious peritonitis virus type II and antigenic relationship between feline, porcine, and canine coronaviruses A study on the mechanism of antibody-dependent enhancement of feline infectious peritonitis virus infection in feline macrophages by monoclonal antibodies
    keywords: assay; cats; detection; fcov; feline; fipv; mrna; pcr; peritonitis; samples; virus
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        item: #550 of 1349
          id: cord-275252-4e3cn50u
      author: Rad SM, Ali Hosseini
       title: Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting
        date: 2020-05-16
       words: 4369
      flesch: 45
     summary: While perfect matches of miRNA to target viral sequences results in miRNA-induced silencing complex (miRISC)-mediate destruction of viral RNA, imperfect matches interfere with translation [15] . C=18.4%) and enrichment of codons in in pyrimidines is likely due to APOBEC editing of viral RNA and the fact that Nsp14 (proof-reading) does not remove U (the product of cytosine deamination)
    keywords: cov-2; figure; genome; host; mirna; mutations; rna; sars; sites; structure; target; virus
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        item: #551 of 1349
          id: cord-275307-d7htyfcl
      author: Gaglia, Marta Maria
       title: Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX
        date: 2015-12-08
       words: 10873
      flesch: 53
     summary: In this study, we address this paradox by using high-throughput sequencing of cleavage intermediates combined with a custom bioinformatics-based analysis pipeline to identify SOX cleavage sites across the mRNA transcriptome. To dissect the specificity of SOX cleavage across the mRNA transcriptome, we designed an approach to map SOX cleavage sites in endogenous mRNAs using PARE
    keywords: analysis; cleavage; cleavage sites; control; cut; cut site; fig; gfp; motif; mrna; rna; sequence; sites; sox; sox cleavage; sox cut; targeting
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        item: #552 of 1349
          id: cord-275403-g4rohhtt
      author: Bautista, Elida M.
       title: Functional Properties of the Predicted Helicase of Porcine Reproductive and Respiratory Syndrome Virus
        date: 2002-07-05
       words: 7486
      flesch: 39
     summary: Kinetic analysis of recombinant helicase ATPase activity revealed dependence on time (Fig. 6A ) and substrate concentration (Fig. 6B) . Coronavirus genome: Prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis RNAstimulated ATPase and RNA helicase activities and RNA binding domain of hepatitis G virus nonstructural protein 3 Characterization of coronavirus RNA polymerase gene products Identification of an ATPase activity associated with a 71-kilodalton polypeptide encoded in gene 1 of the human coronavirus 229E Isolation and genome characterization of porcine reproductive and respiratory syndrome virus in P.R ATPase, GTPase, and RNA binding activities associated with the 206-kilodalton protein of turnip yellow mosaic virus Virus-encoded RNA helicases Enhanced replication of porcine reproductive and respiratory syndrome (Prrs) virus in a homogeneous subpopulation of Ma-104 cell line The serine protease and RNA-stimulated nucleoside triphosphatase and RNA helicase functional domains of dengue virus type 2 NS3 converge within a region of 20 amino acids Firefly and bacterial luminescence: Basic science and applications Lelystad virus, the causative agent of porcine epidemic abortion and respiratory syndrome (PEARS), is related to LDV and EAV Infectious transcripts from cloned genome-length cDNA of porcine reproductive and respiratory syndrome virus Analyzing Data with GraphPad Prism Nucleoside triphosphate specificity of firefly luciferase Comparison of the structural protein coding sequences of the VR-2332 and Lelystad virus strains of the PRRS virus Genetic variation in the PRRS virus Porcine reproductive and respiratory syndrome virus comparison: Divergent evolution on two continents Analysis of ORF 1 in European porcine reproductive and respiratory syndrome virus by long RT-PCR and restriction fragment length polymorphism (RFLP) analysis Lactate dehydrogenaseelevating virus, equine arteritis virus, and simian hemorrhagic fever virus: A new group of positive-strand RNA viruses A steady-state and pre-steady-state kinetic analysis of the NTPase activity associated with the hepatitis C virus NS3 helicase domain ATPase and GTPase activities associated with Semliki Forest virus nonstructural protein nsP2 Molecular Cloning.
    keywords: activity; analysis; atpase; et al; fig; helicase; nsp10; orf1b; protein; prrsv; prrsv-14; recombinant; rna; syndrome; virus
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        item: #553 of 1349
          id: cord-275565-xerr4vki
      author: Kumar, Manish
       title: Decay of SARS-CoV-2 RNA along the wastewater treatment outfitted with Upflow Anaerobic Sludge Blanket (UASB) system evaluated through two sample concentration techniques
        date: 2020-09-15
       words: 3459
      flesch: 38
     summary: These all warrants a study that can track the genetic loading after each wastewater treatment stage in Indian settings and highlight the effects of wastewater treatment on RNA decay of the corona virus. In wastewater treatment ponds, viruses are removed through various mechanisms, including adsorption, predation and sunlight inactivation (Verbyla and Mihelcic, 2015) .
    keywords: cov-2; method; rna; sars; treatment; uasb; wastewater
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        item: #554 of 1349
          id: cord-275602-cog4nma0
      author: Watkins, Kevin
       title: Emerging Infectious Diseases: a Review
        date: 2018-06-22
       words: 4676
      flesch: 47
     summary: Emerging infectious diseases: a CDC perspective Emerging infectious diseases in 2012: 20 years after the Institute of Medicine Report Emerging infectious disease: a proactive approach A novel coronavirus associated with severe acute respiratory syndrome Severe acute respiratory syndrome (SARS): a review of the history, epidemiology, prevention, and concerns for the future Severe acute respiratory syndrome and coronavirus Severe acute respiratory syndrome (SARS) Severe acute respiratory syndrome and influenza: virus incursions from southern China WHO guidelines for the global surveillance of severe acute respiratory syndrome (SARS) Anti-SARS coronavirus agents: a patent review (2008-present) Middle East respiratory syndrome coronavirus: a comprehensive review Middle East respiratory syndrome: what clinicians need to know Middle East respiratory syndrome coronavirus: update for clinicians This article gives the majority of a summary of perhaps most significant recent emerging infectious disease in terms of both mortality and number of cases Middle East respiratory syndrome coronavirus disease is rare in children: an update from Saudi Arabia Risk factors for transmission of Middle East respiratory syndrome coronavirus infection during the 2015 outbreak in South Korea Clinical course and outcomes of critically ill patients with Middle East respiratory syndrome coronavirus infection Infection Prevention and Control Guidelines for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Infection Broad-spectrum antivirals for the emerging Middle East respiratory syndrome coronavirus A review of treatment modalities for Middle East respiratory syndrome Treatment outcomes for patients with middle eastern respiratory syndrome coronavirus (MERS CoV) infection at a coronavirus referral center in the Kingdom of Saudi Arabia A new Phlebovirus associated with severe febrile illness in Missouri Notes from the field: heartland virus disease-United States Heartland virus associated death in Tennessee Update and commentary on four emerging tick-borne infections Novel Thogotovirus associated with febrile illness and death Bourbon virus in field-collected ticks Nipah encephalitis-an update The pandemic potential of Nipah virus Therapeutic treatment of Nipah virus infection in nonhuman primates with a neutralizing human monoclonal antibody Emergomyces canadensis, a dimorphic fungus causing fatal systemic human disease in North America Emergomyces: a new genus of dimorphic fungal pathogens causing disseminated disease among immunocompromised persons globally Global spread of antibiotic resistance: the example of New Delhi metallo-ß-lactamase (NDM)-mediated carbapenem resistance The new medical challenge: why NDM-1? The Centers for Disease Control and Prevention (CDC) recommends evaluation for patients with respiratory symptoms and travel to an affected country within 14 days or for those who are in a cluster of patients with severe acute respiratory disease in which MERS-CoV is being evaluated [14] .
    keywords: cases; coronavirus; disease; east; fever; hemorrhagic; human; infection; middle; patients; syndrome; virus
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        item: #555 of 1349
          id: cord-275683-1qj9ri18
      author: Roux, Simon
       title: Metagenomics in Virology
        date: 2019-06-12
       words: 5893
      flesch: 32
     summary: Viromes provide a deeper description of the virus community, since most of the sequencing data will be obtained from virus genomes. While the analyses outlined above were foundational for our current understanding of virus diversity, they were limited by the short length of next-generation sequencing reads which fragmented the view of viral genomes.
    keywords: diversity; dna; genomes; host; metagenomics; novel; rna; sample; sequencing; time; viruses
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        item: #556 of 1349
          id: cord-275720-kf9m4zho
      author: Cho, Won Kyong
       title: Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection
        date: 2012-05-06
       words: 7177
      flesch: 42
     summary: To identify differentially expressed genes, we first performed hierarchical clustering, which identified gene sets of significantly differentially expressed genes at Figure 2 Differentially expressed F. graminearum genes during FgV1-DK21 infection identified by microarray. Differentially expressed F. graminearum genes at 36 h.Additional file 2: Table S2 .
    keywords: dk21; expression; fgv1; figure; fungal; fusarium; genes; graminearum; host; infection; microarray; time; virus
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        item: #557 of 1349
          id: cord-275795-ee7qyw5h
      author: Monette, Anne
       title: T Lymphocytes as Measurable Targets of Protection and Vaccination Against Viral Disorders
        date: 2018-10-24
       words: 28288
      flesch: 24
     summary: As cellular immunity to VZV wanes in the elderly and immunocompromised populations, latent VZV becomes reactivated and causes zoster (i.e., shingles, herpes zoster), which is usually associated with chronic pain but also numerous other serious neurological and ocular disorders, as well as multiple visceral and gastrointestinal disorders, including ulcers, hepatitis, and pancreatitis (Gershon et al., 2015; Gilden et al., 2010) . Transmission to humans is via the rodent host Mastomys natalensis (Mccormick et al., 1987) .
    keywords: acute; adaptive; antibodies; antibody; cases; cause; cd4; cd8 þ; cell responses; children; clearance; cns; dengue; development; disease; disorders; encephalitis; et al; fever; hbv; hepatitis; human; humoral; ifn; immune; immunity; individuals; infection; influenza; measles; memory; memory t; mortality; populations; protection; proteins; replication; responses; rna; rsv; rubella; specific; system; t cells; term; vaccination; vaccine; varicella; virus; virus infection; viruses; vzv; zoster; þ t
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        item: #558 of 1349
          id: cord-275859-ix8du1er
      author: Mouzakis, Kathryn D.
       title: HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome
        date: 2012-12-15
       words: 6740
      flesch: 42
     summary: key: cord-275859-ix8du1er authors: Mouzakis, Kathryn D.; Lang, Andrew L.; Vander Meulen, Kirk A.; Easterday, Preston D.; Butcher, Samuel E. title: HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome date: 2012-12-15 journal: Nucleic Acids Res DOI: 10.1093/nar/gks1254 sha: doc_id: 275859 cord_uid: ix8du1er The sequence of the frameshift site stemloop was varied to dissect the relative contributions of local and overall RNA stability on HIV-1 frameshift efficiency.
    keywords: base; efficiency; figure; frameshift; frameshift efficiency; frameshifting; loop; ribosomal; ribosome; rna; site; stability; stem; structure
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        item: #559 of 1349
          id: cord-276006-mjjnkqv6
      author: Jarach, Natanel
       title: Polymers in the Medical Antiviral Front-Line
        date: 2020-07-31
       words: 12601
      flesch: 37
     summary: Some other molecules with antiviral effects are 5-(N-ethyl-N-isopropyl)amiloride (EIPA), verapamil, and diltiazem. Silver (Ag) particles have an antiviral effect even in their metal form; Yamamoto et al. showed that the addition of Ag particles to a cotton textile granted it antiviral effect against Influenza A and Feline Calicivirus [76] .
    keywords: acid; activity; addition; ammonium; drugs; effect; et al; figure; influenza; ions; metal; nanoparticles; particles; polymers; properties; rna; sulphate; temperature; virus; viruses
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        item: #560 of 1349
          id: cord-276185-ysspkbj7
      author: Milewska, Aleksandra
       title: APOBEC3-mediated restriction of RNA virus replication
        date: 2018-04-13
       words: 5537
      flesch: 47
     summary: Moreover, APOBEC3 proteins bound to the coronaviral nucleoprotein, and this interaction also affected viral replication. The RNA-editing capability of APOBEC3 proteins was identified in 2004 16 , since when extensive mutational activity of A3A on RNA transcripts in monocytes and macrophages has been demonstrated 17 .
    keywords: a3c; a3f; a3h; apobec3; cells; coronavirus; hcov; human; nl63; proteins; replication; rna; virus
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        item: #561 of 1349
          id: cord-276198-psjua913
      author: V’kovski, Philip
       title: New insights on the role of paired membrane structures in coronavirus replication
        date: 2015-04-16
       words: 6097
      flesch: 30
     summary: related to the replication of potato virus M (PVM) Structural basis of severe acute respiratory syndrome coronavirus ADP-ribose-1 -phosphate dephosphorylation by a conserved domain of nsP3 Properly folded nonstructural polyprotein directs the semliki forest virus replication complex to the endosomal compartment Functional and genetic analysis of coronavirus replicase-transcriptase proteins A positive-strand RNA virus replication complex parallels form and function of retrovirus capsids Alternate, virusinduced membrane rearrangements support positive-strand RNA virus genome replication Nuclear magnetic resonance structure of the N-terminal domain of nonstructural protein 3 from the severe acute respiratory syndrome coronavirus Nuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3 Japanese encephalitis virus replication is negatively regulated by autophagy and occurs on LC3-I-and EDEM1-containing membranes Non-structural proteins 2 and 3 interact to modify host cell membranes during the formation of the arterivirus replication complex Ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex Lymphoid organ virus of Penaeus monodon from Australia Genetic analysis of Murine hepatitis virus nsp4 in virus replication A new cistron in the murine hepatitis virus replicase gene Remodeling the endoplasmic reticulum by poliovirus infection and by individual viral proteins: an autophagy-like origin for virus-induced vesicles The SARS-unique domain (SUD) of SARS coronavirus contains two macrodomains that bind G-quadruplexes Induction of intracellular membrane rearrangements by HAV proteins 2C and 2BC A new nidovirus (NamDinh virus NDiV): its ultrastructural characterization in the C6/36 mosquito cell line Qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirus Deubiquitinase function of arterivirus papain-like protease 2 suppresses the innate immune response in infected host cells Mouse hepatitis coronavirus RNA replication depends on GBF1-mediated ARF1 activation Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome Composition and threedimensional architecture of the dengue virus replication and assembly sites Structure of the X (ADRP) domain of nsp3 from feline coronavirus Papain-like protease 1 from transmissible gastroenteritis virus: crystal structure and enzymatic activity toward viral and cellular substrates Electron microscopic study of tissue cultures infected with simian haemorrhagic fever virus Crystal structures of two coronavirus ADP-ribose-1 -monophosphatases and their complexes with ADP-Ribose: a systematic structural analysis of the viral ADRP domain Crystal structure of the C-terminal cytoplasmic domain of non-structural protein 4 from mouse hepatitis virus A59 Coronavirus replication does not require the autophagy gene ATG5 Recent progress in studies of arterivirus-and coronavirus-host interactions An insect nidovirus emerging from a primary tropical rainforest This work was supported by the Swiss National Science Foundation (SNF; project 149784; VT and PV) and a studentship from the Iraqi Ministry of Higher Education and Scientific Research (HA). These observations parallel the ones seen for MHV but raise further questions whether this feature is even more widespread amongst +RNA viruses.
    keywords: coronavirus; et al; membrane; mhv; organelles; proteins; replication; rna; tm1; tm2; virus; viruses
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        item: #562 of 1349
          id: cord-276364-zyw5aukk
      author: Wong, Ho Him
       title: Manipulation of autophagy by (+) RNA viruses
        date: 2019-08-08
       words: 6910
      flesch: 27
     summary: Cytochemical localization of lysosomal enzymes in infected cells Autophagy is an essential component of Drosophila immunity against vesicular stomatitis virus HSV-1 ICP34.5 confers neurovirulence by targeting the Beclin 1 autophagy protein Autophagy pathway intersects with HIV-1 biosynthesis and regulates viral yields in macrophages Protection against fatal Sindbis virus encephalitis by beclin, a novel Bcl-2-interacting protein Autophagy protects against Sindbis virus infection of the central nervous system PLA2G16 represents a switch between entry and clearance of Picornaviridae CALCOCO2/NDP52 and SQSTM1/p62 differentially regulate coxsackievirus B3 propagation Interferon-inducible protein SCOTIN interferes with HCV replication through the autolysosomal degradation of NS5A Inflammation-induced, STING-dependent autophagy restricts Zika virus infection in the drosophila brain Amino acid substitutions in the non-structural proteins 4A or 4B modulate the induction of autophagy in West Nile virus infected cells independently of the activation of the unfolded protein response The role of secretory autophagy in Zika virus transfer through the placental barrier Japanese encephalitis virus replication is negatively regulated by autophagy and occurs on LC3-I-and EDEM1-containing membranes Rab5 and class III phosphoinositide 3-kinase Vps34 are involved in hepatitis C virus NS4B-induced autophagy Hepatitis C virus upregulates Beclin1 for induction of autophagy and activates mTOR signaling The autophagy elongation complex (ATG5-12/16L1) positively regulates HCV replication and is required for wild-type membranous web formation Coronavirus membraneassociated papain-like proteases induce autophagy through interacting with Beclin1 to negatively regulate antiviral innate immunity Coronaviruses hijack the LC3-I-positive EDEMosomes, ER-derived vesicles exporting short-lived ERAD regulators, for replication Coronavirus nsp6 proteins generate autophagosomes from the endoplasmic reticulum via an omegasome intermediate Cleavage of sequestosome 1/p62 by an enteroviral protease results in disrupted selective autophagy and impaired NFKB signaling Protein 2B of coxsackievirus B3 induces autophagy relying on its transmembrane hydrophobic sequences Enteroviruses remodel autophagic trafficking through regulation of host SNARE proteins to promote virus replication and cell exit Foot-and-mouth disease virus capsid protein VP2 activates the cellular EIF2S1-ATF4 pathway and induces autophagy via HSPB1 Viroporin activity of the foot-and-mouth disease virus non-structural 2B protein Modification of cellular autophagy protein LC3 by poliovirus Double-membraned liposomes sculpted by poliovirus 3AB protein This work was supported by Health and Medical Research Funds (16150592 and 17161202 and 17161032), and partially by Research Grants Council-General research funds (17112617). A similar finding was reported more recently with rotavirus where virus replication benefited from induction of autophagy while blocking degradation [34] .
    keywords: autophagosomes; autophagy; cells; degradation; denv; infection; membrane; pathway; protein; replication; rna; vesicles; virus; viruses
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        item: #563 of 1349
          id: cord-276493-hoaxv5e0
      author: Jeong, Gi Uk
       title: Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review
        date: 2020-07-14
       words: 5702
      flesch: 43
     summary: (Dai et al., 2020; Jin et al., 2020; Zhang et al., 2020b) . (Dai et al., 2020; Jin et al., 2020; Zhang et al., 2020b) .
    keywords: binding; coronavirus; cov-2; covid-19; et al; hace2; pro; protein; rbd; rna; sars; structure
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        item: #564 of 1349
          id: cord-276541-u9ebql5a
      author: Lan, Yungang
       title: Inhibition of porcine hemagglutinating encephalomyelitis virus replication by short hairpin RNAs targeting of the nucleocapsid gene in a porcine kidney cell line
        date: 2011-11-25
       words: 3084
      flesch: 45
     summary: The results (Fig. 3) showed that in control cells transfected with shNC, the PHEV TCID 50 reached 10 4.30 at 48 h postinfection, which was similar to that observed in non-transfected cells. Our results revealed that both shRNAs were highly capable of inhibiting viral RNA genome replication, especially shN2.
    keywords: cells; infection; phev; replication; rna; shn2; virus
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        item: #565 of 1349
          id: cord-276575-jfug80yu
      author: Aigner, Achim
       title: Applications of RNA interference: current state and prospects for siRNA-based strategies in vivo
        date: 2007-04-25
       words: 5255
      flesch: 29
     summary: Bradley et al. 2005a, b; Chien et al. 2005; Ge et al. 2004; Hassan et al. 2005; Miyawaki-Shimizu et al. 2005; Morrissey et al. 2005a, b; Schiffelers et al. 2004; Soutschek et al. 2004; Yano et al. 2004; Takeshita et al. 2005 In situ perfusion/intravenous (pancreatic islet) Bradley et al. 2005a , b Intracardiac Bollerot et al. 2006
    keywords: cancer; cells; delivery; et al; gene; molecules; rnai; sirna; small; target; targeting; tumor; vivo
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        item: #566 of 1349
          id: cord-276739-84vf5bts
      author: Sakurai, Akira
       title: Rapid typing of influenza viruses using super high-speed quantitative real-time PCR
        date: 2011-08-22
       words: 3315
      flesch: 44
     summary: Clinical diagnostic tests for influenza viruses in outpatient departments or clinics are typically based on immunochromatographic detection of influenza virus antigens (Chan et al., 2007) . The analysis targeted the nucleotide sequences of the matrix protein segment of influenza virus A (A-MP), influenza virus B (B-MP), and hemagglutinin (HA) of the 2009 pandemic S-OIV and H5N1 avian influenza viruses.
    keywords: detection; influenza; pcr; reaction; rna; shrt; time; viruses
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        item: #567 of 1349
          id: cord-276908-9jthjf24
      author: Gupta, Akanksha
       title: COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives
        date: 2020-07-06
       words: 5182
      flesch: 52
     summary: [92] Au NPs based materials are well known for the detection of various viruses such as dengue virus, influenza virus, bovine viral diarrhea coronavirus, etc. The viral infection encountered with present‐day challenges and futuristic approaches with the help of nanotechnology to minimize the spread of infectious viruses.
    keywords: antiviral; coronavirus; covid-19; covs; disease; drugs; hcov; host; human; infection; protein; rna; sars; virus; viruses
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        item: #568 of 1349
          id: cord-276914-44ji0g78
      author: Chen, Weilie
       title: Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity
        date: 2020-02-26
       words: 2501
      flesch: 52
     summary: But we believe the existence of virus RNA in the stool samples from these patients because that a large amount of viral RNA was detected in anal swabs and that viral RNA had also been detected in a case reported from the United States [10] . In summary, we find that the presence of viral RNA in the blood and anal swab is positively correlated with the severe disease stage and that early monitoring of virus RNA in blood and the digestive tract on top of the respiratory tract might benefit the disease prediction.
    keywords: blood; day; rna; virus
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        item: #569 of 1349
          id: cord-276988-bvsz5q6d
      author: Neu, Carolin T.
       title: Post-Transcriptional Expression Control in Platelet Biogenesis and Function
        date: 2020-10-15
       words: 11425
      flesch: 33
     summary: The complex transcriptional landscape of the anucleate human platelet Integration of proteomics and genomics in platelets: A profile of platelet proteins and platelet-specific genes Next generation sequencing analysis of human platelet PolyA+ mRNAs and rRNA-depleted total RNA Mapping and quantifying mammalian transcriptomes by RNA-Seq Uncovering the complexity of transcriptomes with RNA-Seq Platelet factor XI: Intracellular localization and mRNA splicing following platelet activation Signal-dependent splicing of tissue factor pre-mRNA modulates the thrombogenicity of human platelets Lipopolysaccharide signaling without a nucleus: Kinase cascades stimulate platelet shedding of proinflammatory IL-1beta-rich microparticles Lipopolysaccharide is a direct agonist for platelet RNA splicing Rigoutsos, I. These molecules, be they platelet proteins, lipids, growth factors, or cytokines, are mainly found in alpha (α) and dense (δ) granules [38] .
    keywords: activation; binding; cancer; cells; coding; control; expression; factor; function; human; mechanisms; megakaryocytes; mirnas; mks; mrna; patients; platelets; protein; rbps; rna; role; transcriptional; translation
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        item: #570 of 1349
          id: cord-276997-hbovh7s9
      author: Alsved, Malin
       title: Aerosolization and recovery of viable murine norovirus in an experimental setup
        date: 2020-09-29
       words: 6035
      flesch: 40
     summary: Linear regression analysis using the ANOVA test on the log-transformed data was used to compare the quantities of nsRNA with inoculation dilutions in Fig. 4 . Detection and quantification of airborne norovirus during outbreaks in healthcare facilities Sources of airborne norovirus in hospital outbreaks Norovirus recovery from floors and air after various decontamination protocols Aerosol generation by modern flush toilets Routes of transmission of influenza A H1N1, SARS CoV, and norovirus in air cabin: comparative analyses Replication of human noroviruses in stem cell-derived human enteroids Surrogates for the study of norovirus stability and inactivation in the environment: a comparison of murine norovirus and feline calicivirus Detection of murine norovirus 1 by using plaque assay, transfection assay, and real-time reverse transcription-PCR before and after heat exposure Murine norovirus detection in the exhaust air of IVCs is more sensitive than serological analysis of soiled bedding sentinels Some factors affecting the survival of airborne viruses Sampling methodologies and dosage assessment techniques for submicrometre and ultrafine virus aerosol particles Comparison of five bacteriophages as models for viral aerosol studies Airborne micro-organisms: survival tests with four viruses Resistance of aerosolized bacterial viruses to relative humidity and temperature Determination of the distribution of infectious viruses in aerosol particles using water-based condensational growth technology and a bacteriophage MS2 model A vibrating mesh nebulizer as an alternative to the Collison 3-jet nebulizer for infectious disease aerobiology Relationship between humidity and influenza A viability in droplets and implications for influenza's seasonality Natural sources and experimental generation of bioaerosols: challenges and perspectives The role of particle size in aerosolised pathogen transmission: a review Concentrations and size distributions of airborne influenza A viruses measured indoors at a health centre, a day-care centre and on aeroplanes Detection and isolation of airborne influenza A H3N2 virus using a sioutas personal cascade impactor sampler Concentration, size distribution, and infectivity of airborne particles carrying swine viruses Aerosolization of particles from a bubbling liquid: characteristics and generator development Design and performance of a single-pass bubbling bioaerosol generator A systematic comparison of four bioaerosol generators: affect on culturability and cell membrane integrity when aerosolizing Escherichia coli bacteria Release of free DNA by membrane-impaired bacterial aerosols due to aerosolization and air sampling Effect of aerosolization and drying on the viability of pseudomonas syringae cells High-flow-rate impinger for the study of concentration, viability, metabolic activity, and ice-nucleation activity of airborne bacteria Host stress and immune responses during aerosol challenge of Brown Norway rats with Yersinia pestis Aerosolisation of Escherichia coli and associated endotoxin using an improved bubbling bioaerosol generator Vesicle-cloaked virus clusters are optimal units for inter-organismal viral transmission The role of jet and film drops in controlling the mixing state of submicron sea spray aerosol particles Development of a strand specific real-time RT-qPCR assay for the detection and quantitation of murine norovirus RNA Assessment of airborne virus contamination in wastewater treatment plants Electrospray versus nebulization for aerosolization and filter testing with bacteriophage particles Collection and measurement of aerosols of viable influenza virus in liquid media in an Andersen cascade impactor An experimental investigation of the performance of a Collison nebulizer generating H1N1 influenza aerosols Gentle sampling of submicrometer airborne virus particles using a personal electrostatic particle concentrator A wind tunnel evaluation of the physical sampling efficiencies of three bioaerosol samplers Evaluation of six inhalable aerosol samplers Biosurfactants change the thinning of contaminated bubbles at bacteria-laden water interfaces As the infectivity was strongly reduced after aerosolization, the nsRNA detection after 24 h was chosen instead of CPE observation after 72 h. The experimental setup described here highlights some difficulties in studies on aerosolized viruses: (1) the lack of standards in how to generate bioaerosol that results in significant differences in aerosol particle size and concentration, (2) the necessity to determine both physical and viral dilution factors, and (3) www.nature.com/scientificreports/ during airborne transport due to the low-solute solution and dilution in the setup.
    keywords: aerosol; aerosolization; collection; detection; dilution; factor; infectivity; liquid; mnv; nsrna; particles; samples; time; virus
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        item: #571 of 1349
          id: cord-277306-r8jki3x4
      author: Osborne, Christina
       title: Alphacoronaviruses in New World Bats: Prevalence, Persistence, Phylogeny, and Potential for Interaction with Humans
        date: 2011-05-12
       words: 5192
      flesch: 52
     summary: Similar findings were made in rhinolophid bats in Asia that harbor SARs-like-bat-CoVs [37] and in fruit bats experimentally infected with bat CoVs which showed no signs of illness [39] . To assess the potential for zoonotic transmission of bat CoVs, we focused part of this present work on North American bats that have the closest contact with humans and sampled roosts where big brown bats had histories of contact or potential for contact with people [30] .
    keywords: bats; brown; colorado; cov; covs; prevalence; rna; sequences; site; species; viruses; world
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        item: #572 of 1349
          id: cord-277318-cwuls6xs
      author: Visscher, Koen
       title: −1 Programmed Ribosomal Frameshifting as a Force-Dependent Process
        date: 2016-02-02
       words: 8572
      flesch: 40
     summary: The elasticity of a single supercoiled DNA molecule Magnetic tweezers: micromanipulation and force measurement at the molecular level Recent advances in magnetic tweezers Atomic force microscope Reversible unfolding of individual titin immunoglobulin domains by AFM Bead movement by single kinesin molecules studied with optical tweezers Direct observation of kinesin stepping by optical trapping interferometry Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads Single kinesin molecules studied with a molecular force clamp Single-molecule studies of DNA mechanics Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA Dynamics of equilibrium folding and unfolding transitions of titin immunoglobulin domain under constant forces Direct observation of chaperoneinduced changes in a protein folding pathway Chaperone action at the singlemolecule level Unusual mechanical stability of a minimal RNA kissing complex Mechanical unfolding of two DIS RNA kissing complexes from HIV-1 Optical trapping and manipulation of neutral particles using lasers Biological applications of optical forces Optical trapping Versatile optical traps with feedback control Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy Passive all-optical force clamp for high-resolution laser trapping Reversible unfolding of single RNA molecules by mechanical force Direct observation of the three-state folding of a single protein molecule Stretching DNA with optical tweezers Versatile optical traps with feedback control Interference model for back-focal-plane displacement detection in optical tweezers Three-dimensional position detection of optically trapped dielectric particles Å ngström-precision optical traps and applications Ultrastable measurement platform: sub-nm drift over hours in 3D at room temperature Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules Direct observation of base-pair stepping by RNA polymerase Differential detection of dual traps improves the spatial resolution of optical tweezers Limitations of constant-forcefeedback experiments Shape-induced force fields in optical trapping Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid Counter-propagating dual-trap optical tweezers based on linear momentum conservation Free-energy inference from partial work measurements in small systems −1 Programmed Ribosomal Frameshifting as a Force-Dependent Process Measuring the folding landscape of a harmonically constrained biopolymer Elongation-competent pauses govern the fidelity of a viral RNA-dependent RNA polymerase Massively parallel single-molecule manipulation using centrifugal force Cantilever springconstant calibration in atomic force microscopy Ultrastable atomic force microscopy: improved force and positional stability Stepwise unfolding of ankyrin repeats in a single protein revealed by atomic force microscopy Order statistics theory of unfolding of multimeric proteins Probing complex RNA structures by mechanical force Microsecond timescale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules Rapid nanopore discrimination between single polynucleotide molecules Ion-beam sculpting at nanometre length scales Fabrication of solid-state nanopores with single-nanometre precision DNA molecules and configurations in a solid-state nanopore microscope Extracting kinetics from singlemolecule force spectroscopy: nanopore unzipping of DNA hairpins Direct force measurements on double-stranded RNA in solid-state nanopores Solid-state nanopores Determination of thermodynamics and kinetics of RNA reactions by force Force unfolding kinetics of RNA using optical tweezers. However, since it was shown that unfolding forces depend upon the number of unfolded domains in a chain, so-called order statistics need to be applied for generating proper parent distribution functions 73 of unfolding forces before such data can further be utilized for analysis and/or predictions of kinetic behavior.
    keywords: codon; constant; dna; energy; experiments; force; molecule; mrna; prf; ribosomal; ribosome; sequence; structure; tweezers; unfolding
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        item: #573 of 1349
          id: cord-277355-si3g5dih
      author: He, Yu
       title: The role of capsid in the flaviviral life cycle and perspectives for vaccine development
        date: 2020-09-17
       words: 6906
      flesch: 40
     summary: capsid protein Spontaneous mutations restore the viability of tick-borne encephalitis virus mutants with large deletions in protein C Solution structure of dengue virus capsid protein reveals another fold Dynamics of zika virus capsid protein in solution: the properties and exposure of the hydrophobic cleft are controlled by the alpha-helix 1 sequence West Nile virus core protein; tetramer structure and ribbon formation Crystal structure of the capsid protein from Zika virus Crystal structure of the Japanese encephalitis virus capsid protein Structural insight into the Zika virus capsid encapsulating the viral genome Dengue virus capsid protein usurps lipid droplets for viral particle formation Maintenance of dimer conformation by the dengue virus core protein alpha 4-alpha 4'= helix pair is critical for nucleocapsid formation and virus production Partial intrinsic disorder governs the dengue capsid protein conformational ensemble Flavivirus immunization with capsid-deletion mutants: basics, benefits, and barriers Capsid protein C of tick-borne encephalitis virus tolerates large internal deletions and is a favorable target for attenuation of virulence Mimicking live flavivirus immunization with a noninfectious RNA vaccine Functional requirements of the yellow fever virus capsid protein Helices alpha 2 and alpha 3 of west Nile virus capsid protein are dispensable for assembly of infectious virions NS2B-3 proteinasemediated processing in the yellow fever virus structural region: in vitro and in vivo studies Signal peptidase cleavage at the flavivirus C-prM junction: dependence on the viral NS2B-3 protease for efficient processing requires determinants in C, the signal peptide, and prM Mutagenesis of the NS2B-NS3-mediated cleavage site in the flavivirus capsid protein demonstrates a requirement for coordinated processing Mutagenesis of the signal sequence of yellow fever virus prM protein: enhancement of signalase cleavage In vitro is lethal for virus production Inefficient signalase cleavage promotes efficient nucleocapsid incorporation into budding flavivirus membranes A flavivirus signal peptide balances the catalytic activity of two proteases and thereby facilitates virus morphogenesis Role of capsid anchor in the morphogenesis of Zika virus Increased expression of capsid protein in trans enhances production of singleround infectious particles by West Nile virus DNA vaccine candidate Production and characterization of vaccines based on flaviviruses defective in replication A single-dose live-attenuated Zika virus vaccine with controlled infection rounds that protects against vertical transmission e485 DENV2 Pseudoviral Particles with Unprocessed Capsid Protein Are Assembled and Infectious Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization Long-range RNA-RNA interactions circularize the dengue virus genome Essential role of cyclization sequences in flavivirus RNA replication The 5' and 3' downstream AUG region elements are required for mosquito-borne flavivirus RNA replication RNA secondary structure in the coding region of dengue virus type 2 directs translation start codon selection and is required for viral replication The capsid-coding region hairpin element (cHP) is a critical determinant of dengue virus and West Nile virus RNA synthesis Novel cis-Acting element within the capsid-coding region enhances flavivirus viral-RNA replication by regulating genome cyclization In addition to having safety and efficiency similar to those of SRIPs, they are more suitable for meeting the challenges of rapid development and large-scale deployment for emerging virus vaccines [99] .
    keywords: assembly; capsid; cps; dengue; flavivirus; particles; protein; replicon; rna; vaccines; virus
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        item: #574 of 1349
          id: cord-277547-2vim1wno
      author: Zandi, Keivan
       title: Antiviral activity of four types of bioflavonoid against dengue virus type-2
        date: 2011-12-28
       words: 4387
      flesch: 47
     summary: Anti-dengue activity of these compounds was determined at different stages of DENV-2 infection and replication cycle. Although there was no significant direct virucidal activity against DENV-2 by quercetin, continuous treatment of cells from 5 h before virus infection up to 4 days post-infection exhibited anti-dengue activity with IC 50 = 28.9 μg mL -1
    keywords: activity; cells; dengue; denv-2; infection; quercetin; replication; rna; vero; virus
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        item: #575 of 1349
          id: cord-277566-j3ehiwn9
      author: Verheije, Monique H.
       title: Mouse Hepatitis Coronavirus RNA Replication Depends on GBF1-Mediated ARF1 Activation
        date: 2008-06-13
       words: 8957
      flesch: 44
     summary: MHV RNA replication was not sensitive to BFA in MDCK cells, which are known to express the BFA-resistant guanine nucleotide exchange factor GBF1. Accordingly, individual knockdown of the Golgi-resident targets of BFA by transfection of small interfering RNAs (siRNAs) showed that GBF1, but not BIG1 or BIG2, was critically involved in MHV RNA replication.
    keywords: arf1; bfa; cells; coronavirus; expression; fig; gbf1; golgi; luciferase; membrane; mhv; p.i; protein; rcs; replication; rna; virus
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        item: #576 of 1349
          id: cord-277687-u3q36o3e
      author: Shean, Ryan C.
       title: VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank
        date: 2019-01-23
       words: 4073
      flesch: 46
     summary: handles batch submissions of multiple viruses of different types without prior knowledge of the viral species, correctly annotates RNA editing and ribosomal slippage, performs spellchecking on annotations, handles batch or individual submission of metadata, runs with a simple one-line command, and creates annotated viral sequence files for GenBank submission. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions.
    keywords: annotation; file; genbank; genome; metadata; ncbi; reference; sequence; vapid; virus
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        item: #577 of 1349
          id: cord-277830-6fsz9iy7
      author: Saikatendu, Kumar Singh
       title: Structural Basis of Severe Acute Respiratory Syndrome Coronavirus ADP-Ribose-1″-Phosphate Dephosphorylation by a Conserved Domain of nsP3
        date: 2005-11-08
       words: 6571
      flesch: 46
     summary: One of its sequence homologs, Poa1p (YBR022) from Saccharomyces cerevisiae, was recently functionally characterized as a highly specific phosphatase that removes the 1 00 phosphate group of ADP-ribose-1 00 -phosphate (Appr-1 00 -p) in the latter half of the tRNA splicing pathway in yeast (Shull et al., 2005) , hinting at a similar substrate specificity for SARS ADRP. (L-SIGN) is a receptor for severe acute respiratory syndrome coronavirus Improved methods for building protein models in electron density maps and the location of errors in these models A novel coronavirus associated with severe acute respiratory syndrome Angiotensin-converting enzyme 2: a functional receptor for SARS coronavirus Structure and mechanism of ADP-ribose-1 00 -monophosphatase (Appr-1 00 -pase), a ubiquitous cellular processing enzyme Coronaviruses Automated refinement for protein crystallography Emergence of epidemic O'nyong-nyong fever in Uganda after a 35-year absence: genetic characterization of the virus PROCHECK: a program to check the stereochemical quality of protein structures Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline SMART 4.0: towards genomic data integration Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus A biochemical genomics approach for identifying genes by the activity of their products A highly specific phosphatase from Saccharomyces cerevisiae implicated in tRNA splicing Peptidase activity of Escherichia coli aminopeptidase
    keywords: adp; adrp; conserved; domain; et al; figure; nsp3; phosphate; protein; residues; ribose; rna; sars; site; structure; yeast
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        item: #578 of 1349
          id: cord-277841-7sp8ftbc
      author: Kumari, Pratibha
       title: Potential diagnostics and therapeutic approaches in COVID-19
        date: 2020-08-12
       words: 4881
      flesch: 40
     summary: While the level of E gene confirms the presence of SARS related virus. Like most immunological diagnostic protocols, Enzyme-Linked Immunosorbent Assay (ELISA) for COVID-19 detection uses IgM and IgG antibody against nucleocapsid (N) and receptor binding domain spike proteins (S) of SARS-CoV-2.
    keywords: clinical; coronavirus; cov-2; covid-19; detection; diagnosis; infection; novel; patients; rna; sars; test; treatment; virus
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        item: #579 of 1349
          id: cord-277874-cr53ycrm
      author: Neault, N.
       title: SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence.
        date: 2020-09-03
       words: 7086
      flesch: 39
     summary: Ultimately, determining to what extent wastewater viral protein can serve as a prevalence leading indicator will require a longer study with more frequent sampling over rising and falling community prevalence in order to assess robustly. Moreover, the PEG precipitated influent solid viral RNA signal when detected did not correlate with viral RNA signal from PEG precipitated primary sludge, viral protein signal, or public health data (data not shown).
    keywords: cov-2; covid-19; influent; license; medrxiv; preprint; primary; protein; rna; samples; sars; signal; sludge; viral; wastewater
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        item: #580 of 1349
          id: cord-278055-v2ed3tei
      author: Sia, Sin Fun
       title: Pathogenesis and transmission of SARS-CoV-2 in golden Syrian hamsters
        date: 2020-05-14
       words: 5406
      flesch: 50
     summary: Contact hamsters showed the maximal mean weight loss (mean ± SD, −10.68 ± 3.42%, N=3) on 6 dpc; all animals returned to the original weight after 11 dpc (Fig. 2d) . c, Transmission of SARS-CoV-2 to naïve hamsters (N=3) that were each co-housed with one inoculated donor on 1 dpi; infectious viral load and viral RNA copy numbers detected in the nasal washes of contact hamsters were shown.
    keywords: cells; contact; cov-2; donor; dpi; fig; hamsters; nasal; rna; sars; virus
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        item: #581 of 1349
          id: cord-278081-tk7vn1v1
      author: Brooks, Wesley H.
       title: Viral Impact in Autoimmune Diseases: Expanding the “X Chromosome–Nucleolus Nexus” Hypothesis
        date: 2017-11-28
       words: 9826
      flesch: 34
     summary: In addition, CDK1 cyclin kinases have a key role in controlling nucleoli during cell cycling, and centromere complexes are generated in the nucleolus giving further importance to nucleoli in cell cycling. F1000Prime Rep The nucleolus: structure/function relationship in RNA metabolism Nucleolus and nuclear periphery: velcro for heterochromatin Proteins of the nucleolus: an introduction The nucleolus -guardian of cellular homeostasis and genome integrity Crosstalk between the nucleolus and the DNA damage response Nucleolar DNA: the host and guests Perinucleolar targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing Regulation of Epstein-Barr virus latency type by the chromatin boundary factor CTCF Alu element-containing RNAs maintain nucleolar structure and function The nucleolus under stress The multifunctional nucleolus NOPdb: nucleolar proteome database-2008 update Role of polyamine in the regulation of RNA synthesis in uterine nucleoli Assembly and disassembly of the nucleolus during the cell cycle Structure of the p53 binding domain of HAUSP/USP7 bound to Epstein-Barr nuclear antigen 1 implications for EBV-mediated immortalization Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome The proto-oncogene c-myc is a direct target of gene of Epstein-Barr virus nuclear antigen 2 Epstein-Barr virus induces cellular transcription factors to allow active expression of EBER genes by RNA polymerase III Direct activation of RNA polymerase III transcription by c-Myc c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I An overview of MYC and its interactome Autoimmune diseases and polyamines The ornithine decarboxylase gene is a transcriptional target of c-Myc c-Myc targets genes involved in cell growth, apoptosis, and metabolism Targeting ornithine decarboxylase in Myc-induced lymphomagenesis prevents tumor formation Ultrastructural changes in vitro of rat liver nucleoli in response to polyamines Relationship between polyamine accumulation and RNA biosynthesis and content during the cell cycle RNA viruses: hijacking the dynamic nucleolus Modifications of both selectivity factor and upstream binding factor contribute to poliovirus-mediated inhibition of RNA polymerase I transcription Viruses and the nucleolus: the fatal attraction Virus infection induces redistribution and membrane localization of the nuclear antigen La (SS-B): a possible mechanism for autoimmunity X chromosome inactivation and autoimmunity Nucleolin: the most abundant multifunctional phosphoprotein of nucleolus Nucleophosmin: from structure and function to disease development Increased polyamines alter chromatin and stabilize autoantigens in autoimmune diseases Noncoding RNAs and epigenetic mechanisms during X-chromosome inactivation X-inactivation profile reveals extensive variability in X-linked gene expression in females Intense correlation between protein-conjugated acrolein and primary Sjogren's syndrome Recent insights into the regulation of X-chromosome inactivation LINE-mediated retrotransposition of marked Alu sequences Plasma DNA in systemic lupus erythematosus Post-translational modifications, subcellular relocation and release in apoptotic microparticles: apoptosis turns nuclear proteins into autoantigens cGAS surveillance of micronuclei links genome instability to innate immunity STING: infection, inflammation and cancer Autoantibodies in patients with Alzheimer's disease: pathogenetic role and potential use as biomarkers of disease progression Brain polyamine levels are altered in Alzheimer's disease Polyamines in frontal cortex of patients with Downs syndrome and Frontiers in Immunology | www Alzheimer disease Acrolein is increased in Alzheimer's disease brain and is toxic to primary hippocampal cultures Brain S-adenosylmethionine levels are severely decreased in Alzheimer's disease Endogenous polyamines reduce the toxicity of soluble Aβ peptide aggregates associated with Alzheier's disease Nucleolar PARP1 expression is decreased in Alzheimer's disease: consequences for epigenetic regulation of rDNA and cognition The disappearing Barr body in breast and ovarian cancers Triple-negative breast cancer Epigenetic connections between autoimmune disorders and haematological malignancies Cancer risk in systemic lupus: an updated international multi-centre cohort study Systemic lupus erythematosus and related autoimmune diseases are antigen-driven epigenetic diseases Autoimmune disorders result from loss of epigenetic control following chromosome damage Rare X chromosome abnormalities in systemic lupus erythematosus and Sjögren's syndrome
    keywords: alu; autoimmune; barr; cell; chromosome; diseases; disruption; dna; genes; nucleolus; polyamines; rna; virus; viruses
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        item: #582 of 1349
          id: cord-278099-ypov9ha3
      author: Kumar, Surender
       title: Molecular characterization of a novel cryptic virus infecting pigeonpea plants
        date: 2017-08-03
       words: 11418
      flesch: 49
     summary: Emaravirus: A novel genus of multipartite negative strand RNA plant viruses The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses Interference with viral infection by defective RNA replicase Effects of mutations in poliovirus 3Dpol on RNA polymerase activityand on polyprotein cleavage Enzymatic activity of poliovirus RNA polymerase mutants with single amino acid changes in the conserved YGDD amino acid motif Biochemical properties of hepatitis C virus NS5B RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity Structure of Foot and mouth disease virus RNA-dependent RNA-polymerase and its complex with a template-primer RNA Site-specific mutagenesis of AIDS virus reverse transcriptase Point mutations which drastically affect the polymerization activity of encephalomyocarditis virus RNA-dependent RNA polymerase correspond to the active site of Escherichia coli DNA polymerase I Defined mutations in a small region of the brome mosaic virus 2a gene cause diverse temperature-sensitive RNA replication phenotypes I-TASSER server for protein 3D structure prediction I-TASSER: a unified platform for automated protein structure & function prediction Structure of the RNA-dependent RNA polymerase of poliovirus Evolution and taxonomy of positive strand RNA viruses: implications of comparative analysis of amino acid sequences A unified polymerase mechanism for non-homologous DNA & RNA polymerases Initiation of viral RNA-dependent RNA polymerization Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site Crystal structure of complete rhinovirus RNA polymerase suggests front-loading of protein primer A comparison of viral RNA-dependent RNA polymerases The structure of a protein primer-polymerase complex in the initiation of genome replication The palm subdomain-based active site is internally permuted in viral RNA-dependent RNA polymerases of an ancient lineage Poliovirus RNA-dependent RNA polymerase (3Dpol): It is of interest to examine if ArCV-1 RNA dependent RNA polymerase (RdRp) structurally resembles the known RdRp of the dsRNA bacteriophage Փ-6, reovirus, or with other viruses like calciviruses and picornaviruses
    keywords: amino; analysis; arcv-1; conserved; cryptic; cryptoviruses; dsrna; fig; genome; identity; motif; picornaviruses; polymerase; protein; rdrp; residues; rna; sequence; structure; thumb; virus; viruses
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        item: #583 of 1349
          id: cord-278123-mq56em3z
      author: Hasan, Mohammad Rubayet
       title: Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA
        date: 2020-07-24
       words: 3941
      flesch: 45
     summary: RNA extraction is preferable to the use of direct specimens because the extraction process concentrates and purifies the RNA targets and excludes PCR inhibitory substances. This could potentially be due to interfering substances concentrated by the SARS-CoV-2 detection by RT-qPCR without RNA extraction extraction process.
    keywords: approach; cov-2; qpcr; rna; sars; specimens; standard
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        item: #584 of 1349
          id: cord-278186-t3izmz6n
      author: Le Naour, Julie
       title: Trial watch: TLR3 agonists in cancer therapy
        date: 2020-06-02
       words: 7636
      flesch: 15
     summary: 77, 78 Finally, several studies have demonstrated that the emission of DAMPs by dying cancer cells, either spontaneously or following treatment, enables the initiation of an efficient and durable anticancer immune response through the activation of TLRs and other PRRs on immune cells of the host. 135, 136 Several laboratories have recently focused their attention on the design of innovative delivery platforms for polyI:C. Thus, Aznar and collaborators have developed a nanoplexed formulation of polyI:C complexed with polyethylenimine (BO-112), which induces the apoptotic demise of cancer cells accompanied by features of immunogenic cell death (ICD).
    keywords: acid; agonists; cancer; cell; clinical; hiltonol; immunity; immunotherapy; melanoma; patients; phase; polyi; receptor; tlr3; toll; trial; tumor; vaccine
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        item: #585 of 1349
          id: cord-278250-dwok857k
      author: Li, Heng
       title: The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites
        date: 2019-08-19
       words: 7468
      flesch: 40
     summary: [16] , and the difference varied more widely between gut viromes than between gut bacterial microbiomes in humans The phylogenetic tree on genus level of gut bacterial microbiome.
    keywords: analysis; antibiotics; bacteria; composition; dna; figure; file; gut; microbiome; monkeys; reads; results; rna; samples; treatment; virome; viruses
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        item: #586 of 1349
          id: cord-278436-job4854r
      author: Xie, Mao-Hua
       title: A phage RNA-binding protein binds to a non-cognate structured RNA and stabilizes its core structure
        date: 2009-01-09
       words: 3404
      flesch: 52
     summary: The binding capacity of MS2 CP with the Candida ribozyme was investigated by gel retardation assay, showing that the level of the MS2-ribozyme complex increased with the concentrations of MS2 protein (Fig. 1A) . Here, we report that bacteriophage MS2 coat protein (MS2 CP) bound and promoted the catalytic activity of Candida group I ribozyme.
    keywords: binding; group; ms2; protein; ribozyme; rna; structure
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        item: #587 of 1349
          id: cord-278482-j5zlismf
      author: Taylor, Raymond
       title: BCX4430 – A broad-spectrum antiviral adenosine nucleoside analog under development for the treatment of Ebola virus disease
        date: 2016-06-30
       words: 2552
      flesch: 41
     summary: Evidence from this research program would provide a sound basis for the selection of BCX4430 doses and regimens for use in an emergency response setting. In fresh hepatocytes from mice, rats, non-human primates and humans in vitro ( Fig. 1 , left panel) and after an IM injection in rats in vivo (Fig. 1 , right panel), BCX4430 is efficiently taken up into cells and converted to BCX4430 triphosphate (TP) [5] .
    keywords: bcx4430; dose; drug; infections; rna; studies; virus
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        item: #588 of 1349
          id: cord-278635-vwdxr1bl
      author: Świętoń, Edyta
       title: Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency
        date: 2020-08-28
       words: 5436
      flesch: 41
     summary: A defective interfering influenza RNA inhibits infectious influenza virus replication in human respiratory tract cells: a potential new human antiviral Cell culture-based production of defective interfering particles for influenza antiviral therapy Influenza virus DI particles: Defective interfering or delightfully interesting? Characterization of virulent and avirulent A/chicken/Pennsylvania/83 influenza A viruses: potential role of defective interfering RNAs in nature Defective viral genomes arising in vivo provide critical danger signals for the triggering of lung antiviral immunity Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients Interfering vaccine: a novel antiviral that converts a potentially virulent infection into one that is subclinical and immunizing Protection of mice from lethal influenza: evidence that defective interfering virus modulates the immune response and not virus multiplication Defective interfering influenza virus confers only short-lived protection against influenza virus disease: evidence for a role for adaptive immunity in DI virus-mediated protection in vivo Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing Defective interfering virus associated with A/Chicken/Pennsylvania/83 influenza virus Avian influenza in Poland Manual of diagnostic tests and vaccines for terrestrial animals chapter Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses Viral population analysis and minority-variant detection using short read next-generation sequencing Trimmomatic: a flexible trimmer for Illumina sequence data Fast and accurate short read alignment with Burrows-Wheeler transform The sequence alignment/map format and SAMtools VarScan: variant detection in massively parallel sequencing of individual and pooled samples Droplet digital PCR: A novel method for detection of influenza virus defective interfering particles convenient online submission • thorough peer review by experienced researchers in your field • rapid publication on acceptance • support for research data, including large and complex data types • gold Open Access which fosters wider collaboration and increased citations maximum visibility for your research: over 100M website views per year • At BMC Development and evaluation of a one-step real-time RT-PCR assay for universal detection of influenza A viruses from avian and mammal species Identification of sensitive and specific avian influenza polymerase chain reaction methods through blind ring trials organized in the European Union Pathogenesis and pathobiology of avian influenza virus infection in birds Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys Infectivity, transmission and pathogenicity of H5 highly pathogenic avian influenza clade 2344 (H5N8 and H5N2) United States index viruses in Pekin ducks and Chinese geese Different pathogenicity of two strains of clade 2.3.4.4c H5N6 highly pathogenic avian influenza viruses bearing different PA and NS gene in domestic ducks Ghedin E; INSIGHT FLU002 Study Group; INSIGHT FLU003 Study Group (2013) In: Swayne DE (ed) Diseases of poultry Influenza virus RNA polymerase: insights into the mechanisms of viral RNA synthesis Population diversity and collective interactions during influenza virus infection The defective component of viral populations Incomplete forms of influenza virus Functional characterization of naturally occurring variants of human hepatitis B virus containing the core internal deletion mutation Defective interfering viral particles in acute dengue infections Internally deleted WNV genomes isolated from exotic birds in New Mexico: function in cells, mosquitoes, and mice SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection Influenza defective interfering viral RNA is formed by internal deletion of genomic RNA Segment-specific noncoding sequences of the influenza virus genome RNA are involved in the specific competition between defective interfering RNA and its progenitor RNA segment at the virion assembly step Defective interfering influenza virus RNAs: time to reevaluate their clinical potential as broad-spectrum antivirals?
    keywords: birds; contact; dpi; high; infection; influenza; low; particles; segments; turkeys; virus
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        item: #589 of 1349
          id: cord-278647-krh63hqp
      author: Carter, Robert W
       title: A new look at an old virus: patterns of mutation accumulation in the human H1N1 influenza virus since 1918
        date: 2012-10-12
       words: 8427
      flesch: 50
     summary: Finally, the correlation between the exponential decline of H1N1-related mortalities and the linear increase in H1N1 mutations is only one of our evidences for the genetic attenuation of H1N1. The exact nature of H1N1 mutation accumulation over time has not been fully explored.
    keywords: accumulation; codon; genome; h1n1; human; influenza; lineage; mutations; pandemic; strains; virus; viruses
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        item: #590 of 1349
          id: cord-278684-txlvla0j
      author: Gonzalez–Dunia, Daniel
       title: Borna Disease Virus and the Brain
        date: 1998-01-30
       words: 13963
      flesch: 39
     summary: Arch Persistent Borna virus infection in adult hamsters Unusually high seroprevalence of Borna disease virus in clade E human immunodeficiency virus type 1-infected patients with sexually transmitted diseases in Thailand Varied prevalence of Borna disease virus infection in Arabic, thoroughbred and their cross-bred horses in Iran Developmental injury to the cerebellum following perinatal Borna disease virus infection Early and persistent abnormalities in rats with neonatally acquired Borna disease virus infection The hippocampus: functional and structural correlations Expanded nuclear magnetic resonance studies in Borna disease virus seropositive psychiatric patients and control probands Findings with nuclear magnetic resonance tomography in psychiatric patients with and without serum antibodies to the virus of Borna disease Possible significance of Borna disease for humans Borna disease virus: An immunohistological and virological study of naturally infected animals Borna disease-Neuropathology and pathogenesis Neuronal birth and death Mood disorders: Biochemical aspects Purification and properties of an intranuclear virus-specific antigen from tissue infected with Borna disease virus Mechanism of glial-guided neuronal migration in vitro and in vivo Die Bornasche Krankheit der Pferde und Schafe Ein Beitrag zur Epizootiologie der Bornaschen Krankheit beim Pferd Studies on the genetic control of resistance of black hooded rats to Borna disease Replication of Borna disease virus in rats: Age-dependent differences in tissue distribution Replication of Borna disease virus in cell cultures Effect of Borna disease virus infection on athymic rats Progressive decline in avoidance learning paralleled by inflammatory neurodegeneration in transgenic mice expressing interleukin 6 in the brain Persistent, tolerant or subacute infection in Borna disease virus-infected rats Genetic diversity of RNA viruses Local nitric oxide production in viral and autoimmune diseases of the central nervous system Viruses, neurosis and fatigue Borna disease virus p24 and p38/40 synthesized in a baculovirus expression system: Virus protein interactions in insect and mammalian cells Borna disease virus and the consumption of raw horse meat Abrogation of tolerance to a chronic viral infection Chimeric Theiler's virus with altered tropism for the central nervous system A single amino acid change determines persistence of a chimeric Theiler's virus Role of VP2 amino acid 141 in tropism of Theiler's virus within the central nervous system Ü ber eigentümliche Kerneinschlüsse der Ganglienzellen bei der enzootischen Gehirn-Rückenmarksentzündung der Pferde Untersuchungen über die pathologische Histologie, Pathogenese und postmortale Diagnose der seuchenhaften Gehirn-Rückenmarksentzündung (Bornasche Krankheit) des Pferdes
    keywords: animals; bdv; bdv infection; borna; borna disease; brain; cells; cns; disease; disease virus; disorders; evidence; expression; human; immune; infection; neurons; patients; pti; rats; specific; studies; system; virus; viruses
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        item: #591 of 1349
          id: cord-279070-cy049zbi
      author: Hewson, I.
       title: Description of viral assemblages associated with the Gorgonia ventalina holobiont
        date: 2011-12-29
       words: 2572
      flesch: 41
     summary: Non-host sequence reads within RNA virus libraries and contiguous sequences [100 bp in the DNA virus libraries were compared against the non-redundant (nr) protein database by BLASTx. The majority of matches for both DNA and RNA viral contigs and reads were to bacterial and metazoan proteins.
    keywords: contigs; dna; libraries; proteins; rna; viruses
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        item: #592 of 1349
          id: cord-279346-7del8d2p
      author: Callendret, Benoît
       title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS
        date: 2007-07-05
       words: 10753
      flesch: 39
     summary: In contrast, S protein expression could be detected in Vero E6 cells after transfection of the pCI-S construct (Fig. 1, lane 4) . In all cell lines examined, the impact of WPRE on S protein expression was consistently better than that of CTE, reflecting synergistic effects of this element on cytoplasmic mRNA levels and mRNA translation.
    keywords: cells; coronavirus; cov; cte; dna; et al; expression; fig; intron; mice; mrna; pci; plasmid; protein; rna; sars; spike; viral; virus; wpre
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        item: #593 of 1349
          id: cord-279404-u0fs6xcj
      author: Carrington, Christine V.F.
       title: Detection and Phylogenetic Analysis of Group 1 Coronaviruses in South American Bats
        date: 2008-12-17
       words: 1765
      flesch: 54
     summary: The search for the animal reservoir of the severe acute respiratory syndrome coronavirus (SARS-CoV) led to extensive surveys of coronaviruses in wild and domestic animal populations in China, resulting in the detection of a wide variety of novel bat coronaviruses (Bt-CoVs) (2) (3) (4) (5) . Additionally antibodies reactive with SARS-CoV have been detected in African bat species (8) .
    keywords: bats; cov; covs; group; sequences
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        item: #594 of 1349
          id: cord-279418-3r1ijafm
      author: Nevers, Quentin
       title: Negri bodies and other virus membrane-less replication compartments()
        date: 2020-08-21
       words: 6446
      flesch: 34
     summary: These structures often referred as viral inclusions, viral factories or viroplasms, concentrate viral proteins, nucleic acids and specific cellular factors. Other DNA viruses belonging to Herpesviridae, Adenoviridae, Parvoviridae, Polyomaviridae and Papillomaviridae families induce the formation of membrane-less assemblies inside the nucleus termed viral replication compartments (or centers), hereafter referred as VRCs [65] , which concentrate viral proteins and nucleic acids, incoming viral genomes and host proteins.
    keywords: bodies; compartments; domain; factories; formation; liquid; membrane; phase; pml; protein; replication; rna; virus; viruses
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        item: #595 of 1349
          id: cord-279623-ezax8c1u
      author: Huang, Yong
       title: Regulatory long non-coding RNA and its functions
        date: 2012-04-26
       words: 3579
      flesch: 41
     summary: The antisense transcriptomes of human cells Cascade transcription of mRNAtype long non-coding RNAs (mlonRNAs) and local chromatin remodeling Biological functions of microRNAs: a review A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response Large non-coding RNAs: missing links in cancer? RNA maps reveal new RNA classes and a possible function for pervasive transcription The majority of total nuclear-encoded nonribosomal RNA in a human cell is 'dark matter' un-annotated RNA Mining mammalian transcript data for functional long non-coding RNAs The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion A novel RNA transcript with antiapoptotic function is silenced in fragile X syndrome Oxytocin stimulates expression of a noncoding RNA tumor marker in a human neuroblastoma cell line Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness Long noncoding RNAs: insights into functions Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1 Long antisense non-coding RNAs function to direct epigenetic complexes that regulate transcription in human cells GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer Long noncoding RNAs with enhancer-like function in human cells Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatinlevel regulation Genome-wide identification of long noncoding RNAs in CD8+ T cells Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling Long, abundantly expressed non-coding transcripts are altered in cancer Evolution and functions of long noncoding RNAs The emergence of lncRNAs in cancer biology Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression Long noncoding RNAs in nervous system function and disease Complex I binding by a virally encoded RNA regulates mitochondria-induced cell death Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs A possible role for long non-coding RNA in modulating signaling pathways Protection from interferon-induced apoptosis by Epstein-Barr virus small RNAs is not mediated by inhibition of PKR Identification of long stress-induced noncoding transcripts that have altered expression in cancer A conserved long noncoding RNA affects sleep behavior in Drosophila New roles for large and small viral RNAs in evading host defences Primary structure, neural-specific expression, and dendritic location of human BC200 RNA Control of translation and mRNA degradation by miRNAs and siRNAs Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression A strategy for probing the function of noncoding RNAs finds a repressor of NFAT Long noncoding RNAs: functional surprises from the RNA world The functional role of long non-coding RNA in human carcinomas Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals )
    keywords: antisense; cancer; cell; expression; functions; gene; human; lncrnas; noncoding; transcription
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        item: #596 of 1349
          id: cord-279691-v5kpmk0b
      author: Hagemeijer, Marne C.
       title: Biogenesis and Dynamics of the Coronavirus Replicative Structures
        date: 2012-11-21
       words: 9053
      flesch: 36
     summary: [151] [152] [153] can all be applied to investigate the CoV RTCs and the membranous replicative structures at the ultrastructural level using fluorescently-tagged proteins, while EU-labeling of viral RNA in combination with correlative light-electron microscopy may provide the resolution to indisputably pinpoint the exact location of viral RNA synthesis [154] . Organelle-Like Membrane Compartmentalization of Positive-Strand RNA Virus Replication Factories Cytoplasmic Viral Replication Complexes Modification of Intracellular Membrane Structures for Virus Replication SARS-Coronavirus Replication is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum Identification of a Novel Coronavirus in Patients with Severe Acute Respiratory Syndrome A Novel Coronavirus Associated with Severe Acute Respiratory Syndrome Isolation and Characterization of Viruses Related to the SARS Coronavirus from Animals in Southern China Bats are Natural Reservoirs of SARS-Like Coronaviruses Evolving the Largest RNA Virus Genome A Contemporary View of Coronavirus Transcription Coronaviruses use Discontinuous Extension for Synthesis of Subgenome-Length Negative Strands Sequence Motifs Involved in the Regulation of Discontinuous Coronavirus Subgenomic RNA synthesis Coronavirus Minus-Strand RNA Synthesis and Effect of Cycloheximide on Coronavirus RNA Synthesis The RNA Structures Engaged in Replication and Transcription of the A59 Strain of Mouse Hepatitis Virus The Primary Structure and Expression of the Second Open Reading Frame of the Polymerase Gene of the Coronavirus MHV-A59; a Highly Conserved Polymerase is Expressed by an Efficient Ribosomal Frameshifting Mechanism Characterization of an Efficient Coronavirus Ribosomal Frameshifting Signal: Requirement for an RNA Pseudoknot Virus-Encoded Proteinases and Proteolytic Processing in the Nidovirales Processing of Open Reading Frame 1a Replicase Proteins nsp7 to nsp10 in Murine Hepatitis Virus Strain A59 Replication Functional and Genetic Analysis of Coronavirus Replicase-Transcriptase Proteins The RNA Polymerase Activity of SARS-Coronavirus nsp12 is Primer Dependent Non-Canonical RNA-Dependent RNA Superfamily 1 Helicase has RNA and DNA Duplex-Unwinding Activities with 5'-to-3' Polarity The Severe Acute Respiratory Syndrome (SARS) Coronavirus NTPase/helicase Belongs to a Distinct Class of 5' to 3' Viral Helicases Multiple Enzymatic Activities Associated with Severe Acute Respiratory Syndrome Coronavirus Helicase Human Coronavirus 229E Nonstructural Protein 13: Characterization of Duplex-Unwinding, Nucleoside Triphosphatase, and RNA 5'-Triphosphatase Activities Functional Screen Reveals SARS Coronavirus Nonstructural Protein nsp14 as a Novel Cap N7 Methyltransferase Coronavirus Nonstructural Protein 16 is a Cap-0 Binding Enzyme Possessing (Nucleoside-2'O)-Methyltransferase Activity In Vitro Reconstitution of SARS-Coronavirus mRNA Cap Methylation Molecular Mapping of the RNA Cap 2'-O-Methyltransferase Activation Interface between Severe Acute Respiratory Syndrome Coronavirus nsp10 and nsp16 Discovery of an RNA Virus 3'→5' Exoribonuclease that is Critically Involved in Coronavirus RNA Synthesis Major Genetic Marker of Nidoviruses Encodes a Replicative Endoribonuclease RNA Recognition and Cleavage by the SARS Coronavirus Endoribonuclease Infidelity of SARS-CoV Nsp14-Exonuclease Mutant Virus Replication is Revealed by Complete Genome Sequencing An RNA Proofreading Machine Regulates Replication Fidelity and Diversity RNA 3'-End Mismatch Excision by the Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein nsp10/nsp14 Exoribonuclease Complex Identification of Severe Acute Respiratory Syndrome Coronavirus Replicase Products and Characterization of Papain-Like Protease Activity Topology and Membrane Anchoring of the Coronavirus Replication Complex:
    keywords: cells; coronavirus; cov; dmvs; hepatitis; membrane; nsp3; nsp4; protein; replication; rna; rna synthesis; sars; sites; structures; synthesis; viruses
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        item: #597 of 1349
          id: cord-279841-oq25o4qr
      author: Ahlquist, Paul
       title: Viral and host determinants of RNA virus vector replication and expression
        date: 2005-03-07
       words: 2272
      flesch: 27
     summary: key: cord-279841-oq25o4qr authors: Ahlquist, Paul; Schwartz, Michael; Chen, Jianbo; Kushner, David; Hao, Linhui; Dye, Billy T. title: Viral and host determinants of RNA virus vector replication and expression date: 2005-03-07 journal: Vaccine DOI: 10.1016/j.vaccine.2004.11.005 sha: doc_id: 279841 cord_uid: oq25o4qr Positive-strand RNA viruses have proven to be valuable vectors for delivery and expression of antigens for direct vaccination of animals and vaccine production in plants. One virus that is being used as a model to study positivestrand RNA virus replication is brome mosaic virus (BMV).
    keywords: bmv; expression; host; replication; rna; virus; viruses
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        item: #598 of 1349
          id: cord-279985-de0b27nq
      author: Anraku, Itaru
       title: Kunjin replicon-based simian immunodeficiency virus gag vaccines
        date: 2008-06-19
       words: 6408
      flesch: 44
     summary: The A20-EGFP-SIV gag challenge model (Fig. 5 ) represents a new model for testing the effectiveness of T cell induction by SIV gag vaccines. The use of peptide pools covering Gag to measure T cell responses in mice has been described previously
    keywords: cells; elispot; expression; fig; gag; kunjin; memory; protein; replicon; responses; rna; siv; vaccines; virus; vlp
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        item: #599 of 1349
          id: cord-280001-y7pvj2l1
      author: Patel, Robin
       title: Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19
        date: 2020-03-26
       words: 1786
      flesch: 38
     summary: Most tests currently used for direct detection of SARS-CoV-2 identify viral RNA through nucleic acid amplification, usually using PCR. An important consideration is exactly what gets tested for viral RNA.
    keywords: patients; rna; testing; tests
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        item: #600 of 1349
          id: cord-280003-ndpuezpo
      author: Lou, Bin
       title: Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset
        date: 2020-03-27
       words: 3027
      flesch: 54
     summary: The serology characteristics and complement diagnosis value of antibody test to RNA test needs to be demonstrated. The diagnosis value of antibody test remains to be clearly demonstrated.
    keywords: antibody; author; funder; medrxiv; perpetuity; preprint
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        item: #601 of 1349
          id: cord-280048-b4dz1lnn
      author: Domingo, Esteban
       title: Viral quasispecies
        date: 2019-10-17
       words: 7969
      flesch: 31
     summary: A model for polynucleotide replication Viral replication modes in singlepeak fitness landscapes: A dynamical systems analysis Quasispecies: From Theory to Experimental Systems Nucleotide sequence heterogeneity of an RNA phage population Subclonal components of consensus fitness in an RNA virus clone Pathogenomics: Genome Analysis of Pathogenic Microbes The proportion of revertant and mutant phage in a growing population, as a function of mutation and growth rate Mutation rates among RNA viruses Correlation between mutation rate and genome size in riboviruses: mutation rate of bacteriophage Qbeta Rapid evolution of RNA genomes The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance-a review Transitions in understanding of RNA viruses: an historical perspective Viral quasispecies evolution Temporal fluctuations in HIV quasispecies in vivo are not reflected by sequential HIV isolations New insights into the HCV quasispecies and compartmentalization Mathematical Models of Quasi-Species Theory and Exact Results for the Dynamics Quasispecies: from theory to experimental systems Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase A conserved 3'5' exonuclease active site in prokaryotic and eukaryotic DNA polymerases High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants A novel 3'-end repair mechanism in an RNA virus Exonucleolytic proofreading by p53 protein Coronaviruses as DNA wannabes: a new model for the regulation of RNA virus replication fidelity Thinking Outside the Triangle: Replication Fidelity of the Largest RNA Viruses Theoretical Models of Generalized Quasispecies Alterations in cellular metabolism triggered by URA7 or GLN3 inactivation cause imbalanced dNTP pools and increased mutagenesis Deep-Sequence Identification and Role in Virus Replication of a JC Virus Quasispecies in Patients with Progressive Multifocal Leukoencephalopathy An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-Cbound viral peptides Differential Shape of Geminivirus Mutant Spectra Across Cultivated and Wild Hosts With Invariant Viral Consensus Sequences Genetic variability: the key problem in the prevention and therapy of RNA-based virus infections Quasispecies and virus Mechanisms of viral mutation Quasispecies theory and the behavior of RNA viruses Quasispecies composition and evolution of a typical Zika virus clinical isolate from Suriname Marine RNA Virus Quasispecies Are Distributed throughout the Oceans Within-Host Variations of Human Papillomavirus Reveal APOBEC Signature Mutagenesis in the Viral Genome In vivo evolution of viral virulence: switching of deformed wing virus between hosts results in virulence changes and sequence shifts PAQ: Collective behavior of viruses was documented with mutant RNA viruses resistant to nucleotide analogues.
    keywords: disease; evolution; fitness; genomes; host; mutant; mutation; population; quasispecies; rate; replication; rna; sequence; spectrum; virus; viruses
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        item: #602 of 1349
          id: cord-280130-ewqe9edq
      author: Weber, Friedemann
       title: Viral suppression of the interferon system
        date: 2007-01-27
       words: 4311
      flesch: 21
     summary: The leader protein of Theiler's virus inhibits immediate-early alpha/beta interferon production Influenza A virus NS1 protein targets poly(A)-binding protein II of the cellular 3 0 -end processing machinery Influenza virus NS1 protein inhibits pre-mRNA splicing and blocks mRNA nucleocytoplasmic transport The 3 0 -end-processing factor CPSF is required for the splicing of single-intron pre-mRNAs in vivo Human influenza viruses activate an interferon-independent transcription of cellular antiviral genes: outcome with influenza A virus is unique Cellular antiviral responses against influenza A virus are countered at the posttranscriptional level by the viral NS1A protein via its binding to a cellular protein required for the 3 0 end processing of cellular pre-mRNAS Variation in the ability of human influenza A viruses to induce and inhibit the IFN-beta pathway Stats: transcriptional control and biological impact Degradation of STAT1 and STAT2 by the V proteins of simian virus 5 and human parainfluenza virus type 2, respectively: consequences for virus replication in the presence of alpha/beta and gamma interferons The V protein of simian virus 5 inhibits interferon signalling by targeting STAT1 for proteasome-mediated degradation All four Sendai Virus C proteins bind Stat1, but only the larger forms also induce its mono-ubiquitination and degradation The V protein of human parainfluenza virus 2 antagonizes type I interferon responses by destabilizing signal transducer and activator of transcription 2 STAT3 ubiquitylation and degradation by mumps virus suppress cytokine and oncogene signaling The STAT2 activation process is a crucial target of Sendai virus C protein for the blockade of alpha interferon signaling Rinderpest virus blocks type I and type II interferon action: role of structural and nonstructural proteins STAT protein interference and suppression of cytokine signal transduction by measles virus V protein Newcastle disease virus (NDV)-based assay demonstrates interferon-antagonist activity for the NDV V protein and the Nipah virus V, W, and C proteins Nipah virus V protein evades alpha and gamma interferons by preventing STAT1 and STAT2 activation and nuclear accumulation Hendra virus V protein inhibits interferon signaling by preventing STAT1 and STAT2 nuclear accumulation Nipah virus V and W proteins have a common STAT1-binding domain yet inhibit STAT1 activation from the cytoplasmic and nuclear compartments, respectively Nuclear localization of the Nipah virus W protein allows for inhibition of both virus-and toll-like receptor 3-triggered signaling pathways Sendai virus C protein physically associates with Stat1 Measles virus suppresses interferon-alpha signaling pathway: suppression of Jak1 phosphorylation and association of viral accessory proteins, C and V, with interferon-alpha receptor complex Inhibition of interferon signaling by rabies virus phosphoprotein P: activation-dependent binding of STAT1 and STAT2 Ebola virus VP24 binds karyopherin alpha1 and blocks STAT1 nuclear accumulation Expression of hepatitis C virus proteins interferes with the antiviral action of interferon independently of PKR-mediated control of protein synthesis Expression of hepatitis C virus proteins inhibits signal transduction through the Jak-STAT pathway Herpes simplex virus 1 gene products occlude the interferon signaling pathway at multiple sites Induction of suppressor of cytokine signaling-3 by herpes simplex virus type 1 contributes to inhibition of the interferon signaling pathway A cytomegalovirus inhibitor of gamma interferon signaling controls immunoproteasome induction A cytomegaloviral protein reveals a dual role for STAT2 in IFN-{gamma} signaling and antiviral responses Vaccinia, cowpox, and camelpox viruses encode soluble gamma interferon receptors with novel broad species specificity The vaccinia virus soluble alpha/ beta interferon (IFN) receptor binds to the cell surface and protects cells from the antiviral effects of IFN Vaccinia virus-encoded cytokine receptor binds and neutralizes chicken interferon-gamma Vaccinia virus encodes a soluble type -Triphosphate RNA is the ligand for RIG-I RIG-I-mediated antiviral responses to single-stranded RNA bearing 5 0 phosphates Inhibition of retinoic acid-inducible gene-I-mediated induction of interferon-{beta} by the NS1 protein of influenza A virus The V proteins of paramyxoviruses bind the IFN-inducible RNA helicase, mda-5, and inhibit its activation of the IFN-beta promoter mda-5, but not RIG-I, is a common target for paramyxovirus V proteins Dissociation of a MAVS/ IPS-1/VISA/Cardif-IKKepsilon molecular complex from the mitochondrial outer membrane by hepatitis C virus NS3-4A proteolytic cleavage Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus Identification of the rabies virus alpha/beta interferon antagonist: phosphoprotein P interferes with phosphorylation of interferon regulatory factor 3 The pathogenic NY-1 hantavirus G1 cytoplasmic tail inhibits RIG-I-and TBK-1-directed interferon responses Role of double-stranded RNA and Npro of classical swine fever virus in the activation of monocyte-derived dendritic cells The NPro product of bovine viral diarrhea virus inhibits DNA binding by interferon regulatory factor 3 and targets it for proteasomal degradation Loss of interferon regulatory factor 3 in cells infected with classical swine fever virus involves the N-terminal protease, Npro N(pro) of classical swine fever virus is an antagonist of double-stranded RNA-mediated apoptosis and IFN-alpha/beta induction Human papillomavirus 16 E6 oncoprotein binds to interferon regulatory factor-3 and inhibits its transcriptional activity Functional analysis of human herpesvirus 8-encoded viral interferon regulatory factor 1 and its association with cellular interferon regulatory factors and p300 Unique properties of a second human herpesvirus 8-encoded interferon regulatory factor (vIRF-2) Inhibition of interferon signaling by the Kaposi's sarcoma-associated herpesvirus full-length viral interferon regulatory factor 2 protein Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor Characterization of a novel human herpesvirus 8-encoded protein, vIRF-3, that shows homology to viral and cellular interferon regulatory factors Kaposi's sarcoma-associated herpesvirus-encoded vIRF-3 stimulates the transcriptional activity of cellular IRF-3 and IRF-7 Human herpesvirus 8 encodes an interferon regulatory factor (IRF) homolog that represses IRF-1-mediated transcription NSs protein of Rift Valley Fever Virus blocks interferon production by inhibiting host gene transcription TFIIH transcription factor, a target for the Rift Valley hemorrhagic fever virus Inhibition of RNA polymerase II phosphorylation by a viral interferon antagonist Genetic evidence for an interferon-antagonistic function of rift valley fever virus nonstructural protein NSs Bunyamwera bunyavirus nonstructural protein NSs counteracts the induction of alpha/beta interferon Inhibition of host RNA polymerase IIdependent transcription by vesicular stomatitis virus results from inactivation of TFIID Inhibition of Ran guanosine triphosphatase-dependent nuclear transport by the matrix protein of vesicular stomatitis virus Vesicular stomatitis virus infection alters the eIF4F translation initiation complex and causes dephosphorylation of the eIF4E binding protein 4E-BP1 The vesicular stomatitis virus matrix protein inhibits transcription from the human beta interferon promoter VSV strains with defects in their ability to shutdown innate immunity are potent systemic anti-cancer agents The leader protein of Theiler's virus interferes with nucleocytoplasmic trafficking of cellular proteins The leader proteinase of foot-and-mouth disease virus inhibits the induction of beta interferon mRNA and blocks the host innate immune response Cytopathogenesis and inhibition of host gene expression by RNA viruses, Microbiol Classical swine fever virus interferes with cellular antiviral defense: evidence for a novel function of N(pro)
    keywords: binding; ifn; influenza; inhibition; interferon; ns1; protein; rna; signaling; virus; viruses
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        item: #603 of 1349
          id: cord-280272-mn596x1p
      author: Akhrymuk, Ivan
       title: Magnetic Nanotrap Particles Preserve the Stability of Venezuelan Equine Encephalitis Virus in Blood for Laboratory Detection
        date: 2020-01-28
       words: 6557
      flesch: 44
     summary: However, despite the existence of the above-mentioned obstacles, we observed efficient separation of VEEV viral particles from blood by NT particles at various temperature and humidity conditions. NT particles have previously been shown to capture and enrich multiple pathogens including respiratory syncytial virus, influenza virus, coronavirus, and Rift Valley fever virus.
    keywords: blood; capsid; cn3080; conditions; detection; figure; particles; protein; rna; samples; temperature; time; veev; virus
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        item: #604 of 1349
          id: cord-280427-smqc23vr
      author: Singla, Rubal
       title: Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence
        date: 2020-09-14
       words: 7198
      flesch: 52
     summary: Various cases of human to animal transmission have also come up indicating the risk of the virus to domestic animals or pets (Oreshkova et al. 2020) . With the increasing reports of transmission of COVID-19 from infected humans to pets (like cats and dogs) and tigers and lions, there is an urgent need for public health officials to identify and investigate the possibility of virus transmission from pets to humans.
    keywords: animals; cats; cov-2; covid-19; et al; ferrets; humans; pets; rna; sars; transmission; virus
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        item: #605 of 1349
          id: cord-280616-9mwr6a4x
      author: Yang, Ying
       title: Small non-coding RNAs-based bone regulation and targeting therapeutic strategies
        date: 2017-11-15
       words: 16983
      flesch: 20
     summary: mitigates glucocorticoid induction of bone loss and fatty marrow by rescuing Runx2 acetylation Costimulatory signals mediated by the itam motif cooperate with rankl for bone homeostasis Dexamethasone promotes osteoclastogenesis by inhibiting osteoprotegerin through multiple levels miR-34a blocks osteoporosis and bone metastasis by inhibiting osteoclastogenesis and Tgif2 Wnt/b-catenin signalling in prostate cancer Down-regulation of Toll-like receptor 4 gene expression by short interfering RNA attenuates bone cancer pain in a rat model p63 regulates cell proliferation and cell cycle progression-associated genes in stromal cells of giant cell tumor of the bone Second generation sequencing of microRNA in human bone cells treated with parathyroid hormone or dexamethasone The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 Enhanced hyaline cartilage matrix synthesis in collagen sponge scaffolds by using siRNA to stabilize chondrocytes phenotype cultured with bone morphogenetic Protein-2 under hypoxia A microRNA signature for a BMP2-induced osteoblast lineage commitment program Biological functions of miR-29b contribute to positive regulation of osteoblast differentiation Diallyl trisulfide inhibits proliferation, invasion and angiogenesis of osteosarcoma cells by switching on suppressor microRNAs and inactivating of Notch-1 signaling Preventive effects of siRNA targeting PPARg gene on steroid-induced osteonecrosis in rabbits MicroRNA-16-5p controls development of osteoarthritis by targeting SMAD3 in chondrocytes microRNA-23a inhibits osteogenic differentiation of human bone marrow-derived mesenchymal stem cells by targeting LRP5 Osteoclast-derived exosomal miR-214-3p inhibits osteoblastic bone formation Healing of osteoporotic bone defects by baculovirus-engineered bone marrow-derived MSCs expressing MicroRNA sponges Aptamer-functionalized lipid nanoparticles targeting osteoblasts as a novel RNA interference based bone anabolic strategy CREB-regulated transcription coactivator 1 enhances CREB-dependent gene expression in spinal cord to maintain the bone cancer pain in mice Redundant mir-3077-5p and mir-705 mediate the shift of mesenchymal stem cell lineage commitment to adipocyte in osteoporosis bone marrow Redundant miR-3077-5p and miR-705 mediate the shift of mesenchymal stem cell lineage commitment to adipocyte in osteoporosis bone marrow TNF-a inhibits FoxO1 by upregulating miR-705 to aggravate oxidative damage in bone marrow-derived mesenchymal stem cells during osteoporosis SIRT1 promotes endometrial tumor growth by targeting SREBP1 and lipogenesis Biochemical principles of small RNA pathways Manifestations and mechanisms of stem cell aging Stabilization and enhancement of the antiapoptotic activity of mcl-1 by TCTP Loss of androgen-regulated MicroRNA 1 activates SRC and promotes prostate Cancer bone metastasis Development of resistance to chemotherapeutic drugs in human osteosarcoma cell lines largely depends on up-regulation of Clusterin/Apolipoprotein MiR-26a inhibits stem cell-like phenotype and tumor growth of osteosarcoma by targeting Jagged1 Toxicity of cationic lipids and cationic polymers in gene delivery MiR-133 is involved in estrogen deficiency-induced osteoporosis through modulating osteogenic differentiation of mesenchymal stem cells Tumour invasion and metastasis initiated by microRNA-10b in breast cancer Nanostructural materials increase mineralization in bone cells and affect gene expression through miRNA regulation An anti-insulin-like growth factor I receptor antibody that is a potent inhibitor of cancer cell proliferation Local delivery of siRNA using a biodegradable polymer application to enhance BMP-induced bone formation From estrogen-centric to aging and oxidative stress: a revised perspective of the pathogenesis of osteoporosis Pathophysiology of osteoarthritis Bone biology and anabolic therapies for bone: current status and future prospects Osteoclast-derived activity in the coupling of bone formation to resorption Intrathecal delivery of PDGF produces tactile allodynia through its receptors in spinal microglia Mechanisms of gene silencing by double-stranded RNA Strontium eluting nanofibers augment stem cell osteogenesis for bone tissue regeneration Identification of miR-194-5p as a potential biomarker for postmenopausal osteoporosis Targeted disruption of the Stat1 gene in mice reveals unexpected physiological specificity in the JAK-STAT signaling pathway MicroRNAs: key players in carcinogenesis and novel therapeutic targets EMT, CTCs and CSCs in tumor relapse and drugresistance Macro view of microRNA function in osteoarthritis Chemerin neutralization blocks hematopoietic stem cell osteoclastogenesis Designing functional siRNA with reduced off-target effects Endothelial NOS, estrogen receptor b, and HIFs cooperate in the activation of a prognostic transcriptional pattern in aggressive human prostate cancer Suppression of bone formation by osteoclastic expression of semaphorin 4D P2X7-induced zeiosis promotes osteogenic differentiation and mineralization of postmenopausal bone marrow-derived mesenchymal stem cells Sustained localized presentation of RNA interfering molecules from in situ forming hydrogels to guide stem cell osteogenic differentiation MicroRNA function and dysregulation in bone tumors: the evidence to date Bone mesenchymal stem cells (BMSCs), originating from the bone marrow possess multiple differentiation potentials.
    keywords: bone; cancer; cells; colleagues; delivery; development; differentiation; effects; et al; expression; factor; formation; gene; growth; hsa; human; mesenchymal; metastasis; mirnas; mmu; osteoblast; osteoporosis; pathway; potential; regulation; resorption; silencing; sirna; stem; targeting; therapeutic; vitro; vivo
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        item: #606 of 1349
          id: cord-280795-wtrt13ij
      author: Han, Yu-Tsung
       title: Mutational analysis of a helicase motif-based RNA 5′-triphosphatase/NTPase from bamboo mosaic virus
        date: 2007-10-10
       words: 5837
      flesch: 43
     summary: RNA 5′-triphosphatase activity of Nsp2 Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism Brome mosaic virus 1a nucleoside triphosphatase/helicase domain plays crucial roles in recruiting RNA replication templates RNA-stimulated NTPase activity associated with yellow fever virus NS3 protein expressed in bacteria Identification of the RNA-binding sites of the 28 kDa movement protein of bamboo mosaic potexvirus Structure of the hepatitis C virus RNA helicase domain This work was supported by grants, NSC 94-2752-B-005-012-PAE, from the National Science Council, Taiwan, Republic of China. In spite of lacking explicit biochemical data, the helicase-like domain of BaMV replicase has been thought to have RNA helicase activity, which may be required for resolving intramolecular base pairing in the template RNA and/or preventing the formation of extensive base pairing between template and the nascent complementary strand during RNA replication process.
    keywords: 5′-triphosphatase; activities; activity; bamv; domain; et al; helicase; motif; protein; rna; virus
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        item: #607 of 1349
          id: cord-280941-ds6x0yym
      author: Kim, Young-Seok
       title: Chaperna-Mediated Assembly of Ferritin-Based Middle East Respiratory Syndrome-Coronavirus Nanoparticles
        date: 2018-05-17
       words: 9430
      flesch: 44
     summary: Six-week-old female BALB/c mice were immunized with 20 µg/ mouse of the RBD-FR, RBD-[SSG]-FR, or RBD protein generated as described above, or with commercially available MERS-CoV RBD protein (MERS-RBD-005P; eEnzyme) as antigen in BSL-2 facility in YLARC. [RBD-[SSG]-FR, RBD-FR, RBD, and FR (negative control)]-immunized mouse serum inhibited binding of RBD protein to hDPP4 receptor (45, 46) .
    keywords: antigens; assembly; binding; cov; figure; folding; hrid; mers; nps; protein; rbd; rbd-[ssg]-fr; receptor; rna; solubility
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        item: #608 of 1349
          id: cord-280994-w8dtfjel
      author: Peng, Qi
       title: Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus
        date: 2020-04-23
       words: 2124
      flesch: 41
     summary: Python-based system for macromolecular structure solution Mechanism of nucleic acid unwinding by SARS-CoV helicase Biochemical characterization of a 555 recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying 556 viral RNA templates Shaping the flavivirus replication complex: It is 558 curvaceous! Fast and accurate defocus estimation from 621 electron micrographs Transmission of 2019-nCoV infection from an 624 asymptomatic contact in Germany Insights into RNA 626 synthesis, capping, and proofreading mechanisms of SARS-coronavirus Viral RNA polymerase: a promising antiviral target 628 for influenza A virus One severe acute respiratory syndrome 631 coronavirus protein complex integrates processive RNA polymerase and exonuclease activities Coronaviridae and SARS-associated coronavirus strain HSR1 Clinical characteristics of 138 hospitalized patients with 2019 novel 638 coronavirus-infected pneumonia in Wuhan, China Structural basis for the inhibition of the RNA-dependent RNA polymerase 641 from SARS-CoV-2 by Remdesivir.
    keywords: cov; nsp12; nsp7; nsp8; polymerase; rna; sars
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        item: #609 of 1349
          id: cord-281020-g1muealp
      author: Belov, George A
       title: (+)RNA viruses rewire cellular pathways to build replication organelles
        date: 2012-10-01
       words: 3977
      flesch: 19
     summary: Below the roles of some common membrane-remodeling host factors identified to be required for (+)RNA virus replication are discussed. Recently, 3D electron tomography (ET) was applied to resolve the complex spatial organization of replication membranes of picorna, flavi, corona, arteri and nodaviruses [1 ,2 ,3 ,4 ,5 ,6 ].
    keywords: gbf1; lipid; membrane; organelles; protein; replication; rna; viruses
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        item: #610 of 1349
          id: cord-281124-4nhy35xn
      author: Soowannayan, Chumporn
       title: RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp
        date: 2011-08-03
       words: 5634
      flesch: 41
     summary: GAV N protein also bound to double-stranded (ds)RNAs prepared to GAV ORF1b gene regions and to bacteriophage M13 genomic ssDNA. GAV N protein binding to two dsRNAs was also assessed (Fig. 3B) .
    keywords: binding; fig; gav; gene; length; protein; rna; sequence; ssrna; virus
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        item: #611 of 1349
          id: cord-281174-3c1vue0y
      author: Greene, Shermalyn R
       title: Evaluation of the NucliSens® Basic Kit assay for detection of Norwalk virus RNA in stool specimens
        date: 2003-01-16
       words: 5258
      flesch: 39
     summary: key: cord-281174-3c1vue0y authors: Greene, Shermalyn R; Moe, Christine L; Jaykus, Lee-Ann; Cronin, Mike; Grosso, Lynell; Aarle, Pierre van title: Evaluation of the NucliSens® Basic Kit assay for detection of Norwalk virus RNA in stool specimens date: 2003-01-16 journal: J Virol Methods DOI: 10.1016/s0166-0934(02)00286-0 sha: doc_id: 281174 cord_uid: 3c1vue0y Norwalk-like viruses (NLVs) are a genetically diverse group of human caliciviruses that are the most common cause of epidemic gastroenteritis and are detected typically in stool by reverse transcription (RT)-PCR or electron microscopy (EM). Primers and probes for the NLV Basic Kit assay were based on the RNA polymerase region of the prototype NLV, Norwalk virus (NV) genome and could consistently detect 10(4) RT-PCR detectable units of NV RNA in a stool filtrate.
    keywords: amplification; assay; basic; detection; kit; nasba; nuclisens; pcr; rna
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        item: #612 of 1349
          id: cord-281254-x7ivjvti
      author: Chang, Zhijie
       title: Therapeutic and Prophylactic Potential of Small Interfering RNAs against Severe Acute Respiratory Syndrome: Progress to Date
        date: 2012-08-16
       words: 3809
      flesch: 48
     summary: This had a further beneficial Therefore, this approach may enhance the development of siRNAs effect since it appears that the combination of the different siRNAs as a therapeutic intervention for SARS-CoV. had a synergistic effect on the inhibition of SARS-CoV replication. Challenges to In Vivo Application of siRNA siRNA duplexes were maintained in the cells.
    keywords: cells; cov; gene; replication; sars; sirna; targeting
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        item: #613 of 1349
          id: cord-281281-knelqmzx
      author: Villas-Boas, Gustavo R.
       title: The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents
        date: 2020-09-07
       words: 15802
      flesch: 36
     summary: Spike features determining 'host jump' of coronaviruses SARS-CoV, MERS-CoV, and beyond The spike protein of SARS-CoV-A target for vaccine and therapeutic development Cell responses to whole SARS coronavirus in Humans T-cell immunity of SARS-CoV: Implications for vaccine development against MERS-CoV Canine coronavirus highly pathogenic for dogs Experimental infection of dogs with a novel strain of canine coronavirus causing systemic disease and lymphopenia Prolonged depletion of circulating CD4+ T lymphocytes and acute monocytosis after pantropic canine coronavirus infection in dogs Canine Coronavirus: Not Only an Enteric Pathogen Molecular characterization of HLJ-073, a recombinant canine coronavirus strain from China with an ORF3abc deletion Genotypic Characterization of Canine Coronaviruses Associated with Fatal Canine Neonatal Enteritis in the United States Natural history of a recurrent feline coronavirus infection and the role of cellular immunity in survival and disease Acquisition of macrophage tropism during the pathogenesis of feline infectious peritonitis is determined by mutations in the feline coronavirus spike protein An update on canine coronaviruses: Viral evolution and pathobiology Epstein-Barr virus-Specific CD8+ T cells that re-express CD45RA are apoptosis-resistant memory cells that retain replicative potential Decreased CCR5 expression on CD4+ T Cells of SIV-Infected sooty mangabeys Expression of lymphocytes and lymphocyte subsets in patients with severe acute respiratory syndrome Renin-angiotensin system: The unexpected flaw inside the human immune system revealed by SARS-CoV-2 Immunity after natural exposure to enteric canine coronavirus does not provide complete protection against infection with the new pantropic CB/05 strain The Thymus Is a Common Target Organ Articles Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding First Cases of Coronavirus Disease (COVID-19) in Brazil, South America (2 Genomes The origins of bioinformatics Multiple sequence alignment modeling: Despite little understanding about the pathophysiology and high pathogenicity of SARS-CoV-2 infection, early studies have shown that increased amounts of proinflammatory cytokines in serum (e.g., (interleukin IL) IL-1β, IL-6, IL-12, interferon-γ (IFNγ), Interferon-inducible protein 10 (IP10), and monocytic chemotactic protein 1 (MCP1)) were associated with pulmonary inflammation and extensive lung damage in patients with Severe Acute Respiratory Syndrome (SARS)
    keywords: analysis; bioinformatics; cell; compounds; coronavirus; cov-2; covid-19; data; development; drugs; figure; host; human; infection; patients; potential; proteins; receptor; sars; spike; studies; system; target; treatment
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        item: #614 of 1349
          id: cord-281285-5g1rw202
      author: Simonis, Alexander
       title: A comparative analysis of remdesivir and other repurposed antivirals against SARS‐CoV‐2
        date: 2020-11-03
       words: 9524
      flesch: 35
     summary: Several studies could show that entry, as shown for SARS-CoV before, depends on binding of the receptor-binding domain (RBD) (subunit S1) of the S-protein to the human angiotensin converting enzyme receptor 2 (ACE2; Hoffmann et al, 2020a; Walls et al, 2020) . intracellular release of genomic RNA Burkard et al, 2014; Ou et al, 2020) .
    keywords: activity; antiviral; cell; coronavirus; cov-2; covid-19; drugs; effects; efficacy; entry; et al; hcq; patients; rdv; replication; rna; sars; treatment; virus
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        item: #615 of 1349
          id: cord-281385-oxohdfpu
      author: Noble, Christian G.
       title: Crystal structure of dengue virus methyltransferase without S-adenosyl-L-methionine
        date: 2014-09-19
       words: 2626
      flesch: 52
     summary: -O MTase (Egloff et al., 2002) , internal RNA MTase (Dong et al., 2012) , and GTase (Bollati et al., 2009; Egloff et al., 2007; Issur et al., 2009 ). To address this question, we investigated the structural and enzymatic integrity of DENV MTase in the absence of SAM.
    keywords: mtase; rna; sam; structure
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        item: #616 of 1349
          id: cord-281565-v8s2ski3
      author: Belmonte-Reche, Efres
       title: Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2
        date: 2020-08-20
       words: 4584
      flesch: 42
     summary: To compare between virus species, we calculated the density of potential quadruplex sequences per 100000 nucleotides (Density = 100000 × ℎ ). So, we investigated the differences between them through genome alignments and found that most of the sequence versions amongst species (6 out of 8) were still able to form potential quadruplex structures even with modifications.
    keywords: 2019; dna; genome; ncov; potential; quadruplex; sequences; structures; viruses
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        item: #617 of 1349
          id: cord-281717-kzd9vvci
      author: Digard, Paul
       title: Intra-genome variability in the dinucleotide composition of SARS-CoV-2
        date: 2020-05-08
       words: 4475
      flesch: 34
     summary: Across the Coronaviridae, E genes display remarkably high variation in CpG composition, with those of SARS and SARS-CoV-2 having much higher CpG content than other coronaviruses isolated from humans. No differences in CpG composition between coronavirus genera were 104 apparent, although the gamma genus exhibited a tighter range (Fig 2B) .
    keywords: composition; coronavirus; cov-2; cpg; host; human; sars; sequences; viruses
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        item: #618 of 1349
          id: cord-282372-nmii30mc
      author: Youk, Jeonghwan
       title: Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection
        date: 2020-07-10
       words: 5127
      flesch: 42
     summary: Bulk RNA and single cell RNA sequencing datasets will be uploaded on the European Genome-Phenome Archive (EGA). We have established feeder-free, 3D hAT2 organoids (hereafter referred to as hAOs; definition of organoid is available at ref. 24 ) with defined factors which support molecular and functional identity of hAT2 cells over multiple passages, showing substantial improvements from the previous application of co-culture models [25] [26] [27] .
    keywords: alveolar; cells; cov-2; data; dpi; fig; genes; haos; hat2; human; infected; infection; rna; sars
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        item: #619 of 1349
          id: cord-282618-tjvjlyn9
      author: Luke, J M
       title: Improved antibiotic-free plasmid vector design by incorporation of transient expression enhancers
        date: 2010-11-25
       words: 6279
      flesch: 35
     summary: Electroporation for the delivery of DNA-based vaccines and immunotherapeutics: current clinical developments Improved antibiotic-free DNA vaccine vectors utilizing a novel RNA based plasmid selection system pDNAVACCultra vector family: high throughput intracellular targeting DNA vaccine plasmids Plasmid DNA vector design; impact on efficacy, safety and upstream production Generic plasmid DNA production platform incorporating low metabolic burden seed-stock and fed-batch fermentation processes Low metabolic burden plasmid production Plasmid DNA production combining antibiotic-free selection, inducible high yield fermentation, and novel autolytic purification Guidance for Industry: Considerations for Plasmid DNA Vaccines for Infectious Disease Indications Non-clinical Studies Required before First Clinical use of Gene Therapy Medicinal Products Detection of integration of plasmid DNA into host genomic DNA following intramuscular injection and electroporation Cryptic open reading frames in plasmid vector backbone sequences can provide highly immunogenic cytotoxic T-lymphocyte epitopes Translation from cryptic reading frames of DNA vaccines generates an extended repertoire of immunogenic, MHC class I-restricted epitopes Robust, vaccine-induced CD8+ T lymphocyte response against an out-of-frame epitope A similar mRNA translation efficiency increase was observed with plasmid vectors incorporating and expressing the protein kinase R-inhibiting adenoviral viral associated (VA)1 RNA.
    keywords: cell; cmv; dna; egfp; enhancer; expression; figure; htlv; human; mrna; ntc8685; plasmid; promoter; rna; sv40; transgene; va1; vector
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        item: #620 of 1349
          id: cord-282742-eyukbot7
      author: Diosa-Toro, Mayra
       title: Arthropod-Borne Flaviviruses and RNA Interference: Seeking New Approaches for Antiviral Therapy
        date: 2013-02-20
       words: 6502
      flesch: 37
     summary: Stepwise processing and subcellular localization MicroRNA genes are transcribed by RNA polymerase II Utilizing liver-specific microRNA-122 to modulate replication of dengue virus replicon Flaviviridae: The viruses and their replication Inhibition of Japanese encephalitis virus NS1 protein expression in cell by small interfering RNAs Nuclear export of microRNA precursors Markers for trans-Golgi membranes and the intermediate compartment localize to induced membranes with distinct replication functions in flavivirus-infected cells Detection of small RNAs containing the 5'-and the 3'-end sequences of viral genome during West Nile virus replication 5'-and 3'-noncoding regions in flavivirus RNA The utility of siRNA transcripts produced by RNA polymerase i in down regulating viral gene expression and replication of negative-and positive-strand RNA viruses Overview: Japanese encephalitis RNA interference modulates replication of dengue virus in Drosophila melanogaster cells Developing arbovirus resistance in mosquitoes Expression of vector-based small interfering RNA against West Nile virus effectively inhibits virus replication Hypersusceptibility to vesicular stomatitis virus infection in Dicer1-deficient mice is due to impaired miR24 and miR93 expression RNA interference inhibits yellow fever virus replication in vitro and in vivo RNA interference mediated silencing of Hsp60 gene in human monocytic myeloma cell line U937 revealed decreased dengue virus multiplication Six RNA viruses and forty-one hosts: Viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems Structural proteomics of dengue virus Impact of microRNAs for pathogenesis and treatment of hepatitis C virus infection Identification of microRNAs of the herpesvirus family Effective inhibition of Japanese encephalitis virus replication by small interfering RNAs targeting the NS5 gene siRNA and innate immunity Functional microRNA generated from a cytoplasmic RNA virus Dengue virus type 2 infections of Aedes aegypti are modulated by the mosquito's RNA interference pathway Evidence that RNA silencing functions as an antiviral defense mechanism in fungi Inhibition of genes expression of SARS coronavirus by synthetic small interfering RNAs Efficient and targeted delivery of siRNA in vivo Endogenous antiviral mechanisms of RNA interference: A comparative biology perspective Viruses, microRNAs, and host interactions Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus Flavivirus cell entry and membrane fusion Induction of the cellular microRNA, Hs_154, by West Nile virus contributes to virusmediated apoptosis through repression of antiapoptotic factors Cellular microRNAs inhibit replication of the H1N1 influenza A virus in infected cells Inhibition of dengue virus infections in cell cultures and in AG129 mice by a small interfering RNA targeting a highly conserved sequence Molecular mechanisms of flavivirus membrane fusion Targeted delivery of small interfering RNA to human dendritic cells to suppress dengue virus infection and associated proinflammatory cytokine production RNA interference targeted to the conserved dimerization initiation site (DIS) of HIV-1 restricts virus escape mutation Suppression of hepatitis C virus replicon by RNA interference directed against the NS3 and NS5B regions of the viral genome How innate immune mechanisms contribute to antibodyenhanced viral infections West Nile virus: The complex biology of an emerging pathogen Recent developments in understanding dengue virus replication Ecology and geographical expansion of Japanese encephalitis virus Genome cyclization as strategy for flavivirus RNA replication RNA silencing as a plant immune system against viruses Water-related diseases. The genus Flavivirus of the family Flaviviridae comprises more than 70 enveloped RNA viruses and depending on the virus can cause disease and mortality in humans and animals.
    keywords: cells; denv; et al; flaviviruses; gene; genome; host; infection; mirnas; replication; rna; rnai; sirna; virus
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        item: #621 of 1349
          id: cord-282764-d9x1wii6
      author: Chang, Chia-Yin
       title: Influence of intron and exon splicing enhancers on mammalian cell expression of a truncated spike protein of SARS-CoV and its implication for subunit vaccine development
        date: 2006-02-20
       words: 4832
      flesch: 44
     summary: Therefore, several different strategies for improving S TR2 protein expression in mammalian cells were investigated in this report, including intron addition and the application of exon splicing enhancers. As the intron and its splicing out was known to enhance each step of RNA metabolism, including transcription, poly(A) tail addition, mRNA exportation, translation, and translated protein stability [12] , hence we first studied the intron-enhancing effect on S TR2 protein expression.
    keywords: cells; cho; eda; expression; fig; intron; protein; rna; tr2
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        item: #622 of 1349
          id: cord-283097-rlf5nv5q
      author: Ganar, Ketan
       title: Newcastle disease virus: Current status and our understanding
        date: 2014-05-12
       words: 8620
      flesch: 35
     summary: A single amino acid change, Q114R, in the cleavage-site sequence of Newcastle disease virus fusion protein attenuates viral replication and pathogenicity Newcastle Disease and Related Avian Paramyxoviruses Entry of Newcastle disease virus into the host cell: role of acidic pH and endocytosis Antitumor effects of Newcastle disease virus in vivo: local versus systemic effects Vaccination with Newcastle disease virus vectored vaccine protects chickens against highly pathogenic H7 avian influenza virus Molecular evolution of the Newcastle disease virus matrix protein gene and phylogenetic relationships among the paramyxoviridae The fusion promotion activity of the NDV HN protein does not correlate with neuraminidase activity The attachment function of the Newcastle disease virus hemagglutinin-neuraminidase protein can be separated from fusion promotion by mutation Isolation of Newcastle disease virus from a non-avian host (sheep) and its implications A single amino acid substitution in the hemagglutinin-neuraminidase of Newcastle disease virus results in a protein deficient in both functions Prostate-specific antigen-retargeted recombinant Newcastle disease virus for prostate cancer virotherapy High genetic diversity of Newcastle disease virus in poultry in West and Central Africa: cocirculation of genotype XIV and newly defined genotypes XVII and XVIII RNA editing in Newcastle disease virus Exploiting tumor-specific defects in the interferon pathway with a previously unknown oncolytic virus Detection of an interaction between the HN and F proteins in Newcastle disease virus-infected cells Mutational analysis of heptad repeats in the membrane-proximal region of Newcastle disease virus HN protein Avian influenza and Newcastle disease Two factors, IRF1 and KBF1/NF-kappa B, cooperate during induction of MHC class I gene expression by interferon alpha beta or Newcastle disease virus Prevalence of avian paramyxovirus type 1 in Mallards during autumn migration in the western Baltic Sea region Alternative mechanisms of interaction between homotypic and heterotypic parainfluenza virus HN and F proteins Structural comparison of the cleavage-activation site of the fusion glycoprotein between virulent and avirulent strains of Newcastle disease virus Use of reverse genetics to enhance the oncolytic properties of Newcastle disease virus Newcastle disease virus: A 15-year follow-up of AJCC stage III malignant melanoma patients treated postsurgically with Newcastle disease virus (NDV) oncolysate and determination of alterations in the CD8T cell repertoire Incorporation of host complement regulatory proteins into Newcastle disease virus enhances complement evasion Newcastle disease virus as a vaccine vector for humans Recombinant Newcastle disease virus expressing a foreign viral antigen is attenuated and highly immunogenic in primates Nonsegmented negative-strand viruses as vaccine vectors The rule of six, a basic feature for efficient replication of Sendai virus defective interfering RNA Newcastle disease virus may enter cells by caveolae-mediated endocytosis Optimization of human immunodeficiency virus gag expression by newcastle disease virus vectors for the induction of potent immune responses Newcastle disease virus as an antineoplastic agent The oncolytic activity of Newcastle disease virus in clear cell renal carcinoma cells in normoxic and hypoxic conditions: the interplay between von Hippel-Lindau and interferon-beta signaling Nucleotide sequence of the gene encoding the matrix protein of Newcastle disease virus Complete genome sequence of a Newcastle disease virus strain isolated from broiler breeder flocks in China Genomic characterisation of a lentogenic Newcastle disease virus strain HX01 isolated from sick pigs in China Molecular epidemiology of Newcastle disease viruses in Vietnam Fusion deficiency induced by mutations at the dimer interface in the Newcastle disease virus hemagglutinin-neuraminidase is due to a temperature-dependent defect in receptor binding Newcastle disease virus fusion and haemagglutinin-neuraminidase proteins contribute to its macrophage host range A single immunization with soluble recombinant trimeric hemagglutinin protects chickens against highly pathogenic avian influenza virus H5N1 Third genome size category of avian paramyxovirus serotype 1 (Newcastle disease virus) and evolutionary implications Complete nucleotide sequence of Newcastle disease virus: evidence for the existence of a new genus within the subfamily Paramyxovirinae Virulence of Newcastle disease virus is determined by the cleavage site of the fusion protein and by both the stem region and globular head of the haemagglutininneuraminidase protein Localization of a domain on the paramyxovirus attachment protein required for the promotion of cellular fusion by its homologous fusion protein spike Characterization of Newcastle disease viruses isolated from cormorant and gull species in the United States in 2010 Newcastle disease virus, a host range-restricted virus, as a vaccine vector for intranasal immunization against emerging pathogens Newcastle disease virus-vectored vaccines expressing the hemagglutinin or neuraminidase protein of H5N1 highly pathogenic avian influenza virus protect against virus challenge in monkeys Virulence of Newcastle disease virus: what is known so far?
    keywords: amino; disease; disease virus; et al; fusion; gene; ndv; newcastle; newcastle disease; protein; recombinant; replication; rna; vaccine; virulence; virus
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        item: #623 of 1349
          id: cord-283132-rfw8njpo
      author: Olsen, Christopher W.
       title: A review of feline infectious peritonitis virus: molecular biology, immunopathogenesis, clinical aspects, and vaccination
        date: 1993-07-31
       words: 13951
      flesch: 29
     summary: The data presented by Scott et al. indicate that the ability of the vaccine to protect cats against experimental challenge is dependent upon the strain and particularly the dose of challenge virus. Similar correlations between host resistance to virus infection in vivo and intrinsic resistance (Morahan, et al., 1985 ) ofmacrophages to infection in vitro have been documented for several other virus families (Mogensen, 1985) .
    keywords: antibodies; antibody; antigenic; cats; cell; coronavirus; disease; enhancement; et al; fecv; feline; fipv; human; infection; mhv; mrna; pedersen; peritonitis; protein; replication; rna; scott; sequence; tgev; virus
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        item: #624 of 1349
          id: cord-283168-kl1hoa1x
      author: Farkas, Tibor
       title: Molecular detection of novel picornaviruses in chickens and turkeys
        date: 2011-12-13
       words: 4036
      flesch: 49
     summary: However, RdRps of RNA viruses because of their common evolutionary origin share several conserved motifs. Indeed, using P289/P290 for the detection of caliciviruses in several previous studies resulted in the unintentional detection of RNA viruses including rotavirus, porcine kobuvirus and astrovirus
    keywords: chicken; genus; picornaviruses; rna; samples; sequences; turkey; viruses
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        item: #625 of 1349
          id: cord-283346-0v4b6do2
      author: Ansari, Abdul Wahid
       title: Host chemokine (C-C motif) ligand-2 (CCL2) is differentially regulated in HIV type 1 (HIV-1)-infected individuals
        date: 2006-08-17
       words: 4357
      flesch: 41
     summary: Genes up-regulated in the viremic state, in particular CCL2, presumably serve as potential enhancing factors in HIV-1 replication, represented by high viral load in HIV-1 viremic patients. In this study, we report that HIV-1 viremic patients show an altered expression of key inflammatory cytokines and chemokines as compared with aviremic individuals.
    keywords: ccl2; cells; expression; genes; hiv-1; host; infection; patients; rna; viremic
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        item: #626 of 1349
          id: cord-283411-40ojqv1y
      author: Ben-Shmuel, Amir
       title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities
        date: 2020-09-10
       words: 1176
      flesch: 46
     summary: 283 International journal of infectious diseases : IJID : official publication of the International Society for 284 Infectious Diseases Detection of airborne severe 286 acute respiratory syndrome (SARS) coronavirus and environmental contamination in SARS outbreak 287 units. In this study, viral RNA contamination was found in 46% of the surface and air samples.
    keywords: contamination; patients; sars
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        item: #627 of 1349
          id: cord-283439-hqdq2qrh
      author: Rahman, Mohammad Tariqur
       title: Can Zn Be a Critical Element in COVID-19 Treatment?
        date: 2020-05-26
       words: 5258
      flesch: 44
     summary: Zinc is widely distributed in human tissues, where virtually all Zn is present in intracellular compartments such as the nucleus (30-40%), cytosol, and other organelles and specialized vesicles (50%), and the rest is bound with cell membrane proteins On March 11, 2020 , the World Health Organization (WHO) declared Coronavirus Disease 2019 (COVID-19) outbreak as pandemic caused by another member of the Coronaviridae family-SARS-CoV-2. SARS-CoV-2 primarily infects cells of the small air sacs known as alveoli consisting of alveolar cells and alveolar macrophages.
    keywords: cells; chloroquine; coronavirus; cov-2; covid-19; hydroxychloroquine; infection; patients; proteins; replication; rna; sars; treatment; zinc
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        item: #628 of 1349
          id: cord-283590-xvnv17zy
      author: Chen, Dabiao
       title: Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report
        date: 2020-03-05
       words: 1506
      flesch: 40
     summary: Oropharyngeal swab tests of SARS-CoV-2 RNA were performed repeatedly for surveillance (Table 1) . Given the possibility of recurrently positive SARS-CoV-2 RNA in the clinical course and to reduce the risk of transmission in other COVID-19 cases, we suggest that: (1) both nasopharyngeal and oropharyngeal swabs test for SARS-CoV-2 RNA should be performed to reduce the false-negative rate.
    keywords: covid-19; national; rna; sars; test
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        item: #629 of 1349
          id: cord-283880-lrrkuist
      author: Kumar, Arvind
       title: Evolution of selective-sequencing approaches for virus discovery and virome analysis
        date: 2017-07-15
       words: 5937
      flesch: 20
     summary: The section below briefly describe different sequencing platforms, their advantages and disadvantages for virus metagenomics based virus identification and virome analysis. To avoid this, several groups developed a positive selection approach for enriching samples for viruses of a defined taxonomic group (family, genus and species) based on DNA microarray (Gardner et al., 2010; Palacios et al., 2007; Wang et al., 2002) .
    keywords: acids; analysis; approach; discovery; dna; et al; human; identification; metagenomics; new; novel; samples; sequences; sequencing; virome; virus; viruses
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        item: #630 of 1349
          id: cord-283895-1p5uog38
      author: Trottier, J.
       title: Post-lockdown detection of SARS-CoV-2 RNA in the wastewater of Montpellier, France
        date: 2020-07-09
       words: 1929
      flesch: 46
     summary: Next, we evaluated the relative efficiency of RNA extraction and RT-qPCR reaction for each sample by adding 10 7 copies of synthetic Ebo Std RNA before RNA extraction. RNA extraction using the NucleoSpin RNA Virus kit (Macherey-Nagel) and RT-qPCR was performed on 10 µl of purified RNA using the TaqPath One-Step RT-qPCR, CG master mix (ThermoFisher Scientific).
    keywords: covid-19; primer; rna; sars; wastewater
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        item: #631 of 1349
          id: cord-283998-whwksoxt
      author: Tannock, Gregory A.
       title: The RNA of human coronavirus OC-43
        date: 1977-12-31
       words: 3982
      flesch: 47
     summary: (1975) reported that RNA complexes from the porcine coronaviruses TGEV and HEV were degraded if extracted by SDS lysis at temperatures above 60, as has been noted for the RNAs of Retroviridae (Duesberg, 1968 ). RNA extraction.
    keywords: complex; fig; method; phenol; rna; sds; virus
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        item: #632 of 1349
          id: cord-284076-087oltss
      author: Patel, Deendayal
       title: Peptide-conjugated morpholino oligomers inhibit porcine reproductive and respiratory syndrome virus replication
        date: 2007-10-04
       words: 7779
      flesch: 50
     summary: PPMO sequences and target site locations in the PRRSV genome are specified in Table 1 and depicted schematically in Fig. Pairs of DNA oligonucleotides corresponding to PPMO target sequence in PRRSV were duplexed and subcloned upstream of luciferase coding sequence in a T7 promoter-containing reporter plasmid, pCiNeoLuc, as described previously (Zhang et al., 2006) .
    keywords: 5hp; 6p1; cells; et al; inhibition; ppmo; prrsv; replication; rna; sequence; study; target; treatment; virus
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        item: #633 of 1349
          id: cord-284118-z8zwjvbu
      author: Baczko, Knut
       title: Measles virus gene expression in subacute sclerosing panencephalitis
        date: 1984-10-31
       words: 3142
      flesch: 51
     summary: Several immunological investigations have demonstrated that the majority of SSPE patients do not mount an immune response to measles virus M protein (Hall and Choppin, 1979; This interpretation is further supported by studies of non-productive cell lines which, although persistently infected with SSPE viruses, do not express measles virus M protein (Lin and Thormar, 1980; Machamer et al., 1981; Carter et al., 1983a) .
    keywords: brain; measles; protein; rna; virus
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        item: #634 of 1349
          id: cord-284156-btb4oodz
      author: Liu, Yiliu
       title: Host and Viral Modulation of RIG-I-Mediated Antiviral Immunity
        date: 2017-01-03
       words: 7075
      flesch: 23
     summary: ISGF3 then translocates to the nucleus and coordinates the transcription of hundreds of ISGs including RIG-I, thus generating an amplifying loop leading to the accumulation of RIG-I during several types of infections (8) (Figure 1B ). On the other hand, some viruses encode enzymes that directly deubiquitinate RIG-I. For instance, KSHV encoded deubiquitinase ORF64 cleaves Lys63-ubiquination chains on CARDs, blocks CARDs interaction between RIG-I and MAVS, thereby downregulating RIG-I signaling (105) .
    keywords: activation; binding; cards; interferon; mavs; protein; recognition; regulation; rig; rna; signaling; trim25; type; ubiquitination; virus; viruses
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        item: #635 of 1349
          id: cord-284549-edliu3it
      author: Zhou, Hui
       title: Hepatitis C Virus NS2 Protein Suppresses RNA Interference in Cells
        date: 2019-11-27
       words: 4710
      flesch: 54
     summary: 1A , HCV NS2 protein can effectively restore the expression of RNAi-silenced EGFP (lane 4). Our results showed that the reversal effect of EGFP silencing could be observed at 48 hpt (Fig. 2C) , indicating that the VSR activity was dependent on the expression level of HCV NS2 protein.
    keywords: cells; dsrna; egfp; fig; hcv; ns2; protein; rnai; sirna
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        item: #636 of 1349
          id: cord-284609-1q75zw6b
      author: King, Andrew M.Q.
       title: Recombination in RNA
        date: 1982-07-31
       words: 4069
      flesch: 45
     summary: RNAase T1 fingerprints of virus RNA, prepared from representatives of each recombinant type, confirmed the approximate crossover sites that had been deduced from the inheritance of proteins. RNAase Tl fingerprints of virus RNA, prepared from representatives of each recombinant type, confirmed the approximate crossover sites that had been deduced from the inheritance of proteins.
    keywords: parent; polypeptides; recombination; ret; rna; temperature; virus
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        item: #637 of 1349
          id: cord-284707-72vx11aq
      author: Leibowitz, Julian L.
       title: Synthesis of virus-specific RNA in permeabilized murine coronavirus-infected cells
        date: 1988-09-30
       words: 5510
      flesch: 45
     summary: 1. Determination of pH optimum for MHV RNA polymerase activity in permeabilized cells. Replicate cultures were assayed for MHV RNA polymerase activity using the original formulation of buffer B (33 mM NH&I, 5 mM NaCI, 20 mM KCI, 4.5 mM MgCIP, as described under Materials and Methods with the exception that the pH was varied between 7.0 and 8.4 among the replicate cultures.
    keywords: a/.; activity; cells; mhv; polymerase; rna; synthesis; system; virus
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        item: #638 of 1349
          id: cord-284933-flbibrcm
      author: Kim, Jong-Oh
       title: Characterization of the Transcriptome and Gene Expression of Brain Tissue in Sevenband Grouper (Hyporthodus septemfasciatus) in Response to NNV Infection
        date: 2017-01-13
       words: 4266
      flesch: 48
     summary: To better understand the infection mechanism of NNV, we performed the transcriptome analysis of sevenband grouper brain tissue, the main target of NNV infection. In this study, several kinds of lectins were found to be highly induced in sevenband grouper brain tissue by NNV infection, such as C-type lectins (CTLs), galectins, fucolectin, and mannose-binding lectin.
    keywords: analysis; grouper; infection; nnv; protein; sevenband; transcriptome; transcripts; unigenes; virus
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        item: #639 of 1349
          id: cord-284941-wfn0pnev
      author: Samal, S.K.
       title: Paramyxoviruses of Animals
        date: 2008-07-30
       words: 4951
      flesch: 38
     summary: The family Paramyxoviridae contains a large number of viruses of animals (Table 1) , including a number of major animal pathogens (such as Newcastle disease virus (NDV), canine distemper virus, and rinderpest virus), zoonotic pathogens (such as Hendra and Nipah viruses), and a number of somewhat obscure viruses whose natural histories are poorly understood. Interestingly, the type of disease caused by Newcastle disease virus can vary, depending on the strain of the virus.
    keywords: animal; bovine; disease; gene; parainfluenza; paramyxoviruses; protein; rna; vaccines; virus
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        item: #640 of 1349
          id: cord-285159-gytebbua
      author: Eydoux, Cecilia
       title: A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex
        date: 2020-07-07
       words: 3620
      flesch: 51
     summary: Picogreen kinetic assay was based on polymerase activity of SARS nsp12 in complex with nsp7L8, which catalyzed the reaction using a poly (A) template and uridine triphosphate (UTP). The current Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic revealed a new pathogen whose RNA synthesis machinery is highly (>96% aa identity) homologous to SARS-CoV.
    keywords: assay; concentration; cov; nsp12; nsp7l8; rna; sars
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        item: #641 of 1349
          id: cord-285262-690kpupt
      author: Imre, Gergely
       title: The involvement of regulated cell death forms in modulating the bacterial and viral pathogenesis
        date: 2020-01-27
       words: 13248
      flesch: 26
     summary: Caspase-2, along with caspase-1 plays a significant role in Brucella abortus and Brucella suis induced cell death (Bronner et al., 2013; Chen et al., 2011) . This chapter discusses the current advances in the research of cell death signaling with regard to viral and bacterial infections and describes the network of the cell death initiating molecular mechanisms that selectively recognize pathogen associated molecular patterns.
    keywords: activation; apoptosis; apoptotic; bacterial; caspase-8; cell; cell death; death; domain; et al; host; human; infected; infection; inflammasome; macrophages; membrane; mice; necroptosis; nlrp3; pathogen; pathway; protein; pyroptosis; response; ripk3; signaling; virus
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        item: #642 of 1349
          id: cord-285290-l7mnq4yb
      author: Warner, Katherine Deigan
       title: Principles for targeting RNA with drug-like small molecules
        date: 2018-07-06
       words: 7569
      flesch: 40
     summary: Inspection of well-researched classic reviews on RNA-targeted small molecules reveals that, up to 2012, efforts to find small-molecule ligands for RNAs mostly identified highly basic (and thus positively charged under physiological conditions) and planar molecules capable of intercalation between and stacking on RNA bases [20] [21] Strong proof of principle for RNA-targeted drugs has been provided by experiments and clinical trials using antisense oligonucleotides (several of which have gained regulatory approval), as well as preclinical studies with synthetic RNAs that redirect the cellular RNA interference (RNAi) machinery or that activate CRISPR-based systems 10, 11, [13]
    keywords: binding; content; drug; fig; human; information; ligand; molecules; protein; rna; rnas; sites; structure; target; targeting
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        item: #643 of 1349
          id: cord-285330-td4vr0zv
      author: Mohammadi, Ali
       title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus
        date: 2015-11-12
       words: 3162
      flesch: 53
     summary: Molecular analysis of the 793/B serotype of infectious bronchitis virus in Great Britain Studies on avian viral infections in Iran Immunohistochemistry for detection of avian infectious bronchitis virus strain M41 in the proventriculus and nervous system of experimentally infected chicken embryos Re-excretion of infectious bronchitis virus in chickens induced by cyclosporin Pathogenesis and tissue distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/b serotype) in experimentally infected broiler chickens Isolation and identification of a new isolate of avian infectious bronchitis virus IRFIBV32 and a study of its pathogenicity Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens Infectious bronchitis Detection of infectious bronchitis virus strain N1/88 from the oviduct and feces of experimentally infected vaccinated and unvaccinated hens LNA probe-based real-time RT-PCR for the detection of infectious bronchitis virus from the oviduct of unvaccinated and vaccinated laying hens Detection the 4/91 strain of infectious bronchitis virus in testicular tissue from experimentally infected rooster by reverse transcription-polymerase chain reaction Virulent avian infectious bronchitis virus, People's Republic of China Pathogenicity of infectious bronchitis virus isolates from Ontario chickens Detection of infectious bronchitis virus by real-time reverse transcriptase-polymerase chain reaction and identification of a quasispecies in the beaudette strain The immunohistochemistry study of lesions due to avian infectious bronchitis (serotype 4/91) on different tissues in specific pathogen free chicks Establishment of persistent avian infectious bronchitis virus infection in antibodyfree and antibody-positive chickens A simple method of estimating fifty percent endpoint Isolation and identification of infectious bronchitis viruses in chickens in Iran Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate… 323 Acknowledgments The authors extend thanks to the School of Veterinary Medicine, Shiraz University, for providing the necessary facilities and financial support to carry out this study. This disease is caused by infectious bronchitis virus (IBV), a member of the family Coronaviridae (order Nidovirales) and
    keywords: bronchitis; dpi; ibv; pcr; rna; trachea; virus
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        item: #644 of 1349
          id: cord-285505-8norumv6
      author: Vere Hodge, R. Anthony
       title: Meeting report: 27th International conference on antiviral research, in Raleigh, NC, USA
        date: 2014-09-16
       words: 10298
      flesch: 57
     summary: These are followed by brief summaries of the keynote addresses and the three mini-symposia on 'Hepatitis B virus', 'Research Triangle Park' and 'Challenges in HIV infection, treatment and prevention'. Although this patient continues to have no sign of HIV infection, this is hardly a viable treatment option for most HIV-infected patients.
    keywords: activity; antiviral; cells; dna; drug; hbv; hiv; infection; nucleotide; phase; polymerase; prodrug; replication; research; rna; studies; tdf; therapy; treatment; trial; usa; virus
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        item: #645 of 1349
          id: cord-285676-4kgy20o9
      author: de Vries, Antoine A.F.
       title: The Genome Organization of the Nidovirales: Similarities and Differences between Arteri-, Toro-, and Coronaviruses
        date: 1997-02-28
       words: 8011
      flesch: 43
     summary: The polymerase in its labyrinth: Mechanisms and implications of RNA recombination Recombination between nonsegmented RNA genomes of murine coronaviruses High-frequency RNA recombination of murine coronaviruses In vivo RNA-RNA recombination of coronavirus in mouse brain Experimental evidence of recombination in coronavirus infectious bronchitis virus Fitness of RNA virus decreased by Muller's ratchet Evidence of natural recombination within the S1 gene of infectious bronchitis virus A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains Molecular cloning and sequence determination of the peplomer protein gene of feline infectious peritonitis virus type I A comparison of the genomes of FECVs and FIPVs and what they tell us about the relationships between feline coronaviruses and their evolution Molecular biology and evolution of closteroviruses: Sophisticated build-up of large RNA genomes Principles of molecular organization, expression, and evolution of closteroviruses: Over the barriers A reevaluation of the higher taxonomy of viruses based on RNA polymerases Repair and mutagenesis of the genome of a deletion mutant of the coronavirus mouse hepatitis virus by targeted RNA recombination Homologous RNA recombination allows efficient introduction of site-specific mutations into the genome of coronavirus MHV-A59 via synthetic co-replicating RNAs The primary structure and expression of the second open reading frame of the polymerase gene of the coronavirus MHV-A59; a highly conserved polymerase is expressed by an efficient ribosomal frameshifting mechanism Hemagglutinin-esterase, a novel structural protein of torovirus Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus An infectious arterivirus cDNA clone: identification of a replicase point mutation that abolishes discontinuous mRNA transcription The authors thank Drs. Protein sequence analysis identified Q 3333 /S
    keywords: cleavage; coronavirus; fig; gene; genome; kda; leader; like; mhv; pol1a; proteins; recombination; rna; sequence; transcription; virus
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        item: #646 of 1349
          id: cord-285785-29ohzeug
      author: Chen, Xiaolan
       title: Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System
        date: 2020-08-12
       words: 9699
      flesch: 42
     summary: LncRNA directly regulates MDV gene expression is another approach for chicken host to response to MD. miRNA transcriptome analysis in chicken kidneys showed 58 DE miRNAs were found and were shown to be mostly associated with immune response, catalytic activities, metabolic processes, and gene expression [119] .
    keywords: alv; analysis; avian; cell; chicken; circrnas; disease; expression; factor; genes; gga; ibdv; immune; infection; mdv; mirnas; protein; replication; response; signaling; target; virus
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        item: #647 of 1349
          id: cord-285868-fz5utxss
      author: Jheng, Jia-Rong
       title: ER stress, autophagy, and RNA viruses
        date: 2014-08-05
       words: 9417
      flesch: 25
     summary: Alteration of ER functions results from stress signals by RNA virus infection, by the exploitation of ER membrane for viral replication, rapid accumulation of viral proteins, imbalance of calcium concentration by viroporin, and the sabotage or depletion of ER membrane for viral release. the synthesis of viral protein and RNA was restored.
    keywords: activation; atf6; autophagy; cells; chop; eif2α; et al; expression; hcv; infection; ire1; kinase; membrane; pathway; phosphorylation; protein; replication; response; role; stress; upr; virus; xbp1
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        item: #648 of 1349
          id: cord-285935-5rsk6g7l
      author: Kinast, Volker
       title: Hepatitis E Virus Drug Development
        date: 2019-05-28
       words: 6651
      flesch: 42
     summary: Part I: Nucleoside analogues Sensitivity of mitochondrial transcription and resistance of RNA polymerase II dependent nuclear transcription to antiviral ribonucleosides Antiviral candidates for treating hepatitis E virus infection The RNA template channel of the RNA-dependent RNA polymerase as a target for development of antiviral therapy of multiple genera within a virus family Resistance analysis and characterization of NITD008 as an adenosine analog inhibitor against hepatitis C virus Combined treatment of adenosine nucleoside inhibitor NITD008 and histone deacetylase inhibitor vorinostat represents an immunotherapy strategy to ameliorate West Nile virus infection Adenosine Analog NITD008 Is a Potent Inhibitor of Zika Virus An adenosine nucleoside inhibitor of dengue virus Screening of novel drugs for inhibiting hepatitis E virus replication Sofosbuvir: A novel oral agent for chronic hepatitis C Pan-Genotype Hepatitis E Virus Replication in Stem Cell-Derived Hepatocellular Systems Distinct Antiviral Potency of Sofosbuvir Against Hepatitis C and E Viruses Genotype 5 Hepatitis E Virus Produced by a Reverse Genetics System Has the Potential for Zoonotic Infection Sofosbuvir and Daclatasvir Anti-Viral Therapy Fails to Clear HEV Viremia and Restore Reactive T Cells in a HEV/HCV Co-Infected Liver Transplant Recipient Chronic hepatitis E in a heart transplant patient: Sofosbuvir and ribavirin regimen not fully effective Combination therapy of sofosbuvir and ribavirin fails to clear chronic hepatitis E infection in a multivisceral transplanted patient Sofosbuvir shows antiviral activity in a patient with chronic hepatitis E virus infection Autochthonous acute hepatitis E: Treatment with sofosbuvir and ribavirin Sofosbuvir and Ribavirin Eradication of Refractory Hepatitis E in an Immunosuppressed Kidney Transplant Recipient Efficacy and safety of sofosbuvir monotherapy in patients with chronic hepatitis E-The HepNet SofE pilot study High-throughput screening (HTS) for the identification of novel antiviral scaffolds Impact of high-throughput screening in biomedical research An ethanol extract of Lysimachia mauritiana exhibits inhibitory activity against hepatitis E virus genotype 3 replication Spicatoside A derived from Liriope platyphylla root ethanol extract inhibits hepatitis E virus genotype 3 replication in vitro Inhibition of HIV-1 infection by zinc group metal compounds 2+) inhibits coronavirus and arterivirus RNA polymerase activity in vitro and zinc ionophores block the replication of these viruses in cell culture Zinc Salts Block Hepatitis E Virus Replication by Inhibiting the Activity of Viral RNA-Dependent RNA Polymerase The relationship between zinc intake and serum/plasma zinc concentration in children: A systematic review and dose-response meta-analysis Failure to respond to ribavirin despite elevated intra-erythrocyte zinc level in transplant-patients with chronic hepatitis E virus infection A screen for novel hepatitis C virus RdRp inhibitor identifies a broad-spectrum antiviral compound Biological and immunological characteristics of hepatitis E virus-like particles based on the crystal structure Structure of the hepatitis E virus-like particle suggests mechanisms for virus assembly and receptor binding Heparan sulfate proteoglycans are required for cellular binding of the hepatitis E virus ORF2 capsid protein and for viral infection The ubiquitous hammerhead ribozyme Development of a chimeric DNA-RNA hammerhead ribozyme targeting SARS virus Berzal-Herranz, A. Inhibition of hepatitis C virus replication and internal ribosome entry site-dependent translation by an RNA molecule Reduction in severity of a herpes simplex virus type 1 murine infection by treatment with a ribozyme targeting the UL20 gene RNA Targeted cleavage of hepatitis E virus 3' end RNA mediated by hammerhead ribozymes inhibits viral RNA replication Antisense Phosphorodiamidate Morpholino Oligomers as Inhibition of hepatitis E virus replication by peptide-conjugated morpholino oligomers Proteasome inhibitors: Valuable new tools for cell biologists Hepatitis E virus replication requires an active ubiquitin-proteasome system Inhibition of hepatitis E virus replication by proteasome inhibitor is nonspecific Tsg101 and the Vacuolar Protein Sorting Pathway Are Essential for HIV-1 Budding Enhanced alpha1 microglobulin secretion from Hepatitis E virus ORF3-expressing human hepatoma cells is mediated by the tumor susceptibility gene 101 ORF3 protein of hepatitis E virus is essential for virion release from infected cells A PSAP motif in the ORF3 protein of hepatitis E virus is necessary for virion release from infected cells Structure of the Tsg101 UEV domain in complex with the PTAP motif of the HIV-1 p6 protein Inhibition of HIV budding by a genetically selected cyclic peptide targeting the Gag-TSG101 interaction Potent Inhibition of Hepatitis E Virus Release by a Cyclic Peptide Inhibitor of the Interaction between Viral Open Reading Frame 3 Protein and Host Tumor Susceptibility Gene 101 Inhibition of dengue virus through suppression of host pyrimidine biosynthesis Anti-HIV-1 activity of leflunomide: A comparison with mycophenolic acid and hydroxyurea Chronic hepatitis E in heart transplant recipients Calcineurin inhibitors stimulate and mycophenolic acid inhibits replication of hepatitis E virus An Early Viral Response Predicts the Virological Response to Ribavirin in Hepatitis E Virus Organ Transplant Patients Cross Talk between Nucleotide Synthesis Pathways with Cellular Immunity in Constraining Hepatitis E Virus Replication Rocaglamide, silvestrol and structurally related bioactive compounds from Aglaia species Therapeutic suppression of translation initiation modulates chemosensitivity in a mouse lymphoma model Silvestrol Inhibits Chikungunya Virus Replication Broad-spectrum antiviral activity of the eIF4A inhibitor silvestrol against corona-and picornaviruses The natural compound silvestrol is a potent inhibitor of Ebola virus replication The natural compound silvestrol inhibits hepatitis E virus (HEV) replication in vitro and in vivo A mutation in the hepatitis E virus RNA polymerase promotes its replication and associates with ribavirin treatment failure in organ transplant recipients Proposed reference sequences for hepatitis E virus subtypes A new hepatitis E virus genotype 2 strain identified from an outbreak in Nigeria A large outbreak of Hepatitis E virus genotype 1 infection in an urban setting in Chad likely linked to household level transmission factors An outbreak of hepatitis E in an urban area of Bangladesh Abravanel, F. HEV and transfusion-recipient risk Chronic Infection With Camelid Hepatitis E Virus in a Liver Transplant Recipient Who Regularly Consumes Camel Meat and Milk Rat Hepatitis E Virus as Cause of Persistent Hepatitis after Liver Transplant Rat hepatitis E virus linked to severe acute hepatitis in an immunocompetent patient Hepatitis E virus infection Hepatitis E and pregnancy: Current state Extrahepatic manifestations of hepatitis E virus Pegylated interferon-alpha for treating chronic hepatitis E virus infection after liver transplantation Treatment of chronic hepatitis E in liver transplant recipients with pegylated interferon α-2b Three-month pegylated interferon-alpha-2a therapy for chronic hepatitis E virus infection in a haemodialysis patient European Association for the Study of the Liver.
    keywords: antiviral; cells; chronic; development; effect; hepatitis; hev; infection; patients; protein; rbv; replication; rna; study; therapy; virus
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        item: #649 of 1349
          id: cord-286103-cgky6ar6
      author: Otaki, Momoko
       title: Inhibition of measles virus and subacute sclerosing panencephalitis virus by RNA interference
        date: 2006-02-13
       words: 3541
      flesch: 42
     summary: To assess the effect of siRNA on SSPE virus replication, SSPE virus-infected cells were transfected with either synthetic siRNA or a pcPUR + U6i expression plasmid, and then cocultured with fresh Vero/SLAM cells. The results obtained clearly demonstrated that both syn-thetic and plasmid-mediated MV-L2 siRNA markedly inhibited SSPE virus replication and/or cell-to-cell spread ( Fig. 3A and B) .
    keywords: cells; mev; replication; sirna; sspe; virus
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        item: #650 of 1349
          id: cord-286149-awhnjwyc
      author: Hoon‐Hanks, L.L.
       title: Metagenomic Investigation of Idiopathic Meningoencephalomyelitis in Dogs
        date: 2017-12-02
       words: 5444
      flesch: 46
     summary: All taxonomic identifications (TAXIDs) present within MUO samples that were also present in NM samples were removed from further analysis. Next, remaining TAXIDs were compared between MUO samples.
    keywords: brain; cases; csf; disease; dna; minutes; muo; rna; samples; sequences
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        item: #651 of 1349
          id: cord-286232-jo24ia4s
      author: Hasebe, Rie
       title: Infectious entry of equine herpesvirus-1 into host cells through different endocytic pathways
        date: 2009-10-25
       words: 7002
      flesch: 45
     summary: EHV-1 entry into E. Derm cells was significantly reduced by ATP depletion and treatments with lysosomotropic agents. Enveloped virions were detected from E. Derm cells by infectious virus recovery assay after viral internalization, suggesting that EHV-1 enters E. Derm cells via energy- and pH-dependent endocytosis.
    keywords: antibodies; caveolae; cells; derm; ebmecs; endocytosis; entry; et al; infected; infection; virus
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        item: #652 of 1349
          id: cord-286243-ddpemgqt
      author: Whitaker, Amy M.
       title: APE1: A skilled nucleic acid surgeon
        date: 2018-11-30
       words: 5876
      flesch: 34
     summary: Since APE1 has roles in both disease suppression and therapeutic agent resistance, it is apparent that if APE1 DNA repair activities can be strategically regulated that the protein would be a potentially druggable target in both preventative and therapeutic treatments. During DNA repair APE1 functions as a nuclease, cleaving at select phosphodiester bonds that compose the DNA backbone.
    keywords: activity; ape1; apurinic; base; ber; cleavage; dna; endonuclease; human; polymerase; repair; rna; site
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        item: #653 of 1349
          id: cord-286298-pn9nwl64
      author: Helmy, Yosra A.
       title: The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control
        date: 2020-04-24
       words: 9320
      flesch: 44
     summary: The other third of SARS CoV-2 includes four genes (in green) that encode four structural proteins (S, M, E, N), and six accessory genes (in blue) that encode six accessory proteins (orf3a, orf6, orf7a, orf7b, orf8, and orf10). While the SARS-CoV-2 S2 subunit was conserved, the S1 subunit shares an overall 70% identity with those of bat and human SARS-CoV.
    keywords: 2019; analysis; bat; cases; china; coronavirus; cov-2; covid-19; disease; genome; human; infection; mers; novel; patients; protein; rna; sars; transmission; viruses
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        item: #654 of 1349
          id: cord-286332-cdg4im5h
      author: van Beurden, Steven J.
       title: A reverse genetics system for avian coronavirus infectious bronchitis virus based on targeted RNA recombination
        date: 2017-06-12
       words: 7008
      flesch: 49
     summary: The most important findings were that (1) murinized IBV contained the correct 5′ S gene sequence (Primer set [F] -with a forward primer located in the IBV 1b gene at a position upstream of the 1b sequence present in p-mIBV and a reverse primer located in the MHV spike gene -resulted in a detectable PCR product for mIBV, but not for IBV or p-mIBV); (2) murizined IBV contained the MHV spike gene at the location of the IBV spike gene (as both primer set [F] and [H] -each with a primer in the MHV spike gene and one in IBV gene 1b [F] or in the M gene [H] -resulted in a detectable PCR product for mIBV, but not for IBV or MHV); (3) the IBV spike gene was absent from the mIBV genome (as primer set [D] targeting the IBV spike gene resulted in a detectable PCR product for IBV, but not for mIBV or MHV(4); recombinant IBV was the result of recombination between genomic RNA from mIBV and RNA transcribed from p-IBV (as primer set [C] -with a forward primer in IBV gene 1b located upstream of the 1b sequence present in p-mIBV and a reverse primer located in the IBV spike gene -resulted in a detectable PCR product for rIBV-wt, but not for mIBV or p-IBV); (5) recombinant IBV contained the IBV spike gene at the location of the MHV-derived spike in mIBV (as both primer set [C] and primer set [E] -each with one primer in the IBV spike gene and the other in IBV ORF
    keywords: avian; bronchitis; cells; coronavirus; gene; genome; h52; ibv; lr7; mhv; mibv; ribv; rna; spike; virus
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        item: #655 of 1349
          id: cord-286343-s8n1ldol
      author: Martin, Javier
       title: Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic
        date: 2020-10-09
       words: 5931
      flesch: 44
     summary: We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations.
    keywords: concentration; cov-2; npcr; nucleotide; results; rna; samples; sars; sequences; sewage; viral; virus; wastewater
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        item: #656 of 1349
          id: cord-286352-uftl1mx5
      author: Baril, Martin
       title: The Frameshift Stimulatory Signal of Human Immunodeficiency Virus Type 1 Group O is a Pseudoknot
        date: 2003-08-15
       words: 5695
      flesch: 48
     summary: The frameshift efficiencies of the constructs containing these mutations were assessed in vitro and in cultured cells and are presented in Figure 4 (b) (see also Table 1 To provide an independent support for the pseudoknot structure in subtype MVP5180 of HIV-1 group O frameshift stimulatory signal, we made a structural probing analysis of an RNA fragment encompassing the gag/pol frameshift region of this subtype. We can thus propose that the protease of HIV-1 group O viruses could be less active than group M protease, and that group O viruses require a Gag -Pol to Gag ratio higher than that of group M members, so as to incorporate more Gag -Pol in their virions for an optimal fitness during infection.
    keywords: frameshift; group; group o; loop; pseudoknot; rna; sequence; signal; stem; structure
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        item: #657 of 1349
          id: cord-286416-8eu6wp9b
      author: Valiente-Echeverría, Fernando
       title: Viral modulation of stress granules
        date: 2012-06-14
       words: 5583
      flesch: 34
     summary: While the details on the mechanisms by which viruses elicit favorable environments in which to replicate will require further work, the sequestration of critical factors for the induction of SGs by viral proteins appears to be an increasingly studied area of research and should yield important new information on how viruses gain control over host cell biology. This observation likely indicates that viral proteins or viral RNA could locally disassemble SG to favor viral translation and this was shown to correlate with increased vRNA levels (McInerney et al., 2005) .
    keywords: assembly; cells; eif2; et al; granules; infection; protein; rna; sgs; stress; virus
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        item: #658 of 1349
          id: cord-286603-4p3t0vre
      author: Duan, Zhiqiang
       title: TMT-based quantitative proteomics analysis reveals the attenuated replication mechanism of Newcastle disease virus caused by nuclear localization signal mutation in viral matrix protein
        date: 2020-06-27
       words: 10709
      flesch: 31
     summary: Taken together, our findings demonstrate that NDV replication is closely related to the nucleocytoplasmic trafficking of M protein, which accelerates our understanding of the molecular functions of NDV M protein. These results suggested that ubiquitin ligases might participate in the nucleocytoplasmic trafficking of M protein and the assembly and budding of NDV progeny virions, but whether NDV M protein interacts with some of these ubiquitin ligasesrelated DEPs and the exact role of their interaction in NDV budding are worth to be deeply studied.
    keywords: analysis; cells; deps; expression; figure; group; host; hpi; infection; m protein; ndv; nlsm; protein; replication; rna; rss1gfp; rss1gfp group; tifa; transcription; virus
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        item: #659 of 1349
          id: cord-286711-nr6vnl9h
      author: None
       title: Other viruses causing gastroenteritis
        date: 2003-12-31
       words: 2187
      flesch: 37
     summary: key: cord-286711-nr6vnl9h authors: nan title: Other viruses causing gastroenteritis date: 2003-12-31 journal: Perspectives in Medical Virology DOI: 10.1016/s0168-7069(03)09037-2 sha: doc_id: 286711 cord_uid: nr6vnl9h Publisher Summary Besides the viruses producing the majority of human viral gastroenteritis, other viruses infect more rarely but are sometimes able to cause epidemics. Cytomegalovirus DNA level on biopsy specimens during treatment of cytomegalovirus gastrointestinal disease Cytomagalovirus colitis in AIDS: presentation in 44 patients and a review of the literature Coronaviridae HIVs and their replication Detection and characterization of bisegmented double stranded RNA viruses (Picobirnavirus) in human faecal specimes Detection and characterization of a novel bisegmented double-stranded RNA virus (Picobirnavirus) from rabbit faeces Human enteric coronaviruses: antigenic relatedness to human coronavirus OC43 and possible etiologic role in viral gastroenteritis Diarrhea and enteric emerging viruses in HIV-infected patients Enteric viruses and diarrhoea in HIV-infected patients Human immunodeficiency virus infection of enterocytes and mononuclear cells in human jejunal mucosa Coronaviruses.
    keywords: cause; diarrhoea; family; patients; viruses
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        item: #660 of 1349
          id: cord-286719-1xjmlwqr
      author: Draz, Mohamed Shehata
       title: Applications of gold nanoparticles in virus detection
        date: 2018-02-15
       words: 19000
      flesch: 33
     summary: In addition, we provide a general summary of the contributions of AuNPs to the mainstream methods of virus detection, technical measures, and recommendations required in guidance toward commercial in-field applications. Toward this endeavor and beyond the pitfalls of current immunological and molecular techniques commonly applied to virus detection, several new approaches based on nanoparticles (NPs) have recently been developed.
    keywords: addition; amplification; antigen; assay; aunps; conjugates; detection; dna; fig; gold; hbv; hepatitis; hiv; human; infection; influenza; metal; molecular; nanoparticles; nucleic; probes; rna; sensitivity; silver; specific; surface; target; target dna; techniques; viral; virus; virus detection; viruses
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        item: #661 of 1349
          id: cord-286842-04cuk2cn
      author: Plyusnina, Angelina
       title: Recombinant Tula hantavirus shows reduced fitness but is able to survive in the presence of a parental virus: analysis of consecutive passages in a cell culture
        date: 2005-02-22
       words: 2148
      flesch: 43
     summary: Recombination in RNA viruses serves two main purposes: (i) it generates and spreads advantageous genetic combinations; and (ii) it counters the deleterious effect of mutations that, due to the low fidelity of viral RNA polymerases and lack of proofreading, occur with high frequency [1] . Taking into account that the in situ formed recombinant S RNA disappeared from the mixture after four passages [11] , one should conclude that the lower competitiveness of the recombinant virus seen earlier did not result from its immature status.
    keywords: hantavirus; recombination; rectulv; rna; virus
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        item: #662 of 1349
          id: cord-286877-0h5vgi5c
      author: Dahiya, Shyam S.
       title: Immunogenicity of a DNA-launched replicon-based canine parvovirus DNA vaccine expressing VP2 antigen in dogs
        date: 2012-10-31
       words: 5273
      flesch: 36
     summary: + effectors cells were significantly higher with repliconbased CPV DNA vaccine compared to conventional CPV DNA vaccine. The VN titer in all groups of CPV vaccine immunized dogs boosted after booster immunization and crossed the protective status.
    keywords: cells; cpv; dna; dogs; palpha; replicon; specific; vaccine; virus; vp2
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        item: #663 of 1349
          id: cord-287018-g4y5kjju
      author: Konstantinova, P
       title: Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA
        date: 2006-05-18
       words: 7236
      flesch: 49
     summary: A Tat-inducible Pol II promoter expressing anti-HIV shRNA has been described for inhibition of HIV-1 gene expression in mammalian cells. Double-stranded RNA nef2 is a duplex of two separate, complementary sense and antisense nef sequences (8416-8695).
    keywords: cells; dsrna; expression; inhibition; lhrna; long; nef; nef1; nef2; pt7; rna; rnai; virus
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        item: #664 of 1349
          id: cord-287093-9mertwj7
      author: Netherton, Christopher L
       title: Virus factories, double membrane vesicles and viroplasm generated in animal cells
        date: 2011-10-12
       words: 4333
      flesch: 34
     summary: This suggests that virus replication occurs in the CM rather than DMVs. The hepatitis NS5A protein also binds PI4KIIIa and stimulates enzyme activity and knockdown of PI4KIIIa prevents formation of the membranous web associated with virus replication [30 ,31 ] .
    keywords: dmvs; formation; membrane; proteins; replicase; replication; rna; vesicles; virus; viruses
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        item: #665 of 1349
          id: cord-287153-jbuuph6w
      author: Lund, Morten
       title: Experimental Piscine orthoreovirus infection mediates protection against pancreas disease in Atlantic salmon (Salmo salar)
        date: 2016-10-21
       words: 7465
      flesch: 51
     summary: Genes were selected based on their correlation with severity of pathological changes in heart induced by SAV infection, as previously reported [41] . Lesions in the pancreas are a hallmark of SAV infection and used diagnostically for separation of PD and HSMI
    keywords: atlantic; fish; groups; heart; infected; infection; prv; rna; salmon; sav; sav2; sav3; wpc
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        item: #666 of 1349
          id: cord-287228-0qm939ve
      author: Hong, Ke
       title: Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness
        date: 2020-10-27
       words: 3623
      flesch: 45
     summary: Our study has its limitation that a relatively small number of patients were included, which makes it difficult to associate any demographic features with increased risk of prolonged viral RNA in COVID-19 patients. Infectiousness in COVID-19 patients with prolonged presence of viral nucleic acid should not solely be evaluated by RT–PCR.
    keywords: cov-2; covid-19; infection; patients; pcr; rna; sars
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        item: #667 of 1349
          id: cord-287275-vwyny1vt
      author: Zhang, Meng-Jia
       title: Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China
        date: 2018-10-30
       words: 5204
      flesch: 52
     summary: A nucleotide sequence alignment showed that the whole genome of CHN-HG-2017 is 97.6%-99.1% identical to other PDCoV strains. Similar to other PDCoV strains, the complete genome sequence of CHN-HG-2017 is 25,399 nt in length, consisting of 5′ UTR-1ab-S-E-M-NS6-N-NS7-3′ UTR, and predicted transcription regulatory sequences (TRSs) were located at the 5′ end of each gene with a highly conserved core sequence of 5′ -ACCAC-3′ (Table 1) .
    keywords: cells; chn; deltacoronavirus; dpi; genome; hg-2017; infected; pdcov; piglets; porcine; rna; strain
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        item: #668 of 1349
          id: cord-287324-ecpicv5v
      author: Qiu, Yuan
       title: Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods
        date: 2017-06-02
       words: 3739
      flesch: 46
     summary: Virome detection has been widely applied to identification of novel RNA viruses and research of RNA viruses (Masson et al., 2014; Paez-Espino et al., 2016; Webster et al., 2015) . key: cord-287324-ecpicv5v authors: Qiu, Yuan; Chen, Ji-Ming; Wang, Tong; Hou, Guang-Yu; Zhuang, Qing-Ye; Wu, Run; Wang, Kai-Cheng title: Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods date: 2017-06-02 journal: Virus Res DOI: 10.1016/j.virusres.2017.05.003 sha: doc_id: 287324 cord_uid: ecpicv5v Virome (viral megagenomics) detection using next generation sequencing has been widely applied in virology, but its methods remain complicated and need optimization.
    keywords: genera; method; rna; sample; sequencing; viral; viruses
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        item: #669 of 1349
          id: cord-287349-1zcq7kzx
      author: Chen, James
       title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex
        date: 2020-07-28
       words: 2970
      flesch: 27
     summary: In Family Coronaviridae Crystal structure of Middle East respiratory syndrome coronavirus helicase From SARS to MERS: 10 years of research on highly 1162 pathogenic human coronaviruses Structure 1165 of replicating SARS-CoV-2 polymerase Dali server update Human Coronavirus 229E Nonstructural Protein 13: 1170 Characterization of Duplex-Unwinding, Nucleoside Triphosphatase, and RNA 5′-Triphosphatase Enzymatic Activities Associated with Severe Acute Respiratory Syndrome Coronavirus Helicase Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus 1179 Nsp13 upon ATP hydrolysis Structural basis of transcription arrest by coliphage HK022 nun in an 1183 DnaB Drives DNA Branch Migration and Dislodges 1186 Structure of the SARS-CoV nsp12 polymerase bound 1192 to nsp7 and nsp8 co-factors Transcriptional arrest: Escherichia coli RNA 1195 polymerase translocates backward, leaving the 3' end of the RNA intact and extruded RNA polymerase switches between inactivated and 1200 activated states By translocating back and forth along the DNA and the RNA Molecular Evolution of Multisubunit RNA Polymerases: 1204 Structural Analysis Cooperative 1207 translocation enhances the unwinding of duplex DNA by SARS coronavirus helicase nsP13 Discovery of an essential nucleotidylating activity associated with a newly delineated conserved 1213 domain in the RNA polymerase-containing protein of all nidoviruses What we know but 1217 do not understand about nidovirus helicases The EMBL-EBI search and sequence analysis tools APIs in 1221 2019 Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to 1229 polydisperse ensembles Discovery of an RNA virus 3'->5' exoribonuclease that is critically involved in 1233 coronavirus RNA synthesis Collaboration gets the most out of software Discovery of the first insect nidovirus, a missing evolutionary 1240 link in the emergence of the largest RNA virus genomes Cell the register of transcription by preventing backtracking of RNA polymerase Structure 1252 and function of the transcription elongation factor GreB bound to bacterial RNA polymerase Sequence 1256 requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA 1257 synthesis Analyzing resistance to 1264 design selective chemical inhibitors for AAA proteins cryoSPARC: algorithms for 1267 rapid unsupervised cryo-EM structure determination High-Throughput Deconvolution of Native Mass Spectra A 1274 planarian nidovirus expands the limits of RNA genome size Mechanistic basis of 1277 5'-3' translocation in SF1B helicases Advances in Experimental Medicine and Biology RELION: implementation of a Bayesian approach to cryo-EM structure 1283 determination Sequence logos: a new way to display consensus 1286 sequences Biochemical Characterization 1289 of the Equine Arteritis Virus Helicase Suggests a Close Functional The human coronavirus 229E superfamily 1 helicase has RNA and DNA duplex-unwinding activities with 5′-to-3′ polarity Remdesivir and SARS-CoV-2: structural requirements at 1302 both nsp12 RdRp and nsp14 Exonuclease active-sites Structure and Mechanism of 1305 Helicases and Nucleic Acid Translocases Coronaviruses lacking exoribonuclease 1308 activity are susceptible to lethal mutagenesis: evidence for proofreading and potential 1309 therapeutics Thinking Outside the Triangle: Replication Coronavirus RNA Synthesis and Processing Continuous and Discontinuous RNA 1318 Synthesis in Coronaviruses Protein AMPylation by an Evolutionarily Conserved 1322 One severe acute respiratory syndrome 1326 coronavirus protein complex integrates processive RNA polymerase and exonuclease activities The Severe Acute Respiratory Syndrome (SARS) In this case backtracking is energetically disfavored since it only 291 shortens the product RNA duplex without recovering duplex nucleic acids somewhere else.
    keywords: coronavirus; figure; helicase; nsp13; polymerase; rdrp; rna; sars; structural; transcription
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        item: #670 of 1349
          id: cord-287372-ya5uvoki
      author: Böszörményi, Kinga P.
       title: Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques
        date: 2020-11-05
       words: 3984
      flesch: 48
     summary: However, in the second week of infection, cynomolgus macaques 188 showed more, but still mild, clinical symptoms than rhesus macaques. Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model Epub 2020/04/19 Hydroxychloroquine use against SARS-CoV-2 infection in non-human primates CoV-2 infection protects against rechallenge in rhesus macaques Ocular conjunctival inoculation of 620 SARS-CoV-2 can cause mild COVID-19 in rhesus macaques 623 Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2 Development of an inactivated 630 vaccine candidate for SARS-CoV-2 Alphavirus-derived replicon RNA vaccine induces SARS-CoV-2 neutralizing antibody and T cell 635 responses in mice and nonhuman primates Ad26 vaccine protects against SARS-CoV-2 in rhesus macaques DNA 642 vaccine protection against SARS-CoV-2 in rhesus macaques Intradermal-646 delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 647 challenge model 649 Evaluation of the mRNA-1273 Vaccine against SARS-CoV-2 in Nonhuman Primates A vaccine targeting the RBD of the S 653 protein of SARS-CoV-2 induces protective immunity A 656 macaque model of HIV-1 infection SIV infection of rhesus macaques of 660 Chinese origin: a suitable model for HIV infection in humans Nonhuman Primate Model of Tuberculosis Experimental animal modelling for TB vaccine development Pandemic Swine-Origin H1N1 Influenza Virus Replicates to Higher Levels and Induces More 671 Fever and Acute Inflammatory Cytokines in Cynomolgus versus Rhesus Monkeys and Can 672 Replicate in Common Marmosets C-reactive protein levels in the early stage of COVID-19 Kidney involvement in COVID-19 and rationale for extracorporeal 679 therapies Management of acute kidney injury in patients with 682 COVID-19 Kidney disease is associated 685 with in-hospital death of patients with COVID-19 Severe Hypercoagulability in Patients Admitted to Intensive Care Unit for Acute Respiratory 690 COVID-19 and its implications for thrombosis and 693 anticoagulation Respiratory disease in rhesus macaques inoculated with SARS-CoV-2 The cytokine storm in COVID-701 19: An overview of the involvement of the chemokine/chemokine-receptor system Clinical features of patients infected 705 with 2019 novel coronavirus in Wuhan A role for CT in COVID-19?
    keywords: animals; cov-2; covid-19; cynomolgus; infection; macaques; rhesus; sars; species; study
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        item: #671 of 1349
          id: cord-287396-18p171nr
      author: Schroyen, Martine
       title: Current transcriptomics in pig immunity research
        date: 2014-11-15
       words: 9828
      flesch: 32
     summary: The making of ENCODE: lessons for big-data projects Evidence for a major QTL associated with host response to porcine reproductive and respiratory syndrome virus challenge Validation and further characterization of a major quantitative trait locus associated with host response to experimental infection with porcine reproductive and respiratory syndrome virus Patterns of cellular gene expression in swine macrophages infected with highly virulent classical swine fever virus strain Brescia Understanding Haemophilus parasuis infection in porcine spleen through a transcriptomics approach A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing Porcine S100A8 and S100A9: molecular characterizations and crucial functions in response to Haemophilus parasuis infection Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples Evaluation of suitable reference genes for gene expression studies in porcine alveolar macrophages in response to LPS and LTA Evaluation of suitable reference genes for gene expression studies in porcine PBMCs in response to LPS and LTA Quantitative analysis of the immune response upon Salmonella typhimurium infection along the porcine intestinal gut Alphacoronavirus protein 7 modulates host innate immune response Transcriptional approach to study porcine tracheal epithelial cells individually or dually infected with swine influenza virus and Streptococcus suis Comparative assessment of the pig, mouse, and human genomes: a structural and functional analysis of genes involved in immunity Analysis of porcine MHC using microarrays MicroRNA 181 suppresses porcine reproductive and respiratory syndrome virus (PRRSV) infection by targeting PRRSV receptor CD163 Cytokines transcript levels in lung and lymphoid organs during genotype 1 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection Enabling a systems biology approach to immunology: focus on innate immunity Direct multiplexed measurement of gene expression with colorcoded probe pairs Genome-wide transcriptional response of primary alveolar macrophages following infection with porcine reproductive and respiratory syndrome virus Gene expression profiling of porcine alveolar macrophages after antibody-mediated crosslinking of Sialoadhesin (Sn, Siglec-1) pandemic H1N1 influenza virus elicits similar clinical course but differential host transcriptional response in mouse, macaque, and swine infection models miRBase: microRNA sequences, targets and gene nomenclature Meta-analysis of molecular response of kidney to ischemia reperfusion injury for the identification of new candidate genes Analyses of pig genomes provide insight into porcine demography and evolution Mannose-specific interaction of Lactobacillus plantarum with porcine jejunal epithelium Increasing expression of MicroRNA 181 inhibits porcine reproductive and respiratory syndrome virus replication and has implications for controlling virus infection Identification of host encoded microRNAs interacting with novel swine-origin influenza A (H1N1) virus and swine influenza virus Molecular characterisation of the early response in pigs to experimental infection with Actinobacillus pleuropneumoniae using cDNA microarrays Intestinal Salmonella typhimurium infection leads to miR-29a induced caveolin 2 regulation Digital gene expression for non-model organisms Distinct peripheral blood RNA responses to Salmonella in pigs differing in Salmonella shedding levels: intersection of IFNG, TLR and miRNA pathways Transcription networks responsible for early regulation of Salmonella-induced inflammation in the jejunum of pigs Expression of toll-like receptors and downstream genes in lipopolysaccharide-induced porcine alveolar macrophages Age-related changes in phagocytic activity and production of pro-inflammatory cytokines by lipopolysaccharide stimulated porcine alveolar macrophages Reactomes of porcine alveolar macrophages infected with porcine reproductive and respiratory syndrome virus Pig bone marrow-derived macrophages resemble human macrophages in their response to bacterial lipopolysaccharide The impact of breed and tissue compartment on the response of pig macrophages to lipopolysaccharide Characterizing the porcine immune response to an environmental and pathogenic challenge: swine barn dust and Salmonella infection. Furthermore, upcoming high-throughput epigenomic studies, which will add greatly to our knowledge concerning the impact of epigenetic modifications on pig immune response, are listed in this review.
    keywords: analysis; array; colleagues; data; et al; expression; genes; genome; host; human; immune; infection; pig; pigs; porcine; response; rna; seq; studies; swine; virus
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        item: #672 of 1349
          id: cord-287466-ag5y781z
      author: Cowley, J.A.
       title: Nidoviruses of Fish and Crustaceans
        date: 2016-09-09
       words: 17742
      flesch: 23
     summary: A constant-temperature RT loop-mediated isothermal amplification (RT-LAMP) test with a sensitivity of ~5 RNA copies has also been developed for FHMNV diagnosis and surveillance (Zhang et al., 2014) . While toroviruses (28.0-28.5 kb) (Snijder et al., 2013) , bafiniviruses (26.6-27.3 kb) (Schütze et al., 2006; Batts et al., 2012) and roniviruses (26.2-26.6 kb) (Cowley et al., 2000a; Cowley and Walker, 2002; Sittidilokratna et al., 2002 Sittidilokratna et al., , 2008 possess similarly long genomes, those of mesoniviruses (20.2 kb) (Nga et al., 2011; Zirkel et al., 2011 Zirkel et al., , 2013 Lauber et al., 2012) and arteriviruses (12.7-15.7 kb) (Snijder et al., 2013) are more compact.
    keywords: cells; cowley et; detection; disease; dsrna; et al; flegel et; gav; gene; genome; gill; head; head virus; infection; lightner; monodon; nadala et; pcr; penaeus; penaeus monodon; rna; sequence; shrimp; sithigorngul et; sittidilokratna et; soowannayan et; spann et; species; virions; virus; viruses; wijegoonawardane et; yellow; yhv
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        item: #673 of 1349
          id: cord-287487-qeltdch7
      author: Graepel, Kevin W.
       title: Proofreading-Deficient Coronaviruses Adapt for Increased Fitness over Long-Term Passage without Reversion of Exoribonuclease-Inactivating Mutations
        date: 2017-11-07
       words: 7563
      flesch: 41
     summary: Research performed with many RNA viruses supports the hypothesis that the mutation rate of RNA virus replicases has evolved to balance multiple characteristics of the viral population such as genetic diversity, genomic integrity, and virulence. Those studies underscored the importance of understanding the molecular mechanisms by which RNA viruses regulate their replication fidelity.
    keywords: cov; exon(-; fidelity; fig; fitness; mhv; mutations; nsp14; nucleoside; p250; polymerase; replication; resistance; rna; virus; viruses
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        item: #674 of 1349
          id: cord-287488-h102xn29
      author: Araujo, Danielle Bastos
       title: SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network
        date: 2020-10-23
       words: 3940
      flesch: 44
     summary: We used NP swab specimen for virus isolation. The preparation of VIS and VLS stocks was performed as described above for virus isolation.
    keywords: brazil; cell; coronavirus; cov-2; genome; isolation; paulo; rna; sars; são; vero; virus
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        item: #675 of 1349
          id: cord-287501-7it4kh0e
      author: Roh, Changhyun
       title: A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide
        date: 2012-05-03
       words: 2965
      flesch: 38
     summary: key: cord-287501-7it4kh0e authors: Roh, Changhyun title: A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide date: 2012-05-03 journal: Int J Nanomedicine DOI: 10.2147/ijn.s31379 sha: doc_id: 287501 cord_uid: 7it4kh0e Hundreds of million people worldwide have been infected with severe acute respiratory syndrome (SARS), and the rate of global death from SARS has remarkably increased. Quantitative and sensitive detection of SARS coronavirus nucleocapsid protein using quantum dots-conjugated RNA aptamer on chip Coronavirus as a possible cause of severe acute respiratory syndrome A novel coronavirus associated with severe acute respiratory syndrome Identification of a novel coronavirus in patients with severe acute respiratory syndrome The spike protein of SARS-CoV -a target for vaccine and therapeutic development Are drugs for SARS on the horizon? Severe acute respiratory syndrome (SARS):
    keywords: coronavirus; cov; gallate; oligonucleotide; protein; qds; rna; sars
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        item: #676 of 1349
          id: cord-287658-c2lljdi7
      author: Lopez-Rincon, Alejandro
       title: Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning
        date: 2020-09-10
       words: 4786
      flesch: 46
     summary: These methods rely on the assumption that cDNA sequences share common features, and their order prevails among different sequences 19, 20 . We then validate the discovered sequences on datasets not used during the training of the CNN, and show how to exploit them to create a novel, highly informative set of sequence features (e.g. viral sequences).
    keywords: bps; coronavirus; cov-2; data; learning; primer; samples; sars; sequences; set; virus
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        item: #677 of 1349
          id: cord-287748-co9j3uig
      author: Kobayashi, Tomoya
       title: Detection of bat hepatitis E virus RNA in microbats in Japan
        date: 2018-05-29
       words: 1390
      flesch: 52
     summary: Although there is no information about migration of E. japonensis and P. sacrimontis, bat species closely related to them were reported to migrate only a few kilometers from their colonies per night key: cord-287748-co9j3uig authors: Kobayashi, Tomoya; Murakami, Shin; Yamamoto, Terumasa; Mineshita, Ko; Sakuyama, Muneki; Sasaki, Reiko; Maeda, Ken; Horimoto, Taisuke title: Detection of bat hepatitis E virus RNA in microbats in Japan date: 2018-05-29 journal: Virus Genes DOI: 10.1007/s11262-018-1577-9 sha: doc_id: 287748 cord_uid: co9j3uig Several recent studies have reported that various bat species harbor bat hepatitis E viruses (BatHEV) belonging to the family Hepeviridae, which also contains human hepatitis E virus (HEV).
    keywords: bat; bats; bthev; species
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        item: #678 of 1349
          id: cord-287758-da11ypiy
      author: Mônica Vitalino de Almeida, Sinara
       title: COVID-19 therapy: what weapons do we bring into battle?
        date: 2020-09-10
       words: 17493
      flesch: 35
     summary: More preclinical and clinical studies are required to prove whether dasatinib is really promising for COVID-19 patient treatment. SBV is also combined with other antiviral drugs, such as ledipasvir, velpatasvir and voxilaprevir.
    keywords: action; activity; antiviral; binding; cells; clinical; coronavirus; cov-2; covid-19; disease; drug; entry; fig; host; human; infection; inhibitor; mechanism; new; novel; patients; potential; pro; protein; receptor; replication; results; rna; sars; studies; study; syndrome; synthesis; targets; therapy; treatment
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        item: #679 of 1349
          id: cord-287931-cxqzac4a
      author: Huang, Weiwei
       title: An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens
        date: 2013-09-20
       words: 5170
      flesch: 42
     summary: The predominant techniques for identification of microbial pathogens depend on conventional clinical microbiology monitoring approaches. Since the first application of a high-throughput, rapid, and unbiased microarray for detecting viral pathogens in 2002
    keywords: analysis; china; eopm; microarray; pathogens; pcr; probes; rna; samples; sequences; species; virus
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        item: #680 of 1349
          id: cord-288093-012ipcdr
      author: Bouvette, Jonathan
       title: High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension
        date: 2018-12-06
       words: 7300
      flesch: 46
     summary: Together, these studies provide an efficient method for high-yield production of human Dicer as well as revised kinetic parameters for Dicer cleavage that should prove useful for future structural and mechanistic studies of Dicer aimed at better understanding how the catalytic production of miRNAs is achieved and regulated. For Dicer purification, large-scale cultures of 150 mL to 1 L were grown in thoroughly rinsed and sterilized 1-L glass Erlenmeyer (Corning #49851 L) or 2.8-L Fernbach culture flasks (Corning #44262×L).
    keywords: binding; cell; cleavage; concentration; dicer; expression; fig; human; let-7a-1; pre; protein; purification; rna; substrate; transfection
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        item: #681 of 1349
          id: cord-288167-976qxja2
      author: Park, Wan Beom
       title: Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection
        date: 2018-05-09
       words: 1373
      flesch: 44
     summary: In sputum and transtracheal aspirate, sub-genomic mRNA was detected for up to 4 weeks after symptoms developed, which correlated with the detection of genomic RNA. The objectives of this study were to examine the duration for detecting MERS-CoV sub-genomic mRNA vs. genomic RNA in different respiratory specimens.
    keywords: cov; genomic; mers; mrna
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        item: #682 of 1349
          id: cord-288390-p1q3v1ie
      author: Habjan, Matthias
       title: Cytoplasmic sensing of viral nucleic acids
        date: 2015-02-07
       words: 4050
      flesch: 39
     summary: dsRNA could be either the result of replication intermediates (for RNA viruses), generation of genomic RNA (for dsRNA viruses), convergent transcription (for DNA viruses), or of the presence of secondary structures found in viral RNAs (e.g. the IRES structure of ssRNA viruses) I interferon signalling Protein kinase PKR and RNA adenosine deaminase ADAR1: new roles for old players as modulators of the interferon response Bevilacqua PC: 5'-Triphosphate-dependent activation of PKR by RNAs with short stem-loops AIM2 activates the inflammasome and cell death in response to cytoplasmic DNA Recognition of RNA virus by RIG-I results in activation of CARD9 and inflammasome signaling for interleukin 1 beta production The DHX33 RNA helicase senses cytosolic RNA and activates the NLRP3 inflammasome IFIT1 is an antiviral protein that recognizes 5 0 -triphosphate RNA Structural basis for viral 5 0 -PPP-RNA recognition by human IFIT proteins Inhibition of translation by IFIT family members is determined by their ability to interact selectively with the 5 0 -terminal regions of cap0-, cap1-and
    keywords: acids; dna; dsrna; mda5; proteins; rig; rna; viral; virus; viruses
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        item: #683 of 1349
          id: cord-288651-bgo8istm
      author: SHI, Yi
       title: Inhibition of genes expression of SARS coronavirus by synthetic small interfering RNAs
        date: 2005-03-17
       words: 3070
      flesch: 47
     summary: Specific inhibition of cellular mRNA by RNAi can be triggered in mammalian cells by the introduction of synthetic 21-to 23-nucleotide duplexes of RNA N genes of SARS-CoV and evaluated their effects on viral genes expression in Vero E6 cells. Results suggest that siRNA is capable of inhibiting SARS coronavirus genes expression and thus may be a new therapeutic strategy for treatment of SARS.
    keywords: cells; cov; duplexes; expression; genes; sars; sirna
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        item: #684 of 1349
          id: cord-288669-46tkedw7
      author: Lee, Changhee
       title: The small envelope protein of porcine reproductive and respiratory syndrome virus possesses ion channel protein-like properties
        date: 2006-11-10
       words: 9372
      flesch: 44
     summary: The results demonstrate that E protein expression is required for PRRSV infectivity, but genome replication and transcription may occur without E protein. As a first step towards understanding the biological role of E protein during PRRSV replication, E gene expression was blocked in a full-length infectious clone by mutating the ATG translational initiation to GTG, such that the full-length mutant genomic clone was unable to synthesize the E protein.
    keywords: cells; e protein; fig; membrane; p129; particles; protein; prrsv; replication; rna; specific; transfected; viral; virus
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        item: #685 of 1349
          id: cord-288701-nx9fg4yn
      author: Mari, Viviana
       title: Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus
        date: 2015-12-17
       words: 4836
      flesch: 33
     summary: The prototype strain (HoBi D32/00) of this emerging group of pestiviruses, also known as BVDV-3 or atypical pestiviruses (Larska et al., 2012; Liu et al., 2009) , was detected as contaminant of a batch of fetal bovine serum (FBS) imported from Brazil (Schirrmeier et al., 2004) . A recently developed real-time RT-PCR assay is able to detect HoBi-like pestiviruses without providing any simultaneous detection of BVDV-1 and BVDV-2 (Liu et al., 2008) .
    keywords: assay; bovine; bvdv-2; decaro; et al; hobi; like; pcr; pestivirus; rna; samples; time
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        item: #686 of 1349
          id: cord-288879-rj03dsib
      author: Schein, Catherine H.
       title: Polyglutamine Repeats in Viruses
        date: 2018-09-04
       words: 6201
      flesch: 38
     summary: Once Q-rich sequences were identified, BLAST searches starting from the viral proteins that contained them were used to determine the extent of their conservation in the same virus family and to find other virus proteins containing similar tracts. As discussed below, the longest repeats were found in DNA virus proteins that function in enhancing transmissibility (cowpox ATI) or contribute to viral latency (herpes viruses).
    keywords: autophagy; disease; dna; genome; herpes; polyq; proteins; repeats; replication; rna; role; segments; sequences; virus; viruses
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        item: #687 of 1349
          id: cord-288960-v6l6o5va
      author: Li, Yang
       title: Regulating STING in health and disease
        date: 2017-06-07
       words: 12330
      flesch: 35
     summary: Many DNA viruses, RNA viruses and bacteria have been implicated in the activation of STING response [55, 56] . [6] , suggesting STING activation pathways may overlap with RNA sensing mechanisms or reverse transcription of viral RNA
    keywords: activation; cells; cgas; cyclic; dna; dsdna; figure; gmp; human; ifn; immune; infection; interferon; irf3; pathway; protein; response; rna; sensing; signalling; sting; tbk1; type; virus
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        item: #688 of 1349
          id: cord-288962-jgtoehcr
      author: Andréoletti, Laurent
       title: Differential detection of rhinoviruses and enteroviruses RNA sequences associated with classical immunofluorescence assay detection of respiratory virus antigens in nasopharyngeal swabs from infants with bronchiolitis
        date: 2000-06-06
       words: 3713
      flesch: 29
     summary: [1988] , that demonstrated by cell culture assays the low prevalence of human rhinovirus respiratory infection in childhood bronchiolitis. Interestingly, positive human rhinovirus and enterovirus RT-PCR results were obtained in 8 of 84 (9.5%) and in 7 of 84 (8.3%) nasopha-ryngeal aspirates samples, and were the only evidence of respiratory viral infection in 15 patients with obstructive bronchiolitis ( Table I) .
    keywords: assay; bronchiolitis; detection; pcr; respiratory; rhinovirus; viral
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        item: #689 of 1349
          id: cord-289038-15yp9uqy
      author: Chow, Jonathan Tak-Sum
       title: Prediction and Analysis of SARS-CoV-2-Targeting MicroRNA in Human Lung Epithelium
        date: 2020-08-26
       words: 5326
      flesch: 47
     summary: For instance, hsa-miR-196, hsa-miR-296, hsa-miR-351, hsa-miR-431, and hsa-miR-448 were observed to attenuate hepatitis C (HCV) viral replication in vitro. hsa-miR-16-1-3p hsa-miR-15b-3p hsa-miR-103a-2-5p hsa-miR-1208 hsa-miR-6736-5p hsa-let-7b-5p hsa-let-7f-5p hsa-miR-1185-2-3p hsa-miR-1273g-3p hsa-miR-122-5p hsa-miR-197-5p hsa-miR-129-5p hsa-miR-1976 hsa-miR-4262 hsa-miR-1229-5p hsa-miR-1322 hsa-miR-1202 hsa-miR-301a-3p hsa-miR-1273e hsa-miR-6511a-5p hsa-miR-1275 hsa-miR-4665-5p hsa-miR-206 hsa-miR-17-3p hsa-miR-1269a hsa-miR-196a-5p hsa-miR-1267 hsa-miR-98-5p hsa-miR-1304-3p hsa-miR-4420 hsa-miR-1305 hsa-miR-1231 hsa-miR-4500 hsa-miR-19a-5p hsa-miR-1301-3p hsa-miR-152-5p hsa-miR-1238-5p hsa-miR-147a hsa-miR-1302 hsa-miR-1256 hsa-miR-3132 hsa-miR-1197 hsa-miR-124-5p hsa-miR-197-5p hsa-miR-129-5p hsa-miR-1976 hsa-miR-4262 hsa-miR-1229-5p hsa-miR-1322 hsa-miR-1202 hsa-miR-301a-3p hsa-miR-1273e hsa-miR-6511a-5p hsa-miR-1275 hsa-miR-4665-5p hsa-miR-206 hsa-miR-17-3p hsa-miR-1269a hsa-miR-196a-5p hsa-miR-1267 hsa-miR-98-5p hsa-miR-1304-3p hsa-miR-4420 hsa-miR-1305 hsa-miR-1231 hsa-miR-4500 hsa-miR-155-3p hsa-miR-145-3p hsa-miR-1233-3p hsa-miR-1293 hsa-miR-203b-3p hsa-miR-4458 hsa-miR-454-3p hsa-miR-4518 hsa-miR-1291 hsa-let-7a-3p hsa-miR-16-2-3p hsa-miR-193b-3p hsa-miR-1283 hsa-miR-1285-5p hsa-miR-1246 hsa-miR-1197 hsa-miR-124-5p To gain insight into the baseline levels of candidate miRNA in human lung epithelia
    keywords: 5p hsa; cov-2; expression; genome; hsa; infection; mirna; sars; target
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        item: #690 of 1349
          id: cord-289093-si8btsab
      author: Beard, Philippa M.
       title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference
        date: 2014-06-05
       words: 6591
      flesch: 44
     summary: To investigate this complex pathogen-host relationship further, a RNAi screen of druggable host targets was carried out to analyse the effect of cellular protein depletion on VACV replication, using a multi-cycle VACV infection assay that monitors all stages of virus replication including virus spread. This resulted in a Pearson product moment correlation coefficient of 0.86, confirming that fluorescence was a reliable determinant of virus replication.
    keywords: analysis; cells; data; figure; gene; hfs; host; infection; proteins; replication; rnai; screen; sirna; vaccinia; vacv; virus
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        item: #691 of 1349
          id: cord-289192-1ecr16a3
      author: Fujita, Motomichi
       title: Development of a homogeneous time-resolved fluorescence assay for detection of viral double-stranded RNA
        date: 2019-02-01
       words: 2380
      flesch: 49
     summary: Further investigations using the dsRNA-HTRF assay are needed to examine the possibility of broad-spectrum detection of RNA viruses, i.e., coronaviruses, togaviruses, and flaviviruses. However, specific antiviral agents are not currently available for many RNA viruses.
    keywords: assay; cells; dsrna; fig; hrv; htrf; viruses
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        item: #692 of 1349
          id: cord-289248-6mx4o0eb
      author: Wang, Yilong
       title: Enhancement of safety and immunogenicity of the Chinese Hu191 measles virus vaccine by alteration of the S-adenosylmethionine (SAM) binding site in the large polymerase protein
        date: 2018-05-01
       words: 7100
      flesch: 52
     summary: A full-length cDNA clone of MV strain Hu191, pYES-MV(+), was constructed by a novel methodology using the GeneArt™ High-Order Genetic Assembly System. Despite the high attenuation phenotype, rMV-Hu191-G1788A grew to high titer compared to parental vaccine virus in Vero cells, the WHO approved cell line for vaccine production.
    keywords: cells; cotton; et al; hu191; mutants; rats; rmv; rna; vaccine; vero; virus
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        item: #693 of 1349
          id: cord-289321-ahl46ql9
      author: van Buuren, Nicholas
       title: Transmission genetics of drug-resistant hepatitis C virus
        date: 2018-03-28
       words: 7846
      flesch: 42
     summary: Finally, the cis-dominance of Daclatasvir-resistant WT-Y93H was observed when coinfected with drug susceptible virus (S) in the absence and presence of Daclatasvir ( Figure 4H ). A Novel RNA ISH Multicolor Application for Flow Cytometry Efficient rescue of hepatitis C virus RNA replication by transcomplementation with nonstructural protein 5A Boceprevir for previously treated chronic HCV genotype 1 infection Kinetic and structural analyses of hepatitis C virus polyprotein processing Daclatasvir-like inhibitors of NS5A block early biogenesis of hepatitis C virus-induced membranous replication factories, independent of RNA replication Permissive secondary mutations enable the evolution of influenza oseltamivir resistance Daclatasvir Prevents Hepatitis C Virus Infectivity by Blocking Transfer of the Viral Genome to Assembly Sites The capsid-spacer peptide 1 Gag processing intermediate is a dominant-negative inhibitor of HIV-1 maturation Complete three-dimensional structures of picornaviral RNA-dependent RNA polymerases Trans-dominant inhibition of RNA viral replication can slow growth of drugresistant viruses Coronaviruses resistant to a 3C-like protease inhibitor are attenuated for replication and pathogenesis, revealing a low genetic barrier but high fitness cost of resistance Daclatasvir plus sofosbuvir for HCV infection General catalytic deficiency of hepatitis C virus RNA polymerase with an S282T mutation and mutually exclusive resistance towards 2'-modified nucleotide van Oral direct-acting agent therapy for hepatitis c virus infection: a systematic review Treatment of HCV with ABT-450/r-ombitasvir and dasabuvir with ribavirin Combining oncolytic virotherapy and cytotoxic therapies to fight cancer Distinct functions of NS5A in hepatitis C virus RNA replication uncovered by studies with the NS5A inhibitor BMS-790052 Chemical genetics strategy identifies an HCV NS5A inhibitor with a potent clinical effect Antiviral activity and resistance of HCV NS5A replication complex inhibitors HCV NS5A replication complex inhibitors Dominant negative effect of wild-type NS5A on NS5A-adapted subgenomic hepatitis C virus RNA replicon Virus mutation frequencies can be greatly underestimated by monoclonal antibody neutralization of virions Telaprevir for previously untreated chronic hepatitis C virus infection Cell culture and infection system for hepatitis C virus Hepatitis C virus RNA replication depends on specific cis-and trans-acting activities of viral nonstructural proteins Origins of combination therapy for tuberculosis: lessons for future antimicrobial development and application My cousin, my enemy: quasispecies suppression of drug resistance Ná jera I. 2006.
    keywords: cells; drug; et al; figure; genomes; hcv; hepatitis; ns3/4a; ns5a; replication; resistance; rna; virus; viruses
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        item: #694 of 1349
          id: cord-289407-8fje16z1
      author: Moore, G.
       title: Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England
        date: 2020-09-25
       words: 4723
      flesch: 48
     summary: [19] [20] [21] The detection of viral RNA in air samples differs with study with some reporting widespread airborne contamination 14, 18, 21 but many reporting low or non-detectable concentrations 13, 15, 16, 19 even in samples collected 10 cm from the face of positive patients. Air samples were taken using two types of active air sampler: a Coriolis µ air sampler (bertin Instruments, Montigny-le-Bretonneux, France), operating at 300 L/min and collecting into 15 ml RNase-free phosphate buffered saline (PBS) and an MD8 air sampler (Sartorius, Göttingen, Germany), operating at 50 L/min and collecting onto a gelatine membrane filter.
    keywords: air; cov-2; medrxiv; patients; preprint; rna; samples; sars; surfaces
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        item: #695 of 1349
          id: cord-289535-srrfr1es
      author: Tregoning, J. S.
       title: Vaccines for COVID‐19
        date: 2020-10-18
       words: 14346
      flesch: 38
     summary: Identity of blood and tissue leukocytes supporting in vitro infection New insights into the immunopathology and control of dengue virus infection Lack of antibody affinity maturation due to poor Toll-like receptor stimulation leads to enhanced respiratory syncytial virus disease Immunization with SARS coronavirus vaccines leads to pulmonary immunopathology on challenge with the SARS virus Immunization with modified vaccinia virus Ankara-based recombinant vaccine against severe acute respiratory syndrome is associated with enhanced hepatitis in ferrets Anti-spike IgG causes severe acute lung injury by skewing macrophage responses during acute SARS-CoV infection Molecular mechanism for antibodydependent enhancement of coronavirus entry A perspective on potential antibody-dependent enhancement of SARS-CoV-2 Is there an ideal animal model for SARS? Lovastatin-mediated G1 arrest is through inhibition of the proteasome, independent of hydroxymethyl glutaryl-CoA reductase Caution urged on SARS vaccines Aged BALB/c mice as a model for increased severity of severe acute respiratory syndrome in elderly humans Lethal infection of K18-hACE2 mice infected with severe acute respiratory syndrome coronavirus Development of animal models against emerging coronaviruses: from SARS to MERS coronavirus Blocking transmission of Middle East respiratory syndrome coronavirus (MERS-CoV) in llamas by vaccination with a recombinant spike protein Humoral immunogenicity and efficacy of a single dose of ChAdOx1 MERS vaccine candidate in dromedary camels The pathogenicity of SARS-CoV-2 in hACE2 transgenic mice SARS-CoV-2 infection in farmed minks, the Netherlands Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2 Reinfection could not occur in SARS-CoV-2 infected rhesus macaques Ethical guidelines for deliberately infecting volunteers with COVID-19 Human challenge studies to accelerate coronavirus vaccine licensure SARS-CoV-2 controlled human infection models: ethics, challenge agent production and regulatory issues Effect of dexamethasone in hospitalized patients with COVID-19 Criner GJet al, for the GSUSI. Clinical vaccine trials conventionally undergo four broad Phases, from early safety in small numbers of volunteers (Phase I) to wide-scale post-licensure monitoring (Phase IV).
    keywords: antibodies; antibody; cell; challenge; coronavirus; cov-2; covid-19; development; disease; dna; human; immune; immunity; infection; mers; mice; phase; protein; responses; rna; sars; spike; studies; syndrome; trials; vaccination; vaccine; virus
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        item: #696 of 1349
          id: cord-289612-4x5t4c5u
      author: Alsuliman, Tamim
       title: COVID-19 paraclinical diagnostic tools: Updates and future trends
        date: 2020-06-20
       words: 7370
      flesch: 45
     summary: Therefore, it may be important to routinely detect viral RNA in stool specimens of COVID-19 patients during the hospitalization and recovery stage, and to perform transmission-based precautions for patients until the negative conversion of viral RNA in feces. Probably, combining RNA and antibody detections may significantly improve the sensitivity of pathogenic diagnosis for COVID-19 patients (p < 0.001), even in the early phase of 1-week since onset (p = 0.007).
    keywords: assay; cases; coronavirus; cov-2; covid-19; diagnosis; disease; infection; patients; pcr; results; rna; rrt; sars; study
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        item: #697 of 1349
          id: cord-289926-y1rjgbui
      author: Veretnik, S.
       title: RNA binding domain of HDV antigen is homologous to the HMG box of SRY
        date: 2014-05-18
       words: 6687
      flesch: 48
     summary: Sequence alignments were performed using programs from the GCG Wisconsin Package version 8. Monte Carlo evaluation of sequence alignments was done using the GAP program with the option '-RANDOM=10000'.
    keywords: alignment; binding; dna; domain; fig; hdag; hmg; rna; sequence; similarity; sry
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        item: #698 of 1349
          id: cord-289965-qcezqpze
      author: Lehmann, Kathleen C.
       title: Arterivirus nsp12 versus the coronavirus nsp16 2′-O-methyltransferase: comparison of the C-terminal cleavage products of two nidovirus pp1ab polyproteins
        date: 2015-09-01
       words: 6624
      flesch: 41
     summary: Unlike AsD, the coronavirus 29-O-MTase has been characterized experimentally (Bouvet et al., 2010; Chen et al., 2011; Decroly et al., 2008 Decroly et al., , 2011 and was found to provide one of the four activities required for the formation of a socalled type I cap (cap-1) (mGpppNm) structure at the 59 end of Two other coronavirus enzymes, HEL1 (nsp13) (Ivanov et al., 2004; Ivanov & Ziebuhr, 2004) and the N7-MTase (nsp14) (Bouvet et al., 2010; Chen et al., 2009) , are also suspected or known to be involved in capping, whereas the fourth enzyme required (guanylyltransferase) remains to be identified.
    keywords: activity; arterivirus; coronavirus; eav; et al; family; fig; mtase; nsp12; protein; replication; residues; rna; virus
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        item: #699 of 1349
          id: cord-290218-dvyeg5fk
      author: Jiang, Yi
       title: RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19
        date: 2020-09-04
       words: 2259
      flesch: 38
     summary: Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency High-throughput screening identification of poliovirus RNA-dependent RNA polymerase inhibitors Favipiravir: Pharmacokinetics and Concerns About Clinical Trials for 2019-nCoV Infection Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods High throughput virtual screening reveals SARS-CoV-2 multi-target binding natural compounds to lead instant therapy for COVID-19 treatment SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective All third-party financial support for the work in the submitted manuscript All financial relationships with any entities that could be viewed as relevant to the general area of the submitted manuscript All sources of revenue with relevance to the submitted work who made payments to you, or to your institution on your behalf Any other interactions with the sponsor of outside of the submitted work should also be reported. China Novel Coronavirus, T. Research, A Novel Coronavirus from Patients with Pneumonia in China A new coronavirus associated with human respiratory disease in China A pneumonia outbreak associated with a new coronavirus of probable bat origin Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak Polymerase as a Target for COVID-19 Drug Discovery Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor Structural basis of receptor recognition by SARS-CoV-2 Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro Washington State -nCo, First Case of 2019 Novel Coronavirus in the United States Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses Structure of the RNA-dependent RNA polymerase from COVID-19 virus Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2 Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV Nonstructural protein 1 of SARS-CoV-2 is a potent pathogenicity factor redirecting host protein synthesis machinery toward viral RNA Crystal structure of the SARS-CoV-2 non-structural protein 9 Structures of the SARS-CoV-2 Endoribonuclease Nsp15 The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant RdRp mutations are associated with SARS-CoV Crystal structure of Zika virus NS5 RNA-dependent RNA polymerase Structural Insights into Bunyavirus Replication and Its Regulation by the vRNA Promoter Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer Viral replication.
    keywords: complex; polymerase; rdrp; replication; rna; sars; structure
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        item: #700 of 1349
          id: cord-290254-m9l8ntur
      author: Rodriguez-Manzano, J.
       title: A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes
        date: 2020-06-30
       words: 5626
      flesch: 47
     summary: In this work, we report the development of a rapid PoC diagnostic test (< 20 min) based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and semiconductor technology for the detection of SARS-CoV-2 from extracted RNA samples. To evaluate performance of the proposed diagnostic test compared to reference methods, a total of 183 extracted RNA samples from nasopharyngeal, throat and nose swabs were screened by RT-qLAMP and RT-qPCR (CDC assay) (9) .
    keywords: amplification; assay; cov-2; detection; fig; poc; qlamp; qpcr; rna; samples; sars; sequences
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        item: #701 of 1349
          id: cord-290472-w77cmljm
      author: Sharon, Donald
       title: Systems Biology Approaches to Disease Marker Discovery
        date: 2010-06-09
       words: 8676
      flesch: 33
     summary: Traditionally, discovery and detection of these disease markers relied on low throughput technologies such as Enzyme-Linked Immunosorbant Assay (ELISA) or 2D-gel plus Edman degradation for protein markers, Reverse Transcription-Polymerase Chain Reaction (RT-PCR) for mRNA markers, and restriction enzyme digestion, cloning and Sanger sequencing for DNA markers. Overall, this study demonstrated for the first time that protein microarrays could be used to diagnose and monitor human antibodies as protein markers that are generated during the course of a disease.
    keywords: autoantibodies; autoantibody; breast; cancer; detection; discovery; disease; genome; identification; markers; mass; microarrays; patients; protein; rna; samples; sequencing; serum; studies; technology
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        item: #702 of 1349
          id: cord-290481-i2ppvsh5
      author: Dolja, Valerian V.
       title: Comparative and functional genomics of closteroviruses
        date: 2006-03-09
       words: 9321
      flesch: 39
     summary: Nevertheless, RNA viruses play a prominent role in our understanding of life's origin and evolution. Because RNA is widely believed to predate DNA as the genetic material, RNA viruses could be living fossils of the primordial RNA world (Joyce, 2002; Koonin and Martin, 2005) .
    keywords: analysis; cell; closterovirus; et al; evolution; fig; gene; genome; plant; proteins; replication; rna; rnas; silencing; tail; virion; viruses; yellows
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        item: #703 of 1349
          id: cord-290550-u8x9drva
      author: Radford, Alan D.
       title: Application of next-generation sequencing technologies in virology
        date: 2012-09-17
       words: 7936
      flesch: 34
     summary: These allowed those interested in understanding viruses first to amplify and then to sequence viral nucleic acids, namely DNA amplification by PCR (Mullis et al., 1986) and DNA sequencing with chain-terminating inhibitors (Sanger sequencing or first-generation sequencing) (Sanger et al., 1977) . In poxviruses, RNA-seq has been used to revisit temporal trends in gene expression (Yang et al., 2011b) , to identify interactions between the host and poxviral transcriptome (Yang et al., 2010) and to map transcription start and stop sites precisely (Yang et al., 2011a) .
    keywords: amplification; analysis; discovery; disease; dna; et al; fig; genome; host; new; ngs; pcr; pyrosequencing; rna; sequence; sequencing; variants; virus; viruses
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        item: #704 of 1349
          id: cord-290744-m0vpizuh
      author: Kindler, E.
       title: Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response
        date: 2016-09-09
       words: 7239
      flesch: 32
     summary: Translation is initiated at the start codon of ORF1a and may continue to ORF1b via a ribosomal frameshift mechanism, ultimately giving rise to two overlapping replicase polyproteins pp1a and pp1ab Perlman and Netland, 2009; Snijder et al., 2003; Thiel et al., 2003) . Moreover, ORF1b harbors several RNA-processing enzymes, including a 3 0 -5 0 exonuclease and a guanosine N7-methyltransferase (associated with the N-and C-terminal domains, respectively, of nsp14), an endoribonuclease (nsp15) and a 2 0 -O-methyltransferase (nsp16) (Chen et al., 2009; Decroly et al., 2008; Ivanov et al., 2004; Kindler and Thiel, 2014; Minskaia et al., 2006; Perlman and Netland, 2009; Snijder et al., 2003; Thiel et al., 2003; Zust et al., 2011) .
    keywords: antiviral; cells; coronavirus; cov; et al; host; human; ifn; induction; interferon; mers; pkr; protein; respiratory; rna; sars; syndrome; type
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        item: #705 of 1349
          id: cord-290801-dv6aak01
      author: Ivanyi-Nagy, Roland
       title: Reprint of: Core protein-mediated 5′–3′ annealing of the West Nile virus genomic RNA in vitro()
        date: 2012-09-27
       words: 6530
      flesch: 32
     summary: A stable full-length yellow fever virus cDNA clone and the role of conserved RNA elements in flavivirus replication The molecular biology of West Nile Virus: a new invader of the western hemisphere Sequence and secondary structure analysis of the 5 -terminal region of flavivirus genome RNA The 3 -nucleotides of flavivirus genomic RNA form a conserved secondary structure A La protein requirement for efficient pre-tRNA folding The capsid-coding region hairpin element (cHP) is a critical determinant of dengue virus and West Nile virus RNA synthesis RNA secondary structure in the coding region of dengue virus type 2 directs translation start codon selection and is required for viral replication Fine mapping of a cis-acting sequence element in yellow fever virus RNA that is required for RNA replication and cyclization The ubiquitous nature of RNA chaperone proteins The hepatitis C virus Core protein is a potent nucleic acid chaperone that directs dimerization of the viral (+) strand RNA in vitro Translation elongation factor-1alpha, La, and PTB interact with the 3 untranslated region of dengue 4 virus RNA The RNA annealing mechanism of the HIV-1 Tat peptide: conversion of the RNA into an annealingcompetent conformation West Nile virus core protein; tetramer structure and ribbon formation Terminal structures of West Nile virus genomic RNA and their interactions with viral NS5 protein Attenuation and immunogenicity in humans of a live dengue virus type-4 vaccine candidate with a 30 nucleotide deletion in its 3 -untranslated region Small noncoding RNA modulates Japanese encephalitis virus replication and translation in trans RNA sequences and structures required for the recruitment and activity of the dengue virus polymerase A 5 RNA element promotes dengue virus RNA synthesis on a circular genome Interplay of RNA elements in the dengue virus 5 and 3 ends required for viral RNA replication Composition of the sequence downstream of the dengue virus 5 cyclization sequence (dCS) affects viral RNA replication The 5 and 3 downstream AUG region elements are required for mosquito-borne flavivirus RNA replication RNA structures required for production of subgenomic flavivirus RNA La protein binds to NS5 and NS3 and to the 5 and 3 ends of Dengue 4 virus RNA Functional RNA elements in the dengue virus genome Autochthonous dengue fever in Croatia Impact of climate change and other factors on emerging arbovirus diseases Pathogenic flaviviruses Viral encephalomyelitis Origin and evolution of flavivirus 5 UTRs and panhandles: trans-terminal duplications? Flaviviruses constitute a large and diverse group within the Flaviviridae family of positive-strand enveloped RNA viruses (Lindenbach et al., 2007) .
    keywords: annealing; core; cyclization; dengue; et al; fig; genome; lanes; protein; region; replication; rna; utr; virus; wnv
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        item: #706 of 1349
          id: cord-290802-761wqgbe
      author: Zhao, Zheng
       title: Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery
        date: 2020-09-18
       words: 3891
      flesch: 45
     summary: A step towards discovering and designing allosteric kinase inhibitors across the human kinome Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach Revealing Acquired Resistance Mechanisms of Kinase-Targeted Drugs Using an on-the-Fly, Function-Site Interaction Fingerprint Approach A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites Detecting evolutionary relationships across existing fold space, using sequence order-independent profileprofile alignments TM-align: a protein structure alignment algorithm based on the TM-score Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity Calculating and scoring high quality multiple flexible protein structure alignments Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions Pythonbased Protein-Ligand Interaction Fingerprinting Optimizing fragment and scaffold docking by use of molecular interaction fingerprints sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank IChem: To summarize, we characterized RDRP binding pockets, suggesting four classes of binding modes (classes I−IV).
    keywords: binding; class; drug; figure; interaction; ligand; motif; rdrp; rna; sars
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        item: #707 of 1349
          id: cord-290813-6ylwj5je
      author: Ng, Enders K. O.
       title: Molecular Diagnosis of Severe Acute Respiratory Syndrome
        date: 2006
       words: 3129
      flesch: 46
     summary: Severe acute respiratory syndrome Identification of a novel coronavirus in patients with severe acute respiratory syndrome Coronavirus as a possible cause of severe acute respiratory syndrome Identification of severe acute respiratory syndrome in Canada Aetiology: Koch's postulates fulfilled for SARS virus Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Coronavirus genomic-sequence variations and the epidemiology of the severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome The genome sequence of the SARS-associated coronavirus Rapid diagnosis of a coronavirus associated with severe acute respiratory syndrome (SARS) Early diagnosis of SARS coronavirus infection by real time RT-PCR Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome Serial analysis of the plasma concentration of SARS coronavirus RNA in pediatric patients with severe acute respiratory syndrome Detection of SARS coronavirus RNA in the cerebrospinal fluid of a patient with severe acute respiratory syndrome Detection of hepatitis B virus DNA by real-time PCR using TaqMan-MGB probe technology TaqMan amplification system with an internal positive control for HCV RNA quantitation Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays ) mRNA of placental origin is readily detectable in maternal plasma Severe acute respiratory syndrome in children: An early study reported that SARS-CoV RNA was detected in 32% of nasopharyngeal aspirates from SARS patients studied at a mean of 3.2 d after the onset of illness, and the detection rate increased to 68% at d 14 (7).
    keywords: cov; pcr; rna; sars; serum; time
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        item: #708 of 1349
          id: cord-290948-cuu78cvl
      author: Imbert, Isabelle
       title: The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein
        date: 2008-02-05
       words: 7117
      flesch: 43
     summary: Interestingly, nsp10 also interacts with nsp9, a single-stranded RNA binding protein (Egloff et al., 2004; Su et al., 2006; Sutton et al., 2004) that in turn interacts with nsp8, the putative RNA primase (Imbert et al., 2006) . One of them reveals a unique spherical dodecamer architecture (Su et al., 2006) and the other shows a monomer (Joseph et al., 2006) .
    keywords: coronavirus; cov; domain; et al; gst; hybrid; interactions; nsp12; nsp3; nsp8; nsp9; protein; replication; rna; sars; yeast
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        item: #709 of 1349
          id: cord-291026-99cit4ig
      author: Lung, O.
       title: Insulated Isothermal Reverse Transcriptase PCR (iiRT‐PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus
        date: 2015-01-27
       words: 4574
      flesch: 44
     summary: In this study, we describe validation of a new probe‐based insulated isothermal reverse transcriptase PCR (iiRT‐PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user‐friendly device (POCKIT (™) Nucleic Acid Analyzer) that does not need data interpretation by the user. Classical swine fever virus (CSFV) is a member of the genus Pestivirus of the family Flaviviridae (Wengler 1991) .
    keywords: assay; csfv; detection; iirt; pcr; samples; swine; time; virus
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        item: #710 of 1349
          id: cord-291029-oldket3n
      author: Sefers, Susan E.
       title: QIAamp MinElute Virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs()
        date: 2005-07-21
       words: 3537
      flesch: 46
     summary: GG167 Influenza Study Group A distinctive property of Tth DNA polymerase: enzymatic amplification in the presence of phenol Identification of human immunodeficiency virus sequences by using in vitro enzymatic amplification and oligomer cleavage detection Evaluation of realtime PCR versus PCR with liquid-phase hybridization for detection of enterovirus RNA in cerebrospinal fluid Measurement of human cytomegalovirus loads by quantitative real-time PCR for monitoring clinical intervention in transplant recipients Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Bedside diagnosis of influenzavirus infections in hospitalized children Impact of a diagnostic cerebrospinal fluid enterovirus polymerase chain reaction test on patient management Recovery efficiencies on nucleic acid extraction kits as measured by quantitative LightCycler PCR Diagnosis of enteroviral meningitis by using PCR with a colorimetric microwell detection assay Monoclonal antibodies versus reverse transcription-PCR for detection of respiratory viruses in a patient population with respiratory tract infections admitted to hospital Acyclovir versus vidarabine in herpes simplex encephalitis. Cost per test was calculated for each extraction kit, which included test kit and additional materials and reagents used for nucleic acid extraction.
    keywords: dna; extraction; minelute; pcr; rna; rnazol
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        item: #711 of 1349
          id: cord-291063-de7v4e5s
      author: Moens, Ugo
       title: Silencing Viral MicroRNA as a Novel Antiviral Therapy?
        date: 2009-05-28
       words: 9133
      flesch: 42
     summary: Hence, neutralizing the action of viral miRNAs expression by complementary single-stranded oligonucleotides or so-called anti-miRNAs may represent a strategy to combat viral infections and viral-induced pathogenesis. Human polyomaviruses: molecular mechanisms for transformation and their association with cancers The role of polyomaviruses in human disease Identification of a third human polyomavirus Identification of a novel polyomavirus from patients with acute respiratory tract infections Clonal integration of a polyomavirus in human Merkel cell carcinoma Molecular biology of BK virus and clinical aspects of BK virus renal infection SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells Evolutionarily conserved function of a viral microRNA Merkel cell polyomavirus encodes a microRNA with the ability to autoregulate viral gene expression MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs Human cytomegalovirus expresses novel microRNAs during productive viral infection Identification and function of human cytomegalovirus microRNAs Identification of virus-encoded microRNAs A microRNA polycistron as a potential human oncogene Hepadnaviruses HBV-encoded microRNA candidate and its target 25 years of HIV-1 research-progress and perspectives RNA silencing and HIV: a hypothesis for the etiology of the severe combined immunodeficiency induced by the virus HIV-1 nef suppression by virally encoded microRNA Human papillomavirus genotype 31 does not express detectable microRNA levels during latent or productive virus replication Adenoviruses Structure, function and evolution of adenovirus virus-associated RNAs Suppression of RNA interference by adenovirus virus-associated RNA Adenovirus virus-associated RNA is processed to functional interfering RNAs involved in virus production Sequence-specific interference by small RNAs derived from adenovirus VAI RNA The family Herpesviridae: a brief introduction Identification of microRNAs of the herpesvirus family Epstein-Barr virus microRNAs are evolutionarily conserved and differentially expressed Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript An acutely and latently expressed herpes simplex virus 2 viral microRNA inhibits expression of ICP34.5, a viral neurovirulence factor Prediction and identification of herpes simplex virus 1-encoded microRNAs Novel less-abundant viral miRNAs encoded by herpes simplex virus 2 latencyassociated transcript and their roles in regulating ICP34.5 and ICP0 mRNAs
    keywords: amos; cells; ebv; expression; gene; host; hsv-1; human; infection; k12; micrornas; mir; mirna; protein; replication; silencing; target; virus; viruses
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        item: #712 of 1349
          id: cord-291225-75ys908n
      author: Martins, Nelson
       title: A Transgenic Flock House Virus Replicon Reveals an RNAi Independent Antiviral Mechanism Acting in Drosophila Follicular Somatic Cells
        date: 2018-12-12
       words: 5971
      flesch: 40
     summary: Virus derived piRNAs have been observed in some Drosophila cell lines (Wu et al. 2010 ) and some arthropod species (Morazzani et al. 2012; Vodovar et al. 2012; Schnettler et al. 2013; Léger et al. 2013; Lewis et al. 2018) , revealing that the piRNA pathway can be activated by viruses. Our hypothesis that the piRNA could play a role in the control of the replicon in this tissue was further strengthened by i) the observation that an FSC derived cell line (the OSS cell line), produces virus derived piRNAs from FHV and DCV (Wu et al. 2010) and ii) the proposed role of the piRNA pathway in the control of viruses (Reviewed in Miesen et al. 2016) .
    keywords: cells; drosophila; et al; expression; fhvδb2egfp; figure; fscs; pathway; replication; replicon; rna; sirna; small; uas; virus
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        item: #713 of 1349
          id: cord-291513-vpehn6nx
      author: Minich, Jeremiah
       title: Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment
        date: 2020-08-18
       words: 6441
      flesch: 47
     summary: We next compared success rates across swab samples from the built environment. The limit of detection (LoD) of SARs-CoV-2 from floor samples collected using the CGp or TMI swabs was similar or better than the CDC standard, further suggesting that swab type does not impact RNA recovery as measured by SARs-CoV-2.
    keywords: cgp; cov-2; detection; eluent; etoh; fig; rna; samples; sars; swab; syn; tmi; types
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        item: #714 of 1349
          id: cord-291590-24psoaer
      author: Ogando, Natacha S.
       title: The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus
        date: 2020-06-20
       words: 4335
      flesch: 33
     summary: Part A: 882 Emergence of the hypercycle Viral quasispecies evolution Mutational fitness effects in RNA and single-stranded DNA viruses: common 886 patterns revealed by site-directed mutagenesis studies Viral mutation rates Lack of evidence for proofreading mechanisms 891 associated with an RNA virus polymerase Mutation rates among RNA viruses Error catastrophe and antiviral strategy Selforganization of matter and the evolution of biological macromolecules Discovery of the first 899 insect nidovirus, a missing evolutionary link in the emergence of the largest RNA virus 900 genomes The 902 footprint of genome architecture in the largest genome expansion in RNA viruses A planarian 905 nidovirus expands the limits of RNA genome size Description and 907 initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new 908 family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus 909 Alphaletovirus Unique and conserved features of genome and proteome of SARS-912 coronavirus, an early split-off from the coronavirus group 2 lineage Exoribonuclease superfamilies: structural analysis and 914 phylogenetic distribution Purification and characterization of Escherichia coli RNase 916 T Structural basis for the 3'-5' exonuclease activity of Escherichia coli 918 DNA polymerase I: a two metal ion mechanism A general two-metal-ion mechanism for catalytic RNA 922 Discovery of an RNA virus 3'->5' exoribonuclease that is critically involved in coronavirus RNA 923 synthesis Structural basis 925 and functional analysis of the SARS coronavirus nsp14-nsp10 complex Structural and molecular basis of mismatch correction 929 and ribavirin excision from coronavirus RNA High fidelity of murine hepatitis virus 931 replication is decreased in nsp14 exoribonuclease mutants Infidelity of SARS-CoV Nsp14-exonuclease mutant 934 virus replication is revealed by complete genome sequencing A live, impaired-936 fidelity coronavirus vaccine protects in an aged, immunocompromised mouse model of lethal 937 disease
    keywords: activity; coronavirus; cov; exon; fig; mers; nsp14; replication; rna; sars
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        item: #715 of 1349
          id: cord-291677-zcbyhsf1
      author: Wilamowski, M.
       title: Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography
        date: 2020-08-16
       words: 5370
      flesch: 45
     summary: We determined crystal structures of Nsp10/16 that revealed the states before and after the methylation reaction, for the first time illustrating coronavirus Nsp10/16 complexes with the m7GpppAm2′-O Cap-1, where 2′OH of ribose is methylated. Extended Data Table 1 contains details of number of chips and detector distances used for data collection for Nsp10/16 SSX structures.
    keywords: 2′-o; cap-1; complex; cov-2; crystallography; data; fig; mrna; nsp10/16; nsp16; rna; sam; sars; ssx; structure
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        item: #716 of 1349
          id: cord-291727-4wfhuvww
      author: Ketteler, Robin
       title: On programmed ribosomal frameshifting: the alternative proteomes
        date: 2012-11-19
       words: 6683
      flesch: 44
     summary: However, it has been proposed that frameshifting may predominantly serve to modulate RNA levels rather than to produce frameshifted proteins (Plant et al., 2004) . Most commonly, an antibody that is specific to the out-of-frame sequence of the frameshifted protein is used to detect frameshifted proteins.
    keywords: et al; expression; frameshifting; gene; genome; peptides; proteins; pseudoknot; ribosomal; rna; sequence
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        item: #717 of 1349
          id: cord-291749-revhbd0q
      author: Mongan, Arthur Elia
       title: Portable sequencer in the fight against infectious disease
        date: 2019-10-03
       words: 3742
      flesch: 38
     summary: Sequencing technique has been around since 1975 by the works of Frederick Sanger, Allan Maxam, and Walter Gilbert Although the running cost of other sequencing platform is cheaper than MinION (for example, $67.82 for MiSeq compared with $71.56 for MinION per sample [28] ), MinION has significantly lower cost to set up.
    keywords: amplification; disease; dna; genome; minion; nanopore; pcr; resistance; rna; sequencing; virus
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        item: #718 of 1349
          id: cord-291754-1zxztadu
      author: Zhao, Ye
       title: Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure
        date: 2019-10-15
       words: 6873
      flesch: 43
     summary: The cDNA samples were submitted for SYBR Green I real-time RT-qPCR to detect the viral load for IBV N gene as described before (Zhao et al., 2015) . To compare the in vitro replication of the rescued virus rYN and its parental strain YN on CEK cells, 200 μl PBS containing 10 3.0 TCID 50 of rYN or YN virus were inoculated onto the CEK cells in 24-well plates, and 200 μl supernatants from three wells from each group were harvested at the time points of 6, 12, 24, 36, 48, and 60 hpi for a real-time PCR detection assay for IBV N gene as described above.
    keywords: bhk-21; bronchitis; cells; et al; gene; genome; ibv; recombinant; rna; ryn; vaccinia; virus
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        item: #719 of 1349
          id: cord-291765-97lk5qfo
      author: Eckerle, Lance D.
       title: Effects of Mutagenesis of Murine Hepatitis Virus NSP1 and NSP14 on Replication in Culture
        date: 2006
       words: 2192
      flesch: 44
     summary: Together, all of these results support the conclusion that nsp14 performs functions essential in the generation of infectious virus either within the cell or in viral RNA synthesis, and that the Asp242, Asp272, Cys206, and Cys209 residues are indispensable for virus replication. Finally, the results suggest that within apparently dispensable protein domains there may exist protein structure or function determinants that in the context of the intact protein may dramatically impact virus replication.
    keywords: nsp14; protein; replication; terminal; virus
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        item: #720 of 1349
          id: cord-291860-dw1sfzqx
      author: van Boheemen, Sander
       title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients
        date: 2019-12-16
       words: 5406
      flesch: 35
     summary: Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study Global and regional burden of hospital admissions for severe acute lower respiratory infections in young children in 2010: a systematic analysis Deaths due to respiratory tract infections in Africa: a review of autopsy studies CDC EPIC Study Team: Community-acquired pneumonia requiring hospitalization among U.S. adults The common cold Aetiology of lower respiratory tract infection in adults in primary care: a prospective study in 11 European countries Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Exploring the potential of next-generation sequencing in detection of respiratory viruses A primer on metagenomics Beer M: Novel orthobunyavirus in cattle Neurobrucellosis: unexpected answer from metagenomic nextgeneration sequencing Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans Protocol for metagenomic virus detection in clinical specimens Application of next generation sequencing for the detection of human viral pathogens in clinical specimens Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique Sequence analysis of the human virome in febrile and afebrile children Diagnosis of human metapneumovirus and rhinovirus in patients with respiratory tract infections by an internally controlled multiplex real-time RNA PCR Validation of clinical application of cytomegalovirus plasma DNA load measurement and definition of treatment criteria by analysis of correlation to antigen detection Zincmediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq Cutadept removes adapter sequences from high-throughput sequencing reads Centrifuge: rapid and sensitive classification of metagenomic sequences Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation Interactive metagenomic visualization in a Web browser Genome Detective: an automated system for virus identification from high-throughput sequencing data. The amount of internal control reads and target virus reads has been reported to be dependent on the amount of background reads (negative correlation).
    keywords: database; detection; dna; mngs; pathogens; pcr; protocol; reads; rna; samples; sensitivity; sequencing; viruses
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        item: #721 of 1349
          id: cord-291916-5yqc3zcx
      author: Hozhabri, Hossein
       title: The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting
        date: 2020-08-05
       words: 16799
      flesch: 39
     summary: This form of adaptation required a series of amino acid changes in the RBD within the S protein of SARS viruses that circulated in bats [56, 68] . Strategies for controlling emerging coronaviruses A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice Cross-species transmission of the newly identified coronavirus 2019-nCoV Towards a solution to MERS:
    keywords: ace2; acute; cases; cell; china; coronavirus; cov-2; covid-19; days; diagnosis; disease; figure; genome; host; human; infection; mers; novel; patients; pneumonia; protein; receptor; rna; sars; study; symptoms; syndrome; transmission; vaccine
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        item: #722 of 1349
          id: cord-291962-rp172ugk
      author: Jing, Huiyuan
       title: Nucleotide-binding oligomerization domain-like receptor X1 restricts porcine reproductive and respiratory syndrome virus-2 replication by interacting with viral Nsp9
        date: 2019-07-15
       words: 5750
      flesch: 40
     summary: Western blot analysis further showed that si-NLRX1-2 # reduced the level of NLRX1 protein by ∼87% compared to the controls cells transfected with NC siRNA (Fig. 3B) . NLRX1 protein levels measured by Western blotting reflected the changes in mRNA observed, suggesting that endogenous NLRX1 expression was upregulated by PRRSV infection (Fig. 1C) .
    keywords: cells; et al; infection; nlrx1; nsp9; porcine; protein; prrsv; replication; rna; syndrome; virus
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        item: #723 of 1349
          id: cord-291965-9r9ll83m
      author: Pfefferle, Susanne
       title: Distant Relatives of Severe Acute Respiratory Syndrome Coronavirus and Close Relatives of Human Coronavirus 229E in Bats, Ghana
        date: 2009-09-17
       words: 4314
      flesch: 50
     summary: Because of the low concentration of RNA in bat samples, generation of long sequences from novel bat CoV is tedious and technically demanding, which may be why some published phylogenies of bat CoV are based on short datasets, making it difficult to use these data for reference. However, the absence of successful virus isolation from bat feces in previous studies (3) (4) (5) (6) 8, 11, 12) may not reflect the incapability of bat CoV to infect human cells.
    keywords: analysis; bats; coronavirus; cov; covs; group; human; samples; sars; study; virus
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        item: #724 of 1349
          id: cord-292045-pnid9dmq
      author: Kumar, Manish
       title: First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2
        date: 2020-07-28
       words: 3040
      flesch: 45
     summary: Detection of, SARS-CoV-2 RNA in wastewater has been reported in Australia, China, France, Israel, Italy, Japan, Netherlands, Spain and the US (Ahmed et al., 2020a,b; Bar-or et al., 2020; Haramoto et al., 2020; La Rosa et al., 2020; Medema et al., 2020; Zheng et al., (2020) , reported detection of SARS-J o u r n a l P r e
    keywords: cov-2; covid-19; detection; et al; rna; sars; wastewater
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        item: #725 of 1349
          id: cord-292112-dejrksum
      author: Wang, Jinglu
       title: Genome-Wide Analysis Reveals Changes in Long Noncoding RNAs in the Differentiation of Canine BMSCs into Insulin-Producing Cells
        date: 2020-08-03
       words: 4716
      flesch: 45
     summary: To the best of our knowledge, this study is the first to focus on lncRNAs during the transdifferentiation of canine BMSCs, and lncRNAs expression changes were acquired and verified. According to many studies in other species and based on existing high-throughput technology, many lncRNAs have been reported in either disease research or basic research areas.
    keywords: analysis; coding; comparison; figure; genes; lncrnas; pathway; protein; signaling; table
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        item: #726 of 1349
          id: cord-292347-d7xq7x5g
      author: Carter, Linda J.
       title: Assay Techniques and Test Development for COVID-19 Diagnosis
        date: 2020-04-30
       words: 3437
      flesch: 38
     summary: This type of testing requires cell culture facilities, 470 and in the case of SARS coronavirus, Biosafety Level 3 (BSL3) 471 laboratories. These tests have a huge potential for the epide-397 miology of COVID-19, 32,42−45 but test results can be impacted by 398 at least three situations: (1) a subset of subjects with a positive 399 result from molecular genetic assays for SARS-CoV-2 infection 400 are seronegative due to the lag in antibody production following 401 infection, (2) the subjects may be seropositive yet negative for 402 molecular genetic assay results reflecting clearance of an earlier, 403 milder infection, and (3) limitation in sensitivity and specificity of 404 the assays.
    keywords: antibodies; assays; coronavirus; cov-2; covid-19; detection; infection; rna; sars; test; testing
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        item: #727 of 1349
          id: cord-292353-z86rjwle
      author: Hussein, Islam T.M.
       title: Recent Advances in Hantavirus Molecular Biology and Disease
        date: 2011-04-01
       words: 13586
      flesch: 33
     summary: The total size of the RNA genomes ranges from 11,845 nucleotides for HTNV to 12,317 nucleotides for SNV (Hooper and Schmaljohn, 2001; Jonsson et al., 2010; Schmaljohn et al., 1985 Schmaljohn et al., , 1986 . Gott et al., 1997; Schmaljohn et al., 1986 Schmaljohn et al., , 1987 Yamada et al., 1995) .
    keywords: cells; conserved; disease; et al; fever; genome; glycoproteins; hantaan; hantavirus; hcps; hfrs; host; infection; mechanism; mrna; nucleocapsid; polymerase; protein; pulmonary; rdrp; replication; rna; rodent; segment; syndrome; transcription; viral; virus; viruses
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        item: #728 of 1349
          id: cord-292416-3hhi4wps
      author: Sarid, Ronit
       title: Investigating an Emerging Virus During a Sudden Pandemic Outbreak
        date: 2020-07-31
       words: 4872
      flesch: 35
     summary: Zoonotic origins of human coronaviruses Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing Cultivation of viruses from a high proportion of patients with colds A new virus isolated from the human respiratory tract Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia Association between a novel human coronavirus and Kawasaki disease Human coronavirus NL63 is not detected in the respiratory tracts of children with acute Kawasaki disease Kawasaki disease lacks association with human coronavirus NL63 and human bocavirus Epidemiology, genetic recombination, and pathogenesis of coronaviruses Update on human rhinovirus and coronavirus infections Human coronavirus infections in Israel: epidemiology, clinical symptoms and summer seasonality of HCoV-HKU1 An outbreak of human coronavirus OC43 infection and serological cross-reactivity with SARS coronavirus Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history Molecular characterization of a canine respiratory coronavirus strain detected in Italy Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARScoronavirus 2 Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target Diagnostic testing for severe acute respiratory syndromerelated coronavirus 2: a narrative review Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease Ribavirin, remdesivir, sofosbuvir, galidesivir, and tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): a molecular docking study SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective Coronaviruses -drug discovery and therapeutic options Treatment with convalescent plasma for influenza A (H5N1) infection Convalescent plasma treatment reduced mortality in patients with severe pandemic influenza A (H1N1) 2009 virus infection Evaluation of convalescent plasma for Ebola virus disease in Guinea Administration of brincidofovir and convalescent plasma in a patient with Ebola virus disease Feasibility, safety, clinical, and laboratory effects of convalescent plasma therapy for patients with Middle East respiratory syndrome coronavirus infection: a study protocol Treatment of 5 critically ill patients with COVID-19 with convalescent plasma Convalescent plasma transfusion for the treatment of COVID-19: systematic review Our understanding of other viruses, in particular regarding coronaviruses, can provide guidance for understanding and control of the SARS-CoV-2 new outbreak.
    keywords: coronaviruses; cov-2; disease; hcov; host; human; infection; potential; rna; sars; virus
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        item: #729 of 1349
          id: cord-292643-n6xp5mlz
      author: Hall, Richard J.
       title: Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery
        date: 2013-09-13
       words: 4829
      flesch: 35
     summary: The application of virus discovery methods using metagenomics has been considered for routine use in diagnostic and reference laboratories to aid in the diagnosis of human (Svraka et al., 2010) and animal disease (Belak et al., 2013) . This finding supports the use of the 3-step procedure for virus enrichment, and similar 3-step procedures have previously been employed in published virus metagenomic studies (Table 1) .
    keywords: dna; enrichment; human; methods; pcr; rna; sample; step; treatment; usa; viruses
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        item: #730 of 1349
          id: cord-292673-00s3wgem
      author: Buonaguro, Luigi
       title: SARS-CoV-2 RNA polymerase as target for antiviral therapy
        date: 2020-05-05
       words: 2064
      flesch: 41
     summary: Moreover, Sofosbuvir has been already shown to be effective for other positivesense RNA viruses, namely Yellow Fever and Hepatitis A virus [23, 24] . In particular, few analogs are already available originally developed to target RdRps of other RNA viruses, such as Remdesivir (Ebola virus)
    keywords: coronaviruses; rdrp; rna; sars; sense; viruses
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        item: #731 of 1349
          id: cord-292751-tk1oggi9
      author: Hosseini, Elahe Seyed
       title: The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies
        date: 2020-09-24
       words: 3817
      flesch: 42
     summary: The Lancet infectious diseases Anti-malaria drug chloroquine is highly effective in treating avian influenza A H5N1 virus infection in an animal model Chloroquine is a potent inhibitor of SARS coronavirus infection and spread Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro Coronaviruses-drug discovery and therapeutic options Treatment of Middle East respiratory syndrome with a combination of lopinavir/ritonavir and interferon-β1b (MIRACLE trial): statistical analysis plan for a recursive two-stage group sequential randomized controlled trial New Nucleoside Analogues for the Treatment of Hemorrhagic Fever Virus Infections Comparative effectiveness of combined favipiravir and oseltamivir therapy versus oseltamivir monotherapy in critically ill patients with influenza virus infection The Novel Chinese Coronavirus (2019-nCoV) Infections: challenges for fighting the storm Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses A randomized, controlled trial of Ebola virus disease therapeutics Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys Initiation, extension, and termination of RNA synthesis by a paramyxovirus polymerase Coronavirus susceptibility to the antiviral remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease Therapeutic options for the 2019 novel coronavirus (2019-nCoV). MedRxiv Prevalence of comorbidities in the Middle East respiratory syndrome coronavirus (MERS-CoV): a systematic review and meta-analysis Sex-based differences in susceptibility to severe acute respiratory syndrome coronavirus infection Sexual dimorphism in innate immunity An ultrasensitive, rapid, and portable coronavirus SARS-CoV-2 sequence detection method based on CRISPR-Cas12.
    keywords: 2019; coronavirus; cov-2; covid-19; infection; ncov; novel; patients; pneumonia; rna; sars
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        item: #732 of 1349
          id: cord-292831-oihcay6w
      author: Choudhary, Manohar L.
       title: Development of a multiplex one step RT-PCR that detects eighteen respiratory viruses in clinical specimens and comparison with real time RT-PCR
        date: 2013-01-08
       words: 3726
      flesch: 44
     summary: CDC protocol of real-time RTPCR for influenza A (H1N1) Comparative analysis of the multiple test methods for the detection of pandemic influenza A/H1N1 2009 virus Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene Simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested-PCR assays Nucleic acid amplification tests for detection of respiratory viruses Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Real time RT PCR detection of 12 respiratory viral infections in four triplex reactions Development and evaluation of a four-tube real time multiplex PCR assay covering fourteen respiratory viruses, and comparison to its corresponding single target counterparts Rapid detection and identification of 12 respiratory viruses using a dual priming oligonucleotide system-based multiplex PCR assay High-throughput, sensitive, and accurate multiplex PCR-microsphere flow cytometry system for large-scale comprehensive detection of respiratory viruses Comparison of a multiplex reverse transcription-PCR-enzyme hybridization assay with conventional viral culture and immunofluorescence techniques for the detection of seven viral respiratory pathogens Real-time reverse transcriptase PCR assay for detection of human metapneumoviruses from all known genetic lineages Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay Rapid detection of respiratory viruses by centrifugation enhanced cultures from children with acute lower respiratory tract infections Comparison of the Luminex xTAG Detection of nine respiratory RNA viruses using three multiplex RT PCR assays incorporating a novel RNA internal control transcript Development of three multiplex RT PCR assays for the detection of 12 respiratory RNA viruses Respiratory viral infections detected by multiplex PCR among pediatric patients with lower respiratory tract infections seen at an urban hospital in Delhi from Detection of influenza virus types A and B and type A subtypes (H1, H3, and H5) by multiplex polymerase chain reaction Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens-duration of symptoms significantly affects detection rate A prospective three-year cohort study of the epidemiology and virology of acute respiratory infections of children in rural India.
    keywords: detection; influenza; mrt; pcr; respiratory; viruses
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        item: #733 of 1349
          id: cord-292983-msuluuuu
      author: Ballesteros-Briones, María Cristina
       title: A new generation of vaccines based on alphavirus self-amplifying RNA
        date: 2020-09-06
       words: 4952
      flesch: 37
     summary: Intradermal electroporation of naked replicon RNA elicits strong immune responses Electroporation of RNA stimulates immunity to an encoded reporter gene in mice Enhanced delivery and potency of self-amplifying mRNA vaccines by electroporation in situ Expression kinetics and innate immune response after electroporation and LNP-mediated delivery of a self-amplifying mRNA in the skin Comparison of the expression kinetics and immunostimulatory activity of replicating mRNA, nonreplicating mRNA, and pDNA after intradermal electroporation in pigs Effects of epigenetic modulation on reporter gene expression: implications for stem cell imaging Improving the repeatability and efficacy of intradermal electroporated selfreplicating mRNA Improved methodology to reduce variability of saRNA in vivo expression delivered by EP in combination with RNAse inhibitors Rapidly produced SAM(J) vaccine against H7N9 influenza is immunogenic in mice CD8 Tcell priming upon mRNA vaccination is restricted to bonemarrow-derived antigen-presenting cells and may involve antigen transfer from myocytes Selfamplifying mRNA vaccines expressing multiple conserved influenza antigens confer protection against homologous and heterosubtypic viral challenge Induction of protective immunity against Toxoplasma gondii in mice by nucleoside triphosphate hydrolase-II (NTPase-II) selfamplifying RNA vaccine encapsulated in lipid nanoparticle (LNP) In vivo electroporation (EP) can enhance the potency of saRNA vaccines, by increasing transfection efficiency as shown for the first time by Piggott et al.
    keywords: delivery; expression; mice; mrna; responses; sarna; self; vaccines; virus
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        item: #734 of 1349
          id: cord-293038-pjjvfdnq
      author: Fontana, Juan
       title: The unique architecture of Bunyamwera virus factories around the Golgi complex
        date: 2008-06-10
       words: 7398
      flesch: 45
     summary: Interestingly, integrity of Golgi actin and viral NSm protein is also important for viral tube structure and normal production of infectious virions. In the present work we have studied a large number of serial sections and discovered that viral tubes actually contain a tubular domain and a bigger globular domain on one of the extremities (Fig. 1L ).
    keywords: actin; assembly; cells; et al; fig; golgi; membranes; nsm; protein; replication; rna; sections; tubes; virus; viruses
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        item: #735 of 1349
          id: cord-293163-udcw1mx5
      author: Lu, Patrick Y.
       title: Modulation of angiogenesis with siRNA inhibitors for novel therapeutics
        date: 2005-02-04
       words: 6393
      flesch: 23
     summary: Clinical translation of angiogenesis inhibitors Lymphangiogenesis and cancer metastasis VEGF-A stimulates lymphangiogenesis and hemangiogenesis in inflammatory neovascularization via macrophage recruitment Gene silencing in mammals by small interfering RNAs siRNA-mediated antitumorigenesis for drug target validation and therapeutics RNA interference for HIF-1a inhibits its downstream signalling and affects cellular proliferation Progestin-dependent induction of vascular endothelial growth factor in human breast cancer cells: preferential regulation by progesterone receptor B siRNA agents inhibit oncogene expression and attenuate human tumor cell growth Differentiated human podocytes endogenously express an inhibitory isoform of vascular endothelial growth factor (VEGF 165b ) mRNA and protein Delivering siRNA to animal disease models for validation of novel drug targets in vivo A small interfering RNA targeting vascular endothelial growth factor as cancer therapeutics Small interfering RNA (siRNA) targeting VEGF effectively inhibits ocular neovascularization in a mouse model Inhibition of ocular angiogenesis by siRNA targeting vascular endothelial growth factor-pathway genes; therapeutic strategy for herpetic stromal keratitis The adaptor protein shb binds to tyrosine 1175 in vascular endothelial growth factor (VEGF) receptor-2 and regulates VEGF-dependent cellular migration QGAP1, a novel vascular endothelial growth factor receptor binding protein, is involved in reactive oxygen species-dependent endothelial migration and proliferation Cancer siRNA therapy by tumor selective delivery with ligand-targeted sterically-stablilized nanoparticle Matrix metalloproteinase-9 triggers the angiogenic switch during carcinogenesis Basement membranes: structure, assembly and role in tumor angiogenesis Matrix metalloproteinase-9 silencing by RNA interference triggers the migratory-adhesive switch in Ewing's sarcoma cells Cyclic strain-induced endothelial MMP-2: role in vascular smooth muscle cell migration Histone deacetylase inhibitor up-regulates RECK to inhibit MMP-2 activation and cancer cell invasion Mint-3 regulates the retrieval of the internalized membrane-type matrix metalloproteinase, MT5-MMP, to the plasma membrane by binding to its carboxyl end motif EWV Engagement of CD44 promotes Rac activation and CD44 cleavage during tumor cell migration CD13/APN transcription is induced by RAS/MAPK-mediated phosphorylation of Ets-2 in activated endothelial cells Role of metalloprotease disintegrin ADAM12 Knocking down 3-phosphoinositide-dependent protein kinase-1 (PDK1) with siRNA demonstrated that PDK1 maintains steady-state phosphorylated MEK levels and cell growth
    keywords: adhesion; angiogenesis; anti; cancer; cells; endothelial; expression; factor; growth; inhibition; inhibitors; protein; sirna; tumor; vegf
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        item: #736 of 1349
          id: cord-293215-6flf5ig0
      author: Eriksson, Klara Kristin
       title: Generation of Recombinant Coronaviruses Using Vaccinia Virus as the Cloning Vector and Stable Cell Lines Containing Coronaviral Replicon RNAs
        date: 2007-11-28
       words: 4694
      flesch: 53
     summary: The following protocols describe the generation of coronavirus replicon cell lines and their use in the evaluation of coronavirus replicase inhibitors. Two selection markers, conferring neomycin/G418 (4) or blasticidin (10) resistance, have been used successfully for establishing stable coronavirus replicon cell lines.
    keywords: cdna; cells; coronavirus; fragments; ligation; plasmid; reaction; replicon; rna; vaccinia
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        item: #737 of 1349
          id: cord-293355-0v71xwqy
      author: Aguiar, Eric Roberto Guimarães Rocha
       title: Virus‐derived small RNAs: molecular footprints of host–pathogen interactions
        date: 2016-05-12
       words: 6840
      flesch: 43
     summary: The germline of the malaria mosquito produces abundant miRNAs, endo-siRNAs, piRNAs and 29-nt small RNAs A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish Piwi proteins and piRNAs in mammalian oocytes and early embryos RNA interference functions as an antiviral immunity mechanism in mammals Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs in Aedes aegypti mosquito cells Knockdown of piRNA pathway proteins results in enhanced Semliki Forest virus production in mosquito cells RNA interference targets arbovirus replication in Culicoides cells Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs Arbovirus-derived piRNAs exhibit a ping-pong signature in mosquito cells Crystal structure of the 2'-specific and double-stranded RNA-activated interferon-induced antiviral protein 2'-5'-oligoadenylate synthetase Expression cloning of 2-5A-dependent RNAase: a uniquely regulated mediator of interferon action 2-5A-dependent RNase molecules dimerize during activation by 2-5A Small self-RNA generated by RNase L amplifies antiviral innate immunity Interferon action: RNA cleavage pattern of a (2'-5')oligoadenylate--dependent endonuclease RNase L mediates the antiviral effect of interferon through a selective reduction in viral RNA during encephalomyocarditis virus infection RNase L releases a small RNA from HCV RNA that refolds into a potent PAMP Alphavirus minus-strand synthesis and persistence in mouse embryo fibroblasts derived from mice lacking RNase L and protein kinase R RNase L plays a role in the antiviral response to West Nile virus Identification of RNase Ldependent, 3'-end-modified, viral small RNAs in Sindbis virus-infected mammalian cells Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage Novel virus discovery and genome reconstruction from field RNA samples reveals highly divergent viruses in dipteran hosts Enhanced arbovirus surveillance with deep sequencing: Identification of novel rhabdoviruses and bunyaviruses in Australian mosquitoes Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing RNA-Seq: a method for comprehensive transcriptome analysis Application of next-generation sequencing technologies in virology Argonaute loading improves the 5' precision of both microRNAs and their miRNA* strands in flies FDF-PAGE: a powerful technique revealing previously undetected small RNAs sequestered by complementary transcripts Advanced Review wires Biases in small RNA deep sequencing data Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses Functional specialization of the small interfering RNA pathway in response to virus infection Broad RNA interference-mediated antiviral immunity and virus-specific inducible responses in Drosophila Characterization of hypovirus-derived small RNAs generated in the chestnut blight fungus by an inducible DCL-2-dependent pathway RNA-based immunity terminates viral infection in adult Drosophila in the absence of viral suppression of RNA interference: characterization of viral small interfering RNA populations in wild-type and mutant flies Induction and suppression of tick cell antiviral RNAi responses by tick-borne flaviviruses Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection Fossil rhabdoviral sequences integrated into arthropod genomes: ontogeny, evolution, and potential functionality Transcriptome analysis of Bombyx mori larval midgut during persistent and pathogenic cytoplasmic polyhedrosis virus infection A virulent strain of deformed wing virus (DWV) of honeybees (Apis mellifera) prevails after Varroa destructor-mediated, or in vitro, transmission Endogenous viral elements in animal genomes Dicer-2 processes diverse viral RNA species The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster Viral suppressors of RNA silencing hinder exogenous and endogenous small RNA pathways in Drosophila Cytoplasmic viral replication complexes Virus factories: associations of cell organelles for viral replication and morphogenesis A call to arms: coevolution of animal viruses and host innate immune responses RNA-based antiviral immunity New insights into the role of RNase L in innate immunity RNA degradation in antiviral immunity and autoimmunity Diagnosis and discovery of fungal viruses using deep sequencing of small RNAs Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host The discovery, distribution, and evolution of viruses associated with Drosophila melanogaster Antiviral RNA interference in mammalian cells
    keywords: decay; host; mechanisms; pathway; pirnas; rna; rnas; sequences; sirna; viral; virus; viruses; vsrnas
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        item: #738 of 1349
          id: cord-293375-qcy56ui7
      author: Strauss, Ellen G.
       title: Identification of the active site residues in the nsP2 proteinase of sindbis virus
        date: 1992-12-31
       words: 5197
      flesch: 47
     summary: Other proposed papain-like proteinases in RNA viruses include two domains within ORFl a of coronaviruses identified by protein modeling studies (Baker et al., 1991; Lee et al., 1991) and the HC-Pro protein of potyviruses, in which the catalytic Cys and His residues have been identified by mutagenesis (Oh and Carrington, 1989) . Structure of Sindbis virus core protein reveals a chymotrypsln-like serine proteinase and the organization of the vlnon Cleavage-site preferences of Slndbis virus polyproteins containing the nonstructural proteinase: Evidence for temporal regulation of polyproteln processing In VIVO Sindbls virus RNA polymerase is degraded by the N-end rule pathway Sequence of the genome RNA of rubella virus: Evidence for genetic rearrangement during togavirus evolution Genome sequences of a mouse-avirulent and a mouse-virulent strain of Ross River virus Convergence of active site geometries Plant viral protelnases Cysteine proteases of positive strand RNA viruses and chymotrypsln-like serine proteases: A distinct protein superfamily with a common structural fold Putative papain-related thiol proteases of positive-strand RNA viruses
    keywords: activity; catalytic; nsp2; papain; proteinase; residues; rna; sindbis; site; virus
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        item: #739 of 1349
          id: cord-293417-oqusfhei
      author: Ma, Yanlin
       title: Structures of the N- and C-terminal domains of MHV-A59 nucleocapsid protein corroborate a conserved RNA-protein binding mechanism in coronavirus
        date: 2010-07-01
       words: 5167
      flesch: 44
     summary: The nucleoprotein is required for efficient coronavirus genome replication Engineering the largest RNA virus genome as an infectious bacterial artificial chromosome The CCP4 suite: programs for protein crystallography Interactions between coronavirus nucleocapsid protein and viral RNAs: implications for viral transcription Importance of MHV-CoV A59 nucleocapsid protein COOH-terminal negative charges Four proteins processed from the replicase gene polyprotein of mouse hepatitis virus colocalize in the cell periphery and adjacent to sites of virion assembly Reverse genetics system for the avian coronavirus infectious bronchitis virus Multiple nucleic acid binding sites and intrinsic disorder of severe acute respiratory syndrome coronavirus nucleocapsid protein: implications for ribonucleocapsid protein packaging Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA Recombinant mouse hepatitis virus strain A59 from cloned, full-length cDNA replicates to high titers in vitro and is fully pathogenic in vivo Identification of nucleocapsid binding sites within coronavirus-defective genomes The PyMOL Molecular Graphics System Identification of a novel coronavirus in patients with severe acute respiratory syndrome Coot: model-building tools for molecular graphics The nucleocapsid protein of coronavirus infectious bronchitis virus: crystal structure of its N-terminal domain and multimerization properties Outbreak of severe acute respiratory syndromeworldwide Coronavirus N protein Nterminal domain (NTD) specifically binds the transcriptional regulatory sequence (TRS) and melts TRS-cTRS RNA duplexes Structure of the N-Terminal RNA-Binding domain of the SARS CoV nucleocapsid protein A major determinant for membrane protein interaction localizes to the carboxy-terminal domain of the mouse coronavirus nucleocapsid protein Minireview:The Structure of Protein-Protein Recognition Sites X-ray structures of the N-and C-terminal domains of a coronavirus nucleocapsid protein: implications for nucleocapsid formation A novel coronavirus associated with severe acute respiratory syndrome Genetic evidence for a structural interaction between the carboxy termini of the membrane and nucleocapsid proteins of mouse hepatitis virus RNA of mouse hepatitis virus Main-chain bond lengths and bond angles in protein structures Carboxyl terminus of severe acute respiratory syndrome coronavirus nucleocapsid protein: self-association analysis and nucleic acid binding characterization Ribonucleoprotein-like structures from coronavirus particles Localization of an RNA-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus Phaser crystallographic software Characterization of the RNA chaperone activity of hantavirus nucleocapsid protein Identification of a specific interaction between the coronavirus mouse hepatitis virus A59 nucleocapsid protein and packaging signal High affinity interaction between nucleocapsid protein and leader/intergenic sequence of mouse hepatitis virus RNA Processing of X-ray diffraction data collected in the oscillation mode Automated protein model building combined with iterative structure refinement RNA-binding proteins of coronavirus MHV: detection of monomeric and multimeric N protein with an RNA overlayprotein blot assay Characterization of a novel coronavirus associated with severe acute respiratory syndrome Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein Functional and genetic analysis of coronavirus replicase-transcriptase proteins Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling Specific interaction between coronavirus leader RNA and nucleocapsid protein The molecular biology of coronaviruses Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method Maximum-likelihood density modification Automated MAD and MIR structure solution Localization of mouse hepatitis virus nonstructural proteins and RNA synthesis indicates a role for late endosomes in viral replication Identification of functionally important negatively charged residues in the carboxy end of mouse hepatitis coronavirus A59 nucleocapsid protein Trafficking motifs in the SARS-coronavirus nucleocapsid protein Crystal structure of the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein dimerization domain reveals evolutionary linkage between corona-and arteriviridae Coronavirus leader RNA regulates and initiates subgenomic mRNA transcription both in trans and in cis Coronavirus nucleocapsid protein is an RNA chaperone ABBREVIATIONS ASU, asymmetric unit; AUC, analytical ultracentrifugation; CTD, Cterminal domain; HCoV-229E, human coronavirus; IBV, avian infectious bronchitis virus; MHV, murine hepatitis virus; N protein, nucleocapsid protein; NTD, N-terminal domain; SAD, single-wavelength anomalous dispersion; SARS-CoV, severe acute respiratory syndrome coronavirus; SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis; TGEV, transmissible gastroenteritis virus; TRS, transcriptional regulatory sequence The structure of Nterminal domain of MHV N protein also implicated its specific affinity with transcriptional regulatory sequence (TRS) RNA.
    keywords: binding; coronavirus; ctd; et al; mhv; ntd; nucleocapsid; protein; residues; rna; structure
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        item: #740 of 1349
          id: cord-293481-bmfj50fb
      author: Malin, Jakob J.
       title: Remdesivir against COVID-19 and Other Viral Diseases
        date: 2020-10-14
       words: 9125
      flesch: 37
     summary: They found that the activity of remdesivir includes both contemporary human and highly divergent zoonotic CoVs and that natural variations in wild-type RdRp do not confer remdesivir resistance. Recently, the efficacy of remdesivir treatment was finally tested in a rhesus macaque model of SARS-CoV-2 infection (53) .
    keywords: antiviral; cell; clinical; cov-2; covid-19; data; drug; efficacy; mers; nucleoside; patients; remdesivir; rna; sars; study; treatment; trial; virus
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        item: #741 of 1349
          id: cord-293525-c7nwygl1
      author: Saldanha, I. F.
       title: Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host
        date: 2019-04-03
       words: 5044
      flesch: 44
     summary: [30] , thus making any association difficult to detect should it occur with EriCoV infection in the hedgehog. Experimental infection studies and the development of in situ hybridisation to localise EriCoV in tissues would be worthwhile in the future to further elucidate the clinical significance of EriCoV infection.
    keywords: association; coronavirus; ericov; faeces; hedgehogs; infection; rna; samples; sequence; species; wildlife
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        item: #742 of 1349
          id: cord-293646-d4qcckh1
      author: Meanwell, Nicholas A.
       title: Chapter 22. Non-HIV antiviral agents
        date: 2003-12-31
       words: 4188
      flesch: 38
     summary: The development of the HCV replicon system and its application to screening for antiviral agents provided tangible benefit with the disclosure of mechanistically and structurally diverse HCV inhibitors. The development of the first HCV replicon system in 1998 and its application to screening for antiviral agents is beginning to provide tangible benefit with the disclosure of mechanistically and structurally diverse HCV inhibitors.
    keywords: antiviral; hbv; hcv; inhibitors; nucleoside; protease; rna; treatment; virus
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        item: #743 of 1349
          id: cord-293651-96cmduez
      author: Callison, Scott A.
       title: Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens
        date: 2006-08-28
       words: 4749
      flesch: 48
     summary: In this study, we developed a TaqMan ®based real-time RT-PCR assay for rapid detection of IBV viral RNA directly from clinical samples. In this report we present the development and evaluation of a real-time Taqman ® -based RT-PCR assay for the detection and quantification of IBV genomic RNA directly from tracheal swabs.
    keywords: assay; birds; ibv; pcr; rna; samples; time; tracheal; viral; virus
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        item: #744 of 1349
          id: cord-293747-ds8rhbkv
      author: Lani, Rafidah
       title: Antiviral activity of silymarin against chikungunya virus
        date: 2015-06-16
       words: 5091
      flesch: 46
     summary: This data also indicates that silymarin can interfere with CHIKV RNA replication by affecting the viral replicase system. This finding is consistent with that from previous assay and confirms that silymarin suppresses CHIKV RNA replication and does it in dose-dependent manner.
    keywords: activity; antiviral; assay; cells; chikungunya; chikv; replication; rna; silymarin; usa; virus
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        item: #745 of 1349
          id: cord-293766-vpfda3pd
      author: Ji, Jingjing
       title: Glucocorticoid therapy does not delay viral clearance in COVID-19 patients
        date: 2020-09-21
       words: 741
      flesch: 56
     summary: The use of antiinflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): the perspectives of clinical immunologists from China Low-dose corticosteroid therapy does not delay viral clearance in patients with COVID-19 Persistence and clearance of viral RNA in 2019 novel coronavirus disease rehabilitation patients National Health Commission of the People's Republic of China. key: cord-293766-vpfda3pd authors: Ji, Jingjing; Zhang, Jinxia; Shao, Ziyun; Xie, Qifeng; Zhong, Li; Liu, Zhifeng title: Glucocorticoid therapy does not delay viral clearance in COVID-19 patients date: 2020-09-21 journal: Crit Care DOI: 10.1186/s13054-020-03287-6 sha: doc_id: 293766 cord_uid: vpfda3pd nan lower respiratory tract samples from confirmed patients were collected and tested by RT-PCR every 2 to 3 days.
    keywords: clearance; days; patients
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        item: #746 of 1349
          id: cord-293790-7hyelm88
      author: Guévin, Carl
       title: Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection
        date: 2010-09-01
       words: 5285
      flesch: 47
     summary: Furthermore, ATG5 protein colocalizes with NS4B, a constituent of the membranous web. To demonstrate a physical interaction between ATG5 and NS5B proteins, we performed co-IP on radio-inert or metabolically labeled yeast cells coexpressing ATG5 and NS5B. We used yeast cells in this study because cotransfection of Huh-7 cells with c-myc-NS5B and HAtagged ATG5 resulted in a low level expression of ATG5 protein.
    keywords: atg5; autophagy; cells; hcv; interaction; ns5b; protein; replication; rna; virus; yeast
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        item: #747 of 1349
          id: cord-293852-r72c6584
      author: Greco, S.
       title: Noncoding RNAs implication in cardiovascular diseases in the COVID-19 era
        date: 2020-10-31
       words: 8171
      flesch: 32
     summary: However, in the heart of both SARS-CoV infected mice and of SARS patients, decreased ACE2-levels were observed [64] , suggesting a complex virus/receptor dynamic that needs to be elucidated. Interestingly, in the hearts of both SARS-CoV infected mice and SARS patients, macrophage infiltration with evidence of myocardial damage was observed [64] .
    keywords: ace2; cardiac; cardiovascular; cells; coronavirus; cov-2; covid-19; disease; expression; heart; human; infection; noncoding; patients; response; rna; rnas; sars
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        item: #748 of 1349
          id: cord-293913-frkb8iso
      author: Gao, Hong-Qiang
       title: Identification of the polymerase polyprotein products p72 and p65 of the murine coronavirus MHV-JHM
        date: 1996-12-31
       words: 3649
      flesch: 45
     summary: To determine if MHV proteinase domains PCP-1 or PCP-2 act in trans to cleave p72, we generated radiolabeled p72 protein and unlabeled pT7-NBgl and pT7-NA6 The translation products were analyzed by 10% SDS-PAGE directly (Lanes 1 and 2) or following immunoprecipitation with anti-647 (Lanes 4 and 5) or anti-p28 (Lanes 6 and 7). The role of MHV proteinases in the processing of p72 and p65 is discussed.
    keywords: mhv; p28; p65; p72; protein
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        item: #749 of 1349
          id: cord-293988-f5gvwjyh
      author: Musso, Nicolò
       title: New SARS-CoV-2 Infection Detected in an Italian Pet Cat by RT-qPCR from Deep Pharyngeal Swab
        date: 2020-09-11
       words: 3229
      flesch: 44
     summary: In particular, viral RNA and infectious viral particles were found in the upper respiratory tract of domestic cats after introduction of SARS-CoV-2 virus samples through their nasal cavities; nevertheless, none of the infected cats showed clinical signs of the disease. In addition, viral RNA was detected in 1:3 healthy cats exposed to infected felines, suggesting that they had contracted the virus from the droplets exhaled by infected cats [13, 19] .
    keywords: cat; cod; coronavirus; cov-2; gene; human; infection; rna; sars; swab
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        item: #750 of 1349
          id: cord-294056-7e477y1x
      author: La Monica, Nicola
       title: Coronavirus mRNA synthesis: Identification of novel transcription initiation signals which are differentially regulated by different leader sequences
        date: 1992-05-31
       words: 3371
      flesch: 54
     summary: A second primer (78) representing leader RNA sequence (nucleotides 22 to 56) was then used for PCR amplification by Ta9 polymerase. To understand the mechanism of MHV mRNA transcription, we have attempted to determine whether the differential regulation of transcription initiation by leader RNA containing different UCUAA copy numbers is unique to mRNA 2-l. In this report, we have identified several additional transcription initiation sites which are regulated in different manners by leader RNA with different copy numbers of the UCUAA sequence.
    keywords: leader; mrna; sequence; transcription; ucuaa
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        item: #751 of 1349
          id: cord-294108-uvnh0s9r
      author: Dube, Taru
       title: Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector
        date: 2020-10-25
       words: 13897
      flesch: 38
     summary: COVID-19 patients seeking intensive care unit (ICU) are particularly older and more likely to carry pre-existing comorbid conditions like hypertension and related heart diseases followed by diabetes. To date, apart from the emergency use approval of the antiviral drug favilavir in China, India, Russia, and parts of the Middle East and the emergency use approval of remdesivir by the US-FDA and Japan in COVID-19 patients, there are no approved therapeutic molecules to treat the COVID-19 pandemic.
    keywords: care; cells; cov-2; covid-19; covid-19 patients; disease; dose; drug; efficacy; host; human; iii; infection; patients; phase; potential; protein; response; rna; safety; sars; therapeutics; treatment; trial; use; vaccine; virus
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        item: #752 of 1349
          id: cord-294138-h7sfd1wa
      author: McIver, David J.
       title: Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents
        date: 2020-06-01
       words: 2787
      flesch: 49
     summary: The 1.4% prevalence of CoV RNA in rodents was much lower than what had been detected in bats in Laos; however, such observations have been made repeatedly, re-emphasizing the role of bats as a primary CoV source [5, [15] Studies in which CoV RNA was more frequently detected in rodents have used intestine or fecal matter for their studies, while we tested oral and rectal swab samples
    keywords: animals; bats; coronavirus; cov; covs; laos; rna; rodents; species; wildlife
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        item: #753 of 1349
          id: cord-294260-g410mavp
      author: Sztuba-Solińska, Joanna
       title: Subgenomic messenger RNAs: Mastering regulation of (+)-strand RNA virus life cycle
        date: 2011-04-10
       words: 9542
      flesch: 39
     summary: The arrow on (−) G RNA diagram indicates the initiation site and the direction of SG RNA synthesis. It was also shown that mutations disrupting the U-turn motif of the 5′ UTR stem-loop 2 (SL2) affected SG RNA synthesis, suggesting that SL2 mediates specific interactions with viral and/or cellular proteins involved in the synthesis of SG RNAs (Liu et al., 2007) .
    keywords: et al; initiation; promoter; protein; replication; rna; rnas; sequence; sg rna; sgp; strand; subgenomic; synthesis; transcription; trs; virus; viruses
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        item: #754 of 1349
          id: cord-294363-bv6xa8v8
      author: Zhou, Hong
       title: Potential Therapeutic Targets and Promising Drugs for Combating SARS‐CoV‐2
        date: 2020-05-05
       words: 8944
      flesch: 34
     summary: Decoupling deISGylating and deubiquitinating activities of the MERS virus papain-like protease Origin and evolution of pathogenic coronaviruses Preparation and anti-HIV activities of aurintricarboxylic acid fractions and analogues: direct correlation of antiviral potency with molecular weight Viral infection modulation and neutralization by camelid nanobodies Discovering drugs to treat coronavirus disease 2019 (COVID-19) Human Coronavirus: Host-Pathogen Interaction Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase A data-driven drug repositioning framework discovered a potential therapeutic agent targeting COVID-19 CAR T cell-induced cytokine release syndrome is mediated by macrophages and abated by IL-1 blockade Camostat mesilate attenuates pancreatic fibrosis via inhibition of monocytes and pancreatic stellate cells activity The course of clinical diagnosis and treatment of a case infected with coronavirus disease 2019 The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY Potent and selective inhibition of SARS coronavirus replication by aurintricarboxylic acid From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor First Case of 2019 Novel Coronavirus in the United States Severe Acute Respiratory Syndrome: Historical, Epidemiologic, and Clinical Features Genetic variability and phylogenetic analysis of Lagovirus europaeus strains GI.1 (RHDV) and GI.2 (RHDV2) based on the RNA-dependent RNA polymerase (RdRp) coding gene Identification of an existing Japanese pancreatitis drug, Nafamostat Contributes to Virus Spread and Immunopathology in the Airways of Murine Models after Coronavirus Infection Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors CD147 (EMMPRIN/Basigin) in kidney diseases: from an inflammation and immune system viewpoint The Use of TKM-100802 and Convalescent Plasma in 2 Patients With Ebola Virus Disease in the United States Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan, China Crystal structures of the main peptidase from the SARS coronavirus inhibited by a substrate-like aza-peptide epoxide Coronavirus infections and immune responses Adjuvant (131)I-metuximab for hepatocellular carcinoma after liver resection: a randomised Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus Nucleic-acid-based antiviral agents against positive single-stranded RNA viruses Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases RNA-based therapeutics for colorectal cancer: Updates and future directions Interaction between heptad repeat 1 and 2 regions in spike protein of SARS-associated coronavirus: implications for virus fusogenic mechanism and identification of fusion inhibitors L (2020) Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS-CoV-2 A (2020a) Coronavirus Disease 2019 and Influenza A (2020b) Coronavirus Disease 2019 and Influenza induces hepatocyte polarity loss by E-cadherin ubiquitination and degradation in hepatocellular carcinoma progress Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding Timely development of vaccines against SARS-CoV-2 The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase L (2020) Clinical Pathology of Critical Patient with Novel Coronavirus Pneumonia (COVID-19) Severe acute respiratory syndrome coronavirus replication inhibitor that interferes with the nucleic acid unwinding of the viral helicase Evaluation of SSYA10-001 as a replication inhibitor of severe acute respiratory syndrome, mouse hepatitis, and Middle East respiratory syndrome coronaviruses Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies RNA aptamer-based sensitive detection of SARS coronavirus nucleocapsid protein THE CONCISE GUIDE TO PHARMACOLOGY 2019/20:
    keywords: ace2; article; cells; copyright; coronavirus; cov-2; drugs; et al; infection; novel; patients; potential; protein; research; rna; sars; targets; treatment
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        item: #755 of 1349
          id: cord-294483-mozabpcs
      author: Choudhary, Manohar Lal
       title: Development of in vitro transcribed RNA as positive control for laboratory diagnosis of SARS-CoV-2 in India
        date: 2020-04-28
       words: 644
      flesch: 56
     summary: In addition, majority of the WHO screening protocols (5 of 6) are based on N gene targeting different nucleotide positions and require multiple specific positive controls 4 . The limit of detection for E gene was 10 6 yielding a cycle threshold (Ct) at cycle 29, RdRP (p1) was 10 5 with 27 Ct, RdRp (p2) was 10 6 with 29 Ct and
    keywords: gene; rna
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        item: #756 of 1349
          id: cord-294592-zwvr57a0
      author: Mukherjee, Moumita
       title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2
        date: 2020-08-11
       words: 6103
      flesch: 48
     summary: We have also looked at the possible regulation of viral genomic RNA through binding of host RNA binding proteins (RBPs) and miR-NAs in specific sequences of the viral UTRs. We also looked at the putative host RNA binding protein (RBP) and microRNA binding sites in these regions by ‘RBPmap’ and ‘RNA22 v2’ respectively.
    keywords: binding; expression; genome; host; mirna; region; rna; sars; sequence; site; variants; virus
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        item: #757 of 1349
          id: cord-294718-n3gx862b
      author: Tam, Patrick C K
       title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19)
        date: 2020-05-30
       words: 1608
      flesch: 52
     summary: This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. Given this uncertainty and detectable viral RNA in human milk, the benefits of human milk likely greatly outweigh risks associated with maternal COVID-19 infection, due to conferring protection to other respiratory illnesses [9] .
    keywords: human
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        item: #758 of 1349
          id: cord-294764-v28wbrqp
      author: Deval, Jerome
       title: Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses
        date: 2017-04-15
       words: 8333
      flesch: 32
     summary: Crystal structures of murine norovirus-1 RNA-dependent RNA polymerase in complex with 2-thiouridine or ribavirin Characterization of lethal Zika virus infection in AG129 mice Development of a reverse-genetics system for murine norovirus 3: long-term persistence occurs in the caecum and colon Favipiravir elicits antiviral mutagenesis during virus replication in vivo Norovirus polymerase fidelity contributes to viral transmission in vivo Norovirus vaccine against experimental human Norwalk virus illness In vitro proteolytic processing of the MD145 norovirus ORF1 nonstructural polyprotein yields stable precursors and products similar to those detected in calicivirus-infected cells Norovirus proteinase-polymerase and polymerase are both active forms of RNA-dependent RNA polymerase Chronic norovirus gastroenteritis in a double hematopoietic stem cell and lung transplant recipient Rapid evolution of pandemic noroviruses of the GII.4 lineage Caliciviruses differ in their functional requirements for eIF4F components High-throughput screening identification of poliovirus RNA-dependent RNA polymerase inhibitors Chronic diarrhea associated with persistent norovirus excretion in patients with chronic lymphocytic leukemia: report of two cases Rapid emergence and predominance of a broadly recognizing and fast-evolving norovirus GII.17 variant in late Interferons and ribavirin effectively inhibit Norwalk virus replication in replicon-bearing cells Stable expression of a Norwalk virus RNA replicon in a human hepatoma cell line Structural basis for initiation of transcription from an RNA polymerase-promoter complex Norovirus infection as a cause of diarrhea-associated benign infantile seizures Organization and expression of calicivirus genes Antiviral activity of nucleoside analogues against norovirus Structural bases of norovirus RNA dependent RNA polymerase inhibition by novel suramin-related compounds PPNDS inhibits murine Norovirus RNA-dependent RNA-polymerase mimicking two RNA stacking bases The genome-linked protein VPg of the Norwalk virus binds eIF3, suggesting its role in translation initiation complex recruitment Antiviral, antimetabolic and antineoplastic activities of 2 -or 3 -amino or -azido-substituted deoxyribonucleosides Viral shape-shifting: norovirus evasion of the human immune system Failure to detect norovirus in a large group of asymptomatic individuals by Adjuvanted intranasal Norwalk virus-like particle vaccine elicits antibodies and antibody-secreting cells that express homing receptors for mucosal and peripheral lymphoid tissues A fluorescence-based high-throughput screen to identify small compound inhibitors of the genotype 3a hepatitis C virus RNA polymerase Nonnucleoside inhibitors of norovirus RNA polymerase: scaffolds for rational drug design Norwalk virus nonstructural protein p48 forms a complex with the SNARE regulator VAP-A and prevents cell surface expression of vesicular stomatitis virus G protein Replication of human noroviruses in stem cell-derived human enteroids Norwalk virus N-terminal nonstructural protein is associated with disassembly of the golgi complex in transfected cells Poly(A)-and primer-independent RNA polymerase of Norovirus Mechanism of action of T-705 against influenza virus T-705 (favipiravir) and related compounds: novel broad-spectrum inhibitors of RNA viral infections Favipiravir (T-705), a novel viral RNA polymerase inhibitor The genome-linked protein VPg of vertebrate viruses-a multifaceted protein Epidemiology of foodborne norovirus outbreaks Synthesis of a universal 5-nitroindole ribonucleotide and incorporation into RNA by a viral RNA-dependent RNA polymerase Lack of norovirus replication and histo-blood group antigen expression in 3-dimensional intestinal epithelial cells The active form of the norovirus RNA-dependent RNA polymerase is a homodimer with cooperative activity Development of a microsphere-based serologic multiplexed fluorescent immunoassay and a reverse transcriptase PCR assay to detect murine norovirus 1 infection in mice Persistent infection with and serologic cross-reactivity of three novel murine noroviruses Studies of promoter recognition and start site selection by T7 RNA polymerase using a comprehensive collection of promoter variants Inhibition of human immunodeficiency virus type I reverse transcriptase by suramin-related compounds The ambiguous base-pairing and high substrate efficiency of T-705 (favipiravir) ribofuranosyl 5 -triphosphate towards influenza A virus polymerase Biochemical evaluation of the inhibition properties of favipiravir and 2 -C-methyl-cytidine triphosphates against human and mouse norovirus RNA polymerases New mouse model for dengue virus vaccine testing Enteric bacteria promote human and mouse norovirus infection of B cells Human norovirus culture in B cells Murine norovirus (MNV-1) exposure in vitro to the purine nucleoside analog Ribavirin increases quasispecies diversity Comparative murine norovirus studies reveal a lack of correlation between intestinal virus titers and enteric pathology STAT1-dependent innate immunity to a Norwalk-like virus Treatment of norovirus infections: moving antivirals from the bench to the bedside De novo initiation of viral RNA-dependent RNA synthesis Gastrointestinal norovirus infection associated with exacerbation of inflammatory bowel disease Inhibition of human norovirus by a viral polymerase inhibitor in the B cell culture system and in the mouse model Norwalk virus does not replicate in human macrophages or dendritic cells derived from the peripheral blood of susceptible humans Structures of the compact helical core domains of feline calicivirus and murine norovirus VPg proteins Subgenomic promoter recognition by the norovirus RNA-dependent RNA polymerases Increase in viral gastroenteritis outbreaks in Europe and epidemic spread of new norovirus variant Environmental transmission of norovirus gastroenteritis The evolution and transmission of epidemic GII.17 noroviruses Trends in statin use and low-density lipoprotein cholesterol levels among US adults: impact of the 2001 National Cholesterol Education Program guidelines Structure-based inhibition of norovirus RNA-dependent RNA polymerases Delivery of suramin as an antiviral agent through liposomal systems Norovirus regulation of the innate immune response and apoptosis occurs via the product of the alternative open reading frame 4 Norovirus RNA in the blood of a child with gastroenteritis and convulsions-a case report Synthesis in vitro of rabbit hemorrhagic disease virus subgenomic RNA by internal initiation on (−)sense genomic RNA: mapping of a subgenomic promoter The trypanocidal drug suramin and other trypan blue mimetics are inhibitors of pyruvate kinases and bind to the adenosine site Crystal structure of norwalk virus polymerase reveals the carboxyl terminus in the active site cleft Suramin prevents duck hepatitis B virus infection in vivo Protein-RNA linkage and posttranslational modifications of feline calicivirus and murine norovirus VPg proteins Challenges of culturing human norovirus in three-dimensional organoid intestinal cell culture models Noroviruses: a comprehensive review Picornaviral polymerase structure, function and fidelity modulation Synthesis and pharmacokinetics of valopicitabine (NM283), an efficient prodrug of the potent anti-HCV agent 2 -C-methylcytidine X-ray crystallographic structure of the Norwalk virus capsid The approved pediatric drug suramin identified as a clinical candidate for the treatment of EV71 infection-suramin inhibits EV71 infection in vitro and in vivo Norovirus virus-like particle vaccines for the prevention of acute gastroenteritis Inhibition of norovirus replication by the nucleoside analogue 2 -C-methylcytidine Favipiravir (T-705) inhibits in vitro norovirus replication The norovirus RdRp (NS7) is the central enzyme in norovirus RNA replication.
    keywords: cells; et al; fig; human; hunov; infection; inhibition; mnv; norovirus; norwalk; polymerase; protein; rdrp; replication; rna; site; structure; suramin; synthesis; vitro; vpg
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        item: #759 of 1349
          id: cord-294800-akr4f5p8
      author: Kabir, Md. Tanvir
       title: nCOVID-19 Pandemic: From Molecular Pathogenesis to Potential Investigational Therapeutics
        date: 2020-07-10
       words: 14110
      flesch: 33
     summary: Recently, it has been observed that nCOVID-19 might predispose to both arterial and venous thromboembolic disease because of immobilization, hypoxia, inflammation, and diffuse intravascular coagulation Guan et al., 2020; Klok et al., 2020; Wang et al., 2020a; Zhou et al., 2020) . Also, the derivatives of teicoplanin including telavancin, dalbavancin, and oritavancin, were also found to block the entry of SARS, MERS, and Ebola viruses (Zhou et al., 2016) .
    keywords: acute; antiviral; cells; coronavirus; cov-2; day; disease; drug; et al; host; human; individuals; infection; influenza; mers; ncovid-19; novel; patients; pneumonia; protein; response; sars; studies; study; syndrome; transmission; treatment; use; vitamin
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        item: #760 of 1349
          id: cord-294842-aesiff1f
      author: Romero-Brey, Inés
       title: Membranous Replication Factories Induced by Plus-Strand RNA Viruses
        date: 2014-07-22
       words: 11053
      flesch: 35
     summary: In addition, after multiple rounds of virus replication, tubular structures were also observed in the vicinity of VPs. As discussed earlier [119] , amongst these viruses two main architectures of remodeled membranes (morphotypes) can be found that may reflect two alternative strategies to induce the membranous microenvironments required to allow virus replication (summarized in Table 1 ).
    keywords: cells; cms; complex; denv; diameter; dmvs; family; formation; hepatitis; infection; membrane; protein; replication; rna; spherules; structures; synthesis; vesicles; virus; viruses
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        item: #761 of 1349
          id: cord-294890-93ldjyi5
      author: Chen, Yan
       title: Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour
        date: 2018-11-06
       words: 8674
      flesch: 48
     summary: lncRNAs acting as eTMs for miRNAs may be an important regulatory mechanism during longan early SE lncRNAs were observed to function as eTMs for miR-NAs, revealing a new mechanism for the regulating of miRNAs by lncRNAs in plants. A common method of trans-regulation is the upregulation of target gene expression by forming dimers with neighboring mRNAs that increase mRNA stability [56, 57] .
    keywords: coding; dlo; early; expression; genes; icpec; lncrnas; longan; mirnas; plant; qpcr; regulation; stage; target; target genes
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        item: #762 of 1349
          id: cord-295019-8tf8ah6g
      author: Weber, Wilfried
       title: Emerging biomedical applications of synthetic biology
        date: 2011-11-29
       words: 9531
      flesch: 28
     summary: A celebration of the genome, part I Genotype and SNP calling from next-generation sequencing data Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing Parallel on-chip gene synthesis and application to optimization of protein expression Creating bacterial strains from genomes that have been cloned and engineered in yeast Evidence for large diversity in the human transcriptome created by Alu RNA editing Hematopoietic stem cell gene therapy with a lentiviral vector in X-linked adrenoleukodystrophy Creation of a bacterial cell controlled by a chemically synthesized genome Life after the synthetic cell Making cellular memories A synchronized quorum of genetic clocks Diversity-based, model-guided construction of synthetic gene networks with predicted functions A synthetic oscillatory network of transcriptional regulators A synthetic gene-metabolic oscillator Construction of a genetic toggle switch in Escherichia coli An engineered mammalian band-pass network Hysteresis in a synthetic mammalian gene network An engineered epigenetic transgene switch in mammalian cells Rationally designed logic integration of regulatory signals in mammalian cells A universal RNAi-based logic evaluator that operates in mammalian cells A fast, robust and tunable synthetic gene oscillator Intron length increases oscillatory periods of gene expression in animal cells A tunable synthetic mammalian oscillator A synthetic-natural hybrid oscillator in human cells A synthetic time-delay circuit in mammalian cells and mice Multi-input RNAi-based logic circuit for identification of specific cancer cells b | Acetylsalicylic acid (Aspirin)-triggered killing of cancer cells after invasion of Salmonella spp.
    keywords: bacteria; biology; cancer; cells; control; devices; drug; example; expression; gene; human; levels; mammalian; mice; networks; production; promoter; protein; synthetic; transcription; tumour; type
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        item: #763 of 1349
          id: cord-295130-e7j7kac0
      author: Moreno-Contreras, Joaquín
       title: Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages
        date: 2020-09-22
       words: 2912
      flesch: 48
     summary: After collection, both swab and saliva samples were stored at 4°C until transported to the Institute of Biotechnology/UNAM for their analysis, which was within 24 to 36 h after sample collection. For saliva samples that had high viscosity, 1 volume of sterile phosphate-buffered saline (PBS) was added and mixed by repeated pipetting, and the diluted saliva sample was extracted as mentioned above.
    keywords: cov-2; rna; saliva; samples; sars; swabs
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        item: #764 of 1349
          id: cord-295217-z2erqkr9
      author: Seow, Justine Jia Wen
       title: Single‐Cell RNA Sequencing for Precision Oncology: Current State-of-Art
        date: 2020-06-02
       words: 4354
      flesch: 41
     summary: Ambient RNA contamination: Background contamination of RNA from dying single cells in droplet-based methods Natural log transform: To transform skewed data to approximately conform to normality. This is used to infer future directionalities of single cells.
    keywords: algorithms; analysis; batch; cell; data; expression; gene; methods; rna; scrna; seq; sequencing
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        item: #765 of 1349
          id: cord-295351-0zr2e8lh
      author: Mohd Ropidi, Muhammad Izzuddin
       title: Endoplasmic reticulum: a focal point of Zika virus infection
        date: 2020-01-20
       words: 7858
      flesch: 32
     summary: ZIKV proteins localize to distinct subcellular compartments ZIKV proteins are primarily distributed within and in close proximity to several endomembrane compartments including the endoplasmic reticulum, Golgi apparatus, endosomes, lysosomes, autophagosomes, and nucleus The subcellular distribution of certain ZIKV proteins was corroborated in a separate study where interatomic analyses using proximity-dependent biotin-identification (BioID) labeling and FLAG-based immunoprecipitation (IP) coupled with mass spectrometry (MS) uncover indepth molecular interactions between ZIKV proteins with various host organelles and proteins.
    keywords: assembly; cells; complex; expression; genome; host; infection; ire1; membrane; protein; replication; response; rna; stress; upr; virus; zika; zikv
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        item: #766 of 1349
          id: cord-295467-9fnis6ci
      author: Botella, Leticia
       title: The European race of Gremmeniella abietina hosts a single species of Gammapartitivirus showing a global distribution and possible recombinant events in its history
        date: 2014-12-12
       words: 5927
      flesch: 42
     summary: A unique species of G. abietina RNA virus–MS1 (GaRV-MS1) appears to occur indistinctly in G. abietina biotypes A and B, without a particular geographical distribution pattern. RNA recombination events are common among plant ssRNA viruses (Chare 2003; Alabi et al. 2010; Sztuba-Solinska et al. 2011 ) and human and animal dsRNA viruses such as rotaviruses (Suzuki et al. 1998; Phan et al. 2007 ), but there is less evidence of recombination in the dsRNAs of plant (Liu et al. 2012) or fungal viruses (Carbone et al. 2004; Feau et al. 2014; Linder-Basso et al. 2005; Voth et al. 2006) , and this phenomenon is particularly scarce in fungal partitiviruses.
    keywords: abietina; biotype; et al; garv; gremmeniella; isolates; ms1; population; rdrp; recombination; rna; sequences
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        item: #767 of 1349
          id: cord-295733-f3rt1fyk
      author: Ge, Tianxiang
       title: Evaluation of disinfection procedures in a designated hospital for COVID-19
        date: 2020-08-22
       words: 2493
      flesch: 43
     summary: WHO Director-General's opening remarks at the media briefing on COVID-19 -11 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan Does SARS-CoV-2 has a longer incubation period than SARS and MERS Temporal dynamics in viral shedding and transmissibility of COVID-19 Presumed Asymptomatic Carrier Transmission of COVID-19 Experimental aerosol survival of SARS-CoV-2 in artificial saliva and tissue culture media at medium and high humidity Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1 Aerosol transmission of infectious disease Coughs and Sneezes: Their Role in Transmission of Respiratory Viral Infections, Including SARS-CoV-2 Laboratory management for SARS-CoV-2 detection: a user-friendly combination of the heat treatment approach and rt-Real-time PCR testing Epidemiologic Features and Clinical Course of Patients Infected With SARS-CoV-2 in Singapore Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients Asymptomatic COVID-19 Patients Can Contaminate Their Surroundings: an Environment Sampling Study Environmental contamination of SARS-CoV-2 in healthcare premises Severe acute respiratory syndrome coronavirus 2 RNA contamination of inanimate surfaces and virus viability in a health care emergency unit Avoiding hospital-related infections during the COVID-19 epidemic SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital Analysis of the infection status of the health care workers in Wuhan during the COVID-19 outbreak: A cross-sectional study The presence of SARS-CoV-2 RNA in the feces of COVID-19 patients Evaluation of SARS-CoV-2 RNA shedding in clinical specimens and clinical characteristics of 10 patients with COVID-19 in Macau Clinical and virological data of the first cases of COVID-19 in Europe: a case series SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases Evaluation of lockdown impact on SARS-CoV-2 dynamics through viral genome quantification in Paris wastewaters First detection of SARS-CoV-2 in untreated wastewaters in Italy Wastewater-Based Epidemiology: Global Collaborative to Maximize Contributions in the Fight Against COVID-19 Coronaviruses in wastewater processes: Source, fate and potential risks Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals The common symptoms of COVID-19 patients include fever, fatigue, dry cough, and the computed tomography scans showed bilateral patchy shadows or ground glass opacity in the lungs, while headache, dizziness, and gastrointestinal symptoms including abdominal pain, diarrhea, and vomiting are less common symptoms
    keywords: cov-2; covid-19; disinfection; patients; samples; sars
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        item: #768 of 1349
          id: cord-296250-7ln7p715
      author: Wang, Sheng-Fan
       title: The pharmacological development of direct acting agents for emerging needed therapy against severe acute respiratory syndrome coronavirus-2
        date: 2020-05-20
       words: 4978
      flesch: 35
     summary: In vitro susceptibility of 10 clinical isolates of SARS coronavirus to selected antiviral compounds Interferon priming enables cells to partially overturn the SARS coronavirus-induced block in innate immune activation Pegylated interferon-alpha protects type 1 pneumocytes against SARS coronavirus infection in macaques Proposal for vaccination against SARS coronavirus using avian infectious bronchitis virus strain H from The Netherlands Interferon alfacon-1 plus corticosteroids in severe acute respiratory syndrome: a preliminary study Current treatment options and the role of peptides as potential therapeutic components for Middle East Respiratory Syndrome (MERS): a review Managing SARS amidst uncertainty Inhibition of SARS coronavirus infection in vitro with clinically approved antiviral drugs Clinical features and short-term outcomes of 144 patients with SARS in the greater Toronto area Critics slam treatment for SARS as ineffective and perhaps dangerous Washington State 2019-nCoV Case Investigation Team. 18 Earlier evidence demonstrated that the combination of ribavirin and IFN-β had a synergistic effect for inhibiting the replication of SARS coronavirus in animal and human cell lines.
    keywords: coronavirus; cov-2; covid-19; development; entry; novel; protein; receptor; replication; rna; sars; treatment; vitro
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        item: #769 of 1349
          id: cord-296309-i1mpov7k
      author: Houldcroft, Charlotte J.
       title: Clinical and biological insights from viral genome sequencing
        date: 2017-01-16
       words: 9059
      flesch: 23
     summary: The concentration of virus particles (see the Zika virus example above 72 ), depletion of host material and/or sequencing to high read depth can increase the amount of virus sequence, but all of these methods add to the cost. This is particularly relevant for rapid responses to emerging threats, such as Zika virus 81 .
    keywords: dna; drug; enrichment; example; genome; hiv; methods; pcr; resistance; rna; sequence; sequencing; target; variants; virus; viruses; wgs; zika
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        item: #770 of 1349
          id: cord-296847-r752bcsu
      author: Campanini, Giulia
       title: Human respiratory syncytial virus (hRSV) RNA quantification in nasopharyngeal secretions identifies the hRSV etiologic role in acute respiratory tract infections of hospitalized infants
        date: 2007-04-23
       words: 3048
      flesch: 37
     summary: Observation of 8 consecutive epidemics between 1982 and 1990 Nasal quantity of respiratory syncytial virus correlates with disease severity in hospitalized infants A randomised, double-blind, placebo-controlled trial of dexamethasone in severe respiratory syncytial virus (RSV) infections: effects on RSV quantity and clinical outcome Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription-nested PCR assay Natural infection of infants with respiratory syncytial virus subgroups A and B: a study of frequency, disease severity and viral load Diagnosis of respiratory syncytial virus infection: comparison of reverse transcription-PCR to viral culture and serology in adults with respiratory illness Comparison of quantitative reverse transcription-PCR to viral culture for assessment of respiratory syncytial virus shedding Evaluation of R-Mix fresh cells in shell vials for detection of respiratory viruses Detection of respiratory syncytial virus by reverse-transcription-PCR and hybridization with a DNA enzyme immunoassay Occurrence of groups A and B respiratory syncytial virus over 15 years: associated epidemiologic and clinical characteristics in hospitalized and ambulatory children Evaluation of five methods for respiratory syncytial virus detection Evaluation of direct immunofluorescence, enzyme immunoassay, centrifugation culture, and conventional culture for the detection of respiratory syncytial virus SimulFluor respiratory screen for rapid detection of multiple respiratory viruses in clinical specimens by immunofluorescence staining Respiratory syncytial virus-coded pediatric hospitalisation, 1997-1999 Reduction of respiratory syncytial virus (RSV) in tracheal aspirates in intubated infants using humanized monoclonal antibody to RSV F protein A singleseason epidemic with respiratory syncytial virus subgroup B2 during 10 epidemic years, 1978 to 1988 Rapid detection of respiratory syncytial virus in nasopharyngeal aspirates by reverse transcription and polymerase chain reaction amplification Comparison of a real-time reverse transcription PCR assay and a culture technique for quantitative assessment of viral load in children naturally infected with respiratory syncytial virus Monoclonal antibodies versus reverse transcription-PCR for detection of respiratory viruses in a patient population with respiratory tract infections admitted to hospital Detection and molecular characterization of Ebola viruses causing disease in human and nonhuman primates Anderson LJ. Bronchiolitis-associated hospitalizations among US children Severity of respiratory virus infection is related to virus strain We thank all the technical staff of the Servizio di Virologia for performing all the assays.
    keywords: hrsv; infants; rna; virus
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        item: #771 of 1349
          id: cord-296977-yzhsdz9c
      author: Soares, R. R. G.
       title: Point-of-care detection of SARS-CoV-2 in nasopharyngeal swab samples using an integrated smartphone-based centrifugal microfluidic platform
        date: 2020-11-06
       words: 6546
      flesch: 41
     summary: We introduce a novel portable bead-based centrifugal microfluidic platform and demonstrate LAMP based viral RNA detection directly from heat-inactivated nasopharyngeal swab samples. These features can potentially pave the way to bring routine and scalable diagnostics to RLS, as well as expanding the current diagnostic capacities in high-income countries by bringing viral RNA detection directly to the field.
    keywords: author; copyright; disc; funder; holder; lamp; license; medrxiv preprint; november; peer; preprint; review; version
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        item: #772 of 1349
          id: cord-297039-vfuem6bk
      author: Beltrán-García, Jesús
       title: Circular RNAs in Sepsis: Biogenesis, Function, and Clinical Significance
        date: 2020-06-25
       words: 7510
      flesch: 35
     summary: The novel roles of circular RNAs in metabolic organs Coordinated circRNA Biogenesis and Function with NF90/NF110 in Viral Infection Cytokine storm and sepsis disease pathogenesis Another Road to Sepsis and Its Therapeutic Targeting Modulation of TNF-α mRNA stability by human antigen R and miR181s in sepsis-induced immunoparalysis miRNA-125b regulates TNF-α production in CD14+ neonatal monocytes via post-transcriptional regulation Glucocorticoid-induced microRNA-511 protects against TNF by down-regulating TNFR1 Multiplex cytokine profiling in patients with sepsis Dysregulation in microRNA expression in peripheral blood mononuclear cells of sepsis patients is associated with immunopathology Attenuation of Cardiac Dysfunction in Polymicrobial Sepsis by MicroRNA-146a Is Mediated via Targeting of IRAK1 and TRAF6 Expression Toll-like receptor-mediated NF-kappaB activation: A phylogenetically conserved paradigm in innate immunity A human homologue of the Drosophila Toll protein signals activation of adaptive immunity Elevation of IL-18 in human sepsis IL-18) levels in patients with sepsis IL-27 Enhances LPS-Induced Proinflammatory Cytokine Production via Upregulation of TLR4 Expression and Signaling in Human Monocytes IL-27, a Heterodimeric Cytokine Composed of EBI3 and p28 Protein, Induces Proliferation of Naive CD4+ T Cells Circular RNA circ-4099 is induced by TNF-α and regulates ECM synthesis by blocking miR-616-5p inhibition of Sox9 in intervertebral disc degeneration Follow-up study identifies two novel susceptibility loci PRKCB and 8p11.21 for systemic lupus erythematosus Calcitonin gene-related peptide induces IL-6 expression in RAW264.7 macrophages mediated by mmu_circRNA_007893 CircRNA hsa_circ_0005105 upregulates NAMPT expression and promotes chondrocyte extracellular matrix degradation by sponging miR-26a The down-regulation of hsa_circ_0012919, the sponge for miR-125a-3p, contributes to DNA methylation of CD11a and CD70 in CD4+ T cells of systemic lupus erythematous Persistent inflammation and immunosuppression: A common syndrome and new horizon for surgical intensive care MyD88-dependent expansion of an immature GR-1(+)CD11b(+) population induces T cell suppression and Th2 polarization in sepsis MicroRNA-155 promotes autoimmune inflammation by enhancing inflammatory T cell development MicroRNA control in the immune system: BBasic principles MicroRNA miR-223 as regulator of innate immunity Impact of miR-223-3p and miR-2909 on inflammatory factors IL-6, IL-1ß, and TNF-α, and the TLR4/TLR2/NF-κB/STAT3 signaling pathway induced by lipopolysaccharide in human adipose stem cells Hsa_circ_0003159 inhibits gastric cancer progression by regulating miR-223-3p/NDRG1 axis Serum miR-146a and miR-223 as potential new biomarkers for sepsis NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses The prognostic value of plasma microRNA-155 and microRNA-146a level in severe sepsis and sepsis-induced acute lung injury patients Circular RNA RSF1 promotes inflammatory and fibrotic phenotypes of irradiated hepatic stellate cell by modulating miR-146a-5p Circular RNA expression alterations in colon tissues of Crohn's disease patients Circular RNA profile identifies circPVT1 as a proliferative factor and prognostic marker in gastric cancer MiR-125b but not miR-125a is upregulated and exhibits a trend to correlate with enhanced disease severity, inflammation, and increased mortality in sepsis patients Circular RNA GLI2 promotes osteosarcoma cell proliferation, migration, and invasion by targeting miR-125b-5p Circulating plasma microRNAs can differentiate human sepsis and Systemic Inflammatory Response Syndrome (SIRS) NSD2 circular RNA promotes metastasis of colorectal cancer by targeting miR-199b-5p-mediated DDR1 and JAG1 signalling Circular RNA 0000096 affects cell growth and migration in gastric cancer Circular RNA circHIPK3 Promotes the Proliferation and Differentiation of Chicken Myoblast Cells by Sponging miR-30a-3p Circular RNA Signature in Hepatocellular Carcinoma CircRNA-9119 regulates the expression of prostaglandin-endoperoxide synthase 2 (PTGS2) by sponging miR-26a in the endometrial epithelial cells of dairy goat Circular RNA circTRIM33-12 acts as the sponge of MicroRNA-191 to suppress hepatocellular carcinoma progression Sepsis: Older and newer concepts Circular RNA circ-Foxo3 induced cell apoptosis in urothelial carcinoma via interaction with miR-191-5p Basophil Recruitment to Skin Lesions of Patients with Systemic Lupus Erythematosus Mediated by CCR1 and CCR2 Sepsis definitions: Time for change The Clinical Challenge of Sepsis Identification and Monitoring Surviving Sepsis Campaign: International Guidelines for Management of Severe Sepsis and Septic Shock Early versus delayed administration of norepinephrine in patients with septic shock Empiric antibiotic treatment reduces mortality in severe sepsis and septic shock from the first hour: Results from a guideline-based performance improvement program Diagnostic and prognostic markers in sepsis New approaches to sepsis: Molecular diagnostics and biomarkers MiR-145 negatively regulates TGFBR2 signaling responsible for sepsis-induced acute lung injury Function and clinical significance of circRNAs in solid tumors Matrix-metalloproteinases and their inhibitors are elevated in severe sepsis: Prognostic value of TIMP-1 in severe sepsis Matrix metalloproteinase-14 triggers an anti-inflammatory proteolytic cascade in endotoxemia Predictive value of miRNA-29a and miRNA-10a-5p for 28-day mortality in patients with sepsis-induced acute kidney injury.
    keywords: biogenesis; biomarkers; cells; circrnas; circular; expression; function; human; linear; patients; process; response; role; sepsis; septic; splicing
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        item: #773 of 1349
          id: cord-297078-pxggjaby
      author: Poole, Anthony M.
       title: Modern mRNA Proofreading and Repair: Clues that the Last Universal Common Ancestor Possessed an RNA Genome?
        date: 2005-03-16
       words: 8291
      flesch: 40
     summary: A glycyl radical site in the crystal structure of a class III ribonucleotide reductase Mutation accumulation in transfer RNAs: molecular evidence for Muller#s ratchet in mitochondrial genomes The genome sequence of the SARS-associated coronavirus Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes The involvement of RNA in ribosome function Viroid replication is inhibited by alpha-amanitin A minimal gene set for cellular life derived by comparison of complete bacterial genomes The driving force for molecular evolution of translation Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase Evolution of the genetic apparatus Intrinsic transcript cleavage activity of RNA polymerase AlkB restores the biological function of mRNA and tRNA inactivated by chemical methylation Characterization of a viroid-derived RNA promoter for the DNA-dependent RNA polymerase from Escherichia coli Binding site of Escherichia coli RNA polymerase to an RNA promoter Overlapping messages and survivability The nature of the last universal common ancestor A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity Early evolution: prokaryotes, the new kids on the block Methyl-RNA: an evolutionary bridge between RNA and DNA? Under Scenario 2, the LUCA possessed an RNA genome, and if the inherent potential for RNA repair by RNA polymerases was realized, both the genome and expressed transcripts would be subject to proofreading and repair, as both would be synthesized by RNA polymerase.
    keywords: apparatus; dna; genome; luca; modern; origin; polymerase; proofreading; repair; replication; rna; rna polymerase; scenario
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        item: #774 of 1349
          id: cord-297092-oq14cwka
      author: Tan, Shaoyuan
       title: Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model
        date: 2020-10-07
       words: 6986
      flesch: 47
     summary: SVA reads were extracted from total sequencing reads and analyzed. SVA reads were extracted from total sequencing reads and analyzed.
    keywords: consensus; drs; genome; pcs; reads; rna; samples; sequence; sequencing; sva; table; total; viral
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        item: #775 of 1349
          id: cord-297323-l3f12hg4
      author: Amor, Sandra
       title: Innate immunity during SARS‐CoV‐2: evasion strategies and activation trigger hypoxia and vascular damage
        date: 2020-09-26
       words: 4990
      flesch: 26
     summary: All rights reserved the Acute COVID-19 Cardiovascular Syndrome Neurological associations of COVID-19 The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19 Breadth of concomitant immune responses prior to patient recovery: a case report of non-severe COVID-19 Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals Marked T cell activation, senescence, exhaustion and skewing towards TH17 in patients with COVID-19 pneumonia Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding 3D Models of glycosylated SARS-CoV-2 spike protein suggest challenges and opportunities for vaccine development Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy Neuropilin-1 is a host factor for SARS-CoV-2 infection Accessory proteins of SARS-CoV and other coronaviruses Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense Identification of Residues of SARS-CoV nsp1 That Differentially Affect Inhibition of Gene Expression and Antiviral Signaling Severe Acute Respiratory Syndrome Coronavirus Evades Antiviral Signaling: Role of nsp1 and Rational Design of an Attenuated Strain Severe acute respiratory syndrome coronavirus nsp1 protein suppresses host gene expression by promoting host mRNA degradation Like many viruses, SARS‐CoV‐2 has evolved strategies to circumvent innate immune detection including low CpG levels in the genome, glycosylation to shield essential elements including the receptor binding domain, RNA shielding and generation of viral proteins that actively impede anti‐viral interferon responses.
    keywords: article; cell; copyright; coronavirus; cov-2; covid-19; host; infection; protein; response; rights; rna; sars; syndrome
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        item: #776 of 1349
          id: cord-297579-ohpm5ys0
      author: Netzler, Natalie E.
       title: Norovirus antivirals: Where are we now?
        date: 2018-12-25
       words: 6479
      flesch: 19
     summary: Curcumin shows antiviral properties against norovirus Antiviral effect of vitamin A on norovirus infection via modulation of the gut microbiome Potential therapeutic agents for feline calicivirus infection Opposing effects of nitazoxanide on murine and human norovirus Nitazoxanide inhibits human norovirus replication and synergizes with ribavirin by activation of cellular antiviral response Nitazoxanide: a new thiazolide antiparasitic agent Nitazoxanide: a first-in-class broad-spectrum antiviral agent Nitazoxanide in the treatment of viral gastroenteritis: a randomized double-blind placebo-controlled clinical trial Norovirus gastroenteritis successfully treated with nitazoxanide Successful treatment of chronic norovirus gastroenteritis with nitazoxanide in a pediatric kidney transplant recipient Chronic diarrhea associated with persistent norovirus excretion in patients with chronic lymphocytic leukemia: report of two cases Chronic norovirus infections in cardiac transplant patients: considerations for evaluation and management Nitazoxanide is an ineffective treatment of chronic norovirus in patients with x-linked agammaglobulinemia and may yield false-negative polymerase chain reaction findings in stool specimens Prolonged norovirus infection after pancreas transplantation: a case report and review of chronic norovirus Her project focuses on identifying antiviral compounds for norovirus and other caliciviruses. Nonnucleoside inhibitors of norovirus RNA polymerase: scaffolds for rational drug design Broad-spectrum antivirals against 3C or 3C-like proteases of picornaviruses, noroviruses, and coronaviruses A fluorescence-based high-throughput screen to identify small compound inhibitors of the genotype 3a hepatitis C virus RNA polymerase In silico screening for human norovirus antivirals reveals a novel non-nucleoside inhibitor of the viral polymerase Model systems for the study of human norovirus Biology STAT1-dependent innate immunity to a Norwalk-like virus Replication of norovirus in cell culture reveals a tropism for dendritic cells and macrophages Characterization of ozone disinfection of murine norovirus Comparison of chlorine and peroxyacetic-based disinfectant to inactivate Feline calicivirus, Murine norovirus and Hepatitis A virus on lettuce Disinfection kinetics of murine norovirus using chlorine and chlorine dioxide Recovery of genetically defined murine norovirus in tissue culture by using a fowlpox virus expressing T7 RNA polymerase Development of an optimized RNA-based murine norovirus reverse genetics system Chimpanzees as an animal model for human norovirus infection and vaccine development Experimental infection of Macaca nemestrina with a Toronto Norwalk-like virus of epidemic viral gastroenteritis Experimental norovirus infections in non-human primates Pathogenesis of a genogroup II human norovirus in gnotobiotic pigs
    keywords: activity; antiviral; cell; compounds; culture; development; human; infection; inhibition; inhibitors; norovirus; norwalk; polymerase; protease; replication; rna; studies; treatment
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        item: #777 of 1349
          id: cord-297760-uzzuoy9v
      author: Naito, Yuki
       title: siVirus: web-based antiviral siRNA design software for highly divergent viral sequences
        date: 2006-07-01
       words: 1143
      flesch: 49
     summary: However, designing functional siRNAs that target viral sequences is problematic because of their extraordinarily high genetic diversity. Highly conserved siRNA sequences are selected based on their degree of conservation, defined as the proportion of viral sequences that are targeted by the corresponding siRNA, with complete matches (i.e. 21/21 matches).
    keywords: sequences; sirnas; target
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        item: #778 of 1349
          id: cord-297776-k38jssr0
      author: Volk, Aaron
       title: Coronavirus Endoribonuclease and Deubiquitinating Interferon Antagonists Differentially Modulate the Host Response during Replication in Macrophages
        date: 2020-05-18
       words: 5851
      flesch: 33
     summary: We used an online tool called Database for Annotation, Visualization and Integrated Discovery (DAVID) to cluster the genes highly upregulated by EndoUmut virus infection (bracket in Fig. 1 ) based on functional similarities (21, 22) . Interestingly, despite of this elevated IFN expression during DUBmut infection, we did not observe a similar increase in ISG15 mRNA, which is upregulated by EndoUmut virus infection (Fig. 2B) .
    keywords: cells; coronavirus; dubmut; endoumut; expression; genes; host; infection; interferon; macrophages; response; type; virus
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        item: #779 of 1349
          id: cord-297790-tpjxt0w5
      author: Mandl, Judith N.
       title: Going to Bat(s) for Studies of Disease Tolerance
        date: 2018-09-20
       words: 9488
      flesch: 28
     summary: Given the diversity of the Chiroptera order (Figure 1) , we may simply see more bat viruses because there are so many (>1,300) species of bats (31) . Fewer studies have examined the adaptive immune system than those probing innate immune pathways, but experimental infections with bat borne viruses have demonstrated that bats generate low or absent antibody responses which often wane rapidly.
    keywords: aegyptiacus; alecto; bats; cell; dna; evidence; genes; host; humans; ifn; infection; reservoir; responses; rna; species; studies; virus; viruses
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        item: #780 of 1349
          id: cord-297834-me1ajoyb
      author: Schountz, Tony
       title: Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions
        date: 2014-03-14
       words: 6426
      flesch: 33
     summary: In addition, antigen presenting cells isolated from Norway rats and infected with SEOV in vitro were resistant to stimulation, suggesting that virus infection inhibits the normal signaling activities of these cells [85] . Kinetics of immune responses in deer mice experimentally infected with Sin Nombre virus Experimental infection with Puumala virus, the etiologic agent of nephropathia epidemica, in bank voles (Clethrionomys glareolus) Intraspecific transmission of Hantaan virus, etiologic agent of Korean hemorrhagic fever, in the rodent Apodemus agrarius Modes of Seoul virus infections: Persistency in newborn rats and transiency in adult rats High levels of cytokine-producing cells in the lung tissues of patients with fatal hantavirus pulmonary syndrome The pathogenesis of nephropathia epidemica: New knowledge and unanswered questions Seoul virus enhances regulatory and reduces proinflammatory responses in male Norway rats Regulatory T cells enhance persistence of the zoonotic pathogen Seoul virus in its reservoir host Seoul virus-infected rat lung endothelial cells and alveolar macrophages differ in their ability to support virus replication and induce regulatory T cell phenotypes A lethal disease model for hantavirus pulmonary syndrome Maporal viral infection in the Syrian golden hamster: A model of hantavirus pulmonary syndrome The delicate pygmy rice rat (Oligoryzomys delicatus) is the principal host of Maporal virus (family Bunyaviridae, genus Hantavirus).
    keywords: antibodies; cells; deer; disease; expression; hantavirus; host; immune; infection; mice; reservoir; response; rodent; species; virus
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        item: #781 of 1349
          id: cord-297880-jlnv90vn
      author: Stewart, Hazel
       title: Transcriptional and Translational Landscape of Equine Torovirus
        date: 2018-08-16
       words: 10309
      flesch: 42
     summary: The viral genome was assembled de novo from RNA-seq reads and confirmed as EToV, Berne isolate. Some of the identified GO categories, including cytokine signaling, innate immune responses, and ribosome biogenesis, have been identified in previous RNA-seq analyses of various coronaviruses (43, 44) .
    keywords: analysis; density; etov; fig; gene; genome; leader; orf1a; protein; reads; ribo; rna; seq; sequence; torovirus; trs
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        item: #782 of 1349
          id: cord-297974-sduz0j35
      author: Bokelmann, L.
       title: Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP)
        date: 2020-08-06
       words: 4771
      flesch: 47
     summary: Amplification in LAMP reactions is often detected colorimetrically by a pH sensitive dye that changes color when extensive DNA synthesis lowers the pH of the reaction (Tanner et al. 2015) . Evaluation of different amounts of Tte UvrD helicase in LAMP reactions.
    keywords: amplification; cov-2; detection; ilamp; preprint; reaction; samples; sars
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        item: #783 of 1349
          id: cord-298032-3zlu8g8y
      author: Nan, Yuchen
       title: Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds
        date: 2018-04-20
       words: 10600
      flesch: 36
     summary: For HSV-1, ICP0 and ICP27 were selected as virus PPMO targets. Thus, both peptide-conjugated PMO (PPMO) and non-conjugated PMOs have been tested against Ebola virus infection in cultured cells and animal models.
    keywords: antisense; cells; et al; genome; infection; inhibition; mice; morpholino; mrna; oligomers; peptide; pmo; ppmo; replication; rna; sequence; targeting; translation; treatment; viral; virus; viruses; vivo
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        item: #784 of 1349
          id: cord-298036-2zurc60t
      author: Imre, Gergely
       title: Cell death signalling in virus infection
        date: 2020-09-12
       words: 8035
      flesch: 31
     summary: [45] , thus only blocking of both pathways at the same time can significantly reduce IAV induced cell death. Conversely, some viruses hijack cell death pathways to selectively destroy cell populations in order to compromise the immune system of the host.
    keywords: activation; apoptosis; apoptotic; caspase-8; cell; death; human; immune; infection; inflammasome; leads; necroptosis; nlrp3; pathways; protein; pyroptosis; response; virus
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        item: #785 of 1349
          id: cord-298078-uqrwq5qk
      author: Kwak, Hoyun
       title: Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus
        date: 2011-08-30
       words: 5377
      flesch: 51
     summary: Since the frameshifting of IBV generates RNA dependent RNA polymerase, which is critical for successful viral replication, the protein that inhibits frameshifting must be a major antiviral regulator in eukaryotic cells. Since translation is a complex process involving many regulatory factors in addition to the ribosome, binding of RNA binding protein (RBP) at a nearby RNA signal could affect RNA conformation and somehow redirect the translational machinery
    keywords: anxa2; binding; cells; efficiency; frameshifting; ibv; mutant; protein; pseudoknot; ribosomal; rna; type
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        item: #786 of 1349
          id: cord-298233-qqhgmqrg
      author: Nan, Yuchen
       title: Molecular Biology and Infection of Hepatitis E Virus
        date: 2016-09-07
       words: 16476
      flesch: 35
     summary: For the detailed geographical distribution of hepatitis E virus genotypes, please refer to these reviews (Dalton et al., 2008; Kamar et al., 2012a) . inhibits type I interferon induction by ORF1 products Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites Hepatitis E virus ORF1 encoded macro domain protein interacts with light chain subunit of human ferritin and inhibits its secretion Genetic variability and evolution of hepatitis E virus Efficient cell culture systems for hepatitis E virus strains in feces and circulating blood Culture systems for hepatitis E virus Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure The hepatitis E virus intraviral interactome Inhibition of alphavirus infection in cell culture and in mice with antisense morpholino oligomers Hepatitis E virus (HEV) protease: a chymotrypsin-like enzyme that processes both non-structural (pORF1) and capsid (pORF2) protein The in vitro-synthesized RNA from a cDNA clone of hepatitis E virus is infectious Molecular characterization of hepatitis E virus ORF1 gene supports a papain-like cysteine protease (PCP)-domain activity The hepatitis E virus ORF1 'X-domain' residues form a putative macrodomain protein/Appr-1-pase catalytic-site, critical for viral RNA replication The intergenic-junction variant (genotype 2 isolate) of hepatitis E virus restores the CREX 'stem-loop' structural integrity, essential for viral life cycle Evidence of MAPK-JNK1/2 activation by hepatitis E virus ORF3 protein in cultured hepatoma cells Hepatitis E virus infection among solid organ transplant recipients, the Netherlands Herpesvirus tegument protein pUL37 interacts with dystonin/BPAG1 to promote capsid transport on microtubules during egress Zoonotic origin of hepatitis E MacroH2A, a core histone containing a large nonhistone region Evolutionary conservation of histone macroH2A subtypes and domains Higher concentrations of histone macroH2A in the Barr body are correlated with higher nucleosome density Early secretory pathway localization and lack of processing for hepatitis E virus replication protein pORF1 Deletions of the hypervariable region (HVR) in open reading frame 1 of hepatitis E virus do not abolish virus infectivity: evidence for attenuation of HVR deletion mutants in vivo Mutational analysis of the hypervariable region of hepatitis e virus reveals its involvement in the efficiency of viral RNA replication Hepatitis E: an emerging awareness of an old disease Evolution of the hepatitis E virus polyproline region: order from disorder The molecular epidemiology of hepatitis E virus infection The hepatitis E virus polyproline region is involved in viral adaptation ADP-ribose-1-monophosphatase: a conserved coronavirus enzyme that is dispensable for viral replication in tissue culture Identification of protease and ADP-ribose 1-monophosphatase activities associated with transmissible gastroenteritis virus non-structural protein 3 Hepatitis E virus produced from cell culture has
    keywords: acute; analysis; capsid; cells; culture; domain; e virus; et al; expression; genome; genotypes; hepatitis; hev; human; infection; orf1; orf2; orf3; patients; product; protease; protein; region; replication; rna; sequence; strain; study; vaccine; virus; vp13
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        item: #787 of 1349
          id: cord-298281-wkje5jyt
      author: Chan, Vinson Wai-Shun
       title: A systematic review on COVID-19: urological manifestations, viral RNA detection and special considerations in urological conditions
        date: 2020-05-27
       words: 3497
      flesch: 50
     summary: 5.74% (95% CI 2.88–9.44%) of COVID-19 patients had positive viral RNA in urine samples, but the duration of viral shedding in urine was unknown. 65.82% (95% CI 45.71–83.51%) of COVID-19 patients had positive viral RNA in stool samples, which were detected from 2 to 47 days from symptom onset.
    keywords: covid-19; et al; patients; rna; sars; studies
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        item: #788 of 1349
          id: cord-298779-0mjizsoo
      author: Narendrula, Rashmi
       title: RNA disruption is associated with response to multiple classes of chemotherapy drugs in tumor cell lines
        date: 2016-02-24
       words: 7177
      flesch: 43
     summary: Annexin-V and PI staining of docetaxel treated cells, along with assessment of caspase-3 activation, showed concurrent initiation of apoptosis and RNA disruption, while inhibition of caspase-3 activity significantly reduced RNA disruption. key: cord-298779-0mjizsoo authors: Narendrula, Rashmi; Mispel-Beyer, Kyle; Guo, Baoqing; Parissenti, Amadeo M.; Pritzker, Laura B.; Pritzker, Ken; Masilamani, Twinkle; Wang, Xiaohui; Lannér, Carita title: RNA disruption is associated with response to multiple classes of chemotherapy drugs in tumor cell lines date: 2016-02-24 journal: BMC Cancer DOI: 10.1186/s12885-016-2197-1 sha: doc_id: 298779 cord_uid: 0mjizsoo BACKGROUND: Cellular stressors and apoptosis-inducing agents have been shown to induce ribosomal RNA (rRNA) degradation in eukaryotic cells.
    keywords: 28s; a2780; apoptosis; cells; chemotherapy; degradation; disruption; docetaxel; drug; fig; rna; rna disruption; rrna; treatment
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        item: #789 of 1349
          id: cord-298820-nogoqyxl
      author: Zhang, Qi
       title: Transcriptome altered by latent human cytomegalovirus infection on THP-1 cells using RNA-seq
        date: 2016-12-05
       words: 4687
      flesch: 36
     summary: The death effector domain protein family Cytomegalovirus: pathogen, paradigm, and puzzle Altered cellular mRNA levels in human cytomegalovirus-infected fibroblasts: viral block to the accumulation of antiviral mRNAs A ribonucleotide reductase homolog of cytomegalovirus and endothelial cell tropism NONCODE v3.0: integrative annotation of long noncoding RNAs Evaluation of the host transcriptional response to human cytomegalovirus infection Kinetics of IgG antibody to cytomegalovirus (CMV) after birth and seroprevalence of anti-CMV IgG in Chinese children Transcriptional regulation of endothelial cell adhesion molecules: NF-kappa B and cytokineinducible enhancers Cyclin A downregulation in TGFbeta1-arrested follicular lymphoma cells Infusion of cytomegalovirus (CMV)-specific T cells for the treatment of CMV infection not responding to antiviral chemotherapy Coupling M phase and S phase: controls maintaining the dependence of mitosis on chromosome replication Human cytomegalovirus latent infection alters the expression of cellular and viral microRNA Extrinsic versus intrinsic apoptosis pathways in anticancer chemotherapy Lost in transcription: p21 repression, mechanisms, and consequences Missing pieces in the NF-κB puzzle A cytomegalovirus-encoded mitochondria-localized inhibitor of apoptosis structurally unrelated to Bcl-2 Human cytomegalovirus persistence Expression of bbc3, a pro-apoptotic BH3-only gene, is regulated by diverse cell death and survival signals Checkpoints: controls that ensure the order of cell cycle events Global analysis of host cell gene expression late during cytomegalovirus infection reveals extensive dysregulation of cell cycle gene expression and induction of Pseudomitosis independent of US28 function Expression of transcription factor E2F1 induces quiescent cells to enter S phase Transcriptome analysis of fibroblast cells immediate-early after human cytomegalovirus infection Transcriptional regulation of the intercellular adhesion molecule-1 gene by inflammatory cytokines in human endothelial cells. At 4 days post HCMV infection, a total of 169,008,624 sequence reads and 180,616 transcripts were obtained, respectively.
    keywords: cell; cycle; cytomegalovirus; et al; expression; genes; hcmv; host; human; infection; lncrnas; response
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        item: #790 of 1349
          id: cord-298847-szezd2vb
      author: Jacomy, Hélène
       title: Vacuolating encephalitis in mice infected by human coronavirus OC43
        date: 2003-10-10
       words: 6907
      flesch: 39
     summary: Although the etiology of most neuroautoimmune, neuroinflammatory, and/or neurodegenerative diseases remains unclear, virus infections could directly trigger neurodegeneration or initiate a CNS-directed inflammatory process leading to central nervous system (CNS) damage, or a combination of both. Histochemical labeling of viral distribution at different times after infection revealed that virus infection initiated by ic inoculation was quickly disseminated throughout the CNS.
    keywords: brain; cells; cns; days; disease; et al; hcov; human; infection; mhv; mice; oc43; postinfection; virus
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        item: #791 of 1349
          id: cord-298905-c2uuvfm5
      author: Horzinek, M. C.
       title: Molecular pathogenesis of virus infections
        date: 1987
       words: 3891
      flesch: 34
     summary: Attachment ofpoliovirus to cultivated cells of primate and non-primate origin Human chromosome 19 carries a poliovirus receptor gene Expression and modulation of virus receptors on lymphoid and myeloid cells: Relationship to infectivity Cell receptors for mammalian reovirus. With increasing knowledge about viral genes and their functions, in-depth study of the pathogenesis of virus diseases has become feasible and, in fact, fashionable.
    keywords: cell; disease; host; infection; membrane; receptor; rna; surface; virus; viruses
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        item: #792 of 1349
          id: cord-298934-vtrfqozl
      author: Makino, Shinji
       title: Primary structure and translation of a defective interfering rna of murine coronavirus
        date: 1988-10-31
       words: 5194
      flesch: 50
     summary: These data suggest that MHV DI RNA may have been generated as a result of the discontinuous and nonprocessive manner of MHV RNA synthesis. Therefore, the DlssE sequence likely contains essential recognition signals for MHV RNA replication.
    keywords: a/.; dlsse; genomic; jhm; makino; mhv; rna; sequence; virus
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        item: #793 of 1349
          id: cord-298938-xemarhlv
      author: Goswami, Biswendu B.
       title: Apoptosis induced by a cytopathic hepatitis A virus is dependent on caspase activation following ribosomal RNA degradation but occurs in the absence of 2′–5′ oligoadenylate synthetase
        date: 2004-04-07
       words: 7468
      flesch: 43
     summary: However, phosphorylated STAT 1, a key regulator of interferon-stimulated gene transcription was not detected in virus infected cells. key: cord-298938-xemarhlv authors: Goswami, Biswendu B.; Kulka, Michael; Ngo, Diana; Cebula, Thomas A. title: Apoptosis induced by a cytopathic hepatitis A virus is dependent on caspase activation following ribosomal RNA degradation but occurs in the absence of 2′–5′ oligoadenylate synthetase date: 2004-04-07 journal: Antiviral Res DOI: 10.1016/j.antiviral.2004.02.004 sha: doc_id: 298938 cord_uid: xemarhlv We have presented previously evidence that the cytopathogenic 18f strain of hepatitis A virus (HAV) induced degradation of ribosomal RNA (rRNA) in infected cells [Arch.
    keywords: 18f; apoptosis; cells; degradation; et al; hepatitis; ifn; infection; rna; rnase; virus
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        item: #794 of 1349
          id: cord-299509-7xjdryoq
      author: Scholte, Florine E. M.
       title: Characterization of Synthetic Chikungunya Viruses Based on the Consensus Sequence of Recent E1-226V Isolates
        date: 2013-08-01
       words: 9731
      flesch: 44
     summary: To examine CHIKV-induced translational shut-off, the synthesis of 35 S-labeled viral and cellular proteins during the course of CHIKV LS3 infection was analyzed by metabolic labeling of infected 293/ACE2 cells with 35 S-Met and 35 S-Cys (Fig. 3C) . CHIKV RNA was isolated from virions using the QIAamp Viral RNA mini kit.
    keywords: cells; chikungunya; chikv; chikv ls3; fig; gfp; host; infection; ita07; ls3; p.i; ra1; replication; rna; sequence; strains; synthetic; vero; virus; viruses
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        item: #795 of 1349
          id: cord-299560-np6nfvf2
      author: Hendaus, Mohamed A.
       title: Remdesivir in the treatment of coronavirus disease 2019 (COVID-19): a simplified summary
        date: 2020-05-20
       words: 2808
      flesch: 40
     summary: Replication of SARS-CoV-2 depends on the viral RNAdependent RNA polymerase (RdRp) (Elfiky & Azzam, 2020) which is the most probable target of the investigational nucleotide analogue remdesivir (RDV) (Agostini et al., 2018; Jordan et al., 2018; Siegel et al.,2017; Tchesnokov et al., 2019) . RDV exhibits broad-spectrum antiviral activity against RNA viruses, and former studies with RdRps from Ebola virus (EBOV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have shown that delayed chain-termination is RDV's conceivable mechanism of action ( Figure 2 ) (Agostini et al., 2018; Jordan et al., 2018; Siegel et al.,2017; Tchesnokov et al., 2019) .
    keywords: coronavirus; covid-19; et al; patients; rdv; rna; sars
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        item: #796 of 1349
          id: cord-299747-qovrstak
      author: Deval, Jerome
       title: Inhibition of viral RNA polymerases by nucleoside and nucleotide analogs: therapeutic applications against positive-strand RNA viruses beyond hepatitis C virus
        date: 2014-09-17
       words: 4345
      flesch: 36
     summary: Cancer-causing Viruses and Their Inhibitors A novel mechanism to ensure terminal initiation by hepatitis C virus NS5B polymerase Hepatitis C virus RNA-dependent RNA polymerase (NS5B) as a mediator of the antiviral activity of ribavirin First transient kinetic study with HCV NS5B showing how deletion of the b-hairpin loop enables the polymerase to readily extend a primer Multiple interactions within the hepatitis C virus RNA polymerase repress primer-dependent RNA synthesis Structure of hepatitis C virus polymerase in complex with primer-template RNA Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase Klumpp K: Assembly, purification, and pre-steady-state kinetic analysis of active RNA-dependent RNA polymerase elongation complex Describes a method to isolate a stable NS5B-RNA elongation complex Contribution of a mutational bias in hepatitis C virus replication to the genetic barrier in the development of drug resistance 3 0 -Deoxynucleosides. -fluoro-2 0 -C-methylcytidine: a specific inhibitor of hepatitis C virus replication Characterization of the metabolic activation of hepatitis C virus nucleoside inhibitor beta-D-2 0 -deoxy-2 0
    keywords: analogs; hcv; hepatitis; ns5b; nucleoside; polymerase; rna; virus
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        item: #797 of 1349
          id: cord-299754-tgexahwd
      author: van Tol, Sarah
       title: The TRIMendous Role of TRIMs in Virus–Host Interactions
        date: 2017-08-22
       words: 18335
      flesch: 37
     summary: Additionally, several TRIMs directly restrict viral replication either through proteasome-mediated degradation of viral proteins or by interfering with different steps of the viral replication cycle. In addition to conferring an antiviral state indirectly by regulating cytokine production downstream of PRR signaling, TRIMs are capable of restricting the effectiveness of pathogens through direct interactions with viral proteins crucial to their entry, dissemination, or life cycle [6] .
    keywords: activation; cells; degradation; domain; host; ifn; infection; interferon; ligase; protein; replication; response; restriction; rig; rna; role; signaling; transcription; trim25; trim5α; trims; type; ubiquitin; virus
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        item: #798 of 1349
          id: cord-299848-fft1brwz
      author: Claridge, Jolyon K.
       title: A picornaviral loop-to-loop replication complex
        date: 2009-03-04
       words: 8836
      flesch: 52
     summary: MBP fusion protein with a viral protease cleavage site: one-step cleavage/purification of insoluble proteins Molecular basis of sequencespecific recognition of pre-ribosomal RNA by nucleolin Identification of the oriI-binding site of poliovirus 3C protein by nuclear magnetic resonance spectroscopy Poliovirus RNA synthesis utilizes an RNP complex formed around the 5 0 -end of viral RNA The program XEASY for computer-supported NMR spectral analysis of biological macromolecules Solving the generalized indirect Fourier transformation (GIFT) by Boltzmann simplex simulated annealing (BSSA) HRV-14 3C pro structure, mutation data and basic residues.
    keywords: 3ci; binding; complex; data; et al; fig; linker; loop; nmr; pro; protein; residues; rna; scattering; site; sld; structure
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        item: #799 of 1349
          id: cord-299943-wzkh04dv
      author: Santhanam, Manikandan
       title: DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment
        date: 2020-08-18
       words: 7358
      flesch: 37
     summary: In electrochemical DNA sensors, nucleic acid hybridization is coupled with the electrochemical reaction for selective detection of target DNA [13, 14] . To simplify DNA detection for point-of-care testing, other alternative approaches are being developed, namely, colorimetric
    keywords: amplification; approach; capture; detection; dna; electrochemical; electrode; hybridization; probe; reporter; rna; signal; surface; target; target dna
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        item: #800 of 1349
          id: cord-300023-2dg7njki
      author: Pillet, S.
       title: Contamination of healthcare workers' mobile phones by epidemic viruses()
        date: 2015-12-20
       words: 3087
      flesch: 46
     summary: We aimed to evaluate the presence of virus RNA from epidemic viruses including metapneumovirus, respiratory syncytial virus, influenza viruses, rotavirus (RV) and norovirus on the MPs used by healthcare workers (HCWs) and to relate it to hygiene measures. The presence of virus RNA was significantly associated with MPs from the paediatric HCWs (p <0.001).
    keywords: contamination; hcws; hospital; mps; study; viruses
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        item: #801 of 1349
          id: cord-300399-21xozruq
      author: Jayamohan, Harikrishnan
       title: SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations
        date: 2020-10-18
       words: 13021
      flesch: 38
     summary: Recent studies on four different commercial antigen tests demonstrated a wide range of sensitivities from 16.7 to 85% (with 100% specificity) in COVID-19 clinical samples [113] . Such methods have been extensively reviewed [44, 163, 164] and will need to be validated with COVID-19 clinical samples.
    keywords: amplification; antibody; antigen; assay; collection; coronavirus; cov-2; covid-19; crispr; detection; diagnostic; novel; pandemic; patients; pcr; rna; samples; sars; sensitivity; sequencing; swabs; testing; tests
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        item: #802 of 1349
          id: cord-300470-vgd1ol2z
      author: Conradie, Andelé M.
       title: Establishment of different plasmid only-based reverse genetics systems for the recovery of African horse sickness virus
        date: 2016-09-19
       words: 7966
      flesch: 35
     summary: During the development of reverse genetics systems for different RNA viruses, instability of cloned cDNA sequences in Escherichia coli have been reported for coronaviruses (Casais et . key: cord-300470-vgd1ol2z authors: Conradie, Andelé M.; Stassen, Liesel; Huismans, Henk; Potgieter, Christiaan A.; Theron, Jacques title: Establishment of different plasmid only-based reverse genetics systems for the recovery of African horse sickness virus date: 2016-09-19 journal: Virology DOI: 10.1016/j.virol.2016.07.010 sha: doc_id: 300470 cord_uid: vgd1ol2z In an effort to simplify and expand the utility of African horse sickness virus (AHSV) reverse genetics, different plasmid-based reverse genetics systems were developed.
    keywords: ahsv-4; bsr; cells; et al; genetics; genome; pjad; plasmid; polymerase; rna; segment; system; virus
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        item: #803 of 1349
          id: cord-300489-gzcb6uqw
      author: Martinez, Mitzi L.
       title: Detection of feline infectious peritonitis virus infection in cell cultures and peripheral blood mononuclear leukocytes of experimentally infected cats using a biotinylated cDNA probe
        date: 1993-03-31
       words: 3710
      flesch: 42
     summary: Feline infectious peritonitis: an immune-mediated coronavirus vasculitis Serodiagnostic aids and management practice for feline retrovirus and coronavirus infections Cats, coronaviruses and coronavirus antibody tests Experimental inoculation of cats with canine coronavirus and subsequent challenge with feline infectious peritonitis virus Genomic organization of a virulent isolate of porcine transmissible gastroenteritis virus cDNA cloning and sequence analysis of the gene encoding the peplomer protein of feline infectious peritonitis virus lntracellular RNAs of the feline infectious peritonitis coronavirus strain 79-1146 Sequence analysis of the 3' end of the feline coronavirus FIPV 79-1146 genome: Comparison with the genome of porcine coronavirus TGEV reveals large insertion Characterization of a feline infectious peritonitis virus isolate Biological and pathological consequences of feline infectious peritonitis virus infection in the cheetah Feline infectious peritonitis: A worldwide serosurvey Feline infectious peritonitis virus Antigenic relationships among homologous StlUClural polypeptides of porcine, feline and canine coronaviruses Isolation of feline coronaviruses from two cats with diverse disease manifestations A fast and sensitive method for detecting specific viral RNA in mammalian cells Morphologic and physical characteristics of feline infectious peritonitis virus and its growth in autochthonous peritoneal cell cultures Virologic and immunologic aspects of feline infectious peritonitis virus infection Coronavirus diseases (coronavirus enteritis, feline infectious peritonitis) Attempted immunization of cats against feline infectious peritonitis, using avirulent live virus or sublethal amounts of virulent virus Experimental studies with three new strains of feline infectious peritonitis virus: FIPV-UCD2, FIPV-UCD3 and FIPV-UCD4 Antigenic relationship of the feline infectious peritonitis virus to coronaviruses of other species An enteric coronavirus infection of cats and its relationship to feline infectious peritonitis Pathogenicity studies of feline coronavirus isolates 79-1146 and 79-1683 The biology of coronaviruses Immunoehemistry of viruses, 1I. The basis for serodiagnosis and vaccines Intrinsic resistance of feline peritoneal macrophages to coronavirus infection correlates with in vivo virulence Antigenic and biological diversity of feline coronaviruses: feline infectious peritonitis and feline enteritis virus Primary structure of the membrane and nucleocapsid protein genes of feline infectious peritonitis virus and immunogenicity of recombinant vaccinia viruses in kittens Pathogenesis of feline infectious peritonitis: Veterinary Microbiology DOI: 10.1016/0378-1135(93)90016-z sha: doc_id: 300489 cord_uid: gzcb6uqw Abstract A dot blot hybridization assay, using a biotinylated cDNA probe, was able to detect feline infectious peritonitis virus (FIPV) RNA in Felis catus whole fetus (fcwf-4) cells infected with the FIPV isolates DF2, 79-1146, UCDI, and UCD2.
    keywords: cats; df2; feline; fipv; pbml; probe; rna; virus
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        item: #804 of 1349
          id: cord-300685-bcjnujlj
      author: Poon, Leo L M
       title: Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS)
        date: 2003-06-01
       words: 2432
      flesch: 50
     summary: The disease is highly infectious, and attach rates Ͼ56% have been reported in healthcare workers caring for SARS patients (2 ) . Recently, we identified a novel virus in the family Coronaviridae in SARS patients (4 ) .
    keywords: assay; patients; pcr; rna; sars; virus
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        item: #805 of 1349
          id: cord-300884-rqfxe0x1
      author: Zhang, Jianqiang
       title: Genomic characterization of equine coronavirus
        date: 2007-12-05
       words: 6808
      flesch: 45
     summary: Improved tools for biological sequence comparison Coronavirus as a possible cause of severe acute respiratory syndrome Identification of a novel coronavirus in bats ADPribose-1ʺ-monophosphatase: a conserved coronavirus enzyme that is dispensable for viral replication in tissue culture Identification of protease and ADP-ribose 1ʺ-monophosphatase activities associated with transmissible gastroenteritis virus non-structural protein 3 Stem-loop IV in the 5′ untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication Stem-loop III in the 5′ untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication Full-length genome sequences of two SARS-like coronaviruses in horseshoe bats and genetic variation analysis A contemporary view of coronavirus transcription Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements Selective replication of coronavirus genomes that express nucleocapsid protein Murine coronavirus nonstructural protein ns2 is not essential for virus replication in transformed cells The human coronavirus 229E superfamily 1 helicase has RNA and DNA duplex-unwinding activities with 5′-to-3′ polarity A complex zinc finger controls the enzymatic activities of nidovirus helicases Comparison of the genome organization of toro-and coronaviruses: evidence for two nonhomologous RNA recombination events during Berne virus evolution Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage A hidden Markov model for predicting transmembrane helices in protein sequences Single-amino-acid substitutions in open reading frame (ORF) 1b-nsp14 and ORF 2a proteins of the coronavirus mouse hepatitis virus are attenuating in mice The severe acute respiratory syndrome (SARS) coronavirus NTPase/helicase belongs to a distinct class of 5′ to 3′ viral helicases On the basis of antigenic and genetic analyses, coronaviruses are divided into three groups (Gonzalez et al., 2003; Gorbalenya et al., 2004; Snijder et al., 2003) .
    keywords: amino; analysis; bcov; coronavirus; ecov; et al; genome; hcov; mrna; nc99; oc43; protein; rna; sequence
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        item: #806 of 1349
          id: cord-300963-1n1f8mf2
      author: Gajendran, Mahesh
       title: Inflammatory bowel disease amid the COVID-19 pandemic: impact, management strategies, and lessons learned
        date: 2020-10-12
       words: 6697
      flesch: 43
     summary: Patients with COVID-19 have lymphopenia, whereas in IBD patients, lymphocyte levels are usually normal or elevated. Hence, there is an ongoing concern over the impact of COVID-19 on IBD patients and their susceptibility to it.
    keywords: bowel; cells; coronavirus; covid-19; disease; ibd; ibd patients; infection; management; pandemic; patients; risk; rna; sars; study
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        item: #807 of 1349
          id: cord-301115-sedfbjlw
      author: Han, Mingfeng
       title: Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity
        date: 2020-08-28
       words: 4582
      flesch: 47
     summary: Severe patients additionally met at least one of the following conditions: (1) shortness of breath, RR ≥ 30 times/min, (2) oxygen saturation (resting state) ≤ 93%, or (3) PaO 2 / FiO 2 ≤ 300 mmHg. PCA was firstly performed with R package factoextra to identify correlating variables for distinguishing severe patients from mild patients (Figure Suppl 3A) .
    keywords: cases; counts; covid-19; disease; fig; levels; patients; sars
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        item: #808 of 1349
          id: cord-301226-hmc2wmst
      author: Randazzo, Walter
       title: Metropolitan Wastewater Analysis for COVID-19 Epidemiological Surveillance
        date: 2020-04-27
       words: 2162
      flesch: 45
     summary: Methods: Here, we have used RT-qPCR for SARS-CoV-2 detection in a series of longitudinal metropolitan wastewaters samples collected during the earliest stages of the epidemic in the Region of Valencia, Spain. Specifically, samples were taken from wastewater treatment plants Pinedo 1, Pinedo 2 and Quart-Benàger, all belonging to the Empresa Pública de Saneamiento de Aguas Residuales (Generalitat Valenciana).
    keywords: cov-2; rna; samples; sars; wastewater
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        item: #809 of 1349
          id: cord-301233-nenw0f81
      author: Naydenova, Katerina
       title: Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP
        date: 2020-10-21
       words: 4082
      flesch: 42
     summary: However, in the influenza RNA polymerase this site is occupied by the trisphosphate of the incoming rNTP (PDB 6SZV [30] ). The RNA template, 5'-rUrUrUrUrUrCrArUrArArCrUrUrArArUrCrUrCrAr CrArUrArGrCrArCrUrG-3', and RNA primer 5'-rCrArGrUrGrCrUrArUrGrUr GrArGrArUrUrArArGrUrUrArU-3' were prepared by solid phase synthesis on anÄKTA oligopilot plus 10 (GE Healthcare).
    keywords: complex; cov-2; favipiravir; fig; polymerase; primer; rdrp; rna; rtp; sars; structure
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        item: #810 of 1349
          id: cord-301285-p83ondy8
      author: Kautz, Tiffany F
       title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy
        date: 2018-03-06
       words: 8856
      flesch: 45
     summary: Resistance of TC-83 mutants to treatment by 5FU (D). Resistance of TC-83 mutants to treatment by Ribavirin (E).
    keywords: cells; diversity; equine; et al; fidelity; fig; mice; mutants; mutations; rdrp; rna; tc-83; virulence; virus; viruses
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        item: #811 of 1349
          id: cord-301362-f3lp10lm
      author: Delgui, Laura R.
       title: A Novel Mechanism Underlying the Innate Immune Response Induction upon Viral-Dependent Replication of Host Cell mRNA: A Mistake of +sRNA Viruses' Replicases
        date: 2017-01-20
       words: 7023
      flesch: 26
     summary: It was shown that several poliovirus and host proteins are involved in the membrane rearrangements that are essential for virus RNA replication (reviewed by Jackson, 2014) . Other +sRNA viruses such as the enterovirus Coxsackievirus (Kemball et al., 2010) , Hepatitis C virus (Flaviviridae family) (Sir et al., 2012) , or Coronavirus such as MVH (Reggiori et al., 2010) also usurp the autophagy pathway and induce remarkably alterations in intracellular membranous components to harbor the sites for viral RNA replication.
    keywords: cell; dsrna; et al; host; membrane; poliovirus; protein; replication; rig; rna; vesicles; viral; virus; viruses
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        item: #812 of 1349
          id: cord-301535-eui41zyg
      author: Chandler-Brown, Devon
       title: A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing
        date: 2020-04-10
       words: 4149
      flesch: 45
     summary: Crucially, our assay was able to detect SARS-CoV-2 RNA from viral particles suspended in transport media that was directly added to the PCR master mix, suggesting that RNA extraction can be skipped entirely without any degradation of test performance. Since a major limitation for increasing testing capacity has been supply chain and lab workflow bottlenecks related to RNA extraction, we next attempted to detect SARS-CoV-2 directly from the specimen matrix (viral transport medium).
    keywords: cov-2; covid-19; gce; qpcr; qsanger; rna; sars; sequence; spike
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        item: #813 of 1349
          id: cord-301904-mjfbvl5n
      author: Schultz-Cherry, S.
       title: Astroviruses
        date: 2014-11-28
       words: 5498
      flesch: 38
     summary: Astrovirus infections are identified in up to 2% of asymptomatic Figure 2 Phylogenetic relationships between representative species and genotypes of the family Astroviridae. Immunodeficient individuals, particularly those that are HIV-positive, appear to be at an increased risk of astrovirus infection.
    keywords: astrovirus; capsid; cells; children; hastv; infection; protein; replication; species; studies; viruses
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        item: #814 of 1349
          id: cord-301997-63160t7f
      author: Schwer, Beate
       title: Discontinuous transcription or RNA processing of vaccinia virus late messengers results in a 5′ poly(A) leader
        date: 1987-07-17
       words: 4746
      flesch: 48
     summary: The reason for this is that primer elongation experiments are complicated by a high degree of complementarity in late vaccinia RNA transcripts, both DNA strands are transcribed, genes can be overlapping, and there is readthrough of the RNA polymerase (Plucienniczak et al., 1985; Smith et al., 1984) . This paper concerns the study of the structure of the 5' terminus of vaccinia virus late RNA transcripts.
    keywords: cdna; et al; late; promoter; rna; transcripts; vaccinia
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        item: #815 of 1349
          id: cord-302020-ypsh3rjv
      author: Kim, Dongwan
       title: The Architecture of SARS-CoV-2 Transcriptome
        date: 2020-04-23
       words: 6130
      flesch: 51
     summary: Viral RNA modification was first described more than 40 years ago (Gokhale and Horner, 2017) . It was recently shown that HCoV-229E nsp8 has an adenylyltransferase activity, which may extend poly(A) tail of viral RNA (Tvarogová et al., 2019) .
    keywords: cov-2; drs; figure; genome; length; modification; poly(a; reads; rna; rnas; sars; sequencing; viral
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        item: #816 of 1349
          id: cord-302047-vv5gpldi
      author: Willemsen, Anouk
       title: On the stability of sequences inserted into viral genomes
        date: 2019-11-14
       words: 12562
      flesch: 34
     summary: However, genomic deletions that disrupt the inserted sequence will be subject to less constraints, as for example they can disrupt the reading frame of the insert without affecting the expression of virus genes. A large number of virus genomes have been engineered to carry additional sequences for a variety of purposes.
    keywords: cells; deletion; et al; evolution; expression; fitness; gene; genome; genomic; host; insert; insertions; recombination; replication; rna; sequences; size; stability; vectors; virus; viruses
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        item: #817 of 1349
          id: cord-302085-xyru2q9o
      author: Shepard, Samuel S.
       title: Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler
        date: 2016-09-05
       words: 10347
      flesch: 47
     summary: Given short read assembly, sensitivity to phased variants will be more difficult as the distance between them increases. However, the disconcerting issue is that genetic variability is compounded with the variability introduced by sequencing error, making the capture of distant reads even more difficult for RNA virus assembly.
    keywords: allele; assembly; consensus; data; error; fig; gene; influenza; irma; iterative; non; quality; read; reference; segments; sequence; sequencing; set; step; variants; viruses
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        item: #818 of 1349
          id: cord-302195-25gjbyi1
      author: Al Huraimel, Khalid
       title: SARS-CoV-2 in the environment: Modes of transmission, early detection and potential role of pollutions
        date: 2020-07-15
       words: 7091
      flesch: 36
     summary: Genetic material of SARS-CoV-2 has already been J o u r n a l P r e -p r o o f detected in wastewater samples from the Region of Valencia, Spain (Randazzo et al., 2020a) , Amsterdam Airport Schiphol, Netherlands (Lodder and de Roda Husman, 2020) , Australia (Ahmed et al., 2020) , Massachusetts, USA (Wu et al., 2020a) , France (Wurtzer et al., 2020) , Milan, Italy (La Rosa et al., 2020; Rimoldi et al., 2020) , Istanbul, Turkey (Kocamemi et al., 2020) and China (Wang et al., 2020d) . Since wastewater contains viruses excreted from infected individuals in a given wastewater treatment plant catchment population, wastewater surveillance and quantification of SARS CoV-2 can be an effective tool in estimating the number of infections in a community at an early stage of the outbreak (Ahmed et al., 2020; Mallapaty, 2020; Wu et al., 2020a) .
    keywords: air; coronavirus; covid-19; et al; evidence; pandemic; pollution; rna; sars; spread; transmission; virus; wastewater
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        item: #819 of 1349
          id: cord-302316-raf5rlkq
      author: Brüssow, Harald
       title: COVID‐19: From pathogenesis models to the first drug trials
        date: 2020-06-23
       words: 6948
      flesch: 40
     summary: A Chinese study used anakinra in severe COVID-19 patients who could not receive intensive care due to overwhelming patient numbers. The Authors Isolation of SARS-CoV-2-related coronavirus from malayan pangolins Pathological findings of COVID-19 associated with acute respiratory distress syndrome Effective treatment of severe COVID-19 patients with tocilizumab Effect of convalescent plasma therapy on viral shedding and survival in COVID-19 patients SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues I thank Jacqueline Steinhauser, and Kenneth Timmis and Lutz Br€ ussow for critical reading of the manuscript.
    keywords: cell; cov-2; covid-19; disease; group; infection; interferon; lung; patients; sars; study; treatment; trial; virus
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        item: #820 of 1349
          id: cord-302355-3se1wp8o
      author: Chen, Yi-Shiuan
       title: The conserved stem-loop II structure at the 3' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA
        date: 2018-07-26
       words: 6032
      flesch: 45
     summary: Furthermore, being infected with RNA viruses induces double membrane vesicles to form replication/transcription complexes that are protease-and nuclease-resistant [27] [28] [29] . The DENV sfRNA is readily formed when treated with XRN1 at concentration as low as 0.01 units (Fig 1E, lane 7) , whereas the 800-nt JEV RNA was relatively resistant to low concentrations of XRN1 (0.01 and 0.1 unit) (Fig 1E, lanes 2 and 3) .
    keywords: accumulation; cells; fig; formation; genome; jev; rdrp; replication; sfrna; structure; virus; vitro; xrn1
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        item: #821 of 1349
          id: cord-302368-uhhtvdif
      author: Longhini, Andrew P.
       title: Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations
        date: 2016-04-07
       words: 6557
      flesch: 38
     summary: Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression Widespread genetic switches and toxicity resistance proteins for fluoride Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy Three-state mechanism couples ligand and temperature sensing in riboswitches The 3 untranslated region of pea enation mosaic virus contains two T-shaped, ribosome-binding, cap-independent translation enhancers Identification of a Minimal Region of the HIV-1 5-Leader Required for RNA Dimerization, NC Binding, and Packaging Flipping of the Ribosomal A-Site Adenines Provides a Basis for tRNA Selection Visualizing transient low-populated structures of RNA Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR Time-resolved structural studies of protein reaction dynamics: A smorgasbord of X-ray approaches Alternate-site isotopic labeling of ribonucleotides for NMR studies of ribose conformational dynamics in RNA Selective 13 C labeling of nucleotides for large RNA NMR spectroscopy using an E. coli strain disabled in the TCA cycle Selective 13 C labeling of nucleotides for large RNA NMR spectroscopy using an E. coli strain disabled in the TCA cycle Three-dimensional heteronuclear NMR studies of RNA Preparation of 13 C and 15 N labelled RNAs for heteronuclear multi-dimensional NMR studies Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA Structure of HCVIRES domain II determined by NMR NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus Solution structure of tRNA(Val) from refinement of homology model against residual dipolar coupling and SAXS data Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3 ' UTR of turnip crinkle virus Structure of the yeast U2/U6 snRNA complex A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure Structure of the HIV-1 RNA packaging signal Key labeling technologies to tackle sizeable problems in RNA structural biology These nucleotides are suitable for use in three key aspects of RNA NMR structural biology: assignment, structural and dynamics measurements.
    keywords: assignment; chemical; dynamics; experiments; labeling; nmr; noesy; nucleotides; relaxation; rna; rnas; site; spin; synthesis
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        item: #822 of 1349
          id: cord-302409-40ktyt5q
      author: Wang, Jie
       title: SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital
        date: 2020-04-18
       words: 2772
      flesch: 44
     summary: key: cord-302409-40ktyt5q authors: Wang, Jie; Feng, Haiting; Zhang, Sheng; Ni, Zuowei; Ni, Lingmei; Chen, Yu; Zhuo, Lixin; Zhong, Zifeng; Qu, Tingting title: SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date: 2020-04-18 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.024 sha: doc_id: 302409 cord_uid: 40ktyt5q OBJECTIVES: The aim of this paper was to monitor the presence of SARS-Cov-2 among hospital environment surfaces, sewage, and personal protective equipment (PPE) of staffs in isolation wards in the First Affiliated Hospital of Zhejiang University, China.
    keywords: cov-2; disinfection; isolation; patients; rna; sars; wards
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        item: #823 of 1349
          id: cord-302425-aaxvlktp
      author: Cortey, Martí
       title: High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea
        date: 2019-12-05
       words: 4999
      flesch: 46
     summary: Most of the viruses causing outbreaks of diarrhoea in neonate piglets are RNA viruses such as Porcine epidemic diarrhoea virus (PEDV), Transmissible gastroenteritis virus (TGEV), Porcine deltacoronavirus (PDCoV) or Rotavirus A, B, C or H (RVA, RVB, RVC, RVH) key: cord-302425-aaxvlktp authors: Cortey, Martí; Díaz, Ivan; Vidal, Anna; Martín-Valls, Gerard; Franzo, Giovanni; Gómez de Nova, Pedro José; Darwich, Laila; Puente, Héctor; Carvajal, Ana; Martín, Marga; Mateu, Enric title: High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea date: 2019-12-05 journal: BMC Vet Res DOI: 10.1186/s12917-019-2204-2 sha: doc_id: 302425 cord_uid: aaxvlktp BACKGROUND: Diarrhoea is a major cause of death in neonate pigs and most of the viruses that cause it are RNA viruses.
    keywords: cases; diarrhoea; porcine; present; reads; rna; samples; sequences; viral; viruses
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        item: #824 of 1349
          id: cord-302830-5psqxxc8
      author: Ávila‐Pérez, Ginés
       title: Ultrastructural characterization of membranous torovirus replication factories
        date: 2016-07-05
       words: 9043
      flesch: 44
     summary: Bromouridine labelling of de novo synthesized viral RNA Infected cells on glass coverslips were incubated with 5 mM 5-BrU (Sigma-Aldrich) and 5 mg ml À1 of actinomycin D (Sigma-Aldrich) for 1 h before fixation and permeabilization for immunofluorescence staining. replication complex function New insights on the structure and morphogenesis of Berne virus Nidovirales: evolving the largest RNA virus genome RNA replication of mouse hepatitis virus takes place at double-membrane vesicles Visualizing coronavirus RNA synthesis in time by using click chemistry Ultrastructure of the replication sites of positive-strand RNA viruses Mutational analysis of the active centre of coronavirus 3C-like proteases SARS-coronavirus replication/transcription complexes are membraneprotected and need a host factor for activity in vitro Torovirus pathogenesis and immune response Genetic and antigenic characterization of newly isolated bovine toroviruses from Japanese cattle Multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase Order -Nidovirales SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum Integrity of the early secretory pathway promotes, but is not required for, severe acute respiratory syndrome coronavirus RNA synthesis and virus-induced remodeling of endoplasmic reticulum membranes Ultrastructural characterization of arterivirus replication structures: reshaping the endoplasmic reticulum to accommodate viral RNA synthesis First isolation of cytopathogenic bovine torovirus in cell culture from a calf with diarrhea Characterization of rubella virus replication complexes using antibodies to double-stranded RNA The transformation of enterovirus replication structures: a three-dimensional study of single-and doublemembrane compartments Immunolocalization of the dengue virus nonstructural glycoprotein NS1 suggests a role in viral RNA replication Equine torovirus (BEV) induces caspase-mediated apoptosis in infected cells Infectious bronchitis virus generates spherules from zippered endoplasmic reticulum membranes Modification of intracellular membrane structures for virus replication Virus factories, double membrane vesicles and viroplasm generated in animal cells Morphogenesis of coronavirus HCoV-NL63 in cell culture: a transmission electron microscopic study A photoactivatable GFP for selective photolabeling of proteins and cells Open reading frame 1a-encoded subunits of the arterivirus replicase induce endoplasmic reticulum-derived double-membrane vesicles which carry the viral replication complex Coronavirus replication complex formation utilizes components of cellular autophagy Where the endoplasmic reticulum and the mitochondrion tie the knot: the mitochondria-associated membrane (MAM) Three-dimensional architecture and biogenesis of membrane structures associated with hepatitis C virus replication Severe acute respiratory syndrome coronavirus replication is severely impaired by MG132 due to proteasome-independent inhibition of M-calpain Colocalization and membrane association of murine hepatitis virus gene 1 products and de novo-synthesized viral RNA in infected cells Coronaviruses, toroviruses, and arteriviruses Mouse hepatitis virus replicase proteins associate with two distinct populations of intracellular membranes Cryosectioning and immunolabeling Characterization of a torovirus main proteinase Toroviruses: replication, evolution and comparison with other members of the coronavirus-like superfamily The carboxyl-terminal part of the putative Berne virus polymerase is expressed by ribosomal frameshifting and contains sequence motifs which indicate that toro-and coronaviruses are evolutionarily related Comparison of the genome organization of toro-and coronaviruses: evidence for two nonhomologous RNA recombination events during Berne virus evolution The arterivirus nsp4 protease is the prototype of a novel group of chymotrypsin-like enzymes, the 3C-like serine proteases Non-structural proteins 2 and 3 interact to modify host cell membranes during the formation of the arterivirus replication complex Ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex Visualization of double-stranded RNA in cells supporting hepatitis C virus RNA replication Qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirus Characterization of Bafinivirus main protease autoprocessing activities Morphogenesis of Berne virus (proposed family Toroviridae) Purification and partial characterization of a new enveloped RNA virus (Berne virus) Ultrastructure of Kunjin virus-infected cells: colocalization of NS1 and NS3 with double-stranded RNA, and of NS2B with NS3, in virusinduced membrane structures Nascent Flavivirus RNA colocalized in situ with doublestranded RNA in stable replication complexes MERS-coronavirus replication induces severe in vitro cytopathology and is strongly inhibited by cyclosporin A or interferon-alpha treatment Coronavirus replication does not require the autophagy gene ATG5 Virusencoded proteinases and proteolytic processing in the Nidovirales We thank Paco Rodriguez for helpful discussions and critical reading of the manuscript.
    keywords: anti; bev; cells; dmvs; et al; fig; infected; membranes; pro; replication; rna; virus
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        item: #825 of 1349
          id: cord-302895-471zei5o
      author: Deng, Zengqin
       title: Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase
        date: 2013-12-24
       words: 8489
      flesch: 43
     summary: Previous studies identified the nsp carrying RNA helicase activity (arterivirus nsp10 and coronavirus nsp13) as one of the two most evolutionarily conserved nidovirus proteins. Therefore, our study not only provides the first insights into the structural basis for nidovirus RNA helicase function, but also creates a basis to propose a role for this protein in the posttranscriptional quality control of viral mRNAs.
    keywords: binding; complex; dna; domain; figure; genome; hel1; helicase; like; nidovirus; nsp10; protein; residues; rna; structure; upf1; zbd; zinc
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        item: #826 of 1349
          id: cord-302980-2jlz4c58
      author: Crucière, C.
       title: Sequence and analysis of bovine enteritic coronavirus (F15) genome I.—Sequence of the gene coding for the nucleocapsid protein; analysis of the predicted protein
        date: 1988-03-31
       words: 3934
      flesch: 59
     summary: CAACCCAAUUCCCCGACUCUCGUUCCCCAUUACUCUU 267 CCUUCUCUCGAAUUACUCAGUUUCAAMIGCGAAACCACUUUGAAUUUGCUGACGCACAAGGUCUCCCUAUUG IIII II II IIIII II II II IIIIIIII IIIIII Ili III IIilliii IIII1 III II IIIII IIII III II III I II IIII 217 CA&ACAAUCACCCCAACCAGACUCCAACUACU
    keywords: becv; coronavirus; dna; f15; genome; iii; protein; rna; sequence
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        item: #827 of 1349
          id: cord-303111-iv4lzpev
      author: Almazán, Fernando
       title: Reprint of: Coronavirus reverse genetic systems: Infectious clones and replicons()
        date: 2014-12-19
       words: 7077
      flesch: 25
     summary: Molecular genetic analysis of the structure and function of RNA virus genomes has been profoundly advanced by the availability of full-length cDNA clones. The large size of the CoV genome and the instability of some CoV replicase gene sequences during its propagation in bacteria, represent serious obstacles for the development of reverse genetic systems similar to those used for smaller positive sense RNA viruses.
    keywords: cdna; coronavirus; cov; et al; gene; genome; infectious; length; recombination; reverse; rna; sars; vaccinia; virus
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        item: #828 of 1349
          id: cord-303153-z7bdiuvx
      author: Ulasli, Mustafa
       title: Qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirus
        date: 2010-01-20
       words: 8723
      flesch: 52
     summary: These are the characteristic DMVs induced by CoV (Svoboda et al., 1962; David-Ferreira and Manaker, 1965; Ruebner et al., 1967; Pedersen et al., 1999; Gosert et al., 2002; Snijder et al., 2006; Knoops et al., 2008) . -Caplen et al., 1984; David-Ferreira and Manaker, 1965; Ruebner et al., 1967; Salanueva et al., 1999; Escorcia et al., 2002; Gosert et al., 2002; Snijder et al., 2006; Stertz et al., 2007; Knoops et al., 2008;
    keywords: cells; cms; coronavirus; dmvs; et al; fig; golgi; infection; lvcvs; mhv; p.i; protein; structures; time; viral; virions
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        item: #829 of 1349
          id: cord-303189-ktl4jw8v
      author: Coccia, Eliana M.
       title: Early IFN type I response: Learning from microbial evasion strategies
        date: 2015-03-31
       words: 15234
      flesch: 32
     summary: Strategies, identified so far, include viral proteins that bind ISG15 or that remove ISG15 from target proteins (reviewed in [237] ). Similarly, some identified targets of viral proteins in PRR signaling pathways might be turned out to be new targets for treating a range of diseases.
    keywords: activation; activity; bacterial; binding; cells; cov; expression; hcv; hepatitis; host; ifn; infection; interferon; irf3; pathway; pkr; production; protein; replication; response; rig; rna; signaling; type; virus; viruses
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        item: #830 of 1349
          id: cord-303265-v6ci69n0
      author: Domingo, Esteban
       title: Introduction to virus origins and their role in biological evolution
        date: 2019-11-08
       words: 15691
      flesch: 36
     summary: Group 1 (with a replicative scheme abbreviated as RNA/RNA) includes RNA viruses whose genomic replication cycle involves only RNA. The extent of genetic variation and its biological consequences have been less investigated for DNA viruses than for RNA viruses.
    keywords: acid; biological; cells; chapter; day; disease; dna; earth; elements; entities; et al; evolution; fig; genome; host; information; life; mechanisms; molecules; origin; present; protein; replication; rna; rna viruses; synthesis; viruses; world
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        item: #831 of 1349
          id: cord-303319-v3iyur78
      author: Abe, Takayuki
       title: Cytosolic DNA‐sensing immune response and viral infection
        date: 2019-02-26
       words: 7830
      flesch: 31
     summary: Another interesting point is that cGAMP may be transferred from virus-infected cells to neighboring uninfected cells via gap-junction channels, thereby promoting STING activation independently of type I IFN signaling mediated by the IFN-receptor/JAK-STAT axis 5 protein inhibits STING activation that restricts viral replication Modulation of the cGAS-STING DNA sensing pathway by gammaherpesviruses Cytoplasmic isoforms of Kaposi sarcoma herpesvirus LANA recruit and antagonize the innate immune DNA sensor cGAS Evasion of innate cytosolic DNA sensing by a gammaherpesvirus facilitates establishment of latent infection Inhibition of cGAS DNA sensing by a herpesvirus virion protein DNA tumor virus oncogenes antagonize the cGAS-STING DNA-sensing pathway Hepatitis C virus NS4B protein targets STING and abrogates RIG-I-mediated type I interferon-dependent innate immunity Hepatitis C virus NS4B blocks the interaction of STING and TBK1 to evade host innate immunity Viral evasion of intracellular DNA and RNA sensing DENV inhibits type I IFN production in infected cells by cleaving human STING Dengue virus targets the adaptor protein MITA to subvert host innate immunity Species-specific disruption of STING-dependent antiviral cellular defenses by the Zika virus NS2B3 protease Zika virus elicits inflammation to evade antiviral response by cleaving cGAS via NS1-caspase-1 axis Coronavirus papain-like proteases negatively regulate antiviral innate immune response through disruption of STING-mediated signaling The papain-like protease of porcine epidemic diarrhea virus negatively regulates type I interferon pathway by acting as a viral deubiquitinase SARS coronavirus papain-like protease inhibits the type I interferon signaling pathway through interaction with the STING-TRAF3-TBK1 complex HTLV-1 Tax impairs K63-linked ubiquitination of STING to evade host innate immunity Influenza A virus targets a cGAS-independent STING pathway that controls enveloped RNA viruses HIV-1 evades innate immune recognition through specific cofactor recruitment The capsids of HIV-1 and HIV-2 determine immune detection of the viral cDNA by the innate sensor cGAS in dendritic cells Dengue virus NS2B protein targets cGAS for degradation and prevents mitochondrial DNA sensing during infection Cytosolic DNA-sensing immune response and viral infection
    keywords: activation; cells; cgas; cytosolic; dna; infection; pathway; protein; response; sensing; signal; sting; type; virus; viruses
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        item: #832 of 1349
          id: cord-303377-lkewcf8a
      author: Dimke, H.
       title: Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems
        date: 2020-05-27
       words: 4115
      flesch: 45
     summary: In comparison to automated RNA extraction systems there is extensive hands-on time and inadvertently risks of human errors. RNA samples were then vortexed 3 sec.
    keywords: agpc; cov-2; extraction; method; rna; sars; systems
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        item: #833 of 1349
          id: cord-303403-9th2jiq6
      author: Qing, Jie
       title: Cyclophilin A Associates with Enterovirus-71 Virus Capsid and Plays an Essential Role in Viral Infection as an Uncoating Regulator
        date: 2014-10-02
       words: 10148
      flesch: 50
     summary: This screen identified compound HL051001P2 (Figs. 1A) as a potent inhibitor of viral proliferation, with an EC 50 value of 780 nM, by measuring EV71 virus RNA through quantitative RT-PCR (qRT-PCR) (Fig. 1C) . Moreover, the augmentation of EV71 virus RNA in RD-sh-control cells indicated that the replication of EV71 RNA began at 4 hpi (Fig. 4C , black line); by contrast, this stage was obviously delayed to 8 hpi in the RD-sh-CypA cells (Fig. 4C , red line).
    keywords: cells; control; cypa; cypa cells; ev71; ev71 virus; fig; infection; protein; rd cells; rna; s243p; uncoating; virus; vp1
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        item: #834 of 1349
          id: cord-303408-coesfldm
      author: Konstantinova, Pavlina
       title: Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome
        date: 2007-03-01
       words: 4902
      flesch: 47
     summary: HIV-1 Nef intersects the macrophage CD40L signalling pathway to promote resting-cell infection HIV-1 Nef enhances both membrane expression and virion incorporation of Env products. However, HIV-lhNef did not replicate to detectable levels in HIV-1 target cells, probably because steps of its replication cycle are affected by the hairpin insertion, e.g. RNA splicing, RNA nuclear export or mRNA translation.
    keywords: cells; escape; hairpin; hiv-1; inhibition; lhnef; replication; rna; type; variants; virus
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        item: #835 of 1349
          id: cord-303533-6s01qplg
      author: Neuman, Benjamin W.
       title: Does form meet function in the coronavirus replicative organelle?
        date: 2014-07-15
       words: 3643
      flesch: 27
     summary: Because +RNA viruses share both the central component of the RNA-making machinery and a common replication strategy, it is useful to consider how coronaviruses fit into the wider world of +RNA viruses. This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle.
    keywords: coronavirus; membrane; nsp3; organelles; protein; replication; rna; viral; virus; viruses
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        item: #836 of 1349
          id: cord-303915-14yfs4pa
      author: Almazán, Fernando
       title: Engineering a Replication-Competent, Propagation-Defective Middle East Respiratory Syndrome Coronavirus as a Vaccine Candidate
        date: 2013-09-10
       words: 7147
      flesch: 42
     summary: A live attenuated SARS coronavirus is immunogenic and efficacious in golden Syrian hamsters Immunization with an attenuated severe acute respiratory syndrome coronavirus deleted in E protein protects against lethal respiratory disease Complete protection against severe acute respiratory syndrome coronavirus-mediated lethal respiratory disease in aged mice by immunization with a mouse-adapted virus lacking E protein Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells Severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp1 and rational design of an attenuated strain A live, impaired-fidelity coronavirus vaccine protects in an aged, immunocompromised mouse model of lethal disease Coronaviruses maintain viability despite dramatic rearrangements of the strictly conserved genome organization Vaccines to prevent severe acute respiratory syndrome coronavirusinduced disease Complete nucleotide sequence of two generations of a bacterial artificial chromosome cloning vector Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) In contrast, rMERS-CoV-⌬E was rescued in E ϩ cells with titers of around 1 ϫ 10 3 TCID 50 /ml but not in control E Ϫ cells, in which the virus was not detectable from passage 1 (limit of detection, 50 TCID 50 /ml)
    keywords: cdna; cells; clone; coronavirus; cov; gene; infectious; mers; pbac; protein; respiratory; virus; viruses
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        item: #837 of 1349
          id: cord-304014-k62mtr9j
      author: Ma, Xuelian
       title: Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection
        date: 2019-11-04
       words: 4482
      flesch: 49
     summary: Among them, 215 were antisense lncRNAs, 1427 long intervening/intergenic non-coding RNAs (lincRNAs), 220 other lncRNAs, 24 Promoter-associated lncRNAs, 115 sense overlapping lncRNAs, and 22 UTR lncRNAs ( Fig. Among 106 lncRNAs, 16 were antisense lncRNAs, 79 lincRNAs, 5 other lncRNAs, 2 Promoter-associated lncRNAs, 3 sense overlapping lncRNAs, and 1 UTR lncRNAs (Fig. 1d) .
    keywords: expression; fig; file; genes; lncrnas; mrnas; pml; response; signaling; table; tgev
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        item: #838 of 1349
          id: cord-304044-i1ikf96b
      author: Wu, Yue
       title: Inhibition of white spot syndrome virus in Litopenaeus vannamei shrimp by sequence-specific siRNA
        date: 2007-10-03
       words: 4744
      flesch: 47
     summary: Moreover, the suppression effect of WSSV gene expression was low at 48 h p.i. To detect the corresponding mRNA expression of WSSV genes in shrimp, 2 μg of RNA extract was used as template for RT-PCR amplification with the one-step RT-PCR system (Invitrogen, USA).
    keywords: et al; expression; genes; replication; sequence; shrimp; sirna; target; virus; wssv
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        item: #839 of 1349
          id: cord-304058-i8cywew0
      author: Pfefferle, Susanne
       title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo
        date: 2009-08-24
       words: 9581
      flesch: 50
     summary: The characterization of virus proteins can be unreliable if only the protein of interest is studied on its own. In CaCo-2 and HUH7 cells, but not in Vero cells, the variant carrying the ORF 7b deletion had a replicative advantage against the parental virus (4- and 6-fold increase of virus RNA in supernatant, respectively).
    keywords: cdna; cells; coronavirus; cov; deletion; figure; fragment; frankfurt-1; genome; infection; interferon; orf; pcr; protein; replication; rna; sars; syndrome; virus
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        item: #840 of 1349
          id: cord-304283-nv4ret1f
      author: Hung, Chuan-Fu
       title: A novel siRNA validation system for functional screening and identification of effective RNAi probes in mammalian cells
        date: 2006-08-04
       words: 7126
      flesch: 33
     summary: As compared with the results obtained from using the active RNAi targeting sequence sisAg3, the inactive sisAg1 totally had no inhibition effects on targeting reporter gene expression in all tested systems including sisAg1 fused at the 5 0 -or 3 0 -UTR of EGFP or firefly luciferase or inserted within EGFP-Fluc+ fusion gene, as well as pHsH1-expressed shsAg1 and pDual-expressed sisAg1 (Fig. S2) . Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans Killing the messenger: short RNAs that silence gene expression Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing A potential role for RNA interference in controlling the activity of the human LINE-1 retrotransposon The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi RNAi-mediated pathways in the nucleus Functional genomics: RNA sets the standard A large-scale RNAi screen in human cells identifies new components of the p53 pathway A resource for large-scale RNA-interference-based screens in mammals RNA-interferencebased functional genomics in mammalian cells: reverse genetics coming of age RNAi: gene-silencing in therapeutic intervention Unlocking the potential of the human genome with RNA interference Approaches for the sequence-specific knockdown of mRNA Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells siRNAs: applications in functional genomics and potential as therapeutics Synthetic shRNA as potent RNAi triggers system for stable expression of short interfering RNAs in mammalian cells A DNA vector-based RNAi technology to suppress gene expression in mammalian cells Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells Effective expression of small interfering RNA in human cells Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells U6 promoter-driven siRNAs with four uridine 3 0 overhangs efficiently suppress targeted gene expression in mammalian cells
    keywords: cells; egfp; expression; gene; inhibition; reporter; rnai; sequence; siakt1; sirna; system; targeting; vector
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        item: #841 of 1349
          id: cord-304306-rxjahqwh
      author: Vlachakis, Dimitrios
       title: Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic
        date: 2020-10-08
       words: 8538
      flesch: 33
     summary: A different function of the N protein is its interaction with the protease subunit p42, which degrades viral proteins . Specifically, this interaction may impair proteolysis of viral proteins and their presentation to Cytotoxic T-Lymphocytes, thus promoting viral evasion from immune effectors .
    keywords: activity; binding; cell; coronavirus; cov-2; covid-19; domain; drug; et al; helicase; inhibitors; membrane; polymerase; protease; protein; replication; rna; sars; spike; structure; target
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        item: #842 of 1349
          id: cord-304356-jyp9gjh9
      author: Grant, Rogan A.
       title: Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells
        date: 2020-08-05
       words: 7464
      flesch: 38
     summary: We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. Single cell RNA-Seq of flow-sorted BAL cells:
    keywords: alveolar; analysis; bal; cells; controls; cov-2; covid-19; data; figure; flow; infection; macrophages; patients; pneumonia; rna; samples; sars; seq; type
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        item: #843 of 1349
          id: cord-304424-048xo7jn
      author: Greninger, Alexander L.
       title: A decade of RNA virus metagenomics is (not) enough
        date: 2018-01-15
       words: 9614
      flesch: 26
     summary: Mining of publicly available transcriptome data has contributed greatly to the discovery of novel RNA viruses (Basler et al., 2005; Schomacker et al., 2004) . The greatest paradigm shifter in recent viral metagenomics work has been the sheer number and diversity of novel RNA viruses present in arthropods and invertebrates.
    keywords: analysis; bats; detection; discovery; diversity; dna; et al; evolution; genome; greninger; host; human; identification; library; metagenomics; new; novel; number; preparation; protein; rna; rna viruses; sequence; sequencing; shi et; species; viruses
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        item: #844 of 1349
          id: cord-304498-ty41xob0
      author: Denison, Mark R
       title: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity
        date: 2011-03-01
       words: 7361
      flesch: 26
     summary: This review will discuss the role of RNA replication fidelity in RNA virus replication and pathogenesis, and will focus on a novel exoribonuclease universally encoded within CoV genomes that likely mediates RNA-dependent RNA proofreading during virus replication. key: cord-304498-ty41xob0 authors: Denison, Mark R; Graham, Rachel L; Donaldson, Eric F; Eckerle, Lance D; Baric, Ralph S title: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date: 2011-03-01 journal: RNA Biology DOI: 10.4161/rna.8.2.15013 sha: doc_id: 304498 cord_uid: ty41xob0 In order to survive and propagate, RNA viruses must achieve a balance between the capacity for adaptation to new environmental conditions or host cells with the need to maintain an intact and replication competent genome.
    keywords: activity; coronavirus; cov; covs; diversity; exon; fidelity; genome; mutation; nsp14; pathogenesis; replication; rna; sars; virus; viruses
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        item: #845 of 1349
          id: cord-304553-gbwb7fqi
      author: Christopher, Mary E.
       title: Broad-Spectrum Drugs Against Viral Agents
        date: 2008-09-01
       words: 11349
      flesch: 31
     summary: Neuraminidase is important for the initiation of influenza virus infection in human airway epithelium Oseltamivir resistance during treatment of influenza A (H5N1) infection Avian flu: isolation of drug-resistant H5N1 virus Incidence of adamantane resistance among influenza A (H3N2) viruses isolated worldwide from Local delivery of CpG oligodeoxynucleotides induces rapid changes in the genital mucosa and inhibits replication, but not entry, of herpes simplex virus type 2 A Toll-like receptor recognizes bacterial DNA Novel adjuvant systems CpG motifs in bacterial DNA and their immune effects Characterization of three CpG oligodeoxynucleotide classes with distinct immunostimulatory activities Recognition of single-stranded RNA viruses by Toll-like receptor 7 Memory CD8+ T cells provide an early source of IFN-gamma Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses Involvement of toll-like receptor 3 in the immune response of lung epithelial cells to doublestranded RNA and influenza A virus Proinflammatory cytokine responses induced by influenza A (H5N1) viruses in primary human alveolar and bronchial epithelial cells CpG and double-stranded RNA trigger human NK cells by Toll-like receptors: induction of cytokine release and cytotoxicity against tumors and dendritic cells Virus-cell interactions in the induction of type 1 interferon by influenza virus in mouse spleen cells Activation of mast cells by doublestranded RNA: evidence for activation through Toll-like receptor 3 Langerhans cells exhibit low responsiveness to double-stranded RNA Viral infection and Toll-like receptor agonists induce a differential expression of type I and lambda interferons in human plasmacytoid and monocyte-derived dendritic cells A modified polyriboinosinic-polyribocytidylic acid complex that induces interferon in primates Prophylactic and therapeutic efficacy of poly(I,C)-LC against Rift Valley fever virus infection in mice Involvement of Toll-like receptors in the immune response of nasal polyp epithelial cells Double-stranded RNA activates RANTES gene transcription through co-operation of nuclear factor-kappaB and interferon regulatory factors in human airway epithelial cells Synthetic double-stranded RNA induces multiple genes related to inflammation through Toll-like receptor 3 depending on NF-kappaB and/or IRF-3 in airway epithelial cells Role of protein kinase R in double-stranded RNA-induced expression of nitric oxide synthase in human astroglia Vaccine adjuvant effects, and immune response, to synthetic polymers MVE and poly ICLC Increase in liver-associated natural killer activity by polyribonucleotides Prophylactic and therapeutic efficacies of poly(IC.LC) against respiratory influenza A virus infection in mice Role of RIG-I, MDA-5, and PKR on the expression of inflammatory chemokines induced by synthetic dsRNA in airway epithelial cells Polyinosinic acid is a ligand for toll-like receptor 3 Lack of correlation between interferon levels induced by polyribonucleotides and their antimetastatic effect A comparison of interferon responses to poly ICLC in males and females A comparison of interferon responses to poly ICLC in males and females Immunoadjuvant effects of polyadenylic:polyuridylic acids through TLR3 and TLR7 Successful prophylaxis against rabies in mice and Rhesus monkeys: the interferon system and vaccine Antiviral and immunomodulating inhibitors of experimentally-induced Punta Toro virus infections Prophylaxis of acute respiratory virus infections using nucleic acid-based drugs Induction of antiviral immunity by double-stranded RNA in a marine invertebrate Effect of a nuclease-resistant derivative of polyriboinosinic-polyribocytidylic acid complex on yellow fever in rhesus monkeys (Macaca mulatta) Protective and toxic effects of a nuclease-resistant derivative of polyriboinosinic-polyribocytidylic acid on Venezuelan equine encephalomyelitis virus in rhesus monkeys The effects of polyinosinic: polycytidylic acid (pI:C) on the GVH reaction: immunopathological observations Liposomemediated immunotherapy against respiratory influenza virus infection using double-stranded RNA poly ICLC Prophylactic and therapeutic efficacy of poly(I,C)-LC against Rift Valley fever virus infection in mice Ranking of prophylactic efficacy of poly(ICLC) against Rift Valley fever virus infection in mice by incremental relative risk of death Correlation between breakdown of the blood-brain barrier and disease outcome of viral encephalitis in mice Evaluation of immunomodulators, interferons and known in vitro SARS-coV inhibitors for inhibition of SARS-coV replication in BALB/c mice Effect of interferon-alpha and interferon-inducers on West Nile virus in mouse and hamster animal models Enhanced therapeutic efficacy of poly(ICLC) and ribavirin combinations against Rift Valley fever virus infection in mice Treatment of advanced ovarian cancer with polyinosinic-polycytidylic lysine carboxymethylcellulose Synthetic double-stranded RNA poly(I:C) combined with mucosal vaccine protects against influenza virus infection Cross-Protection against H5N1 Influenza Virus Infection Is Afforded by Intranasal Inoculation with Seasonal Trivalent Inactivated Influenza Vaccine Intranasal immunization with H5N1 vaccine plus Poly I:Poly C(12)U, a Toll-like receptor agonist, protects mice against homologous and heterologous virus challenge.
    keywords: cells; cpg; dna; h5n1; human; iclc; ifn; infection; influenza; mice; odn; odns; production; response; rna; tlr7; treatment; type; vaccine; virus; viruses
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        item: #846 of 1349
          id: cord-304794-z2kx314h
      author: Métifiot, Mathieu
       title: G-quadruplexes in viruses: function and potential therapeutic applications
        date: 2014-11-10
       words: 9130
      flesch: 38
     summary: Interestingly, TAg can unwind G4 DNA structures (122, 123) ; thus, it might play a crucial role in regulating replication as well as early and late transcription. Even if a 200-bp cis-regulatory element is necessary for efficient initiation, G4 structure formation at ORIs might be the key to selecting the firing origins (67, 68) .
    keywords: activity; binding; cells; dna; figure; formation; g4s; genome; human; promoter; protein; quadruplex; region; replication; rna; role; sequences; structures; transcription; viral; virus
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        item: #847 of 1349
          id: cord-304873-ppb9k3zu
      author: Kang, Hunseung
       title: Direct structural evidence for formation of a stem-loop structure involved in ribosomal frameshifting in human immunodeficiency virus type 1 1 Kumho Life and Environmental Science Laboratory Publication No. 8. 1
        date: 1998-04-01
       words: 2500
      flesch: 60
     summary: The enhancer secondary RNA structure, either a stem-loop or a pseudoknot, downstream of the shift site induces pausing of the ribosome and stimulates w x slippage at the shift sequence 4-7 . Enhancement of ribosomal frameshifting by RNA secondary structures has been studied by many mutational analyses. RNA oligonucleotides were purified by denaturing 20% polyacrylamide gel electrophoresis.
    keywords: frameshifting; rna; sequence; stem; structure
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        item: #848 of 1349
          id: cord-304876-txaoz7oh
      author: Jordan, Paul C
       title: Nucleosides for the treatment of respiratory RNA virus infections
        date: 2018-03-21
       words: 11008
      flesch: 38
     summary: In this review, we summarized the exciting advances in discovery and development of novel nucleoside analogs as potential new treatments for respiratory RNA virus infections. Despite these challenges, the prospect of developing nucleoside analogs directed against respiratory RNA virus infections represents an exciting new avenue in antiviral research.
    keywords: activity; analogs; cov; domain; gs-5734; human; infection; influenza; nucleoside; polymerase; protein; replication; ribavirin; rna; rna polymerase; rsv; structure; synthesis; t-705; treatment; virus; viruses; vitro
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        item: #849 of 1349
          id: cord-305290-xnjwv0d7
      author: Atkins, John F.
       title: Ribosome gymnastics—Degree of difficulty 9.5, style 10.0
        date: 1990-08-10
       words: 8002
      flesch: 57
     summary: Coronaviruses use a combination of the above slippery sequences, namely U UUA AAC, for their frameshifting (Brierley et al., 1987 (Brierley et al., , 1989 Bredenbeek et al., 1990) . The involvement of a pseudoknot has been inferred for another coronavirus, mouse hepatitis virus (Bredenbeek et al., 1990) for some, but not all, retroviral examples (Brierley et al., 1989; ten Dam et al., 1990) and in a variety of other instances (ten Dam et al., 1990) .
    keywords: codon; et al; frameshifting; gene; level; mrna; protein; readthrough; ribosomes; sequence; site; stop; trna; uga; virus
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        item: #850 of 1349
          id: cord-305336-wxiazglk
      author: Li, Ji Lian
       title: Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera
        date: 2014-01-21
       words: 6929
      flesch: 43
     summary: RNA viruses have extremely high mutation rates and thus represent a significant source of these infectious diseases. Among major pathogen groups, RNA viruses have the highest rate of mutation, because the virus-encoded RNA polymerases lack 3=¡5= exonuclease proofreading activity (29) .
    keywords: analysis; bee; colonies; honeybees; host; infection; mites; pcr; plant; pollen; rna; study; tissues; trsv; varroa; viral; virus; viruses
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        item: #851 of 1349
          id: cord-305393-96mrxt8a
      author: Lai, Yvonne
       title: Viral Double-Strand RNA-Binding Proteins Can Enhance Innate Immune Signaling by Toll-Like Receptor 3
        date: 2011-10-10
       words: 9628
      flesch: 53
     summary: The transfected cells were induced 18 to 22 h later by the addition of poly(I:C) or viral dsRNAs to the culture medium to a final concentration of 1 mg/ mL in the presence or absence of 100 nM of RNA binding proteins. (TIF) Plant and animal sensors of conserved microbial signatures Innate immune recognition of viral infection Intracellular pattern recognition receptors in the host response Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing Sensing and signaling in antiviral innate immunity Structure and function of Toll receptors and their ligands A missense mutation of the Toll-like receptor 3 gene in a patient with influenzaassociated encephalopathy TLR3 deficiency in patients with herpes simplex encephalitis Effects of single nucleotide polymorphisms on Toll-like receptor 3 activity and expression in cultured cells The L412F variant of Toll-like receptor 3 (TLR3) is associated with cutaneous candidiasis, increased susceptibility to cytomegalovirus, and autoimmunity Dissecting TLR3 signalling in dendritic cells The Toll-like receptor 3:dsRNA signaling complex Leucinerich repeats and pathogen recognition in Toll-like receptors Predicting Toll-like receptor structures and characterizing ligand binding The TLR3 signaling complex forms by cooperative receptor dimerization Biochemical and functional analyses of the human Toll-like receptor 3 ectodomain mRNA is an endogenous ligand for Toll-like receptor 3 LL37 and cationic peptides enhance TLR3 signaling by viral doublestranded RNAs Replication of hepatitis C virus HCV NS5B polymerase inhibitors Template requirements for RNA synthesis by a recombinant hepatitis C virus RNAdependent RNA polymerase De novo initiation of RNA synthesis by the RNA-dependent RNA polymerase (NS5B) of hepatitis C virus Mechanism of de novo initiation by the hepatitis C virus RNA-dependent RNA polymerase: role of divalent metals Requirements for de novo initiation of RNA synthesis by recombinant flaviviral RNA-dependent RNA polymerases De novo initiation pocket mutations have multiple effects on hepatitis C virus RNAdependent RNA polymerase activities A locking mechanism regulates RNA synthesis and host protein interaction by the hepatitis C virus polymerase Regulation of de novo-initiated RNA synthesis in hepatitis C virus RNA-dependent RNA polymerase by intermolecular interactions De novo initiation of viral RNA-dependent RNA synthesis Structural and functional analysis of hepatitis C virus strain JFH1 polymerase A comprehensive structure-function comparison of hepatitis C virus strain JFH1 and J6 polymerases reveals a key residue stimulating replication in cell culture across genotypes Ross River virus transmission, infection, and disease: a cross-disciplinary review The coat protein leads the way: an update on basic and applied studies with the Brome mosaic virus coat protein Hepatitis B virus infection-natural history and clinical consequences Virus assembly, allostery and antivirals Effects of deletions in the N-terminal basic arm of brome mosaic virus coat protein on RNA packaging and systemic infection Biological significance of the seven aminoterminal basic residues of brome mosaic virus coat protein Fulllength hepatitis B virus core protein packages viral and heterologous RNA with similarly high levels of cooperativity In vitro-assembled alphavirus core-like particles maintain a structure similar to that of nucleocapsid cores in mature virus Cutting Edge:
    keywords: 1bd21; beas-2b; binding; cells; dsrna; fig; hcv; il6; poly(i; polymerase; production; proteins; rna; signaling; tlr3; virus
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        item: #852 of 1349
          id: cord-305591-ir3wz6nr
      author: Ji, Danyang
       title: Discovery of G-quadruplex-forming sequences in SARS-CoV-2
        date: 2020-06-01
       words: 5146
      flesch: 51
     summary: This analysis revealed the presence of 25 four contiguous GG runs (G 2 N x G 2 N y G 2 N z G 2 ) in the genome of SARS-CoV-2. G-quadruplexes are formed by nucleic acid (DNA or RNA) containing the sequences G (≥2)
    keywords: cov-2; genome; helicase; nsp13; pqs; pqss; protein; quadruplex; rna; sars; structures
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        item: #853 of 1349
          id: cord-305737-bnzd7b25
      author: Rehwinkel, Jan
       title: Targeting the viral Achilles’ heel: recognition of 5′-triphosphate RNA in innate anti-viral defence
        date: 2013-05-23
       words: 4140
      flesch: 47
     summary: Selfpropagation allows for sensitive detection of minute amounts of viral RNA: it has been estimated that 20 molecules of 5PPP RNA are sufficient to activate IRF3 via the RIG-I/MAVS pathway IFITs control translation initiation, cell proliferation and cell migration, and exert anti-viral effects against a variety of RNA viruses and human papillomavirus
    keywords: cells; figure; ifit1; recognition; rig; rna; rnas; virus; viruses
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        item: #854 of 1349
          id: cord-305811-987dhnf7
      author: Cho, Che-Pei
       title: Regulation of Programmed Ribosomal Frameshifting by Co-Translational Refolding RNA Hairpins
        date: 2013-04-29
       words: 5863
      flesch: 45
     summary: Because widely distributed RNA structures along an open reading-frame [28] are unwound and refolded repeatedly during translation, the involvement of refolding RNA hairpins in the regulation of translational elongation may be more common than first thought. As E site sequences can affect the potency of downstream stimulators [12, 13] , we ask whether the potency of attenuators can be affected by either proximal E site sequences or downstream stimulators.
    keywords: activity; attenuation; base; fig; frameshifting; hairpin; pairs; prf; ribosomal; ribosome; rna; site; stem
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        item: #855 of 1349
          id: cord-305859-vt8vwo3y
      author: Jung, Kwonil
       title: Calves are susceptible to infection with the newly emerged porcine deltacoronavirus, but not with the swine enteric alphacoronavirus, porcine epidemic diarrhea virus
        date: 2017-04-03
       words: 3251
      flesch: 52
     summary: Our study did not identify which type of cells in the intestines of inoculated calves could be the target for PDCoV replication, resulting in fecal shedding. On the other hand, none of the Gn calves inoculated with PEDV shed detectable PEDV RNA in the feces at PIDs 1-9 (calves #6 and #7) and PIDs 1-17 (calf #5).
    keywords: calf; calves; inoculated; pdcov; pedv; pigs; virus
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        item: #856 of 1349
          id: cord-305871-w1quh4fx
      author: Hindawi, Salwa I.
       title: Inactivation of Middle East respiratory syndrome‐coronavirus in human plasma using amotosalen and ultraviolet A light
        date: 2017-12-14
       words: 4527
      flesch: 41
     summary: Although the potential for MERS‐CoV transmission through blood transfusion is not clear, MERS‐CoV was recognized as a pathogen of concern for the safety of the blood supply especially after its detection in whole blood, serum, and plasma of infected individuals. Currently, there are more than 70 known pathogens that have been recognized by the AABB as pathogens of concern for blood transfusion; 25 however, blood donations are only screened for a small number of pathogens on a regular basis.
    keywords: blood; coronavirus; cov; inactivation; mers; middle; plasma; rna; samples; syndrome; transfusion
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        item: #857 of 1349
          id: cord-306076-ygfnkgqp
      author: Fujita, Yu
       title: RNAi Therapeutic Platforms for Lung Diseases
        date: 2013-02-06
       words: 8427
      flesch: 36
     summary: Strategies for silencing human disease using RNA interference RNAi therapeutics: A potential new class of pharmaceutical drugs Small interfering RNA inhibits hepatitis B virus replication in mice RNAi suppresses polyglutamine-induced neurodegeneration in a model of spinocerebellar ataxia Confirming the RNAi-mediated mechanism of action of siRNA-based cancer therapeutics in mice Chemical modification of siRNA siRNA and isRNA: Two edges of one sword Targeted delivery of antisense oligodeoxynucleotide and small interference RNA into lung cancer cells Poly(ester amine)-mediated, aerosol-delivered Akt1 small interfering RNA suppresses lung tumorigenesis Poly(beta-amino ester) as a carrier for si/shRNA delivery in lung cancer cells Inhibition of non-small cell lung cancer cell proliferation and tumor growth by vector-based small interfering RNAs targeting HER2/neu Rodriguez-Padilla, C. WT1 gene silencing by aerosol delivery of PEI-RNAi complexes inhibits B16-F10 lung metastases growth Inhibition of influenza virus production in virus-infected mice by RNA interference Using siRNA in prophylactic and therapeutic regimens against SARS coronavirus in Rhesus macaque Intrapulmonary delivery of XCL1-targeting small interfering RNA in mice chronically infected with Mycobacterium tuberculosis Effective treatment of respiratory alphaherpesvirus infection using RNA interference A randomized, double-blind, placebo-controlled study of an RNAi-based therapy directed against respiratory syncytial virus RNA interference: new therapeutics in allergic diseases Emerging oligonucleotide therapies for asthma and chronic obstructive pulmonary disease Suppression of plasminogen activator inhibitor-1 In general, both viral and non-viral vectors are being assessed for siRNA delivery to lung cells.
    keywords: asthma; cancer; cells; copd; delivery; development; diseases; expression; gene; lung; mirnas; pulmonary; rnai; sirna; target; therapeutic; therapy
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        item: #858 of 1349
          id: cord-306288-w43wec48
      author: Jang, Sungho
       title: RNA-based dynamic genetic controllers: development strategies and applications
        date: 2017-11-10
       words: 4618
      flesch: 33
     summary: We also discuss computational methods and high-throughput selection approaches for de novo design of dynamic RNA controllers. Finally, we explain applications of dynamic RNA controllers for metabolic engineering and synthetic biology.
    keywords: aptamers; binding; controllers; design; expression; gene; ligand; riboswitches; rna; selection; vivo
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        item: #859 of 1349
          id: cord-306424-gf0bglm0
      author: Scutigliani, Enzo Maxim
       title: Interaction of the innate immune system with positive-strand RNA virus replication organelles
        date: 2017-06-27
       words: 8337
      flesch: 30
     summary: Therefore, detection of viral RNA and the subsequent induction of antiviral effector mechanisms play an important part in the onset of an antiviral state in the context of RNA virus infections. ROs are therefore believed to have a dual role in +RNA virus infection and innate immune evasion, which will be elaborated on further in this review.
    keywords: antiviral; host; ifn; inducible; infection; innate; lc3; membrane; protein; replication; rna; role; ros; signaling; virus; viruses
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        item: #860 of 1349
          id: cord-306535-j26eqmxt
      author: Robertson, Matthew J.
       title: Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets
        date: 2020-08-19
       words: 16775
      flesch: 43
     summary: [28] to create a comprehensive database of mouse gene symbols orthologous to human genes and vice versa. The majority of identified genes were not from a traditional drug target family like kinases or enzymes.
    keywords: analysis; candidate genes; cell; ces5a; datasets; epididymis; expression; fig; file; genes; human; male; mice; mouse; mouse genes; number; protein; reproductive; rna; samples; seq; specific; sperm; spint3; studies; table; testis; tissue; tract
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        item: #861 of 1349
          id: cord-306688-po4p1466
      author: Wang, X.
       title: Brome Mosaic Virus
        date: 2008-07-30
       words: 4574
      flesch: 34
     summary: Studies on BMV RNA replication were greatly advanced by the development and subsequent use of such tools as in vitro RNA-dependent RNA polymerase (RdRp) extracts and cultured plant protoplasts. For BMV, barley protoplast systems developed and refined by the groups of Okuno and Furusawa, Hall and others in the late 1970s have allowed studies of all aspects of BMV RNA replication, subgenomic RNA synthesis, progeny RNA encapsidation, and the like.
    keywords: bmv; host; replication; rna; rnas; strand; virus; viruses
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        item: #862 of 1349
          id: cord-306754-qohrnpgq
      author: Lee, Justin S.
       title: Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species
        date: 2017-05-23
       words: 7194
      flesch: 44
     summary: Despite this limitation, it is encouraging that although the percentage of on-target reads for most samples was low, the number of pathogen reads was sufficient to accurately characterize the pathogens in most samples analyzed. Both DNA and RNA pathogens were detected in this study, although this method was more readily applied to the detection of DNA genomes.
    keywords: dna; enrichment; fold; genome; ngs; pathogens; probe; reads; rna; samples; sequences; sequencing; tgc
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        item: #863 of 1349
          id: cord-306921-3afgpunj
      author: Owino, Collins Oduor
       title: Recent advances on the role of host factors during non-poliovirus enteroviral infections
        date: 2019-06-19
       words: 11752
      flesch: 33
     summary: [165] EV-D68 can disrupt autophagy process downstream Promotes viral replication and egress from infected cells; promoting viral infection within the cells [166] CV-B3 viral protein 3C targets cleavage of SNARE and PLEKHM1 proteins Impairs establishment of SNARE complexes thus providing conducive environment for viral replication [170] CV-B3 viral 2A protease cleaves SQSTM1/p62 a known intermediary of selective autophagy degradation of ubiquitinated proteins Impairs NF-kB signaling and disrupts selective autophagy in infected cells to establish an efficient viral replication/infection [173] CV-B3 interacts with CALCOCO2 and SQSTM1 Targets autophagy receptors; targets mitochondrial antiviral signaling protein for degradation thus blocking establishment of antiviral state in the infected cells [177] targeting different stages of viral infections would be an alternative in targeting different stages of the enteroviral infection cycle. Interplay between viral proteins and human host proteins play a major role in the attachment, entry and internalization of viral infections.
    keywords: a71; autophagy; cell; colleagues; coxsackievirus; cycle; disease; enterovirus; entry; factors; host; human; infections; protein; receptor; replication; rna; study; viruses
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        item: #864 of 1349
          id: cord-306934-29ljbl7g
      author: Tonelli, Michele
       title: Antiviral and cytotoxic activities of aminoarylazo compounds and aryltriazene derivatives
        date: 2009-07-01
       words: 8578
      flesch: 49
     summary: Free energy components and total binding free energies for compounds of the series A-C on BVDV RdRp inhibitor molecules may affect the RdRps interactions with the incoming RNA molecule. Compounds VP32947 (3-[(dipropylaminoethyl)thio]-5H-1,2,4-triazino [5,6-b] indole) 24 and BPIP (5- 23 exhibited EC 50 as low as 30-40 nM. Other compounds (as the thiazolylurea DPC-A69280-29, 25 Table 3 Cytotoxicity against MT-4, MDBK, BHK and Vero-76 cell lines and BVDV, YFV, Reo-1, CVB-2, RSV and HSV-1 inhibitory activity of amino azocompounds of structure A-C the benzimidazolone 1453 26 and 7-amino-1,3-dihydroxy-10methyl-6-[4-(2-pyridinyl)-1-piperazinyl]-9(10H)acridone 27 ) have EC 50 in the range 0.6-1.5 lM, that are comparable with those of the presently described aminoaryl azocompounds 1 and 7 (1.6 and 2.5 lM, respectively).
    keywords: activity; binding; bvdv; cell; compounds; derivatives; energy; hcv; protein; rdrp; rna; rsv; triazene; viruses
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        item: #865 of 1349
          id: cord-306948-wkisfz1m
      author: Han, Mingyuan
       title: Engineering the PRRS virus genome: Updates and perspectives
        date: 2014-12-05
       words: 9532
      flesch: 32
     summary: The coding sequences in the viral genome are flanked by the 5 0 and 3 0 un-translated regions (UTRs) involved in translation, replication, and transcription (see review in Snijder et al., 2013) . The fusion of the common 5 0 sequence (leader TRS) to the different 3 0 -body segments of sg mRNAs is mediated by discontinuous transcription which is a common strategy of nidoviruses (Sawicki et al., 2007; Snijder et al., 2013; Sola et al., 2011) .
    keywords: clones; deletion; et al; gene; genome; genotype; nsp2; porcine; protein; prrsv; regions; replication; rna; sequence; syndrome; syndrome virus; virus; viruses
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        item: #866 of 1349
          id: cord-307354-dkwcheu0
      author: Abernathy, Emma
       title: Emerging roles for RNA degradation in viral replication and antiviral defense
        date: 2015-05-31
       words: 7171
      flesch: 33
     summary: (A) Viral RNA of ( þ ) RNA viruses can be recognized by cellular QC pathways like NMD, in some cases due to long 3 0 UTRs which are inherent to subgenomic RNAs (sgRNA). In addition, several antiviral pathways use RNA degradation as a viral restriction mechanism, and we will summarize new findings related to how these host-encoded ribonucleases target and destroy viral RNA.
    keywords: cellular; cleavage; decay; degradation; et al; expression; host; infection; mrna; protein; translation; viral; virus
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        item: #867 of 1349
          id: cord-307598-p54p7enk
      author: Schlee, Martin
       title: Master sensors of pathogenic RNA – RIG-I like receptors
        date: 2013-07-01
       words: 12877
      flesch: 39
     summary: Hornung et al. , 2002 Judge et al. 2005; Krieg et al. 1995) , reviewed in (Barchet et al. 2008; Schlee et al. 2007 Schlee et al. , 2006 . In contrast to TLR7, 8 and 9, TLR3 is expressed in more cell types (e.g. endothelial cells, fibroblasts, astrocytes) (Barchet et al. 2008; Schlee et al. 2007) and was found to detect long double-stranded RNA (Alexopoulou et al. 2001) .
    keywords: activation; binding; cells; ctd; dna; dsrna; end; et al; ifn; lgp2; ligand; mda5; polymerase; ppp; recognition; response; rig; rna; structure; transcription; triphosphate; type; virus; viruses
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        item: #868 of 1349
          id: cord-307603-uqr6r14u
      author: Kauppinen, S.
       title: Locked Nucleic Acid: High-Affinity Targeting of Complementary RNA for RNomics
        date: 2006
       words: 5812
      flesch: 32
     summary: The focus of this chapter is on LNA antisense, LNA-modified DNAzymes (LNAzymes), LNA-modified small interfering (si)RNA (siLNA), LNA-enhanced expression profiling by real-time RT-PCR and detection and analysis of microRNAs by LNA-modified probes. Several studies in vitro or in cells support the usefulness of LNA antisense for gene silencing (Obika et al. 2001; Hansen et al. 2003) .
    keywords: acid; affinity; antisense; dna; et al; expression; lna; monomers; nucleic; oligonucleotides; rna; targeting
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        item: #869 of 1349
          id: cord-307817-2vy28i4m
      author: Lou, Zhiyong
       title: Current progress in antiviral strategies
        date: 2014-01-14
       words: 7596
      flesch: 32
     summary: This review will highlight recent achievements in antiviral development and discuss various strategies for preventing virus attachment and entry into the host cell, as well as strategies for preventing virus replication and transcription within the host cell. Throughout the life cycle of a negative sense single-stranded RNA (ssRNA) virus, the genome length RNA is encapsidated by a virally encoded nucleoprotein (NP), instead of a naked RNA, and associated with RdRp (polymerase complex) to form a stable ribonucleoprotein (RNP) complex, which is responsible for virus replication, transcription, and assembly
    keywords: activity; binding; complex; function; fusion; hcv; hiv; host; infection; influenza; inhibitors; protein; replication; rna; structure; virus; viruses
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        item: #870 of 1349
          id: cord-307860-iqk1yiw4
      author: Ionescu, Mihaela Ileana
       title: An Overview of the Crystallized Structures of the SARS-CoV-2
        date: 2020-10-24
       words: 9884
      flesch: 50
     summary: The role of programmed-1 ribosomal frameshifting in coronavirus propagation The proteins of severe acute respiratory syndrome coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19 From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design Variable oligomerization modes in coronavirus non-structural protein 9 Dimerization of coronavirus nsp9 with diverse modes enhances its nucleic acid binding affinity Porcine deltacoronavirus nsp15 antagonizes interferon-beta production independently of its endoribonuclease activity Structural and biochemical characterization of endoribonuclease Nsp15 encoded by middle east respiratory syndrome coronavirus Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV -2 Biophysical methods in early drug discovery Pathogens Nonstructural proteins 7 and 8 of feline coronavirus form a 2:1 heterotrimer that exhibits primer-independent RNA polymerase activity The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency Coronavirus susceptibility to the antiviral remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease The antiviral compound remdesivir potently inhibits RNAdependent RNA polymerase from Middle East respiratory syndrome coronavirus Remdesivir for COVID-19: challenges of underpowered studies RNA 3′-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex Mechanism of inhibition of ebola virus RNA-dependent RNA polymerase by remdesivir Bat flight and zoonotic viruses Analysis of coronavirus temperature-sensitive mutants reveals an interplay between the macrodomain and papain-like protease impacting replication and pathogenesis Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation A noncovalent class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication Biochemical and immunological studies of nucleocapsid proteins of severe acute respiratory syndrome and 229E human coronaviruses Structural basis for the identification of the N-terminal domain of coronavirus nucleocapsid protein as an antiviral target A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike Structure, function, and evolution of coronavirus spike proteins Entry of human coronavirus NL63 into the cell Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC Reverse genetics with a full-length infectious cDNA of the Middle East respiratory syndrome coronavirus Host cell proteases: critical determinants of coronavirus tropism and pathogenesis SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor Cell entry mechanisms of SARS-CoV-2 TMPRSS2: a potential target for treatment of influenza virus and coronavirus infections X-ray structures of human furin in complex with competitive inhibitors Novel furin inhibitors with potent anti-infectious activity The biology and therapeutic targeting of the proprotein convertases Potential therapeutic targeting of coronavirus spike glycoprotein priming Structural basis of receptor recognition by SARS-CoV-2 Structure of SARS coronavirus spike receptor-binding domain complexed with receptor A 193-amino acid fragment of the SARS coronavirus S protein efficiently binds angiotensin-converting enzyme 2 CD209L (L-SIGN) is a receptor for severe acute respiratory syndrome coronavirus Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites Computational prediction of furin cleavage sites by a hybrid method and understanding mechanism underlying diseases The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity Evidence for mutations in SARS-CoV-2 Italian isolates potentially affecting virus transmission The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types Interaction of ACE2 and integrin beta1 in failing human heart Focus on receptors for coronaviruses with special reference to angiotensin-converting enzyme 2 as a potential drug target -a perspective SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues A protein complex in the brush-border membrane explains a Hartnup disorder allele Further evidence for allelic heterogeneity in Hartnup disorder Tissue-specific amino acid transporter partners ACE2 and collectrin differentially interact with hartnup mutations Molecular basis for the interaction of the mammalian amino acid transporters B0AT1 and B0AT3 with their ancillary protein collectrin Expression and regulation of the neutral amino acid transporter B0AT1 in rat small intestine Epidermal growth factor receptor is a co-factor for transmissible gastroenteritis virus entry The human coronavirus HCoV-229E S-protein structure and receptor binding CD13 (human aminopeptidase N) mediates human cytomegalovirus infection Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor COVID-19, an emerging coronavirus infection: advances and prospects in designing and developing vaccines, immunotherapeutics, and therapeutics.
    keywords: ace2; antibodies; binding; coronavirus; cov-2; covid-19; covs; host; human; inhibitors; pdb; pro; protease; protein; receptor; rna; sars; spike; structures; studies
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        item: #871 of 1349
          id: cord-307893-mvl0wrsj
      author: Goulter-Thorsen, R.M.
       title: Disciplines Associated with Food Safety: Food Virology
        date: 2014-01-13
       words: 4998
      flesch: 42
     summary: With availability of such a method, or in its absence, availability of better cultivable surrogates or more sensitive detection methods for complex sample matrices, scientists would be able to tackle the challenges associated with trying to control foodborne viruses. Particularly important was the nucleic acid amplification method polymerase chain reaction (PCR), which was readily adapted to the detection of RNA viruses by preceding PCR with a reverse transcription (RT) step, hence the designation RT-PCR.
    keywords: cause; detection; disease; enteric; foodborne; foods; hav; human; hunov; outbreaks; viruses
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        item: #872 of 1349
          id: cord-307904-lnagg1uw
      author: Johnson, Jennifer A
       title: Sequence elements controlling expression of Barley stripe mosaic virus subgenomic RNAs in vivo
        date: 2003-08-15
       words: 10700
      flesch: 48
     summary: Protoplast transfections and RNA blots were carried out as described in Expression of the sgRNA␤1, sgRNA␤2, and sgRNA␥ promoters in the RNA␤ S/B derivative (␤1Ϫ34/ϩ14), which contains a 48-nt deletion inactivating the native sgRNA␤1 promoter. (C) Alignment of the sgRNA␤1, sgRNA␤2, and sgRNA␥ promoter regions of BSMV with mapped (TMV and PVX) or putative (BNYVV, PCV, PMTV, and PVM) sgRNA promoter regions of other viruses.
    keywords: bsmv; bsmv sgrna; deletions; fig; promoter; rnas; sequence; sgrna promoter; sgrna ␤; site; start; transcription; virus
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        item: #873 of 1349
          id: cord-307914-lgprrwee
      author: Bartok, Eva
       title: Immune Sensing Mechanisms that Discriminate Self from Altered Self and Foreign Nucleic Acids
        date: 2020-07-14
       words: 17786
      flesch: 34
     summary: Unless modified nucleotides or specific sequences precluding the formation of the complementary strand are used, IVT can potentially generate RIG-I ligands from a variety of templates (Hornung et al., 2006; Kim et al., 2004; Schlee et al., 2009; Both sensors contribute to the immune response to dsRNA viruses, such as reoviridae (Loo et al., 2008) , but RIG-I-mediated sensing dominates the response to many (-) ssRNA viruses such as influenza, which form shorter dsRNA panhandles in their genomes (Rehwinkel et al., 2010; Schlee et al., 2009) , whereas MDA5 has a greater role in the host defense against (+) ssRNA viruses, many of which are known to generate large amounts of dsRNA during replication .
    keywords: activation; activity; antiviral; binding; cell; cgas; cytosolic; death; dna; dsrna; et al; host; human; ifn; immune; infection; inflammasome; interferon; non; pathway; protein; receptor; response; rig; rna; self; sensing; sensor; signaling; sting; tlr8; toll; type; viral
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        item: #874 of 1349
          id: cord-307934-84zfabti
      author: Lai, Chao-Kuen
       title: Nonstructural Protein 5A Is Incorporated into Hepatitis C Virus Low-Density Particle through Interaction with Core Protein and Microtubules during Intracellular Transport
        date: 2014-06-06
       words: 8230
      flesch: 52
     summary: Processing pathways of the hepatitis C virus proteins Expression and identification of hepatitis C virus polyprotein cleavage products Efficient initiation of HCV RNA replication in cell culture Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line Expression of hepatitis C virus proteins induces distinct membrane alterations including a candidate viral replication complex Identification of the hepatitis C virus RNA replication complex in Huh-7 cells harboring subgenomic replicons Association of hepatitis C virus replication complexes with microtubules and actin filaments is dependent on the interaction of NS3 and NS5A Cytoskeletal requirements for hepatitis C virus (HCV) RNA synthesis in the HCV replicon cell culture system Initiation of hepatitis C virus infection requires the dynamic microtubule network: role of the viral nucleocapsid protein Hepatitis C virus egress and release depend on endosomal trafficking of core protein Hepatitis C virus core protein induces lipid droplet redistribution in a microtubule-and dynein-dependent manner Hepatitis C virus: assembly and release of virus particles Homotypic interaction and multimerization of hepatitis C virus core protein Interaction of hepatitis C virus core protein with viral sense RNA and suppression of its translation The lipid droplet is an important organelle for hepatitis C virus production Subcellular localization of hepatitis C virus structural proteins in a cell culture system that efficiently replicates the virus An in vitro model of hepatitis C virus genotype 3a-associated triglycerides accumulation Essential role of domain III of nonstructural protein 5A for hepatitis C virus infectious particle assembly Interaction of hepatitis C virus nonstructural protein 5A with core protein is critical for the production of infectious virus particles Ultrastructural and biophysical characterization of hepatitis C virus particles produced in cell culture Complete replication of hepatitis C virus in cell culture Cell culture-grown hepatitis C virus is infectious in vivo and can be recultured in vitro Identification of a residue in hepatitis C virus E2 glycoprotein that determines scavenger receptor BI and CD81 receptor dependency and sensitivity to neutralizing antibodies Biochemical and morphological properties of hepatitis C virus particles and determination of their lipidome Characterization of low-and very-low-density hepatitis C virus RNA-containing particles Hepatitis C virus: buoyant density of the factor VIII-derived isolate in sucrose Hepatitis C virus particle detected by immunoelectron microscopic study Identification of hepatitis C virus by immunoelectron microscopy Visualization of hepatitis C virions and putative defective interfering particles isolated from lowdensity lipoproteins Production of infectious hepatitis C virus in tissue culture from a cloned viral genome An in vitro model of hepatitis C virion production B lymphocytes secrete antigen-presenting vesicles Exosomes: endosomal-derived vesicles shipping extracellular messages Shortrange exosomal transfer of viral RNA from infected cells to plasmacytoid dendritic cells triggers innate immunity Highly permissive cell lines for subgenomic and genomic hepatitis C virus RNA replication The heat shock cognate protein 70 is associated with hepatitis C virus particles and modulates virus infectivity Hepatitis C virus NS3/4A protein interacts with ATM, impairs DNA repair and enhances sensitivity to ionizing radiation Construction and characterization of infectious intragenotypic and intergenotypic hepatitis C virus chimeras Robust production of infectious hepatitis C virus (HCV) from stably HCV cDNA-transfected human hepatoma cells Annexin A2 is involved in the formation of hepatitis C virus replication complex on the lipid raft Fluorescent detection of lipid droplets and associated proteins Effect of cell growth on hepatitis C virus (HCV) replication and a mechanism of cell confluence-based inhibition of HCV RNA and protein expression Hepatitis C virus RNA replication occurs on a detergent-resistant membrane that cofractionates with caveolin-2 Molecular determinants and dynamics of hepatitis C virus secretion Regulation of hepatitis C virus secretion by the Hrs-dependent exosomal pathway The ESCRT system is required for hepatitis C virus production Vps4 and the ESCRT-III complex are required for the release of infectious hepatitis C virus particles Membrane fusion and fission: enveloped viruses Association of hepatitis C virus envelope proteins with exosomes Microvesicles and viral infection Hepatitis C virus core particle detected by immunoelectron microscopy and optical rotation technique Buoyant density of hepatitis C virus recovered from infected hosts: two different features in sucrose equilibrium density-gradient centrifugation related to degree of liver inflammation Extraordinarily low density of hepatitis C virus estimated by sucrose density gradient centrifugation and the polymerase chain reaction The Phe105 loop of Alix Bro1 domain plays a key role in HIV-1 release A pathogenic picornavirus acquires an envelope by hijacking cellular membranes HIV and mature dendritic cells: Trojan exosomes riding the Trojan horse? NS2 protein of influenza virus is found in purified virus and phosphorylated in infected cells The paramyxovirus SV5 V protein binds two atoms of zinc and is a structural component of virions Proteomics analysis unravels the functional repertoire of coronavirus nonstructural protein 3 Localization of the Vpx packaging signal within the C terminus of the human immunodeficiency virus type 2 Gag precursor protein Alpha-helical peptide-induced vesicle rupture revealing new insight into the vesicle fusion process as monitored in situ by quartz crystal microbalance-dissipation and reflectometry Mechanism of an amphipathic alpha-helical peptide's antiviral activity involves sizedependent virus particle lysis Hepatitis C virus entry depends on clathrin-mediated endocytosis We thank Dr. Takaji Wakita of National Institute of Infectious Disease, Tokyo, Japan, for plasmid pJFH1, Dr. Charles M. Rice from Center for the Study of Hepatitis C, Rockefeller University, New York, USA, for Huh7.5 cells. None of the fractions obtained from these cells contained HCV NS5A protein (data not shown), consistent with the previous report [34] .
    keywords: anti; cells; core; core protein; density; fig; hcv; hepatitis; membrane; ns5a; particles; protein; rna; virus
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        item: #875 of 1349
          id: cord-308034-9b219k0v
      author: Murray, James L.
       title: A Role for H/ACA and C/D Small Nucleolar RNAs in Viral Replication
        date: 2014-01-30
       words: 3663
      flesch: 4
     summary: siRNAs targeting viral genes were used as positive controls, as follows: Further work is needed to define whether a role in virus infection is unique for the SHNG genes selected in clones resistant to multiple viruses.
    keywords: cells; gene; host; infection; influenza; replication; rnas; snora; snords; trap; virus; viruses
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        item: #876 of 1349
          id: cord-308216-s6rd8p41
      author: Duan, Fang
       title: Small interfering RNA targeting for infected‐cell polypeptide 4 inhibits herpes simplex virus type 1 replication in retinal pigment epithelial cells
        date: 2011-10-20
       words: 5076
      flesch: 45
     summary: First, the ICP4 protein expression was observed by indirect immunofluorescence in HSV-1 infected cells. 37, 38 Many publications have described the inhibition of viruses, including human immunodeficiency virus type 1 (HIV-1), hepers simplex virus (HSV), hepatitis B virus (HBV) and hepatitis C virus (HCV), by targeting and silencing diverse viral genes as well as cell genes that are essential for virus replication.
    keywords: cells; expression; herpes; hsv-1; icp4; infection; replication; simplex; sirna; type; virus
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        item: #877 of 1349
          id: cord-308331-55ge7kmr
      author: Routh, Andrew
       title: Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data
        date: 2013-10-09
       words: 6026
      flesch: 46
     summary: In addition to single recombination events, multiple recombination events within a single read are detected, as are virus-to-host recombination and insertion and substitution events. By mapping the distribution of recombination events in the genome of flock house virus, we demonstrate that this information can be used to discover de novo functional motifs located in conserved regions of the viral genome.
    keywords: events; genome; mapping; nucleotides; read; recombination; rna; virema; virus
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        item: #878 of 1349
          id: cord-308835-999kewdw
      author: Leibowitz, Julian L.
       title: The virus-specific intracellular RNA species of two murine coronaviruses: MHV-A59 and MHV-JHM
        date: 1981-10-15
       words: 6470
      flesch: 52
     summary: I. Characterization of biological behavior in vitro and virus specific intracellular RNA of strongly neurotropic JHMV and weakly neurotropic A59V viruses Pathogenic murine coronaviruses. Molar ratios of RNA species were calculated by dividing the counts per minute or weight of paper in each peak by its molecular weights X lop6 and normalizing all values such that the major RNA species, RNA7 (see Results), was set at 100.
    keywords: a59v; cells; electrophoresis; gel; jhmv; mhv; min; rna; rnas; species; specific; virus
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        item: #879 of 1349
          id: cord-308884-erofmh39
      author: Yang, Seung Won
       title: Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation
        date: 2018-01-08
       words: 11050
      flesch: 46
     summary: Intrinsically, the influenza HAgD proteins were expressed and purified predominantly as trimers (Fig. 3A) . According to some reports, the solubility of fusion proteins is somewhat influenced by the location of the fusion tag (28, 29) .
    keywords: antibody; assembly; fig; folding; fusion; h1n1; hagd; influenza; mice; mouse; mrid; proteins; rid; rna; samples; serum; virus
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        item: #880 of 1349
          id: cord-309043-dlmx12vt
      author: von Brunn, Albrecht
       title: Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome
        date: 2007-05-23
       words: 6742
      flesch: 48
     summary: We therefore cloned the SARS-CoV ORFeome by recombinatorial cloning (GATEWAY technology) and performed a genome-wide analysis for viral protein interactions by yeast-two-hybrid (Y2H) matrix screen. Known virus-host and intraviral interactions of SARS proteins were identified by a literature screen (see Tables S1 and S2).
    keywords: accessory; cells; coronavirus; cov; interactions; network; nsp2; nsp8; number; orf9b; proteins; replication; rna; sars; virus; y2h
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        item: #881 of 1349
          id: cord-309048-emmtplv3
      author: Lomonossoff, George P.
       title: TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications
        date: 2018-07-26
       words: 9028
      flesch: 35
     summary: English translation Display of epitopes on the surface of tobacco mosaic virus: impact of charge and isoelectric point of the epitope on virus-host interactions Expression of tobacco mosaic virus coat protein by a cauliflower mosaic virus promoter in plants transformed by agrobacterium Refined atomic model of the four-layer aggregate of the tobacco mosaic virus coat protein at 2.4 Å resolution Nanoscale science and technology with plant viruses and bacteriophages Protein disk of tobacco mosaic virus at 2.8 Å resolution showing the interactions within and between subunits Role of hexahistidine in directed nanoassemblies of tobacco mosaic virus coat protein Nanomanufacturing of tobacco mosaic virus-based spherical biomaterials using a continuous flow method Tobacco mosaic virus-based protein nanoparticles and nanorods for chemotherapy delivery targeting breast cancer The current picture of the structure and assembly of tobacco mosaic virus Self-assembly of tobacco mosaic virus: the role of an intermediate aggregate in generating both specificity and speed Assembly of the particle of tobacco mosaic virus from RNA and disks of protein Configuration of tobacco mosaic virus RNA during virus assembly The structure of the protein disk of tobacco mosaic virus to 5 Å resolution Biological templates for antireflective current collectors for photo-electrochemical cell applications Plant virus directed fabrication of nanoscale materials and devices Plant viruses and bacteriophages for drug delivery in medicine and biotechnology Tobacco mosaic virus delivery of phenanthriplatin for cancer therapy Plant-derived vaccine protects target animals against a virus disease cDNA cloning of the complete genome of tobacco mosaic virus and production of infectious transcripts A chemoselective biomolecular template for assembling diverse nanotubular materials β-Structure of the coat protein subunits in spherical particles generated by tobacco mosaic virus thermal denaturation Analysis of the aphthovirus 2A/2B polyprotein 'cleavage' mechanism indicates not a proteolytic reaction, but a novel translational effect: a putative ribosomal 'skip Virus particles as templates for materials synthesis Organization of metallic nanoparticles using tobacco mosaic virus templates States of aggregation of tobacco mosaic virus protein Bottom-up-assembled nanostar colloids of gold cores and tubes derived from tobacco mosaic virus RNA-controlled assembly of tobacco mosaic virus-derived complex structures: from nanoboomerangs to tetrapods Tailoring the surface properties of tobacco mosaic virions by the integration of bacterially expressed mutant coat protein Tobacco mosaic virus: a biological building block for micro/nano/biosystems Electrochemically-driven insertion of biological nanodiscs into solid state membrane pores as a basis for pore-in-pore Stable disk assemblies of a tobacco mosaic virus mutant as nanoscale scaffolds for applications in drug delivery Plant virus expressing hybrid coat protein with added murine epitope elicits autoantibody response Tobacco mosaic virus liquid crystals as templates for the interior design of silica mesophases and nanoparticles Reconstitution of active tobacco mosaic virus from its inactive protein and nucleic acid components Tobacco mosaic virus-delivered cisplatin restores efficacy in platinum-resistant ovarian cancer cells Structure of tobacco mosaic virus: location of the ribonucleic acid in the tobacco mosaic virus particle Targeting cancer with 'smart bombs': equipping plant virus nanoparticles for a 'seek and destroy' mission Trastuzumab-binding peptide display by tobacco mosaic virus Seeing tobacco mosaic virus through direct electron detectors The 5 0 -leader sequence of tobacco mosaic virus RNA enhances the expression of foreign gene transcripts in vitro and in vivo In vivo uncoating and efficient expression of foreign mRNAs packaged in TMV-like particles The effect of multiple dispersed copies of the origin-of-assembly sequence from TMV RNA on the morphology of pseudovirus particles assembled in vitro TMV nanorods with programmed longitudinal domains of differently addressable coat proteins Nucleotide sequence of tobacco mosaic virus RNA Plants transformed with a tobacco mosaic virus nonstructural gene sequence are resistant to the virus Evidence for incorporation of disks in 5 0 -elongation along the major RNA tail Malarial epitopes expressed on the surface of recombinant tobacco mosaic virus Design of virus-based nanomaterials for medicine, biotechnology, and energy Immunoabsorbent nanoparticles based on a tobamovirus displaying protein A Plant viruses: a tool-box for genetic engineering and crop protection Fabrication and characterization of gold nano-wires template on virus-like arrays of tobacco mosaic virus coat proteins Expression of foot-and-mouth disease virus epitopes in tobacco by a tobacco mosaic virus-based vector Enhancing the magnetoviscosity of ferrofluids by the addition of biological nanotubes Electrospinning fabrication, structural and mechanical characterization of rod-like virus-based composite nanofibers Patterned assembly of genetically modified viral nanotemplates via nucleic acid hybridization TMV microarrays: hybridization-based assembly of DNA-programmed viral nanotemplates Tobacco mosaic virus replicase and replicative structures Virus-based scaffolds for tissue engineering applications Disulfide bond: dramatically enhanced assembly capability and structural stability of tobacco mosaic virus nanorods Site-selective nucleation and controlled growth of gold nanostructures in tobacco mosaic virus nanotubulars The nucleotide sequence at the origin for assembly on tobacco mosaic virus RNA The isolation of tobacco mosaic virus RNA fragments containing the origin for viral assembly Location of the origin for viral reassembly on tobacco mosaic virus RNA and its relation to stable fragment
    keywords: amino; assembly; et al; fig; mosaic; mosaic virus; particles; peptides; plants; protein; rna; rods; structure; surface; tmv; tobacco; tobacco mosaic; virus
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        item: #882 of 1349
          id: cord-309469-2naxn580
      author: An, Hongliu
       title: Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus
        date: 2019-01-05
       words: 3609
      flesch: 40
     summary: Noncoding RNAs of plant viruses and viroids: sponges of host translation and RNA interference machinery Noncoding RNAs of plant viruses and viroids: sponges of host translation and RNA interference machinery A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity RNA of low molecular weight in KB cells infected with adenovirus type 2 A contemporary view of coronavirus transcription Noncoding flavivirus RNA displays RNA interference suppressor activity in insect and Mammalian cells West Nile virus noncoding subgenomic RNA contributes to viral evasion of the type I interferon-mediated antiviral response Towards construction of viral vectors based on avian coronavirus infectious bronchitis virus for gene delivery and vaccine development EBV noncoding RNAs Role of nucleotides immediately flanking the transcription-regulating sequence core in coronavirus subgenomic mRNA synthesis Noncoding RNPs of viral origin Decoding human cytomegalovirus Polyadenylylated nuclear RNA encoded by Kaposi sarcoma-associated herpesvirus Parvovirus expresses a small noncoding RNA that plays an essential role in virus replication Dissection of the adenoviral VA RNAI central domain structure reveals minimum requirements for RNA mediated inhibition of PKR Identification of a noncanonical signal for transcription of a novel subgenomic mRNA of mouse hepatitis virus: implication for the mechanism of coronavirus RNA transcription Characterization of ribonucleoprotein complexes containing an abundant polyadenylated nuclear RNA encoded by Kaposi's sarcoma-associated herpesvirus (human herpesvirus 8) Sequence motifs involved in the regulation of discontinuous coronavirus subgenomic RNA synthesis This work was financially supported by grants from the National Natural Science Foundation of China (No. 31572490) and the Department of Science and Technology, Hubei Provincial People's Government, China (No. 2013BHE020) For example, subgenomic RNA (sfRNA) produced by Flaviviruses, such as Dengue virus (DENV), West Nile virus (WNV), Yellow fever virus (YFV), and Zika virus [reviewed in (Bidet and Garcia-Blanco, 2014; Roby et al., 2014; Pijlman et al., 2008; Akiyama et al., 2016) , and subgenomic ncRNA generated by some plant viruses such as Barley yellow dwarf virus and Red clover necrotic mosaic virus using similar mechanism (Miller et al., 2016a) .
    keywords: cells; ibv; ncrna; rna; sequence; sgrna; transcription; vero; virus
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        item: #883 of 1349
          id: cord-309722-04pp3lv0
      author: Qiu, Yingshan
       title: Delivery of RNAi Therapeutics to the Airways—From Bench to Bedside
        date: 2016-09-20
       words: 13217
      flesch: 36
     summary: tablets Nanomedicine as an emerging platform for metastatic lung cancer therapy Aerosol gene delivery using viral vectors and cationic carriers for in vivo lung cancer therapy Akt/protein kinase B is constitutively active in non-small cell lung cancer cells and promotes cellular survival and resistance to chemotherapy and radiation Dual expression of shAkt1 and Pdcd4 suppresses lung tumorigenesis in K-ras LA1 mice Suppression of lung cancer progression by biocompatible glycerol triacrylate-spermine-mediated delivery of shAkt1 Lentivirus-AIMP2-DX2 shRNA suppresses cell proliferation by regulating Akt1 signaling pathway in the lungs of AIMP2+/-Mice Factors involved in the aerosol transmission of infection and control of ventilation in healthcare premises Pulmonary codelivery of doxorubicin and siRNA by pH-sensitive nanoparticles for therapy of metastatic lung cancer A novel platform to enable inhaled naked RNAi medicine for lung cancer In vivo tumor targeting via nanoparticle-mediated therapeutic siRNA coupled to inflammatory response in lung cancer mouse models Knockdown of the sodium-dependent phosphate co-transporter 2b (NPT2b) suppresses lung tumorigenesis Gene silencing in a mouse lung metastasis model by an inhalable dry small interfering RNA powder prepared using the supercritical carbon dioxide technique Nanostructured lipid carriers as multifunctional nanomedicine platform for pulmonary co-delivery of anticancer drugs and siRNA Modelling Myc inhibition as a cancer therapy Co-delivery of doxorubicin and Bcl-2 siRNA by mesoporous silica nanoparticles enhances the efficacy of chemotherapy in multidrug-resistant cancer cells RPN2 gene confers docetaxel resistance in breast cancer Prognostic and therapeutic impact of RPN2-mediated tumor malignancy in non-small-cell lung cancer Co-delivery of chemosensitizing siRNA and an anticancer agent via multiple monocomplexation-induced hydrophobic association Polypeptide cationic micelles mediated co-delivery of docetaxel and siRNA for synergistic tumor therapy Co-delivery of siRNAs and anti-cancer drugs using layered double hydroxide nanoparticles Bcl-2 inhibitors: Targeting mitochondrial apoptotic pathways in cancer therapy Akt1 is an important mediator of cell growth, proliferation and survival of non-small cell lung cancer (NSCLC).
    keywords: administration; asthma; cancer; cells; clinical; delivery; disease; drug; effect; expression; gene; infection; inflammation; lung; molecules; protein; rnai; sirna; targeting; tgf; therapeutic; therapy; treatment; virus
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        item: #884 of 1349
          id: cord-310086-9e4txeck
      author: Fu, Wei
       title: Letter to the Editor: Three cases of re‐detectable positive SARS‐CoV‐2 RNA in recovered COVID‐19 patients with antibodies
        date: 2020-05-05
       words: 1150
      flesch: 49
     summary: However, there have been reports that several cases of re‐detectable positive SARS‐CoV‐2 RNA in recovered COVID‐19 patients, the potential reasons of re‐detectable positive patients remained elusive. These cases suggested that the reasons for re‐detectable positive patients with profile of antibodies may be related to several factors.
    keywords: patients; rna; sars
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        item: #885 of 1349
          id: cord-310141-2jofy8fo
      author: Qureshi, Abid
       title: A review on current status of antiviral siRNA
        date: 2018-04-15
       words: 3384
      flesch: 19
     summary: Short interfering RNAs developed against the helicase and replicase genes of hepatitis E virus were found to be effective in inhibiting virus replication in A549 as well as HepG2 cells. Primate hepatitis B viruses-genetic diversity, geography and evolution Small interfering RNA inhibits hepatitis B virus replication in mice siRNAs against the Epstein Barr virus latency replication factor, EBNA1, inhibit its function and growth of EBVdependent tumor cells Short interfering RNA-mediated inhibition of herpes simplex virus type 1 gene expression and function during infection of human keratinocytes RNA composition of Junin virus Identification and molecular characterization of 18 paramyxoviruses isolated from snakes RNA interference inhibits respiratory syncytial virus replication and disease pathogenesis without inhibiting priming of the memory immune response Emerging viruses: the Bunyaviridae An siRNA against JC virus (JCV) agnoprotein inhibits JCV infection in JCV-producing cells inoculated in nude mice Filoviridae: a taxonomic home for Marburg and Ebola viruses? Use of siRNAs to prevent and treat influenza virus infection Inhibition of influenza virus production in virus-infected mice by RNA interference Molecular detection and typing of human picornaviruses A small interfering RNA targeting coxsackievirus B3 protects permissive HeLa cells from viral challenge Viruses of the Bunya-and Togaviridae families: potential as bioterrorism agents and means of control Inhibition of SARS-CoV replication by siRNA Using siRNA in prophylactic and therapeutic regimens against SARS coronavirus in Rhesus macaque New drug targets for hepatitis C and other Flaviviridae viruses Small interfering RNAmediated inhibition of hepatitis C virus replication in the human hepatoma cell line Huh-7 Effective siRNA targeting of the 3′ untranslated region of the West Nile virus genome Inhibition of dengue virus infections in cell cultures and in AG129 mice by a small interfering RNA targeting a highly conserved sequence An update on Zika virus infection A computational approach to design potential antiviral RNA for 3'UTR post transcriptional gene silencing of different strains of Zika virus ZikaVR: an integrated Zika virus resource for genomics, proteomics, phylogenetic and therapeutic analysis Identification of Zika virus and dengue virus dependency factors using functional genomics Emergence of vertebrate retroviruses and envelope capture siRNA-directed inhibition of HIV-1 infection A randomized, double-blind, placebo-controlled study of an RNAi-based therapy directed against respiratory syncytial virus RNA interference and its potential applications to chronic HBV treatment: results of a phase I safety and tolerability study SPC3649) can inhibit the biogenesis of miR-122 Current prospects for RNA interferencebased therapies Emerging targets and novel approaches to Ebola virus prophylaxis and treatment Targeting Marek's disease virus by RNA interference delivered from a herpesvirus vaccine Adenovirus-mediated RNA interference against foot-and-mouth disease virus infection both in vitro and in vivo RNA interference acts as a natural antiviral response to O'nyongnyong virus (Alphavirus; Togaviridae) infection of Anopheles gambiae The role of RNAi and microRNAs in animal virus replication and antiviral immunity siRNA efficiency: structure or sequence-that is the question Selection of hyperfunctional siRNAs with improved potency and specificity Universal and mutation-resistant antienteroviral activity: potency of small interfering RNA complementary to the conserved cis-acting replication element within the enterovirus coding region Position-specific chemical modification of siRNAs reduces off-target transcript silencing siRNA-optimized modifications for enhanced in vivo activity siRNAmod: a database of experimentally validated chemically modified siRNAs Activity of stabilized short interfering RNA in a mouse model of hepatitis B virus replication Delivery of siRNA therapeutics: barriers and carriers siRNA delivery strategies: a comprehensive review of recent developments.
    keywords: cells; inhibition; interference; replication; rna; rnai; rnas; silencing; sirna; target; virus; viruses
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        item: #886 of 1349
          id: cord-310192-8x37nx4s
      author: Zhang, Huaqun
       title: Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy
        date: 2019-04-25
       words: 7237
      flesch: 29
     summary: eLife, 3, e03678 NMR probing of invisible excited states using selectively labeled RNAs Imino proton exchange rates imply an induced-fit binding mechanism for the VEGF165-targeting aptamer Epigenetic regulation by long noncoding RNAs Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics Riboswitch structure in the ligand-free state Incorporation of isotopic, fluorescent, and heavy-atommodified nucleotides into RNAs by position-selective labeling of RNA Synthesis and applications of RNAs with positionselective labelling and mosaic composition Applications of PLOR in labeling large RNAs at specific sites Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations NMR detection of structures in the HIV-1 5 0 -leader RNA that regulate genome packaging Isotope labeling strategies for NMR studies of RNA Structure of HCV IRES domain II determined by NMR Structure determination of large biological RNAs Measurement of carbonyl chemical shifts of excited protein states by relaxation dispersion NMR spectroscopy: Comparison between uniformly and selectively 13 C labeled samples Accurate measurement of residual dipolar couplings in large RNAs by variable flip angle NMR Visualizing group II intron catalysis through the stages of splicing An introduction to biological NMR spectroscopy RNA structure analysis at single nucleotide resolution by selective 2 0 -hydroxyl acylation and primer extension (SHAPE) Speciation of a group I intron into a lariat capping ribozyme A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography Cryo EM structure of intact rotary H(+)-ATPase/synthase from Thermus thermophilus Multiple segmental and selective isotope labeling of large RNA for NMR structural studies Crystal structure of Pistol, a class of self-cleaving ribozyme RNA dynamics: Perspectives from spin labels Preparation of 13C and 15N labelled RNAs for heteronuclear multi-dimensional NMR studies Cryo-EM: A unique tool for the visualization of macromolecular complexity Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy Metals induce transient folding and activation of the twister ribozyme RNA labeling, conjugation and ligation Chemical probes for higher-order structure in RNA NMR scaler couplings across Watson-Crick base pair hydrogen bonds in DNA observed by transverse relaxation optimized spectroscopy Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands Group II intron self-splicing Structure of a group II intron in complex with its reverse transcriptase Three-state mechanism couples ligand and temperature sensing in riboswitches Structure-based mechanistic insights into catalysis by small self-cleaving ribozymes RNA structure: Software for RNA secondary structure prediction and analysis Mapping the landscape of RNA dynamics with NMR spectroscopy Probing the structural dynamics of proteins and nucleic acids with optical tweezers Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM The structural and functional diversity of metabolite-binding riboswitches Synthesis and NMR of RNA with selective isotopic enrichment in the bases Preparation of specifically 2 H-and 13 C-labeled ribonucleotides Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension Crystal structure of the Varkud satellite ribozyme RNA structure through multidimensional chemical mapping Major groove width variations in RNA structures determined by NMR and impact of 13 C residual chemical shift anisotropy and 1 H-13 C residual dipolar coupling on refinement Crystal structure of a self-spliced group II intron Structural basis for exon recognition by a group II intron Preparation of large RNA oligonucleotides with complementary isotope-labeled segments for NMR structural studies NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation site Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: A primer NMR investigation of RNA structure Structure-activity relationship of flavin analogues that target the flavin mononucleotide riboswitch Single particle electron cryomicroscopy: Trends, issues and future perspective Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution A method for helical RNA global structure determination in solution using small-angle X-ray scattering and NMR measurements Principles for targeting RNA with drug-like small molecules Architecture and secondary structure of an entire HIV-1 RNA genome Advances in RNA structure analysis by chemical probing NMR of proteins and nucleic acids Determining RNA solution structure by segmental isotopic labeling and NMR: Application to Caenorhabditis elegans spliced leader RNA 1 Characterizing RNA excited states using NMR relaxation dispersion Nmr experiments for the measurement of carbon relaxation properties in highly enriched, uniformly 13 C, 15 N-labeled proteins-Application to 13 C(alpha) carbons MQ-HCN-based pulse sequences for the measurement of 13 C1'-1 H1 Structure of the 30 kDa HIV-1 RNA dimerization signal by a hybrid Cryo-EM, NMR, and molecular dynamics approach An excited state underlies gene regulation of a transcriptional riboswitch Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R (1rho) NMR spectroscopy Crystal structure of group II intron domain 1 reveals a template for RNA assembly Measurement of small scalar and dipolar couplings in purine and pyrimidine bases NMR studies of HAR1 RNA secondary structures reveal conformational dynamics in the human RNA DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy key: cord-310192-8x37nx4s authors: Zhang, Huaqun; Keane, Sarah C. title: Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy date: 2019-04-25 journal:
    keywords: analysis; approach; base; chemical; cryo; data; dynamics; et al; experiments; labeling; method; molecules; nmr; rna; rna structure; rnas; spectroscopy; structure; studies; study
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        item: #887 of 1349
          id: cord-310268-8q4tk6fd
      author: Zhu, Qinchang
       title: DNA Aptamers in the Diagnosis and Treatment of Human Diseases
        date: 2015-11-25
       words: 8657
      flesch: 42
     summary: DNA polymerase In vitro selection of RNA molecules that bind specific ligands Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures Selection of single-stranded DNA molecules that bind and inhibit human thrombin Aptamers as therapeutics Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications A Highlight of Recent Advances in Aptamer Technology and Its Application Aptamers and their biological applications Applications of aptamers for chemistry analysis, medicine and food security Outlook for Aptamers after Twenty Five Years RNA aptamers as genetic control devices: The potential of riboswitches as synthetic elements for regulating gene expression Pegaptanib (Macugen): Treating neovascular age-related macular degeneration and current role in clinical practice Aptamer nanomedicine for cancer therapeutics: Barriers and potential for translation Aptamers Market-Global Forecast to 2020 Post-SELEX chemical optimization of a trypanosome-specific RNA aptamer Building oligonucleotide therapeutics using non-natural chemistries Inhibition of HIV-1 protease expression in T cells owing to DNA aptamer-mediated specific delivery of siRNA Improving the Stability of Aptamers by Chemical Modification Influence of the 2 1 -hydroxyl group conformation on the stability of A-form helices in RNA Oligonucleotide Aptamers: New Tools for Targeted Cancer Therapy In vitro selection of functional nucleic acids Aptamers Overview: Selection, Features and Applications Single-stranded DNA (ssDNA) production in DNA aptamer generation Development of a novel DNA aptamer ligand targeting to primary cultured tumor endothelial cells by a cell-based SELEX method DNA aptamer evolved by cell-SELEX for recognition of prostate cancer Development of an efficient targeted cell-SELEX procedure for DNA aptamer reagents A two-step stimulus-response cell-SELEX method to generate a DNA aptamer to recognize inflamed human aortic endothelial cells as a potential in vivo molecular probe for atherosclerosis plaque detection Evolution of DNA aptamers through in vitro metastatic-cell-based systematic evolution of ligands by exponential enrichment for metastatic cancer recognition and imaging In silico maturation of binding-specificity of DNA aptamers against Proteus mirabilis A novel protocol for generating high-affinity ssDNA aptamers by using alternating magnetic fields Magnetic-assisted rapid aptamer selection (MARAS) for generating high-affinity DNA aptamer using rotating magnetic fields Rapid one-step selection method for generating nucleic acid aptamers: Development of a DNA aptamer against alpha-bungarotoxin Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape Single-Round Patterned DNA Library Microarray Aptamer Lead Identification The application of a modified nucleotide in aptamer selection: Novel thrombin aptamers containing 5-(1-pentynyl)-2 1 -deoxyuridine Molecular evolution of functional nucleic acids with chemical modifications Novel combinatorial selection of phosphorothioate oligonucleotide aptamers Chemically modified nucleic acid aptamers for in vitro selections: Evolving evolution Effect of 3 1 -end capping of aptamer with various 2 1 ,4 1 -bridged nucleotides: Enzymatic post-modification toward a practical use of polyclonal aptamers Application of locked nucleic acids to improve aptamer in vivo stability and targeting function Locked nucleic acids: A promising molecular family for gene-function analysis and antisense drug development Selection of LNA-containing DNA aptamers against recombinant human CD73 Synthesis and properties of mirror-image DNA Simple PEG Modification of DNA Aptamer Based on Copper Ion Coordination for Tumor Targeting A multivalent DNA aptamer specific for the B-cell receptor on human lymphoma and leukemia Affinity analysis of DNA aptamer-peptide interactions using gold nanoparticles Aptamer-functionalized PEG-PLGA nanoparticles for enhanced anti-glioma drug delivery Selective Delivery of an Anticancer Drug with Aptamer-Functionalized Liposomes to Breast Cancer Cells in vitro and in vivo DNA aptamer-micelle as an efficient detection/delivery vehicle toward cancer cells Applications of Aptasensors in Clinical Diagnostics In vitro selection of DNA aptamers to anthrax spores with electrochemiluminescence detection DNA Aptamer Selected against Pancreatic Ductal Adenocarcinoma for in vivo Imaging and Clinical Tissue Recognition Cell-SELEX based selection and characterization of DNA aptamer recognizing human hepatocarcinoma Molecular Recognition of Human Liver Cancer Cells Using DNA Aptamers Generated via Cell-SELEX Cell-SELEX based selection and optimization of DNA aptamers for specific recognition of human cholangiocarcinoma QBC-939 cells A cell-based single-stranded DNA aptamer specifically targets gastric cancer A DNA aptamer with high affinity and specificity for molecular recognition and targeting therapy of gastric cancer In Vitro Selection of DNA Aptamers for Metastatic Breast Cancer Cell Recognition and Tissue Imaging Selection of DNA Aptamers against Glioblastoma Cells with High Affinity and Specificity DNA aptamers that target human glioblastoma multiforme cells overexpressing epidermal growth factor receptor variant III in vitro Selection of DNA Aptamers against Epithelial Cell Adhesion Molecule for Cancer Cell Imaging and Circulating Tumor Cell Capture Probing high affinity sequences of DNA aptamer against VEGF165 Selection of DNA aptamers against VEGF(165) using a protein competitor and the aptamer blotting method In Vitro Selection of DNA Aptamers to Glioblastoma Multiforme Selection and characterization of DNA aptamers for use in detection of avian influenza virus H5N1 Development of a fluorescent enzyme-linked DNA aptamer-magnetic bead sandwich assay and portable fluorometer for sensitive and rapid leishmania detection in sandflies Label-free detection of prion protein with its DNA aptamer through the formation of T-Hg2+-T configuration Application of a novel in vitro selection technique to isolate and characterise high affinity DNA aptamers binding mammalian prion proteins Structural basis for discriminatory recognition of Plasmodium lactate dehydrogenase by a DNA aptamer Screening of DNA Aptamers against Myoglobin Using a Positive and Negative Selection Units Integrated Microfluidic Chip and Its Biosensing Application Development of a DNA aptamer for direct and selective homocysteine detection in human serum DNA aptamer-based detection of prostate cancer DNA aptamers against the MUC1 tumour marker: Design of aptamer-antibody sandwich ELISA for the early diagnosis of epithelial tumours Sensitive point-of-care monitoring of cardiac biomarker myoglobin using aptamer and ubiquitous personal glucose meter C-reactive protein, inflammation and coronary heart disease DNA aptamer-based surface plasmon resonance sensing of human C-reactive protein Homocysteine level and coronary heart disease incidence: A systematic review and meta-analysis Thrombin, inflammation, and cardiovascular disease: An epidemiologic perspective Aptamer binding assays for proteins: The thrombin example-A review Design strategies for aptamer-based biosensors Aptamer-based molecular recognition for biosensor development Aptamer in bioanalytical applications Aptamer-based biosensors for biomedical diagnostics Structure-switching signaling aptamers Structure-switching signaling aptamers: Transducing molecular recognition into fluorescence signaling Enzyme-Linked Small-Molecule Detection Using Split Aptamer Ligation Target-induced conjunction of split aptamer fragments and assembly with a water-soluble conjugated polymer for improved protein detection An aptamer-based biosensor for sensitive thrombin detection
    keywords: aptamers; binding; cancer; cells; delivery; dna; dna aptamers; human; method; mode; rna; selection; selex; sequences; specific; target
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        item: #888 of 1349
          id: cord-310371-pylrg91h
      author: Bishop, R.F.
       title: Enteric Viruses
        date: 2008-07-30
       words: 4469
      flesch: 38
     summary: The recent demonstration that human noroviruses can infect and replicate in a three-dimensional cell culture model of human intestinal epithelium, should improve our understanding of the pathogenesis, and antigenic diversity of this important group of enteric viruses. key: cord-310371-pylrg91h authors: Bishop, R.F.; Kirkwood, C.D. title: Enteric Viruses date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00386-1 sha: doc_id: 310371 cord_uid: pylrg91h Many viruses use the enteric tract as a route of entry to the human, animal, or avian host.
    keywords: caliciviruses; cause; children; diarrhea; disease; enteric; gastroenteritis; human; infection; rotavirus; viruses
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        item: #889 of 1349
          id: cord-310605-r63sg73c
      author: Dorward, D. A.
       title: Tissue-specific tolerance in fatal Covid-19
        date: 2020-07-04
       words: 4484
      flesch: 31
     summary: A marked increase in the number of plasma cells (10% or more) was seen in 7/8 bone marrow trephines but these plasma cells had a normal phenotype, being negative for CD56 and cyclin D1, and were polytypic with light chain immunohistochemistry. Splenic red pulp was congested and, in all cases, contained an increased number of plasma cells with similar features to those observed in mediastinal nodes.
    keywords: cells; cov-2; covid-19; inflammation; lung; presence; sars; tissue; viral
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        item: #890 of 1349
          id: cord-310748-ao29zx1u
      author: Banner, Lisa R.
       title: Random nature of coronavirus RNA recombination in the absence of selection pressure
        date: 1991-11-30
       words: 2860
      flesch: 49
     summary: Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. These results suggest that RNA recombination is common and random in nature, but only certain recombinants can be selected.
    keywords: crossover; pcr; recombinant; recombination; rna; viruses
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        item: #891 of 1349
          id: cord-310771-tnwfp1je
      author: Revilla-Fernández, Sandra
       title: The use of endogenous and exogenous reference RNAs for qualitative and quantitative detection of PRRSV in porcine semen
        date: 2005-02-23
       words: 5961
      flesch: 40
     summary: A method was developed for qualitative and quantitative detection of the seminal cell-associated PRRSV RNA in relation to endogenous and exogenous reference RNAs. Particularly for the analysis of persistent infections associated with low copy numbers of PRRSV RNA, UBE2D2 mRNA is an ideal control due to its low expression in seminal cells and its detection in all samples analysed (n = 36).
    keywords: assays; boars; detection; expression; mrna; pcr; porcine; prrsv; reference; rna; semen; time; ube2d2; viral; virus
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        item: #892 of 1349
          id: cord-310861-9kb0b6rq
      author: Koo, Bonhan
       title: An isothermal, label-free, and rapid one-step RNA amplification/detection assay for diagnosis of respiratory viral infections
        date: 2017-04-15
       words: 5588
      flesch: 51
     summary: iROAD assay for viral RNA detection Fig. 1 illustrates the iROAD assay that was designed for the clinical detection of viral RNAs, which were extracted from the nasopharyngeal swab samples with either Influenza (IFN)-A/B or human coronavirus (HCoV)-OC43/229E or respiratory syncytial virus (RSV)-A/B, by the QIAamp viral RNA mini kit. Furthermore, we demonstrated the clinical utility of the iROAD assay by detecting respiratory viral RNAs extracted from the 63 nasopharyngeal samples with either IFN-A/B or HCoV-OC43/229E or RSV-A/B. The iROAD assay combines amplification and detection mechanism of RNA, resulting in increased sensitivity and specificity of viral RNA detection.
    keywords: amplification; assay; detection; fig; ifn; iroad; rna; samples; time; viral
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        item: #893 of 1349
          id: cord-310920-itqwhi6a
      author: Haddad, Christina
       title: Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment
        date: 2020-07-02
       words: 3701
      flesch: 35
     summary: Thus, studying viral RNA structures and their interactions with cognate RBPs are essential to understanding the pathogenesis of RNA viruses and to further assist the design of novel antivirals. It is therefore no surprise that RNA viruses use this functional diversity to their advantage to sustain chronic or lifelong infections.
    keywords: genome; host; interactions; protein; replication; rna; sars; structural; virus; viruses
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        item: #894 of 1349
          id: cord-310947-aqau2n7q
      author: Pan, Ji'An
       title: Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication
        date: 2008-10-01
       words: 6850
      flesch: 39
     summary: In our screen, 1.4 protein interactions per viral protein on the average was detected, and this result is in the upper range of the detection rates of viral protein interactions obtained by yeast two-hybrid systems Nsp11 is a small polypeptide containing only 13 amino acids and no interaction was detected with it in various assays but nsp11 in the fusion with nsp10 (nsp10/ 11) could significantly enhance the binding capability of nsp10 with either nsp14 or nsp16, indicating that the small nsp11 may also play important roles in viral protein interactions and replication.
    keywords: activity; coronavirus; cov; genome; hybrid; interactions; nsp10; protein; replication; rna; sars; syndrome; system; transcription
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        item: #895 of 1349
          id: cord-310967-15mv5yx7
      author: Morris, Vincent L.
       title: Characterization of coronavirus JHM variants isolated from wistar furth rats with a viral-induced demyelinating disease
        date: 1989-03-31
       words: 5853
      flesch: 50
     summary: However, ATllf brain virus, ATlIe brain virus, and wild-type JHM virus-infected oligodendroglioma cells (G26-24) resembled uninfected G26-24 cultures except individual cells rounded up and lifted off from the monolayer ( Fig. 1 ; data not shown for JHM virus). A littermate of ATllf (designated ATlle) was also inoculated ic at 10 days of age with the same cloned stock of JHM virus.
    keywords: atllf; brain; cord; jhm; mrna; rats; variants; virus
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        item: #896 of 1349
          id: cord-311007-0i1abjfa
      author: Schwarz, Megan C.
       title: Rescue of the 1947 Zika Virus Prototype Strain with a Cytomegalovirus Promoter-Driven cDNA Clone
        date: 2016-09-28
       words: 4869
      flesch: 44
     summary: Parallel infection of 293T cells with the parent MR766 virus resulted in supernatants containing between 2.6 ϫ 10 7 and 2.2 ϫ 10 8 TCID 50 /ml. To compare the fitness levels of our parental and rescued MR766 viruses, we first calculated their Vero cell specific infectivities.
    keywords: cdna; cells; fig; mr766; plasmid; rna; system; type; viral; virus; zikv
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        item: #897 of 1349
          id: cord-311625-d7iycdyh
      author: Choong, Oi Kuan
       title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication
        date: 2014-02-20
       words: 4024
      flesch: 48
     summary: Both ends of the duplex TFOs were ligated with a linker sequence or clamps (C-C) to construct circular TFO RNA. One hundred nM of circular TFO RNA was transfected into MDCK cells.
    keywords: binding; cells; feline; fipv; rna; target; tfo; tfo1; tfos; virus
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        item: #898 of 1349
          id: cord-311628-ep795pil
      author: Fu, Yu
       title: A novel delivery platform based on Bacteriophage MS2 virus-like particles
        date: 2016-01-04
       words: 6025
      flesch: 36
     summary: In order to determine the role of MS2 RNA in capsid stability, the experiment was repeated with wild-type phage particles, prepared for electron microscopy in the same way as the empty capsids. The use of armored RNA as a multi-purpose internal control for RT-PCR A simple, RNA-mediated allosteric switch controls the pathway to formation of a T = 3 viral capsid Molecular mechanism of RNA phage morphogenesis Molecular mechanism of RNA-phage morphogenesis Effects of amino acid substitution on the thermal stability of MS2 capsids lacking genomic RNA Crystal structures of MS2 capsids with mutations in the subunit FG loop Ribonucleoprotein complexes formed between bacteriophages MS2 RNA and MS2 protein in vitro A new RNA vaccine platform based on MS2 virus-like particles produced in saccharomyces cerevisiae MicroRNA-146A contributes to abnormal activation of the type I interferon pathway in human lupus by targeting the key signaling proteins The three-dimensional structure of genomic RNA in bacteriophage MS2: implications for assembly Visualising a viral RNA genome poised for release from its receptor complex VLPs displaying a single L2 epitope induce broadly cross-neutralizing antibodies against human papilloma virus A coat for all sequences RNA-based vaccines Structure determination of the bacteriophage MS2 The three-dimensional structure of the bacterial virus MS2 Proliferative lymphocyte responses to foot-and-mouth disease virus and three FMDV peptides after vaccination or immunization with these peptides in cattle mRNA: from a chemical blueprint for protein production to an off-the-shelf therapeutic mRNA: delivering an antitumor message External quality assessment of molecular detection of ebola virus in China Delivery of siRNA therapeutics: barriers and carriers Development of an antisense RNA delivery system using conjugates of the MS2 bacteriophage capsids and HIV-1 TAT cell-penetrating peptide RNase-resistant virus-like particles containing long chimeric RNA sequences produced by two-plasmid coexpression system Plasmids encoding foot-and-mouth disease virus VP1 epitopes elicited immune responses in mice and swine and protected swine against viral infection Delivery of antisense oligonucleotides to leukemia cells by RNA bacteriophage capsids Using a novel MicroRNA delivery system to inhibit osteoclastogenesis Cancer therapy using a self-replicating RNA vaccine Construction and characterization of virus-like particles: a review Armored long RNA controls or standards for branched DNA assay for detection of human immunodeficiency virus type 1 External quality assessment for the detection of measles virus by reverse transcription-PCR using armored RNA A novel method to produce armored double-stranded DNA by encapsulation of MS2 viral capsids RNA melanoma vaccine: induction of antitumor immunity by human glycoprotein 100 mRNA immunization Virus assembly, allostery and antivirals This work was supported by the grant from the National Natural Science Foundation of China (No. 81171981).
    keywords: assembly; bacteriophage; capsid; delivery; et al; mrna; ms2; particles; protein; rna; vaccine; virus; vlps
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        item: #899 of 1349
          id: cord-311982-wkg56xeq
      author: Dye, Charlotte
       title: Genomic RNA sequence of feline coronavirus strain FCoV C1Je
        date: 2007-06-17
       words: 5243
      flesch: 46
     summary: key: cord-311982-wkg56xeq authors: Dye, Charlotte; Siddell, Stuart G. title: Genomic RNA sequence of feline coronavirus strain FCoV C1Je date: 2007-06-17 journal: J Feline Med Surg DOI: 10.1016/j.jfms.2006.12.002 sha: doc_id: 311982 cord_uid: wkg56xeq Comparison of the FCoV C1Je genomic RNA sequence with that of the laboratory strain FCoV FIP virus (FIPV) 79-1146 showed that both viruses have a similar genome organisation and predictions made for the open reading frames and cis-acting elements of the FIPV 79-1146 genome hold true for FCoV C1Je.
    keywords: c1je; coronavirus; fcov; feline; fipv; genomic; rna; sequence; strain
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        item: #900 of 1349
          id: cord-312001-8p7scli8
      author: Majzoub, Karim
       title: The Innate Antiviral Response in Animals: An Evolutionary Perspective from Flagellates to Humans
        date: 2019-08-16
       words: 10087
      flesch: 37
     summary: [corrected] gene induction by the interferon regulatory factor family of transcription factors Cutting edge: TNFR-associated factor (TRAF) 6 is essential for MyD88-dependent pathway but not toll/IL-1 receptor domain-containing adaptor-inducing IFN-beta (TRIF)-dependent pathway in TLR signaling Interferon-alpha induction through Toll-like receptors involves a direct interaction of IRF7 with MyD88 and TRAF6 Helical assembly in the MyD88-IRAK4-IRAK2 complex in TLR/IL-1R signalling Protein kinase IKKbeta-catalyzed phosphorylation of IRF5 at Ser462 induces its dimerization and nuclear translocation in myeloid cells An oligomeric signaling platform formed by the Toll-like receptor signal transducers MyD88 and IRAK-4 IKKbeta is an IRF5 kinase that instigates inflammation Interleukin-1 receptor-associated kinase-1 plays an essential role for Toll-like receptor (TLR)7-and TLR9-mediated interferon-{alpha} induction Structural basis of RNA recognition and activation by innate immune receptor RIG-I Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA MDA5 assembles into a polar helical filament on dsRNA Cooperative assembly and dynamic disassembly of MDA5 filaments for viral dsRNA recognition TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity Ubiquitin-induced oligomerization of the RNA sensors RIG-I and MDA5 activates antiviral innate immune response Riplet/RNF135, a RING finger protein, ubiquitinates RIG-I to promote interferon-beta induction during the early phase of viral infection The ubiquitin ligase Riplet is essential for RIG-I-dependent innate immune responses to RNA virus infection IPS-1, an adaptor triggering RIG-I-and Mda5-mediated type I interferon induction Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-kappaB and IRF 3 Essential role of IPS-1 in innate immune responses against RNA viruses An autoinhibitory mechanism modulates MAVS activity in antiviral innate immune response MAVS forms functional prion-like aggregates to activate and propagate antiviral innate immune response Structural basis for the prion-like MAVS filaments in antiviral innate immunity MAVS recruits multiple ubiquitin E3 ligases to activate antiviral signaling cascades Activation of IKK by TNFalpha requires site-specific ubiquitination of RIP1 and polyubiquitin binding by NEMO Sensing of Lys 63-linked polyubiquitination by NEMO is a key event in NF-kappaB activation Key role of Ubc5 and lysine-63 polyubiquitination in viral activation of IRF3 STING is an endoplasmic reticulum adaptor that facilitates innate immune signalling The adaptor protein MITA links virus-sensing receptors to IRF3 transcription factor activation STING regulates intracellular DNA-mediated, type I interferon-dependent innate immunity STING is a direct innate immune sensor of cyclic di-GMP Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. cholerae virulence MPYS is required for IFN response factor 3 activation and type A conserved Toll-like receptor-to-NF-kappaB signaling pathway in the endangered coral Orbicella faveolata Genomic insights into the immune system of the sea urchin Massively parallel RNA sequencing identifies a complex immune gene repertoire in the lophotrochozoan Mytilus edulis Massive expansion and functional divergence of innate immune genes in a protostome Teleost TLR22 recognizes RNA duplex to induce IFN and protect cells from birnaviruses Adaptive evolution of virus-sensing toll-like receptor 8 in bats The evolution of bat nucleic acid-sensing Toll-like receptors Immune system modulation and viral persistence in bats: Understanding viral spillover Origin and evolution of the RIG-I like RNA helicase gene family Characterization of the mollusc RIG-I/MAVS pathway reveals an archaic antiviral signalling framework in invertebrates Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) in fish: Current knowledge and future perspectives Chicken cells sense influenza A virus infection through MDA5 and CARDIF signaling involving LGP2 Association of RIG-I with innate immunity of ducks to influenza Genome of the Chinese tree shrew Loss of RIG-I leads to a functional replacement with MDA5 in the Chinese tree shrew The kinase IKKbeta regulates a STING-and NF-kappaB-dependent antiviral response pathway in Drosophila The Jak-STAT signaling pathway is required but not sufficient for the antiviral response of drosophila The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila Sensing viral RNAs by Dicer/RIG-I like ATPases across species The DExD/H-box helicase Dicer-2 mediates the induction of antiviral activity in drosophila Secreted Vago restricts West Nile virus infection in Culex mosquito cells by activating the Jak-STAT pathway Dicer-2-dependent activation of Culex Vago occurs via the TRAF-Rel2 signaling pathway Nucleic acid sensing in invertebrate antiviral immunity The RIG-I ATPase core has evolved a functional requirement for allosteric stabilization by the Pincer domain The selective footprints of viral pressures at the human RIG-I-like receptor family Evolution and functional impact of rare coding variation from deep sequencing of human exomes Cyclic di-nucleotide signaling enters the eukaryote domain Evolutionary origins of cGAS-STING signaling Toll signaling: The TIReless quest for specificity Analysis of Drosophila STING reveals an evolutionarily conserved antimicrobial function Modular architecture of the STING C-terminal tail allows interferon and NF-kappaB signaling adaptation Dampened STING-dependent interferon activation in bats Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity ] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase Structural mechanism of cytosolic DNA sensing by cGAS Overlapping patterns of rapid evolution in the nucleic acid sensors cGAS
    keywords: activation; antiviral; cells; cgas; dna; domain; evolution; ifn; immune; immunity; mda5; receptor; response; rig; rlrs; rna; sensing; signaling; species; sting; toll; viruses
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        item: #901 of 1349
          id: cord-312223-qgwzgazd
      author: Shafagati, Nazly
       title: The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus
        date: 2013-07-04
       words: 8854
      flesch: 55
     summary: Viral inactivation was assayed by plaque assays (C) and viral RNA was extracted from the particles with Ambion's MagMax 96-well Viral RNA extraction kit and quantitated by qRT-PCR (D Comparison of capture efficacy of NanoTrap particles and commercially available beads for RVFV capture NanoTrap particles have unique properties not demonstrated in other beads that are used for protein purification and albumin exclusion such as dye baits that make them an ideal candidate in virus capture. Characterization of RVFV NanoTrap particle capture.
    keywords: assays; capture; minutes; nanotrap; nanotrap particles; nt53; particles; pcr; plaque; qrt; rna; rvfv; samples; virus
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        item: #902 of 1349
          id: cord-312240-0k8y86pf
      author: Schlaberg, Robert
       title: Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology
        date: 2017-05-01
       words: 4842
      flesch: 41
     summary: We cannot exclude that highly diverse viruses without homology to known human viral pathogens may have caused CAP in some of the children. Although both RNA-seq and PVG PCR provide broadrange detection of respiratory viruses, each method has potential advantages and disadvantages.
    keywords: cap; children; control; patients; pcr; pvg; rna; seq; subjects; viruses
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        item: #903 of 1349
          id: cord-312332-rwmuucsp
      author: Dicker, Kate
       title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity
        date: 2020-09-10
       words: 9241
      flesch: 41
     summary: The human RNA-Binding proteome and its dynamics during translational arrest Purification of cross-linked RNA-protein complexes by phenol-toluol extraction Comprehensive identification of RNA-Binding domains in human cells High-resolution mapping of RNA-Binding regions in the nuclear proteome of embryonic stem cells The new (dis)order in RNA regulation Two RNA polymerase complexes from vesicular stomatitis virus-infected cells that carry out transcription and replication of genome RNA Identification of cellular interaction partners of the influenza virus ribonucleoprotein complex and polymerase complex using proteomic-based approaches Comprehensive proteomic analysis of influenza virus polymerase complex reveals a novel association with mitochondrial proteins and RNA polymerase accessory factors Discovery of widespread host protein interactions with the prereplicated genome of CHIKV using VIR-CLASP Fields Virology Diverse roles of host RNA binding proteins in RNA virus replication https://doi.org/10.1016/j.semcdb.2020.08.002. Thiouracil cross-linking mass spectrometry: a cell-based method to identify host factors involved in viral amplification Identification of proteins bound to dengue viral RNA in vivo reveals new host proteins important for virus replication Identification of RNA binding proteins associated with dengue virus RNA in infected cells reveals temporally distinct host factor requirements Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry Unconventional RNA-binding proteins step into the virus-host battlefront Identification and characterization of sindbis virus RNA-Host protein interactions System-wide profiling of RNA-Binding proteins uncovers key regulators of virus infection An RNA-centric dissection of host complexes controlling flavivirus infection Viruses seen by our cells: the role of viral RNA sensors Intracellular sensing of viral genomes and viral evasion To translate, or not to translate: viral and host mRNA regulation by interferon-stimulated genes The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts Insights into RNA biology from an atlas of mammalian mRNAbinding proteins A brave new world of RNAbinding proteins Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS)
    keywords: assembly; binding; cell; hiv-1; host; human; infection; particles; proteins; rbps; replication; rna; role; transcription; virion; virus; viruses; vrna
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        item: #904 of 1349
          id: cord-312392-8zxl48af
      author: Buonavoglia, Canio
       title: Canine Coronavirus Highly Pathogenic for Dogs
        date: 2006-03-17
       words: 1172
      flesch: 43
     summary: CCoV type II RNA was also detected in lungs (median 1.08 × 10 6 RNA copies/µL of template), spleen (median 4.46 × 10 6 RNA copies/µL of template), liver (median 9.02 × 10 4 RNA copies/µL of template), kidney (median 7.54 × 10 4 RNA copies/µL of template), and brain (median 5.23 × 10 3 RNA copies/µL of template). Virus-induced cytopathic effect was observed in A-72 cells, and CCoV type II strain (CB/05) was isolated from all tissues examined except brain tissue.
    keywords: canine; ccov; dogs; type
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        item: #905 of 1349
          id: cord-312431-de7zhswl
      author: Ganesh, Atheesha
       title: Detecting Virus‐Like Particles from the Umgeni River, South Africa
        date: 2013-08-30
       words: 7133
      flesch: 42
     summary: Phages share many properties with human viruses, particularly composition, morphology and structure Human viruses seen in negative stains fall into one of two major morphological categories: enveloped or naked [64] .
    keywords: cell; enteric; fig; human; microscopy; particles; phage; river; samples; seasons; umgeni; viruses; vlps; water
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        item: #906 of 1349
          id: cord-312461-5qzpo6l1
      author: Adalja, Amesh A.
       title: Characteristics of Microbes Most Likely to Cause Pandemics and Global Catastrophes
        date: 2019-08-30
       words: 6830
      flesch: 35
     summary: Other factors that may increase a virus' potential to cause a global catastrophic risk include a segmented genome (as exemplified by influenza viruses), a comparatively smaller genome size, and high host viremia (e.g., vector-borne flaviviruses). Nontraditional molecules, such as monoclonal antibodies and immunomodulators, should also be investigated for a role in the treatment and prevention of RNA virus respiratory infections (Walker and Burton 2018) .
    keywords: cause; disease; human; influenza; microbe; pandemic; preparedness; respiratory; risk; rna; spread; transmission; viruses
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        item: #907 of 1349
          id: cord-312517-b24zlaqt
      author: Kim, Denny
       title: The Brighton collaboration standardized template for collection of key information for benefit-risk assessment of nucleic acid (RNA and DNA) vaccines
        date: 2020-06-19
       words: 1950
      flesch: 37
     summary: DNA vaccines have been under development since the early 1990s. The 2019 proposed revision of the WHO guidelines on DNA vaccines lists the approaches being employed to enhance the immunogenicity of a DNA vaccine [9] .
    keywords: dna; rna; safety; template; vaccine
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        item: #908 of 1349
          id: cord-312544-vip4jtlv
      author: Ng, Lisa FP
       title: Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay
        date: 2006-03-02
       words: 2145
      flesch: 52
     summary: A total of 145 field samples comprising of known and suspect cases from chickens, ducks and muscovies isolated from Vietnam and Malaysia during the 2004 to 2005 outbreak were tested for H5N1 RNA (Table Detection of H5N1 avian influenza key: cord-312544-vip4jtlv authors: Ng, Lisa FP; Barr, Ian; Nguyen, Tung; Noor, Suriani Mohd; Tan, Rosemary Sok-Pin; Agathe, Lora V; Gupta, Sanjay; Khalil, Hassuzana; To, Thanh Long; Hassan, Sharifah Syed; Ren, Ee-Chee title: Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay date: 2006-03-02 journal: BMC Infect Dis DOI: 10.1186/1471-2334-6-40 sha: doc_id: 312544 cord_uid: vip4jtlv BACKGROUND: Continuous outbreaks of the highly pathogenic H5N1 avian influenza A in Asia has resulted in an urgent effort to improve current diagnostics to aid containment of the virus and lower the threat of a influenza pandemic.
    keywords: avian; detection; h5n1; human; influenza; rna; virus
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        item: #909 of 1349
          id: cord-312688-12san3m7
      author: Martin, Baptiste
       title: Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry
        date: 2016-09-14
       words: 10232
      flesch: 36
     summary: Côt e et al., 2011; Kolokoltsov et al., 2012; Lee et al., 2013; Shoemaker et al., 2013; Basu et al., 2015) GP2 inhibitors compound 7 (Basu et al., 2011) Several compounds have been described targeting NPC1, such as U18666A, imipramine, cathionic amphiphiles Ro48-8071 and the terconazole adamantane class of compounds like benzylpiperazine adamantane diamides 3.47 and 3.0, or the lately discovered sulfonamide derivative MBX2254 and the triazole thioether derivative MBX2270 (Rodriguez-Lafrasse et al., 1990; Cenedella, 2009; Côt e et al., 2011; Lee et al., 2013; Shoemaker et al., 2013; Basu et al., 2015) .
    keywords: 1,2; antiviral; attachment; cell; compounds; ebola; ebolavirus; entry; et al; fig; filovirus; fusion; glycoprotein; host; infection; inhibitors; marburg; membrane; molecules; protein; receptor; rna; sgp; surface; virus
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        item: #910 of 1349
          id: cord-312741-0au4nctt
      author: Lin, Panpan
       title: Coronavirus in human diseases: Mechanisms and advances in clinical treatment
        date: 2020-10-01
       words: 14692
      flesch: 30
     summary: The 9-kDa hydrophobic protein encoded at the 3' end of the porcine transmissible gastroenteritis coronavirus genome is membrane-associated Mouse hepatitis virus gene 5b protein is a new virion envelope protein Infectious bronchitis virus E protein is targeted to the Golgi complex and directs release of virus-like particles A comprehensive comparison of transmembrane domains reveals organelle-specific properties Subcellular location and topology of severe acute respiratory syndrome coronavirus envelope protein Induction of apoptosis in murine coronavirus-infected cultured cells and demonstration of E protein as an apoptosis inducer Assembly of the coronavirus envelope: homotypic interactions between the M proteins SARS coronavirus E protein forms cation-selective ion channels Differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins S, M and E Bcl-xL inhibits T-cell apoptosis induced by expression of SARS coronavirus E protein in the absence of growth factors The transmembrane domain of the infectious bronchitis virus E protein is required for efficient virus release Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells Role of the coronavirus E viroporin protein transmembrane domain in virus assembly Severe acute respiratory syndrome coronavirus envelope protein regulates cell stress response and apoptosis Heterologous gene expression from transmissible gastroenteritis virus replicon particles Generation of a replication-competent, propagation-deficient virus vector based on the transmissible gastroenteritis coronavirus genome The small envelope protein E is not essential for murine coronavirus replication A severe acute respiratory syndrome coronavirus that lacks the E gene is attenuated in vitro and in vivo Absence of E protein arrests transmissible gastroenteritis coronavirus maturation in the secretory pathway Characterization of severe acute respiratory syndrome coronavirus membrane protein Sequence and topology of a model intracellular membrane protein, E1 glycoprotein, from a coronavirus Genetic evidence for a structural interaction between the carboxy termini of the membrane and nucleocapsid proteins of mouse hepatitis virus The molecular biology of coronaviruses A structural analysis of M protein in coronavirus assembly and morphology Envelope glycoprotein interactions in coronavirus assembly Efficient assembly and release of SARS coronavirus-like particles by a heterologous expression system Coronaviruses: an overview of their replication and pathogenesis Nucleocapsidindependent assembly of coronavirus-like particles by co-expression of viral envelope protein genes Coronavirus pseudoparticles formed with recombinant M and E proteins induce alpha interferon synthesis by leukocytes The cytoplasmic tails of infectious bronchitis virus E and M proteins mediate their interaction The missing link in coronavirus assembly. syndrome coronavirus nucleocapsid protein modulates its multimerization, translation inhibitory activity and cellular localization Identification of in vivointeracting domains of the murine coronavirus nucleocapsid protein Glycogen synthase kinase-3 regulates the phosphorylation of severe acute respiratory syndrome coronavirus nucleocapsid protein and viral replication Oligomerization of the carboxyl terminal domain of the human coronavirus 229E nucleocapsid protein Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method High affinity interaction between nucleocapsid protein and leader/intergenic sequence of mouse hepatitis virus RNA The nucleocapsid protein of SARS coronavirus has a high binding affinity to the human cellular heterogeneous nuclear ribonucleoprotein A1 Theoretical aspects of virus capsid assembly Analysis of multimerization of the SARS coronavirus nucleocapsid protein Mass spectroscopic characterization of the coronavirus infectious bronchitis virus nucleoprotein and elucidation of the role of phosphorylation in RNA binding by using surface plasmon resonance Mapping of the coronavirus membrane protein domains involved in interaction with the spike protein Envelope protein palmitoylations are crucial for murine coronavirus assembly The hydrophobic domain of infectious bronchitis virus E protein alters the host secretory pathway and is important for release of infectious virus The coronavirus E protein: assembly and beyond Mouse hepatitis virus replicase proteins associate with two distinct populations of intracellular membranes The intracellular sites of early replication and budding of SARS-coronavirus Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer Glycan shield and epitope masking of a coronavirus spike protein observed by cryoelectron microscopy Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains A human homolog of angiotensin-converting enzyme.
    keywords: binding; cells; coronavirus; cov; covid-19; covs; domain; east; entry; fusion; host; human; infection; inhibitors; membrane; mers; middle; novel; patients; protein; receptor; replication; rna; sars; sars coronavirus; spike; syndrome; syndrome coronavirus; treatment
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        item: #911 of 1349
          id: cord-312886-o3ipzn05
      author: Onomoto, Koji
       title: Antiviral innate immunity and stress granule responses
        date: 2014-08-19
       words: 5143
      flesch: 27
     summary: The mitochondrial targeting chaperone 14-3-3epsilon regulates a RIG-I translocon that mediates membrane association and innate antiviral immunity Reconstitution of the RIG-I pathway reveals a signaling role of unanchored polyubiquitin chains in innate immunity RIG-I forms signaling-competent filaments in an ATP-dependent, ubiquitin-independent manner Structural basis for ubiquitin-mediated antiviral signal activation by RIG-I Type I interferon gene induction by the interferon regulatory factor family of transcription factors Antiviral effect of the mammalian translation initiation factor 2alpha kinase GCN2 against RNA viruses Encephalomyocarditis virus disrupts stress granules, the critical platform for triggering antiviral innate immune responses Inhibition of cytoplasmic mRNA stress granule formation by a viral proteinase Production of a dominant-negative fragment due to G3BP1 cleavage contributes to the disruption of mitochondriaassociated protective stress granules during CVB3 infection Mammalian orthoreovirus particles induce and are recruited into stress granules at early times postinfection Importance of eIF2alpha phosphorylation and stress granule assembly in alphavirus translation regulation Dynamic oscillation of translation and stress granule formation mark the cellular response to virus infection Regulation of PKR by HCV IRES RNA: importance of domain II and NS5A Hepatitis C virus (HCV) induces formation of stress granules whose proteins regulate HCV RNA replication and virus assembly and egress The leader protein of cardioviruses inhibits stress granule assembly The mengovirus leader protein blocks interferon-alpha/beta gene transcription and inhibits activation of interferon regulatory factor 3 Stress granule formation induced by measles virus is protein kinase PKR dependent and impaired by RNA adenosine deaminase ADAR1 Measles virus nonstructural C protein modulates viral RNA polymerase activity by interacting with host protein Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies The translational regulator CPEB1 provides a link between dcp1 bodies and stress granules The DEAD-box RNA helicase DDX3 associates with export messenger ribonucleoproteins as well as tip-associated protein and participates in translational control Determination of the role of DDX3 a factor involved in mammalian RNAi pathway using an shRNA-expression library Cellular microRNA and P bodies modulate host-HIV-1 interactions RNA-associated protein 55 (RAP55) localizes to mRNA processing bodies and stress granules The dsRNA protein kinase PKR: virus and cell control PKR; a sentinel kinase for cellular stress Identification and characterization of pancreatic eukaryotic initiation factor 2 alpha-subunit kinase, PEK, involved in translational control Protein translation and folding are coupled by an endoplasmic-reticulum-resident kinase Regulation of protein synthesis by hypoxia via activation of the endoplasmic reticulum kinase PERK and phosphorylation of the translation initiation factor eIF2alpha Uncharged tRNA activates GCN2 by displacing the protein kinase moiety from a bipartite tRNA-binding domain Heme-regulated inhibitor kinase-mediated phosphorylation of eukaryotic translation initiation factor 2 inhibits translation, induces stress granule formation, and mediates survival upon arsenite exposure Regulation of protein synthesis by heme-regulated eIF-2 alpha kinase Analysis of subcellular G3BP redistribution during rubella virus infection Cell proteins TIA-1 and TIAR interact with the 3 0 stem-loop of the West Nile virus complementary minus-strand RNA and facilitate virus replication Modulation of hepatitis C virus RNA abundance and virus release by dispersion of processing bodies and enrichment of stress granules Hepatitis C virus hijacks P-body and stress granule components around lipid droplets The polypyrimidine tract-binding protein affects coronavirus RNA accumulation levels and relocalizes viral RNAs to novel cytoplasmic domains different from replication-transcription sites Mouse hepatitis coronavirus replication induces host translational shutoff and mRNA decay, with concomitant formation of stress granules and processing bodies Induction of stress granule-like structures in vesicular stomatitis virus-infected cells Respiratory syncytial virus induces host RNA stress granules to facilitate viral replication Activation of protein kinase R is required for induction of stress granules by respiratory syncytial virus but dispensable for viral replication Roles of the respiratory syncytial virus trailer region: effects of mutations on genome production and stress granule formation Arenavirus infection induces discrete cytosolic structures for RNA replication Mammalian orthoreovirus escape from host translational shutoff correlates with stress granule disruption and is independent of eIF2alpha phosphorylation and PKR Reovirus induces and benefits from an integrated cellular stress response Formation of antiviral cytoplasmic granules during orthopoxvirus infection Colocalization of transcription and translation within cytoplasmic poxvirus factories coordinates viral expression and subjugates host functions Modulation of stress granules and P bodies during dicistrovirus infection We were supported by the following grants: the Ministry of Education, Culture, Sports
    keywords: cells; formation; granules; ifn; infection; pkr; protein; rig; rna; sgs; stress; viral; virus
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        item: #912 of 1349
          id: cord-312892-p72zwmtb
      author: Chen, Nanhua
       title: RNA sensors of the innate immune system and their detection of pathogens
        date: 2017-04-04
       words: 4243
      flesch: 31
     summary: Cold Spring Harbor Perspect TLR8: the forgotten relative revindicated Master sensors of pathogenic RNA -RIG-I like receptors RIG-I in RNA virus recognition The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses Regulating intracellular antiviral defense and permissiveness to hepatitis C virus RNA replication through a cellular RNA helicase, RIG-I Filament assemblies in foreign nucleic acid sensors How RIG-I like receptors activate MAVS Sensing microbial RNA in the cytosol International Union of Basic and Clinical Pharmacology. RNA are the major PAMPs of RNA viruses, to which most severe disease causing viruses belong thus posing a tougher challenge to human and animal health.
    keywords: activation; cells; prrs; receptors; recognition; rig; rna; signaling; tlr7; tlr8; virus; viruses
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        item: #913 of 1349
          id: cord-313138-y485ev30
      author: Magor, Katharine E.
       title: Defense genes missing from the flight division
        date: 2013-04-24
       words: 10647
      flesch: 40
     summary: In comparison with mammals, birds have partial repertoires of pattern recognition receptors including TLR receptors (Boyd et al., 2007; Brownlie and Allan, 2011; Cormican et al., 2009 ) and RIG-like receptors (Barber et al., 2010; Karpala et al., 2012) . We demonstrated that ducks have a functional RIG-I (Barber et al., 2010) .
    keywords: avian; birds; cells; chicken; class; ducks; et al; family; genes; human; igd; igy; influenza; interferon; mhc; receptor; response; rig; rna; tapasin; tlr8; viral; virus
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        item: #914 of 1349
          id: cord-313161-07iwwsfz
      author: Lundstrom, Kenneth
       title: Alphavirus-Based Vaccines
        date: 2014-06-16
       words: 6857
      flesch: 24
     summary: Treatment efficacy and evidence for immunoediting in a stringent rat mammary tumor model Alphaviral vector-transduced dendritic cells are successful therapeutic vaccines against neu-overexpressing tumors in wild-type mice Immunization strategy against cervical cancer involving an alphavirus vector expressing high levels of a stable fusion protein of human papillomavirus 16 E6 and E7 Superior therapeutic efficacy of alphavirus-mediated immunization against human papilloma virus type 16 antigens in a murine tumour model: Effects of the route of immunization Sindbis virus replicon particles encoding calreticulin linked to a tumor antigen generate long-term tumor-specific immunity Eradication of established tumors by vaccination with Venezuelan equine encephalitis virus replicon particles delivering human papillomavirus 16 E7 RNA Augmentation of alphavirus vector-induced human papilloma virus-specific immune and anti-tumour responses by coexpression of interleukin-12 Cancer immunotherapy using Sindbis virus replicon particles encoding a VP22-antigen fusion Treatment of rapidly growing K-BALB and CT26 mouse tumours using Semliki Forest virus and its derived vector Inhibition of angiogenesis by a Semliki Forest virus vector expressing VEGFR-2 reduces tumour growth and metastasis in mice Induction of a therapeutic antitumor immunological response by intratumoral injection of genetically engineered Semliki Forest virus to produce interleukin-12 Biology and application of alphaviruses in gene therapy Immunotherapeutic synergy between anti-CD137 mAb and intratumoral administration of a cytopathic Semliki Forest virus encoding IL-12 Immunization against MUC18/MCAM, a novel antigen that drives melanoma invasion and metastasis An alphavirus vector overcomes the presence of neutralizing antibodies and elevated numbers of Tregs to induce immune responses in humans with advanced cancer A phase I dose escalation trial of vaccine replicon particles (VRP) expressing prostatespecific membrane antigen (PSMA) in subjects with prostate cancer A novel alphavirus vaccine encoding prostate-specific membrane antigen elicits potent cellular and humoral immune responses In vivo effects of vaccination with six-transmembrane epithelial antigen of the prostate: A candidate antigen for treating prostate cancer Prostate stem cell antigen vaccination induces a long-term protective immune response against prostate cancer in the absence of autoimmunity Immunotherapy with recombinant SFV-replicons expressing the P815A tumor antigen or IL-12 induces tumor regression Innovative cancer vaccine strategies based on the identification of tumour-associated antigens Induction of P815 tumor immunity by recombinant Semliki Forest virus expressing the P1A gene Enhancement of tumorspecific immune response with plasmid DNA replicon vectors Genetic immunization against cervical carcinoma: induction of cytotoxic T lymphocyte activity with a recombinant alphavirus vector expressing human papillomavirus type 16 E6 and E7 Enhancement of sindbis virus self-replicating RNA vaccine potency by targeting antigen to endosomal/lysosomal compartments Establishment of an HLA-A*0201 human papillomavirus type 16 tumor model to determine the efficacy of vaccination strategies in HLA-A*0201 transgenic mice Antitumor efficacy of Venezuelan equine encephalitis virus replicon particles encoding mutated HPV16 E6 and E7 genes Induction of an antitumor immunological response by an intratumoral injection of dendritic cells pulsed with genetically engineered Semliki Forest virus to produce interleukin-18 combined with the systemic administration of interleukin-12 An immunological profile of Balb/c mice protected from airborne challenge following vaccination with a live attenuated Venezuelan equine encephalitis virus vaccine Improved mucosal protection against Venezuelan equine encephalitis virus is induced by the molecularly defined, live-attenuated V3526 vaccine candidate Recombinant chimeric western and eastern equine encephalitis viruses as potential vaccine candidates Phase II safety and immunogenicity study of live chikungunya virus vaccine TSI-GSD-218 A DNA vaccine against chikungunya virus is protective in mice and induces neutralizing antibodies in mice and nonhuman primates Design of chimeric alphaviruses with a programmed, attenuated, cell type-restricted phenotype Development of a stable virus-like particle vaccine formulation against Chikungunya virus and investigation of the effects of polyanions RNA interference mediated inhibition of Chikungunya virus replication in mammalian cells In vitro and in vivo characterization of microRNAtargeted alphavirus replicon and helper RNAs Role for mucosal immune responses and cell-mediated immune functions in protection from airborne challenge with Venezuelan equine encephalitis virus Immunogenicity and protective efficacy of a DNA vaccine against Venezuelan equine encephalitis virus aerosol challenge in nonhuman primates Transmission potential of two chimeric Chikungunya vaccine candidates in the urban mosquito vectors, Aedes aegypti and Ae. albopictus Artificial microRNAs can effectively inhibit replication of Venezuelan equine encephalitis virus Nanopatch-targeted skin vaccination against West Nile Virus and Chikungunya virus in mice Semliki Forest virus expression system: Production of conditionally infectious recombinant particles In another study, DNA vaccines based on the SAV E1 and E2 spike proteins were compared to whole virus vaccine in Atlantic salmon [65] .
    keywords: alphavirus; dna; expression; immunization; mice; particles; protection; replicon; sfv; tumor; vaccination; vaccine; vectors; vee; virus
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        item: #915 of 1349
          id: cord-313301-7mkadtp9
      author: Duffy, Siobain
       title: EVOLUTION OF HOST SPECIFICITY DRIVES REPRODUCTIVE ISOLATION AMONG RNA VIRUSES
        date: 2007-08-23
       words: 6098
      flesch: 38
     summary: Although there was no direct selection acting on host range in our experiment, three of the four populations lost the ability to infect one or more alternative hosts. To more closely examine host range of an evolved virus clone, we first obtained a high-titer lysate (∼10 10 virus particles per mL) of the clone on the selected host, P. pseudoalcaligenes ERA.
    keywords: adaptation; evolution; host; isolation; populations; range; selection; virus; viruses
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        item: #916 of 1349
          id: cord-313439-cadyykks
      author: Felten, Sandra
       title: Diagnosis of Feline Infectious Peritonitis: A Review of the Current Literature
        date: 2019-11-15
       words: 12473
      flesch: 40
     summary: Pathogenesis of feline enteric coronavirus infection Common virus infections in cats, before and after being placed in shelters, with emphasis on feline enteric coronavirus Pathogenic characteristics of persistent feline enteric coronavirus infection in cats Feline infectious peritonitis viruses arise by mutation from endemic feline enteric coronaviruses Infection studies in kittens, using feline infectious peritonitis virus propagated in cell culture An enteric coronavirus infection of cats and its relationship to feline infectious peritonitis Clinical and laboratory features of cats with feline infectious peritonitis-a retrospective study of 231 confirmed cases (2000-2010) Prevalence of feline infectious peritonitis in specific cat breeds Epidemiology of feline infectious peritonitis among cats examined at veterinary medical teaching hospitals The inheritance of susceptibility to feline infectious peritonitis in purebred catteries Performances of different diagnostic tests for feline infectious peritonitis in challenging clinical cases A review of feline infectious peritonitis virus infection: 1963-2008 Feline infectious peritonitis: Still an enigma? Immunologic phenomena in the effusive form of feline infectious peritonitis Levels of feline infectious peritonitis virus in blood, effusions, and various tissues and the role of lymphopenia in disease outcome following experimental infection Experimental feline enteric coronavirus infection reveals an aberrant infection pattern and shedding of mutants with impaired infectivity in enterocyte cultures Cats inoculated with feline infectious peritonitis virus exhibit a biphasic acute phase plasma protein response Serologic studies of naturally occurring feline infectious peritonitis Feline coronavirus antibodies in cats Utility of feline coronavirus antibody tests Seroepidemiology of feline infectious peritonitis virus infections using transmissible gastroenteritis virus as antigen Feline infectious peritonitis: A worldwide serosurvey Feline coronavirus serotypes 1 and 2: Seroprevalence and association with disease in switzerland Evaluation of an in-practice test for feline coronavirus antibodies Comparison of serologic techniques for the detection of antibodies against feline coronaviruses The history and interpretation of feline coronavirus serology A. Cats and coronaviruses Long-term impact on a closed household of pet cats of natural infection with feline coronavirus, feline leukaemia virus and feline immunodeficiency virus A study of naturally occurring feline coronavirus infections in kittens Risk of feline infectious peritonitis in cats naturally infected with feline coronavirus Coronavirus serology in healthy pedigree cats
    keywords: cats; coronavirus; detection; diagnosis; effusion; fcov; feline; fip; gene; mutations; pcr; peritonitis; samples; study
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        item: #917 of 1349
          id: cord-313541-fpqwzf9k
      author: Ulloa, S.
       title: A simple method for SARS-CoV-2 detection by rRT-PCR without the use of a commercial RNA extraction kit
        date: 2020-08-22
       words: 1780
      flesch: 48
     summary: SARS-CoV-2 detection by direct rRT-PCR without RNA extraction and inactivating samples at 95 °C for 5 minutes, was showed from specimens placed in UTM and molecular water, but not from samples in Hanks medium and saline buffer (Merindol et al., 2020) . Moreover, SARS-CoV-2 detection without RNA extraction was described by mixing respiratory samples in a 1:1 (v/v) ratio with Sputasol (Oxoid, Basingstoke, England) before adding it directly to the rRT-PCR reaction mix (Wee et al., 2020) .
    keywords: extraction; pcr; rrt; samples; sars
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        item: #918 of 1349
          id: cord-313684-61hkogdh
      author: Samaddar, Arghadip
       title: Pathophysiology and Potential Therapeutic Candidates for COVID-19: A Poorly Understood Arena
        date: 2020-09-17
       words: 11716
      flesch: 34
     summary: There are currently four ongoing clinical trials of umifenovir for COVID-19 treatment: one in comparison with the basic treatment 6 , and the other three comparing the effects in combination with oseltamivir 7 , lopinavir/ ritonavir 8 , and carrimycin. Currently, there are no clinically proven antiviral drugs or biologics for the treatment of COVID-19 patients.
    keywords: acute; antiviral; cells; combination; coronavirus; cov-2; covid-19; covid-19 patients; disease; et al; host; immune; infection; mers; patients; protein; receptors; response; rna; sars; therapy; treatment; trial; viral; virus
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        item: #919 of 1349
          id: cord-314019-8n0jafsk
      author: Feng, Qian
       title: Induction and suppression of innate antiviral responses by picornaviruses
        date: 2014-07-18
       words: 7235
      flesch: 40
     summary: In fact, the L proteins RIG-I-like receptors (RLRs) are cytoplasmic RNA sensors that initiate a type I interferon response upon RNA virus infections. Additionally, these viral proteinases also cleave host factors to aid virus RNA replication and/or to evade host antiviral responses.
    keywords: activation; cells; formation; ifn; infection; mda5; pathway; pro; rig; rna; stress; virus
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        item: #920 of 1349
          id: cord-314254-9ye8tfvz
      author: Pfaender, Stephanie
       title: Natural reservoirs for homologs of hepatitis C virus
        date: 2014-03-26
       words: 6843
      flesch: 42
     summary: I. Transmission of disease, serial passages, and description of liver lesions Identification of two flavivirus-like genomes in the GB hepatitis agent Isolation of novel virus-like sequences associated with human hepatitis Molecular cloning and disease association of hepatitis G virus: a transfusion-transmissible agent Identification of GBV-D, a novel GB-like flavivirus from old world frugivorous bats (Pteropus giganteus) in Bangladesh Molecular characterization of the hepatitis G virus Sequence and genomic organization of GBV-C: a novel member of the flaviviridae associated with human non-A-E hepatitis Characterization of hepatitis G virus (GB-C virus) particles: evidence for a nucleocapsid and expression of sequences upstream of the E1 protein The GB viruses: a review and proposed classification of GBV-A, GBV-C (HGV), and GBV-D in genus Pegivirus within the family Flaviviridae Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and assignment web resource Hepatitis C viral dynamics in vivo and the antiviral efficacy of interferon-alpha therapy Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes Genetic diversity and evolution of hepatitis C virus-15 years on New insights into the HCV quasispecies and compartmentalization Epidemiology of hepatitis C: geographic differences and temporal trends The epidemic behavior of the hepatitis C virus The origin and evolution of hepatitis viruses in humans Glycosylation of hepatitis C virus envelope proteins Role of N-linked glycans in the functions of hepatitis C virus envelope proteins incorporated into infectious virions Nonprimate hepaciviruses in domestic horses, United kingdom A novel hepacivirus with an unusually long and intrinsically disordered NS5A protein in a wild Old World primate Bats: important reservoir hosts of emerging viruses Bats and their virome: an important source of emerging viruses capable of infecting humans Bats carry pathogenic hepadnaviruses antigenically related to hepatitis B virus and capable of infecting human hepatocytes Analysis of hepatitis C virus intrahost diversity across the coding region by ultradeep pyrosequencing Identification of a previously undescribed divergent virus from the Flaviviridae family in an outbreak of equine serum hepatitis Identification of a pegivirus (GB virus-like virus) that infects horses A cross-species view on viruses Global trends in emerging infectious diseases A strategy to estimate unknown viral diversity in mammals Virology: the virus whose family expanded Bats and viruses: friend or foe? To date, there is no evidence for an animal reservoir of viruses closely related to hepatitis C virus which may have crossed the species barrier to cause disease in humans and resulted in the current pandemic.
    keywords: bats; gbv; hcv; hepaciviruses; hepatitis; horses; infection; liver; nphv; proteins; rna; species; virus; viruses
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        item: #921 of 1349
          id: cord-314316-hsspggp8
      author: Sirinarumitr, Theerapol
       title: Rapid in situ hybridization technique for the detection of ribonucleic acids in tissues using radiolabelled and fluorescein-labelled riboprobes
        date: 1997-08-31
       words: 3844
      flesch: 44
     summary: For the fluorescein-labelled RNA probe, we incubated with hybridization buffer for 20 h, 2 h, 1 h or 30 min. Sections were treated with 20 g ml −1 used a hybridization buffer-free probe as an additional control. Sections that hybridized with hybridization buffer at 52°C.
    keywords: buffer; hybridization; probe; reh; rna; sections
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        item: #922 of 1349
          id: cord-314369-o4nis91y
      author: Lopez-Lopes, G. I. S.
       title: Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19.
        date: 2020-08-01
       words: 3687
      flesch: 46
     summary: Among with cost, availability of reagents, equipment, specialized personnel and different logistic aspects that constrain RNA testing, one other limitation is sample collection. Limitations in PPE and safe areas for sample collection add to the current limitations.
    keywords: cases; collection; preprint; rna; sars; swabs
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        item: #923 of 1349
          id: cord-314560-rswa5zdn
      author: Manjunath, N.
       title: Interfering antiviral immunity: application, subversion, hope?
        date: 2006-06-06
       words: 5889
      flesch: 39
     summary: In the context of RNA viruses, siRNAs can be designed to degrade not only viral mRNA Similarly, Ge et al. achieved and Polio), for which a single mRNA is used to transcribe viral proteins, targeting any part of the coding sequence should result in degradation (scissors) of viral genomic RNA and/or progeny mRNA.
    keywords: cells; delivery; gene; infection; interference; protein; rnai; sequence; silencing; sirna; targeting; virus; viruses
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        item: #924 of 1349
          id: cord-314567-purplsjn
      author: Fernández-Ponce, Cecilia
       title: Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells
        date: 2018-01-04
       words: 7982
      flesch: 24
     summary: Among them, HCV core protein has been widely associated with pathogenicity, virulence, immune evasion and immune regulation (Dominguez-Villar et al., 2007 , 2012a Waggoner et al., 2007; However, the underlying molecular processes, as well as the behavior of HCV core protein or its interactions with host cell components, remain unclear.
    keywords: c virus; cd4; cells; core; core protein; cycle; et al; figure; gfp; hcv; hcv core; hepatitis; jurkat; localization; nucleolar; nucleolus; protein; rna; t cells; virus; virus core
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        item: #925 of 1349
          id: cord-314572-1pou702r
      author: Lin, Ya-Hui
       title: Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator
        date: 2016-10-14
       words: 7213
      flesch: 40
     summary: In addition, dual-luciferase based −1 PRF activity obtained from 293T cells transfected by Switch-1 containing reporter possessed a similar dosagedependent trend toward theophylline as that of the in vitro analysis, whereas cells transfected by Switch-1M1 reporter lost theophylline-dependency for −1 PRF activity ( Figure 4D ). The ligand-binding pocket of theophylline aptamer is composed of an internal-loop and an adjacent bulge with conserved key theophyllinecontact sequences distributed within the two motifs.
    keywords: activity; aptamer; binding; figure; ligand; prf; pseudoknot; rna; sars; stem; switch-1; theooff2; theophylline; −1 prf
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        item: #926 of 1349
          id: cord-314753-xflhxb13
      author: Manso, Carmen F.
       title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples
        date: 2017-06-23
       words: 6344
      flesch: 38
     summary: key: cord-314753-xflhxb13 authors: Manso, Carmen F.; Bibby, David F.; Mbisa, Jean L. title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date: 2017-06-23 journal: Sci Rep DOI: 10.1038/s41598-017-02239-5 sha: doc_id: 314753 cord_uid: xflhxb13 RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. The percentage of reads mapping to RNA virus genomes in the rRNA-depleted BBV Panel samples was between 40 and 150-fold higher than in corresponding untreated controls.
    keywords: genome; hcv; hiv; human; mapping; panel; plasma; reads; rna; rrna; samples; sequences; virus; viruses
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        item: #927 of 1349
          id: cord-314833-6fue84x6
      author: Chang, Chung-ke
       title: The SARS coronavirus nucleocapsid protein – Forms and functions
        date: 2014-01-11
       words: 9469
      flesch: 38
     summary: Although the model provided a general overview of coronavirus N protein structure at the time, it lacked the necessary details to provide a clear picture of the structure-function relationship of the protein. There have been several excellent reviews on the coronavirus N protein (Laude and Masters, 1995; Masters, 2006) , including one on SARS-CoV N protein (Surjit and Lal, 2008) .
    keywords: binding; coronavirus; cov; cov n; crystal; ctd; domain; et al; interaction; n protein; ntd; nucleic; nucleocapsid; protein; rna; rnp; sars; structure
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        item: #928 of 1349
          id: cord-314877-db7tze8j
      author: Chkuaseli, Tamari
       title: Activation of viral transcription by stepwise largescale folding of an RNA virus genome
        date: 2020-08-12
       words: 8613
      flesch: 40
     summary: The functional RNA domain 5BSL3.2 within the NS5B coding sequence influences hepatitis C virus IRES-mediated translation A long-range RNA-RNA interaction between the 5 and 3 ends of the HCV genome A twist in the tail: SHAPE mapping of long-range interactions and structural rearrangements of RNA elements involved in HCV replication Hepatitis C virus RNA: molecular switches mediated by long-range RNA-RNA interactions? Identification of a coronavirus transcription enhancer Gene N proximal and distal RNA motifs regulate coronavirus nucleocapsid mRNA transcription Long distance RNA-RNA interactions in the coronavirus genome form high-order structures promoting discontinuous RNA synthesis during transcription Advances in the molecular biology of tombusviruses: gene expression, genome replication and recombination Tomato bushy stunt virus at 2.9 A resolution A defective interfering RNA that contains a mosaic of a plant virus genome Recognition of small interfering RNA by a viral suppressor of RNA silencing A host Ca 2+ /Mn 2+ ion pump is a factor in the emergence of viral RNA recombinants The glycolytic pyruvate kinase is recruited directly into the viral replicase complex to generate ATP for RNA synthesis Tombusvirus-host interactions: co-opted evolutionarily conserved host factors take center court Exploring the architecture of viral RNA genomes Context-influenced cap-independent translation of Tombusvirus mRNAs in vitro Tombusvirus Y-shaped translational enhancer forms a complex with eIF4F and can be functionally replaced by heterologous translational enhancers Tombusvirus recruitment of translational machinery via the 3 UTR Multifaceted regulation of translational readthrough by RNA replication elements in a tombusvirus Subgenomic mRNA transcription in Tombusviridae Uncoupling RNA virus replication from transcription via the polymerase: functional and evolutionary insights Subgenomic mRNA regulation by a distal RNA element in a (+)-strand RNA virus Effects of inactivation of the coat protein and movement genes of Tomato bushy stunt virus on early accumulation of genomic and subgenomic RNAs Long-distance base pairing in flock house virus RNA1 regulates subgenomic RNA3 synthesis and RNA2 replication Discontinuous and non-discontinuous subgenomic RNA transcription in a nidovirus The premature termination model: a possible third mechanism for subgenomic mRNA transcription in (+)-strand RNA viruses A complex network of RNA-RNA interactions controls subgenomic mRNA transcription in a tombusvirus Global organization of a positive strand RNA virus genome An RNA activator of subgenomic mRNA1 transcription in Tomato bushy stunt virus Molecular cloning and complete nucleotide sequence of carnation Italian ringspot tombusvirus genomic and defective interfering RNAs Nonhomologous RNA recombination in tombusviruses: generation and evolution of defective interfering RNAs by stepwise deletions Regulatory activity of distal and core RNA elements in tombusvirus subgenomic mRNA2 transcription Analysis of a 3 -translation enhancer in a tombusvirus: a dynamic model for RNA-RNA interactions of mRNA termini Long-range RNA-RNA interactions between distal regions of the hepatitis C virus internal ribosome entry site element RNA purification by preparative polyacrylamide gel electrophoresis in Laboratory methods in enzymology Structural analysis of RNA backbone using in-line probing in laboratory methods in enzymology In-line probing analysis of riboswitches in Post transcriptional gene regulation Denaturing gel electrophoresis for sequencing RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences Global architecture of viral RNA genomes can contribute significantly to the regulation of critical viral functions.
    keywords: as1; complex; core; figure; formation; genome; interaction; ld2; mrna1; rna; rtsl; sl59; structure; transcription; virus
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        item: #929 of 1349
          id: cord-314891-brgtwxhe
      author: Fumian, Tulio M.
       title: Potential Therapeutic Agents for Feline Calicivirus Infection
        date: 2018-08-16
       words: 5496
      flesch: 37
     summary: In addition to the polymerase inhibition assay, using the purified FCV Pro-Pol, we also described a FRET protease assay for high throughput screening of FCV protease inhibitors. Of the six NNI compounds tested in the current study, PPNDS and quercetagetin showed an inhibition of FCV RdRp activity with IC 50 values in the low micromolar range (Figure 2 and Table 1 ).
    keywords: activity; antiviral; calicivirus; cell; fcv; feline; inhibition; nitazoxanide; norovirus; polymerase; protease; rna
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        item: #930 of 1349
          id: cord-315054-kji2kfek
      author: Chakraborty, Nabarun
       title: Protocol Improvement for RNA Extraction From Compromised Frozen Specimens Generated in Austere Conditions: A Path Forward to Transcriptomics-Pathology Systems Integration
        date: 2020-07-22
       words: 4466
      flesch: 37
     summary: Extra care during tissue handling was needed to avoid tissue damage, and to retain whole-organ tissue architecture for handling, collection, and processing prior to fixation. Extra care during tissue handling and collection was required to avoid tissue damage and loss of tissue architecture prior to fixation.
    keywords: analysis; carcasses; et al; handling; omics; rna; samples; space; thawing; tissue
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        item: #931 of 1349
          id: cord-315069-xo4mbxei
      author: Knorr, D. A.
       title: De novo generation of defective interfering RNAs of tomato bushy stunt virus by high multiplicity passage
        date: 1991-03-31
       words: 5142
      flesch: 43
     summary: Comparisons of nucleotide sequences of 10 cDNA clones from 2 DI RNA populations and with a previously characterized TBSV DI RNA revealed the same four regions of sequence from the TBSV genome were strictly conserved in each of the DI RNAs: the virus 5′ leader sequence of 168 bases; a region of approximately 200–250 bases from the viral polymerase gene; approximately 70 bases from the 3′ terminus of the viral pl9 and p22 genes; and approximately 130 bases from the 3′terminal noncoding region. Interestingly, the homogeneous DI RNA inoculum derived from cloned cDNAs (Fig. 4 , lane 2) gave rise to a complex pattern of smaller RNA spe- ties in the infected plants, suggesting that DI RNAs may be capable of sequence evolution upon reintroduction into plants.
    keywords: high; isolates; m.o.i; passage; regions; rnas; sequence; tbsv; virus
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        item: #932 of 1349
          id: cord-315072-b28yikvj
      author: Giotis, Efstathios S.
       title: Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α)
        date: 2016-08-05
       words: 5889
      flesch: 42
     summary: A virus polymerase host restriction Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources Differential expression in SAGE: accounting for normal between-library variation Involvement of the IRF-1 transcription factor in antiviral responses to interferons Constitutive expression of an ISGF2/IRF1 transgene leads to interferon-independent activation of interferon-inducible genes and resistance to virus infection IFN regulatory factor-1 All things being equal, RNA-seq would seem to be the method of choice for transcriptomic analysis of chicken IFN responses, particularly given its ability to produce high-resolution quantitative and qualitative data.
    keywords: analysis; chicken; data; expression; genes; genome; ifn; induction; interferon; isgs; rna; seq; technologies; virus
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        item: #933 of 1349
          id: cord-315085-rucfowvv
      author: Sekulic, Miroslav
       title: Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases
        date: 2020-05-26
       words: 5033
      flesch: 40
     summary: Sequencing of viral RNA from FFPE lung tissue from the case 1 autopsy showed mutations most consistent with a subset of the Western European Clade A2a (C3037T, C14408T, A23403G), 16 with mutations enriched in New York State A2a cases (C1059T and G25563T). Lung tissue samples from 2 non-SARS-CoV-2 patients with DAD were run as controls and were negative.
    keywords: acute; case; cov-2; findings; heart; image; infection; lung; patient; postmortem; rna; sars
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        item: #934 of 1349
          id: cord-315384-eqiokrub
      author: van der Hoek, Lia
       title: Croup Is Associated with the Novel Coronavirus NL63
        date: 2005-08-23
       words: 4429
      flesch: 54
     summary: An 11-year study in a pediatric practice Asthma in childhood The association of viral and bacterial respiratory infections with exacerbations of wheezing in young asthmatic children New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia Detection of human coronavirus NL63 in young children with bronchiolitis Human coronavirus NL63 infection in Canada Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children A novel pancoronavirus RT-PCR assay: Frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium Financial support was received from Wyeth Pharma, Mü nster, Germany. Screening of respiratory samples in Amsterdam and Rotterdam confirmed that HCoV-NL63 is circulating among humans with respiratory disease in the Netherlands
    keywords: croup; hcov; nl63; patients; respiratory; rna; samples; study
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        item: #935 of 1349
          id: cord-315483-l6dm82pp
      author: Santhakumar, Diwakar
       title: Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses
        date: 2018-05-01
       words: 10827
      flesch: 39
     summary: The second exon codes the rest of the ORF (1435 bps) and 3′ untranslated regions (UTR) for chicken IFIT5 gene. Chicken cells were transfected with 500 ng of mammalian expression vectors encoding V5-tagged chIFIT5 for 24 hours and were left untreated (NDV-) or were treated with 1 MOI of NDV-GFP (NDV+) for another 24 hours before fixation, staining for nucleus (blue), chIFIT5 (red) and GFP marker (NDV).
    keywords: cells; chicken; chifit5; control; df-1; dsrna; embryos; expression; fig; gene; gfp; human; ifn; infection; ndv; promoter; protein; replication; rna; sequence; supplementary; virus; viruses
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        item: #936 of 1349
          id: cord-315611-xbj41ekc
      author: Ahmad, Mohammed
       title: Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase
        date: 2020-07-14
       words: 5088
      flesch: 41
     summary: Directing Coronavirus RNA Synthesis and Processing The RNA Polymerase Activity of SARS-Coronavirus Nsp12 Is Primer Dependent De Novo Initiation of RNA Synthesis by the Arterivirus RNA-Dependent RNA Polymerase The SARS-Coronavirus Nsp7+nsp8 Complex Is a Unique Multimeric RNA Polymerase Capable of Both de Novo Initiation and Primer Extension The Structure of the RNA-Dependent RNA Polymerase from Bovine Viral Diarrhea Virus Establishes the Role of GTP in de Novo Initiation Insights into SARS-CoV Transcription and Replication from the Structure of the Nsp7-Nsp8 Hexadecamer Nonstructural Proteins 7 and 8 of Feline Coronavirus Form a 2:1 Heterotrimer That Exhibits Primer-Independent RNA Polymerase Activity Structure of the SARS-CoV Nsp12 Polymerase Bound to Nsp7 and Nsp8 Co-Factors Crystal Structure of the Dengue Virus RNA-Dependent RNA Polymerase Catalytic Domain at 1.85-Angstrom Resolution Crystal Structure of the RNA-Dependent RNA Polymerase from Hepatitis C Virus Reveals a Fully Encircled Active Site Non-Nucleoside Inhibitors Binding to Hepatitis C Virus NS5B Polymerase Reveal a Novel Mechanism of Inhibition Crystal Structures of the RNA-Dependent RNA Polymerase Genotype 2a of Hepatitis C Virus Reveal Two Conformations and Suggest Mechanisms of Inhibition by Non-Nucleoside Inhibitors Structural Basis for Active Site Closure by the Poliovirus RNA-Dependent RNA Polymerase Requirements for De Novo Initiation of RNA Synthesis by Recombinant Flaviviral RNA-Dependent RNA Polymerases De Novo Initiation of RNA Synthesis by the RNA-Dependent RNA Polymerase (NS5B) of Hepatitis C Virus Structures of EV71 RNA-Dependent RNA Polymerase in Complex with Substrate and Analogue Provide a Drug Target against the Hand-Foot-and-Mouth Disease Pandemic in China Structural Basis for Proteolysis-Dependent Activation of the Poliovirus RNA-Dependent RNA Polymerase RNA Synthesis in a Cage -Structural Studies of Reovirus Polymerase Λ3 RNA-Dependent RNA Polymerase of Japanese Encephalitis Virus Binds the Initiator Nucleotide GTP to Form a Mechanistically Important Pre-Initiation State Conservative Transcription in Three Steps Visualized in a Double-Stranded RNA Virus A Mechanism for Initiating RNA-Dependent RNA Polymerization Structural Basis for the Inhibition of the RNA-Dependent RNA Polymerase from SARS-CoV-2 by Remdesivir Mechanism of Hepatitis C Virus RNA Polymerase Inhibition with Dihydroxypyrimidines Non-nucleoside Analogue Inhibitors Bind to an Allosteric Site on HCV NS5B Polymerase Benzimidazole Derivatives Bearing Substituted Biphenyls as Hepatitis C Virus NS5B RNA-Dependent RNA Polymerase Inhibitors: Structure-Activity Relationship Studies and Identification of a Potent and Highly Selective Inhibitor JTK-109 Inhibition of RNA Binding to Hepatitis C Virus RNA-Dependent RNA Polymerase: A New Mechanism for Antiviral Intervention NS5B RNA Dependent RNA Polymerase Inhibitors: The Promising Approach to Treat Hepatitis C Virus Infections Sofosbuvir, a NS5B Polymerase Inhibitor in the Treatment of Hepatitis C: Additionally, there is a significant rise in the accessible surface area of the GTPbound complex, suggesting that the RdRp assumes an open conformation following the binding of GTP, possible assuming a preinitiation state in order to accommodate the incoming template and/or the primer RNA molecule.
    keywords: binding; complex; cov2; figure; gtp; inhibitors; initiation; molecule; rdrp; rna; rna polymerase; sars; site; structure
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        item: #937 of 1349
          id: cord-315616-pvt0amth
      author: Poole, Anthony
       title: Methyl-RNA: an evolutionary bridge between RNA and DNA?
        date: 2004-06-17
       words: 5630
      flesch: 49
     summary: Completeness of genomic RNA methylation depends on the processivity of the methylase, and if it is non-speci¢c, it may not necessarily methylate every residue. The importance of being modi¢ed: roles of mod-i¢ed nucleosides and Mg 2 in RNA structure and function Small nucleolar RNAs guide the ribose methylations of eukaryotic rRNAs On the function of modi¢ed nucleosides in the RNA world Modi¢ed nucleotides always were: an evolutionary model Divided genomes and intrinsic noise Parsimony, likelihood and the role of models in molecular phylogenetics Prospects for understanding the origin of the RNA world Peptide nucleic acids rather than RNA may have been the ¢rst genetic molecule Birth of the snoRNPs: the evolution of the modi¢cation-guide snoRNAs Homologues of small nucleolar RNAs in Archaea Modi¢cation of U6 spliceosomal RNA is guided by other small RNAs The speci¢city of interaction between S-adenosyl-L-methionine and a nucleolar 2P-O-methyltransferase Crystal structure of catechol O-methyltransferase The 1.85 A î structure of Vaccinia protein VP39: a bifunctional enzyme that participates in the modi¢cation of both mRNA ends Stereochemical course of the transmethylation catalysed by catechol O-methyltransferase Instability and decay of the primary structure of DNA Spontaneous methylation of hemoglobin by S-adenosyl-methionine by a speci¢c and saturable mechanism Nonenzymatic methylation of DNA by S-adenosylmethionine in vitro The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2P-O-Me(CGCGCG)2 under low salt conditions Crystal structure of 2P-O-Me-(CGCGCG)2, an RNA duplex at 1.30 A î resolution.
    keywords: capacity; dna; genome; methylation; radical; ribonucleotide; rna; speci¢c; structure; world
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        item: #938 of 1349
          id: cord-315909-vwugf0wp
      author: Letko, Michael
       title: Studying Evolutionary Adaptation of MERS-CoV
        date: 2019-09-14
       words: 1239
      flesch: 44
     summary: Semi-permissive cells: baby hamster kidney (BHK) cells which have been transduced to stably express Desmodus rotundus DPP4 (drDPP4 At least three replicates (well of semi-permissive cells) for each forced adaptation experiment should be performed in parallel.
    keywords: cells; culture; mers; mutations; virus
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        item: #939 of 1349
          id: cord-316134-lkd2mj27
      author: Sungsuwan, Suttipun
       title: Nucleocapsid proteins from other swine enteric coronaviruses differentially modulate PEDV replication
        date: 2020-01-15
       words: 9264
      flesch: 41
     summary: No detectable fluorescence was observed from co-transfection with the empty pCAGGS vector, confirming the role of PEDV N protein during at least the first round of viral RNA transcription and viral protein translation (Fig. 7A ). Specifically, we asked if N proteins from TGEV or PDCoV can interact with PEDV N and possibly affect PEDV replication.
    keywords: cells; et al; expression; fig; mcherry; nucleocapsid; pcaggs; pdcov; pedv; proteins; replication; rna; tgev; veroe6; virus
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        item: #940 of 1349
          id: cord-316179-kmdxltie
      author: Fozouni, P.
       title: Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone
        date: 2020-09-30
       words: 8259
      flesch: 47
     summary: The need for SARS-CoV-2 tests that are rapid, widespread, and able to identify infectious individuals has motivated efforts to explore new strategies for viral RNA detection based on CRISPR technology. https://doi.org/10.1101 Reporter RNA Reporter RNA .
    keywords: assay; cov-2; crrna; detection; et al; figure; license; medrxiv; preprint; rna; rnp; sars; target
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        item: #941 of 1349
          id: cord-316503-wtmmewiz
      author: Warren, Travis K.
       title: Advanced morpholino oligomers: A novel approach to antiviral therapy
        date: 2012-02-14
       words: 6829
      flesch: 27
     summary: Deas et al., 2005; Holden et al., 2006; Kinney et al., 2005) . In rats, administration of 30 or 150 mg/kg of an anti-c-myc PPMO (containing an arginine-rich peptide) produced reduction in body weight and elevation of serum blood urea nitrogen and creatinine concentrations, changes not observed following dose-matched administration of an unconjugated version of this PMO (Amantana et al., 2007) .
    keywords: administration; agents; antisense; antiviral; efficacy; et al; infection; morpholino; oligomers; peptide; pmoplus; pmos; rna; therapeutics; treatment; virus; viruses
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        item: #942 of 1349
          id: cord-317037-1qydcc5e
      author: Kumar, Asit
       title: Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention
        date: 2020-08-13
       words: 9424
      flesch: 28
     summary: Notably, EVs can enhance viral infection by: (1) mediating transfer of chemokine co-receptors or cell surface proteins to null-target cells that do not express endogenous viral co-receptors; (2) helping viruses to evade the host immune system; (3) transferring of viral components (viral proteins and RNAs) to recipient cells, which induce cytotoxic effects on infected cells, leading to progressive loss of immune cells resulting from the apoptosis of uninfected bystander cells. Notably, EVs can enhance viral infection by: (1) mediating transfer of chemokine co-receptors or cell surface proteins to null-target cells that do not express endogenous viral co-receptors; (2) helping viruses to evade the host immune system; (3) transferring of viral components (viral proteins and RNAs) to recipient cells, which induce cytotoxic effects on infected cells, leading to progressive loss of immune cells resulting from the apoptosis of uninfected bystander cells.
    keywords: cells; delivery; drug; evs; exosomes; extracellular; hiv; human; immune; infected; infection; isolation; membrane; plasma; proteins; replication; rna; sars; size; vesicles; virus; viruses
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        item: #943 of 1349
          id: cord-317244-4su5on6s
      author: Maganga, Gael D.
       title: Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity
        date: 2014-12-31
       words: 3483
      flesch: 45
     summary: A new mouse paramyxovirus (J virus) Isolation and molecular characterization of a novel cytopathogenic paramyxovirus from tree shrews Complete genome sequence of a novel paramyxovirus, Tailam virus, discovered in Sikkim rats Identification and phylogenetic comparison of Salem virus, a novel paramyxovirus of horses Reproduction and nutritional stress are risk factors for Hendra virus infection in little red flying foxes Bats host major mammalian paramyxoviruses Encephalitis caused by a lyssavirus in fruit bats in Australia Airborne transmission of lyssaviruses Rabies in nonhematophagous bats Guidelines of the American Society of Mammalogists for the use of wild mammals in research Ecological and behavioral methods for the study of bats Sensitive and broadly reactive reverse transcription-PCR assays to detect novel paramyxoviruses Marburg virus infection detected in a common African bat Newly discovered ebola virus associated with hemorrhagic Fever outbreak in Uganda Basic local alignment search tool MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance and Maximum Parsimony Methods MRBAYES: Bayesian inference of phylogenetic trees Isolation of Genetically Diverse Marburg Viruses from Egyptian Fruit Bats Studies of Reservoir Hosts for Marburg Virus Genomic characterizations of bat coronaviruses (1A, 1B and HKU8) and evidence for co-infections in Miniopterus bats Isolation of Hendra virus from pteropid bats: a natural reservoir of Hendra virus Bats are natural reservoirs of SARS-like coronaviruses Bats: important reservoir hosts of emerging viruses Novel astroviruses in insectivorous bats Bat white-nose syndrome: an emerging fungal pathogen? Inoculation of bats with European Geomyces destructans supports the novel pathogen hypothesis for the origin of white-nose syndrome Pathogenesis studies with Australian bat lyssavirus in grey-headed flying foxes (Pteropus poliocephalus) Bats and Lyssaviruses Discovery of an Ebolavirus-Like Filovirus in Europe Nipah virus infection in bats (Order Chiroptera) in Peninsular Malaysia Fruit bats as reservoirs of Ebola virus Is Marburg Virus Enzootic in Gabon? Bats as a continuing source of emerging infections in humans Risk factor for Nipah virus encephalitis in Bangladesh Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats Paramyxovirus and Pneumovirus diseases of animals and birds: comparatives aspects and diagnosis Dionisia bunoi n. g. n. sp., Haemoproteidae parasite du microchiroptè re Hipposideros cyclops au Gabon The chiropteran haemosporidian Polychromophilus melanipherus: A worldwide species complex restricted to the family Many authors suggested that persistence in the absence of pathology or disease appears to be a common characteristic of bat viruses in their natural host population [28, 29] .
    keywords: afra; bats; belpv; host; paramyxovirus; pcr; rna; species; virus; viruses
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        item: #944 of 1349
          id: cord-317455-6qx0v28w
      author: Brown, Paul A.
       title: Transmission Kinetics and histopathology induced by European Turkey Coronavirus during experimental infection of specific pathogen free turkeys
        date: 2018-09-10
       words: 3574
      flesch: 39
     summary: Salamanca Spain First complete genome sequence of European turkey coronavirus suggests complex recombination history related with US turkey and guinea fowl coronaviruses A nomenclature for avian coronavirus isolates and the question of species status Detection of a coronavirus from turkey poults in Europe genetically related to infectious bronchitis virus of chickens Viral agents associated with outbreaks of diarrhea in turkey flocks in Quebec Turkey coronavirus in Horizontal transmission of the virus via the airborne route was not observed however, via the oro‐faecal route this proved to be extremely rapid (one infectious individual infecting another every 2.5 hr) and infectious virus was excreted for at least 6 weeks in several birds.
    keywords: coronavirus; rna; subjects; tcov; transmission; turkey; virus
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        item: #945 of 1349
          id: cord-317537-wgu5cd0y
      author: Lu, Hsiang-Chia
       title: Cymbidium mosaic potexvirus isolate-dependent host movement systems reveal two movement control determinants and the coat protein is the dominant
        date: 2009-05-25
       words: 8201
      flesch: 47
     summary: Our data indicated that CymMV M1 CP has a higher binding affinity as compared to CymMV M2 CP (Fig. 7D, lanes 1-4) . The amino acids within the CP, TGBp1 and TGBp3 which are required or important for CymMV M2 movement in N. benthamiana plants were mapped.
    keywords: benthamiana; cell; et al; fig; movement; pcymmv; plants; rna; tgbp1; virus
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        item: #946 of 1349
          id: cord-317591-qa6oxy4j
      author: Fukushima, Akiko
       title: Development of a Chimeric DNA-RNA Hammerhead Ribozyme Targeting SARS Virus
        date: 2009-05-07
       words: 3609
      flesch: 49
     summary: RNA ribozymes are rapidly degraded in both culture medium and living cells by RNase, which diminishes copy number of the ribozyme. Hammerhead ribozymes contain two functional modules: a catalytic core which cleaves the target RNA and contains several conserved bases, and flanking regions which, through nucleic acid complementarity, direct the ribozyme core to a specific target site.
    keywords: cells; chimeric; cov; dna; hammerhead; ribozyme; rna; sars; target
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        item: #947 of 1349
          id: cord-317715-xtsi663k
      author: Ortiz-Riaño, Emilio
       title: D471G Mutation in LCMV-NP Affects its Ability to Self-associate and Results in a Dominant Negative Effect in Viral RNA Synthesis
        date: 2012-10-16
       words: 9191
      flesch: 46
     summary: Puromycin resistant clones were screened for NP expression by immunofluorescence and WB using a polyclonal antibody against the HA epitope (Sigma H6908). At 48 hpt, cell lysates were prepared and analyzed for NP expression levels by WB using an anti-HA antibody (A).
    keywords: cells; d471; expression; figure; gfp; interaction; lcmv; mutant; protein; rna; virus
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        item: #948 of 1349
          id: cord-317720-gbi11oxx
      author: Lefferts, Joel A.
       title: Implementation of an Emergency Use Authorization Test During an Impending National Crisis
        date: 2020-05-14
       words: 2150
      flesch: 32
     summary: As each swab type used in clinical laboratory testing was eventually approved for use in assays, national supplies became exhausted. As laboratories began to place orders for the RNA control, another bottleneck in the development and validation of laboratory testing became evident, as the supplier could not distribute this required material at a sufficient pace.
    keywords: fda; laboratories; laboratory; rna; testing; use
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        item: #949 of 1349
          id: cord-317773-jdq1d98i
      author: Meng, Qing-Wen
       title: Enhanced inhibition of Avian leukosis virus subgroup J replication by multi-target miRNAs
        date: 2011-12-22
       words: 3639
      flesch: 48
     summary: The strategy of multi-target miRNAs might be an effective method for inhibiting ALV replication and the acquisition of resistant mutations. In this study, we used RNAi technology to inhibit ALV replication and screened the effective target sites for their ability to inhibit ALV replication at a cellular level.
    keywords: alv; cells; expression; gene; replication; rna; target; virus
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        item: #950 of 1349
          id: cord-317851-lj07947c
      author: Elena, S F
       title: Experimental evolution of plant RNA viruses
        date: 2008-02-06
       words: 4186
      flesch: 34
     summary: A Darò s for helping us in setting up the lab for plant virus work and for fruitful discussion and Fernando García-Arenal for many enlightening discussions about plant virus evolution. Our goal was not to provide an exhaustive review of all the relevant literature but, instead, to illustrate the advantages of plant RNA viruses as model systems for experimental evolution studies.
    keywords: evolution; fitness; host; mutation; plant; rna; virulence; viruses
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        item: #951 of 1349
          id: cord-318164-6rqi17oz
      author: Paoli, D.
       title: Sperm cryopreservation during the SARS-CoV-2 pandemic
        date: 2020-10-10
       words: 3262
      flesch: 41
     summary: First, it comprises a preliminary biomonitoring for SARS CoV-2 in the semen of asymptomatic cancer patients. Furthermore, the current evidence seems increasingly to point to the absence of SARS CoV-2 in semen.
    keywords: cov-2; covid-19; cryopreservation; patients; samples; sars; semen; sperm
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        item: #952 of 1349
          id: cord-318276-so5jooj0
      author: Bertholet, Christine
       title: Vaccinia virus produces late mRNAs by discontinuous synthesis
        date: 1987-07-17
       words: 6229
      flesch: 53
     summary: Another interesting question is whether the leader RNA sequences are also translated. Synthesis of polyriboadenylic acid How do eucaryotic ribosomes select initiation regions in messenger RNA? Bifunctional messenger RNAs in eukaryotes The role of RNA priming rn viral and trypanosomal mRNA synthesis Characterization of leader RNA sequences on the virion and mRNAs of mouse hepatitis virus, a cytoplasmic RNA virus Arrangement of late mRNAs transcribed from a 7.1-kilobase EcoRl vaccinia virus DNA fragment Molecular Cloning: A Laboratory Manual Control of induced thymidine kinase activity rn the poxvirus infected cell The induction and repression of thymidine kinase in the poxvirus-infected HeLa cell Analysis of single-and double-stranded nucleic acids on polyacrylamide and agarose gels by using glyoxal and acridine orange Reproduction of poxviruses Replication of poxviruses Identification of a novel Y branch structure as an intermediate in trypanosome mRNA processing: evidence for Pans splicing Hybridization and sedimentation studies on early and late vaccinia messenger RNA A cDNA clomng vector that permrts expression of cDNA inserts in mammalian cells Soluble endoribonuclease activity from vaccinia virus: specific cleavage of virion-assocrated highmolecular weight RNA La crosse virions contain a primer-stimulated RNA polymerase and a methylated cap-dependent endonuclease A unique cap (m7GpppXm)-dependent influenza vrnon endonuclease cleaves capped RNAs to generate the primers that rmtiate vrral RNA transcnption Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase
    keywords: cdna; dna; figure; gene; late; rna; rnas; sequences; vaccinia; virus
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        item: #953 of 1349
          id: cord-318359-41h90h05
      author: Irigoyen, Nerea
       title: Ribosome profiling of the retrovirus murine leukemia virus
        date: 2018-01-22
       words: 4500
      flesch: 48
     summary: Mapping was performed in the following order: host rRNA; virus RNA; host Ref-Seq mRNA; host non-coding RNA. MuLV: murine leukemia virus; uORF: upstream ORF; CHX: cycloheximide; HAR: harringtonine.
    keywords: codon; env; fig; gag; gene; initiation; mulv; pol; reads; rna; translation; virus
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        item: #954 of 1349
          id: cord-318478-fn0gcxbb
      author: Ziv, Omer
       title: The short- and long-range RNA-RNA Interactome of SARS-CoV-2
        date: 2020-10-07
       words: 5768
      flesch: 44
     summary: RNA viruses comprise the dominant component of the eukaryotic virome (Dolja and Koonin, 2018) . Genome cyclization plays an essential role in the replication of a number of RNA viruses, including flaviviruses (Hahn et al., 1987; Ziv et al., 2018) .
    keywords: chimeric; coronavirus; cov-2; et al; figure; genome; interactions; rna; sars; sequence; sgmrna; structure
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        item: #955 of 1349
          id: cord-318495-1w74wf02
      author: Vignuzzi, Marco
       title: Defective viral genomes are key drivers of the virus–host interaction
        date: 2019-06-03
       words: 8880
      flesch: 20
     summary: Biologic role in homologous interference Viral interference by defective particles of vesicular stomatitis virus measured in individual cells Analysis of extracellular West Nile virus particles produced by cell cultures from genetically resistant and susceptible mice indicates enhanced amplification of defective interfering particles by resistant cultures Replication signals in the genome of vesicular stoma titis virus and its defective interfering particles: identification of a sequence element that enhances DI RNA replication Functional characterisation of the genomic and antigenomic promoters of Sendai virus Homologous interference by incomplete Sendai virus particles: changes in virus-specific ribonucleic acid synthesis Defective viral genomes alter how Sendai virus interacts with cellular trafficking machinery leading to heterogeneity in the production of viral particles among infected cells Replication defective viral genomes exploit a cellular pro-survival mechanism to establish paramyxovirus persistence MDA5 participates in the detection of paramyxovirus infection and is essential for the early activation of dendritic cells in response to Sendai virus defective interfering particles Sendai virus defective-interfering genomes and the activation of interferon-beta Induction of dendritic cell production of type I and type III interferons by wild-type and vaccine strains of measles virus: role of defective interfering RNAs Highly immunostimulatory RNA derived from a Sendai virus defective viral genome A novel role for viral-defective interfering particles in enhancing dendritic cell maturation Modulation of a systemic Semliki Forest virus infection in mice by defective interfering virus Identification of a natural viral RNA motif that optimizes sensing of viral RNA by RIG.-I. mBio Activation of the beta interferon promoter by unnatural Sendai virus infection requires RIG-I and is inhibited by viral C proteins PACT-and RIG-I-dependent activation of Type I interferon production by a defective interfering RNA derived from measles virus vaccine Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing TLR-independent induction of dendritic cell maturation and adaptive immunity by negative-strand RNA viruses In vivo ligands of MDA5 and RIG-I in measles virusinfected cells Nonencapsidated 5′ Copy-Back Defective Interfering Genomes Produced by Recombinant Measles Viruses Are Recognized by RIG-I and LGP2 but Not MDA5 ATPase-driven oligomerization of RIG-I on RNA allows optimal activation of type-I interferon Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses Dicer-2-dependent generation of viral DNA from defective genomes of RNA viruses modulates antiviral immunity in insects Role of defective interfering particles of Sendai virus in persistent infections Comparative study of rabies virus persistence in human and hamster cell lines Subclinical infections in mice resulting from the modulation of a lethal dose of Semliki Forest virus with defective interfering viruses: neurochemical abnormalities in the central nervous system Defective interfering particles: effects in modulating virus growth and persistence Persistence of virulent Semliki Forest virus in mouse brain following co-inoculation with defective interfering particles Defective interfering virus particles modulate virulence Continuous influenza virus production in cell culture shows a periodic accumulation of defective interfering particles Multiple-hit inhibition of infection by defective interfering particles Defective interfering particles of human parainfluenza virus type 3 are associated with persistent infection in cell culture Defective interfering influenza virus RNAs: time to reevaluate their clinical potential as broad-spectrum antivirals? Targeting expression of the leukemogenic PML-RARalpha fusion protein by lentiviral vector-mediated small interfering RNA results in leukemic cell differentiation and apoptosis Ebola virus defective interfering particles and persistent infection Defective interfering viral particles in acute dengue infections Generation of measles virus defective interfering particles and their presence in a preparation of attenuated live-virus vaccine Effects of defective interfering viruses on virus replication and pathogenesis in vitro and in vivo Defective interfering particles of respiratory syncytial virus Induction and biological properties of defective interfering particles of rabies virus Defective T particles of vesicular stomatitis virus.
    keywords: cells; copy; defective; dvgs; generation; genomes; infection; influenza; interfering; particles; persistent; production; replication; rna; rnas; type; virus; viruses
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        item: #956 of 1349
          id: cord-318551-c1qr27lg
      author: Boguszewska‐Chachulska, Anna M.
       title: Rna Viruses Redirect Host Factors to Better Amplify Their Genome
        date: 2005-12-29
       words: 10689
      flesch: 33
     summary: The incoming genome of many (þ) strand RNA viruses ( Fig. 1 ) serves as mRNA for virus protein synthesis including the RdRp, and is then replicated yielding the complementary (À) RNA strand. key: cord-318551-c1qr27lg authors: Boguszewska‐Chachulska, Anna M.; Haenni, Anne‐Lise title: Rna Viruses Redirect Host Factors to Better Amplify Their Genome date: 2005-12-29 journal: Adv Virus Res DOI: 10.1016/s0065-3527(05)65002-6 sha: doc_id: 318551 cord_uid: c1qr27lg This chapter provides an updated view of the host factors that are, at present, believed to participate in replication/transcription of RNA viruses.
    keywords: binding; cell; et al; factors; genome; host; polymerase; protein; replication; rna; rna synthesis; strand; synthesis; transcription; translation; viral; virus; viruses
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        item: #957 of 1349
          id: cord-318576-dc5n6ni4
      author: Jitobaom, Kunlakanya
       title: Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation
        date: 2020-05-08
       words: 6824
      flesch: 48
     summary: In this study, we investigated the relationship between the codon usage bias of human genes and human RNA viruses. In this study, we demonstrated that the codon usage of human RNA viruses is similar to that of some human genes, especially those involved in the cell cycle.
    keywords: bias; cell; codon; codon usage; cycle; genes; human; protein; rna; rna viruses; usage; viruses
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        item: #958 of 1349
          id: cord-318749-k91oku7h
      author: Dong, Hui-Jun
       title: Selective regulation in ribosome biogenesis and protein production for efficient viral translation
        date: 2020-10-29
       words: 7270
      flesch: 22
     summary: IRES) Host targeted antiviral (HTA): functional inhibitor compounds of scaffold protein RACK1 inhibit herpes simplex virus proliferation Arabidopsis receptor of activated C kinase1 phosphorylation by WITH NO LYSINE8 KINASE Viral ribonucleoprotein complex formation and nucleolar-cytoplasmic relocalization of nucleolin in poliovirus-infected cells RNA-binding properties of influenza A virus matrix protein M1 Ribosomal protein RPL26 is the principal target of UFMylation Cloning of mouse genomic ribosomal protein L6 gene and analysis of its promoter The association of ribosomal protein L18 (RPL18) with infectious bursal disease virus viral protein VP3 enhances viral replication UFMylation of RPL26 links translocation-associated quality control to endoplasmic reticulum protein homeostasis Interferon production and inhibition of host synthesis in cells infected with vesicular stomatitis virus Impact of RNA polymerase I inhibitor CX-5461 on viral kinase-dependent and -independent cytomegalovirus replication New mRNAs are preferentially translated during vesicular stomatitis virus infection The structure and function of the eukaryotic ribosome Hepatitis C virus 3'X region interacts with human ribosomal proteins Specialized ribosomes: a new frontier in gene regulation and organismal biology RNA regulons in Hox 5' Ribosomal protein L4 (RPL4) ) and ribosomal protein L18 were identified as interacting partners of VP3 protein and as being involved in the regulation of IBDV replication.
    keywords: antiviral; biogenesis; cells; et al; host; infection; ires; mrna; protein; replication; ribosomal; ribosome; rna; rps; synthesis; translation; virus; viruses
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        item: #959 of 1349
          id: cord-318751-4v2tl0gi
      author: Arias, Armando
       title: Progress towards the prevention and treatment of norovirus infections
        date: 2013-11-17
       words: 6844
      flesch: 32
     summary: Preceding the initiation of viral RNA replication, VPg must be guanylated in a step carried out by the virus polymerase NS7 pol or its precursor NS6-NS7 [55] . In addition to its capacity to inhibit viral RNA replication, suramin has been found to inhibit HuNoV capsid binding to heparan sulphate [32] .
    keywords: activity; cell; culture; hunov; infection; inhibition; inhibitors; mnv; norovirus; protein; replication; rna; translation; use; viruses; vpg
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        item: #960 of 1349
          id: cord-318853-mxyxwkhx
      author: Sallie, Richard
       title: Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases
        date: 2005-08-22
       words: 10548
      flesch: 17
     summary: Of necessity, some receptor affinity studies have used cloned viral protein ligands, an artificial situation that cannot approach the phenotypic complexity of RNA viral protein quasispecies. Viral receptor disease is a unifying hypothesis that may also explain some diseases with well-established, but multi-factorial and apparently unrelated aetiologies – like coronary artery and other vascular diseases – in addition to diseases like schizophrenia that are poorly understood and lack plausible, coherent, pathogenic explanations.
    keywords: cell; disease; envelope; fidelity; hcv; hepatitis; infection; leptin; patients; pol; proteins; quasispecies; receptor; replication; responses; rna; rna pol; sequence; type; variant; virus; viruses
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        item: #961 of 1349
          id: cord-319100-3gdawhfn
      author: Kirkland, P.D.
       title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses
        date: 2020-06-10
       words: 4628
      flesch: 41
     summary: Finally, to establish whether these effects were limited to testing of RNA viruses, a sample of bovine herpesvirus-1 was tested in the same model and range of dilutions. It is also important to recognise that these observations reflect the outcome of contact between viral nucleic acid and VTM for less than 1 hour in each instance.
    keywords: acid; nucleic; results; rna; samples; sars; transport; virus; vtm
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        item: #962 of 1349
          id: cord-319116-2ts6zpdb
      author: Ruggiero, Emanuela
       title: G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy
        date: 2018-04-20
       words: 9174
      flesch: 33
     summary: Mass spectrometry competition analysis revealed a stronger preference for HIV-1 G4s over HSV-1, but generally, viral G4s were preferentially bound, when compared to the telomeric G4. Since c-exNDI selectivity towards HSV-1 G4s in vitro resulted to be good but not outstanding, the marked anti-HSV-1 activity was likely due also to the massive presence of viral G4s in the cell nucleus, which was demonstrated to occur during HSV-1 replication (70) .
    keywords: activity; binding; cell; dna; g4s; genome; human; ligands; ltr; quadruplex; replication; rna; sequences; structures; telomerase; virus; viruses
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        item: #963 of 1349
          id: cord-319179-gqaxf7mz
      author: Denison, M.
       title: Identification of putative polymerase gene product in cells infected with murine coronavirus A59
        date: 1987-04-30
       words: 1642
      flesch: 53
     summary: p28 was detected in L-2 cells labeled between 5 and 8 hr p.i., the time of maximal viral RNA and protein synthesis, but could not be detected in either uninfected cells or infected cells labeled prior to 5 hr p.i. MHV does not efficiently shut off host cell protein synthesis until very late times after infection, making the analysis of virus-specific proteins difficult.
    keywords: cells; p28; rna
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        item: #964 of 1349
          id: cord-319194-ukuia48s
      author: Liò, Pietro
       title: Phylogenomics and bioinformatics of SARS-CoV
        date: 2004-02-04
       words: 4490
      flesch: 42
     summary: For example, many predicted protein sequences for the oxidation of inorganic compounds including thiosulfate and hydrogen, which provide reducing energy for carbon dioxide and nitrogen fixation are encoded, and also carbon monoxide and formate dehydrogenases. The low conservation of the S1A region among coronavirus sequences suggests that once more strains of SARS-CoV or other closely related species are available it will become possible to use innovative comparative sequence analyses to examine positive selection that acts in this region
    keywords: coronavirus; cov; genome; mutation; protein; region; rna; s1b; sars; sequences; structure
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        item: #965 of 1349
          id: cord-319501-a2x1hvkk
      author: Wong, Lok-Yin Roy
       title: A molecular arms race between host innate antiviral response and emerging human coronaviruses
        date: 2016-01-15
       words: 7773
      flesch: 38
     summary: In a previous study, MERS-CoV M is shown to impede IFN production by preventing IRF3 translocation into the nucleus (Yang et al., 2013) . Among the five accessory proteins, ORF4a, ORF4b and ORF5 show the ability to dampen IFN production (Yang et al., 2013) .
    keywords: activation; coronavirus; cov; covs; et al; host; human; ifn; mers; production; proteins; rig; rna; sars; syndrome; type
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        item: #966 of 1349
          id: cord-319635-kh99n7q2
      author: Chiang, Wei-Wei
       title: Cell Type-Dependent RNA Recombination Frequency in the Japanese Encephalitis Virus
        date: 2014-07-22
       words: 5136
      flesch: 48
     summary: Notably, viral RNAs usually accumulated at a lower amount in mosquito cells through RNase cleavage as well as RNA-mediated pathways, leading to stagnancy of RNA recombination which may brake evolution of the JEV and probably most, if not all, arboviruses which are maintained in nature by alternate cycles involving mosquitoes and vertebrates [28] . Autoimmunity-related demyelination in infection by Japanese encephalitis virus Flavivirus encephalitis Flaviviridae: the viruses and their replication Complete nucleotide sequence of the Japanese encephalitis virus genome RNA Quasispecies theory in virology Rapid fitness losses in mammalian RNA virus clones due to Muller's ratchet Genetic diversity in RNA virus quasispecies is controlled by host-virus interactions Mosquitoes put the brake on arbovirus evolution: experimental evolution reveals slower mutation accumulation in mosquito than vertebrate cells E/NS1 modifications of dengue 2 virus after serial passages in mammalian and/or mosquito cells The advantage of sex in the RNA virus 6 Genetic evolution of Japanese encephalitis virus Evolutionary aspects of recombination in RNA viruses A genetic map of poliovirus temperaturesensitive mutants Heterologous recombination in the double-stranded RNA bacteriophage 6 RNA recombination in brome mosaic virus, a model plus strand RNA virus How RNA viruses exchange their genetic material The extent of homologous recombination in members of the genus Flavivirus A phylogenetic survey of recombination frequency in plant RNA viruses Western equine encephalitis virus is a recombinant virus Evidence for recombination in natural populations of dengue virus type 1 based on the analysis of complete genome suquences Phylogenetic evidence for recombination in dengue virus RNA recombination between persisting pestivirus and a vaccine strain: generation of cytopathogenic virus and induction of lethal disease Adaptation of two flaviviruses results in differences in genetic heterogeneity and virus adaptability Quasispecies of dengue virus Experimental evidence that RNA recombination occurs in the Japanese encephalitis virus Genetic diversity and slow rates of evolution in new world alphaviruses Mutations in the NS3 gene and 3 -NCR of Japanese encephalitis virus isolated from an unconventional ecosystem and implications for natural attenuation of the virus Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis Mutation rates among RNA viruses Why do RNA viruses recombine? RNA viruses generate new genetic strains with approximately 6 orders of magnitude higher rates of nucleotide substitutions compared to DNA viruses [28] .
    keywords: c6/36; cells; fragment; jev; mosquito; recombination; rna; strains; virus
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        item: #967 of 1349
          id: cord-319649-d6dqr03e
      author: Yang, Jie
       title: A cypovirus VP5 displays the RNA chaperone-like activity that destabilizes RNA helices and accelerates strand annealing
        date: 2013-12-05
       words: 7891
      flesch: 43
     summary: Our disorder prediction of CPV VP5 using PONDR VL-XT (51, 53, 54) indicates that VP5 proteins from three different types of cypoviruses-CPV-5, CPV-1 and CPV-18-contain similar distribution patterns of potentially disordered regions (data not shown), thereby suggesting that the 'entropy transfer' applies to HaCPV-5 VP5, and VP5 proteins of other CPVs may also contain RNA chaperone activity. This phenomenon is consistent with our previous observation of Ectropis obliqua picorna-like virus (EoV) nonstructural protein 2C, which also displays RNA chaperone activity (32) .
    keywords: activity; capsid; chaperone; cpv; dsrna; figure; helix; mbp; panhandle; protein; replication; rna; vp5
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        item: #968 of 1349
          id: cord-319664-gyktrd36
      author: Mancini, Fabiola
       title: Laboratory management for SARS-CoV-2 detection: a user-friendly combination of the heat treatment approach and rt-Real-time PCR testing
        date: 2020-06-18
       words: 2091
      flesch: 47
     summary: A lower efficiency was observed with the commercial kit where it was registered a range of 1.2 × 10 6 to 70 copies/reaction for purified samples and 4.5 × 10 5 to 80 copies/reaction for heat samples. Realtime rRT-PCR Panel Primers and Probes Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR Comparative performance of SARS CoV-2 detection assays using seven different primer/probe sets and one assay kit An alternative workflow for molecular detection of SARS CoV-2 -escape from the NA extraction kit-shortage The authors thank Alessia Caratelli, Marina Sbattella and Ambrogio Carlei of the Department of Infectious Disease, Istituto Superiore di Sanità, for technical support.
    keywords: cov-2; pcr; rna; samples; sars
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        item: #969 of 1349
          id: cord-319681-kjet3e50
      author: Lin, Zhaoru
       title: Spacer-length dependence of programmed −1 or −2 ribosomal frameshifting on a U(6)A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting
        date: 2012-06-28
       words: 8876
      flesch: 47
     summary: These data suggested strongly that the +1/ À2 FS product results from À2 FS and this was confirmed by MS (for convenience, these data are presented at the end of the 'Results' section, since acquisition of sufficient trans-frame protein for MS analysis required additional knowledge obtained from experiments outlined in the following sections). Examination of known viral À1 FS sites possessing a U 6 A or A 6 C slippery sequence, however, reveals that in most cases the spacing distances seem inappropriately long for efficient À2 FS.
    keywords: aon; figure; frameshifting; mrna; pfshiv; product; pseudoknot; ribosomal; sequence; site; slippery; spacer; à2 fs
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        item: #970 of 1349
          id: cord-319729-6lzjhn8j
      author: Tian, Bin
       title: Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway
        date: 2018-01-19
       words: 7820
      flesch: 42
     summary: Notably, B2c titers were significantly increased in MAVS−/− astrocytes compared with wt astrocytes (Figures 5A,B) . Moreover, the cell numbers of immunofluorescence plaques in MAVS−/− astrocytes caused by B2c infection were significantly more than those in wt astrocytes (Figures 5E,F) .
    keywords: astrocytes; b2c; cells; drv; dsrna; expression; infection; lab; protein; rabies; rabv; rig; rna; signaling; virus
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        item: #971 of 1349
          id: cord-319780-rfj9t99r
      author: Alexander, S.P.H.
       title: A rational roadmap for SARS‐CoV‐2/COVID‐19 pharmacotherapeutic research and development. IUPHAR Review 29
        date: 2020-05-01
       words: 15233
      flesch: 30
     summary: A truncated version of human recombinant ACE2, lacking the transmembrane domain, mitigated against SARS-CoV infection of cells (Li et al., 2003) and has been used in animal models to reduce symptoms of severe acute lung failure , diabetic nephropathy (Oudit et al., 2010) and cardiac hypertrophy and fibrosis . It has been used to treat influenza A infection through targeting the M2 ion channel (Pinto et al., 1992; Wang et al., 1993; Holsinger et al., 1994) , although it is no longer recommended in the UK or US because of drug resistance (for review, see Li et al., 2015) .
    keywords: ace2; activity; acute; angiotensin; binding; cells; converting; coronavirus; cov-2; covid-19; domain; drug; entry; enzyme; et al; host; human; infection; inhibitors; interferon; membrane; mers; protease; protein; receptor; replication; review; rna; sars; sars coronavirus; spike; structure; syndrome; target; tmprss2
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        item: #972 of 1349
          id: cord-319781-6thdg2up
      author: Payne, Kelly
       title: Twenty-First Century Viral Pandemics: A Literature Review of Sexual Transmission and Fertility Implications in Men
        date: 2020-07-24
       words: 8239
      flesch: 45
     summary: SARS-Cov-2, the most recent viral pandemic included in this review, is expected to behave similar to SARS virus, but further data are required to validate these assumptions. ELevated 17b-estradiol protects females from influenza A virus pathogenesis by suppressing inflammatory responses Critically ill children during the 2009-2010 influenza pandemic in the United States Correlates of severe disease in patients with 2009 pandemic influenza (H1N1) virus infection Probable noneVectorborne transmission of Zika virus Persistence and clinical relevance of Zika virus in the male genital tract Zika virus shedding in semen of symptomatic infected men Effect of acute Zika virus infection on sperm and virus clearance in body fluids: a prospective observational study Sexual transmission of Zika virus and other flaviviruses: a living systematic review Persistence of Zika virus in body fluids -Final report Zika virus infects human testicular tissue and germ cells Sexually acquired Zika virus: a systematic review Low risk of a sexuallytransmitted Zika virus outbreak The dual role of the immune response in reproductive organs during Zika virus infection Zika virus causes testicular atrophy Zika virus infection damages the testes in mice Zika virus in semen: a prospective cohort study of symptomatic travellers returning to Belgium Potential effect of Zika virus infection on human male fertility? Ebola (Ebola Virus Disease)
    keywords: days; disease; ebola; fertility; immune; infection; influenza; rna; sars; semen; studies; transmission; virus; wnv; zika
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        item: #973 of 1349
          id: cord-319821-ij34t1ae
      author: Bauer, Lisa
       title: Direct-acting antivirals and host-targeting strategies to combat enterovirus infections
        date: 2017-04-12
       words: 4057
      flesch: 34
     summary: The sweet spot: defining virus-sialic acid interactions A phase II study of DAS181, a novel host directed antiviral for the treatment of influenza infection The use of sialidase therapy for respiratory viral infections In vitro efficacy of antiviral compounds against enterovirus D68 Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes Conservation of amino acids in human rhinovirus 3C protease correlates with broad-spectrum antiviral activity of rupintrivir, a novel human rhinovirus 3C protease inhibitor In vitro activity of pleconaril and AG7088 against selected serotypes and clinical isolates of human rhinoviruses In vitro antiviral activity of AG7088, a potent inhibitor of human rhinovirus 3C protease Pharmacokinetics and safety of an antirhinoviral agent, ruprintrivir, in healthy volunteers Liquid chromatography-mass spectrometry and liquid chromatography-NMR characterization of in vitro metabolites of a potent and irreversible peptidomimetic inhibitor of rhinovirus 3C protease Phase II, randomized, double-blind, placebo-controlled studies of ruprintrivir nasal spray 2-percent suspension for prevention and treatment of experimentally induced rhinovirus colds in healthy volunteers In vitro antiviral activity and single-dose pharmacokinetics in humans of a novel, orally bioavailable inhibitor of human rhinovirus 3C protease 3C protease of enterovirus 68: structure-based design of Michael acceptor inhibitors and their broad-spectrum antiviral effects against picornaviruses Antiviral activities of peptidebased covalent inhibitors of the Enterovirus 71 3C protease Fragment-wise design of inhibitors to 3C proteinase from enterovirus 71 Identification and biochemical characterization of DC07090 as a novel potent small molecule inhibitor against human enterovirus 71 3C protease by structure-based virtual screening Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases A single mutation in poliovirus RNAdependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity Peginterferon alfa-2b plus ribavirin compared with interferon alfa-2b plus ribavirin for initial treatment of chronic hepatitis C: a randomised trial Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection Inhibition of enterovirus 71 by adenosine analog NITD008 Synergistic antiviral activity of gemcitabine and ribavirin against enteroviruses Cell-based high-throughput screening assay identifies 2 0 ,2 0 -difluoro-2 0 -deoxycytidine Gemcitabine as potential anti-poliovirus agent The RNA template channel of the RNA-dependent RNA polymerase as a target for development of antiviral therapy of multiple genera within a virus family SUMO modification stabilizes enterovirus 71 polymerase 3D to facilitate viral replication Screening of a library of FDA-approved drugs identifies several enterovirus replication inhibitors that target viral protein 2C Selective serotonin reuptake inhibitor fluoxetine inhibits replication of human enteroviruses B and D by targeting viral protein 2C Fluoxetine is a potent inhibitor of coxsackievirus replication 11:e1005067. Lately, several enterovirus inhibitors have been discovered in drug repurposing screens.
    keywords: activity; antiviral; capsid; enterovirus; host; inhibitors; protein; replication; rhinovirus; rna
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        item: #974 of 1349
          id: cord-319842-4mnaicki
      author: Jackson, William T
       title: Subversion of Cellular Autophagosomal Machinery by RNA Viruses
        date: 2005-04-26
       words: 6959
      flesch: 33
     summary: As can be seen in Figure 1 , the punctate GFP-LC3 signal colocalized with that of poliovirus RNA replication protein 3A, as visualized by immunofluorescence. It is thought that one function for membrane localization of viral RNA replication proteins is to promote their oligomerization [6, 7] .
    keywords: autophagosome; autophagy; cells; figure; formation; infection; lc3; membranes; pathway; poliovirus; protein; replication; rna; structures; vesicles
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        item: #975 of 1349
          id: cord-319906-s7kzp795
      author: Zemla, Adam T
       title: StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase
        date: 2011-06-02
       words: 7498
      flesch: 35
     summary: Twilight zone of protein sequence alignments Local alignment refinement using structural assessment Structural proteomics: a tool for genome annotation The structural alignment between two proteins: is there a unique answer Comparative analysis of protein structure alignments Flexible protein alignment and hinge detection Flexible structure alignment by chaining aligned fragment pairs allowing twists Matt: local flexibility aids protein multiple structure alignment Circular permutations of natural protein sequences: structural evidence Common structural cliques: a tool for protein structure and function analysis Connectivity independent protein-structure alignment: a hierarchical approach Topology independent protein structural alignment FlexSnap: Flexible non-sequential protein structure alignment Automated clustering of ensembles of alternative models in protein structure databases Iterative refinement of structure-based sequence alignments by seed extension LGA: a method for finding 3D similarities in protein structures STRALCP-structure alignment-based clustering of proteins A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features Structure of the RNA-dependent RNA polymerase of poliovirus A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure Molecular model of SARS coronavirus polymerase: implications for biochemical functions and drug design Oligomeric structures of poliovirus polymerase are important for function Clustered charged-to-alanine mutagenesis of poliovirus RNA-dependent RNA polymerase yields multiple temperature sensitive mutants defective in RNA synthesis Crystal structure of poliovirus 3CD protein: virally encoded protease and precursor to the RNA-dependent RNA polymerase Mutation of lysine residues in the nucleotide binding segments of the poliovirus RNA-dependent RNA polymerase Poliovirus RNA-dependent RNA polymerase (3Dpol): Structural, biochemical, and biological analysis of conserved structural motifs A and B Crystal structure of the RNA-dependent RNA polymerase form hepatitis C virus reveals a fully encircled active site Effects of mutations in poliovirus 3Dpol on RNA polymerase activity and on polyprotein cleavage SCOP: a structural classification of proteins database for the investigation of sequences and structures A mechanism for initiating RNA-dependent RNA polymerization Our StralSV algorithm detects structurally similar regions within a given pair of protein structures, and reports residue-residue correspondences only from those local regions that are contained within a larger, similar structural context.
    keywords: fragments; hits; polymerase; positions; protein; residue; rna; sequence; stralsv; structure; variability; window_size
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        item: #976 of 1349
          id: cord-320169-dtv7to3l
      author: Liu, Yen-Chin
       title: COVID-19: the First Documented Coronavirus Pandemic in History
        date: 2020-05-05
       words: 1943
      flesch: 41
     summary: Bats are likely reservoir hosts for SARS-CoV-2; however, whether Bat-CoV humans because of the similarity of the pangolin coronavirus to SARS-CoV-2 [32, 33] . Replication of RNA viruses could generate mutations due to the low proofreading ability of their RdRP.
    keywords: coronavirus; cov-2; human; novel; pandemic; sars
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        item: #977 of 1349
          id: cord-320212-fw51w4nm
      author: Friedman, Stephanie D.
       title: Genomic Sequences of two Novel Levivirus Single-Stranded RNA Coliphages (Family Leviviridae): Evidence for Recombinationin Environmental Strains
        date: 2012-09-13
       words: 5367
      flesch: 46
     summary: The first indication of RNA recombination in a male-specific FRNA phage was the report of small, non homologous, recombinant RNA molecules produced from a purified template-free Qβ replicase molecule A final report submitted to the NOAA/UNH Cooperative Institute for Coastal and Estuarine Environmental Technology (CICEET) Evaluation of RT-PCR and reverse line blot hybridization for detection and genotyping F+ RNA coliphages from estuarine waters and molluscan shellfish RNA recombination in animal and plant viruses Evidence of structural genomic region recombination in Hepatitis C virus Phylogenetic analysis of turkey astroviruses reveals evidence of recombination Phylogenetic evidence for recombination in Dengue virus Evidence for frequent recombination within species Human Enterovirus B based on complete genomic sequences of all thirty-seven serotypes Random nature of coronavirus RNA recombination in the absence of selection pressure Natural genetic recombination between co-circulating heterotypic enteroviruses Molecular characterization of a novel recombinant strain of human astrovirus associated with gastroenteritis in children Characterization of a novel human calicivirus that may be a naturally occurring recombinant Detection and genetic differentiation of human astroviruses: Phylogenetic grouping varies by coding region Genetic recombination with Newcastle disease virus, polioviruses, and influenza Genetic recombination with poliovirus type 1 studies of crosses between a normal horse serum-resistant mutant and several guanidine-resistant mutants of the same strain Outbreak of poliomyelitis in Hispaniola associated with circulating type 1 vaccine-derived poliovirus RB-finder: An improved distance-based sliding window method to detect recombination breakpoints Sequence variation among group III F-specific RNA coliphages from water samples and swine lagoons BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Evolution of Protein Molecules Full-length human immunodeficiency virus type 1 genomes from subtype c-infected seroconverters in India, with evidence of intersubtype recombination Recombination analysis tool (RAT): A program for the high-throughput detection of recombination RDP2: Recombination detection and analysis from sequence alignments Recombination analysis using cost optimization This research was funded, in part, through EPA's New England Regional Applied Research Effort (RARE).
    keywords: acid; amino; dl52; genogroup; nucleotide; recombination; replicase; rna; sequences; strains
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        item: #978 of 1349
          id: cord-320325-sjab8zsk
      author: Mendez, Aaron S
       title: Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX
        date: 2018-12-14
       words: 6521
      flesch: 45
     summary: Our data suggest that this is likely because the K2-31 RNA lacks the additional residues necessary for SOX binding site found in both LIMD1 and GFP. This mutant has been previously identified to block SOX cleavage in vivo (20) .
    keywords: binding; cells; cleavage; figure; limd1; loop; mrna; protein; rna; sequence; site; sox; structure; targeting
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        item: #979 of 1349
          id: cord-320351-47d0nby0
      author: Li, Zhouxiao
       title: The emerging landscape of circular RNAs in immunity: breakthroughs and challenges
        date: 2020-07-10
       words: 5982
      flesch: 31
     summary: Here, we primarily elucidated the status and effect of cir-cRNAs on a wide variety of types of immune cells in cancer, autoimmune diseases, and infections, which can present a novel perspective and lay a theoretical foundation in treating diseases. Based on the type of foreign antigen, the immune response can perform antiviral, antibacterial, and anti-tumor functions, depending on the synthesis of a wide range of immune cells that build the immune defense
    keywords: cancer; cd8; cells; circrnas; circular; diseases; expression; functions; immune; macrophages; process; regulating; response; system; tumor
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        item: #980 of 1349
          id: cord-320501-xqgqq55q
      author: Theobald, Nigel
       title: Emerging vaccine delivery systems for COVID-19: Functionalised silica nanoparticles offer a potentially safe and effective alternative delivery system for DNA/RNA vaccines and may be useful in the hunt for a COVID-19 vaccine
        date: 2020-06-24
       words: 1204
      flesch: 41
     summary: A DNA/RNA vaccine introduces the DNA/RNA into the cell to produce the spike protein, which will then be internally processed by the cell and presented on the cell surface to immune cells. The presence of PEI will facilitate the endosomal disruption and release of nucleic acid but also presents a danger signal that will up regulate surface markers and hence attract immune cells and boost the immune response.
    keywords: cell; dna; rna; virus
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        item: #981 of 1349
          id: cord-320709-2pnqpljt
      author: Munster, Vincent J.
       title: Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis)
        date: 2016-02-22
       words: 3954
      flesch: 42
     summary: In vitro, the MERS-CoV spike glycoprotein interacted with Jamaican fruit bat (Artibeus jamaicensis) dipeptidyl peptidase 4 (DPP4) receptor and MERS-CoV replicated efficiently in Jamaican fruit bat cells, suggesting there is no restriction at the receptor or cellular level for MERS-CoV. MERS-CoV replicated efficiently to high titers in both cell lines (Fig. 1B) , indicating that there is no restriction at the receptor or cellular level for MERS-CoV replication in Jamaican fruit bat cells.
    keywords: bats; cells; coronavirus; cov; dpi; fruit; mers; middle; respiratory; syndrome
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        item: #982 of 1349
          id: cord-320713-b37c8aye
      author: Roberts, Lisa O.
       title: Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery
        date: 2009-10-27
       words: 20235
      flesch: 41
     summary: A study to understand the components of the eIF4F complex that are required for translation of viral mRNAs has recently demonstrated that influenza virus translation has no requirement for eIF4E, as viral mRNAs are translated in cells depleted of eIF4E and in cells treated with rapamycin. 48 Members of several different families of RNA viruses are able to bypass the canonical, cap-dependent, translation initiation process by employing this strategy of internal initiation of protein synthesis.
    keywords: binding; cells; cellular; cleavage; complex; eif4e; expression; host; host translation; human; infected; infection; ires; kinase; mechanisms; mrnas; pabp; phosphorylation; pkr; protein; protein synthesis; ribosomal; ribosome; rna; sequence; site; translation; translation initiation; virus; viruses
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        item: #983 of 1349
          id: cord-320921-eumuid3r
      author: Widagdo, W.
       title: Lack of Middle East Respiratory Syndrome Coronavirus Transmission in Rabbits
        date: 2019-04-24
       words: 4834
      flesch: 47
     summary: Using immunohistochemistry, we analyzed the DPP4 expression in rabbit respiratory tract tissues. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia Isolation of MERS coronavirus from a dromedary camel Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia Geographic distribution of MERS coronavirus among dromedary camels Zoonotic origin and transmission of Middle East respiratory syndrome coronavirus in the UAE Middle East respiratory syndrome coronavirus in dromedary camels: An outbreak investigation Reported Direct and Indirect Contact with Dromedary Camels among Laboratory-Confirmed MERS-CoV Cases Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis) Experimental Infection and Response to Rechallenge of Alpacas with Middle East Respiratory Syndrome Coronavirus Middle East respiratory syndrome coronavirus specific antibodies in naturally exposed Israeli llamas, alpacas and camels Infection, Replication, and Transmission of Middle East Respiratory Syndrome Coronavirus in Alpacas Asymptomatic Middle East respiratory syndrome coronavirus infection in rabbits Airborne transmission of influenza A/H5N1 virus between ferrets New case-Qatari Supreme Council of Health Pathogenesis and transmission of swine-origin 2009 A(H1N1) influenza virus in ferrets Differential Expression of the Middle East Respiratory Syndrome Coronavirus Receptor in the Upper Respiratory Tracts of Humans and Dromedary Camels Prophylaxis With a Middle East Respiratory Syndrome Coronavirus (MERS-CoV)-Specific Human Monoclonal Antibody Protects Rabbits From MERS-CoV Infection Enhanced inflammation in New Zealand white rabbits when MERS-CoV reinfection occurs in the absence of neutralizing antibody Deletion Variants of Middle East Respiratory Syndrome Coronavirus from Humans Epidemiology of a Novel Recombinant Middle East Respiratory Syndrome Coronavirus in Humans in Saudi Arabia Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels:
    keywords: cov; mers; nasal; rabbits; swabs; transmission; viral; virus
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        item: #984 of 1349
          id: cord-320935-3n157yl4
      author: Kumar, Manish
       title: Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic
        date: 2020-09-12
       words: 6629
      flesch: 37
     summary: Although SARS viruses are of zoonotic origin and several countries have already facing secondary transmission of SARS-COV-2, developing an early warning system always presents a challenge. Previous studies have highlighted the persistence of coronavirus and SARS virus in the wastewater, which ranged from hours to several days in the absence of disinfection practices [31, 37] .
    keywords: coronavirus; cov-2; covid-19; disease; infection; models; patients; population; sars; spread; temperature; time; transmission; virus; wastewater
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        item: #985 of 1349
          id: cord-321013-8pkrg0mx
      author: McBride, Ruth
       title: The Coronavirus Nucleocapsid Is a Multifunctional Protein
        date: 2014-08-07
       words: 10773
      flesch: 40
     summary: IBV N protein contains a functional nuclear export signal (NES) to traffic N protein to the cytoplasm [68, 71] , and an 8 amino acid NoRS motif at its NTD and is necessary and sufficient for nucleolar retention [68] . It has been proposed that the flexible, positively charged finger-like β-hairpin extension in the NTD of both IBV and SARS-CoV N protein is able to grasp RNA by neutralizing its phosphate groups, while the base moieties can make contact with exposed aromatic residues from the hydrophobic palm [16, 21] .
    keywords: assembly; binding; cell; coronavirus; cov; cov n; ctd; domain; interaction; localization; mhv; n protein; nucleocapsid; protein; residues; rna; sars; structure
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        item: #986 of 1349
          id: cord-321053-lgae22f8
      author: Gerold, Gisa
       title: Opportunities and Risks of Host-targeting Antiviral Strategies for Hepatitis C
        date: 2013-10-04
       words: 9425
      flesch: 38
     summary: Notably, recent evidence suggests that among the different factors of the VLDL pathway implicated in HCV virus production, only ApoE is absolutely essential, since production of infectious HCV can be reconstituted in an engineered human kidney derived cell line (293 T), which does not produce VLDL and lacks endogenous expression of MTTP and ApoB A recent study suggests that several lab-generated variants of SCARB1 all efficiently support HCV cell entry
    keywords: cell; effects; entry; factors; hcv; hepatitis; host; infection; inhibitors; mir-122; ns5a; patients; pi4kiiiα; replication; resistance; rna; therapy; treatment; virus
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        item: #987 of 1349
          id: cord-321155-dty18esg
      author: Zhang, Rongxin
       title: Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2
        date: 2020-06-05
       words: 4936
      flesch: 47
     summary: G-Quadruplex Telomere DNA-and TERRA-Binding Protein TLS/FUS G-quadruplex preferentially forms at the very 3′ end of vertebrate telomeric DNA An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation UTR of the BAG-1 mRNA affects both its cap-dependent and cap-independent translation through global secondary structure maintenance A Gquadruplex structure within the 5′-UTR of TRF2 mRNA represses translation in human cells RNA Gquadruplexes at upstream open reading frames cause DHX36-and DHX9-dependent translation of human mRNAs More Than Just a Kink in Microbial Genomes G-quadruplexes in viruses: function and potential therapeutic applications G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy The SARS-unique domain (SUD) of SARS coronavirus contains two macrodomains that bind G-quadruplexes LTR Reveals a (3 + 1) Folding Topology Containing a Stem-Loop U3 Region in the HIV-1 Genome Adopts a G-Quadruplex Structure in Its RNA and DNA Sequence HIV-1 Nucleocapsid Protein Unfolds Stable RNA G-Quadruplexes in the Viral Genome and Is Inhibited by G-Quadruplex Ligands Anti-HIV-1 activity of the G-quadruplex ligand BRACO-19 Zika Virus Genomic RNA Possesses Conserved G-Quadruplexes Characteristic of the Flaviviridae Family The effect of single nucleotide polymorphisms in G-rich regions of high-risk human papillomaviruses on structural diversity of DNA Chemical Targeting of a G-Quadruplex RNA in the Ebola Virus L Gene New scoring system to identify RNA G-quadruplex folding An <em&gt rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome UTR G-quadruplex structures acting as translational repressors Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations G-quadruplex DNA: a potential target for anti-cancer drug design Quadruplex nucleic acids as targets for anticancer therapeutics G-quadruplexes: We noticed that the PG4s in SARS-CoV-2 are all in the two-quartet style.
    keywords: cov-2; genome; human; pg4s; potential; quadruplexes; rna; sars; sequence; sud
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        item: #988 of 1349
          id: cord-321505-m40s6uw9
      author: Sakamoto, Naoya
       title: Inhibition of hepatitis C virus infection and expression in vitro and in vivo by recombinant adenovirus expressing short hairpin RNA
        date: 2007-08-07
       words: 4429
      flesch: 37
     summary: 14 Briefly, five siRNA targeting the 5′-UTR of HCV RNA were tested for their efficiency to inhibit HCV replication, and the most effective sequence, which targeted nucleotide position of 331 though 351, was used in the present study. Similarly, infection of AxshRNA-HCV into Huh7.5.1/ HCV-JFH1 cells specifically suppressed expression of HCV RNA (Fig. 6b) .
    keywords: adenovirus; cells; control; expression; fig; hcv; hepatitis; protein; replication; shrna; virus
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        item: #989 of 1349
          id: cord-321607-3r736dnk
      author: Ezelle, Heather J.
       title: The Roles of RNase-L in Antimicrobial Immunity and the Cytoskeleton-Associated Innate Response
        date: 2016-01-08
       words: 11712
      flesch: 34
     summary: Fractionation of the endonucleaseint system into two macromolecular components; role of a small molecule in nuclease activation Expression cloning of 2-5A-dependent RNaase: A uniquely regulated mediator of interferon action Germline mutations in the ribonuclease L gene in families showing linkage with HPC1 The role of 2 1 -5 1 oligoadenylate-activated ribonuclease L in apoptosis A study of the interferon antiviral mechanism: Apoptosis activation by the 2-5A system A dominant negative mutant of 2-5A-dependent RNase suppresses antiproliferative and antiviral effects of interferon Interferon action and apoptosis are defective in mice devoid of 2 1 ,5 1 -oligoadenylate-dependent RNase L Ribonuclease L proteolysis in peripheral blood mononuclear cells of chronic fatigue syndrome patients Characterization of a 2 1 ,5 1 -oligoadenylate (2-5A)-dependent 37-kDa RNase L: Azido photoaffinity labeling and 2-5A-dependent activation Biochemical evidence for a novel low molecular weight 2-5A-dependent RNase L in chronic fatigue syndrome Role of 2-5A-dependent RNase-L in senescence and longevity Defects in TLR3 expression and RNase L activation lead to decreased mnsod expression and insulin resistance in muscle cells of obese people RNase L controls terminal adipocyte differentiation, lipids storage and insulin sensitivity via CHOP10 mRNA regulation RNase L mediated protection from virus induced demyelination RNase-L deficiency exacerbates experimental colitis and colitis-associated cancer RNase L contributes to experimentally induced type 1 diabetes onset in mice RNase-L control of cellular mRNAs: Roles in biologic functions and mechanisms of substrate targeting An essential role for the antiviral endoribonuclease, RNase-L, in antibacterial immunity Small self-RNA generated by RNase L amplifies antiviral innate immunity RNase L interacts with filamin a to regulate actin dynamics and barrier function for viral entry RNase L induces autophagy via c-jun N-terminal kinase and double-stranded RNA-dependent protein kinase signaling pathways RNase L cleavage products promote switch from autophagy to apoptosis by caspase-mediated cleavage of beclin-1 Skin allograft rejection is suppressed in mice lacking the antiviral enzyme, 2 1 ,5 1 -oligoadenylate-dependent RNase L Lack of RNase L attenuates macrophage functions Interferons at age 50: Past, current and future impact on biomedicine Interferon-inducible antiviral effectors The human 2 1 ,5 1 -oligoadenylate synthetase family: Interferon-induced proteins with unique enzymatic properties The human 2 1 -5 1 oligoadenylate synthetase family: Unique bond formation Antiviral activity of human OASL protein is mediated by enhancing signaling of the RIG-I RNA sensor Activation of 2 1 -5 1 oligoadenylate synthetase by single-stranded and double-stranded RNA aptamers Selection and cloning of poly(rC)-binding protein 2 and raf kinase inhibitor protein RNA activators of 2 1 ,5 1 -oligoadenylate synthetase from prostate cancer cells Heterogeneous nuclear RNA from hairy cell leukemia patients activates 2 1 ,5 1 -oligoadenylate synthetase Ribosomal protein mRNAs are primary targets of regulation in RNase-L-induced senescence Germline mutation in RNase L predicts increased risk of head and neck, uterine cervix and breast cancer A bipartite model of 2-5A-dependent RNase L radiobinding and hplc analysis of 2-5A and related oligonucleotides from intact cells Identification of 2 1 -phosphodiesterase, which plays a role in the 2-5A system regulated by interferon Synthesis, characterization and properties of ppp(A2 1 p)nApCp and related high-specific-activity 32P-labelled derivatives of ppp(A2 1 p)nA The role of phosphodiesterase 12 (PDE12) as a negative regulator of the innate immune response and the discovery of antiviral inhibitors Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response Innate immune messenger 2-5A tethers human RNase L into active high-order complexes Dimeric structure of pseudokinase RNase L bound to 2-5A reveals a basis for interferon-induced antiviral activity Interferon action: RNA cleavage pattern of a (2 1 -5 1 )oligoadenylate-dependent endonuclease Interferon action-Sequence specificity of the ppp(A2 1 p)nA-dependent ribonuclease RNase L mediates the antiviral effect of interferon through a selective reduction in viral RNA during encephalomyocarditis virus infection RNase L attenuates mitogen-stimulated gene expression via transcriptional and post-transcriptional mechanisms to limit the proliferative response A transcriptional signaling pathway in the IFN system mediated by 2 1 -5 1 -oligoadenylate activation of RNase L Mapping of the human RNase L promoter and expression in cancer and normal cells Overexpression of the transcription factor sp1 activates the OAS-RNase L-RIG-I pathway Regulation of human RNase-L by the mir-29 family reveals a novel oncogenic role in chronic myelogenous leukemia Post-transcriptional regulation of RNase-L expression is mediated by the 3 1 -untranslated region of its mRNA Posttranscriptional regulation of cancer traits by HuR Proteasome-mediated degradation of RNase L in response to phorbol-12-myristate-13-acetate (PMA) treatment of mouse l929 cells Decreased proteasomal activity causes age-related phenotypes and promotes the development of metabolic abnormalities Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins Cloning and characterization of a RNase L inhibitor. RNase L inhibitor is induced during human immunodeficiency virus type 1 infection and down regulates the 2-5A/RNase L pathway in human T cells RNase L inhibitor (RLI) antisense constructions block partially the down regulation of the 2-5A/RNase L pathway in encephalomyocarditisvirus-(EMCV)-infected cells A newly discovered function for RNase L in regulating translation termination 2 1 ,5 1 -oligoadenylate-dependent RNase L is a dimer of regulatory and catalytic subunits Eukaryotic release factors (ERFS) history RNase Lregulates the stability of mitochondrial DNA-encoded mRNAs in mouse embryo fibroblasts Regulation of mitochondrial mRNA stability by RNase L is translation-dependent and controls IFNα-induced apoptosis Ultrastructural localization of interferon-inducible double-stranded RNA-activated enzymes in human cells Human 2 1 -phosphodiesterase localizes to the mitochondrial matrix with a putative function in mitochondrial RNA turnover The mRNA-destabilizing protein tristetraprolin is suppressed in many cancers, altering tumorigenic phenotypes and patient prognosis TTP): Interactions with mRNA and proteins, and current thoughts on mechanisms of action Zinc-finger antiviral protein mediates retinoic acid inducible gene I-like receptor-independent antiviral response to murine leukemia virus mRNA degradation by the endoribonuclease Regnase-1/ZC3H12a/MCPIP-1 RNase L activates the NLRP3 inflammasome during viral infections Enteropathogenic escherichia coli inhibits type I interferon-and RNase L-mediated host defense to disrupt intestinal epithelial cell barrier function Viral encounters with 2 1 ,5 1 -oligoadenylate synthetase and RNase L during the interferon antiviral response Interferon action: Binding of viral RNA to the 40-kilodalton 2 1 -5 1 -oligoadenylate synthetase in interferon-treated hela cells infected with encephalomyocarditis virus Natural occurrence of 2-5A in interferon-treated emc virus-infected l cells A phylogenetically conserved RNA structure in the poliovirus open reading frame inhibits the antiviral endoribonuclease RNase L Evasion of antiviral innate immunity by theiler's virus l* protein through direct inhibition of RNase L A viral RNA competitively inhibits the antiviral endoribonuclease domain of RNase L A putative loop E motif and an H-H kissing loop interaction are conserved and functional features in a group C enterovirus RNA that inhibits ribonuclease L Activation and evasion of the antiviral 2 1 -5 1 oligoadenylate synthetase/ribonuclease L pathway by hepatitis c virus mRNA Hepatitis c virus RNA: Dinucleotide frequencies and cleavage by RNase L Clinical relevance of the 2 1 -5 1 -oligoadenylate synthetase/RNase L system for treatment response in chronic hepatitis c RNase L targets distinct sites in influenza a virus RNAs The primary function of RNA binding by the influenza A virus NS1 protein in infected cells: Inhibiting the 2 1 -5 1 oligo (A) synthetase/RNase L pathway Mechanisms of IFN resistance by influenza virus Diagnostic value of the determination of an interferon-induced enzyme activity: Decreased 2 1 ,5 1 -oligoadenylate dependent binding protein activity in aids patient lymphocytes Antagonism of the interferon-induced OAS-RNase L pathway by murine coronavirus ns2 protein is required for virus replication and liver pathology Inhibition of the OAS/RNase L pathway by viruses Caspase-dependent apoptosis by 2 1 ,5 1 -oligoadenylate activation of RNase L is enhanced by IFN-β Viruses and the autophagy pathway RNase L triggers autophagy in response to viral infections The crosstalk between autophagy and apoptosis: Where does this lead Regulation of antiviral T cell responses by type I interferons Transcription factor STAT3 and type I interferons are corepressive insulators for differentiation of follicular helper and T helper
    keywords: actin; activation; activity; antiviral; binding; cell; cytoskeleton; expression; function; infection; interferon; lnx; protein; response; rig; rnase; rnase l; role; signaling; virus
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        item: #990 of 1349
          id: cord-321773-5fw9abzl
      author: Cheng, Wenyu
       title: DDX5 RNA Helicases: Emerging Roles in Viral Infection
        date: 2018-04-09
       words: 6757
      flesch: 42
     summary: DDX5 binds to the viral 3 -UTR and colocalize with viral RNA, which promotes virus RNA replication but not in viral protein translation. By exploiting the driving force of DDX5-mediated ATP hydrolysis or assembling large ribonucleoprotein complexes, RNA viruses can complete their life cycles.
    keywords: box; cells; ddx5; function; hcv; helicase; hepatitis; host; human; infection; proteins; replication; rev; rna; transcription; virus
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        item: #991 of 1349
          id: cord-321938-pda4a5n7
      author: Weisshoff, Hardy
       title: Aptamer BC 007 - Efficient binder of spreading-crucial SARS-CoV-2 proteins
        date: 2020-11-02
       words: 5099
      flesch: 47
     summary: Even though the RNA dependent RNA polymerase occurring peptidesequence, HRFYRLAN, showed the highest amount of folded BC 007, the maximal folding capacity was subsequently induced simply by adding 5 mM KCl to the peptide-aptamer mixture ( Figure 5A ). key: cord-321938-pda4a5n7 authors: Weisshoff, Hardy; Krylova, Oxana; Nikolenko, Heike; Düngen, Hans-Dirk; Dallmann, Andre; Becker, Susanne; Göttel, Peter; Müller, Johannes; Haberland, Annekathrin title: Aptamer BC 007 - Efficient binder of spreading-crucial SARS-CoV-2 proteins date: 2020-11-02 journal: Heliyon DOI: 10.1016/j.heliyon.2020.e05421 sha: doc_id: 321938 cord_uid: pda4a5n7 Corona virus disease 2019 (COVID-19) is a respiratory disease caused by a new coronavirus (SARS-CoV-2) which causes significant morbidity and mortality.
    keywords: 007; aptamer; binding; cov-2; data; hrfyrlan; peptide; polymerase; protein; rna; sars
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        item: #992 of 1349
          id: cord-321957-ybtk9cp1
      author: Carey, Brian D.
       title: Protein Kinase C subtype δ interacts with Venezuelan equine encephalitis virus capsid protein and regulates viral RNA binding through modulation of capsid phosphorylation
        date: 2020-03-09
       words: 6736
      flesch: 45
     summary: Protein Kinase C modulates VEEV capsid phosphorylation However, it should be noted that a similar phenomenon was observed for SINV (27). To determine the impact of VEEV capsid phosphorylation on vRNA binding, we utilized quantitative RNA-IP experiments to probe the interaction between the capsid protein and the vRNA at sites identified as highly enriched, intermediately enriched, and non-enriched by our CLIP-seq studies.
    keywords: anti; binding; capsid; cells; cpd; data; fig; kinase; phosphorylation; pkcδ; protein; rna; tc-83; veev; virus
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        item: #993 of 1349
          id: cord-322062-nnefbeo6
      author: Tam, Albert W.
       title: Hepatitis E virus (HEV): Molecular cloning and sequencing of the full-length viral genome
        date: 1991-11-30
       words: 5759
      flesch: 39
     summary: With the acquisition of BET-SPl, the composite cDNA map (omitting overlaps) spanned approximately 7.4 kb from the 5' end of BET-SPl to the polyadenylated 3'end of clone BET1 ; in good agreement with the maximum length of HEV RNA as detected on Northern blots. These findings on the genetic organization and expression strategy of HEV suggest that it is the prototype human pathogen for a new class of RNA virus or perhaps a separate genus within the Caliciviridae family Viral hepatitis results from infection with one of at least four very different viral agents.
    keywords: cdna; end; fig; genome; hepatitis; hev; non; orf2; rna; sequence; virus
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        item: #994 of 1349
          id: cord-322084-gkg1059v
      author: JEONG, YONG SEOK
       title: Coronavirus Transcription Mediated by Sequences Flanking the Transcription Consensus Sequence
        date: 1996-03-01
       words: 6362
      flesch: 43
     summary: By using PCR-based sequences flanking the same intergenic region between site-directed mutagenesis, a 12-nucleotide-long segenes 6 and 7 do not affect the efficiency of subgenomic quence, TCTAATCTAAAC, was inserted into DI cDNA DI RNA transcription (Makino and Joo, 1993) . To directly compare the efficiency of subgenomic DI RNA transcription, we used RNAs were synthesized in vitro and transfected by lipofection into DBT cell monolayers that were infected with the same membrane in the experiments documented in Figs.
    keywords: fdi; flanking; intergenic; mhv; rna; rnas; sequence; subgenomic; transcription
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        item: #995 of 1349
          id: cord-322206-roxa3ix6
      author: I. Sardi, Silvia
       title: High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics
        date: 2020-07-21
       words: 4203
      flesch: 39
     summary: Virome of > 12 thousand Culex mosquitoes from throughout California Southern tomato virus: The link between the families Totiviridae and Partitiviridae Expanding our Understanding of the Seaweed Holobiont: RNA Viruses of the Red Alga Delisea pulchra This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license We thank all the members of Virology and Allergy and Acarology laboratories. Due to their worldwide occurrence and fast adaptation to environmental changes, mosquitoes from the Aedes genus play an important role in the transmission of viral etiological agents of emerging human infections, including Dengue virus (DENV), Zika virus (ZIKV), Chikungunya virus (CHYKV) and 2 of 10 Yellow fever virus (YFV)
    keywords: analysis; figure; genomes; reads; regions; rna; sequences; sequencing; virus; viruses; zika
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        item: #996 of 1349
          id: cord-322234-1zyy536y
      author: Lorusso, Alessio
       title: One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples
        date: 2009-12-17
       words: 4171
      flesch: 40
     summary: In that case, two consequences will be obvious: first, a reservoir of H1N1 virus in the swine population poses an elevated risk for human infection via aerosol transmission from clinically ill pigs, and second, dramatic economic losses for the pork industry due to direct disease related costs as well as indirect market losses. Although the 2009 H1N1 is related genetically to swine influenza viruses, human infection has not been connected to pig exposure.
    keywords: assay; h1n1; influenza; pandemic; pcr; pigs; rna; swine; virus; viruses
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        item: #997 of 1349
          id: cord-322240-z8zkl2xh
      author: Maeda, Ken
       title: Isolation of Novel Adenovirus from Fruit Bat (Pteropus dasymallus yayeyamae)
        date: 2008-02-17
       words: 1689
      flesch: 42
     summary: Until now, a number of RNA viruses have been isolated from bats, but isolation of DNA virus is rare (1) . The isolation of the novel adenovirus seems to be possible because of usage of the primary cells originated from the host; DNA viruses might have more restricted host range than RNA viruses and require host-originated cells for the growth.
    keywords: adenovirus; bats; oxacin; rna; rv1; viruses
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        item: #998 of 1349
          id: cord-322410-k23engcx
      author: Naguib, Mahmoud M.
       title: New real time and conventional RT-PCRs for updated molecular diagnosis of infectious bronchitis virus infection (IBV) in chickens in Egypt associated with frequent co-infections with avian influenza and Newcastle Disease viruses
        date: 2017-03-21
       words: 5022
      flesch: 43
     summary: Conventional RT-PCRs amplifying hypervariable regions (HVRs 1–2 and 3) of the IBV S1 gene were developed and amplificates used for nucleotide sequence-based typing of IBV field strains in Egyptian chickens directly from clinical samples. No RT-PCR amplicates were obtained from two further samples that showed Cq values <32 in IBV RT-qPCR; failure to amplify IBV S1-specific RNA from these samples may be related to advanced RNA degradation.
    keywords: avian; bronchitis; egypt; egyptian; ibv; rna; samples; specific; virus; viruses
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        item: #999 of 1349
          id: cord-322756-ouvn71r9
      author: Chow, Michael Y.T.
       title: Inhaled RNA Therapy: From Promise to Reality
        date: 2020-09-04
       words: 7289
      flesch: 36
     summary: In this review, we highlight recent developments in pulmonary RNA delivery systems with the use of nonviral vectors. In this review, we highlight recent developments in pulmonary RNA delivery systems with the use of nonviral vectors.
    keywords: administration; cell; delivery; gene; lung; mrna; naked; pulmonary; rna; sirna; studies; table; therapy; transfection; use; vectors
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        item: #1000 of 1349
          id: cord-323029-7hqp8xuq
      author: Bognár, Zsófia
       title: Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications
        date: 2020-08-11
       words: 19355
      flesch: 41
     summary: In case of IgE aptamers, however, a salt induced aggregation can readily occur due to intermolecular hybridization of the AuNP modifying aptamer strands that was called hairpin aptamer sticky-end pairing effect by the authors. A method with wide applicability was published by He et al. where a mixture of fluorescentand quencher-labeled nucleic acid strands were able to hybridize to IgE aptamers in the absence of the target molecule bringing the labels in close proximity, which results in a very low fluorescence backgorund signal.
    keywords: acid; affinity; amplification; antibodies; antibody; aptamer; assay; binding; complex; concentration; detection; dna; figure; fluorescence; gold; human; ige; ige aptamer; ige binding; ige detection; igg; immunoglobulin; method; nanoparticles; protein; selection; signal; specific; surface; target
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        item: #1001 of 1349
          id: cord-323585-iv2dcpqj
      author: Li, Su
       title: eEF1A Interacts with the NS5A Protein and Inhibits the Growth of Classical Swine Fever Virus
        date: 2015-08-10
       words: 6175
      flesch: 52
     summary: In The Springer Index of Viruses Pestivirus internal ribosome entry site (IRES) structure and function: Elements in the 5 1 -untranslated region important for IRES function Specific interaction between the classical swine fever virus NS5B protein and the viral genome Essential and nonessential elements in the 3 1 nontranslated region of bovine viral diarrhea virus Characterization of NS3, NS5A and NS5B of classical swine fever virus through mutation and complementation analysis Classical swine fever virus NS5A regulates viral RNA replication through binding to NS5B and 3 1 UTR The NS5A protein of hepatitis C virus is a zinc metalloprotein Hepatitis C virus (HCV) NS5A protein downregulates HCV IRES-dependent translation Hepatitis C virus NS5A protein down-regulates the expression of spindle gene Aspm through PKR-p38 signaling pathway Interaction of hepatitis C virus nonstructural protein 5A with core protein is critical for the production of infectious virus particles Domain III of NS5A contributes to both RNA replication and assembly of hepatitis C virus particles Regulation of the production of infectious genotype 1a hepatitis C virus by NS5A domain III Influence of NS5A protein of classical swine fever virus (CSFV) on CSFV internal ribosome entry site-dependent translation Determination of the amounts of the protein synthesis initiation and elongation factors in wheat germ Elongation factor 1 alpha, translation and the cytoskeleton Thinking Outside the Ribosome Actin bundling and polymerisation properties of eukaryotic elongation factor 1 alpha (eEF1A), histone H2A-H2B and lysozyme in vitro The many roles of the eukaryotic elongation factor 1 complex Translation elongation factor 1A facilitates the assembly of the tombusvirus replicase and stimulates minus-strand synthesis Inhibition of ER stress-mediated apoptosis in macrophages by nuclear-cytoplasmic relocalization of eEF1A by the HIV-1 Nef protein Eukaryotic elongation factor 1 complex subunits are critical HIV-1 reverse transcription cofactors The NS5A protein of bovine viral diarrhoea virus interacts with the alpha subunit of translation elongation factor-1 Evaluation of a multiplex real-time RT-PCR for quantitative and differential detection of wild-type viruses and C-strain vaccine of classical swine fever Screening of cellular proteins that interact with the classical swine fever virus non-structural protein 5A by yeast two-hybrid analysis Heat shock protein 70 is associated with CSFV NS5A protein and enhances viral RNA replication The nucleocapsid protein of severe acute respiratory syndrome coronavirus inhibits cell cytokinesis and proliferation by interacting with translation elongation factor 1alpha EF1A interacting with nucleocapsid protein of transmissible gastroenteritis coronavirus and plays a role in virus replication Identification of cis-acting nucleotides and a structural feature in West Nile virus 3 1 -terminal RNA that facilitate viral minus strand RNA synthesis Eukaryotic elongation factor 1A interacts with Turnip mosaic virus RNA-dependent RNA polymerase and VPg-Pro in virus-induced vesicles In vivo interaction between Tobacco mosaic virus RNA-dependent RNA polymerase and host translation elongation factor 1A Translation elongation factor 1A is a component of the tombusvirus replicase complex and affects the stability of the p33 replication cofactor Hepatitis C virus NS4A inhibits cap-dependent and the viral IRES-mediated translation through interacting with eukaryotic elongation factor 1A RNA-mediated response to heat shock in mammalian cells Translation elongation factor-1 alpha interacts with the 3 1 stem-loop region of West Nile virus genomic RNA Interaction between the cellular protein eEF1A and the 3 1 -terminal stem-loop of West Nile virus genomic RNA facilitates viral minus-strand RNA synthesis A simple method of estimating fifty percent endpoints Thioredoxin 2 is a novel E2-interacting protein that inhibits the replication of classical swine fever virus Modulation of translation initiation efficiency in classical swine fever virus Rapid recovery of classical swine fever virus directly from cloned cDNA We thank Graham J. Belsham from the National Veterinary Institute, Technical University of Denmark, for kindly providing the plasmid pFluc/IRES/Rluc. To examine the colocalization of NS5A protein with eEF1A, the subcellular localization of 3ˆFlag-NS5A and Myc-eEF1A was examined by confocal microscopy.
    keywords: anti; catalog; cells; csfv; eef1a; figure; ires; myc; ns5a; protein; replication; rna; virus
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        item: #1002 of 1349
          id: cord-323668-evzzfu04
      author: Yin, Zhixin
       title: lncRNA expression signatures in response to enterovirus 71 infection
        date: 2013-01-11
       words: 3513
      flesch: 46
     summary: To identify the cellular long noncoding RNAs (lncRNAs) involved in the host response to EV71 infection, we performed comprehensive lncRNA and mRNA profiling in EV71-infected rhabdomyosarcoma cells through microarray. The results provided information for further research on the prevention and treatment of EV71 infection, as well as on distinguishing severe and mild EV71 cases.
    keywords: analysis; cells; ev71; expression; genes; host; infection; lncrnas; pairs; response
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        item: #1003 of 1349
          id: cord-323691-5s5almd2
      author: Mishin, Vasiliy P
       title: A ‘minimal’ approach in design of flavivirus infectious DNA
        date: 2001-12-04
       words: 5068
      flesch: 41
     summary: Hum Intron insertion facilitates amplification of cloned virus cDNA in Escherichia coli while biological activity is reestablished after transcription in vivo An enhancer in the first intron of the human purine nucleoside phosphorylase-encoding gene Synthesis and characterization of an infectious dengue virus type-2 RNA genome Phylogeny of the genus Flavivirus Construction of a stable and highly infectious intron-containing cDNA clone of plum pox potyvirus and its use to infect plants by particle bombardment An artificial enhancer with multiple response elements stimulates prokaryotic transcriptional activation medicated by various regulatory proteins Nucleotide sequence of the virulent SA-14 strain of Japanese encephalitis virus and its attenuated vaccine derivative, SA-14-14-2 Nucleotide sequence and infectious cDNA clone of the L1 isolate of Pea seed-borne mosaic potyvirus Infectious RNA transcripts from full-length dengue virus type 2 cDNA clones made in yeast In vitro processing of dengue virus type 2 nonstructural proteins NS2A, NS2B, and NS3 Cloned poliovirus complementary DNA is infectious in mammalian cells Flaviviridae: the viruses and their replication Transcription of infectious yellow fever RNA from fulllength cDNA templates produced by in vitro ligation Modulations of the in vitro translational efficiencies of Yellow Fever virus mRNAs: interactions between coding and noncoding regions Assaying the polyadenylation state of mRNAs Molecular Cloning: A Laboratory Manual Alphavirus vectors for gene expression and vaccines Production of infectious poliovirus from cloned cDNA is dramatically increased by SV40 transcription and replication signals Infectious Japanese encephalitis virus RNA can be synthesized from in vitro-ligated cDNA templates Complete nucleotide sequence of the Japanese encephalitis virus genome RNA Promoter-regulatory region of the major immediate early gene of human cytomegalovirus Stable high-level expression of heterologous genes In vitro and In vivo by noncytopathic DNA-based kunjin virus replicon vectors A new strategy in design of +RNA virus infectious clones enabling their stable propagation in E. coli We thank Dr S. Schlesinger for BHK-21 cells, Dr D. Trent for pM343 and pH756 plasmids, and Jennifer Ascañ o for help in manuscript preparation. key: cord-323691-5s5almd2 authors: Mishin, Vasiliy P; Cominelli, Fabio; Yamshchikov, Vladimir F title: A ‘minimal’ approach in design of flavivirus infectious DNA date: 2001-12-04 journal: Virus Research DOI: 10.1016/s0168-1702(01)00371-9 sha: doc_id: 323691 cord_uid: 5s5almd2 Abstract The ‘infectious DNA’ approach, which is based on in vivo transcription of (+)RNA virus genome cDNA cassettes from eukaryotic promoters in transfected cells, became a popular alternative to the classical scheme in the infectious clone methodology.
    keywords: cells; cmv; dna; genome; infectious; plasmid; promoter; rna; virus
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        item: #1004 of 1349
          id: cord-323737-6ajqy0ch
      author: Jiang, Yuanyuan
       title: Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus
        date: 2020-10-04
       words: 6807
      flesch: 40
     summary: All seven of these drugs are adenosine receptor agonists that were clinically investigated for treating various diseases, including cardiac arrhythmias, neuropathic pain, inflammatory diseases, and cancer (Gao & Jacobson, 2011; Jacobson et al., 2019) . These 2 0 -O-MTases regulate important cellular functions, and are associated with developmental disorders and cancer (B€ ugl et al., 2000; Hager et al., 2002; Lee & Bogenhagen, 2014; Ringeard et al., 2019) .
    keywords: analysis; binding; compounds; cov-2; drugs; et al; figure; hesperidin; mtase; nsp16; protein; rna; sam; sars
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        item: #1005 of 1349
          id: cord-323756-atnrw9ew
      author: Vabret, Nicolas
       title: Sensing Microbial RNA in the Cytosol
        date: 2013-12-25
       words: 6419
      flesch: 31
     summary: A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells Length-dependent recognition of double-stranded ribonucleic acids by retinoic acid-inducible gene-I and melanoma differentiation-associated gene Nonself RNA-sensing mechanism of RIG-I helicase and activation of antiviral immune responses The thermodynamic basis for viral RNA detection by the RIG-I innate immune sensor RIG-I detects viral genomic RNA during negative-strand RNA virus infection Incoming RNA virus nucleocapsids containing a 5'-triphosphorylated genome activate RIG-I and antiviral signaling Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing Epstein-Barr virus-encoded small RNA induces IL-10 through RIG-I-mediated IRF-3 signaling Adenovirus virus-associated RNAs induce type I interferon expression through a RIG-I-mediated pathway The 5' ends of RNA oligonucleotides in Escherichia coli and mRNA degradation Extracellular and intracellular pattern recognition receptors cooperate in the recognition of Helicobacter pylori IFNgamma inhibits the cytosolic replication of Shigella flexneri via the cytoplasmic RNA sensor RIG-I Essential role of mda-5 in type I IFN responses to polyriboinosinic:polyribocytidylic acid and encephalomyocarditis picornavirus Structural basis for dsRNA recognition, filament formation, and antiviral signal activation by MDA5 Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses Activation of MDA5 requires higher-order RNA structures generated during virus infection MDA5 detects the double-stranded RNA replicative form in picornavirus-infected cells Innate immune response after adenoviral gene delivery into skin is mediated by AIM2, NALP3, DAI and mda5 Visualisation of direct interaction of MDA5 and the dsRNA replicative intermediate form of positive strand RNA viruses Activation of IFN-&#946; expression by a viral mRNA through RNase L and MDA5 New insights into the role of RNase L in innate immunity Ribose 2'-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5 MAVS forms functional prion-like aggregates to activate and propagate antiviral innate immune response Intracellular pathogen detection by RIG-I-like receptors The adaptor MAVS promotes NLRP3 mitochondrial localization and inflammasome activation Recognition of RNA virus by RIG-I results in activation of CARD9 and inflammasome signaling for interleukin 1 beta production Type I IFN triggers RIG-I/TLR3/NLRP3-dependent inflammasome activation in influenza A virus infected cells The RIG-I-like receptor LGP2 recognizes the termini of double-stranded RNA The regulatory domain of the RIG-I family ATPase LGP2 senses doublestranded RNA LGP2 is a positive regulator of RIG-I-and MDA5-mediated antiviral responses ATP hydrolysis enhances RNA recognition and antiviral signal transduction by the innate immune sensor, laboratory of genetics and physiology 2 (LGP2) RNA ligands can be generated by DNA viruses and retroviruses via genome transcription, or by synthesis of mRNA and replication intermediates by RNA-dependent RNA polymerases (RdRps) of RNA viruses (8) .
    keywords: activation; cells; cytosolic; dsrna; ifn; infection; mda5; microbial; protein; recognition; rig; rna; virus; viruses
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        item: #1006 of 1349
          id: cord-323845-s78t5qxj
      author: Soliman, H.
       title: Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS)
        date: 2006-05-31
       words: 3912
      flesch: 43
     summary: The specificity of the VHS-LAMP primers and conditions to VHS virus was confirmed by its aptitude to amplify only RNA from VHS virus serotypes, with no amplification of IHNVor non-infected fish (Fig. 5) . Agarose gel highlighting the specificity of the RT-LAMP primers to VHS virus RNA.
    keywords: amplification; detection; lamp; loop; reaction; rna; vhs; virus
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        item: #1007 of 1349
          id: cord-323973-wszo9s3d
      author: Zhu, Hanliang
       title: The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond
        date: 2020-07-20
       words: 9786
      flesch: 42
     summary: This is an old technique that was used in the early days of PCR systems, with three baths with different temperatures and a laboratory technician or robot to move a basket with samples from bath to bath. There was another push to release PCR systems for POC applications and this has contributed to disease diagnosis during pandemics such as the 2014 Ebola outbreak.
    keywords: amplification; analysis; cartridge; chamber; chip; detection; dna; nucleic; pcr; poc; polymerase; preparation; reaction; rna; sample; system; temperature; test; time; viral; virus
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        item: #1008 of 1349
          id: cord-323987-gh1m05gi
      author: Dziąbowska, Karolina
       title: Detection Methods of Human and Animal Influenza Virus—Current Trends
        date: 2018-10-18
       words: 11146
      flesch: 43
     summary: Influenza Other Respir Bioassay Development for Ultrasensitive Detection of Influenza A Nucleoprotein Using Digital ELISA Highly sensitive colorimetric immunosensor for influenza virus H5N1 based on enzyme-encapsulated liposome A highly sensitive europium nanoparticle-based immunoassay for detection of influenza A/B virus antigen in clinical specimens Identification and subtyping of avian influenza viruses by reverse transcription-PCR Evaluation of saliva as diagnostic materials for influenza virus infection by PCR-based assays Nucleic acid dipstick test for molecular diagnosis of pandemic H1N1 Development and evaluation of a real-time nucleic acid sequence based amplification assay for rapid detection of influenza A Detection of human influenza A viruses by loop-mediated isothermal amplification Development and evaluation of reverse transcription loop-mediated isothermal amplification assay for rapid and real-time detection of the swine-origin influenza A H1N1 virus Comparison of Next-Generation Sequencing Systems A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing Electrochemical Sensors for Detections of Influenza Viruses: Fundamentals and Applications Novel Nano Biosensor Developed for Rapid Detection of Flu Virus Applying the miniaturization technologies for biosensor design Rapid detection for primary screening of influenza A virus: Microfluidic RT-PCR chip and electrochemical DNA sensor Use of semiconductor-based oligonucleotide microarrays for influenza a virus subtype identification and sequencing Detection of viruses with molecularly imprinted polymers integrated on a microfluidic biochip using contact-less dielectric microsensors Evaluation of a smartphone-based rapid fluorescent diagnostic system for H9N2 virus in specific-pathogen-free chickens A paper-based microfluidic Dot-ELISA system with smartphone for the detection of influenza A. Microfluid Electrochemical assay to detect influenza viruses and measure drug susceptibility The phenomenon of fluorescence in immunosensors Electrochemical Sensors and Biosensors for Influenza Detection-Literature Survey Direct and label-free influenza virus detection based on multisite binding to sialic acid receptors A rapid-response ultrasensitive biosensor for influenza virus detection using antibody modified boron-doped diamond A PCR-free point-of-care capacitive immunoassay for influenza A virus Electrochemical immunosensor for detection of antibodies against influenza A virus H5N1 in hen serum An amplified electrochemical immunosensor based on in situ-produced 1-naphthol as electroactive substance and graphene oxide and Pt nanoparticles functionalized CeO2 nanocomposites as signal enhancer Dual immunosensor based on methylene blue-electroadsorbed graphene oxide for rapid detection of the influenza A virus antigen Label-free Detection of Influenza Viruses using a Reduced Graphene Oxide-based Electrochemical Immunosensor Integrated with a Microfluidic Platform Highly sensitive detection of influenza virus by boron-doped diamond electrode terminated with sialic acid-mimic peptide Universal biosensor for detection of influenza virus Electrochemical Biosensing for the Diagnosis of Viral Infections and Tropical Diseases Electrochemical biosensing of influenza A subtype genome based on meso/macroporous cobalt (II) oxide nanoflakes-applied to human samples Role of metal and metal oxide nanoparticles as diagnostic and therapeutic tools for highly prevalent viral infections Amperometric bioaffinity sensing platform for avian influenza virus proteins with aptamer modified gold nanoparticles on carbon chips Carbon nanotag based visual detection of influenza A virus by a lateral flow immunoassay In situ self-assembly of gold nanoparticles on hydrophilic and hydrophobic substrates for influenza virus-sensing platform Highly Uniform Gold Nanobipyramids for Ultrasensitive Colorimetric Detection of Influenza Virus Hewlett, I. Sensitive detection of influenza viruses with Europium nanoparticles on an epoxy silica sol-gel functionalized polycarbonate-polydimethylsiloxane hybrid microchip Aptasensors for Detection of Avian Influenza Virus H5N1 Rapid detection of avian influenza virus H5N1 in chicken tracheal samples using an impedance aptasensor with gold nanoparticles for signal amplification Aptamer-based 'point-of-care testing Specific Recognition of Human Influenza Virus with PEDOT Bearing Sialic Acid-Terminated Trisaccharides Silver nanoparticles coated graphene electrochemical sensor for the ultrasensitive analysis of avian influenza virus H7 A nanohybrid of platinum nanoparticles-porous ZnO-hemin with electrocatalytic activity to construct an amplified immunosensor for detection of influenza LabVIEW-based impedance biosensing system for detection of avian influenza virus A multi-virus detectable microfluidic electrochemical immunosensor for simultaneous detection of H1N1, H5N1, and H7N9 virus using ZnO nanorods for sensitivity enhancement Label-free electrochemical detection of neuraminidase activity: A facile whole blood diagnostic probe for infectious diseases Ultrasensitive detection of influenza viruses with a glycan-based impedimetric biosensor Influenza A Virus-Host Protein Interactions Control Viral Pathogenesis Immunomodulatory Nonstructural Proteins of Influenza A Viruses Identification of Novel Influenza A Virus Proteins Translated from PA mRNA PA-X is a virulence factor in avian H9N2 influenza virus Direct electrochemical detection of PB1-F2 protein of influenza A virus in infected cells Extrinsic surface-enhanced Raman scattering detection of influenza A virus enhanced by two-dimensional gold@silver core-shell nanoparticle arrays Surface-enhanced Raman scattering based lateral flow immunochromatographic assay for sensitive influenza detection Fluorescent Neuraminidase Assay Based on Supramolecular Dye Capture After Enzymatic Cleavage A promising magnetic SERS immunosensor for sensitive detection of avian influenza virus Early Diagnosis of Influenza Virus A Using Surface-enhanced Raman Scattering-based Lateral Flow Assay Rapid detection of avian influenza A virus by immunochromatographic test using a novel fluorescent dye Enhanced catalytic activity of gold nanoparticle-carbon nanotube hybrids for influenza virus detection Detection of influenza virus using peroxidase-mimic of gold nanoparticles Upconversion luminescence resonance energy transfer (LRET)-based biosensor for rapid and ultrasensitive detection of avian influenza virus H7 subtype Detection and differentiation of influenza viruses with glycan-functionalized gold nanoparticles Neuraminidase Resistant Sialosides for the Detection of Influenza Viruses
    keywords: acid; amplification; analysis; antibodies; assay; authors; detection; diagnosis; gold; influenza; influenza virus; methods; pcr; rapid; results; sensitivity; sensor; surface; tests; time; virus; viruses
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        item: #1009 of 1349
          id: cord-324137-nau83mjv
      author: Saranathan, Nandhini
       title: G-Quadruplexes: More Than Just a Kink in Microbial Genomes
        date: 2018-09-14
       words: 6751
      flesch: 38
     summary: An earlier study reports that, following concatemeric replication of HHV-1, the cleavage of unit length genomes and their encapsidation is achieved by the binding of virus proteins to a DNA secondary structure formed by a DNA packaging sequence (pac-1) Taken together, these results suggest that G4s in virus genomes may interact with host proteins not only to facilitate virus latency but also to revoke viruses from latency.
    keywords: binding; dna; g4s; gene; genome; host; motifs; promoter; proteins; quadruplex; recombination; replication; rna; structures; transcription; virus
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        item: #1010 of 1349
          id: cord-324212-aqp73hi9
      author: Wyszko, Eliza
       title: Leadzyme formed in vivo interferes with tobacco mosaic virus infection in Nicotiana tabacum
        date: 2006-10-09
       words: 4475
      flesch: 53
     summary: TMV genomic RNA is enclosed within the protein capsid, and as a result, leadzyme formation and TMV RNA cleavage is possible only within host cells. Thirty thousand counts per minute of the labeled and 250 nm unlabeled RNA substrate was mixed with 25 lm RNA leadzyme catalytic strand, heated up to 90°C for 2 min, cooled slowly (1°C AEmin )1 ) to 25°C, and incubated at 25°C for 60 min.
    keywords: catalytic; cleavage; fig; leadzyme; leaves; rna; tmv; tobacco; virus
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        item: #1011 of 1349
          id: cord-324324-8ybfiz8f
      author: Decaro, Nicola
       title: Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses
        date: 2020-04-14
       words: 14950
      flesch: 34
     summary: After 2002-2003 SARS epidemic, the renovated interest in HCoVs allowed the discovery of two additional viruses, the alphacoronavirus HCoV-NL63 and the betacoronavirus HCoV-HKU1, derived from bats and rodents, respectively (Tao et al., 2017) . NL63 (Tao et al., 2017) .
    keywords: animals; avian; bats; betacoronavirus; canine; ccov; china; coronavirus; cov; cov-2; covs; disease; enteric; et al; gene; genome; genus; host; human; ibv; infection; mers; novel; origin; protein; recombination; sars; species; strains; subgenus; syndrome; viruses; wild
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        item: #1012 of 1349
          id: cord-324495-0pee1i3o
      author: Kang, Hyeonjeong
       title: Sasa quelpaertensis Nakai extract suppresses porcine reproductive and respiratory syndrome virus replication and modulates virus-induced cytokine production
        date: 2015-06-06
       words: 6132
      flesch: 43
     summary: Our results demonstrated that SQE treatment suppressed the replication of PRRSV in a dose-dependent manner. PAM-KNU cells were infected with PRRSV along with SQE treatment as described above.
    keywords: cells; infection; knu; pam; porcine; presence; prrsv; replication; rna; sqe; syndrome; virus
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        item: #1013 of 1349
          id: cord-324638-gwd8qin6
      author: Chiu, Rossa WK
       title: Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study
        date: 2006-02-09
       words: 3361
      flesch: 43
     summary: WHO: Summary of probable SARS cases with onset of illness from 1 A major outbreak of severe acute respiratory syndrome in Hong Kong Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome Serial analysis of the plasma concentration of SARS coronavirus RNA in pediatric patients with severe acute respiratory syndrome Effects of early corticosteroid treatment on plasma SARSassociated Coronavirus RNA concentrations in adult patients Fully automated nucleic acid extraction: MagNA Pure LC SARS molecular detection external quality assurance A new biometrical procedure for testing the equality of measurements from two different analytical methods. For serum SARS-CoV concentration at 10 5 copies/mL, the assay coefficient of variation was 47.4% for the manual RNA extraction and 51.0% when automated RNA extraction was used.
    keywords: cov; extraction; kit; protocol; rna; sars
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        item: #1014 of 1349
          id: cord-324640-2zhaknbi
      author: Munday, Diane C.
       title: Quantitative Proteomic Analysis of A549 Cells Infected with Human Respiratory Syncytial Virus
        date: 2010-07-20
       words: 12374
      flesch: 31
     summary: The relative level of host cell proteins can have a direct effect on HRSV disease progression where secondary bacterial infections are observed. These included mitochondrial proteins, cell cycle regulatory proteins, ND10s, components of the nuclear pore complex, and nucleocytoplasmic trafficking proteins.
    keywords: a549; abundance; analysis; cells; complex; cytoplasmic; data; fig; fraction; host; hrsv; infection; mock; nuclear; nucleus; pml; pore; proteins; response; rna; study; virus
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        item: #1015 of 1349
          id: cord-324697-c0dv1zmi
      author: Rodriguez, William
       title: Fated for decay: RNA elements targeted by viral endonucleases
        date: 2020-06-07
       words: 6417
      flesch: 43
     summary: Furthermore, while this review focuses on host RNA elements that escape viral endonucleases, there also exist several examples of RNA structures that escape from host nucleases to benefit viral infection. mRNA degradation by the virion host shutoff (Vhs) protein of herpes simplex virus: genetic and biochemical evidence that Vhs is a nuclease Lytic KSHV infection inhibits host gene expression by accelerating global mRNA turnover Host shutoff during productive Epstein-Barr virus infection is mediated by BGLF5 and may contribute to immune evasion An overlapping protein-coding region in influenza A virus segment 3 modulates the host response C19ORF66 broadly escapes viral-induced endonuclease cleavage and restricts Kaposi sarcoma associated herpesvirus (KSHV) Transcriptome-wide cleavage site mapping on cellular mRNAs reveals features underlying sequence-specific cleavage by the viral ribonuclease SOX The influenza a virus endoribonuclease PA-X usurps host mRNA processing machinery to limit host gene expression Selective degradation of host RNA polymerase II transcripts by influenza a virus PA-X host shutoff protein KSHV SOX mediated host shutoff: the molecular mechanism underlying mRNA transcript processing Nuclease escape elements protect messenger RNA against cleavage by multiple viral endonucleases Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX RNA splicing by the spliceosome RNA localization: making its way to the center stage Communication is key: 5″-3″ interactions that regulate mRNA translation and turnover The hDcp2 protein is a mammalian mRNA decapping enzyme XRN 5″→3″ exoribonucleases: structure, mechanisms and functions Decapitation: poxvirus makes RNA lose its head Characterization of a second vaccinia virus mRNA-decapping enzyme conserved in poxviruses Vaccinia virus D10 protein has mRNA decapping activity, providing a mechanism for control of host and viral gene expression The Nudix hydrolase superfamily Decapping the message: a beginning or an end
    keywords: cleavage; decay; elements; expression; gene; host; mrna; protein; rna; sox; targeting; vhs; virus
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        item: #1016 of 1349
          id: cord-324928-cpryxa6p
      author: Lello, Laura Sandra
       title: Cross-utilisation of template RNAs by alphavirus replicases
        date: 2020-09-04
       words: 13793
      flesch: 45
     summary: For making SINV/CHIKV swapped templates the region corresponding to the 5' end of CHIKV template RNA was extended from nucleotide 307 to nucleotide 412; obtained plasmid was designated as HSPolI-FG-C � CC. Mutations introduced into these elements had a severe impact on template RNA replication and on the rescue of recombinant SINV from infectious transcripts.
    keywords: alphaviruses; cells; chikv; expression; fig; hspoli; human; onnv; replicase; replication; rna; rnas; sfv; sinv; template; template rna; trans; virus
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        item: #1017 of 1349
          id: cord-324944-ixh3ykrc
      author: Mitsakakis, Konstantinos
       title: Diagnostic tools for tackling febrile illness and enhancing patient management
        date: 2018-12-05
       words: 20813
      flesch: 41
     summary: This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. Nucleic acid amplification technologies (NAATs) are based on sequence-specific recognition and amplification of unique target regions in the genome of pathogens to be detected.
    keywords: acid; amplification; assay; blood; care; cartridge; detection; diagnosis; diseases; dna; e.g.; febrile; fever; fig; health; infections; malaria; management; nucleic; patients; pcr; platform; point; process; reaction; reagents; sample; specific; system; target; technologies; technology; test; time; tools; use; virus
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        item: #1018 of 1349
          id: cord-324984-ojrpsdt9
      author: Ji, Xingyue
       title: Medicinal chemistry strategies toward host targeting antiviral agents
        date: 2020-02-14
       words: 16870
      flesch: 33
     summary: HSP-90 inhibitors reduce CHIKV infection and inflammation in vivo Hsp90 inhibitors exhibit resistance-free antiviral activity against respiratory syncytial virus Molecular chaperone Hsp90 is a therapeutic target for noroviruses Heat shock protein 90 facilitates formation of the HBV capsid via interacting with the HBV core protein dimers Hsp90, an unlikely ally in the war on cancer Geldanamycin, a ligand of heat shock protein 90, inhibits herpes simplex virus type 2 replication both in vitro and in vivo Geldanamycin, a ligand of heat shock protein 90, inhibits the replication of herpes simplex virus type 1 in vitro Inhibition of heat-shock protein 90 reduces Ebola virus replication Heat shock protein 90 controls HIV-1 reactivation from latency Hsp90 inhibitors reduce influenza virus replication in cell culture Hsp90 inhibitors exhibit resistance-free antiviral activity against respiratory syncytial virus Evolutionary constraints on chaperone-mediated folding provide an antiviral approach refractory to development of drug resistance A novel class of geldanamycin derivatives as HCV replication inhibitors targeting on Hsp90: synthesis, structure-activity relationships and anti-HCV activity in GS4.3 replicon cells Synthesis and biological evaluation of heat-shock protein 90 inhibitors: geldanamycin derivatives with broad antiviral activities Hsp90 inhibitor AT-533 blocks HSV-1 nuclear egress and assembly Inhibition of heat-shock protein 90 reduces Ebola virus replication Inhibition of HSP90 attenuates porcine reproductive and respiratory syndrome virus production in vitro Hsp90 molecular chaperone inhibitors: are we there yet? but not in patients in a randomized clinical trial Herpes simplex virus type 1 DNA polymerase requires the mammalian chaperone hsp90 for proper localization to the nucleus Nuclear transport of Epstein-Barr virus DNA polymerase is dependent on the BMRF1 polymerase processivity factor and molecular chaperone Hsp90 Involvement of Hsp90 in assembly and nuclear import of influenza virus RNA polymerase subunits Geldanamycin, a potent and specific inhibitor of Hsp90, inhibits gene expression and replication of human cytomegalovirus Human butyrate-induced transcript 1 interacts with hepatitis C virus NS5A and regulates viral replication Antiviral activity and RNA polymerase degradation following Hsp90 inhibition in a range of negative strand viruses Chikungunya virus nsP3 & nsP4 interacts with HSP-90 to promote virus replication:
    keywords: activity; antiviral; compound; cxcr4; development; drug; effects; hbv; hcv; hepatitis; hiv-1; host; hsp90; human; inhibition; inhibitors; kinase; patients; potent; protein; replication; rna; spectrum; targeting; treatment; trial; virus; viruses; vitro
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        item: #1019 of 1349
          id: cord-325043-vqjhiv7p
      author: Gorbalenya, Alexander E.
       title: An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication
        date: 1989
       words: 6807
      flesch: 42
     summary: In fact, in recent studies, protein sequences were searched for the A consensus alone as the B consensus in its loosest form is obviously too degenerate to be unequivocally recognized, except in a family of diverged proteins (see below). Protein sequences were extracted from the current literature (for references see Table 1 ).
    keywords: consensus; et al; families; family; motif; ntp; proteins; residues; rna; sequence; viruses
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        item: #1020 of 1349
          id: cord-325113-sou8xyld
      author: Kuiper, Johannes W. P.
       title: Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification
        date: 2020-11-02
       words: 4980
      flesch: 43
     summary: A RNA-and DNA-reading heat-stable polymerase reverse transcribes and amplifies viral RNA Evidence of an acute SARS-CoV-2 infection depends on the detection of viral RNA species in patient samples, which necessitates reverse transcription of RNA followed by PCR amplification of the resulting DNA. When 5000 genome equivalents of the purified, in vitro transcribed viral RNA was used as a PCR template for a generic, heat-stable DNA-dependent DNA polymerase (Taq DNA polymerase)
    keywords: dna; fig; patient; pcr; polymerase; rna; samples; sars; temperature; volcano3
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        item: #1021 of 1349
          id: cord-325137-6c6er06a
      author: Moser, Lindsey A.
       title: A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses
        date: 2016-06-07
       words: 9977
      flesch: 48
     summary: In summary, we describe a rapid, universal standard operating procedure that generates high-quality NGS libraries free of infectious virus and infectious viral RNA. Applying NGS to sequencing RNA viruses represents an unparalleled capacity to generate large amounts of sequence data, which can be used to identify consensus sequences as well as minor sequence variants, or quasispecies, present in a viral population (25) .
    keywords: cells; cpe; data; fig; fmdv; genomic; hrv-16; infectivity; material; pcr; rna; samples; sequence; sequencing; sispa; sop; viral; virus; viruses
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        item: #1022 of 1349
          id: cord-325197-j1uo8qmf
      author: Crimi, Ettore
       title: Epigenetic susceptibility to severe respiratory viral infections: pathogenic and therapeutic implications: a narrative review
        date: 2020-08-20
       words: 6080
      flesch: 21
     summary: The architecture of SARS-CoV-2 transcriptome Control of viral infections by epigenetic-targeted therapy Epigenetic mechanisms of importance for drug treatment Curcumin alleviates macrophage activation and lung inflammation induced by influenza virus infection through inhibiting the NF-kB signaling pathway. key: cord-325197-j1uo8qmf authors: Crimi, Ettore; Benincasa, Giuditta; Figueroa-Marrero, Neisaliz; Galdiero, Massimiliano; Napoli, Claudio title: Epigenetic susceptibility to severe respiratory viral infections: pathogenic and therapeutic implications: a narrative review date: 2020-08-20 journal:
    keywords: coronavirus; cov-2; covid-19; disease; host; human; immune; infections; influenza; mechanisms; patients; response; sars; virus; viruses
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        item: #1023 of 1349
          id: cord-325230-3kg4oe4g
      author: Agol, Vadim I.
       title: Viral security proteins: counteracting host defences
        date: 2010-11-09
       words: 8721
      flesch: 30
     summary: At the same time, however, there is a certain division of labour between viral proteins. The reasons for this variability are poorly understood, although receptor compatibility and effects on viral protein and RNA synthesis that are caused by differences in the availability of host factors are surely important contributors.
    keywords: cardiovirus; disease; host; interferon; leader; picornavirus; poliovirus; proteins; replication; rna; security; security proteins; translation; virus; viruses
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        item: #1024 of 1349
          id: cord-325280-4whzcmqv
      author: Takizawa, Naoki
       title: Current landscape and future prospects of antiviral drugs derived from microbial products
        date: 2017-10-11
       words: 6633
      flesch: 28
     summary: In addition, the current state of development of antiviral drugs that target influenza virus and hepatitis B virus, and the future prospects for antivirals from natural products are described and discussed. Approximately 90 drugs have been approved to treat human infectious diseases caused by the following nine viruses: HIV, human cytomegalovirus, hepatitis B virus (HBV), hepatitis C virus (HCV), herpes simplex virus, influenza virus, respiratory syncytial virus, varicella zoster virus and human papillomavirus.
    keywords: activity; dna; drugs; hbv; hepatitis; hiv; host; influenza; inhibitors; microbial; polymerase; products; rna; virus; viruses
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        item: #1025 of 1349
          id: cord-325326-2bbqz4o7
      author: Beitzel, Brett F.
       title: High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing
        date: 2010-10-14
       words: 7802
      flesch: 45
     summary: The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket Phosphorylation of Sindbis virus nsP3 in vivo and in vitro Phosphorylation site analysis of Semliki forest virus nonstructural protein 3 Deletion and duplication mutations in the C-terminal nonconserved region of Sindbis virus nsP3: effects on phosphorylation and on virus replication in vertebrate and invertebrate cells The crystal structure of the Venezuelan equine encephalitis alphavirus nsP2 protease Demonstration in vitro of temperature-sensitive elongation of RNA in Sindbis virus mutant ts6 Sequence analysis of three Sindbis virus mutants temperature-sensitive in the capsid protein autoprotease Mapping of RNA-temperaturesensitive mutants of Sindbis virus: assignment of complementation groups A, B, and G to nonstructural proteins Synthesis and processing of the nonstructural polyproteins of several temperature-sensitive mutants of Sindbis virus Functional defects of RNA-negative temperature-sensitive mutants of Sindbis and Semliki Forest viruses Temperature sensitive shut-off of alphavirus minus strand RNA synthesis maps to a nonstructural protein A second nonstructural protein functions in the regulation of alphavirus negative-strand RNA synthesis Mutants of sindbis virus. I. Isolation and partial characterization of 89 new temperature-sensitive mutants Roles of nonstructural polyproteins and cleavage products in regulating Sindbis virus RNA replication and transcription Novel Functions of the Alphavirus Nonstructural Protein nsP3 C-Terminal Region Functional analysis of nsP3 phosphoprotein mutants of Sindbis virus High-resolution functional profiling of hepatitis C virus genome Highresolution functional profiling of a gammaherpesvirus RTA locus in the context of the viral genome Replicon-helper systems from attenuated Venezuelan equine encephalitis virus: expression of heterologous genes in vitro and immunization against heterologous pathogens in vivo Specific restrictions in the progression of Venezuelan equine encephalitis virus-induced disease resulting from single amino acid changes in the glycoproteins Gapped BLAST and PSI-BLAST: a new generation of protein database search programs The mouse research protocol was approved by the US Army Medical Research Institute of Infectious Disease Institutional Animal Care and Use Committee in compliance with the Animal Welfare Act and other federal statutes and regulations relating to animals and experiments involving animals and adheres to principles stated in The Guide for the Care and Use of Laboratory Animals, National Research Council, 1996.
    keywords: 30uc; analysis; genome; insertions; library; mice; mutants; nsp3; regions; replication; rna; sequencing; transposon; veev; virus
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        item: #1026 of 1349
          id: cord-325328-3l3jznkj
      author: Holbrook, Stephen R
       title: RNA structure: the long and the short of it
        date: 2005-05-16
       words: 3714
      flesch: 38
     summary: A database of non-canonical base pairs in RNA structures [30] , coupled with tools for the automatic identification and classification of RNA base pairs [31] , provides an initial description of RNA secondary structure. key: cord-325328-3l3jznkj authors: Holbrook, Stephen R title: RNA structure: the long and the short of it date: 2005-05-16 journal: Curr Opin Struct Biol DOI: 10.1016/j.sbi.2005.04.005 sha: doc_id: 325328 cord_uid: 3l3jznkj The database of RNA structure has grown tremendously since the crystal structure analyses of ribosomal subunits in 2000–2001.
    keywords: base; crystal; interaction; loops; motifs; ribosomal; rna; rnas; structure
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        item: #1027 of 1349
          id: cord-325479-2r4oomdp
      author: Torii, Shotaro
       title: Applicability of polyethylene glycol precipitation followed by acid guanidinium thiocyanate-phenol-chloroform extraction for the detection of SARS-CoV-2 RNA from municipal wastewater
        date: 2020-10-17
       words: 5906
      flesch: 47
     summary: Katayama Hiroyuki: Resources, Project administration, Funding Acquisition, Supervision, Writing -review & editing First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A Comparison of virus concentration methods for the RT-qPCR-based recovery of murine hepatitis virus The MIQE Guidelines : Minimum Information for Publication of Quantitative Real-Time PCR Experiments Inactivation of an Enveloped Surrogate Virus in Human Sewage Evaluation of eluents for the recovery of an enveloped virus from hands by whole-hand sampling CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction An optimized method to detect influenza virus and human rhinovirus from exhaled breath and the airborne environment Evaluation of Filters for the Sampling and Quantification of RNA Phage Aerosols Southeastern Virginia using wastewater-based epidemiology Development of a novel method for simultaneous concentration of viruses and protozoa from a single water sample A review on recent progress in the detection methods and prevalence of human enteric viruses in water First environmental surveillance for the presence of SARS-CoV-2 RNA in wastewater and river water in Japan Identification of SARS-CoV-2 in wastewater in Japan by multiple molecular assays-implication for wastewater-based epidemiology (WBE) Validation of Internal Controls for Extraction and Amplification of Nucleic Acids from Enteric Viruses in Water Samples Temporal dynamics of norovirus determined through monitoring of municipal wastewater by pyrosequencing and virological surveillance of gastroenteritis cases SARS-CoV-2 in wastewater: State of the knowledge and research needs Use of Murine Norovirus as a Novel Surrogate to Evaluate Resistance of Human Norovirus to Free Chlorine Disinfection in Drinking Water Supply System in India through detection of genetic material of SARS-CoV-2 First detection of SARS-CoV-2 in untreated wastewaters in Italy Minimized virus binding for tests of barrier materials Presence of SARS-Coronavirus-2 RNA in Sewage and Correlation with Reported COVID-19 Prevalence in the Early Stage of the Epidemic in The Netherlands Sensitive and specific quantitative detection of rotavirus A by one-step real-time reverse transcription-PCR assay without antecedent double-stranded-RNA denaturation Wastewater-Based Epidemiology Can Overcome Representativeness and Stigma Issues Related to COVID-19 R: A Language and Environment for Statistical Computing SARS-CoV-2 RNA in wastewater anticipated COVID-19 occurrence in a low prevalence area Concentration methods for the quantification of coronavirus and other potentially pandemic enveloped virus from wastewater First detection of SARS-CoV-2 RNA in wastewater in North America: A study in Louisiana Elution Is a Critical Step for Recovering Human Adenovirus 40 from Tap Water and Surface Water by Cross-Flow Ultrafiltration Development of Genetic Diagnostic Methods for Novel Coronavirus 2019 (nCoV-2019) in Japan Cross-platform evaluation of commercial real-time reverse transcription PCR master mix kits using a quantitative 5′nuclease assay for Ebola virus Impact of repeated pressurization on virus removal by reverse osmosis membranes for household water treatment Viral multiplex quantitative PCR assays for tracking sources of fecal contamination Virological assessment of hospitalized patients with COVID-2019 SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases Survivability, Partitioning, and Recovery of Enveloped Viruses in Untreated Municipal Wastewater Shotaro Torii: Investigation, Resources, Funding Acquisition Writing -review & editing. The comparison of virus concentrations between concentrated samples and control allows for the evaluation of the whole process recovery ratio as described below. where C obs_WPC indicates the cDNA concentration of WPC in concentrated samples (copies/mL), C ini_WPC indicates the cDNA concentration of WPC in the control sample (copies/mL), x the concentration factor during the whole process (primary concentration, RNA extraction, and RT), C obs_MPC indicates the cDNA concentration of MPC in concentrated samples (copies/mL), C ini_MPC indicates the cDNA concentration of MPC in the control sample (copies/mL) and ALOD indicates the assay limit of detection defined as the minimum copy number with a 95% probability detection (copies/mL).
    keywords: concentration; cov-2; process; recovery; rna; sars; sewage
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        item: #1028 of 1349
          id: cord-325529-pid58g2r
      author: Ben-Ami, Roni
       title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection
        date: 2020-06-23
       words: 2830
      flesch: 45
     summary: Here we describe and demonstrate practical pooling solutions that save time and reagents by performing RNA extraction and RT-PCR on pooled samples. Alternatively, it is possible to dynamically adapt pooling sizes, when the measured rate of positive samples is different than expected.
    keywords: covid-19; pooling; rna; samples; sars; testing
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        item: #1029 of 1349
          id: cord-325624-6anybxnk
      author: Ireland, Derek D. C.
       title: RNase L Mediated Protection from Virus Induced Demyelination
        date: 2009-10-02
       words: 8100
      flesch: 39
     summary: Cell type specific effects of anti-viral RNase L activity are also clearly evident from studies with West Nile virus (WNV). While mouse embryonic fibroblasts display RNase L dependent anti-viral activity [10] , IFN-b treatment revealed no affect of RNase L in reducing WNV replication in either cortical or peripheral motor neurons [11] .
    keywords: brain; cells; ifn; infected; infection; matter; mice; microglia; p.i; rnase; spinal; virus
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        item: #1030 of 1349
          id: cord-325736-gs9d8y55
      author: Marin, J
       title: Persistence of Viruses in Upper Respiratory Tract of Children with Asthma
        date: 2000-07-31
       words: 1875
      flesch: 50
     summary: In addition to allergens, respiratory viruses have been proven to be important factors in provoking asthmatic attacks. Due to the high viral NAs detection rate in asthmatic children compared to the lower detection rate in the control group, we can speculate that the results could be related to the disease itself or to the glucocorticoid treatment, since there is data which suggests that glucocorticoid therapy increases the titre of respiratory viruses and prolongs viral shedding.
    keywords: asthma; children; dna; pcr; viruses
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        item: #1031 of 1349
          id: cord-325820-tnyzmrm8
      author: Kovacikova, Kristina
       title: 6′-β-Fluoro-Homoaristeromycin and 6′-Fluoro-Homoneplanocin A Are Potent Inhibitors of Chikungunya Virus Replication through Their Direct Effect on Viral Nonstructural Protein 1
        date: 2020-03-24
       words: 9868
      flesch: 48
     summary: Recently, a similar assay with CHIKV nsP1 has been used to screen for CHIKV nsP1 inhibitors (28) . By selection of escape mutants and reverse engineering we identified CHIKV nsP1 as the viral target for these compounds.
    keywords: activity; assay; cells; chikv; compound; fhna; fig; mutations; nsp1; resistance; rna; sah; sfv; sfv nsp1; virus
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        item: #1032 of 1349
          id: cord-325925-010xj69x
      author: Mordecai, Gideon J
       title: Endangered wild salmon infected by newly discovered viruses
        date: 2019-09-03
       words: 5556
      flesch: 39
     summary: The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture. Together, sequencing of dead or moribund aquaculture salmon and live-sampled wild salmon, in-situ hybridization, and epidemiological surveys revealed that previously unknown viruses, some of which are associated with disease, infect wild salmon from different populations.
    keywords: chinook; disease; et al; farmed; figure; fish; juvenile; pacific; populations; rna; salmon; samples; sockeye; viruses; wild
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        item: #1033 of 1349
          id: cord-325954-rhrkr97h
      author: Han, Mi Seon
       title: Viral RNA Load in Mildly Symptomatic and Asymptomatic Children with COVID-19, Seoul, South Korea
        date: 2020-10-17
       words: 1429
      flesch: 50
     summary: Viral RNA load in the nasopharyngeal swabs peaked early at median 7.56 (range 6.19-10.56) log 10 copies/mL and decreased over time (p<0.001 for trend) (Figure, panel A) . However, viable virus was isolated in feces in previous studies, and infectivity was dependent on viral RNA load (3, 5, 6) .
    keywords: children; cov-2; rna; sars
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        item: #1034 of 1349
          id: cord-325958-1v1pg2z0
      author: Lange, Clemens
       title: Expression of the COVID‐19 receptor ACE2 in the human conjunctiva
        date: 2020-05-06
       words: 2676
      flesch: 35
     summary: Our results show that the SARS‐CoV‐2 receptor ACE2 is not substantially expressed in conjunctival samples on the mRNA (median 0.0 transcripts per million (TPM), min 0.0 TPM, max 1.7 TPM) and protein levels. In conclusion, this study finds no evidence for a significant expression of ACE2 and its auxiliary mediators for cell entry in conjunctival samples, making conjunctival infection with SARS‐CoV‐2 via these mediators unlikely.
    keywords: ace2; conjunctival; cov-2; expression; human; patients; rna; samples; sars
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        item: #1035 of 1349
          id: cord-325966-0g7a9s5z
      author: Shih, Hsin-I.
       title: Fighting COVID-19: a quick review of diagnoses, therapies, and vaccines
        date: 2020-05-30
       words: 7334
      flesch: 33
     summary: For COVID-19 patients, fever and cough are the two most common symptoms, and some patients might also suffer from sputum production, sore throat, headache, myalgia/arthralgia, rhinorrhea, and diarrhea An earlier study demonstrated that hydroxychloroquine was significantly associated with viral load reduction/disappearance in COVID-19 patients and its effect was strengthened by azithromycin [25] .
    keywords: antibodies; bcg; cells; coronavirus; cov-2; covid-19; immunity; infection; patients; protein; rna; sars; syndrome; treatment; vaccination; vaccine; virus
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        item: #1036 of 1349
          id: cord-326017-qw4qynqv
      author: Laskar, Partha
       title: “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies
        date: 2020-08-06
       words: 14817
      flesch: 35
     summary: Thus, early, rapid, and accurate diagnosis of COVID-19 patients is becoming very crucial to control the sources of infection and to prevent further community spread. Such tests have proven lung histology (lung damage or holes/honeycomb-like appearance) of COVID-19 patients [70] .
    keywords: 2019; amplification; antiviral; cases; coronavirus; cov-2; covid-19; data; detection; development; disease; drug; health; human; iii; infection; methods; number; pandemic; patients; pcr; pneumonia; research; rna; sars; time; treatment; use
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        item: #1037 of 1349
          id: cord-326217-ji0njeha
      author: Saleh, Maged
       title: Glycogen Synthase Kinase 3β Enhances Hepatitis C Virus Replication by Supporting miR-122
        date: 2018-11-27
       words: 4744
      flesch: 37
     summary: To assess whether both GSK3 isoforms are required for HCV replication, we silenced GSK3α and / or GSK3β gene expression by transfecting siRNAs and quantified HCV RNA in Huh-7.5 cells harboring HCV subgenomic replicon (Con1) or infectious HCV (Jc1). As shown in Figure 4A (upper panel), silencing of GSK3β gene expression resulted in a substantial decrease of HCV RNA levels of both the subgenomic replicon and the full-length HCV construct, whereas silencing of GSK3α gene expression had only a minor effect on HCV replication.
    keywords: et al; gsk3; hcv; hepatitis; inhibition; insulin; mir-122; replication; rna; synthase; virus
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        item: #1038 of 1349
          id: cord-326225-crtpzad7
      author: Neill, John D.
       title: Simultaneous rapid sequencing of multiple RNA virus genomes
        date: 2014-06-01
       words: 3807
      flesch: 49
     summary: These include methodologies based on PCR amplification of viral sequences, both in fragments (Rao et al., 2013) or fulllength genome amplification (Christenbury et al., 2010) . This was modified for amplification of viral sequences from serum to include a step where DNase I was used to first degrade host DNA (Allander et al., 2001) .
    keywords: dna; genomic; library; rna; sequences; sequencing; viruses
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        item: #1039 of 1349
          id: cord-326257-rcv8sh22
      author: Simmonds, P.
       title: Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories
        date: 2020-05-01
       words: 3506
      flesch: 37
     summary: Repeated cycles of mutation and reversion in favoured mutational hotspots and the widespread occurrence of amino acid changes with no adaptive value for the virus represents a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks that are typically used in molecular epidemiology investigations. Sequence substitutions were characterised by a preponderance of cytidine to uridine (C->U) transitions.
    keywords: c->u; changes; coronaviruses; cov-2; fig; rna; sars; sequence; substitutions
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        item: #1040 of 1349
          id: cord-326719-p1ma4akz
      author: Enjuanes, Luis
       title: Virus-based vectors for gene expression in mammalian cells: Coronavirus
        date: 2003-12-31
       words: 5934
      flesch: 51
     summary: The coronaviruses have been classified into three groups (1, 2 and 3) based on sequence analysis of a number of coronavirus genes [1] . key: cord-326719-p1ma4akz authors: Enjuanes, Luis; Almazán, Fernando; Ortego, Javier title: Virus-based vectors for gene expression in mammalian cells: Coronavirus date: 2003-12-31 journal: New Comprehensive Biochemistry DOI: 10.1016/s0167-7306(03)38010-x sha: doc_id: 326719 cord_uid: p1ma4akz Publisher Summary The coronavirus and the torovirus genera form the Coronaviridae family, which is closely related to the Arteriviridae family.
    keywords: cdna; cells; coronavirus; expression; gene; genome; infectious; protein; rna; tgev; transcription
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        item: #1041 of 1349
          id: cord-326911-va3x6au2
      author: Ramos-Mandujano, G.
       title: A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples
        date: 2020-06-29
       words: 4430
      flesch: 49
     summary: https://doi.org/10.1101/2020.06.28.20141945 doi: medRxiv preprint RNA produced by MAVRICS is free of contaminants and maintains good integrity. Both rRT-PCR testing and high-throughput sequencing of SARS-CoV-2 require RNA extraction from nasopharyngeal swab samples.
    keywords: author; funder; june; license; medrxiv; medrxiv preprint; perpetuity; preprint; rna
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        item: #1042 of 1349
          id: cord-327000-oyg3oyx1
      author: Li, Shasha
       title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response
        date: 2020-05-11
       words: 11139
      flesch: 41
     summary: These cap structures enhance the initiation of translation of viral proteins, protect viral mRNAs against cellular 5 -3 -exoribonuclease and limit the recognition of viral RNA by host innate system [120, 121] . Although several studies have been performed to understand the pathogenicity of PEDV, there remains limited information about the interaction between viral proteins and host cell factors during viral infection.
    keywords: activity; coronavirus; cov; covs; diarrhea; epidemic; expression; host; ifn; nsp1; pedv; porcine; production; protein; replication; response; rna; sars; signaling; type; virus
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        item: #1043 of 1349
          id: cord-327024-1k5jucae
      author: Zhang, Qingshui
       title: Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings
        date: 2018-04-19
       words: 4173
      flesch: 41
     summary: Bidin et al. 18 reported the detection of avian nephritis virus infection in Croatian goose flocks and provided evidence that this AstV was associated with stunting and prehatching mortality of goose embryos. Infected goslings exhibited signs of depression from 3 dpi and this symptom persisted for 3-4 days.
    keywords: astrovirus; astv; birds; dpi; fig; goose; goslings; infection; isolate; rna; virus
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        item: #1044 of 1349
          id: cord-327259-7o7fs4yb
      author: Correa, I. A.
       title: Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling
        date: 2020-08-19
       words: 4586
      flesch: 50
     summary: key: cord-327259-7o7fs4yb authors: Correa, I. A.; Rodrigues, T. d. S.; Queiroz, A.; Nascimento, L. d. F.; Wolff, T.; Akamine, R. N.; Kuriyama, S. N.; Costa, L.; Fidalgo-Neto, A. A. title: Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date: 2020-08-19 journal: nan DOI: 10.1101/2020.08.16.20167536 sha: doc_id: 327259 cord_uid: 7o7fs4yb qRT-PCR is the gold standard technique available for SARS-CoV-2 detection. Coronavirus Disease (COVID-19) Dashboard Considerations in adjusting public health and social measures in the context of COVID-19 COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation per million population Clinical management of COVID-19: interim guidance Coronavirus disease (COVID-19) technical guidance: Laboratory testing for 2019-nCoV in humans Pooling of sera for human immunodeficiency virus (HIV) testing: an economical method for use in developing countries Pooling Nasopharyngeal/Throat Swab Specimens To Increase Testing Capacity for Influenza Viruses by PCR Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources The Detection of Defective Members of Large Populations Pooling Samples: the Key to Sensitive, Specific and Cost-effective Genetic Diagnosis of Chlamydia trachomatis in Low-Resource Countries Utility of Pooled Urine Specimens for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Men Attending Public Sexually Transmitted Infection Clinics in Mumbai, India, by PCR Optimal pooled testing Evaluation of Group Testing for SARS-CoV-2 RNA.
    keywords: cost; pooling; pools; preprint; prevalence; rna; samples; sars; testing
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        item: #1045 of 1349
          id: cord-327272-fspxett8
      author: Buonaguro, Luigi
       title: Knowledge-based repositioning of the anti-HCV direct antiviral agent Sofosbuvir as SARS-CoV-2 treatment
        date: 2020-05-12
       words: 1440
      flesch: 34
     summary: In the specific case of SARS-CoV-2, and in general in the case of RNA viruses, the most specific target is represented by the RNA-dependent RNA-polymerase (RdRp) which is specific to each RNA virus, regardless the polarity of the viral RNA genome [10, 11] . The alignment of RdRp sequences from HCV and the three epidemic/pandemic coronaviruses, confirms the high homology and conservation in several residues along the sequence and in particular in the Motif B and C. On the contrary, such homology is almost lost when RdRp sequences from the three epidemic/pandemic coronaviruses are aligned with those from negativesense RNA viruses, namely Ebola, Influenza, Rabies and Vesicular Stomatitis viruses
    keywords: cov-2; rdrp; rna; sars; sofosbuvir
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        item: #1046 of 1349
          id: cord-327518-yilv9z2m
      author: None
       title: Coronaviridae
        date: 2011-11-23
       words: 7138
      flesch: 44
     summary: l Envelope: contains a variable number of viral membrane protein species, two of which seem to be conserved family-wide and are essential for virion morphogenesis and/or infectivity (at least in coronaviruses): l a 200-to 250-aa triple-spanning N exo C endo integral membrane protein M l an extensively N-glycosylated, 1100-to 1600-aa class I fusion protein S which forms peplomers. PL (green) papain-like proteinase 1 (PL1 pro ); PL (red), papain-like proteinase 2 (PL2 pro ); A, ADP-ribose-1phosphatase (macrodomain); M pro , 3C-like main protease; Pr, noncanonical RNA-dependent RNA polymerase, putative primase; RdRp, RNA-dependent RNA polymerase; Z, zinc-binding domain; Hel, helicase domain; Exo, 3 to-5 exoribonuclease domain; N7, guanine-N7-methyltransferase; U, nidoviral uridylate-specific endoribonuclease (NendoU); MT, ribose-2-O-methyltransferase domain; HE, hemagglutinin-esterase; S, spike protein; E, envelope protein; M, membrane protein, N, nucleocapsid protein; I, internal ORF.
    keywords: coronavirus; figure; genome; membrane; minus; mrna; protein; replicase; rna; sequence; species; strand; synthesis; torovirus
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        item: #1047 of 1349
          id: cord-327660-p1b07b4t
      author: Wolf, Yuri I.
       title: Origins and Evolution of the Global RNA Virome
        date: 2018-11-27
       words: 13936
      flesch: 36
     summary: The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). The prospects of substantial progress appeared dim because of the extreme sequence divergence among RNA viruses, which could amount to irrevocable loss of evolutionary information.
    keywords: analysis; branch; branches; dsrna; evolution; fig; gene; genomes; groups; like; members; protein; rdrp; rna; rna viruses; sjr; supergroup; tree; viruses; ϩrna; ϩrna viruses; ϫrna
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        item: #1048 of 1349
          id: cord-327855-txryqil7
      author: Kulka, M.
       title: The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells
        date: 2003
       words: 8717
      flesch: 43
     summary: Degradation of rRNA has not been reported previously in HAV infected cells, therefore, the rRNA origin of the observed degradation The probe for 18S RNA was a 1.2 kb fragment of the mouse 18S The parental HM175/clone 1 virus (clone 1), also used in the present study, produced no changes in cell morphology after several months of continuous culture of infected cells, although viral antigens could be detected by EIA after four weeks of weekly subculture following the initial infection.
    keywords: 18f; apoptosis; cells; clone; degradation; fig; frhk4; hav; hepatitis; infected; infection; protein; replication; rna; rrna; virus
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        item: #1049 of 1349
          id: cord-327997-noqbcxua
      author: Wu, Kevin E.
       title: RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus
        date: 2020-06-20
       words: 7209
      flesch: 35
     summary: In this work, we apply computational models of human RNA transcript localization to better understand the subcellular localization behavior of the SARS-CoV-2 genome and its constituent sgRNAs. A limitation of our work lies in that it applies models trained on human RNA transcript localization data to viral transcripts.
    keywords: cov-2; data; figure; gps; human; localization; matrix; nucleolus; predictions; residency; rna; sars; subcellular; transcripts
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        item: #1050 of 1349
          id: cord-328042-e1is656g
      author: Klein, Steffen
       title: SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP
        date: 2020-08-07
       words: 6357
      flesch: 47
     summary: Magnetic bead RNA extraction was benchmarked against the commercial QIAcube extraction platform. Magnetic bead RNA extraction was performed in 96-well plates in combination with a magnet plate optimized for 96 deep-well plates.
    keywords: bead; cov-2; detection; extraction; figure; lamp; plate; qpcr; rna; samples; sars
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        item: #1051 of 1349
          id: cord-328085-7wp18qb6
      author: Barage, Sagar
       title: Identification and characterization of novel RdRp and Nsp15 inhibitors for SARS-COV2 using computational approach
        date: 2020-11-06
       words: 6079
      flesch: 45
     summary: The variation in binding mode results in altered RdRp residue interaction with Alectinib. The first compound, namely, Chlorohexidine with binding free energy -10.11 Kcal/mol efficiently accommodated in the active site of RdRp and do molecular mimicry of nucleotides in terms of substructure interactions with RdRp residues (Figure 2(A) ).
    keywords: coronavirus; energy; et al; figure; interaction; ligand; naldemedine; nsp15; protein; rdrp; residues; rna; simulation; structure
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        item: #1052 of 1349
          id: cord-328252-dk54w8z9
      author: Kikkert, Marjolein
       title: Innate Immune Evasion by Human Respiratory RNA Viruses
        date: 2019-10-14
       words: 11567
      flesch: 34
     summary: Although the exact mechanism of inhibition is still not clear for several of the viruses inhibited by Mx proteins, Mx GTPase family members bind to intracellular membranes, and in cytosolic +RNA virus infections Mx proteins could target the ROs As discussed in the beginning of this review, the type I IFN antiviral pathway is very relevant for RNA virus infections, and an essential adaptor that enables downstream signaling in this pathway is IPS-1 (also called MAVS).
    keywords: cells; cov; evasion; formation; host; immune; immunity; infection; influenza; innate; protein; replication; respiratory; responses; rna; role; stress; translation; viruses
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        item: #1053 of 1349
          id: cord-328259-3g4klpyg
      author: Guajardo-Leiva, Sergio
       title: Metagenomic Insights into the Sewage RNA Virosphere of a Large City
        date: 2020-09-21
       words: 7642
      flesch: 43
     summary: Viral sequences can also be misannotated to homologous cellular genes [36, 39] , which relies on the low number and diversity of viral sequences in the databases. Viral sequences identified as Partitiviridae-like viruses included in the unclassified RNA viruses ShiM-2016 category in the NCBI taxonomy (~25% abundance; Figure 2B ) and Totiviriade family were also highly abundant in treated and untreated sewage samples from the EU
    keywords: abundance; database; family; figure; human; ncbi; proteins; rdrp; rna; rotavirus; samples; sequences; sewage; trebal; viral; viruses; wastewater
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        item: #1054 of 1349
          id: cord-328300-zehltghv
      author: Lin, Shing-Yen
       title: Structural Basis for the Identification of the N-Terminal Domain of Coronavirus Nucleocapsid Protein as an Antiviral Target
        date: 2014-02-24
       words: 6649
      flesch: 47
     summary: We found that PJ34 at 10 μM inhibits coronavirus replication and potently interferes with the RNAbinding activity of HCoV OC43 N protein by targeting the N-NTD ribonucleotide-binding pocket. 29, 30 Previous studies showed that HCoV N protein has high affinity for the intergenic sequence.
    keywords: amp; binding; complex; coronavirus; figure; hcov; n protein; ntd; nucleocapsid; oc43 n; pj34; protein; replication; rna; structure
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        item: #1055 of 1349
          id: cord-328460-thx9zh11
      author: Zanoli, Laura Maria
       title: Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices
        date: 2012-12-27
       words: 8976
      flesch: 31
     summary: Although PCR is the most widespread technology for DNA amplification, the need for an electrically powered thermal cycler with a precise temperature control and for an optimized experimental setup makes the use of PCR at point-of-care settings more complex and increases the cost of PCR-based devices. Symmetrical mode of DNA replication TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing Optimization of the polymerase chain reaction with regard to fidelity: Modified T7, Taq, and vent DNA polymerases Fidelity of DNA polymerases in DNA amplification Unbiased whole genome amplification directly from clinical samples Genomic DNA amplification from a single bacterium Nanoliter reactors improve multiple displacement amplification of genomes from single cells Single-Molecule DNA Amplification and analysis using microfluidics DNA detection using recombination proteins A phaseguided passive batch microfluidic mixing chamber for isothermal amplification Phaseguides: A paradigm shift in microfluidic priming and emptying Hot start PCR Digital isothermal quantification of nucleic acids via simultaneous chemical initiation of recombinase polymerase amplification reactions on SlipChip Nucleic acid sequence-based amplification Characteristics and applications of nucleic acid sequence-based amplification (NASBA) Quantitative detection of hepatitis B virus DNA by real-time nucleic acid sequence-based amplification with molecular beacon detection A one-tube quantitative HIV-1 RNA NASBA nucleic acid amplification assay using electrochemiluminiscent (ECL) labelled probes Comparison of nucleic acid-based detection of avian influenza H5N1 with virus isolation Human pathogenic Cryptosporidium species bioanalytical detection method with single oocyst detection capability PMMA biosensor for nucleic acids with integrated mixer and electrochemical detection Strategy for molecular beacon binding readout: Separating molecular recognition element and signal reporter Molecular engineering of DNA: Molecular beacons Real-time molecular beacon NASBA reveals hblc expression from Bacillus spp.
    keywords: acid; amplification; detection; device; dna; dna amplification; helicase; isothermal; nasba; nucleic; pcr; polymerase; reaction; rna; sample; sequence; target; temperature; time
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        item: #1056 of 1349
          id: cord-328471-oz99upzz
      author: Ahmad, Jamshaid
       title: SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp) – A drug repurposing study
        date: 2020-07-23
       words: 5094
      flesch: 50
     summary: During protein preparation, different combinations of enantiomers and tautomers were generated, which ultimately enhanced the total number of drug molecules. Although, designing and developing a panel of new drugs molecules are always encouraged.
    keywords: binding; docking; drugs; efficiency; ligand; molecules; protein; rdrp; residues; rna; score; site
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        item: #1057 of 1349
          id: cord-328633-c31xsyeo
      author: Moser, Michael J.
       title: Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme
        date: 2012-06-04
       words: 7878
      flesch: 48
     summary: The AMV and MMLV had higher RT activity at 37uC while the 3173 Pol RT was much more active at 65uC using the fluorogenic incorporation assay ( Figure 3A ). Soluble proteins were collected from the supernatant after centrifugation at 11,000 rcf for 10 minutes and assayed for DNA Pol activity based on their ability to extend a 59 fluorescently labeled oligonucleotide primer.
    keywords: activity; amplification; dna; enzyme; exonuclease; fidelity; figure; mmlv; ms2; pcr; pol; polymerase; primer; reverse; rna; step; taq; target
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        item: #1058 of 1349
          id: cord-328659-miujzgtd
      author: Mishra, Akhilesh
       title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions
        date: 2020-07-27
       words: 6074
      flesch: 47
     summary: Individual mutations as well as co-occurring mutations can act as lineage defining mutations. A single lineage defining mutation G26144T first reported from North America on the 22 nd January 2020 represents our C1 lineage.
    keywords: cov-2; defining; editing; figure; genomes; lineage; mutations; nucleotide; rna; sars; sequences; substitutions; virus
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        item: #1059 of 1349
          id: cord-328686-5ik5em5a
      author: Zhao, L.
       title: First study on surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: Post-lockdown
        date: 2020-08-21
       words: 1607
      flesch: 47
     summary: Indeed, a recently conducted study has inferred that risk of 111 infection from wastewater and river is insignificant due to the low success rate in cell culture of SARS-CoV-2 112 from water samples in spite of the high RNA copies (Rimoldi et al. 2020) . https://doi.org/10.1101/2020.08.19.20172924 doi: medRxiv preprint Wuhan, and it was lowered from high to medium risk on 25 th March 2020, and thereafter lowered it from 64 medium to low risk on 8 th April.
    keywords: license; medrxiv; preprint; sars
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        item: #1060 of 1349
          id: cord-328737-6mcefqn5
      author: Lee, Eun Yeong
       title: A novel nucleic acid amplification system based on nano-gap embedded active disk resonators
        date: 2020-05-26
       words: 4152
      flesch: 40
     summary: To form silicon nanoclusters uniformly in a resonator, silicon-rich silicon nitride (SRSN) film is deposited on a substrate and fabricated into disk resonators. These complexes bind to the target nucleic acids and enable the strand exchange which will begin the amplification process both on the surface of disk resonator (solid) and solution simultaneously ( Fig. 1-rectangle) , with the temperature maintained at isothermal conditions (38°C or 43°C for DNA or RNA, respectively).
    keywords: amplification; detection; disk; fig; gap; nucleic; resonator; surface; target
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        item: #1061 of 1349
          id: cord-328768-2qk884x2
      author: Sabatier, Marina
       title: Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses
        date: 2020-10-06
       words: 5364
      flesch: 38
     summary: To determine potential bias in the detection of DNA or RNA viruses, the relative abundance of Levivirus (Internal Quality Control) and targeted viruses in each triplicate were then compared ( Figure 4) . The highest relative abundance of RNA viruses was observed using the QIAamp method (8.2% Enterovirus, 2.2% Alphainfluenzavirus, and 0.6% Orthopneumovirus), which was not significantly different from that of eMAG (5% Enterovirus, 1.4% Alphainfluenzavirus, and 0.4% Orthopneumovirus).
    keywords: contamination; emag; extraction; methods; qiaamp; reads; rna; rpm; samples; viral; viruses
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        item: #1062 of 1349
          id: cord-328947-3l9ydspz
      author: Webb, L. G.
       title: Chikungunya virus antagonizes cGAS-STING mediated type-I interferon responses by degrading cGAS
        date: 2020-10-15
       words: 9891
      flesch: 45
     summary: Because CHIKV can inhibit cellular transcription, the reduction in cGAS expression over time in CHIKV infected cells could also be due to reduced cGAS transcripts, ultimately leading to reduced newly translated cGAS. mRNA levels of cGAS were quantified and there were no differences in CHIKV infected cells when compared to mock or NDV at 4 hpi (Fig 4B) indicating that a decrease in cGAS transcripts is not responsible for the rapid loss of cGAS expression following CHIKV infection.
    keywords: cells; cgas; chikungunya; chikv; data; degradation; dna; expression; fig; infection; interaction; nsp1; pathway; protein; rna; sensing; sting; type; viral; virus
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        item: #1063 of 1349
          id: cord-328960-46zui1sl
      author: Hillen, Hauke S.
       title: Structure of replicating SARS-CoV-2 polymerase
        date: 2020-04-27
       words: 4556
      flesch: 54
     summary: From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses A new coronavirus associated with human respiratory disease in China A pneumonia outbreak associated with a new coronavirus of probable bat origin The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing Nidovirus RNA polymerases: Complex enzymes handling exceptional RNA genomes SARS-CoV ORF1b-encoded nonstructural proteins 12-16: replicative enzymes as antiviral targets Nucleosides for the treatment of respiratory RNA virus infections Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses Coronavirus Susceptibility to the Antiviral Remdesivir (GS-5734) Is Mediated by the Viral Polymerase and the Proofreading Exoribonuclease The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus Race to find COVID-19 treatments accelerates Arguments in favour of remdesivir for treating SARS-CoV-2 infections Remdesivir for severe acute respiratory syndrome coronavirus 2 causing COVID-19: An evaluation of the evidence Biochemical characterization of a recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying viral RNA templates One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities Structure of the RNA-dependent RNA polymerase from COVID-19 virus Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer Nonstructural proteins 7 and 8 of feline coronavirus form a 2:1 heterotrimer that exhibits primer-independent RNA polymerase activity Viral replication. When added to a minimal RNA substrate (Fig. 1b) , the purified proteins gave rise to RNA-dependent RNA extension activity, which depended on the presence of nsp8 and nsp7 (Fig. 1c) .
    keywords: buffer; ml-1; nsp12; nsp7; nsp8; rdrp; rna; sars; structure
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        item: #1064 of 1349
          id: cord-329041-coryaz2s
      author: Brown, Ariane J.
       title: Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase
        date: 2019-09-30
       words: 5956
      flesch: 44
     summary: We developed multiple assays to further define the breadth of RDV antiviral activity against the CoV family. Upon passage of MHV in the presence of RDV, resistance mutations arise in the RNA dependent RNA polymerase (RdRp) that confer resistance (i.e. up to a 5-fold shift in EC 50 ) demonstrating that the RdRp is a target of RDV antiviral activity (Agostini et al., 2018) .
    keywords: activity; antiviral; cells; cov; et al; fig; human; oc43; rdv; rna; sars; thermofisher
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        item: #1065 of 1349
          id: cord-329102-2y49kcwu
      author: Lan, Tammy C. T.
       title: Structure of the full SARS-CoV-2 RNA genome in infected cells
        date: 2020-06-30
       words: 9327
      flesch: 53
     summary: Interactive drawing and editing of the RNA secondary structure Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond Simplified Estimation from Censored Normal Samples CONTRAfold: RNA secondary structure prediction without physics-based models Implications of RNA structure on the annealing of a potent antisense RNA directed against the human immunodeficiency virus type 1 MUSCLE: Like many other RNA viruses, RNA structures in coronaviruses regulate gene expression and are crucial for viral replication.
    keywords: base; cov-2; dms; et al; figure; fse; genome; rna; sars; sequence; stem; structure; î¼l
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        item: #1066 of 1349
          id: cord-329107-43e2lkht
      author: Pawlicka, Kamila
       title: Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics
        date: 2020-03-24
       words: 6727
      flesch: 37
     summary: The role of NMD pathway in tumours is complex. Cardiac glycosides (e.g., digoxin, ouabain) increase cytoplasmic calcium, which represses NMD pathway
    keywords: cancer; cells; decay; gene; human; inhibition; mrna; mutations; nonsense; pathway; protein; ptc; response; transcripts; tumour; upf1
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        item: #1067 of 1349
          id: cord-329311-p68kr4ga
      author: Prebensen, Christian
       title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19
        date: 2020-09-05
       words: 1459
      flesch: 52
     summary: c e p t e d M a n u s c r i p t Multiorgan and Renal Tropism of SARS-CoV-2 Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR High frequency of SARS-CoV-2 RNAemia and association with severe disease Impact of neuraminidase inhibitor treatment on outcomes of public health importance during the 2009-2010 influenza A(H1N1) pandemic: a systematic review and meta-analysis in hospitalized patients Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases Virological assessment of hospitalized patients with COVID-2019 A c c e p t e d In this prospective study of patients hospitalized with COVID-19 we detected SARS-CoV-2 RNAemia in 47% of included patients, and a significantly higher frequency of RNAemia and higher RNA loads in and similarly found that RNAemia was associated with ICU admission and hospital mortality
    keywords: patients; rna; sars
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        item: #1068 of 1349
          id: cord-329361-0mpbau1b
      author: Bennasser, Yamina
       title: RNAi Therapy for HIV Infection: Principles and Practicalities
        date: 2012-08-16
       words: 2651
      flesch: 45
     summary: HIV-1 tar RNA subverts RNA interferencein tion transfected cells through sequestration of tar RNA binding protein interference: viral diversion of a cellular pathway or evasion from antiviral 75 Conserved seed pairing, often flanked by HIV shRNA, anti-CCR5 ribozyme, and a nucleolar-localizing TAR decoy. The introduction of small uses its guide RNA for base-pairing-mediated recognition of target RNA duplexes of 19 to 21 nucleotides into cells can elicit specific messenger RNA (mRNA).
    keywords: cells; hiv; infection; protein; rnai; sirna; target; virus
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        item: #1069 of 1349
          id: cord-329366-xuszdrsa
      author: Hackbart, Matthew
       title: Coronavirus endoribonuclease targets viral polyuridine sequences to evade activating host sensors
        date: 2020-04-07
       words: 7216
      flesch: 48
     summary: both reduces PUN RNA abundance and suppresses host MDA5 activation, we hypothesized that CoV PUN RNA is a PAMP. We found that the presence of PUN RNAs increased IFNβ1 expression by 2,000-fold (Fig. 7B) , which was fourfold higher than any other in vitro transcribed viral RNA, indicating that PUN RNA is a PAMP.
    keywords: activity; cells; coronavirus; cov; dsrna; endou; endoumut; fig; ifn; mda5; polyu; pun; rna; rnas; sense; virus
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        item: #1070 of 1349
          id: cord-329429-ur8g68vp
      author: Miłek, Justyna
       title: Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds
        date: 2018-12-10
       words: 3814
      flesch: 40
     summary: Emerg Infect Dis Emergence of a group 3 coronavirus through recombination Molecular identification and characterization of novel coronaviruses infecting graylag geese (Anser anser), feral pigeons (Columbia livia) and mallards (Anas platyrhynchos) Identification of avian coronavirus in wild aquatic birds of the Central and Eastern USA Surveillance of avian coronaviruses in wild bird populations of Korea Novel avian coronavirus and fulminating disease in guinea fowl Diverse gammacoronaviruses detected in wild birds from Madagascar First characterization of a Middle-East GI-23 lineage (Var2-like) of infectious bronchitis virus in Europe Isolation of avian infectious bronchitis coronavirus from domestic peafowl (Pavo cristatus) and teal (Anas) Retrospective testing and case series study of porcine delta coronavirus in US swine herds Identification of a novel coronavirus from a beluga whale by using a panviral microarray Broadly targeted multiprobe QPCR for detection of coronaviruses: coronavirus is common among mallard ducks (Anas platyrhynchos) Prevalence and phylogeny of coronaviruses in wild birds from the Bering Strait area (Beringia) Birds, migration and emerging zoonoses: West Nile Virus, Lyme disease, influenza A, and enteropathogens Reverse spillover of avian viral vaccine strains from domesticated poultry to wild birds Phylogenetic analysis of a highly conserved region of the polymerase gene from 11 coronaviruses and development of a consensus polymerase chain reaction assay A Massachusetts prototype like coronavirus isolated from wild peafowls is pathogenic to chickens An avian coronavirus in quail withr respiratory and reproductive signs Gammacoronavirus and deltacoronavirus in quail Gamma and deltacoronaviruses in quail and pheasants from Northern Italy S1 gene-based phylogeny of infectious bronchitis virus: an attempt to harmonize virus classification A case for the ancient origin of coronaviruses The avian coronavirus spike protein Novel receptor specificity of avian gammacoronaviruses that cause enteritis Temporal dynamics, diversity, and interplay in three components of the virodiversity of a Mallard population: influenza A virus, avian paramyxovirus and avian coronavirus High prevalence and putative lineage maintenance of avian coronaviruses in Scandinavian waterfowl Urbanization and the dynamics of RNA viruses in Mallards (Anas platyrhynchos) Coronavirus diversity, phylogeny and interspecies jumping Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus Discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus Genomic analysis and surveillance of the coronavirus dominant in ducks in China Moreover, CoVs other than IBVs, are identified in wild birds, which suggests that wild birds play a key role in the epidemiology of other gammaCoVs and deltaCoVs.
    keywords: avian; birds; coronaviruses; covs; gene; genome; ibv; novel; species; strains
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        item: #1071 of 1349
          id: cord-329493-ueqlhgn0
      author: Stadler, Konrad
       title: SARS — beginning to understand a new virus
        date: 2003
       words: 5153
      flesch: 43
     summary: Coronavirus as a possible cause of severe acute respiratory syndrome Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong Clinical presentations and outcome of severe acute respiratory syndrome in children Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Acute respiratory syndrome in China Summary of probable SARS cases with onset of illness from 1 Identification of a novel coronavirus in patients with severe acute respiratory syndrome A Nnvel coronavirus associated with severe acute respiratory syndrome Aetiology: Koch's postulates fulfilled for SARS virus Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome Transmission dynamics of the etiological agent of SARS in Hong Kong: impact of public health interventions Transmission dynamics and control of severe acute respiratory syndrome Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China SARS in China: tracking the roots of a killer Severe acute respiratory syndrome (SARS) in Singapore Virus Taxonomy The genome sequence of the SARSassociated coronavirus References 17 and 18 are the first reports of the complete genome sequences of two SARS-CoV isolates (TOR2 and Urbani strains, respectively) The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39) Mechanisms and enzymes involved in SARS coronavirus genome expression The complete genome sequence of a SARS-CoV isolate (FRA) and experimental data on its key RNA elements and protein functions are described. Their efficacy still needs to be shown, but our laboratory (and possibly others) are in the process of testing vaccines on the basis of inactivated SARS virus in pre-clinical models.
    keywords: coronavirus; cov; domain; genome; group; protein; rna; sars; sequence; spike; syndrome; virus
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        item: #1072 of 1349
          id: cord-329494-cdn52epy
      author: Artuso, María C.
       title: Inhibition of Junín virus replication by small interfering RNAs
        date: 2009-07-08
       words: 4784
      flesch: 39
     summary: JUNV is an enveloped, single stranded, ambisense RNA virus with a segmented genome consisting of two segments, designated large (L) and small (S). Role for a bidentate ribonuclease in the initiation step of RNA interference An arenavirus RING (zincbinding) protein binds the oncoprotein promyelocyte leukemia protein (PML) and relocates PML nuclear bodies to the cytoplasm The lymphocytic choriomeningitis virus RING protein Z associates with eukaryotic initiation factor 4E and selectively represses translation in a RING-dependent manner Antigenic relationships between attenuated and pathogenic strains of Junin virus Silencing E1A mRNA by RNA interference inhibits adenovirus replication Characterization of the arenavirus RING finger Z protein regions required for Z-mediated inhibition of viral RNA synthesis RING finger Z protein of Lymphocytic Choriomeningitis virus (LCMV) inhibits transcription and RNA replication of an LCMV S-segment minigenome Treatment of arenavirus infections: from basic studies to the challenge of antiviral therapy The first targeted delivery of siRNA in humans via a selfassembling, cyclodextrin polymer-based nanoparticle: from concept to clinic The proline-rich homeodomain (PRH/HEX) protein is down-regulated in liver during infection with lymphocytic choriomeningitis virus Functional anatomy of siRNA for mediating efficient RNAi in Drosophila melanogaster embryo lysate Inhibition of Marburg virus protein expression and viral release by RNA interference Differential inhibitory action of two azoic compounds against arenaviruses Arenavirus Z protein as an antiviral target: virus inactivation and protein oligomerization by zinc finger-reactive compounds Poliovirus escape from RNA interference: short interfering RNA-target recognition and implications for therapeutic approaches An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells Unlocking the potential of the human genome with RNA interference A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA Selective silencing of viral gene expression in HPV-positive human cervical carcinoma cells treated with siRNA, a primer of RNA interference RNA interference: from gene silencing to genespecific therapeutics Combination of small interfering RNA and lamivudine on inhibition of human B virus replication in HepG2.2.15 cells RNA interference effectively inhibits mRNA accumulation and protein expression of hepatitis C virus core and E2 genes in human cells Transcription and RNA replication of Tacaribe virus genome and antigenome analogs require N and L proteins: Z protein is an inhibitor
    keywords: cells; expression; inhibition; junv; protein; sirna; vero; virus
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        item: #1073 of 1349
          id: cord-329504-91te3nu8
      author: Croll, Tristan
       title: Making the invisible enemy visible
        date: 2020-10-07
       words: 4827
      flesch: 47
     summary: Visualizing an unseen enemy; mobilizing structural biology to counter COVID-19 RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education Announcing the worldwide Protein Data Bank Xtriage and Fest: automatic assessment of X-ray data and substructure structure factor estimation AUSPEX: a graphical tool for X-ray diffraction data analysis The PDB_REDO Server for Macromolecular Structure Model Optimization Errors in protein structures This has included a number of posts on our homepage aimed at non-scientists and live streaming the reprocessing of data on Twitch, as well as the design, production, and public release of an accurate 3D printed model of SARS-CoV-2 based on deposited structures for use as a prop for outreach activities.
    keywords: cov-2; data; errors; map; model; pdb; polymerase; protein; rna; sars; structures
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        item: #1074 of 1349
          id: cord-329527-0rlotyz3
      author: Bohmwald, Karen
       title: Neurologic Alterations Due to Respiratory Virus Infections
        date: 2018-10-26
       words: 11066
      flesch: 38
     summary: Besides respiratory tract infections, these viruses have been associated with neurological clinical manifestations in patients with a severe occurrence of the respiratory disease (Antonucci and Fanos, 2005; Akins et al., 2010; Antonucci et al., 2010; Desforges et al., 2014a; Fok et al., 2015; Algahtani et al., 2016) . Commonly, the invasion of the central nervous system (CNS) and the subsequent pathology have been more studied in infection caused by Japanese encephalitis virus (JEV), Varicella-Zoster virus (VZV), measles virus (MV) and human immunodeficiency virus (HIV), among others (Koyuncu et al., 2013) .
    keywords: brain; cells; cns; csf; detection; encephalitis; et al; hmpv; hrsv; human; infection; influenza; mice; patients; respiratory; viral; virus; viruses; year
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        item: #1075 of 1349
          id: cord-329618-kywhulpc
      author: Xu, Cheng
       title: A de novo transcriptome analysis shows that modulation of the JAK-STAT signaling pathway by salmonid alphavirus subtype 3 favors virus replication in macrophage/dendritic-like TO-cells
        date: 2016-05-23
       words: 8333
      flesch: 45
     summary: The type II receptor genes were subdivided into two groups namely the interleukin (IL) and IFN receptor genes. [45] suggest that Atlantic salmon possess two clusters type I IFN receptor genes located on different chromosomes which allow for a large repertoire of IFN receptors than mammals and zebrafish.
    keywords: analysis; cells; data; genes; ifn; infection; jak; pathway; receptor; rna; sav3; signaling; stat; table; treatment; type
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        item: #1076 of 1349
          id: cord-329687-vhi4tbnc
      author: Verdugo, C.
       title: A comparative evaluation of dye-based and probe-based RT-qPCR assay for the screening of SARS-CoV-2 using individual and pooled-sample testing.
        date: 2020-06-03
       words: 3506
      flesch: 54
     summary: Since the dye-based assay was not able to perform adequately using this approach, we do not recommend the use of this protocol in pooled pre-RNA extraction samples. A total of 5 µL of RNA sample was added to the final RT-qPCR mix.
    keywords: assay; dye; extraction; rna; samples
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        item: #1077 of 1349
          id: cord-329707-89zyu8bl
      author: Zhang, Xue
       title: Inhibition of SARS-CoV Gene Expression by Adenovirus-Delivered Small Hairpin RNA
        date: 2006-11-30
       words: 3220
      flesch: 49
     summary: 3 d, lane 3) , but To determine effects of shRNAs on viral RNA expression, total RNAs isolated from transfected cells were used as templates to synthesize cDNA. With availability of high titers of adenoviruses and uniform and rapid infection, this technology will have a foreseeable wide application both in experimental biology and molecular medicine. Identification of a novel coronavirus in patients with severe acute respiratory syndrome Coronavirus as a possible cause of severe acute respiratory syndrome Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study A novel coronavirus associated with severe acute respiratory syndrome Characterization of a novel coronavirus associated with severe acute respiratory syndrome The genome sequence of the SARS-associated coronavirus Philadelphia, Lippincott Williams & Wilkins Ribonucleoprotein-like structures from coronavirus particles The molecular biology of coronaviruses The nucleocapsid protein of coronavirus mouse hepatitis virus interacts with the cellular heterogeneous nuclear ribonucleoprotein A1 in vitro and in vivo Activation of AP-1 signal transduction pathway by SARS coronavirus nucleocapsid protein A highly conserved region of the Sendai virus nucleocapsid protein contributes to the NP-NP binding domain Hantavirus nucleocapsid protein coiled-coil domains
    keywords: cells; cov; expression; fig; gene; rna; sars; shrna; virus
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        item: #1078 of 1349
          id: cord-329710-vqorb6j7
      author: Kumar, Krishna
       title: Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment
        date: 2020-05-27
       words: 2481
      flesch: 42
     summary: By discussing the current inventory of viral inhibitors, we identify molecular scaffolds that may be improved by medicinal chemistry efforts for effective therapeutics to treat current and future coronavirus-caused diseases. Given that approximately a quarter of human proteases are predicted to belong to this class, design of specific viral inhibitors remains a challenge.
    keywords: coronavirus; cov-2; covid-19; helicase; host; inhibitors; sars
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        item: #1079 of 1349
          id: cord-329794-msxrdhb3
      author: Lu, Aili
       title: Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase
        date: 2004-06-20
       words: 2693
      flesch: 52
     summary: To test this possibility, in the present study, HeLa cells and 293 cells were transfected with SARS coronavirus RDRP, and the effect of RNAi on inhibition of RDRP of coronavirus was tested. shRNA reduced the production of SARS RDRP proteins To confirm the effect of shRNA on RDRP expression, we performed Western blot analysis.
    keywords: cells; coronavirus; expression; plasmid; rdrp; rna; sars
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        item: #1080 of 1349
          id: cord-329866-io9fvy58
      author: Lorusso, Eleonora
       title: Discrepancies between feline coronavirus antibody and nucleic acid detection in effusions of cats with suspected feline infectious peritonitis
        date: 2019-08-31
       words: 2812
      flesch: 36
     summary: Additional 13 samples presented FCoV antibody titres between 1:200 and 1:800, which are quite high for an enteric infection but cannot be considered enough high for a systemic infection. 1:1600 as cut-off (Fig. 1B) , 6 samples tested negative by both assays (no viral RNA and no FCoV antibodies), possibly accounting for diseases other than FIP, and 3 samples tested negative only by qRT-PCR, although they contained FCoV antibody titres between 1:3200 and 1:12,800, which were highly suggestive of FIP.
    keywords: antibody; effusions; fcov; fip; rna
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        item: #1081 of 1349
          id: cord-330045-4gj9d181
      author: Sun, Jiufeng
       title: Prolonged Persistence of SARS-CoV-2 RNA in Body Fluids
        date: 2020-08-17
       words: 1545
      flesch: 48
     summary: The estimated time until loss of virus RNA detection ranged from 45.6 days for nasopharyngeal swab samples to 46.3 days for feces samples in mild cases and from 48.9 days for nasopharyngeal swab samples to 49.4 days for feces samples in severe cases, which was longer than those of SARS-CoV and MERS-CoV (10,11). We found differences in median time until loss of virus RNA detection among respiratory specimen types in mild cases but not in severe cases (Table) .
    keywords: cov-2; rna; samples; sars
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        item: #1082 of 1349
          id: cord-330131-yfhrmbvx
      author: Danchin, Antoine
       title: Cytosine drives evolution of SARS‐CoV‐2
        date: 2020-04-27
       words: 5338
      flesch: 31
     summary: As parasites, viruses-especially those with small genomes, such as RNA viruses-do not generally code for functions that result in the construction of metabolic pathways. Viruses tap into the cell's resources, and this original setup of intermediary metabolism creates an intracellular chemical pressure that must constrain the evolution of the genome sequence of RNA viruses, in particular SARS-CoV-2.
    keywords: antiviral; cell; ctp; cytosine; et al; evolution; genome; growth; metabolism; rna; sars; viral; virus
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        item: #1083 of 1349
          id: cord-330200-l6bnxi40
      author: Huang, Jianping
       title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study
        date: 2020-04-27
       words: 4480
      flesch: 55
     summary: In addition, the seropositive rate for anti-S and anti-RBD IgM was significantly higher in viral RNA long persistence patients. Anti-RBD IgM and IgG levels, including anti-RBD IgM levels at presentation and peak time, were significantly higher in viral RNA short persistence patients than in long persistence patients.
    keywords: anti; cov-2; igm; patients; preprint; rna; sars
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        item: #1084 of 1349
          id: cord-330213-reb9vo7x
      author: Miladi, Milad
       title: The landscape of SARS-CoV-2 RNA modifications
        date: 2020-07-18
       words: 3215
      flesch: 47
     summary: RNA modifications are essential modulators of RNA stability and function. The recent invention of direct RNA sequencing protocols using nanopores enable unbiased detection of RNA modification.
    keywords: data; genome; modification; reads; rna; sars; sgrnas; sites; trs
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        item: #1085 of 1349
          id: cord-330800-s91zfzfi
      author: Reta, Daniel Hussien
       title: Molecular and Immunological Diagnostic Techniques of Medical Viruses
        date: 2020-09-04
       words: 10553
      flesch: 40
     summary: A H1N1 Virus 2009 by reverse-transcription loop-mediated isothermal amplification with hydroxynaphthol blue dye An updated loop-mediated isothermal amplification method for rapid diagnosis of H5N1 avian influenza viruses Loop-mediated isothermal amplification assay for rapid detection of hepatitis C virus Detection of acute HIV-1 infection by RT-LAMP Detection of Zika virus using reverse-transcription LAMP coupled with reverse dot blot analysis in saliva Infectious diseases detection by microarray: an overview of clinical relevant infections Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children Detection of herpesvirus and adenovirus co-infections with diagnostic DNA-microarrays DNA microarrays for virus detection in cases of central nervous system infection DNA microarray for detection of gastrointestinal viruses DNA microarray platform for detection and surveillance of viruses transmitted by small mammals and arthropods DNA probe array for the simultaneous identification of herpesviruses, enteroviruses, and flaviviruses Characterization of real-time microarrays for simultaneous detection of HIV-1, HIV-2, and hepatitis viruses A DNA microarray-based assay to detect dual infection with two dengue virus serotypes An efficient microarray-based genotyping platform for the identification of drug-resistance mutations in majority and minority subpopulations of HIV-1 Quasispecies Development of a simple microarray for genotyping HIV-1 drug resistance mutations in the reverse transcriptase gene in rural Tanzania Microarray-based genotyping and detection of drug-resistant HBV mutations from 620 Chinese patients with chronic HBV infection Development of a single nucleotide polymorphism DNA microarray for the detection and genotyping of the SARS coronavirus Diagnostic microarray for influenza B viruses Viral discovery and sequence recovery using DNA microarrays Metagenomics and the molecular identification of novel viruses DNA microarrays: types, applications and their future Next-generation sequencing for infectious disease diagnosis and management Current approaches for diagnosis of influenza virus infections in humans Application of next generation sequencing in clinical microbiology and infection prevention Assessing the performance of the Oxford nanopore technologies MinION Nanopore sequencing and assembly of a human genome with ultra-long reads Rapid and accurate sequencing of enterovirus genomes using MinION nanopore sequencer Whole genome sequencing of influenza A and B viruses with the MinION sequencer in the clinical setting: a pilot study Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples A method to identify respiratory virus infections in clinical samples using nextgeneration sequencing Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis First evaluation of the Next-Generation Sequencing platform for the detection of HIV-1 drug resistance mutations in Belgium Newly discovered Ebola virus associated with hemorrhagic fever outbreak in Uganda Next-generation sequencing and bioinformatic approaches to detect and analyze influenza virus in ferrets Metagenomic nextgeneration sequencing aids the diagnosis of viral infections in febrile returning travellers Nucleoprotein-based indirect enzyme-linked immunosorbent assay (indirect ELISA) for detecting antibodies specific to Ebola virus and Marbug virus Evaluation of antibody testing for SARS-CoV-2 using ELISA and lateral flow immunoassays Evaluation of ELISA tests for the qualitative determination of IgG, IgM and IgA to SARS-CoV-2 Development of an enzyme-linked immunosorbent assay for rapid detection of dengue virus (DENV) NS1 and differentiation of DENV serotypes during early infection Transmission of Herpes simplex virus type 2 among factory workers in Ethiopia Detection of severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in SARS patients by enzyme-linked immunosorbent assay Detection of hepatitis A, B, and C virus-specific antibodies using oral fluid for epidemiological studies Newly established monoclonal antibodies for immunological detection of H5N1 influenza virus High specificity of a novel Zika virus ELISA in European patients after exposure to different flaviviruses Laboratory diagnostics for HIV infection Development of a Western blot assay for detection of antibodies against coronavirus causing severe acute respiratory syndrome Western blot detection of human anti-Chikungunya virus antibody with recombinant envelope 2 protein Western blot-based logistic regression model for the identification of recent HIV-1 infection: a promising HIV-1 surveillance approach for resource-limited regions Early detection of anti-HCc antibody in acute hepatitis C virus (HCV) by western blot (immunoblot) using a recombinant HCV core protein fragment Detection of human immunodeficiency virus type 1 (HIV-1) antibody by western blotting and HIV-1 DNA by PCR in patients with AIDS Western blot profile in HIV infection Accuracy of rapid influenza diagnostic test and immunofluorescence assay compared to real time RT-PCR in children with influenza A(H1N1)pdm09 infection Immunofluorescence assay for serologic diagnosis of SARS Detection of herpes simplex virus in direct specimens by immunofluorescence assay using a monoclonal antibody Comparative evaluation of a simple indirect immunofluorescence test and mouse neutralization test for assaying rabies antibodies Molecular diagnostic techniques provide rapid viral detection in patient sample.
    keywords: amplification; assay; detection; diagnosis; dna; elisa; human; infection; influenza; pcr; reaction; rna; samples; sars; sensitivity; specificity; time; virus; viruses
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        item: #1086 of 1349
          id: cord-330847-a84pcc9z
      author: Edwards, M. C.
       title: RNA recombination in the genome of Barley stripe mosaic virus
        date: 1992-07-31
       words: 2353
      flesch: 57
     summary: Analysis of the resulting cDNA clones suggested that CV17 RNA y is a naturally occurring chimeric recombinant, composed of a 70nucleotide (nt) a-specific leader sequence preceding a r-specific coding region. Using an M 13 universal primer, six of these putative CV17 y clones were then sequenced in the region of the cDNA insert corresponding to the 5'-end of CV17 RNA y.
    keywords: cdna; clones; cv17; leader; rna; rnas
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        item: #1087 of 1349
          id: cord-330954-ft14aa2n
      author: Liu, B. M.
       title: Epidemiological characteristics of COVID-19 patients in convalescence period
        date: 2020-06-03
       words: 3791
      flesch: 49
     summary: key: cord-330954-ft14aa2n authors: Liu, B. M.; Yang, Q. Q.; Zhao, L. Y.; Xie, W.; Si, X. Y. title: Epidemiological characteristics of COVID-19 patients in convalescence period date: 2020-06-03 journal: Epidemiol Infect DOI: 10.1017/s0950268820001181 sha: doc_id: 330954 cord_uid: ft14aa2n However, the epidemiological characteristics of COVID-19 patients in isolation period have not been clarified.
    keywords: covid-19; detection; patients; rna
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        item: #1088 of 1349
          id: cord-331066-ediowz4s
      author: Chechetkin, Vladimir R.
       title: Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting
        date: 2020-09-09
       words: 7045
      flesch: 48
     summary: The interactions between genomic RNA and N proteins are assumed to be nonspecific and governed mainly by electrostatic effects. The proximal origin of SARS-CoV-2 Practical applications of DNA genotyping in diagnostic pathology DNA polymorphism in the b-esterase gene cluster of Drosophila melanogaster Entropy and GC content in the beta-esterase gene cluster of the Drosophila melanogaster subgroup Computational methods of identification of pseudogenes based on functionality: Entropy and GC content Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression Advanced topics in forensic DNA typing: Methodology Computational inference of selection underlying the evolution of the novel coronavirus, severe acute respiratory syndrome coronavirus 2 The SARS coronavirus nucleocapsid protein-forms and functions Multiple nucleic acid binding sites and intrinsic disorder of severe acute respiratory syndrome coronavirus nucleocapsid protein: Implications for ribonucleocapsid protein packaging Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein Spectral sum rules and search for periodicities in DNA sequences Levels of ordering in coding and non-coding regions of DNA sequences Large-scale chromosome folding versus genomic DNA sequences: A discrete double Fourier transform technique Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences Detection of large-scale noisy multi-periodic patterns with discrete double Fourier transform.
    keywords: cov-2; genomes; motifs; packaging; patterns; rna; sars
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        item: #1089 of 1349
          id: cord-331076-ak481qew
      author: Eskier, Doğa
       title: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load
        date: 2020-10-12
       words: 3865
      flesch: 39
     summary: We propose nsp14 as a priority research target for understanding genomic variance rate in SARS-CoV-2 isolates and nsp14 mutations as potential predictors for high mutability strains. Our results show that nsp14 mutations show the most consistent association with mutations between MoE and the whole genome.
    keywords: cov-2; genome; isolates; moe; mutation; nsp14; sars
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        item: #1090 of 1349
          id: cord-331414-i0oxm5mr
      author: Kautz, Tiffany F.
       title: A Low Fidelity Virus Shows Increased Recombination during the Removal of an Alphavirus Reporter Gene
        date: 2020-06-19
       words: 5071
      flesch: 40
     summary: RNA virus recombination primarily occurs when the RdRp switches from the template RNA strand to an acceptor RNA strand (i.e., copy choice recombination) or, less frequently, by ligation of cleaved RNA strands [8] . key: cord-331414-i0oxm5mr authors: Kautz, Tiffany F.; Jaworski, Elizabeth; Routh, Andrew; Forrester, Naomi L. title: A Low Fidelity Virus Shows Increased Recombination during the Removal of an Alphavirus Reporter Gene date: 2020-06-19 journal: Viruses DOI: 10.3390/v12060660 sha: doc_id: 331414 cord_uid: i0oxm5mr Reporter genes for RNA viruses are well-known to be unstable due to putative RNA recombination events that excise inserted nucleic acids.
    keywords: deletions; events; fidelity; fidelity tc-83; gene; gfp; passage; recombination; rna; tc-83; virus
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        item: #1091 of 1349
          id: cord-331509-p19dg1jw
      author: Bigault, Lionel
       title: Porcine epidemic diarrhea virus: Viral RNA detection and quantification using a validated one-step real time RT-PCR
        date: 2020-05-31
       words: 4322
      flesch: 50
     summary: In this study we described the development and validation of a SYBR™ Green one-step RT-qPCR according to the French norm NF U47-600, for the detection and quantification of PEDV viral RNA. This method is the first, validated according a norm for PEDV and may serve as a global reference method to harmonize detection and quantification of PEDV viral RNA in both field and experimental settings.
    keywords: detection; epidemic; indel; method; pedv; porcine; rna; strains; virus
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        item: #1092 of 1349
          id: cord-331607-2h56vb0n
      author: Jin, Xuejiao
       title: Three-Dimensional Architecture and Biogenesis of Membrane Structures Associated with Plant Virus Replication
        date: 2018-01-30
       words: 10726
      flesch: 25
     summary: The COPI system: molecular mechanisms and function Membrane curvature induced by Arf1-GTP is essential for vesicle formation Complex dynamic development of poliovirus membranous replication complexes Ion-abrasion scanning electron microscopy reveals surface-connected tubular conduits in HIV-infected macrophages Organization of the ER-Golgi interface for membrane traffic control The 5'-terminal region of a tombusvirus genome determines the origin of multivesicular bodies Morphogenesis of endoplasmic reticulum membrane-invaginated vesicles during beet black scorch virus infection: role of auxiliary replication protein and new implications of three-dimensional architecture The complete nucleotide sequence of beet black scorch virus (BBSV), a new member of the genus Necrovirus Cowpea mosaic virus infection induces a massive proliferation of endoplasmic reticulum but not Golgi membranes and is dependent on de novo membrane synthesis Relation of barley stripe mosaic virus to plastids A vicilin-like seed storage protein, PAP85, is involved in tobacco mosaic virus replication Inactivation of the host lipin gene accelerates RNA virus replication through viral exploitation of the expanded endoplasmic reticulum membrane Ultrastructural characterization of Zika virus replication factories Turnip mosaic virus RNA replication complex vesicles are mobile, align with microfilaments, and are each derived from a single viral genome Lipins: multifunctional lipid metabolism proteins Whole cell cryo-electron tomography reveals distinct disassembly intermediates of vaccinia virus Rtn1p is involved in structuring the cortical endoplasmic reticulum Cytoplasmic viral replication complexes Role of host reticulon proteins in rearranging membranes for positive-strand RNA virus replication Bromovirus-induced remodeling of host membranes during viral RNA replication Bromovirus RNA replication compartment formation requires concerted action of 1a's self-interacting RNA capping and helicase domains Membrane-shaping host reticulon proteins play crucial roles in viral RNA replication compartment formation and function Host ESCRT proteins are required for Bromovirus RNA replication compartment assembly and function Unconventional protein secretion Three-dimensional imaging of HIV-1 virological synapses reveals membrane architectures involved in virus transmission Electron tomography of ER, Golgi and related membrane systems Imaging of intracellular spherical lamellar structures and tissue gross morphology by a focused ion beam/scanning electron microscope (FIB/SEM) However, in yeast mutants in which peroxisome biogenesis is defective, TBSV replication sites are derived from the ER, which provides an optional subcellular membrane for virus replication (Jonczyk et al., 2007; Chuang et al., 2014) .
    keywords: cells; electron; et al; factories; formation; host; infection; membrane; mosaic; plant; proteins; replication; rna; sem; sites; spherules; structures; tbsv; vesicles; virus; viruses; yeast
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        item: #1093 of 1349
          id: cord-331680-qlzhtxs0
      author: Goryachev, A.N.
       title: Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model
        date: 2020-11-03
       words: 4113
      flesch: 43
     summary: antisense oligonucleotides consists in administering to the body of the patient a drug containing single-strand DNA chains which is complementary to any site of single-strand DNA or RNA, for example, virus RNA. Table 2 Genetic target sequences of the coronavirus genome for TRS1 and TRS2 drugs Name Nucleotide sequence of virus RNA (5 '-3') site trs1 GATCTGTTCTCTAAACGAAC site trs2 CTGTTCTCTAAACGAACTTTA *
    keywords: antisense; cells; drug; oligonucleotide; rna; sars; sequence; study; virus
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        item: #1094 of 1349
          id: cord-331802-wo462anq
      author: Xia, Hongjie
       title: Human Enterovirus Nonstructural Protein 2C(ATPase) Functions as Both an RNA Helicase and ATP-Independent RNA Chaperone
        date: 2015-07-28
       words: 9420
      flesch: 41
     summary: It is very likely that the RNA helicase activity of 2C ATPase plays such a dsRNA unwinding role during enteroviral RNA replication, which is consistent with our observations that 2C ATPase can facilitate RdRP-mediated enteroviral RNA synthesis in vitro by promoting the recycling of vRNA template (Fig 9) , and disrupting 2C ATPase RNA helicase activity in EV71 resulted in an almost complete loss of enteroviral RNA replication and virus production in cells (Fig 10) . The long unwinding road of RNA helicases RNA helicase proteins as chaperones and remodelers RNA helicases at work: binding and rearranging A guanosine-centric mechanism for RNA chaperone function RNA chaperones, RNA annealers and RNA helicases RNA chaperones exist and DEAD box proteins get a life Virus-encoded RNA helicases RNA remodeling by chaperones and helicases The hepatitis C virus NS3 protein: a model RNA helicase and potential drug target NTPase and 5'-RNA triphosphatase activities of Chikungunya virus nsP2 protein Cooperative translocation enhances the unwinding of duplex DNA by SARS coronavirus helicase nsP13 Identification and characterization of RNA duplex unwinding and ATPase activities of an alphatetravirus superfamily 1 helicase Philadelphia:
    keywords: 2c atpase; activities; activity; atpase; chaperone; ev71; ev71 2c; fig; helicase; helix; poliovirus; protein; remodeling; replication; rna; rna helicase; unwinding
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        item: #1095 of 1349
          id: cord-331916-n744pymd
      author: Liu, Jue
       title: Inhibition of porcine circovirus type 2 replication in mice by RNA interference
        date: 2006-04-10
       words: 6710
      flesch: 42
     summary: Inhibition of PCV2 viral protein synthesis in cell culture by shRNA is sequence-specific and dose-dependent To test whether RNAi could inhibit PCV2 in cell culture, we generated six shRNA-expressing plasmids targeting the ORF1 and ORF2 regions of the PCV2 genome (Fig. 1A) for their ability to suppress expression of PCV2 viral proteins. A dose -response analysis ( Fig. 2A ) was conducted by transfecting PK15 cells with increasing amounts of pSIR3, pSIR6, or negative control pVP2-expressing plasmid followed by measuring the numbers of PCV2 antigen cells by IFA 72 h post-transfection.
    keywords: cells; et al; expression; fig; infection; mice; pcv2; porcine; protein; psir3; replication; shrna; virus
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        item: #1096 of 1349
          id: cord-332003-67e9fchy
      author: Boisguérin, Prisca
       title: Delivery of therapeutic oligonucleotides with cell penetrating peptides()
        date: 2015-06-29
       words: 13090
      flesch: 35
     summary: key: cord-332003-67e9fchy authors: Boisguérin, Prisca; Deshayes, Sébastien; Gait, Michael J.; O'Donovan, Liz; Godfrey, Caroline; Betts, Corinne A.; Wood, Matthew J.A.; Lebleu, Bernard title: Delivery of therapeutic oligonucleotides with cell penetrating peptides() date: 2015-06-29 journal: Among the many proposed tools for delivery, cell penetrating peptides (CPPs) have appeared as an easy to implement strategy and have led to encouraging data at least in murine models of human diseases, as will be reviewed later in this chapter.
    keywords: activity; antisense; cell; complexes; conjugates; conjugation; covalent; cpp; cpps; delivery; dystrophin; exon; gene; mdx; mice; morpholino; mouse; ons; penetrating; peptide; pmo; pna; protein; sirna; splicing; uptake; vivo
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        item: #1097 of 1349
          id: cord-332006-if46jycd
      author: Whitehead, Kathryn A.
       title: Knocking down barriers: advances in siRNA delivery
        date: 2009
       words: 6667
      flesch: 29
     summary: The ease of siRNA delivery is partly dependent on the accessibility of the target organ or tissue within the body. Viral vectors, which were among the first vehicles to be studied for siRNA delivery, can induce unacceptable levels of toxicity through the activation of immune responses 66 .
    keywords: administration; cells; delivery; gene; lipid; liposomes; mice; nanoparticles; rnai; silencing; sirna; specific; target; targeting; therapeutic; vivo
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        item: #1098 of 1349
          id: cord-332024-jk983q4p
      author: Briese, Thomas
       title: Diagnostic System for Rapid and Sensitive Differential Detection of Pathogens
        date: 2005-02-17
       words: 1745
      flesch: 26
     summary: Multiplex primer sets were designed to identify up to 22 respiratory pathogens in a single Mass Tag PCR reaction; sensitivity was established by using synthetic DNA and RNA standards as well as titered viral stocks; the utility of Mass Tag PCR was determined in blinded analysis of previously diagnosed clinical specimens. After quantita-tion by UV spectrometry, RNA was serially diluted in 2.5µg/mL yeast tRNA (Sigma), reverse transcribed with random hexamers by using Superscript II (Invitrogen, Carlsbad, CA, USA), and used as template for Mass Tag PCR.
    keywords: detection; mass; multiplex; pathogens; pcr; rna; tag
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        item: #1099 of 1349
          id: cord-332270-fusfdkjw
      author: Lukiw, Walter J.
       title: Biomarkers for Alzheimer’s Disease (AD) and the Application of Precision Medicine
        date: 2020-09-21
       words: 5198
      flesch: 21
     summary: AD biomarkers also include protein, lipid, proteolipid, inflammatory cytokine, chemokine, carbohydrate, microRNA (miRNA), and messenger RNA (mRNA) abundance, speciation, and complexity, as well as an evolving assortment of neuro-radiological and neuroimaging technologies (Table 1) . AD biomarkers are certainly useful in the detection of dementing illness during its progressive course, and their appearance and magnitude correlate with cognitive loss in a dynamic way, allowing clinicians to monitor responses to therapeutic intervention across a background of aging of the AD patient.
    keywords: age; alzheimer; biomarkers; blood; brain; data; diagnosis; disease; mrna; neuroimaging; patient; rna
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        item: #1100 of 1349
          id: cord-332356-au7s3dmp
      author: Strandin, Tomas
       title: The cytoplasmic tail of hantavirus Gn glycoprotein interacts with RNA
        date: 2011-09-15
       words: 6576
      flesch: 43
     summary: Surprisingly, the antibodies against N protein precipitated exogenous RNA-N protein complexes very weakly if at all. The same pattern of RNA-bound proteins was observed with exogenous hantavirus S segment and the unRNA.
    keywords: binding; et al; genomic; hantavirus; protein; puuv; rna; tulv; virus
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        item: #1101 of 1349
          id: cord-332484-qy8vj6uu
      author: Pierini, Roberto
       title: Modulation of membrane traffic between endoplasmic reticulum, ERGIC and Golgi to generate compartments for the replication of bacteria and viruses
        date: 2009-04-01
       words: 4260
      flesch: 36
     summary: Targeting of host Rab GTPase function by the intravacuolar pathogen Legionella pneumophila Legionella pneumophila proteins that regulate Rab1 membrane cycling A bifunctional bacterial protein links GDI displacement to Rab1 activation The Legionella pneumophila effector protein DrrA is a Rab1 guanine nucleotideexchange factor Legionella subvert the functions of Rab1 and Sec22b to create a replicative organelle RNA interference analysis of Legionella in Drosophila cells: exploitation of early secretory apparatus dynamics Legionella pneumophila replication vacuole formation involves rapid recruitment of proteins of the early secretory system Parallels among positive strand RNA viruses, reverse transcribing viruses and double strand RNA viruses Inhibition of poliovirus RNA synthesis by brefeldin A Involvement of cellular membrane traffic proteins in poliovirus replication COPI activity coupled with fatty acid biosynthesis is required for viral replication Identification of essential host factors affecting tombusvirus RNA replication based on the yeast Tet promoters Hughes collection Poliovirus proteins induce membrane association of GTPase ADP ribosylation factor Hijacking components of the cellular secretory pathway for replication of poliovirus RNA A critical role of a cellular membrane traffic protein in poliovirus RNA replication Inhibition of cellular protein secretion by poliovirus proteins 2B and 3A A viral protein that blocks Arf-1 mediated COP-I assembly by inhibiting the guanine nucleotide exchange factor GBF1 Effects of picornavirus 3A proteins on protein transport and GBFIdependent COP-I recruitment Molecular determinants of the interaction between coxsackievirus protein 3A and guanine nucleotide exchange factor GBF1 Poliovirus protein 3A binds and inactivates LIS1, causing block of membrane protein trafficking and deregulation of cell division Poliovirus infection blocks ERGIC-to-Golgi trafficking and induces microtubule-dependent disruption of the Golgi complex Inhibition of cellular protein secretion by picornaviral 3A proteins Effects of foot-and-mouth disease virus nonstructural proteins on the structure and function of the early secretory pathway: 2BC but not 3A blocks endoplasmic reticulum-to-Golgi transport Differential requirements for COPI coats in formation of replication complexes among three genera of Picornaviridae Cellular COPII proteins are involved in production of the vesicles that form the poliovirus replication complex Intracellular location and translocation of silent and active poliovirus replication complexes Biogenesis of cytoplasmic membranous vesicles for plant potyvirus replication occurs at endoplasmic reticulum exit sites in a COPI-and COPII-dependent manner Subversion of cellular autophagosomal machinery by RNA viruses Inhibition of the secretory pathways by foot-and-mouth disease virus 2BC protein is reproduced by coexpression of 2B with 2C, and the site of inhibition is determined by the subcellular localisation of 2C Inhibition of protein trafficking by coxsackievirus b3: multiple viral proteins target a single organelle Reticulon 3 binds the 2C protein of enterovirus 71 and is required for viral replication Hepatitis C virus RNA polymerase and NS5A complex with a SNARE-like protein Human VAP-B is involved in hepatitis C virus replication through interaction with NS5A and NS5B Norwalk virus nonstructural protein p48 forms a complex with the SNARE regulator VAP-A and prevents cell surface expression of vesicular stomatitis virus G protein TBC1D20 is a Rab1 GTPase-activating protein that mediates hepatitis C virus replication A Rab-GAP TBC domain protein binds Hepatitis C virus NS5A and mediates virus replication Participation of Rab5, an early endosome protein, in hepatitis C virus RNA replication machinery Brucella intracellular replication requires trafficking through the late endosomal/lysosomal compartment Lounging in a lysosome: the intracellular lifestyle of Coxiella burnetii SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum Mouse hepatitis coronavirus RNA replication depends on GBF1-mediated ARF1 activation Localization and membrane topology of coronavirus nonstructural protein 4: involvement of the early secretory pathway in replication The unique architecture of Bunyamwera virus factories around the Golgi complex Fowlpox virus encodes nonessential homologs of cellular alpha-SNAP, PC-1, and an orphan human homolog of a secreted nematode protein African Swine Fever virus causes microtubule-dependent dispersal of the trans-Golgi network and slows delivery of membrane protein to the plasma membrane The subcellular distribution of multigene family 110 proteins of African Swine Fever virus is determined by differences in C-terminal KDEL endoplasmic reticulum retention motifs
    keywords: golgi; membrane; pathway; proteins; rab1; recruit; replication; rna; salmonella; vesicles; virus
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        item: #1102 of 1349
          id: cord-332632-u2ud0vmq
      author: Lussi, Carmela
       title: What can pestiviral endonucleases teach us about innate immunotolerance?
        date: 2016-03-17
       words: 8710
      flesch: 36
     summary: The replicative intermediate molecule of bovine viral diarrhoea virus contains multiple nascent strands Characterization of RNA synthesis during a one-step growth curve and of the replication mechanism of bovine viral diarrhoea virus Properties of the bovine viral diarrhoea virus replicase in extracts of infected MDBK cells Doublestranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses Role of doublestranded RNA and N pro of classical swine fever virus in the activation of monocyte-derived dendritic cells The viral RNase E rns prevents IFN type-I triggering by pestiviral single-and doublestranded RNAs Morphogenesis of pestiviruses: new insights from ultrastructural studies of strain giraffe-1 A cellular Jdomain protein modulates polyprotein processing and cytopathogenicity of a pestivirus The double-stranded RNA-induced apoptosis pathway is involved in the cytopathogenicity of cytopathogenic Bovine viral diarrhea virus Intracellular detection of viral nucleic acids BVDV: a pestivirus inducing tolerance of the innate immune response Self and nonself manipulation of interferon defense during persistent infection: bovine viral diarrhea virus resists alpha/beta interferon without blocking antiviral activity against unrelated viruses replicating in its host cells Classical swine fever virus N pro limits type I interferon induction in plasmacytoid dendritic cells by interacting with interferon regulatory factor 7 The amino-terminal domain of bovine viral diarrhea virus N pro protein is necessary for alpha/beta interferon antagonism RNasedependent inhibition of extra-but not intracellular, dsRNA-induced IFN synthesis by E rns of pestiviruses Classical swine fever virus interferes with cellular antiviral defense: evidence for a novel function of N pro No love lost between viruses and interferons Interferons and viruses: an evolutionary arms race of molecular interactions Microbial sensing by toll-like receptors and intracellular nucleic acid sensors, Cold Spring Harbor Perspect Viral RNA detection by RIG-I-like receptors Identification of the role of RIG-I, MDA-5 and TLR3 in sensing RNA viruses in porcine epithelial cells using lentivirus-driven RNA interference Efficient sensing of infected cells in absence of virus particles by plasmacytoid dendritic cells is blocked by the viral ribonuclease E rns Fc gamma RII-dependent sensitisation of natural interferonproducing cells for viral infection and interferon-alpha responses Extracellular dsRNA: its function and mechanism of cellular uptake Autophagydependent viral recognition by plasmacytoid dendritic cells Autophagy during early stages contributes to bovine viral diarrhea virus replication in MDBK cells N pro expressed in virus infected cells is responsible for polyubiquitinylation and proteasomal degradation of the transcription factor IRF-3 in an as yet unknown manner but without requiring its proteolytic activity.
    keywords: acids; activation; bovine; cells; dsrna; e rns; host; ifn; infection; rna; rnase; rns; self; type; virus; viruses
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        item: #1103 of 1349
          id: cord-332710-2s14knw6
      author: Lai, Michael M.C.
       title: Recombination in large RNA viruses: Coronaviruses
        date: 1996-12-31
       words: 4205
      flesch: 34
     summary: Recombination between nonsegmented RNA genomes of murine coronaviruses Coronavirus: organization, replication and expression of genome Evidence for coronavirus discontinuous transcription Coronavirus leader RNA regulates and initiates subgenomic mRNA transcription, both in trans and in cis Multiple recombination sites at the 5'-end of murine coronavirus RNA In vivo RNA-RNA recombination of coronavirus in mouse brain RNA recombination of murine coronaviruses: Recombination between fusion-positive MHV-A59 and fusion-negative MHV-2 Highfrequency RNA recombination of murine coronaviruses RNA recombination of coronaviruses: Localization of neutralizing epitopes and neuropathogenic determinants on the carboxyl terminus of peplomers Recombination between Sindbis virus RNA Generation and analysis of nonhomologous RNA-RNA recombinants in brome mosaic virus: Sequence complementarities at crossover sites Recombination between satellite RNAs of turnip crinkle virus RNA recombination in animal and plant viruses Establishing a genetic recombination map for murine coronavirus strain A59 complementation groups Genetics of picronaviruses Evidence for variable rates of recombination in the MHV genome Map locations of mouse hepatitis virus temperature-sensitive mutants: Confirmation of variable rates of recombination Phylogeny of antigenic variants of avian coronavirus IBV Sequence analysis of strains of avian infectious bronchitis coronavirus isolated during the 1960s in the UK Evidence of natural recombination within the S1 gene of the infectious bronchitis virus Evolutionary implications of genetic variations in the S1 gene of infectious bronchitis virus A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains Experimental evidence of recombination in coronavirus infectious bronchitis virus Structure of the intracellular defective viral RNAs of defective interfering particles of mouse hepatitis virus Natural evolution of coronavirus defective-interfering RNA involves RNA recombination Translation but not the encoded sequence is essential for the efficient propagation of the defective interfering RNAs of the coronavirus mouse hepatitis virus A cis-acting viral protein is not required for the replication of a coronavirus defective-interfering RNA The fitness of defective interfering murine coronavirus DI-a and its derivatives is decreased by nonsense and frameshift mutations Generation and selection of coronavirus defective interfering RNA with large open reading frame by RNA recombination and possible editing High-frequency leader sequence switching during coronavirus defective interfering RNA replication The UCUAAAC promoter motif is not required for high-frequency leader recombination in bovine coronavirus defective interfering RNA Repair and mutagenesis of the genome of a deletion mutant of the coronavirus mouse hepatitis virus by targeted RNA recombination RNA recombination in a coronavirus: Recombination between viral genomic RNA and transfected RNA fragments Homologous RNA recombination allows efficient introduction of site-specific mutations into the genome of coronavirus MHV-A59 via synthetic co-replicating RNAs Optimization of targeted RNA recombination and mapping of a novel nucleocapsid gene mutation in the coronavirus mouse hepatitis virus Analysis of second-site revertants of a murine coronavirus nucleocapsid protein deletion mutant and construction of nucleocapsid protein mutants by targeted RNA recombination Deletion mapping of a mouse hepatitis virus defective-interfering RNA reveals the requirement of an internal and discontiguous sequence for replication Analysis of cis-acting sequences essential for coronavirus defective interfering RNA replication Construction of murine coronavirus mutants containing interspecies chimeric nucleocapsid proteins Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Sequence of mouse hepatitis virus A59 mRNA 2: Indications for RNA-recombination between coronavirus and influenza C virus Comparison of the genome organization of toro-and coronaviruses: evidence for two nonhomologous RNA recombination events during Berne virus evolution Analysis of intracellular small RNAs of mouse hepatitis virus: Evidence for discontinuous transcription Template-determined, variable rate of RNA chain elongation A clustering of RNA recombination sites adjacent to a hypervariable region of the peplomer gene of murine coronavirus Random nature of coronavirus RNA recombination in the absence of selection pressure The mechanism of RNA recombination in poliovirus Identification of a 3'-→5' exonuclease activity associated with human RNA polymerase II RNA cleavage and chain elongation by Escherichia coli DNAdependent RNA polymerase in a binary enzyme-RNA complex Sequences and structures required for recombination between virus-associated RNAs RNA determinants of junction site selection in RNA virus recombinants and defective interfering RNAs I would like to thank Daphne Shimoda for editorial assistance. Thus, coronavirus RNA recombination is an important biological phenomenon for coronavirus and serves as an excellent model for viral RNA recombination in general.
    keywords: coronavirus; gene; recombination; rna; rnas; sequence; viruses
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        item: #1104 of 1349
          id: cord-332747-u46xryoo
      author: Mingorance, Lidia
       title: Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation
        date: 2018-09-18
       words: 10427
      flesch: 31
     summary: These results underscore the role that lipin1 plays at early steps of HCV infection and indicate that either viral entry or a step leading to efficient HCV RNA replication is impaired in these cells. Infection of control and lipin1 isoform-deficient cells with HCV tcp revealed that lipin1α silencing resulted in a strong (85%) reduction in HCV infection while lipin1β silencing resulted in a milder (55%) but significant reduction in HCV infection efficiency ( Fig 4B) .
    keywords: accumulation; activity; cells; control; expression; fig; hcv; hepatitis; hours; infection; levels; lipin1; luciferase; ns3; post; protein; replicase; replication; rna; shlpin1; silencing; virus
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        item: #1105 of 1349
          id: cord-332844-2se4d1yp
      author: Yun, Sang-Im
       title: Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses
        date: 2015-12-29
       words: 4809
      flesch: 34
     summary: Recover the cloned BAC DNA from the host cells by a column-based purification method (Figure 1C) Pick six to eight bacterial colonies from the LB-Cml agar plates and inoculate them into 3 ml of 2xYT broth containing 10 µg/ml Cml Perform two analytical restriction enzyme digestions of the isolated BACs for ~6 hr in a total volume of 10 µl, one to identify the presence of the vector with a correct insert using the same enzymes used for cloning (see Protocol 3.1), and the other to test the integrity of the cloned BACs with an appropriate enzyme Propagate the correctly cloned BACs by inoculating 500 µl of the positive bacterial cultures (from Protocol 3.5.1) in 500 ml of 2xYT-Cml medium and cultivating the inoculum for 6 hr at 35 °C while shaking at 225-250 rpm Reverse genetics of RNA viruses: applications and perspectives QB DNA-containing hybrid plasmids giving rise to QB phage formation in the bacterial host Cloned poliovirus complementary DNA is infectious in mammalian cells RNA virus reverse genetics and vaccine design Infectious transcripts and cDNA clones of RNA viruses Multicomponent RNA plant virus infection derived from cloned viral cDNA cDNA cloning and in vitro transcription of the complete brome mosaic virus genome Functional cDNA clones of the Flaviviridae: strategies and applications Construction of a severe acute respiratory syndrome coronavirus infectious cDNA clone and a replicon to study coronavirus RNA synthesis Systematic assembly of a full-length infectious cDNA of mouse hepatitis virus strain A59 Reverse genetics with a full-length infectious cDNA of severe acute respiratory syndrome coronavirus Coronavirus reverse genetics by targeted RNA recombination Reverse genetics of coronaviruses using vaccinia virus vectors Systematic assembly of a full-length infectious clone of human coronavirus NL63 Reverse genetics with a full-length infectious cDNA of the Middle East respiratory syndrome coronavirus Engineering the largest RNA virus genome as an infectious bacterial artificial chromosome Engineering a replication-competent, propagation-defective Middle East respiratory syndrome coronavirus as a vaccine candidate The making of infectious viral RNA: No size limit in sight Construction of large DNA segments in Escherichia coli Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector Construction of a 750-kb bacterial clone contig and restriction map in the region of human chromosome 21 containing the progressive myoclonus epilepsy gene PACs and MACs: artificial chromosomes as research tools Choosing a cloning vector Generation of recombinant pestiviruses using a full-genome amplification strategy An improved reverse genetics system for generation of bovine viral diarrhea virus as a BAC cDNA Construction of an infectious cDNA clone for a Brazilian prototype strain of dengue virus type 1: characterization of a temperature-sensitive mutation in NS1 Development and application of a reverse genetics system for Japanese encephalitis virus A molecularly cloned, live-attenuated Japanese encephalitis vaccine SA 14 -14-2 virus: a conserved single amino acid in the ij hairpin of the viral E glycoprotein determines neurovirulence in mice Development of a novel DNA-launched dengue virus type 2 infectious clone assembled in a bacterial artificial chromosome Identification of 5' and 3' cis-acting elements of the porcine reproductive and respiratory syndrome virus: acquisition of novel 5' AU-rich sequences restored replication of a 5'-proximal 7-nucleotide deletion mutant Recovery of a neurovirulent human coronavirus OC43 from an infectious cDNA clone Molecular characterization of feline infectious peritonitis virus strain DF-2 and studies of the role of ORF3abc in viral cell tropism Virus taxonomy: eighth report of the International Committee on Taxonomy of Viruses. For RNA virologists, the advent of recombinant DNA technology in the late 1970s made it possible to convert viral RNA genomes into cDNA clones, which could then be propagated as plasmids in bacteria for the genetic manipulation of RNA viruses.
    keywords: bac; cdna; cells; encephalitis; figure; genome; length; rna; strand; virus; viruses
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        item: #1106 of 1349
          id: cord-332992-8rmqg4rf
      author: de Vries, A. A. F.
       title: SARS-CoV-2/COVID-19: a primer for cardiologists
        date: 2020-07-15
       words: 9215
      flesch: 31
     summary: Front Public Health Trained immunity: a tool for reducing susceptibility to and the severity of SARS-CoV-2 infection Complement as a target in COVID-19? COVID-19: immunopathology and its implications for therapy Immune-inflammatoryparameters in COVID-19 cases: a systematic review and meta-analysis AntibodyresponsestoSARS-CoV-2 in patients with COVID-19 IgA-Ab response to spike glycoprotein of SARS-CoV-2 in patients with COVID-19: a longitudinal study Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals Detection of SARS-CoV-2-specific humoral and cellular immunity in COVID-19 convalescent individuals Diagnostic testing for severe acute respiratory syndrome-related coronavirus 2: a narrative review Towards effective diagnostic assays for COVID-19: a review Coronavirus pandemic-therapy and vaccines Vaccines for SARS-CoV-2: lessons from other coronavirus strains AreviewofSARS-CoV-2 and the ongoing clinical trials Early death after feline infectious peritonitis virus challenge due to recombinant vaccinia virus immunization The challenges of vaccine development against a new virus during a pandemic The current and future state of vaccines, antivirals and gene therapies against emerging coronaviruses A systematic review of antibody mediated immunity to coronaviruses: antibody kinetics, correlates of protection, and association of antibody responses with severity of disease COVID-19: Transmission, prevention, and potential therapeutic opportunities Renin-angiotensin system inhibition in COVID-19 patients A systematic review on use of aminoquinolines for the therapeutic management of COVID-19: efficacy, safety and clinical trials The possible mechanisms of action of 4-aminoquinolines (chloroquine/hydroxychloroquine) against SARS-CoV-2 infection (COVID-19): a role for iron homeostasis? Based on previous research on SARS-CoV and MERS-CoV and various animal models of virus-induced acute lung injury as well as haematological and biochemical laboratory findings in COVID-19 patients, the following scenarios can be envisioned [33, 34, 48, 49] .
    keywords: antibody; cells; coronavirus; cov-2; covid-19; disease; human; immune; infection; injury; onset; particles; patients; protein; rna; sars; transmission; vaccines; viral; virus
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        item: #1107 of 1349
          id: cord-333080-qytwbsne
      author: Alahari, Suresh K.
       title: SARS-CoV infection crosstalk with human host cell noncoding-RNA machinery: An in-silico approach
        date: 2020-07-28
       words: 2246
      flesch: 43
     summary: Also, significant GO categories for overlapped genes using the threshold of P < 0.05 and FDR < 0.05 showed meaningful predicted changes in enriched GO functions of the genes involved in interaction network, including those controlling the transforming growth factor-beta, transforming growth factor-beta receptor cytoplasmic mediator activity, and cellular response to endogenous stimulus. The COVID-19 pandemic in the US: a clinical update Regulation of microRNA biogenesis and its crosstalk with other cellular pathways Long noncoding RNAs and exosomal lncRNAs: classification, and mechanisms in breast cancer metastasis and drug resistance Non-coding RNAs in human disease Functional Interplay between RNA Viruses and Non-Coding RNA in Mammals Viral perturbations of host networks reflect disease etiology Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing STRING:
    keywords: cov; host; protein; sars
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        item: #1108 of 1349
          id: cord-333261-knj2rrut
      author: Albright, Catherine J.
       title: An exercise in molecular epidemiology: Human rhinovirus prevalence and genetics
        date: 2011-11-11
       words: 3417
      flesch: 56
     summary: HRV PCR products were sequenced to determine the genetic makeup of each field isolate. The average symptom, sleep, and stress scores were compared between HRV positive and HRV negative subjects and between reported sick and healthy subjects (Figs. 4a-4c) .
    keywords: hrv; pcr; rna; samples; stress; students; subjects; viruses
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        item: #1109 of 1349
          id: cord-333429-bq7kfpby
      author: Shi, Ding
       title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study
        date: 2020-07-02
       words: 3517
      flesch: 49
     summary: Underlying diseases has been shown to be related to prolonged viral shedding in SARS patients [6] . Several studies have reported that the use of corticosteroids is associated with delayed viral RNA clearance in MERS or SARS patients and even with higher mortality in influenza pneumonia
    keywords: group; patients; rna; sars; shedding; virus
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        item: #1110 of 1349
          id: cord-333473-c1lykari
      author: Irigoyen, Nerea
       title: High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling
        date: 2016-02-26
       words: 18283
      flesch: 51
     summary: [8] . Despite the very high MOI, virus RNA levels were low except, unexpectedly, in the N region where the mean RNASeq density was~27 times that in the ORF1a region. This study also provides insights into the challenges associated with the profiling of RNA viruses and suggests strategies that may prove beneficial in future studies.
    keywords: aug; codon; coronavirus; density; fig; host; initiation; length; mhv; mrna; orf; p.i; profiling; protein; reads; repeat; riboseq; ribosomal; ribosome; rna; rnaseq; rpfs; sequence; site; time; translation; upstream; virus
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        item: #1111 of 1349
          id: cord-333515-llqpfhwg
      author: Zhao, Juanjuan
       title: Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019
        date: 2020-03-03
       words: 3583
      flesch: 51
     summary: https://doi.org/10.1101/2020.03.02.20030189 doi: medRxiv preprint 15 Third, although it had shown good specificity in healthy people, the cross-reactivity among the different coronaviruses cannot be accurately assessed because we cannot obtain blood samples from SARS-CoV-1 and other coronaviruses infection patients. The total antibody (Ab), IgM antibody and IgG antibody against SARS-CoV-2 in plasma samples were tested using enzyme linked immunosorbent assay (ELISA) kits supplied All rights reserved.
    keywords: antibody; author; funder; license; medrxiv; patients; preprint
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        item: #1112 of 1349
          id: cord-333524-a6p6ma8r
      author: Khan, Pavana
       title: Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings
        date: 2020-09-23
       words: 8847
      flesch: 42
     summary: Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV Virus An Ultrasensitive, Rapid, and Portable Coronavirus SARS-CoV SARS-CoV-2 Detection with CRISPR Diagnostics CDetection: CRISPR-Cas12b-Based DNA Detection with Sub-Attomolar Sensitivity and Single-Base Specificity Development and Evaluation of Recombinase-Aided Amplification Assays Incorporating Competitive Internal Controls for Detection of Human Adenovirus Serotypes 3 and 7 Direct Observation of DNA Target Searching and Cleavage by CRISPR-Cas12a SHERLOCK: Nucleic Acid Detection with CRISPR Nucleases Pointof-Care Testing for COVID-19 Using SHERLOCK. CRISPR-based detection uses both primer-specific amplification and guide RNA directed detection, thus increasing sequence specificity in two different ways.
    keywords: amplification; cov-2; crispr; detection; dna; isothermal; lamp; nucleic; pcr; polymerase; primers; reaction; rna; rpa; sars; sequence; use
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        item: #1113 of 1349
          id: cord-333547-88dkh6xd
      author: Hasan, Shadi W.
       title: Detection and Quantification of SARS-CoV-2 RNA in Wastewater and Treated Effluents: Surveillance of COVID-19 Epidemic in the United Arab Emirates
        date: 2020-10-19
       words: 3982
      flesch: 41
     summary: Different methods for wastewater virus concentration have been adopted by different groups around the world It was also observed that the precautionary measures implemented by the UAE government correlated with a drop in the measured viral load in wastewater samples, which were in line with the reduction of COVID-19 cases reported in the population.
    keywords: cases; cov-2; covid-19; method; rna; sars; virus; viruses; wastewater
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        item: #1114 of 1349
          id: cord-333636-h2sg6shp
      author: Kochan, G.
       title: Characterization of the RNA-binding activity of VP3, a major structural protein of Infectious bursal disease virus
        date: 2003
       words: 6013
      flesch: 47
     summary: The affinity of VP3 protein to ssRNA was estimated from three independent experiments using 32 P-labeled virus ssRNA probes. Assuming that the plateau reached represented the complete binding of the RNA, the apparent Kd corresponded to the concentration of VP3 protein required to reach half saturation [21] .
    keywords: activity; binding; bursal; complexes; disease; fig; ibdv; probe; protein; purified; ssrna; virus; vp3
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        item: #1115 of 1349
          id: cord-333979-bx2xspbe
      author: Kalikiri, Mahesh K R
       title: High-throughput extraction of SARS-CoV-2 RNA from nasopharyngeal swabs using solid-phase reverse immobilization beads
        date: 2020-04-11
       words: 2031
      flesch: 46
     summary: For all subsequent experiments we added 0.5 µg of carrier RNA per extraction sample, mixed into the RLT buffer. The increased demand for laboratory testing has led to global shortages of all the required supplies, from personal protective equipment such as N95 masks, to swabs, and even the reagents required for viral RNA extraction.
    keywords: extraction; method; rna; samples
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        item: #1116 of 1349
          id: cord-334082-fyxn0g3v
      author: O’Carroll, I.P.
       title: Viral Nucleic Acids
        date: 2015-08-20
       words: 5500
      flesch: 50
     summary: In contrast, cells do not normally make copies of RNA molecules; thus, RNA viruses must encode the proteins needed for RNA replication, including the RNA-dependent RNA polymerase. Another striking difference between DNA and RNA viruses is in the range of their genome sizes: while the largest RNA virus genomes, those of the coronaviruses, are approximately 32 kb, DNA viral genomes can be nearly 100 times larger, as Pandoravirus DNA is approximately 2.5 Â 10 6 bp.
    keywords: cell; dna; genomes; proteins; replication; rna; rnas; strand; viruses
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        item: #1117 of 1349
          id: cord-334123-wb45ww7f
      author: Schimmel, Paul
       title: RNA pseudoknots that interact with components of the translation apparatus
        date: 1989-07-14
       words: 3336
      flesch: 56
     summary: Regardless of the detailed interpretation of the experiments, the analysis of RNA structure by these methods is instructive and has provided one of the first examples of a functional probe for pseudoknot formation. key: cord-334123-wb45ww7f authors: Schimmel, Paul title: RNA pseudoknots that interact with components of the translation apparatus date: 1989-07-14 journal: Cell DOI: 10.1016/0092-8674(89)90395-4 sha: doc_id: 334123 cord_uid: wb45ww7f nan It is not a long extrapolation to recognize that the unanticipated structural motifs that were found in tRNA are underpinnings of the RNA pseudoknot.
    keywords: et al; pseudoknot; structure; trna
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        item: #1118 of 1349
          id: cord-334299-0zn1z7rc
      author: Ahmed, Warish
       title: Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information
        date: 2020-09-30
       words: 1374
      flesch: 35
     summary: The review highlights areas for potential standardization including considerations related to sampling timing and frequency relative to peak fecal loading times; inclusion of appropriate information on sample volume collected; sample collection points; transport and storage conditions; sample concentration and processing; RNA extraction process and performance; effective volumes; PCR inhibition; process controls throughout sample collection and processing; PCR standard curve performance; and recovery efficiency testing. In order to obtain high quality RNA of SARS-CoV-2 for RT-qPCR analysis, several factors need to be 279 considered, including the RNA extraction procedures, the concentration, purity, and integrity of the While wastewater surveillance for SARS-CoV-2 has the potential to act as an early warning system, 329 the merit for WBE will be influenced by site selection and can only be realised with rapid turnround.
    keywords: cov-2; rna; sars; wastewater
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        item: #1119 of 1349
          id: cord-334315-ymkrgj0h
      author: Moon, Stephanie L.
       title: Cytoplasmic Viruses: Rage against the (Cellular RNA Decay) Machine
        date: 2013-12-05
       words: 1998
      flesch: 37
     summary: Picornaviruses use an aggressive mechanism for suppression of host RNA decay factors. The dispersal of P-bodies (cytoplasmic aggregates of host RNA decay factors) in several viral infections is also evidence of disruption of cellular RNA decay activities [6] .
    keywords: cellular; decay; host; rna; viruses
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        item: #1120 of 1349
          id: cord-334394-qgyzk7th
      author: Edgar, Robert C.
       title: Petabase-scale sequence alignment catalyses viral discovery
        date: 2020-08-10
       words: 8139
      flesch: 49
     summary: Innovative fields such as high-throughput functional viromics [39] leverage these broad and rapidly growing collections of viral sequences, and can inform evidence-based policies responding to emerging pandemics [40, 41] . Accurate annotation of CoV genomes is challenging due to ribosomal frameshifts and polyproteins which are cleaved into maturation proteins [56] , and thus previously-annotated viral genomes offer a guide to accurate gene-calls and protein functional predictions.
    keywords: alignment; annotation; assembly; contigs; cov; coverage; data; family; figure; genome; identity; rdrp; reads; reference; rna; sequence; sequencing; serratus; sra; study; tree; virus
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        item: #1121 of 1349
          id: cord-334463-nvu5tqxb
      author: Kim, Chonsaeng
       title: Echovirus 7 Entry into Polarized Intestinal Epithelial Cells Requires Clathrin and Rab7
        date: 2012-04-10
       words: 6232
      flesch: 40
     summary: To monitor requirements for uncoating, we pretreated Caco-2 cells with inhibitors, exposed them to NR-EV7, and allowed infection to proceed in the dark for 90 min. Cells were then exposed to light, harvested, replated on cell monolayers, overlaid with agar, and incubated to permit the appearance of infectious centers. tracellular trafficking events required for EV7 entry, we tested whether Rab5 and Rab7 were required for virus infection.
    keywords: cells; clathrin; cvb3; daf; dynamin; endosomes; entry; ev7; fig; infection; rna; uncoating; virus
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        item: #1122 of 1349
          id: cord-334771-uy3s6443
      author: Rao, BL
       title: A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus
        date: 2004-09-09
       words: 3675
      flesch: 45
     summary: Virus was isolated from six patients with encephalitis and was identified as Chandipura virus by electron microscopy, complement fixation, and neutralisation tests. Neutralising, IgG, and IgM antibodies to Chandipura virus were present in some patients' serum samples.
    keywords: antibodies; chandipura; encephalitis; igm; outbreak; patients; rna; samples; serum; virus
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        item: #1123 of 1349
          id: cord-334891-4jgtxg07
      author: Choudhury, Abhigyan
       title: In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human
        date: 2020-11-11
       words: 2937
      flesch: 43
     summary: The Brazilian Journal of Infectious Diseases Recognition of GU-rich polyadenylation regulatory 13 elements by human CstF-64 protein Coronavirus infections and immune responses The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 18 (SARS CoV-2 or n-COV19), the Cause of COVID-19 Identifying discriminative classification-based motifs 21 in biological sequences Learning Framework for 1 Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary 2 Information Predicting RNA-Protein Interactions Using Only 5 Sequence Information HDOCK: a web server for protein-protein 8 and protein-DNA/RNA docking based on a hybrid strategy PLIP: fully automated 11 protein-ligand interaction profiler iMODS: internal coordinates 14 normal mode analysis server Designing of a novel multi-epitope peptide based 17 vaccine against Brugia malayi: 15 Our study focuses principally on the interactions of the intracellular TLRs with the mRNA 16 fragments, and molecular docking studies play a pivotal role in this study by precisely Table S1 .
    keywords: binding; complex; cov-2; figure; mrna; protein; sars; studies; tlrs
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        item: #1124 of 1349
          id: cord-334947-pa0p5dif
      author: Rozen-Gagnon, Kathryn
       title: Alphavirus Mutator Variants Present Host-Specific Defects and Attenuation in Mammalian and Insect Models
        date: 2014-01-16
       words: 8911
      flesch: 37
     summary: The broadspectrum antiviral ribonucleoside ribavirin is an RNA virus mutagen The mechanism of action of ribavirin: lethal mutagenesis of RNA virus genomes mediated by the viral RNA-dependent RNA polymerase Deduced consensus sequence of Sindbis virus strain AR339: mutations contained in laboratory strains which affect cell culture and in vivo phenotypes Isolation of fidelity variants of RNA viruses and characterization of virus mutation frequency Command-line tools for processing biological sequencing data Fast and accurate short read alignment with Burrows-Wheeler transform The Sequence Alignment/Map format and SAMtools ANDES: Statistical tools for the ANalyses of DEep Sequencing Development of a highly protective combination monoclonal antibody therapy against Chikungunya virus Chikungunya virus in US travelers returning from India Changing patterns of chikungunya virus: reemergence of a zoonotic arbovirus Entry is a rate-limiting step for viral infection in a Drosophila melanogaster model of pathogenesis Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity Engineering attenuated virus vaccines by controlling replication fidelity Determinants of RNA-dependent RNA polymerase (in)fidelity revealed by kinetic analysis of the polymerase encoded by a foot-and-mouth disease virus mutant with reduced sensitivity to ribavirin Structure-function relationships of the viral RNA-dependent RNA polymerase: fidelity, replication speed, and initiation mechanism determined by a residue in the ribose-binding pocket RNA virus error catastrophe: direct molecular test by using ribavirin Mosquitoes put the brake on arbovirus evolution: experimental evolution reveals slower mutation accumulation in mosquito than vertebrate cells The West Nile virus mutant spectrum is host-dependant and a determinant of mortality in mice Genetic diversity and purifying selection in West Nile virus populations are maintained during host switching Finescale genetic variation and evolution of West Nile Virus in a transmission 'hot spot Adaptation of two flaviviruses results in differences in genetic heterogeneity and virus adaptability West Nile virus genetic diversity is maintained during transmission by Culex pipiens quinquefasciatus mosquitoes Natural resistance-associated macrophage protein is a cellular receptor for sindbis virus in both insect and mammalian hosts Beyond RNAi: antiviral defense strategies in Drosophila and mosquito Belshaw R (2010) The cost of replication fidelity in human immunodeficiency virus type 1 The cost of replication fidelity in an RNA virus A Polymerase mechanism-based strategy for viral attenuation and vaccine development Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population Error thresholds and the constraints to RNA virus evolution Mutation rates and rapid evolution of RNA viruses Mutation frequencies at defined single codon sites in vesicular stomatitis virus and poliovirus can be increased only slightly by chemical mutagenesis Lethal mutagenesis of HIV with mutagenic nucleoside analogs Increased fidelity reduces poliovirus fitness and virulence under selective pressure in mice Arbovirus high fidelity variant loses fitness in mosquitoes and mice Evolution of pig influenza viruses Ribavirin and lethal mutagenesis of poliovirus: molecular mechanisms, resistance and biological implications Viral error catastrophe by mutagenic nucleosides Theory of lethal mutagenesis for viruses Therapeutically targeting RNA viruses via lethal mutagenesis Back to the future: revisiting HIV-1 lethal mutagenesis Interrelationship between HIV-1 fitness and mutation rate Host alternation of chikungunya virus increases fitness while restricting population diversity and adaptability to novel selective pressures Factors shaping the adaptive landscape for arboviruses: implications for the emergence of disease Arbovirus evolution in vivo is constrained by host alternation Characterization of mosquito-adapted West Nile virus Effect of alternating passage on adaptation of sindbis virus to vertebrate and invertebrate cells West Nile virus experimental evolution in vivo and the trade-off hypothesis Vectorborne transmission imposes a severe bottleneck on an RNA virus population Genetic diversity and slow rates of evolution in New World alphaviruses Role of the mutant spectrum in adaptation and replication of West Nile virus Study of sequence variation of dengue type 3 virus in naturally infected mosquitoes and human hosts: implications for transmission and evolution Genetic variation in West Nile virus from naturally infected mosquitoes and birds suggests quasispecies structure and strong purifying selection Quasispecies of dengue virus Cooperative interactions in the West Nile virus mutant swarm NTPase and 59-RNA triphosphatase activities of Chikungunya virus nsP2 protein Differential unfolded protein response during Chikungunya and Sindbis virus infection: CHIKV nsP4 suppresses eIF2alpha phosphorylation The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket Chikungunya virus nsP3 blocks stress granule assembly by recruitment of G3BP into cytoplasmic foci BST-2/ tetherin-mediated restriction of chikungunya (CHIKV) VLP budding is counteracted by CHIKV non-structural protein 1 (nsP1) Biology and pathogenesis of chikungunya virus Replication cycle of chikungunya: a re-emerging arbovirus Role for conserved residues of sindbis virus nonstructural protein 2 methyltransferase-like domain in regulation of minus-strand synthesis and development of cytopathic infection Roles of nonstructural polyproteins and cleavage products in regulating Sindbis virus RNA replication and transcription O'nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3 Conservation of a packaging signal and the viral genome RNA packaging mechanism in alphavirus evolution Catalytic core of alphavirus nonstructural protein nsP4 possesses terminal adenylyltransferase activity
    keywords: cells; chikv; defects; fidelity; figure; frequencies; mosquito; mutation; mutator; polymerase; position; replication; rna; sinv; strains; variants; virus; viruses; wildtype
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        item: #1125 of 1349
          id: cord-335040-1qa6pe4v
      author: Rogstam, Annika
       title: Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2
        date: 2020-10-06
       words: 7436
      flesch: 52
     summary: Proteins with a significant z-score >20 included SARS nsp10 in the unbound form; SARS, MERS and SARS-CoV-2 nsp16-nsp10 complexes; and the SARS nsp14-nsp10 complex. The protein sequence of SARS nsp10 (NP_828868, 139 residues) was aligned with the Open Reading Frame 1ab (ORF1aB) of SARS-CoV-2 (GenBank: MN908947.3) to identify the location and sequence for nsp10.
    keywords: cov-2; data; figure; nsp10; protein; residues; rna; sars; sedimentation; structure; zinc
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        item: #1126 of 1349
          id: cord-335067-tg66h99q
      author: Woolhouse, Mark E.J.
       title: Ecological and taxonomic variation among human RNA viruses
        date: 2013-03-19
       words: 1396
      flesch: 53
     summary: The remaindercomprising almost half the total of human RNA virus species -is not known to be transmissible between humans at all. We can distinguish three categories of human RNA viruses based on their basic reproduction number in human populations (R 0 ).
    keywords: human; rna; viruses
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        item: #1127 of 1349
          id: cord-335231-617e5dcy
      author: Pettersson, Lisa
       title: Hantavirus RNA in Saliva from Patients with Hemorrhagic Fever with Renal Syndrome
        date: 2008-03-17
       words: 3335
      flesch: 46
     summary: The project was approved by the Research Ethics Committee of Umeå University and all patients gave written and informed consent. RNA from 140 μL of patient saliva and plasma was extracted by using a QIAamp Viral RNA kit (QIAGEN, Valencia, CA, USA) according to the manufacturer's instructions. Sequencing cDNA from patient saliva and plasma were amplifi ed by using Pfu DNA Polymerase (Fermentas Life Sciences, Helsingbord, Sweden), and the sequencing reactions were performed by using the Big Dye Terminator v 1.1 Cycle Sequencing kit (Applied Biosystems).
    keywords: hantavirus; human; patients; pcr; person; puuv; rna; saliva
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        item: #1128 of 1349
          id: cord-335377-zrbn637z
      author: Ishimaru, Daniella
       title: RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus
        date: 2012-12-26
       words: 7763
      flesch: 45
     summary: A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal An atypical RNA pseudoknot stimulator and an upstream attenuation signal for -1 ribosomal frameshifting of SARS coronavirus Mechanisms and enzymes involved in SARS coronavirus genome expression Comparative study of the effects of heptameric slippery site composition on -1 frameshifting among different eukaryotic systems Frameshifting RNA pseudoknots: structure and mechanism Programmed ribosomal frameshifting in decoding the SARS-CoV genome Mutational analysis of the RNA pseudoknot component of a coronavirus ribosomal frameshifting signal Ecoepidemiology and complete genome comparison of different strains of severe acute respiratory syndrome-related Rhinolophus bat coronavirus in China reveal bats as a reservoir for acute, self-limiting infection that allows recombination events A review of studies on animal reservoirs of the SARS coronavirus Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA Evidence that a kissing loop structure facilitates genomic RNA dimerisation in HIV-1 A 19-nucleotide sequence upstream of the 5 0 major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro Impact of human immunodeficiency virus type 1 RNA dimerization on viral infectivity and of stem-loop B on RNA dimerization and reverse transcription and dissociation of dimerization from packaging Dimerization of retroviral RNA genomes: an inseparable pair Genome of infectious bronchitis virus Biochemical aspects of coronavirus replication and virus-host interaction RNA structure determination by NMR NMRPipe: a multidimensional spectral processing system based on UNIX pipes University of California Absorption mode two-dimensional NOE spectroscopy of exchangeable protons in oligonucleotides Use of a water flip-back pulse in the homonuclear noesy experiment Pattern of 4-thiouridine-induced cross-linking in 16S ribosomal RNA in the Escherichia coli 30S subunit Systematic analysis of bicistronic reporter assay data Severe acute respiratory syndrome coronavirus infection of human ciliated airway epithelia: role of ciliated cells in viral spread in the conducting airways of the lungs Identification and characterization of severe acute respiratory syndrome coronavirus replicase proteins Clustal W and Clustal X version 2.0 Mfold web server for nucleic acid folding and hybridization prediction Dimerization of a pathogenic human mitochondrial tRNA Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets RNA LEGO: magnesium-dependent formation of specific RNA assemblies through kissing interactions Bipartite signal for genomic RNA dimerization in Moloney murine leukemia virus Hepatitis C virus genomic RNA dimerization is mediated via a kissing complex intermediate Kissing-loop model of HIV-1 genome dimerization: RNA pseudoknots implicated in -1
    keywords: cov; dimerization; figure; formation; frameshifting; imino; kissing; loop; pseudoknot; rna; s3l2; sars; sequence; stem; structure; type; virus
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        item: #1129 of 1349
          id: cord-335441-bj3me7p8
      author: Jourdain, Elsa
       title: Influenza Virus in a Natural Host, the Mallard: Experimental Infection Data
        date: 2010-01-28
       words: 6383
      flesch: 48
     summary: A virus A/Turkey/Minn/BF/72 (Hv6Neq2) Highly pathogenic avian influenza virus infection of Mallards with homo-and heterosubtypic immunity induced by low-pathogenic avian influenza viruses Effects of influenza A virus infection on migrating mallard ducks Electrocardiography, heart rates, and heart weights of free-living birds Characteristics of the febrile response in Pekin ducks Ecologic immunology of avian influenza (H5N1) in migratory birds Ecological immunology: life-history trade-offs and immune defense in birds Effect of intravenous inoculation of avian influenza virus on reproduction and growth in mallard ducks Hampered foraging and migratory performance in swans infected with lowpathogenic avian influenza A virus Practical considerations for high-throughput influenza A virus surveillance studies of wild birds by use of molecular diagnostic tests Sampling for low-pathogenic avian influenza A virus in wild Mallard ducks: oropharyngeal versus cloacal swabbing Coinfection of wild ducks by influenza A viruses: distribution patterns and biological significance Immunology of avian influenza virus: a review Bile immunoglobulin of the duck (Anas platyrhynchos). Likewise, local immunity may influence the outcome of duck infections and provide protection against further infections.
    keywords: birds; body; day; days; ducks; h7n7; infection; influenza; inoculation; mallards; study; temperature; viral; virus
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        item: #1130 of 1349
          id: cord-335443-iv2gs3kg
      author: Kim, Youngchang
       title: Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
        date: 2020-06-28
       words: 5475
      flesch: 48
     summary: Protein science : a publication of the Biochemical characterization of arterivirus nonstructural protein 11 reveals the nidovirus-wide conservation of a replicative endoribonuclease Trifluridine/Tipiracil (Lonsurf) for the Treatment of Metastatic Colorectal Cancer Turkey coronavirus non-structure protein NSP15--an endoribonuclease The severe acute respiratory syndrome coronavirus Nsp15 protein is an endoribonuclease that prefers manganese as a cofactor Mutational analysis of the SARS virus Nsp15 endoribonuclease: identification of residues affecting hexamer formation Functional plasticity of antibacterial EndoU toxins Structural and functional analyses of the severe acute respiratory syndrome coronavirus endoribonuclease Nsp15 Major genetic marker of nidoviruses encodes a replicative endoribonuclease Bovine pancreatic ribonuclease: fifty years of the first enzymatic reaction mechanism Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism Bovine pancreatic ribonuclease A as a model of an enzyme with multiple substrate binding sites Crystal structure of ribonuclease A.d(ApTpApApG) complex. Tipiracil, an uracil derivative, binds to Nsp15 uracil site in a manner consistent with competitive inhibition.
    keywords: base; binding; cov-2; endoribonuclease; fig; nsp15; rna; rnase; sars; site; structures; tipiracil; uracil
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        item: #1131 of 1349
          id: cord-335482-nx7odchj
      author: Makino, Shinji
       title: Defective interfering particles of mouse hepatitis virus
        date: 1984-02-29
       words: 3848
      flesch: 57
     summary: These results indicated that defective interfering particles were generated by serial undiluted passages of JHM virus. We have observed marked reduction of infectivity in the course od serial undiluted passages of JHM virus in DBT cell culture.
    keywords: cells; jhm; particles; passage; rna; standard; virus
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        item: #1132 of 1349
          id: cord-335614-qh98622y
      author: Xu, Puzhi
       title: A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus
        date: 2019-11-16
       words: 6557
      flesch: 35
     summary: To further study the biochemical metabolic pathway and signal transduction pathways related to NIBV infection, KEGG analysis and pathway enrichment analysis were conducted in the KEGG pathway database. MetaboAnalyst (http: //www.metaboanalyst.ca) was used for pathway enrichment analysis.
    keywords: acid; analysis; chicken; data; figure; gene; gout; group; gut; infection; kidney; metabolism; metabolites; nibv; pathways; receptor; rna; signalling; study
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        item: #1133 of 1349
          id: cord-335864-392xmrq0
      author: Sun, Yu-Meng
       title: Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application
        date: 2020-08-10
       words: 13950
      flesch: 41
     summary: Expression and association with the vault complex Vault ribonucleoprotein particles from rat and bullfrog contain a related small RNA that is transcribed by RNA polymerase III Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs Characterization of the RNA content of chromatin Df31 protein and snoRNAs maintain accessible higher-order structures of chromatin Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs Mapping the genome landscape using tiling array technology Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 genomes data A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome Identification of fusion genes in breast cancer by paired-end RNAsequencing TopHat: discovering splice junctions with RNA-Seq Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses omiRas: a web server for differential expression analysis of miRNAs derived from small RNA-Seq data piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome-and CAGEseq, ChIP-seq and genomic DNA sequencing FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq highthroughput data tsRNAs: new players in mammalian retrotransposon control A survey of best practices for RNA-seq data analysis MicroRNA profiling: separating signal from noise Evidence for human microRNA-offset RNAs in small RNA sequencing data Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods Single-cell RNA sequencing for the study of development, physiology and disease Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR Adapting the smart-seq2 protocol for robust single worm RNA-seq Technical variations in low-input RNA-seq methodologies Metabolic tagging and purification of nascent RNA: implications for transcriptomics Nascent RNA analyses: tracking transcription and its regulation Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells RNA dynamics revealed by metabolic RNA labeling and biochemical nucleoside conversions Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome Decrypting noncoding RNA interactions, structures, and functional networks Non-coding RNA: a new frontier in regulatory biology Genome regulation by long noncoding RNAs The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites Systematic mapping of RNA-chromatin interactions in vivo The genomic binding sites of a noncoding RNA Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions [58] RNA capture sequencing A derivative technology combining RNA-seq with tilling arrays.
    keywords: cancer; cdna; cell; chromatin; circrnas; coding; database; expression; fig; functional; gene; human; identification; interactions; method; ncrnas; noncoding; novel; protein; rna; rnas; seq; sequencing; small; transcription; transcripts
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        item: #1134 of 1349
          id: cord-336012-8klkojpo
      author: Harilal, Divinlal
       title: SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission
        date: 2020-06-18
       words: 3042
      flesch: 36
     summary: Results We show a significant improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. Even with higher throughput sequencing (NovaSeq SP flowcell), shotgun sequencing requires an allocation of 1TB of data for ~250 sequenced samples.
    keywords: cost; cov-2; data; genome; sars; sequencing; table; usa; virus
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        item: #1135 of 1349
          id: cord-336093-ic6q6ke8
      author: Sun, Ying
       title: Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase
        date: 2014-02-11
       words: 6442
      flesch: 45
     summary: It has been shown that the capping functions in yeast cells can be replaced by the cap-forming enzymes of mammals or DNA viruses (Ho et al., 2000; Saha et al., 1999 Saha et al., , 2003 , and we previously found that coronavirus nsp14 could replace yeast cap N7-MTase in vivo (Chen et al., 2009 (Chen et al., , 2013 . After incubation, yeast cells were collected and then ground in liquid nitrogen.
    keywords: coronavirus; et al; human; inhibitors; mtase; rna; sars; sinefungin; system; yeast
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        item: #1136 of 1349
          id: cord-336319-8068s9a3
      author: Graci, Jason D.
       title: Mechanisms of action of ribavirin against distinct viruses
        date: 2005-11-15
       words: 6502
      flesch: 33
     summary: Mathematical modelling has been used to approximate the contribution of immunomodulatory effects towards ribavirin antiviral activity. key: cord-336319-8068s9a3 authors: Graci, Jason D.; Cameron, Craig E. title: Mechanisms of action of ribavirin against distinct viruses date: 2005-11-15 journal: Rev Med Virol DOI: 10.1002/rmv.483 sha: doc_id: 336319 cord_uid: 8068s9a3 The nucleoside analogue ribavirin has antiviral activity against many distinct viruses both in vitro and in vivo.
    keywords: action; activity; antiviral; cells; effect; gtp; hepatitis; impdh; inhibition; mechanism; ribavirin; rna; virus; viruses
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        item: #1137 of 1349
          id: cord-336447-hpnkou41
      author: Pitlik, Silvio Daniel
       title: COVID-19 Compared to Other Pandemic Diseases
        date: 2020-07-31
       words: 6150
      flesch: 44
     summary: 87, 88 Readers can visit these sites to access updates regarding ongoing developments related to COVID-19 vaccines and treatments. Excess mortality estimation during the COVID-19 pandemic: preliminary data from Portugal Diagnostic performance of COVID-19 serology assays Cholera and the water supply in the South districts of London UCLA Department of Epidemiology, Fielding School of Public Health New insights on the emergence of cholera in Latin America during 1991: the Peruvian experience Impact of complete lockdown on total infection and death rates: a hierarchical cluster analysis The Jenner Society and the Edward Jenner Museum: tributes to a physicianscientist Smallpox vaccines for biodefense Draft landscape of COVID-19 candidate vaccines The race for coronavirus vaccines: a graphical guide The COVID-19 vaccine development landscape The SARS-CoV-2 vaccine pipeline: an overview Remdesivir for the treatment of COVID-19 -preliminary report Deployment of convalescent plasma for the prevention and treatment of COVID-19 Economics in the Age of COVID-19 The economic impact of COVID-19 COVID-19: in the footsteps of Ernest Shackleton Coronavirus drug and treatment tracker Coronavirus vaccine tracker.
    keywords: cases; coronavirus; cov-2; covid-19; disease; history; human; new; number; pandemic; sars; vaccine; virus; viruses
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        item: #1138 of 1349
          id: cord-336554-n8n5ii5k
      author: Singh, Thakur Uttam
       title: Drug repurposing approach to fight COVID-19
        date: 2020-09-05
       words: 13068
      flesch: 39
     summary: Further, darunavir has been used (600 mg tablet every 12 h) along with other anti-viral drugs and supportive therapy in the clinical management of COVID-19 patients presented with a range of MEWS from less than 3 to more than 4 in Italy [33] . Hydroxychloroquine phosphate (400 mg tablet every 12 h as a loading dose followed 200 mg tablet every 12 h for 10 days) or chloroquine phosphate (250 mg of two tablet every 12 h for 10 days) along with other anti-viral drugs and supportive therapy have been used in the clinical management of COVID-19 patients presented with a range of MEWS from less than 3 to more than 4 in Italy
    keywords: antiviral; arbidol; clinical; coronavirus; cov2; covid-19; disease; dose; drug; effects; hydroxychloroquine; infection; inhibitors; interferon; lopinavir; patients; protease; remdesivir; ribavirin; ritonavir; sars; study; therapy; tocilizumab; treatment; trial; use
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        item: #1139 of 1349
          id: cord-336560-m5u6ryy9
      author: Boudewijns, Robbert
       title: STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters
        date: 2020-07-02
       words: 5039
      flesch: 37
     summary: Of note, these receptor knockouts did not affect ACE2 expression in hamster lungs (Fig. S9A ), while interferon-stimulated genes (ISG) 27 such as MX-2 (strongly induced by IFNα/STAT2 signaling) and IP-10 (induced by both type I and type II IFNs) showed a differential expression pattern when comparing the different genotypes, triggered by SARS-CoV-2 infection (Fig. S9B) . The lack of readily accessible serum markers or the absence of overt disease symptoms in hamsters prompted us to establish a non-invasive means to score for lung infection and SARS-CoV-2 induced lung disease by computed tomography (CT) as used in standard patient care to aid COVID-19 diagnosis with high sensitivity and monitor progression/recovery 7, 33, 35, 36 .
    keywords: covid-19; disease; fig; hamsters; infection; interferon; levels; lung; mice; rna; sars; stat2; type; virus
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        item: #1140 of 1349
          id: cord-336628-0evl3wnd
      author: Neufeldt, Christopher J.
       title: SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB
        date: 2020-07-21
       words: 5906
      flesch: 41
     summary: One hour after infection cells were treated with the indicated drugs at the given concentrations. We also demonstrate that SARS-CoV-2 infection leads specifically to NF-κB but not IRF3 nuclear localization and that poly(I:C)-induced pathway activation is attenuated in infected cells.
    keywords: activation; cells; cgas; cov-2; infection; levels; response; rna; sars; sting; virus
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        item: #1141 of 1349
          id: cord-336775-d4hi9myk
      author: Kirtipal, Nikhil
       title: From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses
        date: 2020-08-13
       words: 8621
      flesch: 29
     summary: bat-SL-CoVZX45 and bat-SL-CoVZX2 from bats Zhou et al., 2020b) . (E), nucleocapsid (N) proteins, and hemagglutinin (HA), where S, M, and E proteins are embedded in viral envelop while N protein protects viral RNA genome located as core of virus ( Fig. 3 ) (Zhou et al., 2020b) .
    keywords: ace2; bats; cells; coronavirus; cov; cov-2; covs; et al; genome; host; human; immune; infection; mers; patients; protein; receptor; respiratory; responses; rna; sars; syndrome
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        item: #1142 of 1349
          id: cord-336986-rmxin1da
      author: De Clercq, Erik
       title: New Nucleoside Analogues for the Treatment of Hemorrhagic Fever Virus Infections
        date: 2019-08-07
       words: 2730
      flesch: 50
     summary: [3] In their final remarks, Sidwell et al. (1972) stated, rightfully that the antiviral spectrum of Virazole was the broadest ever reported for any syntheticm aterial that does not induce interferon, although the eventual clinicalu se of Virazole would eventually be limited to RNA virus infections. That T-705 (Favipiravir), as av iral RNA polymerase inhibitor, offers great potential in the treatment of aw idev ariety of RNA virus infections, has been reviewed repeatedly.
    keywords: activity; ebov; favipiravir; fever; infections; remdesivir; ribavirin; rna; treatment; virus
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        item: #1143 of 1349
          id: cord-337026-osgi06o4
      author: Panoutsopoulos, Alexios A.
       title: Conjunctivitis as a Sentinel of SARS-CoV-2 Infection: a Need of Revision for Mild Symptoms
        date: 2020-06-19
       words: 3183
      flesch: 38
     summary: The Molecular Biology of Coronaviruses and SARS-CoV-2 Coronaviruses (CoVs) are RNA viruses with the largest RNA in base length identified so far and belong to the Coronaviridae family. Except for DNA viruses though, RNA viruses are often associated with conjunctivitis.
    keywords: cell; conjunctivitis; coronavirus; cov-2; covid-19; host; protein; receptor; sars; virus
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        item: #1144 of 1349
          id: cord-337199-mbv8kd1k
      author: Ballarín-González, Borja
       title: Clinical translation of RNAi-based treatments for respiratory diseases
        date: 2012-09-07
       words: 10562
      flesch: 35
     summary: [47] that present a barrier to siRNA delivery. The effects of thiophosphate substitutions on native siRNA gene silencing Asymmetric shorter-duplex siRNA structures trigger efficient gene silencing with reduced nonspecific effects Asymmetric RNA duplexes mediate RNA interference in mammalian cells Potent RNAi by short RNA triggers Improved silencing properties using small internally segmented interfering RNAs Strand-specific 5′-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity Improved specificity of gene silencing by siRNAs containing unlocked nucleobase analogs Position-specific chemical modification of siRNAs reduces off-target transcript silencing Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced offtarget effect Viral load drives disease in humans experimentally infected with respiratory syncytial virus
    keywords: activity; administration; aln; cells; delivery; dose; effects; gene; immune; infection; lung; mucus; reduction; rnai; rsv; rsv01; silencing; sirna; study; system; virus
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        item: #1145 of 1349
          id: cord-337285-t6qr41wc
      author: Ikeda, Masanori
       title: Modulation of host metabolism as a target of new antivirals()
        date: 2007-10-10
       words: 8192
      flesch: 43
     summary: Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome Prevalence of antibody against non-A, non-B hepatitis virus in Japanese patients with hepatocellular carcinoma Global surveillance and control of hepatitis C, Report of a WHO Consultation organized in collaboration with the Viral Hepatitis Prevention Board Antiviral therapy for chronic hepatitis C: past, present, and future Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line Complete replication of hepatitis C virus in cell culture Production of infectious hepatitis C virus in tissue culture from a cloned viral genome Robust hepatitis C virus infection in vitro A critical role for the chimpanzee model in the study of hepatitis C Transmission of hepatitis C virus infection to tree shrews Toward a surrogate model for hepatitis C virus: An infectious molecular clone of the GB virus-B hepatitis agent Development of a GB virus B marmoset model and its validation with a novel series of hepatitis C virus NS3 protease inhibitors Hepatitis C virus replication in mice with chimeric human livers Recent advances in the analysis of HCV NS5B RNA-dependent RNA polymerase Structure and function of the hepatitis C virus NS3-NS4A serine proteinase Discovery of SCH446211 (SCH6): a new ketoamide inhibitor of the HCV NS3 serine protease and HCV subgenomic RNA replication In vitro antiviral activity of SCH446211 (SCH6), a novel inhibitor of the hepatitis C virus NS3 serine protease Discovery of (1R,5S VX-950, a novel hepatitis C virus (HCV) NS3-4A protease inhibitor, exhibits potent antiviral activities in HCV replicon cells Rapid decline of viral RNA in hepatitis C patients treated with VX-950: a phase Ib, placebo-controlled, randomized study An NS3 protease inhibitor with antiviral effects in humans infected with hepatitis C virus Synthesis and pharmacokinetics of valopicitabine (NM283), an efficient prodrug of the potent anti-HCV agent 2′-Cmethylcytidine Clearance of replicating hepatitis C virus replicon RNAs in cell culture by small interfering RNAs Interference of hepatitis C virus RNA replication by short interfering RNAs Small interfering RNA targeted to hepatitis C virus 5′ nontranslated region exerts potent antiviral effect cDNA microarray analysis to compare HCV subgenomic replicon cells with their cured cells NIM811, a cyclophilin inhibitor, exhibits potent in vitro activity against hepatitis C virus alone or in combination with alpha interferon Cyclophilin B is a functional regulator of hepatitis C virus RNA polymerase Cyclosporin A suppresses replication of hepatitis C virus genome in cultured hepatocytes Specific inhibition of hepatitis C virus replication by cyclosporin A Suppression of hepatitis C virus replication by cyclosporin a is mediated by blockade of cyclophilins Diverse effects of cyclosporine on hepatitis C virus strain replication Evaluation of the anti-hepatitis C virus effects of cyclophilin inhibitors, cyclosporin A, and NIM811 The non-immunosuppressive cyclosporin DEBIO-025 is a potent inhibitor of hepatitis C virus replication in vitro Combined interferon alpha2b and cyclosporin The effect of ribavirin and IMPDH inhibitors on hepatitis C virus subgenomic replicon RNA Glycosylation of hepatitis C virus envelope proteins Antiviral effect of alphaglucosidase inhibitors on viral morphogenesis and binding properties of hepatitis C virus-like particles S-Adenosylmethionine and betaine correct hepatitis C virus induced inhibition of interferon signaling in vitro Anti-HCV activities of selective polyunsaturated fatty acids Oral prostaglandin (PGE2) therapy for chronic viral hepatitis B and C Regulation of interferon regulatory factor-3 by the hepatitis C virus serine protease Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus Genetic variation and dynamics of hepatitis C virus replicons in long-term cell culture Comprehensive analysis of the effects of ordinary nutrients on hepatitis C virus RNA replication in cell culture
    keywords: activity; cell; culture; hcv; hcv rna; hepatitis; ifn; proteins; replication; replicon; ribavirin; rna; rna replication; system; virus
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        item: #1146 of 1349
          id: cord-337339-0vkigjv2
      author: Osterrieder, Nikolaus
       title: Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters
        date: 2020-07-20
       words: 4355
      flesch: 39
     summary: Histopathology revealed clear age-dependent differences, with young hamsters launching earlier and stronger immune cell influx than aged hamsters. Association between age and clinical characteristics and outcomes of COVID-19 Coronavirus Infections-More Than Just the Common Cold SARS and MERS: recent insights into emerging coronaviruses A Genomic Perspective on the Origin and Emergence of SARS-CoV-2 Clinical Characteristics of Coronavirus Disease 2019 in China SARS-CoV-2 and COVID-19 in older adults: what we may expect regarding pathogenesis, immune responses, and outcomes Clinical features of COVID-19 in elderly patients: A comparison with young and middle-aged patients Estimating excess 1-year mortality associated with the COVID-19 pandemic according to underlying conditions and age: a population-based cohort study The search for a COVID-19 animal model Animal models for emerging coronavirus: progress and new insights SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study Respiratory disease in rhesus macaques inoculated with SARS-CoV-2 Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model Ocular conjunctival inoculation of SARS-CoV-2 can cause mild COVID-19 in 2 Rhesus macaque Age-related rhesus macaque models of COVID-19 A mouse-adapted SARS-CoV-2 model for the evaluation of COVID-19 medical countermeasures Rapid adaptation of SARS-CoV-2 in BALB/c mice: Novel mouse model for vaccine efficacy The pathogenicity of SARS-CoV-2 in hACE2 transgenic mice The battle against SARS and MERS coronaviruses: Reservoirs and Animal Models Animal models for SARS and MERS coronaviruses Infection and Rapid Transmission of SARS-CoV-2 in Ferrets Is there an ideal animal model for SARS? Severe acute respiratory syndrome coronavirus infection of golden Syrian hamsters Pathogenesis and transmission of SARS-CoV-2 in golden hamsters Simulation of the clinical and pathological manifestations of Coronavirus Disease 2019 (COVID-19) in golden Syrian hamster model: implications for disease pathogenesis and transmissibility Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform Virological assessment of hospitalized patients with COVID-2019 Effects of a mixture of medetomidine, midazolam and butorphanol on anesthesia and blood biochemistry and the antagonizing action of atipamezole in hamsters Spectrum of pathogen-and model-specific histopathologies in mouse models of acute pneumonia The Family of Chloride Channel Regulator, Calcium-activated Proteins in the Feline Respiratory Tract: A Comparative Perspective on Airway Diseases in Man and Animal Models Pulmonary immunostimulation with MALP-2 in influenza virus-infected mice increases survival after pneumococcal superinfection IL-37 Causes Excessive Inflammation and Tissue Damage in Murine Pneumococcal Pneumonia Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR Validation of assays to monitor immune responses in the Syrian golden hamster (Mesocricetus auratus) Tropism, replication competence, and innate immune responses of the coronavirus SARS-CoV-2 in human respiratory tract and conjunctiva: an analysis in ex-vivo and in-vitro cultures Syrian hamsters as a small animal model for SARS-CoV-2 infection and countermeasure development This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license The authors acknowledge the excellent technical assistance by Ann Reum, Annett Neubert, and Simon Dökel.
    keywords: age; animals; cells; cov-2; dpi; germany; hamsters; infection; lung; rna; sars; young
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        item: #1147 of 1349
          id: cord-337361-salby0fu
      author: Bujarski, Jozef J.
       title: Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives
        date: 2013-03-26
       words: 6867
      flesch: 30
     summary: From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented.
    keywords: bmv; events; factors; genome; host; mechanisms; plant; recombination; replicase; replication; rna; rnas; sequences; viral; virus; viruses
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        item: #1148 of 1349
          id: cord-337508-nfzaw8gg
      author: Kirkland, P.D.
       title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2
        date: 2020-10-05
       words: 2715
      flesch: 45
     summary: The special requirements for products that are suitable for nucleic acid testing have been recognised by some manufacturers who have developed specific transport media to inactivate the viruses of interest and to minimise the degradation of nucleic acid. It is also important to recognise that these observations reflect the outcome of contact between viral nucleic acid and VTM for less than 1 hour in each instance.
    keywords: acid; nucleic; results; rna; vtm
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        item: #1149 of 1349
          id: cord-337673-1nau263l
      author: Wu, Chang-Jer
       title: Antiviral applications of RNAi for coronavirus
        date: 2006-01-24
       words: 4333
      flesch: 45
     summary: The final structural protein, N protein, with a molecular mass of 50 -60 kDa, probably associates with viral RNA to form a long and flexible helical nucleocapsid These plasmids were also able to block viral replication, as shown by both the titre and levels of viral RNA and protein.
    keywords: cells; coronavirus; cov; expression; gene; protein; rna; rnai; sars; sirna; virus
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        item: #1150 of 1349
          id: cord-337879-liqhbqxl
      author: Kriesel, John D.
       title: Deep Sequencing for the Detection of Virus-Like Sequences in the Brains of Patients with Multiple Sclerosis: Detection of GBV-C in Human Brain
        date: 2012-03-08
       words: 5064
      flesch: 49
     summary: A new arenavirus in a cluster of fatal transplant-associated diseases The complete genome of klassevirus -a novel picornavirus in pediatric stool Human enterovirus 109: a novel interspecies recombinant enterovirus isolated from a case of acute pediatric respiratory illness in Nicaragua Hepatitis G virus Identification of GBV-D, a novel GB-like flavivirus from old world frugivorous bats (Pteropus giganteus) in Bangladesh The natural history of nonhuman GB Virus C (GBV-Ccpz) in captive chimpanzees Review of the epidemiology, molecular characterization and tropism of the hepatitis G virus/GBV-C Evidence that the GBV-C/hepatitis G virus is primarily a lymphotropic virus Lack of GB virus C/hepatitis G virus sequences in cerebrospinal fluid in patients with central nervous system infections GB virus type C/Hepatitis G virus GBV-C/hepatitis G virus infection and non-Hodgkin lymphoma: a case control study The prevalence of hepatitis C and hepatitis G virus infection in patients with B cell non-Hodgkin lymphomas in Greece: a Hellenic Cooperative Oncology Group Study High prevalence of hepatitis G virus infection in Hodgkin's disease and Bcell lymphoproliferative disorders: absence of correlation with hepatitis C virus infection GB Virus Type C Envelope Protein E2 Elicits Antibodies That React with a Cellular Antigen on HIV-1 Particles and Neutralize Diverse HIV-1 Isolates Cluster analysis and display of genome-wide expression patterns Java Treeview-extensible visualization of microarray data Effect of primer selection on estimates of GB virus C (GBV-C) prevalence and response to antiretroviral therapy for optimal testing for GBV-C viremia Development of GBV-C E2 Monoclonal Antibodies that Precipitate HIV-1 Particles and Neutralize Diverse HIV-1 Isolates. [14] The GB viruses are approximately 10 kb in size and are most closely related to hepatitis C virus.
    keywords: brain; control; gbv; hepatitis; human; reads; rna; sequences; specimens; virus
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        item: #1151 of 1349
          id: cord-337899-w5zh40gv
      author: Bissoyi, Akalabya
       title: Alphavirus Nonstructural Proteases and Their Inhibitors
        date: 2017-07-14
       words: 7315
      flesch: 41
     summary: Alphaviruses are generally RNA viruses with a positive-sense, and single-stranded RNA genome (Koonin et al., 1993) . The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket Novel trends in high-throughput screening Proteolytic processing of Semliki Forest virus-specific non-structural polyprotein by nsP2 protease Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites Discovery of in silico hits targeting the nsP3 macro domain of Chikungunya virus The nsP3 macro domain is important for Sindbis virus replication in neurons and neurovirulence in mice Exploring the polymerase activity of Chikungunya viral nonstructural protein 4 (nsP4) using molecular modeling, e-pharmacophore and docking studies Effect of water on solvation structure and dynamics of ions in the peptide bond environment: importance of hydrogen bonding and dynamics of the solvents A molecular dynamics simulations study on the behavior of liquid N-methylacetamide in presence of NaCl: structure, dynamics and H-bond properties Evolutionary conservation of histone macroH2A subtypes and domains Identification of thieno[3, 2-b]pyrrole derivatives as novel small molecule inhibitors of neurotropic alphaviruses The Alphavirus replicase protein nsP1 is membrane-associated and has affinity to endocytic organelles Nuclear localization of Semliki Forest virus-specific nonstructural protein nsP2 Semliki Forest virus-specific nonstructural protein nsP3 is a phosphoprotein UCSF Chimera-a visualization system for exploratory research and analysis Alphavirus vectors and vaccination Functional significance of the nuclear-targeting and NTP-binding motifs of Semliki Forest virus nonstructural protein nsP2 Characterization of purified Sindbis virus nsP4 RNA-dependent RNA polymerase activity in vitro Properly folded nonstructural polyprotein directs the Semliki Forest virus replication complex to the endosomal compartment Computational approach towards exploring potential anti-Chikungunya activity of selected flavonoids Requirement for an aromatic amino acid or histidine at the N terminus of Sindbis virus RNA polymerase Suppressor mutations that allow Sindbis virus RNA polymerase to function with nonaromatic amino acids at the N-terminus: evidence for interaction between nsP1 and nsP4 in minus-strand RNA synthesis Homology modeling, molecular dynamics, e-pharmacophore mapping and docking study of Chikungunya virus nsP2 protease The alphaviruses: gene expression, replication, and evolution High-throughput and ultra-high-throughput screening: solution-and cellbased approaches High levels of GDF15 in thalassemia suppress expression of the iron regulatory protein hepcidin Antiviral activity of the interferoninduced cellular protein BST-2/tetherin Catalytic core of Alphavirus nonstructural protein nsP4 possesses terminal adenylyltransferase activity Amino acid mutations in the replicase protein nsP3 of Semliki Forest virus cumulatively affect neurovirulence Preoperative gemcitabine and cisplatin followed by gemcitabine-based chemoradiation for resectable adenocarcinoma of the pancreatic head Phosphorylation site analysis of Semliki Forest virus nonstructural protein 3 Elimination of phosphorylation sites of Semliki Forest virus replicase protein nsP3 Induction of autophagy in axonal dystrophy and degeneration Mutagenesis of the Sindbis virus nsP1 protein: effects on methyltransferase activity and viral infectivity Gene silencing as an adaptive defence against viruses Inhibitors of hiv-1 protease: a major success of structureassisted drug design 1 I-TASSER server for protein 3D structure prediction Mutations at the palmitoylation site of non-structural protein NSP1 of Semliki Forest virus attenuate virus replication and cause accumulation of compensatory mutations ChemDraw Ultra 10.0 A. Bissoyi expresses his gratefulness to the Department of Science and Technology (DST), Government of India, for the financial support to this work through Grant No.
    keywords: activity; alphavirus; binding; chikv; et al; fig; inhibitors; nsp1; nsp2; nsp3; nsp4; protease; protein; replication; rna; virus; viruses
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        item: #1152 of 1349
          id: cord-337976-c2auspti
      author: Weiss, Susan R.
       title: Coronaviruses SD and SK share extensive nucleotide homology with murine coronavirus MHV-A59, more than that shared between human and murine coronaviruses
        date: 1983-04-30
       words: 3824
      flesch: 55
     summary: Intraeellular RNAs extracted from eells infected with SD or SK, were eleetrophoresed in parallel with MHV-A59 RNA, blotted onto nitrocellulose and the virusspecific species detected by hybridization with MHV-A59 eDNA. L Characterization of biological behavior in vitro and virus specific intracellular RNA of strongly neurotropic JHMV and weakly neurotropic A59V viruses Plaque assay and improved yield of human coronaviruses in a human rhabdomyosarcoma cell line Sequence relationship between the genome segments of human and animal rotavirus strains Isolation and identification of virus-specific mRNAs in cells infected with mouse hepatitis virus (MHV-A59) Chronic central nervous system demyelination in mice after JHM virus infection Intracisternal virus-like particles in the brain of a multiple sclerosis patient Efficient transcription of RNA into DNA by avian sarcoma virus polymerase Hybridization of denatured RNA and small DNA fragments transferred to nitrocellulose.
    keywords: a59; cells; mhv; rna; virus
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        item: #1153 of 1349
          id: cord-337998-08tknscm
      author: Sztuba-Solinska, Joanna
       title: A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8
        date: 2016-11-16
       words: 8292
      flesch: 42
     summary: The NCRs of RNA virus genomes have highly conserved primary and secondary structures (4) (5) (6) (7) . Reactivity to the SHAPE reagent 1M7 for EBOV minigenome RNA is shown in Figure 4A (Supplementary Figure S2) .
    keywords: a30u; analysis; cells; ebov; figure; host; hspa8; leader; loop; minigenome; motif; probe; protein; replication; rna; structure; trailer; transcription; virus
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        item: #1154 of 1349
          id: cord-338083-77re4l0w
      author: Bolin, Steven R.
       title: Origination and consequences of bovine viral diarrhea virus diversity
        date: 2005-03-04
       words: 6749
      flesch: 39
     summary: The causative agent of BVD: its epidemiology and pathogenesis Thrombocytopenia and hemorrhages in veal calves infected with bovine viral diarrhea virus Thrombocytopenia associated with acute bovine virus diarrhea infection in cattle Phylogenetic, antigenic and clinical characterization of type 2 BVDV from North America Immunology of bovine viral diarrhea virus Differences in virulence between two noncytopathic bovine viral diarrhea viruses in calves The effect of different bovine viral diarrhea virus genotypes and biotypes on the metabolic activity and activation status of bovine peripheral blood mononuclear cells Relationship between degree of viremia and disease manifestation in calves with experimentally induced bovine viral diarrhea virus infection Comparative virulence of isolates of bovine viral diarrhea virus type II in experimentally inoculated sixto nine-month-old calves Role of bovine viral diarrhea virus in the bovine respiratory disease complex Experimental production of bovine respiratory tract disease with bovine viral diarrhea virus Effect of bovine viral diarrhea virus infection on the distribution of infectious bovine rhinotracheitis virus in calves Effect of concurrent experimentally induced bovine respiratory syncytial virus and bovine viral diarrhea virus infection on respiratory tract and enteric diseases in calves Comparison of the pneumopathogenicity of two strains of bovine viral diarrhea virus Differences in experimental virulence of bovine viral diarrhoea viral strains isolated from haemorrhagic syndromes Development of a fetal challenge method for the evaluation of bovine viral diarrhea virus vaccines Variation in neuropathogenicity in sheep fetuses transplacentally infected with non-cytopathogenic and cytopathogenic biotypes of bovine-virus diarrhoea virus BVDV fetal infection with selected isolates. Bovine viral diarrhea virus infections also have been associated with concurrent salmonellosis, Escherichia coli, bovine papular stomatitis, rotavirus, and coronavirus infections.
    keywords: bovine; bvdv; cattle; diarrhea; disease; infection; isolates; rna; type; viral; virus; viruses
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        item: #1155 of 1349
          id: cord-338307-vfutmwxq
      author: Sturman, Lawrence S.
       title: The Molecular Biology of Coronaviruses
        date: 1983-12-31
       words: 21989
      flesch: 46
     summary: Although in moderate infection of MHV-A59 in 17 C1 1 cells, little or no 90K E2 was detected at 8-10 hours after infection (Holmes et al., 1981b; Fig. 16) , in Sac ( -) cells infected with MHV-JHM or -A59, a substantial amount of 90K E2 was detected after 60-to 90-minute chase (Siddell et al., 1981c; Rottier et al., 1981b) . The same conclusion was reached by others (Holmes et al., 1981a,b; Siddell et al., 1981c; Rottier et al., 1981b) based on the resistance of the glycosylation of E l to tunicamycin, an inhibitor specific for N-glycosylation.
    keywords: 1981b; a59; cells; coronavirus; e l; et al; fig; fusion; glycoprotein; hepatitis; holmes; holmes et; human; ibv; infection; jhm; mhv; mouse; proteins; rna; siddell et; species; strain; structural; studies; sturman; synthesis; viral; virions; virus; viruses
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        item: #1156 of 1349
          id: cord-338345-mr1orklo
      author: Adedeji, Adeyemi O.
       title: Biochemical Characterization of Middle East Respiratory Syndrome Coronavirus Helicase
        date: 2016-09-07
       words: 4278
      flesch: 47
     summary: Characterization of helicase activity. Helicase activity was measured by incubating 20 nM M-nsp13 with a 5 nM concentration of an RNA substrate (Fig.
    keywords: activity; atp; duplex; helicase; nsp13; rna; substrate; unwinding
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        item: #1157 of 1349
          id: cord-338358-ppjxo2di
      author: Whitworth, Kristin M.
       title: Zygote injection of CRISPR/Cas9 RNA successfully modifies the target gene without delaying blastocyst development or altering the sex ratio in pigs
        date: 2016-10-15
       words: 4966
      flesch: 47
     summary: In the past 3 years there have been numerous reports of production of modified pig embryos either by direct zygote injection of CRISPR/Cas9 RNA or by somatic cell nuclear transfer with CRISPR/Cas9 modified cells. The rate of blastocyst development was not significantly different between CRISPR injection embryos or the non-injected controls at day 5, 6 or 7 (p = 0.36, 0.09, 0.63, respectively).
    keywords: blastocyst; cas9; crispr; dna; embryos; guides; injection; pigs; rna; sex; tmprss2
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        item: #1158 of 1349
          id: cord-338582-o976nab9
      author: Dahlhausen, Bob
       title: Future Veterinary Diagnostics
        date: 2010-09-19
       words: 9203
      flesch: 30
     summary: Antibodies in an immunoassay format have been widely used and are well established as highly sensitive tools for disease detection. 26, 27 Researchers led by Joseph DeRisi of the University of California at San Francisco have combined genome databases of sequenced viruses with DNA microarray technology.
    keywords: amplification; analysis; cancer; detection; diagnostic; disease; dna; expression; gene; microarrays; nucleic; pcr; protein; rna; sequence; target; technology; testing; viral; viruses
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        item: #1159 of 1349
          id: cord-338680-wwlttymp
      author: Khonyongwa, K.
       title: Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence
        date: 2020-07-30
       words: 4841
      flesch: 47
     summary: Bed occupancy was derived from the Business Intelligence Unit of the Hospital and community incidence was derived from national population data (10) and Department of Health reports of COVID-19 cases (1) Statistical methods: Categorical variables were compared using the chi square test or Fisher's exact test. Healthcare associated COVID-19 infections (HA-COVID-19) have been reported in other studies (5) but the literature on epidemiology, risk factors and outcomes of healthcare acquisition of COVID-19 among healthcare inpatients is lacking.
    keywords: cases; covid-19; incidence; license; medrxiv; patients; preprint; rna; staff
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        item: #1160 of 1349
          id: cord-338727-1kodz527
      author: Ilinskaya, O. N.
       title: Ribonucleases as antiviral agents
        date: 2014-10-11
       words: 4605
      flesch: 37
     summary: Furthermore, it has been found that siRNAs specific to a conserved region of influenza virus RNA introduced into a cell decreased the titer of the virus The study of the molecular mechanism of the action of antiviral RNases is undoubtedly an urgent task, the solution of which may promote the develop ment of novel antiviral preparations capable of pro tecting the organism independently of changes in the virus genome.
    keywords: activity; binase; cell; domain; effect; human; infection; influenza; protein; replication; ribonuclease; rnase; virus; viruses
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        item: #1161 of 1349
          id: cord-338812-q24jycgk
      author: Zakaryan, H.
       title: Nuclear remodelling during viral infections
        date: 2011-04-28
       words: 4470
      flesch: 24
     summary: For example, it is still unclear why RNA virus proteins localize to the nucleolus or whether the PML NBs play a role for establishing herpesviral latency. For this reason, viruses rely on the utilization of host cell proteins and cellular structures to facilitate their own replicative processes.
    keywords: cell; nbs; nuclear; nucleolus; nucleus; pml; proteins; rna; virus; viruses
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        item: #1162 of 1349
          id: cord-338901-1kzy7rts
      author: Li, Heng
       title: Overview of therapeutic drug research for COVID-19 in China
        date: 2020-06-17
       words: 5106
      flesch: 44
     summary: Molecular basis of ribavirin resistance Comparative effectiveness of aerosolized versus oral ribavirin for the treatment of respiratory syncytial virus infections: a single-center retrospective cohort study and review of the literature Ideal oral combinations to eradicate HCV: the role of ribavirin A major outbreak of severe acute respiratory syndrome in Hong Kong Clinical features and short-term outcomes of 144 patients with SARS in the greater Toronto area Short term outcome and risk factors for adverse clinical outcomes in adults with severe acute respiratory syndrome (SARS) Severe acute respiratory syndrome: report of treatment and outcome after a major outbreak Ribavirin and interferonbeta synergistically inhibit SARS-associated coronavirus replication in animal and human cell lines Ribavirin and interferon alfa-2a for severe Middle East respiratory syndrome coronavirus infection: a retrospective cohort study Use of chloroquine in viral diseases Effects of chloroquine on viral infections: an old drug against today's diseases? Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro Evidence for a common evolutionary origin of coronavirus spike protein receptor-binding subunits Chloroquine is a potent inhibitor of SARS coronavirus infection and spread Progress in antiviral therapy of new coronavirus pneumonia Arbidol as a broad-spectrum antiviral: an update Arbidol: a broad-spectrum antiviral compound that blocks viral fusion The synthetic antiviral drug arbidol inhibits globally prevalent pathogenic viruses Comparison of inhibitory effects of arbidol and Lianhuaqingwen Capsules on Middle East respiratory syndrome coronavirus in vitro and in vivo Clinical characteristics and therapeutic procedure for four cases with 2019 novel coronavirus pneumonia receiving combined Chinese and Western medicine treatment Dancing with chemical formulae of antivirals: a personal account Dancing with chemical formulae of antivirals: A panoramic view (Part 2) Mechanism of action of T-705 against influenza virus. In vitro susceptibility of 10 clinical isolates of SARS coronavirus to selected antiviral compounds Combined adjuvant effect of ginseng stem-leaf saponins and selenium on immune responses to a live bivalent vaccine of Newcastle disease virus and infectious bronchitis virus in chickens Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor Structural basis of receptor recognition by SARS-CoV-2 Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds Learning from the past: possible urgent prevention and treatment options for severe acute respiratory infections caused by 2019-nCoV Nucleotide analogues as inhibitors of viral polymerases SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor
    keywords: antiviral; chinese; clinical; coronavirus; cov-2; covid-19; medicine; pneumonia; rna; sars; treatment
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        item: #1163 of 1349
          id: cord-339172-210dwhgj
      author: Knoops, Kèvin
       title: SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum
        date: 2008-09-16
       words: 9958
      flesch: 39
     summary: For MHV, based on IF microscopy studies using the nsp13 helicase and viral membrane (M) protein as markers for RTCs and virus assembly sites [21] , respectively, such a connection was previously proposed [54] , but could not be corroborated in our studies using the same protein markers in SARS-CoV-infected cells [28] . Alternatively, the conspicuous absence of ribosomes from DMV inner membranes lends some credibility to a scenario involving a preformed inner vesicle derived from another membrane source.
    keywords: cells; coronavirus; cov; dmvs; dsrna; figure; inner; membrane; outer; replicase; replication; rna; sars; structures; synthesis; vesicles; virus
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        item: #1164 of 1349
          id: cord-339209-oe8onyr9
      author: Vasilakis, Nikos
       title: Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range
        date: 2014-05-20
       words: 5821
      flesch: 41
     summary: Mesoniviridae: a proposed new family in the order Nidovirales formed by a single species of mosquito-borne viruses Examining landscape factors influencing relative distribution of mosquito genera and frequency of virus infection Discovery of the first insect nidovirus, a missing evolutionary link in the emergence of the largest RNA virus genomes An insect nidovirus emerging from a primary tropical rainforest Identification and characterization of genetically divergent members of the newly established family mesoniviridae Molecular biology and pathogenesis of roniviruses A new nidovirus (NamDinh virus NDiV): its ultrastructural characterization in the C6/36 mosquito cell line A new species of mesonivirus from the northern territory, australia Supramolecular architecture of severe acute respiratory syndrome coronavirus revealed by electron cryomicroscopy Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming A Wolbachia symbiont in Aedes aegypti limits infection with dengue, Chikungunya, and Plasmodium The relative importance of innate immune priming in Wolbachia-mediated dengue interference The native Wolbachia endosymbionts of Drosophila melanogaster and Culex quinquefasciatus increase host resistance to West Nile virus infection Negevirus: a proposed new taxon of insect-specific viruses with wide geographic distribution The footprint of genome architecture in the largest genome expansion in RNA viruses Isolation of a Singh's Aedes albopictus cell clone sensitive to dengue and Chikungunya viruses SMART 7: recent updates to the protein domain annotation resource SMART, a simple modular architecture research tool: identification of signaling domains MUSCLE: multiple sequence alignment with high accuracy and high throughput New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing SSE: a nucleotide and amino acid sequence analysis platform Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range Additional file 5: Figure S5 . The compiled sequences had their relationship to other viruses determined by a BLASTX search.
    keywords: alignment; analysis; conserved; domains; figure; genome; isolates; mesoniviruses; ndiv; orf1a; region; sequence; species; structure
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        item: #1165 of 1349
          id: cord-339288-y8woqsii
      author: Tews, Birke Andrea
       title: Self-Replicating RNA
        date: 2016-06-11
       words: 7569
      flesch: 38
     summary: Due to the technical difficulties, RNA is not amenable to site specific manipulation so that reverse genetics systems for RNA viruses always rely on a cDNA intermediate The history of reverse genetic systems for positive strand RNA viruses highlights the pitfalls that may be encountered in the design of a reverse genetic system and show solutions how to circumvent these difficulties.
    keywords: cdna; cells; end; genome; replication; rna; sequences; strand; transcription; translation; vaccine; virus; viruses
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        item: #1166 of 1349
          id: cord-339431-kyr5lv15
      author: Saçar Demirci, Müşerref Duygu
       title: Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection
        date: 2020-03-17
       words: 2325
      flesch: 35
     summary: Since viruses would need to use at least some members of host miRNA biogenesis pathway elements, viral miRNAs should be similar to host miRNAs to a certain degree. For instance, through targeting specific human genes by viral miRNAs, it is possible to form an environment suitable for survival and replication of the virus.
    keywords: coronavirus; cov-2; genes; human; mirnas; sars; virus
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        item: #1167 of 1349
          id: cord-339456-82iks0xf
      author: Mikel, P.
       title: Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens
        date: 2015-02-25
       words: 10037
      flesch: 42
     summary: Process control viruses can also be constructed artificially using technology for production of MS2 phage-like particles, which have many advantages in comparison with other used controls and are especially suited for controlling the detection and quantification of certain types of RNA viruses. The use of process control virus in RT-PCR and qRT-PCR detection of RNA viruses from clinical specimens is necessary, but so far there is no ISO/TS, which would describe the use of specific process control viruses.
    keywords: bacteriophage; coat; control; control viruses; detection; et al; ms2; ms2 phage; packaging; particles; pcr; phage; process; process control; protein; rna; system; virus; viruses
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        item: #1168 of 1349
          id: cord-339782-rybjc58j
      author: Carmo, Anália
       title: Clearance and Persistence of SARS‐CoV‐2 RNA in COVID‐19 patients
        date: 2020-06-02
       words: 1846
      flesch: 43
     summary: The clearance and persistence of viral RNA was evaluated in two groups of positive patients: those who achieved two negative RT‐PCR tests and those who kept testing positive. The study evidenced that most patients tested positive for more than two weeks and that persistence of viral RNA is not necessarily associated with severe disease but may result from a weaker immune response instead.
    keywords: clearance; days; patients; rna; sars
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        item: #1169 of 1349
          id: cord-339976-tg2jkss7
      author: Wang, Haibin
       title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome
        date: 2004-07-01
       words: 2582
      flesch: 36
     summary: RT-PCR was successfully used to detect SARS CoV in nasopharyngeal aspirates, nasopharyngeal swabs, throat swabs, and broncheoalveolar lavage of SARS patients (6, 7 ) . This finding provides evidence that lymphocytes are a target or reservoir for SARS CoV and that they are a better sample source than plasma for detecting SARS CoV.
    keywords: acute; cov; patients; pcr; plasma; sample; sars
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        item: #1170 of 1349
          id: cord-340046-kgbvld0y
      author: Houspie, Lieselot
       title: Exhaled breath condensate sampling is not a new method for detection of respiratory viruses
        date: 2011-03-04
       words: 4082
      flesch: 48
     summary: key: cord-340046-kgbvld0y authors: Houspie, Lieselot; De Coster, Sarah; Keyaerts, Els; Narongsack, Phouthalack; De Roy, Rikka; Talboom, Ive; Sisk, Maura; Maes, Piet; Verbeeck, Jannick; Van Ranst, Marc title: Exhaled breath condensate sampling is not a new method for detection of respiratory viruses date: 2011-03-04 journal: Virol J DOI: 10.1186/1743-422x-8-98 sha: doc_id: 340046 cord_uid: kgbvld0y BACKGROUND: Exhaled breath condensate (EBC) sampling has been considered an inventive and novel method for the isolation of respiratory viruses. This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways.
    keywords: collection; detection; ebc; pcr; samples; study; viruses; volunteers
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        item: #1171 of 1349
          id: cord-340189-jo38hjqa
      author: Bar-On, Yinon M
       title: SARS-CoV-2 (COVID-19) by the numbers
        date: 2020-04-02
       words: 7253
      flesch: 52
     summary: Early epidemiological assessment of the transmission potential and virulence ofcoronavirus disease 2019 (COVID-19 Public health responses to COVID-19 outbreaks on cruise ships -Worldwide A structural analysis of M protein in coronavirus assembly and morphology Early events of SARS coronavirus infection in vero cells SARS-CoV-2 RNA has been detected on various surfaces several weeks after they were last touched (Moriarty et al., 2020) , but infectiousness appears to degrade more quickly than RNA.
    keywords: cell; coronavirus; cov-2; data; days; et al; infection; number; period; rate; sars; time; virus
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        item: #1172 of 1349
          id: cord-340325-0oh40b6r
      author: Witzigmann, Dominik
       title: Lipid nanoparticle technology for therapeutic gene regulation in the liver
        date: 2020-07-02
       words: 11255
      flesch: 27
     summary: Impact on Physicochemical Properties, Cytokine Induction, and Efficacy Hypersensitivity and Loss of Disease Site Targeting Caused by Antibody Responses to PEGylated Liposomes Synthesis and characterization of novel poly(ethylene glycol)-lipid conjugates suitable for use in drug delivery On the role of helper lipids in lipid nanoparticle formulations of siRNA Design of lipid nanoparticles for in vitro and in vivo delivery of plasmid DNA A combinatorial library of lipid-like materials for delivery of RNAi therapeutics Rational design of cationic lipids for siRNA delivery Maximizing the potency of siRNA lipid nanoparticles for hepatic gene silencing in vivo Patisiran, an RNAi Therapeutic, for Hereditary Transthyretin Amyloidosis The Onpattro® story and the clinical translation of nanomedicines containing nucleic acid-based drugs Hereditary transthyretin amyloidosis: a model of medical progress for a fatal disease Advances in microfluidics for lipid nanoparticles and extracellular vesicles and applications in drug delivery systems State-of-the-Art Design and Rapid-Mixing Production Techniques of Lipid Nanoparticles for Nucleic Acid Delivery The liver The Global Burden of Liver Disease: The Major Impact of China Structural and functional hepatocyte polarity and liver disease Hepatocytes: a key cell type for innate immunity Nanoparticle-liver interactions: Cellular uptake and hepatobiliary elimination Elimination Pathways of Nanoparticles Modifying a Commonly Expressed Endocytic Receptor Retargets Nanoparticles in Vivo Lipidoid Nanoparticles Containing PD-L1 siRNA Delivered In Vivo Enter Kupffer Cells and Enhance NK and CD8(+) T Cellmediated Hepatic Antiviral Immunity Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations A human liver cell atlas reveals heterogeneity and epithelial progenitors Addressing liver disease in the UK: a blueprint for attaining excellence in health care and reducing premature mortality from lifestyle issues of excess consumption of alcohol, obesity, and viral hepatitis Burden of liver diseases in the world RNA-Targeted Therapeutics GalNAc-siRNA Conjugates: Leading the Way for Delivery of RNAi Therapeutics Lipid Nanoparticle Technology for Clinical Translation of siRNA Therapeutics Gene therapy comes of age Adeno-associated virus vector as a platform for gene therapy delivery mRNA vaccines-a new era in vaccinology Personalized vaccines for cancer immunotherapy Rational designs of in vivo CRISPR-Cas delivery systems Delivery Aspects of CRISPR/Cas for in Vivo Genome Editing Overcoming cellular barriers for RNA therapeutics Safety profile of RNAi nanomedicines Knocking down disease: a progress report on siRNA therapeutics Delivery of oligonucleotides with lipid nanoparticles Liposomal drug delivery systems: from concept to clinical applications Lipid Nanoparticle Systems for Enabling Gene Therapies Lipid Nanoparticles Enabling Gene Therapies: From Concepts to Clinical Utility Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells Strategies, design, and chemistry in siRNA delivery systems Chemical and structural modifications of RNAi therapeutics Influence of Polyethylene Glycol Lipid Desorption Rates on Pharmacokinetics and Pharmacodynamics of siRNA Lipid Nanoparticles Shielding of Lipid Nanoparticles for siRNA Delivery:
    keywords: acid; cationic; cell; delivery; development; disease; formulations; gene; hepatic; hepatocytes; lipid; liver; lnp; mrna; nanoparticles; nucleic; onpattro; protein; rnai; silencing; sirna; study; systems; therapeutic; therapy; vivo
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        item: #1173 of 1349
          id: cord-340422-8f5xe4zc
      author: Rowland, R. R. R.
       title: Inhibition of porcine reproductive and respiratory syndrome virus by interferon-gamma and recovery of virus replication with 2-aminopurine
        date: 2001
       words: 4757
      flesch: 45
     summary: key: cord-340422-8f5xe4zc authors: Rowland, R. R. R.; Robinson, B.; Stefanick, J.; Kim, T. S.; Guanghua, L.; Lawson, S. R.; Benfield, D. A. title: Inhibition of porcine reproductive and respiratory syndrome virus by interferon-gamma and recovery of virus replication with 2-aminopurine date: 2001 journal: Arch Virol DOI: 10.1007/s007050170161 sha: doc_id: 340422 cord_uid: 8f5xe4zc Porcine reproductive and respiratory syndrome virus (PRRSV) belongs to a group of RNA viruses that establish persistent infections. The effect of IFN-γ on virus replication included reductions in the number of infected cells, virus yield, and RNA content in single cells.
    keywords: cells; fig; ifn-; infection; pkr; prrsv; replication; virus
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        item: #1174 of 1349
          id: cord-340423-f8ab7413
      author: Barr, J.N.
       title: Genetic Instability of RNA Viruses
        date: 2016-09-09
       words: 9780
      flesch: 40
     summary: Sequence analysis of RNA virus genomes has revealed that they preferentially accumulate A-to-G transitions, which are characteristic hallmarks of ADAR activity. Because the majority of nucleotide changes in RNA virus genomes are either strongly deleterious or lethal, the population is perpetually refined as deleterious genomes become purged through selection, leaving only mutations with phenotypically neutral or advantageous consequences to persist [69, 70] .
    keywords: cell; cycle; fidelity; genome; host; infection; mutation; polymerase; rate; recombination; replication; rna; rna viruses; robustness; viruses
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        item: #1175 of 1349
          id: cord-340475-h0q1m3ed
      author: Carnero, Elena
       title: Type I Interferon Regulates the Expression of Long Non-Coding RNAs
        date: 2014-11-06
       words: 10174
      flesch: 49
     summary: The multilayered complexity of ceRNA crosstalk and competition Long noncoding RNA HOTAIR reprograms chromatin state to promote cancer metastasis A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response Role of human noncoding RNAs in the control of tumorigenesis Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells Long non-coding RNAs in haematological malignancies Non-coding RNAs: regulators of disease Long noncoding RNAs and human disease Long non-coding RNAs: new players in cell differentiation and development Control of Cdc28 CDK1 by a stress-induced lncRNA Long noncoding RNAs in innate and adaptive immunity Unliganded progesterone receptor-mediated targeting of an RNA-containing repressive complex silences a subset of hormone-inducible genes Noncoding RNA and its associated proteins as regulatory elements of the immune system A long noncoding RNA mediates both activation and repression of immune response genes Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes The human long noncoding RNA lnc-IL7R regulates the inflammatory response The long noncoding RNA THRIL regulates TNFalpha expression through its interaction with hnRNPL A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics Role of microRNAs and long-non-coding RNAs in CD4(+) T-cell differentiation Genome-wide identification of long noncoding RNAs in CD8+ T cells Cutting edge: influence of Tmevpg1, a long intergenic noncoding RNA, on the expression of Ifng by Th1 cells The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation lncRNA expression signatures in response to enterovirus 71 infection Evidence for a crucial role of a host non-coding RNA in influenza A virus replication Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling Annotation of long non-coding RNAs expressed in Collaborative Cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts Hepatitis B virus X protein (HBx)-related long noncoding RNA (lncRNA) down-regulated expression by HBx (Dreh) inhibits hepatocellular carcinoma metastasis by targeting the intermediate filament protein vimentin Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans Elevation of highly up-regulated in liver cancer (HULC) by hepatitis B virus X protein promotes hepatoma cell proliferation via down-regulating p18 NEAT1 long noncoding RNA and paraspeckle bodies modulate HIV-1 posttranscriptional expression Regulation of type I interferon responses Synergistic activation of inflammatory cytokine genes by interferon-gamma-induced chromatin remodeling and toll-like receptor signaling Complex modulation of cell typespecific signaling in response to type I interferons SOCS proteins, cytokine signalling and immune regulation Alpha interferon induces long-lasting refractoriness of JAK-STAT signaling in the mouse liver through induction of USP18/UBP43 Fine tuning type I interferon responses Interferons and microRNAs Production of infectious hepatitis C virus in tissue culture from a cloned viral genome Influenza A virus lacking the NS1 gene replicates in interferon-deficient systems Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair Effect of adenovirus-mediated RNA interference on endogenous microRNAs in a mouse model of multidrug resistance protein 2 gene silencing Linear models and empirical Bayes methods for assessing differential expression in microarray experiments Data Analysis Tools for DNA Microarrays GENCODE: the reference human genome annotation for the ENCODE project The UCSC genome browser database: 2014 update CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine Coding-potential assessment tool using an alignment-free logistic regression model LNCipedia: a database for annotated human lncRNA transcript sequences and structures ISR2 and 12 also shared a negative correlation with response to viral infection and IFN pathway genes.
    keywords: analysis; cells; coding; data; expression; figure; genes; hcv; ifn; irf1; isgs; isr2; isr8; levels; lncrnas; long; response; virus
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        item: #1176 of 1349
          id: cord-340489-yo3cp5vs
      author: None
       title: KAPITEL 13 Infektionskrankheiten
        date: 2008-12-31
       words: 26587
      flesch: 38
     summary: ASL spielt in der Diagnostik des rheumatischen Fiebers nur eine geringe Rolle, ADB hat in der Diagnostik der akuten Glomerulonephritis größere Bedeutung. Antikörpernachweisverfahren (Mikroagglutination, ELISA, Westernblot) spielen in der Diagnostik der akuten Enterokolitiden keine wesentliche Rolle.
    keywords: abb; aber; aids; alle; als; anderen; antibiotika; antikörper; antiretroviralen; antivirale; auch; auch bei; auf; auf der; auftreten; aus; bedeutung; behandelt; behandlung; bei; bei der; bei hiv; beim; bekannt; bereits; besteht; bild; bis; bisher; blut; bzw; cd4; chemotherapie; cmv; daher; damit; dann; das; dass; dem; denen; der; der hiv; der infektion; der therapie; des; deutschland; diagnose; diagnostik; die; diese; dna; durch; durch den; durch die; durchgeführt; ebenfalls; ebv; eine; eingesetzt; einige; erfolgen; erfolgt; erkrankungen; erreger; erwachsenen; evtl; fieber; fällen; führen; führt; für; für die; für eine; gabe; gegen; gibt; haben; hat; hbv; hcv; hemmung; hepatitis; herpesviren; heute; hier; hiv; hoher; hpv; hsv; häufig; ifn; immer; immunsupprimierten; impfstoff; impfung; infektion; infizierten; interferone; ist; ist das; ist der; ist die; ist eine; ist es; jahren; jedoch; kann; kap; kindern; klinischen; kommen; kommt; kommt es; können; lassen; letzten; liegt; lymphozyten; man; maßnahmen; mehr; meist; meisten; menschen; mit; mit der; mit einer; monate; muss; möglich; müssen; nach; nachgewiesen; nachweis; nachweis von; neben; nebenwirkungen; nicht; noch; nukleosidanaloga; nur; nur bei; oder; oft; patienten; pcr; pneumokokken; prionen; prognose; prp; relativ; ribavirin; risiko; rna; rolle; schweren; sehr; sein; seit; selten; sich; sie; sind; sollte; spezifische; substanzen; symptome; tab; tage; therapie; therapie ist; und; und bei; und der; und eine; und mit; unter; untersuchung; verlauf; verschiedene; verursacht; veränderungen; viele; viren; virus; virusvermehrung; von; von der; vor; war; weitere; wenn; werden; werden die; werden können; wie; wird; wochen; wurde; während; z. b.; zahl; zellen; zns; zum; zunächst; zur; zwischen; über; übertragung
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        item: #1177 of 1349
          id: cord-340554-7cwp2xbw
      author: Yamasaki, Satoshi
       title: ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow
        date: 2019-03-06
       words: 5383
      flesch: 46
     summary: Those small structural elements were derived from RNA structures found in the PDB. Rascal can predict tertiary structures with any secondary structures because the single stranded three-base fragments derived from RNA structures found in the PDB are not based on their secondary structure like RASSIE.
    keywords: acid; analysis; aptamer; complex; drugs; node; nucleic; prediction; protein; rascal; rna; simulations; structure; workflow
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        item: #1178 of 1349
          id: cord-341029-49360l2a
      author: Nasir, Arshan
       title: A phylogenomic data-driven exploration of viral origins and evolution
        date: 2015-09-25
       words: 14420
      flesch: 43
     summary: [as previously argued (40) (41) (42) ], albeit cautiously for RNA viruses with small proteome complements (read below). Surprisingly, FSFs shared with RNA viruses were also enriched in archaeal proteomes.
    keywords: archaea; bacteria; cells; data; dna; domains; evolution; example; fig; fsfs; genomes; groups; life; number; origin; proteins; proteomes; rna; table; venn; viruses
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        item: #1179 of 1349
          id: cord-341034-2oigu75k
      author: Moser, Theresa S.
       title: AMP-Activated Kinase Restricts Rift Valley Fever Virus Infection by Inhibiting Fatty Acid Synthesis
        date: 2012-04-19
       words: 9953
      flesch: 41
     summary: tumour suppressor provokes intestinal polyposis but resistance to transformation Autophagy is an essential component of Drosophila immunity against vesicular stomatitis virus A vesicular stomatitis virus recombinant expressing granulocyte-macrophage colony-stimulating factor induces enhanced T-cell responses and is highly attenuated for replication in animals Natural resistance-associated macrophage protein is a cellular receptor for sindbis virus in both insect and Mammalian hosts Heterogeneous nuclear ribonuclear protein K interacts with Sindbis virus nonstructural proteins and viral subgenomic mRNA RNAi screening for host factors involved in Vaccinia virus infection using Drosophila cells Genomewide RNAi screen reveals a specific sensitivity of IRES-containing RNA viruses to host translation inhibition Ars2 regulates both miRNA-and siRNA-dependent silencing and suppresses RNA virus infection in Drosophila Unsaturated fatty acids down-regulate srebp isoforms 1a and 1c by two mechanisms in HEK-293 cells We would like to thank members of Cherry lab for helpful discussions; Sheri Hanna, Maggie Nakamoto, and Patrick Rose for growing viruses; Robert Rawson for fatty acid reagents; Craig Thompson, Tullia Lindsten, and Heesun Cheong for autophagy-deficient MEFs; Bernard Moss and Stuart Isaacs for vaccinia reagents; Russell Jones, Morrie Birnbaum, and Russell Miller for AMPK reagents, technical help and suggestions. To explore the mechanism by which AMPK restricts RVFV replication, we examined the impact of AMPK on translation and lipid biogenesis, both of which contribute to important steps in virus infection.
    keywords: acid; activation; ampk; cells; fatty; figure; infection; kinase; lipid; lkb1; mefs; protein; replication; rna; rvfv; synthesis; virus; viruses
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        item: #1180 of 1349
          id: cord-341050-hnuogpqn
      author: Acharya, Dhiraj
       title: An Overview of Current Approaches Toward the Treatment and Prevention of West Nile Virus Infection
        date: 2016-05-18
       words: 10749
      flesch: 23
     summary: inhibitors Investigators of The Multicenter Study of Perioperative Ischemia Research Group, Ischemia Research, and Education Foundation (2007) Mortality associated with aprotinin during 5 years following coronary artery bypass graft surgery Discovery of a non-peptidic inhibitor of West Nile virus NS3 protease by high-throughput docking Identifi cation and biochemical characterization of small-molecule inhibitors of West Nile virus serine protease by a high-throughput screen Characterization of the West Nile virus protease substrate specifi city and inhibitors Synthesis and in vitro evaluation of West Nile virus protease inhibitors based on the 2-{6 Structure-activity relationship and improved hydrolytic stability of pyrazole derivatives that are allosteric inhibitors of West Nile Virus NS2B-NS3 proteinase Inhibitors of Dengue virus and West Nile virus proteases based on the aminobenzamide scaffold Synthesis and in vitro evaluation of West Nile virus protease inhibitors based on the 1,3,4,5-tetrasubstituted 1H-pyrrol-2(5H)-one scaffold Design, synthesis and characterization of novel 1,2-benzisothiazol-3(2H)-one and 1,3,4-oxadiazole hybrid derivatives: potent inhibitors of Dengue and West Nile virus NS2B/NS3 proteases Small molecule pan-dengue and West Nile virus NS3 protease inhibitors Flexibility between the protease and helicase domains of the dengue virus NS3 protein conferred by the linker region and its functional implications Structure of West Nile virus NS3 protease: ligand stabilization of the catalytic conformation dengue virus NS5 RNA capping enzyme West Nile virus methyltransferase domain interacts with protein kinase G A single amino acid in nonstructural protein NS4B confers virulence to dengue virus in AG129 mice through enhancement of viral RNA synthesis A single amino acid substitution in the central portion of the West Nile virus NS4B protein confers a highly attenuated phenotype in mice Inhibition of dengue virus by targeting viral NS4B protein Chemical genetics strategy identifi es an HCV NS5A inhibitor with a potent clinical effect B cells and antibody play critical roles in the immediate defense of disseminated infection by West Nile encephalitis virus A critical role for induced IgM in the protection against West Nile virus infection The memory T cell response to West Nile virus in symptomatic humans following natural infection is not infl uenced by age and is dominated by a restricted set of CD8+ T cell epitopes Comprehensive mapping of West Nile virus (WNV)-and Japanese encephalitis virus serocomplex-specifi c linear B-cell epitopes from WNV non-structural protein 1 Identifi cation of two linear B-cell epitopes from West Nile virus NS1 by screening a phage-displayed random peptide library Mapping and analysis of West Nile virus-specifi c monoclonal antibodies: prospects for vaccine development Fusion loop peptide of the West Nile virus envelope protein is essential for pathogenesis and is recognized by a therapeutic cross-reactive human monoclonal antibody Role of IFN-gamma in an experimental murine model of West Nile virus-induced seizures Role of CD8+ T cells in control of West Nile virus infection The relative contribution of antibody and CD8+ T cells to vaccine immunity against West Nile encephalitis virus Gamma interferon plays a crucial early antiviral role in protection against West Nile virus infection Pattern recognition receptor MDA5 modulates CD8+ T cell-dependent clearance of West Nile virus from the central nervous system Attenuation and immunogenicity in humans of a live dengue virus type-4 vaccine candidate with a 30 nucleotide deletion in its 3′-untranslated region The live attenuated chimeric vaccine rWN/ DEN4Delta30 is well-tolerated and immunogenic in healthy fl avivirus-naive adult volunteers Chimeric dengue 2 PDK-53/West Nile NY99 viruses retain the phenotypic attenuation markers of the candidate PDK-53 vaccine virus and protect mice against lethal challenge with West Nile virus An attenuated West Nile prototype virus is highly immunogenic and protects against the deadly NY99 strain: a candidate for live WN vaccine development Liveattenuated recombinant equine herpesvirus type 1 (EHV-1) induces a neutralizing antibody response against West Nile virus (WNV) Equine vaccine for West Nile virus The effi cacy of inactivated West Nile vaccine (WN-VAX) in mice and monkeys Safety and effi cacy in geese of a PER.C6-based inactivated West Nile virus vaccine A hydrogen peroxide-inactivated virus vaccine elicits humoral and cellular immunity and protects against lethal West Nile virus infection in aged mice Development of a new hydrogen peroxidebased vaccine platform Phylogeny and molecular epidemiology of West Nile and Kunjin viruses West Nile virus (Kunjin subtype) disease in the northern territory of Australia-a case of encephalitis and review of all reported cases An inactivated West Nile virus vaccine derived from a chemically synthesized cDNA system Immunization with West Nile virus envelope domain III protects mice against lethal infection with homologous and heterologous virus Preparation and immunogenic properties of a recombinant West Nile subunit vaccine A West Nile virus recombinant protein vaccine that coactivates innate and adaptive immunity A VLP-based vaccine targeting domain III of the West Nile virus E protein protects from lethal infection in mice A novel platform for virus-like particle-display of fl aviviral envelope domain III: induction of Dengue and West Nile virus neutralizing antibodies Dhiraj Acharya and Fengwei Bai duction of detection and diagnostic reagents of West Nile virus in plants Plant-made vaccines against West Nile virus are potent, safe, and economically feasible Monoclonal antibody produced in plants efficiently treats West Nile virus infection in mice The structural immunology of antibody protection against West Nile virus The molecular basis of antibody-mediated neutralization of West Nile virus Antibody engineering Antibody engineering and modifi cation technologies Glycoengineering of therapeutic antibodies enhances monocyte/macrophage-mediated phagocytosis and cytotoxicity A paradoxical role for neutrophils in the pathogenesis of West Nile virus
    keywords: activity; antiviral; cell; dengue; development; host; identifi; infection; inhibitors; nile; nile virus; ns3; protease; protein; replication; rna; screening; structural; vaccine; virus; west; west nile; wnv
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        item: #1181 of 1349
          id: cord-341071-nwrl1qws
      author: Berzal-Herranz, Alfredo
       title: Two Examples of RNA Aptamers with Antiviral Activity. Are Aptamers the Wished Antiviral Drugs?
        date: 2020-07-22
       words: 5443
      flesch: 42
     summary: This work describes two well documented examples of RNA aptamers with antiviral activity against highly conserved structural domains of the HIV-1 and HCV RNA genome, respectively, performed in our laboratory. We applied the previously described SELEX strategy to identify RNA aptamers against a 194 nt-long subgenomic RNA comprising the CRE
    keywords: aptamers; hcv; molecules; rna; selection; sequence; target; viral
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        item: #1182 of 1349
          id: cord-341171-s8vkgdhf
      author: Kojima, Mizuki
       title: Irradiation by a Combination of Different Peak-Wavelength Ultraviolet-Light Emitting Diodes Enhances the Inactivation of Influenza A Viruses
        date: 2020-07-08
       words: 6580
      flesch: 47
     summary: The effects of the LED irradiations on viral inactivation were determined by the infection ratio (log 10 FFU ratio), which was calculated as log 10 FFU ratio = log 10 (Nt/N 0 ), where N t is the FFU of the UV-irradiated sample, and N 0 is the FFU of the sample without UV irradiation. [22] , and the effects of the LED irradiations were determined by the infection ratio (log 10 EID 50 ratio) calculated as log 10 EID 50 ratio = log 10 (N t /N 0 ), where N t is the EID 50 of the UV-irradiated sample, and N 0 is the EID 50 of the sample without UV irradiation.
    keywords: effect; figure; inactivation; irradiation; lamp; leds; nm uv; rna; spectrum; uv lamp
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        item: #1183 of 1349
          id: cord-341176-83khavoh
      author: Lotfi, Melika
       title: CRISPR/Cas13: A potential therapeutic option of COVID-19
        date: 2020-09-17
       words: 5308
      flesch: 36
     summary: Moreover, Cas13 can process its CRISPR array and release individual CRISPR RNA (crRNAs), so it can be used for multiplexed targeting applications (76) . They applied the class 2 type VI-D CRISPR (CRISPR/Cas13d) system derived from Ruminococcus flavefaciens XPD3002 to inhibit RNA viruses in human cells (13, 68) .
    keywords: cas13; cells; coronavirus; cov-2; covid-19; crispr; genome; novel; proteins; rna; sars; system
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        item: #1184 of 1349
          id: cord-341321-paucodwz
      author: Finkbeiner, Stacy R
       title: Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea
        date: 2008-10-14
       words: 3620
      flesch: 44
     summary: In this paper, we report the full sequencing and characterization of the genome of this astrovirus, referred to hereafter as astrovirus MLB1 (AstV-MLB1). Alignment between AstV-MLB1 and other human astroviruses of the highly conserved 52 nt at the ORF1b/ORF2 junction revealed that AstV-MLB1 possessed only 61.5% identity in this region (Fig. 1B) .
    keywords: astroviruses; astv; diarrhea; genome; human; mlb1; rna; sequence
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        item: #1185 of 1349
          id: cord-341324-f9g9gitn
      author: Rojas, José M.
       title: Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway
        date: 2020-10-21
       words: 10861
      flesch: 35
     summary: The measles virus V protein binding site to STAT2 overlaps with that of IRF9 STAT2 is a primary target for measles virus V protein-mediated alpha/ beta interferon signaling inhibition The interferon signaling antagonist function of yellow fever virus NS5 protein is activated by type I interferon Dengue virus co-opts UBR4 to degrade STAT2 and antagonize type I interferon signaling Nonstructural protein 11 of porcine reproductive and respiratory syndrome virus induces STAT2 degradation to inhibit interferon signaling The V protein of simian virus 5 inhibits interferon signalling by targeting STAT1 for proteasome-mediated degradation Association of mumps virus V protein with RACK1 results in dissociation of STAT-1 from the alpha interferon receptor complex The human papillomavirus type 16 E7 protein binds human interferon regulatory factor-9 via a novel PEST domain required for transformation Expression of hepatitis C virus proteins interferes with the antiviral action of interferon independently of PKR-mediated control of protein synthesis Herpes simplex virus 1 gene products occlude the interferon signaling pathway at multiple sites Human cytomegalovirus inhibits IFN-alpha-stimulated antiviral and immunoregulatory responses by blocking multiple levels of IFN-alpha signal transduction The polyoma virus T antigen interferes with interferon-inducible gene expression Foot-and-mouth disease virus leader protease cleaves G3BP1 and G3BP2 and inhibits stress granule formation Stress granule formation induced by measles virus is protein kinase PKR dependent and impaired by RNA adenosine deaminase ADAR1 G3BP1, G3BP2 and CAPRIN1 are required for translation of interferon stimulated mRNAs and are targeted by a dengue virus non-coding RNA Inhibitory activity for the interferoninduced protein kinase is associated with the reovirus serotype 1 sigma 3 protein Site-directed mutagenic analysis of reovirus sigma 3 protein binding to dsRNA Rift Valley fever virus NSs protein functions and the similarity to other bunyavirus NSs proteins RNA-specific adenosine deaminase ADAR1 suppresses measles virus-induced apoptosis and activation of protein kinase PKR Double-stranded RNA deaminase ADAR1 increases host susceptibility to virus infection ADAR1 interacts with PKR during human immunodeficiency virus infection of lymphocytes and contributes to viral replication Silencing the alarms: Innate immune antagonism by rotavirus NSP1 and VP3 Homologous 2',5'-phosphodiesterases from disparate RNA viruses antagonize antiviral innate immunity Rotavirus open cores catalyze 5′-capping and methylation of exogenous RNA: evidence that VP3 is a methyltransferase 2′-O methylation of the viral mRNA cap evades host restriction by IFIT family members Attenuation and restoration of severe acute respiratory syndrome coronavirus mutant lacking 2'-o-methyltransferase activity Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus Interferon induction of IFITM proteins promotes infection by human coronavirus OC43 HIV-1 mutates to evade IFITM1 restriction In vivo evasion of MxA by avian influenza viruses requires human signature in the viral nucleoprotein Irreversible inactivation of ISG15 by a viral leader protease enables alternative infection detection strategies Consecutive inhibition of ISG15 expression and ISGylation by cytomegalovirus regulators The abundant tegument protein pUL25 of human cytomegalovirus prevents proteasomal degradation of pUL26 and supports its suppression of ISGylation Transmembrane protein pUL50 of human cytomegalovirus inhibits ISGylation by downregulating UBE1L ISG15, a ubiquitin-like interferon-stimulated gene, promotes hepatitis C virus production in vitro: implications for chronic infection and response to treatment For instance, Ebola virus VP35 protein, Middle East respiratory syndrome Viral interference with accessory cellular components involved in PRR activation.
    keywords: activation; activity; binding; cell; degradation; human; ifn; induction; interferon; mechanism; phosphorylation; protease; protein; receptor; recognition; response; rig; rna; signaling; type; viral; virus; viruses
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        item: #1186 of 1349
          id: cord-341330-31ngknq4
      author: Sarma, Phulen
       title: In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain)
        date: 2020-05-18
       words: 3626
      flesch: 55
     summary: key: cord-341330-31ngknq4 authors: Sarma, Phulen; Shekhar, Nishant; Prajapat, Manisha; Avti, Pramod; Kaur, Hardeep; Kumar, Subodh; Singh, Sanjay; Kumar, Harish; Prakash, Ajay; Dhibar, Deba Prasad; Medhi, Bikash title: In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain) date: 2020-05-18 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1753580 sha: doc_id: 341330 cord_uid: 31ngknq4 The N terminal domain (NTD) of Nucleocapsid protein (N protein) of coronavirus (CoV) binds to the viral (+) sense RNA and results in CoV ribonucleoprotien (CoV RNP) complex, essential for the virus replication. Two NTD structures of N proteins were selected (2OFZ and 1SSK, 92% homology) for virtual screening of 56,079 compounds from Asinex and Maybridge library to identify top 15 hits for each of the targets based on ‘docking score’.
    keywords: binding; cov; domain; ligands; ntd; protein; rna
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        item: #1187 of 1349
          id: cord-341342-kyavg4vu
      author: Masters, P. S.
       title: Localization of an RNA-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus
        date: 1992
       words: 5909
      flesch: 50
     summary: Interferon-mediated inhibition of simian virus-40 early RNA accumulation Zinc fingers: a novel protein motif for nucleic acid recognition Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Characterization of leader RNA sequences on the virion and mRNAs of mouse hepatitis virus, a cytoplasmic RNA virus Sequence-specific recognition of RNA hairpins by bacteriophage antiterminators requires a conserved arginine-rich motif The complete sequence (22 kilobases) of murine coronavirus gene I encoding the putative proteases and RNA polymerase Plus and minus strand leader RNAs in negative strand virus-infected cells Ribonucleoprotein-like structures from coronavirus particles RNA-binding domain of MHV N protein 159 Analysis of efficiently packaged defective interfering RNAs of murine coronavirus: localization of a possible packaging signal Molecular cloning: a laboratory manual Resolution of multiple complexes of phosphoprotein NS with nucleocapsid protein N of vesicular stomatitis virus Complex formation with vesicular stomatitis virus phosphoprotein NS prevents binding of nucleocapsid protein N to nonspecific RNA Structure and function studies of the nucleocapsid protein of mouse hepatitis virus Efficient in vitro synthesis of biological active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter Molecular cloning of the gene encoding the putative polymerase of mouse hepatitis coronavirus, strain A59 Sequence comparison of the N genes of five strains of the coronavirus mouse hepatitis virus suggests a three domain structure for the nucleocapsid protein A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP protein RNA-binding proteins of coronavirus MHV: detection of monomeric and multimeric N protein with an RNA overlay-protein blot assay The 54-kD protein of signal recognition particle contains a methionine-rich RNA binding domain DNA sequencing with chain terminating inhibitors Identification and primary structure of the gene encoding the Berne virus nucleocapsid protein Coronaviruses: structure and genome expression Assembly of nucleocapsidlike struct~es in animal cells infected with a vaccinia virus recombinant encoding the measles virus nucleoprorein Expression of a recombinant DNA gene coding for the vesicular stomatitis virus nucleocapsid protein Deans ILl (1988) By contrast, internal deletions or truncations extending beyond these two limits effectively abolished RNA binding by N protein.
    keywords: ability; amino; binding; fig; gel; mhv; molecule; n protein; page; protein; rna
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        item: #1188 of 1349
          id: cord-341502-jlzufa28
      author: Lee, Sungyul
       title: The SARS-CoV-2 RNA interactome
        date: 2020-11-02
       words: 5853
      flesch: 37
     summary: As for viral proteins, the N protein was the most strongly enriched one, as expected ( Figure 1D ). PARP12, a cytoplasmic mono-ADP-ribosylation (MARylation) enzyme, is also known to have broad antiviral activity against RNA viruses such as Venezuelan equine encephalitis virus (Togaviridae), vesicular stomatitis virus (Rhabdoviridae), Rift Valley fever virus (Phenuiviridae), encephalomyocarditis virus (Picornaviridae), and Zika virus (Flaviviridae) by multiple mechanisms including blocking cellular RNA translation (Atasheva et al., 2014; Welsby et al., 2014) or triggering proteasome-mediated destabilization of viral proteins (Li et al., 2018) .
    keywords: cells; cov-2; figure; host; interactome; mrna; probe; proteins; rna; rnas; rnp; sars; translation; viral; virus
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        item: #1189 of 1349
          id: cord-341513-e6p3lrlf
      author: Li, Yunchuan
       title: Microarray Analysis Identifies the Potential Role of Long Non-Coding RNA in Regulating Neuroinflammation during Japanese Encephalitis Virus Infection
        date: 2017-09-29
       words: 6143
      flesch: 40
     summary: First, we used mice brain to understand the regulation of host lncRNAs upon JEV infection. Collectively, we first demonstrated the transcriptomic landscape of lncRNAs in mice brain infected with JEV and analyzed the coexpression network of differentially regulated lncRNAs and mRNAs during JEV infection.
    keywords: analysis; brain; cells; expression; genes; infection; jev; lncrnas; mice; mrnas; non; pathway; response; virus
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        item: #1190 of 1349
          id: cord-341541-3l6tjf3t
      author: Hajijafari Anaraki, Mozafar
       title: Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene
        date: 2020-05-26
       words: 1276
      flesch: 43
     summary: Based on the RT-PCR detection and sequence analysis of IBV RdRp gene, an overall prevalence of field strains estimated as 44.2%. Phylogenetic analysis of RdRp gene sequences resulted in clustering the IBV strains related to each area.
    keywords: gene; ibv; rdrp; strains
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        item: #1191 of 1349
          id: cord-341804-rnj3wtg4
      author: Jin, Zhe
       title: Drug treatment of coronavirus disease 2019 (COVID-19) in China.
        date: 2020-06-27
       words: 2054
      flesch: 15
     summary: key: cord-341804-rnj3wtg4 authors: Jin, Zhe; Liu, Jing-Yi; Feng, Rang; Ji, Lu; Jin, Zi-Li; Li, Hai-Bo title: Drug treatment of coronavirus disease 2019 (COVID-19) in China. 7 authorization for the treatment of adults and children with severe COVID-19 disease 20 (Hendaus, 2020) .
    keywords: coronavirus; covid-19; disease; patients; treatment
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        item: #1192 of 1349
          id: cord-342117-r2chpw7y
      author: Wu, Xinwei
       title: Inhibitory effect of small interfering RNA on dengue virus replication in mosquito cells
        date: 2010-10-14
       words: 2933
      flesch: 50
     summary: Our data showed that synthetic siRNA against the DEN membrane glycoprotein precursor gene effectively inhibited DEN viral RNA replication and increased C6/36 cell survival rate. Our data showed that synthetic siRNA against the DEN-1 membrane glycoprotein precursor gene effectively inhibited DEN-1 viral RNA replication and increased C6/36 cell survival rate.
    keywords: c6/36; cells; dengue; group; replication; rna; sirna; virus
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        item: #1193 of 1349
          id: cord-342145-cq6xe5r7
      author: Dao Thi, Viet Loan
       title: A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples
        date: 2020-08-12
       words: 9345
      flesch: 52
     summary: Therefore, it appeared that the N-A primer set used for the RT-LAMP assay performed equally well with either IVT RNA or RNA samples isolated from the pharyngeal swab specimens. For samples with a CT ≤ 30 as measured by RT-qPCR with E-Sarbeco primers, we found overall satisfactory sensitivity and specificity values for SARS-CoV-2 RNA detection by the RT-LAMP assay using RNA samples isolated from pharyngeal swab specimens ( Fig. 3 and Table 1 ).
    keywords: cov-2; detection; fig; lamp; lamp assay; positive; primer; qpcr; reaction; rna; samples; sars; sensitivity; sequencing; specimens; swab
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        item: #1194 of 1349
          id: cord-342189-ya05m58o
      author: Banerjee, Abhik K.
       title: SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses
        date: 2020-10-08
       words: 11499
      flesch: 45
     summary: Because viral membrane proteins also require trafficking to the ER, viral disruption of SRP might negatively impact viral propagation, unless viral proteins are trafficked in an SRP-independent manner ( Figure S7E ) or if NSP8/9 selectively impacts host (but not viral) proteins. Understanding the interactions between viral proteins and components of human cells is essential for elucidating their pathogenic mechanisms and for development of effective therapeutics.
    keywords: binding; cells; cov-2; et al; expression; figure; gene; gfp; host; human; ifn; infection; membrane; mrna; nsp1; protein; ribosome; rna; sars; splicing; srp; translation
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        item: #1195 of 1349
          id: cord-342344-jjnf4yje
      author: Mello, C. J.
       title: Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR
        date: 2020-06-26
       words: 3130
      flesch: 45
     summary: The coronavirus pandemic and aerosols: Does COVID-19 transmit via expiratory particles? Temporal dynamics in viral shedding and transmissibility of COVID-19 SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Detection of a novel human coronavirus by real-time reversetranscription polymerase chain reaction Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections Identification of a novel coronavirus in patients with severe acute respiratory syndrome A one step quantitative RT-PCR for detection of SARS coronavirus with an internal control for PCR inhibitors Talking the talk, but not walking the walk: RT-qPCR as a paradigm for the lack of reproducibility in molecular research How good is a PCR efficiency estimate: 56% linked molecules) between these sequences (Fig. 4b, Table 1) , similar to the level of linkage (58%) was detected in a control RNA sample that was not exposed to saliva (Fig. 4c, Table 1 ). .
    keywords: cov-2; droplets; license; positive; preprint; rna; sars; sequences
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        item: #1196 of 1349
          id: cord-342412-azkamnpa
      author: Ecker, David J
       title: The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents
        date: 2005-04-25
       words: 7212
      flesch: 37
     summary: Infectious disease agents important to the public health in the U.S. are monitored by the CDC and listed in Additional File 2 The goal of the database is to provide an informative, readily accessible, single location for basic information on a broad range of important disease causing agents.
    keywords: agents; database; disease; figure; file; food; health; human; information; list; organisms; pathogens; plant; potential; public; rna; species; toxins; viruses
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        item: #1197 of 1349
          id: cord-342456-5gp3cry0
      author: Hoagland, Daisy A.
       title: Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds
        date: 2020-07-13
       words: 4520
      flesch: 37
     summary: We then searched for FDA-approved compounds that induce or suppress the expression of these genes using drug signatures extracted from other independent transcriptome studies . Consensus analysis was performed by counting gene overlap in the top 50 up or down differentially expressed genes based on the consensus L1000FWD and RNA-seq signatures generated from the A549-ACE2 cells.
    keywords: cells; cov-2; drugs; rna; sars; seq; signatures; virus
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        item: #1198 of 1349
          id: cord-342634-4ouhdjsr
      author: Semrad, Katharina
       title: Proteins with RNA Chaperone Activity: A World of Diverse Proteins with a Common Task—Impediment of RNA Misfolding
        date: 2010-12-26
       words: 7147
      flesch: 46
     summary: RNA chaperones and the RNA folding problem A DEAD-Box protein functions as an ATP-dependent RNA chaperone in group I intron splicing Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones Escherichia coli protein StpA stimulates self-splicing by promoting RNA assembly in vitro RNA chaperone activity and RNA-binding properties of the E. coli protein StpA Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator Geometric nomenclature and classification of RNA base pairs RNA tertiary interactions in the large ribosomal subunit: the A-minor motif Two interconvertible forms of tryptophanyl sRNA in E. coli Native and renatured transfer ribonucleic acid A ribosomal function is necessary for efficient splicing of the T4 phage thymidylate synthase intron in vivo Alternative secondary structures in the 5 exon affect both forward and reverse self-splicing of the Tetrahymena intervening sequence RNA A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core Domain structure and RNA annealing activity of the Escherichia coli regulatory protein StpA RNA annealing activities in HeLa nuclei HIV-1 nucleocapsid protein as a nucleic acid chaperone: spectroscopic study of its helix-destabilizing properties, structural binding specificity, and annealing activity Coupling RNA annealing and strand displacement: a FRET-based microplate reader assay for RNA chaperone activity Dissecting RNA chaperone activity An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis RNA chaperone activity of large ribosomal subunit proteins from Escherichia coli RNA chaperone activity of protein components of human Ro RNPs Assaying RNA chaperone activity in vivo in bacteria using a ribozyme folding trap Escherichia coli CspA-family RNA chaperones are transcription antiterminators Transcription antitermination by translation initiation factor IF1 Assay of transcription antitermination by proteins of the CspA family RNA chaperones, RNA annealers and RNA helicases Protein enhancement of hammerhead ribozyme catalysis Identification and characterization of the RNA chaperone activity of hepatitis delta antigen peptides The hepatitis C virus Core protein is a potent nucleic acid chaperone that directs dimerization of the viral (+) strand RNA in vitro RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae Role of RNA chaperones in virus replication Coronavirus nucleocapsid protein is an RNA chaperone Coronavirus nucleocapsid protein facilitates template switching and is required for efficient transcription Assaying RNA chaperone activity in vivo using a novel RNA folding trap Assays for the RNA chaperone activity of proteins RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo The role of structural disorder in the function of RNA and protein chaperones How common are extraribosomal functions of ribosomal proteins? Recently, it was demonstrated that E. coli ribosomal proteins L15, L16, L18, and L19, that showed RNA chaperone activity in vitro, further possess protein chaperone activity comparable to other protein chaperones such as Hsp90 [43] .
    keywords: activity; annealing; assay; chaperone; chaperone activity; folding; group; intron; proteins; ribosomal; rna; splicing; structure; vivo
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        item: #1199 of 1349
          id: cord-342649-ysossker
      author: Scagnolari, Carolina
       title: Evaluation of viral load in infants hospitalized with bronchiolitis caused by respiratory syncytial virus
        date: 2012-03-10
       words: 3766
      flesch: 36
     summary: Furthermore, we found a signiWcant correlation between RSV viral load and the length of hospital stay (r = 0.16, p = 0.038), and levels of hemoglobin (r = ¡0.18, p = 0.024) or glycemia (r = 0.24, p = 0.028). To this regard, some studies revealed signiWcant association between disease severity and RSV load in nasopharyngeal secretion of infants with primary respiratory tract infection
    keywords: bronchiolitis; infants; load; rna; rsv; severity; virus
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        item: #1200 of 1349
          id: cord-342653-bpyc2gbl
      author: Wang, Hai-Tao
       title: Substrate recognition by TRIM and TRIM-like proteins in innate immunity
        date: 2020-10-20
       words: 8610
      flesch: 44
     summary: The tripartite motif family identifies cell compartments Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties The tripartite motif: structure and function The interferon-inducible ubiquitin-protein isopeptide ligase (E3) EFP also functions as an ISG15 E3 ligase Innate immunity to RNA virus is regulated by temporal and reversible sumoylation of RIG-I and MDA5 Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity Mechanism of TRIM25 catalytic activation in the antiviral RIG-I pathway Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5alpha Structural determinants of TRIM protein function Structural insights into the TRIM family of ubiquitin E3 ligases The tripartite motif coiled-coil is an elongated antiparallel hairpin dimer Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition TRIM5alpha SPRY/coiled-coil interactions optimize avid retroviral capsid recognition Ubiquitin-dependent and -independent roles of E3 ligase RIPLET in innate immunity Hierarchical assembly governs TRIM5alpha recognition of HIV-1 and retroviral capsids TRIM family: pleiotropy and diversification through homomultimer and heteromultimer formation TRIM family proteins and their emerging roles in innate immunity TRIM family proteins: roles in autophagy, immunity, and carcinogenesis Genomics and evolution of the TRIM gene family Relationship between SPRY and B30.2 protein domains. Thus, TRIM CC plays diverse functions in regulating the overall architecture and functions of TRIM proteins.
    keywords: activation; domain; dsrna; fig; proteins; recognition; rig; rna; signaling; spry; trim; trim21; trim5α
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        item: #1201 of 1349
          id: cord-342676-ykog278j
      author: Stewart, H.
       title: Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging
        date: 2016-03-14
       words: 6864
      flesch: 40
     summary: The presence of multiple, weak-affinity packaging signals in other RNA virus genomes has recently been reported 19, 29 , which represents a novel mechanism for viral packaging in viruses which do not possess a readily identifiable prototypic packaging signal. 6 .0 × 10 6 Huh-7 cells were electroporated with 5 μg of viral RNA at 975 μF and 260 V for 25 ms.
    keywords: assembly; cells; core; genome; hcv; hepatitis; jfh-1; motif; packaging; ppss; protein; region; replication; rna; structures; virus
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        item: #1202 of 1349
          id: cord-342681-pqzcy9wu
      author: Pongpirul, Wannarat A.
       title: Clinical Characteristics of Patients Hospitalized with Coronavirus Disease, Thailand
        date: 2020-07-17
       words: 1745
      flesch: 28
     summary: The required duration of hospitalization and observed period of viral RNA positivity for these patients underscore the potential burden of COVID-19 patients on hospital, diagnostic, treatment, and isolation capacities. Despite mild-to-moderate illness, the protracted period of SARS-CoV-2 RNA positivity in these patients' specimens might indicate a lengthy period of infectiousness and highlights risks to providers caring for COVID-19 patients.
    keywords: days; patients; rna; sars; specimens; virus
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        item: #1203 of 1349
          id: cord-342756-rgm9ffpk
      author: Senger, Mario Roberto
       title: COVID-19: molecular targets, drug repurposing and new avenues for drug discovery
        date: 2020-10-02
       words: 16157
      flesch: 39
     summary: Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19 Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/ NSP16 methyltransferase and main protease of SARS CoV-2 Targeting SARS-COV-2 non-structural protein 16: a virtual drug repurposing study Ready, set, fuse! (148) Other targets -Apart from SARS-CoVs infection, some relevant molecular targets of other viral diseases and host metabolism have also been investigated in COVID-19 drug discovery, such as viral neuraminidases and the DPP4 cell receptor.
    keywords: ace2; activity; cells; coronavirus; cov-2; covid-19; disease; drug; fig; host; human; infection; inhibitors; lopinavir; mers; new; patent; patients; potential; protease; protein; remdesivir; replication; repurposing; ritonavir; rna; sars; structure; studies; syndrome; target; treatment; trials
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        item: #1204 of 1349
          id: cord-342800-62jklwiy
      author: Xu, Shuqin
       title: mRNA Vaccine Era—Mechanisms, Drug Platform and Clinical Prospection
        date: 2020-09-09
       words: 13604
      flesch: 36
     summary: Self-adjuvanting properties of mRNA have both advantages and disadvantages in mRNA vaccine applications, therefore, it is necessary to form mRNA immunogenic regulations according to different medical demands, which in return would effectively improve the application efficacy of mRNA vaccines. The extraordinary advantages associated with mRNA vaccines, including their high efficacy, a relatively low severity of side effects, and low attainment costs, have enabled them to become prevalent in pre-clinical and clinical trials against various infectious diseases and cancers.
    keywords: antigen; cancer; cap; cationic; cells; clinical; delivery; efficiency; encoding; expression; ifn; immune; mice; mrna; mrna vaccines; protein; responses; self; sequence; specific; translation; vaccines; virus; vitro; vivo
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        item: #1205 of 1349
          id: cord-342901-ca2xxkb2
      author: Lloyd, Richard E.
       title: Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses
        date: 2015-05-31
       words: 16231
      flesch: 39
     summary: The cytoplasmic milieu encountered by plus strand RNA virus genomes as they are released from capsids is poised to greet the interloper as any other mRNA, with a ready store of RNA binding proteins ready to interact and impart functions. However, translation does not occur on transcripts that are naked and devoid of RNA-binding proteins, rather, cellular transcripts are continually bound to a host of RNA binding proteins from the instant they emerge from RNA polymerase during their synthesis.
    keywords: binding; cells; complex; et al; factors; hcv; hepatitis; hnrnp; host; infection; initiation; interaction; ires; nuclear; poliovirus; protein; ptb; region; replication; rna; rna replication; roles; strand; synthesis; translation; utr; viral; virus; viruses
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        item: #1206 of 1349
          id: cord-342902-y1v8wzxq
      author: Yuan, Shuofeng
       title: Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters
        date: 2020-10-07
       words: 5699
      flesch: 35
     summary: The effective concentration of clofazimine against SARS-CoV-2 (half maximal effective concentration 310 nM) is clinically achievable with standard dosage in patients (peak serum concentration 861 nM) 13 . Clofazimine has a relatively long duration of action with the mean elimination half-life approximately 25 days, thus we performed prophylactic treatment of hamsters with clofazimine before intranasally challenged with 10 5 PFU of SARS-CoV-2 ( Figure 4a ).
    keywords: antiviral; cells; clofazimine; cov-2; covid-19; drug; figure; human; infection; lung; patients; remdesivir; replication; rna; sars; treatment
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        item: #1207 of 1349
          id: cord-343221-e29of29o
      author: Kindler, Eveline
       title: Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication
        date: 2017-02-03
       words: 7936
      flesch: 44
     summary: MHV H277A replication was not detectable in spleen and liver of C57BL/6 mice at two days post intraperitoneal infection with 500 plaque-forming units (pfu), demonstrating that the EndoU activity is required for efficient replication and spread in vivo. Interestingly, concerning the role of Mda5 and TLR7, which are known as main cytoplasmic and endosomal PRRs for coronaviral RNA, respectively, MHV H277A replication was not restored in Mda5-deficient, TLR7-deficient, or Mda5-and TLR7-deficient mice.
    keywords: a59; cells; coronavirus; deficient; dsrna; endou; expression; fig; h277a; ifn; infection; macrophages; mhv; mhv h277a; replication; rna; rnase
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        item: #1208 of 1349
          id: cord-343350-04e6wvov
      author: Liu, Haipeng
       title: Antiviral immunity in crustaceans
        date: 2009-02-15
       words: 8014
      flesch: 38
     summary: A gene named as PmAV was found to be up-regulated in virus resistant shrimp and the PmAV protein has a C-type lectinlike domain (CTLD). Taura syndrome of marine penaeid shrimp: characterization of the viral agent Shrimp taura syndrome virus: genomic characterization and similarity with members of the genus Cricket paralysis-like viruses Virus taxonomy: the classification and nomenclature of viruses Special topic review: major viral diseases of the black tiger prawn (Penaeus monodon) in Thailand Epizootiology, distribution, and the impact on international trade of two penaeid shrimp viruses in the Shrimp diseases and current diagnostic methods Mechanisms of enveloped virus entry into animal cells Coronaviruses: structure and genome expression Antiserum to the gp116 glycoprotein of yellow head virus neutralizes infectivity in primary lymphoid organ cells of Penaeus monodon PmRab7 is a VP28-binding protein involved in white spot syndrome virus infection in shrimp Suppression of PmRab7 by dsRNA Inhibits WSSV or YHV Infection in Shrimp Antiviral phagocytosis is regulated by a novel Rab-dependent complex in shrimp Penaeus japonicus Vp28 of shrimp white spot syndrome virus is involved in the attachment and penetration into shrimp cells White spot syndrome virus (WSSV) infects specific hemocytes of the shrimp Penaeus merguiensis Sö derhä
    keywords: antiviral; cells; crayfish; crustaceans; dsrna; infection; monodon; penaeus; protein; rna; shrimp; spot; syndrome; virus; viruses; white; wssv
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        item: #1209 of 1349
          id: cord-343448-xhm97wy2
      author: Rinaldi, Andrea
       title: RNA to the rescue: RNA is one of the most promising targets for drug development given its wide variety of uses
        date: 2020-06-26
       words: 2940
      flesch: 41
     summary: Moreover, RNA vaccines may be able to elicit a stronger and broader immune response since they stimulate both the adaptive and innate immune systems. In addition, RNA vaccines are cell-free, non-infectious, and not-integrating, thus eliminating the risks of infection and insertional mutagenesis that comes with viral vectors.
    keywords: cancer; covid-19; gene; mrna; phase; protein; rna; vaccines
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        item: #1210 of 1349
          id: cord-343470-w215pzdc
      author: Tsai, Kevin
       title: Epigenetic and epitranscriptomic regulation of viral replication
        date: 2020-06-12
       words: 9796
      flesch: 31
     summary: Whereas cellular gene expression may be either enhanced or inhibited by specific epigenetic modifications deposited on histones (in particular, histone H3), these epigenetic modifications can also repress viral gene expression, potentially functioning as a potent antiviral innate immune response in DNA virus-infected cells. By contrast, the various covalent modifications added to RNAs, termed epitranscriptomic modifications, can positively regulate mRNA translation and/or stability, and both DNA and RNA viruses have evolved to utilize epitranscriptomic modifications as a means to maximize viral gene expression.
    keywords: cells; chromatin; dna; expression; gene; histone; host; ifi16; infection; modifications; pml; proteins; replication; residues; rna; virus; viruses
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        item: #1211 of 1349
          id: cord-343604-v986m9jd
      author: Vijayakumar, Balaji Gowrivel
       title: In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2
        date: 2020-08-06
       words: 1261
      flesch: 10
     summary: Hence, these flavonoids and structurally similar indole chalcones derivatives were studied in silico for their pharmacokinetic properties including absorption, distribution, metabolism, excretion, toxicity (ADMET) and anti-SARS-CoV-2 properties against their proteins, namely, RNA dependent RNA polymerase (rdrp), main protease (M(pro)) and Spike (S) protein via homology modelling and docking. Cyanidin may inhibit RNA polymerase function and, Quercetin is found to block interaction sites on the viral spike.
    keywords: coronavirus; flavonoids; indole; proteins; rna; sars
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        item: #1212 of 1349
          id: cord-343632-cv3qgno3
      author: Zhang, Yinhua
       title: Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP
        date: 2020-02-29
       words: 2347
      flesch: 42
     summary: This test was additionally verified using RNA samples purified from respiratory swabs collected from COVID-19 patients in Wuhan, China with equivalent performance to a commercial RT-qPCR test while requiring only heating and visual inspection. This study describes testing and validation of 5 sets LAMP primers targeting two fragments of the SARS-CoV-2 genome using short (~300bp) RNA fragments made with in vitro transcription and RNA samples from patients.
    keywords: amplification; detection; lamp; license; preprint; rna
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        item: #1213 of 1349
          id: cord-343662-scn7b4c6
      author: Delli Ponti, Riccardo
       title: A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs
        date: 2018-12-03
       words: 6575
      flesch: 45
     summary: 2018.00111/full#supplementary-material X-inactivation: quantitative predictions of protein interactions in the Xist network RNA STRAND: the RNA secondary structure and statistical analysis database Predicting protein associations with long noncoding RNAs A hierarchical model for evolution of 23S ribosomal RNA Comparative transcriptomics in human and mouse X-chromosome inactivation: closing in on proteins that bind Xist RNA Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution Quantitative predictions of protein interactions with long noncoding RNAs A highthroughput approach to profile RNA structure The four dimensions of noncoding RNA conservation Probing Xist RNA structure in cells using targeted structure-Seq Computing and visualizing dynamic time warping alignments in R: the dtw package Regulation of microRNA biogenesis Analysis of energy-based algorithms for RNA secondary structure prediction BLAT-The BLAST-Like Alignment Tool Scaling up dynamic time warping for datamining applications Genome-wide measurement of RNA secondary structure in yeast Global or local? Predicting secondary structure and accessibility in mRNAs Clustal W and Clustal X version 2.0 Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA Visualizing the secondary and tertiary architectural domains of lncRNA RepA ViennaRNA Package 2.0 SHAPE directed RNA folding Structural Determinants and mechanism of HIV-1 genome packaging Improved RNA secondary structure prediction by maximizing expected pair accuracy HIV-1 and Ebola virus encode small peptide motifs that recruit Tsg101 to sites of particle assembly to facilitate egress Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure Infernal 1.1: 100-fold faster RNA homology searches History of the ribosome and the origin of translation Function by structure: spotlights on xist long non-coding Word image matching using dynamic time warping RNAstructure: software for RNA secondary structure prediction and analysis A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs Simian immunodeficiency virus RNA is efficiently encapsidated by human immunodeficiency virus type 1 particles High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface Origins of HIV and the AIDS Pandemic SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells HOTAIR forms an intricate and modular secondary structure Structural imprints in vivo decode RNA regulatory mechanisms Evolution to the rescue: using comparative genomics to understand long non-coding RNAs Landscape and variation of RNA secondary structure across the human transcriptome Viral lncRNA: A regulatory molecule for controlling virus life cycle Architecture and secondary structure of an entire HIV-1 RNA genome Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data Xist Exon 7 contributes to the stable localization of xist RNA on the inactive x-chromosome CMfinder-a covariance model based RNA motif finding algorithm RNA secondary structure prediction guided by chemical shifts
    keywords: crossalign; dtw; figure; human; profiles; repa; rna; sequence; similarity; structure
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        item: #1214 of 1349
          id: cord-343918-5yk1j4ms
      author: Gorbalenya, A.E.
       title: Phylogeny of Viruses
        date: 2008-07-30
       words: 3892
      flesch: 37
     summary: Comparison of nucleotide and amino acid sequences, and, occasionally, other quantitative characteristics such as distances between three-dimensional structures of biopolymers, have been used to reconstruct virus phylogeny. With few exceptions, virus phylogeny follows the theory and practice developed for phylogeny of cellular life forms.
    keywords: analysis; evolution; phylogeny; rna; species; tree; virus; viruses
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        item: #1215 of 1349
          id: cord-343963-99rd3o79
      author: Wong, Mun-Teng
       title: Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection
        date: 2014-12-29
       words: 17306
      flesch: 34
     summary: RIG-I-mediated type I interferon-dependent innate immunity Phosphorylation of hepatitis C virus-encoded nonstructural protein NS5A Phosphorylation of the hepatitis C virus NS5A protein in vitro and in vivo: properties of the NS5A-associated kinase Phosphorylation of hepatitis C virus NS5A nonstructural protein: a new paradigm for phosphorylation-dependent viral RNA replication? Reduction of hepatitis C virus NS5A hyperphosphorylation by selective inhibition of cellular kinases activates viral RNA replication in cell culture Hepatitis C virus NS5A: tales of a promiscuous protein Hepatitis C virus nonstructural protein 5A modulates the Toll-like receptor-MyD88-dependent signaling pathway in macrophage cell lines Evidence that hepatitis C virus resistance to interferon is mediated through repression of the PKR protein kinase by the nonstructural 5A protein How hepatitis C virus counteracts the interferon response: the jury is still out on NS5A Control of PKR protein kinase by hepatitis C virus nonstructural 5A protein: molecular mechanisms of kinase regulation Hepatitis C virus nonstructural 5A protein induces interleukin-8, leading to partial inhibition of the interferoninduced antiviral response Relationships between hepatitis C virus replication and CXCL-8 production in vitro Hepatitis C virus NS5A protein interacts with 29,59-oligoadenylate synthetase and inhibits antiviral activity of IFN in an IFN sensitivity-determining region-independent manner Activation and evasion of the antiviral 29-59 oligoadenylate synthetase/ribonuclease L pathway by hepatitis C virus mRNA Hepatitis C virus NS5A protein protects against TNF-alpha mediated apoptotic cell death Inhibition of intrahepatic gamma interferon production by hepatitis C virus nonstructural protein 5A in transgenic mice Hepatitis C virus nonstructural protein 5A inhibits tumor necrosis factor-a-mediated apoptosis in Huh7 cells Activation of endoplasmic reticulum stress response by hepatitis viruses upregulates protein phosphatase 2A Protein phosphatase 2A: a highly regulated family of serine/threonine phosphatases implicated in cell growth and signalling PP2A targeting by viral proteins: a widespread biological strategy from DNA/RNA tumor viruses to HIV-1 Hepatitis C virus inhibits interferon signaling through upregulation of protein phosphatase 2A Upregulation of protein phosphatase 2Ac by hepatitis C virus modulates NS3 helicase activity through inhibition of protein arginine methyltransferase 1 Transcriptional induction of two genes in human cells by b interferon Functional classification of interferon-stimulated genes identified using microarrays A central role for RNA in the induction and biological activities of type 1 interferons Targeted impairment of innate antiviral responses in the liver of chronic hepatitis C patients Negative feedback regulation of RIG-I-mediated antiviral signaling by interferoninduced ISG15 conjugation Immune signaling by RIG-I-like receptors Retinoic acid inducible gene-I (RIG-I) signaling of hepatic stellate cells inhibits hepatitis C virus replication in hepatocytes Interferon-b pretreatment of conventional and plasmacytoid human dendritic cells enhances their activation by influenza virus A structure-based model of RIG-I activation Emerging role of ubiquitination in antiviral RIG-I signaling DDX60, a DEXD/H box helicase, is a novel antiviral factor promoting RIG-I-like receptor-mediated signaling Hepatitis C virus induces interferon-and interferon-stimulated genes in primary liver cultures IRF family of transcription factors as regulators of host defense Regulation of PKR and IRF-1 during hepatitis C virus RNA replication Constitutive expression of an ISGF2/IRF1 transgene leads to interferon-independent activation of interferon-inducible genes and resistance to virus infection Regulation of hepatitis C virus replication by interferon regulatory factor 1 IRF-7 is the master regulator of type-I interferon-dependent immune responses Hepatitis C virus infection impairs IRF-7 translocation and Alpha interferon synthesis in immortalized human hepatocytes IRF-3, IRF-5, and IRF-7 coordinately regulate the type I IFN response in myeloid dendritic cells downstream of MAVS signaling Hepatitis C virus inhibits intracellular interferon alpha expression in human hepatic cell lines Serum-derived hepatitis C virus infectivity in interferon regulatory factor-7-suppressed human primary hepatocytes Interferon regulatory factor IRF-7 induces the antiviral alpha interferon response and protects against lethal West Nile virus infection Antiviral actions of interferons Impact of protein kinase PKR in cell biology: from antiviral to antiproliferative action dsRNA-dependent protein kinase PKR and its role in stress, signaling and HCV infection PKR protein kinase is activated by hepatitis C virus and inhibits viral replication through translational control PKR-dependent mechanisms of gene expression from a subgenomic hepatitis C virus clone Identification of three interferon-inducible cellular enzymes that inhibit the replication of hepatitis C virus Alpha interferon induces distinct translational control programs to suppress hepatitis C virus RNA replication New antiviral pathway that mediates hepatitis C virus replicon interferon sensitivity through ADAR1 Hepatitis C virus controls interferon production through PKR activation Translational resistance of late alphavirus mRNA to eIF2a phosphorylation: a strategy to overcome the antiviral effect of protein kinase PKR Initiation of protein synthesis by hepatitis C virus is refractory to reduced eIF2.GTP.Met-tRNA(i)(Met) ternary complex availability Translational insensitivity to potent activation of PKR by HCV IRES RNA HCV NS5A co-operates with PKR in modulating HCV IRES-dependent translation Eukaryotic translation initiation machinery can operate in a bacterial-like mode without eIF2 Hepatitis C virus blocks interferon effector function by inducing protein kinase R phosphorylation Hepatitis C virus (HCV) induces formation of stress granules whose proteins regulate HCV RNA replication and virus assembly and egress P bodies, stress granules, and viral life cycles Stress granules: sites of mRNA triage that regulate mRNA stability and translatability Stress granules Eukaryotic stress granules: the ins and outs of translation Regulation of stress granules and P-bodies during RNA virus infection Diversion of stress granules and P-bodies during viral infection Dynamic oscillation of translation and stress granule formation mark the cellular response to virus infection Hepatitis C virus hijacks P-body and stress granule components around lipid droplets Hepatitis C virus coopts Ras-GTPase-activating protein-binding protein 1 for its genome replication Viral encounters with 29,59-oligoadenylate synthetase and RNase L during the interferon antiviral response New insights into the role of RNase L in innate immunity The oligoadenylate synthetase family: an ancient protein family with multiple antiviral activities The ribonuclease Ldependent antiviral roles of human 29,59-oligoadenylate synthetase family members against hepatitis C virus 59-Oligoadenylate synthetaselike gene highly induced by hepatitis C virus infection in human liver is inhibitory to viral replication in vitro Antiviral activities of ISG20 in positive-strand RNA virus infections ISG20, an actor of the innate immune response Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral Adenosine deaminases acting on RNA, RNA editing, and interferon action RNA-specific adenosine deaminase ADAR1 suppresses measles virus-induced apoptosis and activation of protein kinase PKR Expression of interferoninducible RNA adenosine deaminase ADAR1 during pathogen infection and mouse embryo development involves tissueselective promoter utilization and alternative splicing RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase A specific base transition occurs on replicating hepatitis delta virus RNA RNA editing in hepatitis delta virus HCV-induced ER stress HCV protein expression can induce an ER stress response and lead to calcium release from the ER, which in turn activates the cyclic AMP responsive element-binding protein that binds to the cyclic AMP responsive element in the promoter of protein phosphatase 2A (PP2A), resulting in upregulation of PP2A. 114 Expressed in essentially all cell types, PP2A is a serine/threonine phosphatase that is involved in multiple cellular processes, such as the cell cycle, signal transduction and stress response.
    keywords: activation; activity; antiviral; autophagy; c virus; cells; expression; hcv; hepatitis; host; ifn; immunity; infection; innate; interferon; isgs; ns5a; pkr; production; protein; replication; response; rig; rna; signaling; type; virus; virus infection; virus replication; viruses
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        item: #1216 of 1349
          id: cord-344006-0iq9s94n
      author: Atzrodt, Cassandra L.
       title: A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2
        date: 2020-05-23
       words: 7289
      flesch: 47
     summary: Presenting Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With COVID-19 in the Race to find COVID-19 treatments accelerates Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase Accepted Article RNA-Dependent RNA Polymerase by Remdesivir 120 Gilead Sciences Gilead Announces Results From Phase 3 Trial of Investigational Antiviral Remdesivir in Patients With Severe COVID-19 Some FDA Approved drugs exhibit binding affinity as high as kcal/mol against COVID-19 Main Protease (Mpro): A Molecular Docking Study IndiaRxiv Major ongoing clinical trials for COVID-19 treatment and studies currently being conducted or scheduled in Japan. CNN Kamisar B Oxford scientist says its vaccine is making headway, could show efficacy by WSJ News Exclusive | Drugmaker Moderna Delivers First Experimental Coronavirus Vaccine for Human Testing Long-term protection from SARS coronavirus infection conferred by a single immunization with an attenuated VSV-based vaccine Live bacterial vaccines -a review and identification of potential hazards.
    keywords: article; cell; copyright; coronavirus; cov-2; covid-19; disease; drugs; human; patients; rights; rna; sars; symptoms; testing; vaccine; virus
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        item: #1217 of 1349
          id: cord-344321-fjer281d
      author: Ning, Yi
       title: Aptamers used for biosensors and targeted therapy
        date: 2020-10-20
       words: 16982
      flesch: 45
     summary: Inhibition of receptor binding and VEGF-induced vascular permeability through interactions requiring the exon 7-encoded domain Characterization and application of a novel RNA aptamer against the mouse prion protein In vitro selection of RNA molecules that inhibit the activity of ricin A-chain Methods developed for SELEX Analytical applications of aptamers Gold nanoparticle-based colorimetric detection of kanamycin using a DNA aptamer In vitro selection and characterization of RNA aptamers binding thyroxine hormone In vitro selection of DNA aptamers that bind Ltyrosinamide Automated selection of anti-protein aptamers Use of magnetic beads in selection and detection of biotoxin aptamers by electrochemiluminescence and enzymatic methods RNA aptamers specifically interact with the prion protein PrP Binding of herpes simplex virus-1 US11 to specific RNA sequences FluMag-SELEX as an advantageous method for DNA aptamer selection Isolation and characterization of enantioselective DNA aptamers for ibuprofen Selection of DNA aptamers against polychlorinated biphenyls as potential biorecognition elements for environmental analysis Rapid fluorescent detection of Escherichia coli K88 based on DNA aptamer library as direct and specific reporter combined with immuno-magnetic separation In addition to maintaining the affinity between the aptamer and its target, this method can reduce the number of rounds of aptamer selection from 15 in traditional SELEX to four in CE-SELEX [67]
    keywords: amplification; aptamer; aptasensor; atp; binding; cancer; cells; complex; conjugate; delivery; detection; dna; dox; drug; fig; fluorescence; graphene; oxide; probe; ref; rna; selection; selex; signal; sirna; specific; structure; surface; target
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        item: #1218 of 1349
          id: cord-344410-yo9libo0
      author: Zhou, Yan
       title: Mutational analysis of the SDD sequence motif of a PRRSV RNA-dependent RNA polymerase
        date: 2011-09-16
       words: 5866
      flesch: 52
     summary: Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure Mutations in the GDD motif of rubella virus putative RNA-dependent RNA polymerase affect virus replication. RNA-dependent RNA polymerases (RdRps) function as the catalytic subunit of the viral replicase.
    keywords: cells; conserved; gdd; motif; pcr; prrsv; rdrp; replication; rna; sdd; viruses
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        item: #1219 of 1349
          id: cord-344421-rmnck42f
      author: Theuns, Sebastiaan
       title: Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus
        date: 2018-06-29
       words: 8656
      flesch: 46
     summary: Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus date: 2018-06-29 journal: Sci Rep DOI: 10.1038/s41598-018-28180-9 sha: doc_id: 344421 cord_uid: rmnck42f Enteric diseases in swine are often caused by different pathogens and thus metagenomics are a useful tool for diagnostics. metagenomics is a valuable asset for diagnostics in pigs, leading to discovery of novel viruses and identification of porcine viral enteric disease complexes.
    keywords: analysis; diarrheic; enteric; genome; high; kobuvirus; piglets; pigs; porcine; reads; rotavirus; rva; sample; sequencing; shedding; study; viruses
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        item: #1220 of 1349
          id: cord-344464-if6js43s
      author: Cowley, J. A.
       title: The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report
        date: 2002
       words: 3525
      flesch: 45
     summary: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility Evidence for a separate signal sequence for the carboxy-terminal envelope glycoprotein E1 of Semliki Forest virus TMbase -A database of membrane spanning protein segments Complete sequence of the glycoproteins and M RNA of Punta Toro phlebovirus compared to those of Rift Valley fever virus A simple method for displaying the hydropathic character of a protein Coronavirus: organization, replication and expression of genome The molecular biology of coronaviruses Handbook for cultivation of black tiger prawns Predicting coiled coils from protein sequences Yellow-head virus: A rhabdovirus-like pathogen of penaeid shrimp Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Nucleotide sequence of the 26S mRNA of Sindbis virus and deduced sequence of the encoded virus structural protein Complete nucleotide sequence of the M RNA segment of Uukuniemi virus encoding the membrane glycoproteins G1 and G2 Molecular cloning: a laboratory manual A new model for coronavirus transcription A phosphatocopid crustacean with appendages from the Lower Cambrian Identification and primary structure of the gene encoding the Berne virus nucleocapsid protein Primary structure and post-translational processing of the Berne virus peplomer protein A 3 -coterminal nested set of independently transcribed mRNAs is generated during Berne virus replication The molecular biology of arteriviruses A hidden Markov model for predicting transmembrane helices in protein sequences Proc Sixth International Conference on Intelligent Systems for Molecular Biology Lymphoid organ virus of Penaeus monodon from Australia Gill-associated virus (GAV), a yellow head-like virus from Penaeus monodon cultured in Australia A yellow head virus probe: application to in situ hybridization and determination of its nucleotide sequence Arterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences Yellow head complex viruses: transmission cycles an topographical distribution in the Asia-Pacific region Yellow head virus infection in the giant tiger prawn Penaeus monodon cultured in Taiwan Yellow-head virus of Penaeus monodon is an RNA virus Author's address: Jeff Cowley, CSIRO Livestock Industries, 120 Meiers Road We kindly thank Dr. Sigrid Lehnert for providing the prawn cDNA phage library and Dr. Ross Tellam for helpful discussions on glycoprotein processing. The S glycoprotein gene of coronaviruses encodes polypeptides that range in size from 1160 aa for Infectious bronchitis virus [3] to 1452 aa for Feline infectious peritoneal virus [11] , while the cognate genes of the toroviruses Berne virus and Breda virus [14, 35] encode polypeptides (1581-1583 aa) approaching the size of GAV ORF3.
    keywords: cdna; gav; gene; genome; monodon; orf3; protein; sequence; virus
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        item: #1221 of 1349
          id: cord-344636-go5cw92q
      author: Huang, Wei E.
       title: RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2
        date: 2020-04-25
       words: 4780
      flesch: 56
     summary: However, this extreme sensitivity is also a double-edged sword: carry-over contamination was common in LAMP reactions, which usually cause false positive results (Hsieh et al., 2014; Ma et al., 2017) . Primers were designed using LAMP primer designing software, PrimerExplorer (http:// primerexplorer.jp/e/; Tomita et al., 2008) .
    keywords: amplification; cov-2; gene; lamp; primers; reaction; rna; sars
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        item: #1222 of 1349
          id: cord-344714-0cam9ipf
      author: Russo, Maria
       title: Roles of flavonoids against coronavirus infection
        date: 2020-07-28
       words: 8426
      flesch: 41
     summary: The effect of quercetin on different viruses Activity of some flavonoids against viruses Antiviral effect of flavonoids on human viruses Vanden Berghe, Can ethnopharmacology contribute to the development of antiviral drugs? Effects of propolis flavonoids on virus infectivity and replication An in vitro study of theaflavins extracted from black tea to neutralize bovine rotavirus and bovine coronavirus infections Antiviral activity of quercetin 7-rhamnoside against porcine epidemic diarrhea virus In vitro susceptibility of 10 clinical isolates of SARS coronavirus to selected antiviral compounds Small molecules blocking the entry of severe acute respiratory syndrome coronavirus into host cells Procyanidins and butanol extract of Cinnamomi Cortex inhibit SARS-CoV infection SARS--beginning to understand a new virus Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity Isotope dilution tandem mass spectrometric method for T4/T3 Binding interaction of quercetin-3-beta-galactoside and its synthetic derivatives with SARS-CoV 3CL(pro): structure-activity relationship studies reveal salient pharmacophore features Biflavonoids from Torreya nucifera displaying SARS-CoV 3CL(pro) inhibition Flavonoid-mediated inhibition of SARS coronavirus 3C-like protease expressed in Pichia pastoris Phenolic phytochemical displaying SARS-CoV papain-like protease inhibition from the seeds of Psoralea corylifolia Geranylated flavonoids displaying SARS-CoV papain-like protease inhibition from the fruits of Paulownia tomentosa Evaluation of polyphenols from Broussonetia papyrifera as coronavirus protease inhibitors Characteristics of flavonoids as potent MERS-CoV 3C-like protease inhibitors Inhibition of SARS-CoV 3CL protease by flavonoids Chalcones isolated from Angelica keiskei inhibit cysteine proteases of SARS-CoV Dissection and identification of regions required to form pseudoparticles by the interaction between the nucleocapsid (N) and membrane (M) proteins of SARS coronavirus A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide Development of chemical inhibitors of the SARS coronavirus: viral helicase as a potential target NTPase/helicase by dihydroxychromone derivatives Synthesis and antiviral evaluation of 7-Oarylmethylquercetin derivatives against SARS-associated coronavirus (SCV) and hepatitis C virus (HCV) Identification of myricetin and scutellarein as novel chemical inhibitors of the SARS coronavirus helicase, nsP13 Traditional Chinese medicine for COVID-19 treatment Chemical composition and pharmacological mechanism of Qingfei Paidu Decoction and Ma Xing Shi Gan Decoction against Coronavirus Disease 2019 (COVID-19): In terms of public health, the 21st century has been characterized by coronavirus pandemics: in 2002-03 the virus SARS-CoV caused SARS; in 2012 MERS-CoV emerged and in 2019 a new human betacoronavirus strain, called SARS-CoV-2, caused the unprecedented COVID-19 outbreak.
    keywords: 3cl; activity; binding; coronavirus; cov; cov-2; covid-19; domain; flavonoids; host; infection; pro; protease; protein; quercetin; replication; residues; rna; sars; site
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        item: #1223 of 1349
          id: cord-344749-omzhhr0k
      author: Kaya, Sariye Irem
       title: Electrochemical virus detections with nanobiosensors
        date: 2020-02-14
       words: 8406
      flesch: 32
     summary: key: cord-344749-omzhhr0k authors: Kaya, Sariye Irem; Karadurmus, Leyla; Ozcelikay, Goksu; Bakirhan, Nurgul K.; Ozkan, Sibel A. title: Electrochemical virus detections with nanobiosensors date: 2020-02-14 journal: Nanosensors for Smart Cities DOI: 10.1016/b978-0-12-819870-4.00017-7 sha: doc_id: 344749 cord_uid: omzhhr0k Infectious diseases are caused from pathogens, which need a reliable and fast diagnosis. Recent progress in electrochemical studies shows that biosensors are very simple, accurate, precise, and cheap at virus detection, for which researchers find great interest in this field.
    keywords: antigen; biosensor; carbon; cells; detection; disease; dna; electrochemical; electrode; gold; hepatitis; humans; immunosensor; influenza; methods; nanoparticles; pcr; rna; surface; virus; viruses
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        item: #1224 of 1349
          id: cord-344782-ond1ziu5
      author: Zhang, Jing
       title: Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi)
        date: 2018-10-24
       words: 6005
      flesch: 45
     summary: Similarity to other viruses for each of the ORFs and their predicted amino acid sequences were determined by searches using BLASTn and BLASTp [13] algorithms through the NCBI server (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Ball Python Nidovirus: a Candidate Etiologic Agent for Severe Respiratory Disease in Python regius Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius) Novel divergent nidovirus in a python with pneumonia Nidovirus-Associated Proliferative Pneumonia in the Green Tree Python (Morelia viridis) Discovery and partial genomic characterisation of a novel nidovirus associated with respiratory disease in wild shingleback lizards (Tiliqua rugosa) Redefining the invertebrate RNA virosphere The evolutionary history of vertebrate RNA viruses Programmed translational frameshifting Ribosomal frameshifting on viral RNAs The primary structure and expression of the second open reading frame of the polymerase gene of the coronavirus MHV-A59 a highly conserved polymerase is expressed by an efficient ribosomal frameshifting mechanism An RNA Pseudoknot in the 3' end of the Arterivirus genome has a critical role in regulating viral RNA synthesis Changes to taxonomy and the international code of virus classification and Nomenclature ratified by the international committee on taxonomy of viruses Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates Molecular comparison of isolates of an emerging fish pathogen, Koi herpesvirus, and the effect of water temperature on mortality of experimentally infected Koi Is horizontal transmission of the ostreid herpesvirus OsHV-1 in Crassostrea gigas affected by unselected or selected survival status in adults to juveniles?
    keywords: acid; animals; disease; georgesi; min; nidovirus; pcr; python; river; rna; samples; sequence; species; tissues; turtle; virus
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        item: #1225 of 1349
          id: cord-345157-fhmhpobi
      author: Qi, Dan
       title: Virus infection-induced host mRNA degradation and potential application of live cell imaging
        date: 2018-12-12
       words: 2629
      flesch: 42
     summary: Elife A common strategy for host RNA degradation by divergent viruses Bacteriophage T4-induced shut-off of hostspecific translation Phage-induced change in the stability of mRNAs A tale of two RNAs during viral infection: how viruses antagonize mRNAs and small non-coding RNAs in the host cell Emerging roles for RNA degradation in viral replication and antiviral defense Interplay between viruses and host mRNA degradation Messenger RNA degradation in bacterial cells RNase E: at the interface of bacterial RNA processing and decay The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal Herpes simplex virus virion host shutoff function Herpes simplex virus mutants defective in the virion-associated shutoff of host polypeptide synthesis and exhibiting abnormal synthesis of alpha (immediate early) viral polypeptides The role of the UL41 gene of herpes simplex virus type 1 in evasion of non-specific host defence mechanisms during primary infection The herpes simplex virus host shutoff RNase degrades cellular and viral mRNAs Nsp1, a protein with no known similarity to cellular or viral nucleases from severe acute respiratory syndrome (SARS) coronavirus (SCoV) belonging to betacoronavirus family, is reported to induce host mRNA degradation by binding to 40S ribosome
    keywords: degradation; host; infection; mrna; protein; shutoff; virus; viruses
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        item: #1226 of 1349
          id: cord-345204-ch0e6lzl
      author: Scarlata, S.
       title: Design Of A Rapid And Reversible Fluorescence Assay To Detect COVID-19 And Other Pathogens
        date: 2020-10-05
       words: 2920
      flesch: 54
     summary: To optimize beacon use, it is useful to estimate the density of beacon that must be attached to a test strip. Previously, our lab has used molecular beacons to isolate stem cells induced to express exogenous genes [3] .
    keywords: beacon; covid-19; fluorescence; mrna; rna; saliva; stem
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        item: #1227 of 1349
          id: cord-345302-wbkfjz8r
      author: Devaney, Ryan
       title: A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds
        date: 2016-10-04
       words: 7875
      flesch: 29
     summary: The present study detected two viral contigs exhibiting similarity (96-99% nucleotide identity) to the Gyrovirus genus in only one RSS-affected sample, VF14-92 A1, which specifically showed similarity to chicken anaemia virus (CAV, genus: Gyrovirus) while the unaffected samples displayed no Circoviridae contigs. Infections Caliciviruses: an overview A very small porcine virus with circular singlestranded DNA Development and application of an RT-PCR test for detecting avian nephritis virus Capsid protein sequence diversity of avian nephritis virus Genome sequence determinations and analyses of novel circoviruses from goose and pigeon Genetic characterization of chicken anaemia virus from commercial broiler chickens in Alabama Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies Coronavirus pathogenesis Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus The complete sequence of a human astrovirus Genetic characterization of a novel calicivirus from a chicken Molecular detection of norovirus in sheep and pigs in New Zealand farms Characterization of a picornavirus isolated from broiler chicks Isolation and some characteristics of an agent inducing anaemia in chicks Velvet: algorithms for de novo short read assembly using de Bruijn graphs Identification and genome characterization of the first sicinivirus isolate from chickens in mainland China by using viral metagenomics Chicken parvovirusinduced runting-stunting syndrome in young broilers The authors would like to acknowledge the Department of Agriculture, Environment, and Rural Affairs (DAERA) for funding this study.
    keywords: avian; birds; broiler; chicken; contigs; enteric; et al; family; rna; rss; samples; sequencing; study; vf14; viruses
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        item: #1228 of 1349
          id: cord-345371-pjbviagq
      author: Lisi, Lucia
       title: Approaching Coronavirus Disease 2019: mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2
        date: 2020-07-23
       words: 10674
      flesch: 18
     summary: Among them, the international Solidarity trial launched by the WHO on March 2020 with the aim to find an effective treatment for COVID-19 patients by comparing four different treatments (i.e., lopinavir/ritonavir, lopinavir/ritonavir plus interferon-β, chloroquine/hydroxychloroquine or remdesivir) against standard of care (see also sections 2 and 3). Besides exerting potential direct antiviral effects, baricitinib might prevent the dysregulated production of pro-inflammatory cytokines typically observed in COVID-19 patients via the inactivation of interleukin-6 (IL6)-JAK-signal transducer and activator of transcription (STAT) pathway (this activity will be more deeply discussed in section 3, especially regarding the JAK inhibitor ruxolitinib).
    keywords: acute; cells; coronavirus; cov-2; covid-19; covid-19 patients; disease; hydroxychloroquine; infection; interferon; patients; pneumonia; protein; remdesivir; ritonavir; rna; sars; study; syndrome; tocilizumab; treatment; use
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        item: #1229 of 1349
          id: cord-345413-bsd32j8r
      author: Terada, Yutaka
       title: Establishment of a Virulent Full-Length cDNA Clone for Type I Feline Coronavirus Strain C3663
        date: 2019-08-02
       words: 8053
      flesch: 48
     summary: While sg mRNA6 expression levels in A72 cells were lower than in Fcwf-4 cells, the expression ratio of sg mRNA6 to sg mRNA7 in infected A72 cells was different from that in infected Fcwf-4 cells (Fig. 5A ). Although the expression levels of sg mRNA6 and sg mRNA7 in A72 cells infected with rC3663 were low (Fig. 5A) , the ratio of sg mRNA6 expression to sg mRNA7 expression in infected A72 cells was different from that in infected Fcwf-4 cells.
    keywords: a72; cells; coronavirus; expression; fcov; fcwf-4; feline; fig; infected; levels; nluc; rc3663; rna; type; virus
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        item: #1230 of 1349
          id: cord-345630-bam3pa70
      author: Lee, Han-Jung
       title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase
        date: 1991-02-28
       words: 5981
      flesch: 59
     summary: This possibility is consistent with the finding that MHV RNA synthesis occurs on the membrane fractions in the infected cells (Brayton et al., 1982) . It has been shown that there are at least five to six complementation groups involving MHV RNA synthesis, five of which have been mapped within gene 1 (Leibowitz eta/., 1982; Baric eta/., 1990) .
    keywords: amino; coronavirus; gene; ibv; jhm; mhv; orf; rna; sequence
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        item: #1231 of 1349
          id: cord-345647-h3imwhss
      author: Gao, Wen-Hua
       title: Newly identified viral genomes in pangolins with fatal disease
        date: 2020-04-12
       words: 5066
      flesch: 45
     summary: We named these Dongyang pangolin virus (DYPV) and Lishui pangolin virus (LSPV) based on the sampling site and hosts. Considering that they are related, yet clearly genetically distinct, from known members of Pestivirus and Coltivirus (see below), we designated these two newly identified viruses as Dongyang pangolin virus (DYPV) and Lishui pangolin virus (LSPV), respectively, reflecting their hosts species and the geographic location of sampling.
    keywords: disease; dongyang; et al; novel; pangolins; rna; sequences; ticks; virus; viruses
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        item: #1232 of 1349
          id: cord-345654-vyz6f3he
      author: Dennehy, John J.
       title: Evolutionary ecology of virus emergence
        date: 2016-12-30
       words: 11489
      flesch: 36
     summary: Though it is recognized that host populations must overlap in order for virus emergence to take place, virus host alternation has seldom been explored outside of a few laboratory and theoretical studies. Perhaps the most famous case of reassortment leading to the expansion of virus host range comes from the 2009 IAV H1N1 pandemic.
    keywords: ability; binding; changes; disease; emergence; evolution; example; fitness; genome; host; human; influenza; mutations; novel; populations; range; rates; receptor; recombination; rna; spread; transmission; virus; viruses
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        item: #1233 of 1349
          id: cord-345817-rrf3dbnb
      author: WOOD, Lisa G.
       title: Persistence of rhinovirus RNA and IP‐10 gene expression after acute asthma
        date: 2011-01-27
       words: 3747
      flesch: 41
     summary: After RSV infection, viral persistence can occur despite the presence of virus-specific IgG. 26 Effective T-cell responses are critical to eradicate acute viral infections and prevent viral persistence. 9 Persistence of RNA viral infection has been previously reported.
    keywords: asthma; hrv; infection; persistence; recovery; rna; subjects; virus; visit
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        item: #1234 of 1349
          id: cord-345863-j01l71dh
      author: Drechsler, Yvonne
       title: Host Gene Expression of Macrophages in Response to Feline Coronavirus Infection
        date: 2020-06-09
       words: 5533
      flesch: 36
     summary: A study of naturally occurring feline coronavirus infections in kittens Serologic studies of naturally occurring feline infectious peritonitis Risk factors for feline coronavirus seropositivity in cats relinquished to a UK rescue charity Feline coronavirus in multicat environments An enteric coronavirus infection of cats and its relationship to feline infectious peritonitis Risk factors for feline infectious peritonitis among cats in multiple-cat environments with endemic feline enteric coronavirus Feline Infectious Peritonitis Replication of feline coronaviruses in peripheral blood monocytes Sites of feline coronavirus persistence in healthy cats Pathogenic characteristics of persistent feline enteric coronavirus infection in cats Feline infectious peritonitis: Role of the feline coronavirus 3c gene in intestinal tropism and pathogenicity based upon isolates from resident and adopted shelter cats Prevalence of feline infectious peritonitis in specific cat breeds Clinicopathological findings associated with feline infectious peritonitis in Clinicopathological findings and disease staging of feline infectious peritonitis: 51 cases from 2003 to 2009 in Taiwan Preliminary studies on feline coronavirus distribution in naturally and experimentally infected cats An overview of feline enteric coronavirus and infectious peritonitis virus infections Antibody-dependent enhancement of serotype II feline enteric coronavirus infection in primary feline monocytes Antibody-dependent enhancement of feline infectious peritonitis virus infection in feline alveolar macrophages and human monocyte cell line U937 by serum of cats experimentally or naturally infected with feline coronavirus A possible involvement of TNF-alpha in apoptosis induction in peripheral blood lymphocytes of cats with feline infectious peritonitis Natural feline coronavirus infection: Differences in cytokine patterns in association with the outcome of infection In vivo cytokine response to experimental feline infectious peritonitis virus infection Disease outcome and cytokine responses in cats immunized with an avirulent feline infectious peritonitis virus (FIPV)-UCD1 and challenge-exposed with virulent FIPV-UCD8 Natural history of a recurrent feline coronavirus infection and the role of cellular immunity in survival and disease Apoptosis and T-cell depletion during feline infectious peritonitis Transcriptome analysis of feline infectious peritonitis virus infection Transcriptional profiling of feline infectious peritonitis virus infection in CRFK cells and in PBMCs from FIP diagnosed cats Characterization of peritoneal cells from cats with experimentally-induced feline infectious peritonitis (FIP) using RNA-seq A rapid and simple method to obtain canine peripheral blood-derived macrophages Trimmomatic: A flexible trimmer for Illumina sequence data Near-optimal probabilistic RNA-seq quantification Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package limma powers differential expression analyses for RNA-sequencing and microarray studies ClueGO: Therefore, macrophage gene expression from cats #1, 2, and 5 was compared.
    keywords: cats; cells; feline; genes; host; immune; infection; macrophages; responses; rna; virus
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        item: #1235 of 1349
          id: cord-345898-a6vt8kso
      author: Ren, Linzhu
       title: Live Cell Reporter Systems for Positive-Sense Single Strand RNA Viruses
        date: 2016-01-04
       words: 6005
      flesch: 32
     summary: Moreover, the replicon-defective reporter gene assay could detect a variety of Alphaviruses from tissue cultures with a limit of detection between one and ten (plaque-forming unit) PFU for SINV while other RNA viruses, such as the Japanese encephalitis virus and Tahyna virus, displayed negative results with this system [44] . Cell-based reporter systems have enhanced our understanding of the molecular mechanisms of virus replication and pathogenesis as well as virus interactions with host cells. N pro of CSFV was not only involved with virus RNA translation in the cytoplasm [27] but also counteracted double-stranded RNAmediated apoptosis and IFN-α/β induction
    keywords: cells; csfv; dengue; gene; infection; protease; protein; replication; replicon; reporter; rna; systems; virus
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        item: #1236 of 1349
          id: cord-345957-wuk2arf9
      author: Mohamed, Fakry F.
       title: Detection and genetic characterization of bovine kobuvirus from calves in Egypt
        date: 2018-02-08
       words: 4254
      flesch: 58
     summary: BKoV VP1 sequences from Egypt belonged to lineage 1 (Genotype A), which includes BKoVs from Brazil, Japan (only U-1 strain), and Scotland. Based on phylogenetic analysis of 35 GenBank reference strains, BKoV sequences from Cairo (n = 5) clustered with Chinese strains Table 2
    keywords: bkov; genome; kobuvirus; ky407744; sequences; strains; study; vp1
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        item: #1237 of 1349
          id: cord-346138-ip42zcld
      author: Zhurakivska, Khrystyna
       title: An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens
        date: 2020-08-20
       words: 3956
      flesch: 48
     summary: All patients, except one in Kim's report (12) and four reported by Liu et al. (27) had negative viral detection in urine. Results on viral RNA detection in saliva are reported in two papers (17, 18) . Aimed at identifying viral RNA in the various compartments of the organism of sick subjects, diagnostic tests are carried out.
    keywords: disease; load; patients; rna; sars; studies; virus
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        item: #1238 of 1349
          id: cord-346267-l08ld2cy
      author: Wertheim, Joel O.
       title: Purifying Selection Can Obscure the Ancient Age of Viral Lineages
        date: 2011-06-24
       words: 6416
      flesch: 38
     summary: For each data set and substitution model, four independent BMCMC runs of 25 or 50 million generations were performed. In this study, we demonstrate the need to include relevant biological and evolutionary forces in substitution models.
    keywords: branches; gtr; model; purifying; rate; selection; site; substitution; viruses
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        item: #1239 of 1349
          id: cord-346314-o9fjpqaj
      author: Jarboui, Mohamed Ali
       title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus
        date: 2012-11-15
       words: 10059
      flesch: 29
     summary: The proteasome regulates HIV-1 transcription by both proteolytic and nonproteolytic mechanisms Oncogenic activity of MCM7 transforming cluster Unzipped and loaded: the role of DNA helicases and RFC clamp-loading complexes in sister chromatid cohesion The XRCC genes: expanding roles in DNA double-strand break repair Role of the non-homologous DNA end joining pathway in the early steps of retroviral infection Lupus autoantigen Ku protein binds HIV-1 TAR RNA in vitro Effect of Ku80 depletion on the preintegrative steps of HIV-1 replication in human cells Identification of cellular cofactors for human immunodeficiency virus replication via a ribozyme-based genomics approach siRNA screening of a targeted library of DNA repair factors in HIV infection reveals a role for base excision repair in HIV integration The dynamics of HMG proteinchromatin interactions in living cells Retroviral cDNA integration: stimulation by HMG I family proteins HIV-1 cDNA integration: requirement of HMG I(Y) protein for function of preintegration complexes in vitro Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors Fuel feeds function: energy metabolism and the T-cell response Human immunodeficiency virus type 1, human protein interaction database at NCBI Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems The biological context of HIV-1 host interactions reveals subtle insights into a system hijack HIVhost interactions: a map of viral perturbation of the host system Cataloguing the HIV type 1 human protein interaction network Retroviral proteomics and interactomes: intricate balances of cell survival and viral replication Dual role of host cell factors in HIV-1 replication: restriction and enhancement of the viral cycle Decoding the multifaceted HIV-1 virus-host interactome Functions of Tat: the versatile protein of human immunodeficiency virus type 1 Chromatin dynamics associated with HIV-1 Tat-activated transcription Modifications in host cell cytoskeleton structure and function mediated by intracellular HIV-1 Tat protein are greatly dependent on the second coding exon Pathway analysis in HEK 293T cells overexpressing HIV-1 tat and nucleocapsid Expression profiles and pathway analysis in HEK 293 T cells overexpressing HIV-1 Tat and nucleocapsid using cDNA microarray Proliferative activity of extracellular HIV-1 Tat protein in human epithelial cells: expression profile of pathogenetically relevant genes Proteomics analysis of human astrocytes expressing the HIV protein Tat HIV-1 Tat reprograms immature dendritic cells to express chemoattractants for activated T cells and macrophages Gene expression profile of HIV-1 Tat expressing cells: a close interplay between proliferative and differentiation signals Modifications in the human T cell proteome induced by intracellular HIV-1 Tat protein expression Cell-type-specific proteome and interactome: using HIV-1 Tat as a test case Differentially expressed genes in HIV-1 tat-expressing CD4(+) T-cell line HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP The histone chaperone protein Nucleosome Assembly Protein-1 (hNAP-1) binds HIV-1 Tat and promotes viral transcription Genome-wide binding map of the HIV-1 Tat protein to the human genome Jurkat T cells and development of the T-cell receptor signalling paradigm Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling A genome-wide short hairpin RNA screening of jurkat T-cells for human proteins contributing to productive HIV-1 replication Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity DEDD and DEDD2 associate with caspase-8/10 and signal cell death Chaperones and multitasking proteins in the nucleolus: networking together for survival? Protein B23 is an important human factor for the nucleolar localization of the human immunodeficiency virus protein Tat Spatial association of HIV-1 tat protein and the nucleolar transport protein B23 in stably transfected Jurkat T-cells Specific complex of human immunodeficiency virus type 1 rev and nucleolar B23 proteins: dissociation by the Rev response element Effects of a highly basic region of human immunodeficiency virus Tat protein on nucleolar localization A region of basic amino-acid cluster in HIV-1 Tat protein is essential for trans-acting activity and nucleolar localization Intracellular trafficking and interactions of the HIV-1 Tat protein Phosphatidylinositol-(4,5)-bisphosphate enables efficient secretion of HIV-1 Tat by infected T-cells The ins and outs of HIV-1 Tat Tuning the transport properties of HIV-1 Tat arginine-rich motif in living cells In vivo study of HIV-1 Tat arginine-rich motif unveils its transport properties Direct interaction of the human I-mfa domain-containing protein Tat results in cytoplasmic sequestration and control of Tat activity The arginine-rich domains present in human immunodeficiency virus type 1 Tat and Rev function as direct importin betadependent nuclear localization signals The HIV-1 Tat nuclear localization sequence confers novel nuclear import properties Global enhancement of nuclear localization-dependent nuclear transport in transformed cells Intermolecular masking of the HIV-1 Rev NLS by the cellular protein HIC: novel insights into the regulation of Rev nuclear import Nuclear Factor 90, a cellular dsRNA binding protein inhibits the HIV Rev-export function Functional analysis of the interaction of the human immunodeficiency virus type 1 Rev nuclear export signal with its cofactors The ins and outs of HIV Rev The HIV-1 Rev protein The specificity of the CRM1-Rev nuclear export signal interaction is mediated by RanGTP Requirement of DDX3 DEAD box RNA helicase for HIV-1 Rev-RRE export function Mechanisms of receptor-mediated nuclear import and nuclear export The nuclear pore component Nup358 promotes transportin-dependent nuclear import A nucleolar TAR decoy inhibitor of HIV-1 replication Ribozyme-mediated inhibition of HIV 1 suggests nucleolar trafficking of HIV-1 RNA Constitutive expression of HIV-1 tat protein in human Jurkat T cells using a BK virus vector Gautier VW Proteomic profiling of the human T-cell nucleolus
    keywords: abundance; analysis; anti; cells; enrichment; expression; figure; fold; gene; human; jurkat; nuclear; nucleolar; nucleolus; pathway; proteins; replication; ribosomal; rna; tap; tat; tat expression; tat protein; virus
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        item: #1240 of 1349
          id: cord-346514-vyo8l14p
      author: Chen, I-Hsuan
       title: Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants
        date: 2013-06-13
       words: 5153
      flesch: 48
     summary: Models of the mechanism for BaMV RNA polyadenylation are proposed and discussed in this paper. We conducted a polyadenylation activity assay for BaMV RNA by using a partially purified BaMV replicase complex.
    keywords: bamv; complex; et al; polyadenylation; replicase; replication; rna; sequence; strand
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        item: #1241 of 1349
          id: cord-346544-kk7qyn4w
      author: Andersson, M.
       title: SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus
        date: 2020-05-26
       words: 5001
      flesch: 47
     summary: Protocols to underpin the safe handling of blood samples need to consider the best evidence for routes and risks of transmission in order to mandate safe laboratory practice, being informed by the nature of the samples and the specific task being undertaken (including any risk of aerosol generation), while also maintaining optimum cost effective workflow of clinical samples. 21.20105486 doi: medRxiv preprint Here we assimilate the peer-reviewed literature describing the presence of SARS CoV-2 RNA in human blood, with the aim of providing a pooled dataset to provide improved insights into the causes and correlates of RNA-aemia.
    keywords: blood; clinical; cov-2; covid-19; license; medrxiv; pcr; preprint; rna; samples; sars
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        item: #1242 of 1349
          id: cord-346697-ixho9t5g
      author: Guo, Hua
       title: Novel hepacivirus in Asian house shrew, China
        date: 2019-01-28
       words: 1655
      flesch: 49
     summary: Due to the pathogenesis of SmHCV in liver tissue, Asian shrews could be a potential animal model for hepacivirus study as well as transgenic mice. key: cord-346697-ixho9t5g authors: Guo, Hua; Cai, Chunlin; Wang, Bo; Zhuo, Fei; Jiang, Rendi; Wang, Ning; Li, Bei; Zhang, Wei; Zhu, Yan; Fan, Yi; Chen, Wushen; Chen, Weihong; Yang, Xinglou; Shi, Zhengli title: Novel hepacivirus in Asian house shrew, China date: 2019-01-28 journal: Sci China Life Sci DOI: 10.1007/s11427-018-9435-7 sha: doc_id: 346697 cord_uid: ixho9t5g nan Hepatitis C virus (HCV) is a leading global cause of various liver diseases, including chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma.
    keywords: asian; hepacivirus; liver; rna; shrews
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        item: #1243 of 1349
          id: cord-346853-0c1qdjb5
      author: Holmes, E. C.
       title: The Evolutionary Genetics of Viral Emergence
        date: 2007
       words: 6127
      flesch: 35
     summary: Although the engine of RNA virus evolution is undoubtedly their high mutation rate, there is mounting evidence that the genetic variability observed in RNA virus populations can be shaped, in part, by recombination. The broadest division in virus classification is between those viruses in which the genome is composed of DNA (DNA viruses) and those where the genomic nucleic acid comprises RNA (RNA viruses), with the latter also usually considered to include retroviruses that make a DNA copy of the RNA genome through reverse transcription.
    keywords: emergence; et al; evolution; host; human; rna; species; transmission; viruses
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        item: #1244 of 1349
          id: cord-346916-jj4l9ydl
      author: Girardi, Erika
       title: Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell
        date: 2020-08-23
       words: 13150
      flesch: 37
     summary: genomic RNA Protein kinase r degradation is essential for rift valley fever virus infection and is regulated by SKP1-CUL1-F-box (SCF)FBXW11-NSs E3 ligase Viral encounters with 2',5'-oligoadenylate synthetase and RNase L during the interferon antiviral response New insights into the role of RNase L in innate immunity Molecular mechanisms for the adaptive switching between the OAS/RNase l and OASL/RIG-I pathways in birds and mammals Homologous 2',5'-phosphodiesterases from disparate RNA viruses antagonize antiviral innate immunity Attacked from all sides: RNA decay in antiviral defense The host nonsense-mediated mRNA decay pathway restricts Mammalian RNA virus replication Competing and noncompeting activities of miR-122 and the 5' exonuclease Xrn1 in regulation of hepatitis C virus replication Stabilization of hepatitis C virus RNA by an Ago2-miR-122 complex Zika virus produces noncoding RNAs using a multipseudoknot structure that confounds a cellular exonuclease The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA Full genome sequence and sfRNA interferon antagonist activity of zika virus from Recife, Brazil RNA structures required for production of subgenomic flavivirus RNA Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity An RNA pseudoknot is required for production of yellow fever virus subgenomic RNA by the host nuclease XRN1 Zika virus noncoding RNA suppresses apoptosis and is required for virus transmission by mosquitoes Noncoding flavivirus RNA displays RNA interference suppressor activity in insect and mammalian cells Viruses: overturning RNA turnover Stem-loop recognition by DDX17 facilitates miRNA processing and antiviral defense The zinc-finger antiviral protein recruits the RNA processing exosome to degrade the target mRNA CG dinucleotide suppression enables antiviral defence targeting non-self RNA KHNYN is essential for the zinc finger antiviral protein (ZAP) to restrict HIV-1 containing clustered CpG dinucleotides ZAP's stress granule localization is correlated with its antiviral activity and induced by virus replication RNA-binding activity of TRIM25 is mediated by its PRY/ SPRY domain and is required for ubiquitination TRIM25 enhances the antiviral action of zinc-finger antiviral protein (ZAP) MCPIP1 ribonuclease exhibits broad-spectrum antiviral effects through viral RNA binding and degradation MCPIP1 suppresses hepatitis C virus replication and negatively regulates virus-induced proinflammatory cytokine responses RNase L releases a small RNA from HCV RNA that refolds into a potent PAMP Activation and evasion of the antiviral 2'-5' oligoadenylate synthetase/ribonuclease L pathway by hepatitis C virus mRNA Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila Cross-species comparative analysis of Dicer proteins during Sindbis virus infection RNA interference functions as an antiviral immunity mechanism in mammals Antiviral RNA interference in mammalian cells Flavivirus induces and antagonizes antiviral RNA interference in both mammals and mosquitoes The evolution of antiviral defense systems Human virus-derived small RNAs can confer antiviral immunity in mammals Induction and suppression of antiviral RNA interference by influenza A virus in mammalian cells Viruses and RNA interference: issues and controversies No evidence for viral small RNA production and antiviral function of Argonaute 2 in human cells RNase III nucleases from diverse kingdoms serve as antiviral effectors Making the mark: the role of adenosine modifications in the life cycle of RNA viruses Innate immune restriction and antagonism of viral RNA lacking 2‫-׳‬O methylation RNA modifications: what have we learned and where are we headed? Host factors in positive-strand RNA virus genome replication Human host factors required for influenza virus replication Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens Diverse roles of host RNA binding proteins in RNA virus replication CRISPR-Cas immunity in prokaryotes Antiviral immunity directed by small RNAs Combating emerging viral threats The global distribution and burden of dengue Virus: new clinical syndromes and its emergence in the western hemisphere Emergence of a novel human coronavirus threatening human health Sensing of RNA viruses: a review of innate immune receptors involved in recognizing RNA virus invasion The innate antiviral response in animals: an evolutionary perspective from flagellates to humans Discriminating self from non-self in nucleic acid sensing Toll-like receptor control of the adaptive immune responses Toll-like receptors in antiviral innate immunity Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8 Toll-like receptor 3 is an essential component of the innate stress response in virus-induced cardiac injury Human TLR3 recognizes dengue virus and modulates viral replication in vitro Zika virus depletes neural progenitors in human cerebral organoids through activation of the innate immune receptor TLR3 Toll-like receptor 3 in viral pathogenesis: friend or foe? RIG-I-like receptors: their regulation and roles in RNA sensing 5'-Triphosphate RNA is the ligand for RIG-I RIG-I-mediated antiviral responses to single-stranded RNA bearing 5'-phosphates Recognition of 5' triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus 5'-triphosphate RNA requires base-paired structures to activate antiviral signaling via RIG-I Processing of genome 5' termini as a strategy of negative-strand RNA viruses to avoid RIG-I-dependent interferon induction Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses Cell type-specific involvement of RIG-I in antiviral response RIG-I recognizes the 5' region of dengue and Zika virus genomes Balancing act: MDA5 in Antiviral Immunity and Autoinflammation MDA5 assembles into a polar helical filament on dsRNA Enterovirus 2Apro targets MDA5 and MAVS in infected cells MDA5 detects the double-stranded RNA replicative form in picornavirus-infected cells How flaviviruses activate and suppress the interferon response MDA5 is critical to host defense during infection with murine coronavirus LGP2 is a positive regulator of RIG-I-and MDA5-mediated antiviral responses The RNA helicase Lgp2 inhibits TLR-independent sensing of viral replication by retinoic acid-inducible gene-I Loss of DExD/H box RNA helicase LGP2 manifests disparate antiviral responses The RIG-I-like receptor LGP2 inhibits Dicer-dependent processing of long double-stranded RNA and blocks RNA interference in mammalian cells DEAD-box helicases: sensors, regulators, and effectors for antiviral defense Type 1 interferons and the virus-host relationship: a lesson in détente Interferon-inducible antiviral effectors Involvement of the interferon-regulated antiviral proteins PKR and RNase L in reovirus-induced shutoff of cellular translation Doublestranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses RNA dimerization promotes PKR dimerization and activation Viral double-stranded RNAs from vaccinia virus early or intermediate gene transcripts possess PKR activating function, resulting in NF-kappaB activation, when the K1 protein is absent or mutated Regulation of innate immunity through RNA structure and the protein kinase PKR Translational control in virus-infected cells A cap-to-Tail guide to mRNA translation strategies in virus-infected cells Viral noncoding RNAs: more surprises Inhibition of the protein kinase PKR by the internal ribosome entry site of hepatitis C virus
    keywords: antiviral; binding; cap; cells; cellular; dsrna; factors; fig; host; infection; initiation; interactions; mrna; pkr; protein; rbps; replication; ribosome; rig; rna; rnas; translation; viral; virus; viruses; vrna
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        item: #1245 of 1349
          id: cord-346930-gl573ip9
      author: Hussain, Azhar
       title: Emerging Pharmaceutical Treatments of Novel COVID-19: A Review
        date: 2020-05-24
       words: 4181
      flesch: 43
     summary: Remdesivir is metabolized into its active form, GS-441524, that obscures viral RNA polymerase and evades proofreading by viral exonuclease, causing a decrease in viral RNA production [31] . With the increased risk of anemia at the doses necessary, ribavirin should not be implicated as the first drug of choice in COVID-19 patients.
    keywords: cov-2; covid-19; dose; lopinavir; patients; rna; sars; treatment; virus
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        item: #1246 of 1349
          id: cord-346978-ubkqny8j
      author: Ranoa, Diana Rose E.
       title: Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction
        date: 2020-06-18
       words: 6480
      flesch: 41
     summary: We next sought to evaluate saliva collection buffers as a means to enhance viral RNA stability, but also to increase uniformity between saliva samples and to decrease sample viscosity. 35 Using intact, γ-irradiated SARS-CoV-2 spiked into fresh human saliva, which was then heat treated at 95°C for 30 min, we observed outstanding virus detection when saliva samples were combined with either Tris-Borate-EDTA (TBE) or TE buffer ( Figure 3A) .
    keywords: control; cov-2; detection; ms2; qpcr; saliva; samples; sars
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        item: #1247 of 1349
          id: cord-347128-6lyoz8nn
      author: Kim, Cheorl-Ho
       title: SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction
        date: 2020-06-26
       words: 15614
      flesch: 50
     summary: CoV 3CLpro (PDB: 6WX4) and the PLpro cleave the polyproteins to assemble virus proteins. The CTD of S1 recognizes protein receptors via RBDs.
    keywords: ace2; acetyl; acid; attachment; binding; cells; clq; coronavirus; cov; cov-2; covs; entry; glycoprotein; host; human; infection; influenza; membrane; mers; protein; receptor; sars; sas; tmprss2; viral; virus; viruses
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        item: #1248 of 1349
          id: cord-347221-g98q9cga
      author: Piyush, Ravikant
       title: Nucleic acid-based therapy for coronavirus disease 2019
        date: 2020-09-19
       words: 4221
      flesch: 43
     summary: The potential risk of infection and insertion induced mutagenesis are minimized by mRNA based vaccines due to its natural degradation in cells [167] . Front Immunol Immune response in severe infection: could life-saving drugs be potentially harmful? New Vaccine Technologies to Combat Outbreak Situations A comparison of plasmid DNA and mrna as vaccine technologies RNA: the new revolution in nucleic acid vaccines.
    keywords: acid; cov-2; covid-19; development; dna; mrna; nucleic; protein; sars; vaccine; virus
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        item: #1249 of 1349
          id: cord-347302-ylnb6qfl
      author: van der Schaar, Hilde M.
       title: Fat(al) attraction: Picornaviruses Usurp Lipid Transfer at Membrane Contact Sites to Create Replication Organelles
        date: 2016-03-22
       words: 5359
      flesch: 31
     summary: A complex comprising phosphatidylinositol 4-kinase IIIbeta, ACBD3, and Aichi virus proteins enhances phosphatidylinositol 4-phosphate synthesis and is critical for formation of the viral replication complex Differential effects of the putative GBF1 inhibitors Golgicide A and AG1478 on enterovirus replication Involvement of membrane traffic in the replication of poliovirus genomes: Effects of brefeldin A Modulation of the host lipid landscape to promote RNA virus replication: The picornavirus encephalomyocarditis virus converges on the pathway used by hepatitis C virus Recruitment and activation of a lipid kinase by Hepatitis C Virus NS5A is essential for integrity of the membranous replication compartment Cholesterol biosynthesis modulation regulates dengue viral replication Cholesterol manipulation by West Nile Virus perturbs the cellular immune response West Nile Virus replication requires fatty acid synthesis but is independent on phosphatidylinositol-4-phosphate lipids Co-opted oxysterol-binding ORP and VAP proteins channel sterols to RNA virus replication sites via membrane contact sites Comparative RNAi screening reveals host factors involved in enterovirus infection of polarized endothelial monolayers Differential permissivity of human cerebrovascular endothelial cells to enterovirus infection and specificities of serotype EV-A71 in crossing an in vitro model of the human blood-brain barrier Pancreatic acinar cell-specific autophagy disruption reduces coxsackievirus replication and pathogenesis in vivo Fitness and virulence of a coxsackievirus mutant that can circumnavigate the need for phosphatidylinositol 4-kinase class III beta Inactivation of the host lipin gene accelerates RNA virus replication through viral exploitation of the expanded endoplasmic reticulum membrane Organization and function of membrane contact sites Three-dimensional architecture of extended synaptotagmin-mediated endoplasmic reticulum-plasma membrane contact sites this, other studies showed that enterovirus replication is not sensitive to Arf1 depletion and that overexpression of different Arf proteins cannot relieve virus replication from BFA inhibition [42, 43] .
    keywords: cells; cholesterol; enterovirus; gbf1; host; lipid; membrane; pi4p; proteins; replication; rna; ros
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        item: #1250 of 1349
          id: cord-347351-emdj66vj
      author: Kampf, Günter
       title: Potential sources, modes of transmission and effectiveness of prevention measures against SARS-CoV-2
        date: 2020-09-18
       words: 10293
      flesch: 41
     summary: [Chinese journal of preventive medicine Indirect Virus Transmission in Cluster of COVID-19 Cases Familial cluster of COVID-19 infection from an asymptomatic Potential Presymptomatic Transmission of SARS-CoV-2 Asymptomatic and Human-to-Human Transmission of SARS-CoV-2 in a 2-Family Cluster Presumed Asymptomatic Carrier Transmission of COVID-19 The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) Covid-19: four fifths of cases are asymptomatic, China figures indicate COVID-19 transmission through asymptomatic carriers is a challenge to containment. Table III summarizes the frequency and magnitude of SARS-CoV-2 viral RNA loads in respiratory tract samples obtained from COVID-19 patients.
    keywords: air; asymptomatic; cases; coronavirus; cov-2; covid-19; detection; disease; infection; patients; respiratory; rna; samples; sars; study; surfaces; transmission
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        item: #1251 of 1349
          id: cord-347472-n6811ens
      author: Rosebrock, Adam P.
       title: Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results
        date: 2020-05-15
       words: 6274
      flesch: 49
     summary: DNA samples were diluted in nuclease free water supplemented with 0.01% Tween-20, RNA samples were diluted in nuclease-free water. All samples contained genomic DNA and generated extraction control positive signals well above the CDC assay threshold (40 cycles, horizontal dashed line).
    keywords: assay; cdc; control; dna; extraction; probe; qpcr; reverse; rna; samples; signal
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        item: #1252 of 1349
          id: cord-347532-n51qv9pp
      author: Wacharapluesadee, Supaporn
       title: Group C Betacoronavirus in Bat Guano Fertilizer, Thailand
        date: 2013-08-17
       words: 1194
      flesch: 38
     summary: To assess pathogens in bat guano, we examined bat guano from a cave in the Khao Chong Phran Non-hunting Area (KCP-NHA) in Ratchaburi Province, Thailand, where bat guano was sold as agricultural fertilizer, for the presence of NiV, CoV, and H. capsulatum fungi. To detect H. capsulatum and other fungi, we extracted genomic DNA directly from bat guano by using the silica-guanidine thiocyanate protocol, NucliSense Isolation Reagent (bioMérieux, Boxtel, the Netherlands), according to the manufacturer's protocol.
    keywords: bat; bats; cov; guano; pcr; rna
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        item: #1253 of 1349
          id: cord-347710-ff64y6ef
      author: Wan, Qianya
       title: Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development
        date: 2020-07-13
       words: 36727
      flesch: 38
     summary: First, Hsp90 works as a classic chaperone protein to stabilize virus proteins. 57, 473 Except for promoting viral protein translation by binding with the viral IRES sequence, hnRNPs can directly bind with virus proteins to facilitate virus replication.
    keywords: a71; activation; activity; antiviral; apoptosis; atp; binding; c virus; cells; chaperone; complex; diseases; dna; domain; entry; expression; factor; family; folding; formation; function; gene; hbv; hcv; heat; heat shock; hepatitis; hnrnp; hnrnp a1; host; hsc70; hsp27; hsp90; human; infection; influenza; influenza virus; inhibitors; interaction; kinase; mrna; nuclear; nucleus; polymerase; protein; response; rna; role; shock protein; splicing; stress; terminal; transcription; translation; type; viral; virus; virus infection; virus replication; virus rna; virus type; viruses
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        item: #1254 of 1349
          id: cord-347917-fmb5nyxu
      author: Liu, Junli
       title: Comprehensive Genomic Characterization Analysis of lncRNAs in Cells With Porcine Delta Coronavirus Infection
        date: 2020-01-28
       words: 4655
      flesch: 42
     summary: Meanwhile, an inducible program of inflammatory gene expression is central to antiviral defense. As shown in Figure 4A , 26% of DE lncRNAs were located in the same strand but upstream of protein-coding genes and 24% were located downstream, while antisense-upstream and antisense-overlapping comprised 27 and 1%, respectively, and the remaining 22% were antisensedownstream lncRNAs.
    keywords: analysis; cells; expression; genes; genome; infection; lncrnas; long; pdcov; protein
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        item: #1255 of 1349
          id: cord-347992-coby2m6e
      author: Marton, Soledad
       title: In Vitro and Ex Vivo Selection Procedures for Identifying Potentially Therapeutic DNA and RNA Molecules
        date: 2010-06-28
       words: 10046
      flesch: 39
     summary: It has been shown that an antagonist RNA aptamer against CTLA-4, a negative regulator of T-cell activation, inhibits its function [101] , while an agonistic aptamer against 4-1BB, a major co-stimulatory receptor, leads to the activation of T cells RNA aptamers have been selected against different viral enzymes and proteins involved in host-cell interactions, such as HIV-1 reverse transcriptase (RT), HIV-1 glycoprotein 120, HCV RNA-dependent RNA polymerase (RdRp), SARS coronavirus NTPase/helicase, and the hemagglutinin protein of human influenza virus B, all of which show efficient viral inhibition [138]
    keywords: acids; activity; anti; aptamer; binding; cells; dna; factor; growth; hcv; human; inhibition; molecules; protein; receptor; rna; rna aptamers; selection; specific; target; therapeutic; tumor; vitro; vivo
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        item: #1256 of 1349
          id: cord-348147-leni23pa
      author: Müller, B.
       title: Genetic diversity and recombination of murine noroviruses in immunocompromised mice
        date: 2007-05-29
       words: 3493
      flesch: 47
     summary: Amplification of partial ORF1 and ORF2 sequences ORF1 (RNA polymerase region) and ORF2 (capsid) were amplified by nested RT-PCRs. However, the divergences of partial ORF1 and ORF2 sequences of MNV isolates investigated here reveal a high degree of variability among murine noroviruses.
    keywords: mnv; murine; norovirus; orf1; orf2; rna; strains
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        item: #1257 of 1349
          id: cord-348204-365z3qxz
      author: Harun, Mohammad Syamsul Reza
       title: Transcriptional profiling of feline infectious peritonitis virus infection in CRFK cells and in PBMCs from FIP diagnosed cats
        date: 2013-11-09
       words: 4693
      flesch: 46
     summary: Prevalence of feline coronavirus in two cat populations in Malaysia A review of feline infectious peritonitis virus infection: 1963-2008 Feline infectious peritonitis The molecular genetics of feline coronaviruses: comparative sequence analysis of the ORF7a/7b transcription unit of different biotypes Feline infectious peritonitis viruses arise by mutation from endemic feline enteric coronaviruses Mutation in spike protein cleavage site and pathogenesis of feline coronavirus Natural history of a recurrent feline coronavirus infection and the role of cellular immunity in survival and disease Apoptosis and T-cell depletion during feline infectious peritonitis A possible involvement of TNF-alpha in apoptosis induction in peripheral blood lymphocytes of cats with feline infectious peritonitis Kinetic analysis of a complete poxvirus transcriptome an immediate early class of gene Hepatic transcriptome analysis of hepatitis C virus infection in chimpanzees defines unique gene expression patterns associated with viral clearance Gene-expression changes induced by Feline immunodeficiency virus infection differ in epithelial cells and lymphocytes Viral transcriptome analysis of feline immunodeficiency virus infected cells using second generation sequencing technology A greedy algorithm for aligning DNA sequences Attachment and internalization of feline infectious peritonitis virus in feline blood monocytes and Crandell feline kidney cells Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources Functions, structure, and read-through alternative splicing of feline APOBEC3 genes Increased PD-L1 expression and PD-L1/CD86 ratio on dendritic cells were associated with impaired dendritic cells function in HCV infection Polymorphism in human APOBEC3H affects a phenotype dominant for subcellular localization and antiviral activity Reduced APOBEC3H variant antiviral activities are associated with altered RNA binding activities Feline programmed death and its ligand: characterization and changes with feline immunodeficiency virus infection Upregulation of PD-1 expression on HIV-specific CD8+ T cells leads to reversible immune dysfunction PD-1 and its ligands in tolerance and immunity Blockade of programmed death-1 ligands on dendritic cells enhances T cell activation and cytokine production Regulation of cysteine-rich intestinal protein, a zinc finger protein, by mediators of the immune response Cellular composition and interferon-γ expression of the local inflammatory response in feline infectious peritonitis (FIP) Replication of feline coronaviruses in peripheral blood monocytes Andes virus stimulates interferon-inducible MxA protein expression in endothelial cells West Nile virusinduced cytoplasmic membrane structures provide partial protection against the interferon-induced antiviral MxA protein Identification of five interferon-induced cellular proteins that inhibit west nile virus and dengue virus infections Analysis of ISG expression in chronic hepatitis C identifies viperin as a potential antiviral effector The neutrophil serine protease inhibitor SerpinB1 protects against inflammatory lung injury and morbidity in influenza virus infection SerpinB1 protects the mature neutrophil reserve in the bone marrow Akt phosphorylates the Yes-associated protein, YAP, to induce interaction with 14-3-3 and attenuation of p73-mediated apoptosis The UCSC felCat4 data from the Dec. 2008 catChrV17e draft assembly Mapping and quantifying mammalian transcriptomes by RNA-Seq Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C(T)) Based on Kal’s Z-test, with False Discovery Rate (FDR) <0.05 and >1.99 fold change on gene expressions, a total of 61 genes were differentially expressed by both samples, where 44 genes were up-regulated and the remainder were down-regulated.
    keywords: analysis; cats; cells; expression; feline; fipv; genes; infected; infection; rna; virus
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        item: #1258 of 1349
          id: cord-348243-e5tdb08v
      author: Schermer, Bernhard
       title: Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay
        date: 2020-11-02
       words: 3962
      flesch: 48
     summary: Next, the reaction was diluted with 80 μl of HybriDetect Buffer (Milenia), mixed, and then a HybriDetect dipstick (Milenia) was placed in the reaction tube and incubated at RT. Transferring such assays to automated microfluidic formats [11] can become an important tool to support disease control strategies.
    keywords: assays; cov-2; detection; lamp; reaction; rna; sars
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        item: #1259 of 1349
          id: cord-348669-mizygp4j
      author: Beall, Anne
       title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A
        date: 2016-01-05
       words: 6058
      flesch: 35
     summary: in conventional 9-day-old nursing piglets vs. 26-day-old weaned pigs Swine enteric coronavirus diseases (SECD), including porcine epidemic diarrhea virus (PEDv) Origin, evolution, and virulence of porcine deltacoronaviruses in the United States A novel pathogenic mammalian orthoreovirus from diarrheic pigs and swine blood meal in the United States Distinct characteristics and complex evolution of PEDV strains Understanding human coronavirus HCoV-NL63 Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines Outbreak of porcine epidemic diarrhea in suckling piglets Origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the United States US-like strain of porcine epidemic diarrhea virus outbreaks in Taiwan Porcine epidemic diarrhea: a review of current epidemiology and available vaccines Receptor usage and cell entry of porcine epidemic diarrhea coronavirus Porcine epidemic diarrhea virus uses cellsurface heparan sulfate as an attachment factor Genome organization of porcine epidemic diarrhoea virus Mutations in the spike gene of porcine epidemic diarrhea virus associated with growth adaptation in vitro and attenuation of virulence in vivo Receptor-bound porcine epidemic diarrhea virus spike protein cleaved by trypsin induces membrane fusion Porcine epidemic diarrhea virus E protein causes endoplasmic reticulum stress and up-regulates interleukin-8 expression Porcine epidemic diarrhea virus N protein prolongs S-phase cell cycle, induces endoplasmic reticulum stress, and up-regulates interleukin-8 expression Completion of the porcine epidemic diarrhoea coronavirus (PEDV) genome sequence PEDV ORF3 encodes an ion channel protein and regulates virus production Manipulation of the porcine epidemic diarrhea virus genome using targeted RNA recombination Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene Reverse genetics with a full-length infectious cDNA of the Middle East respiratory syndrome coronavirus Systematic assembly of a full-length infectious clone of human coronavirus NL63 Development of mouse hepatitis virus and The appearance of the porcine respiratory coronavirus has created new problems and perspectives Detection and genetic characterization of deltacoronavirus in pigs Genetic manipulation of porcine epidemic diarrhea virus (PEDV) recovered from a full-length infectious cDNA clone Determination of the infectious titer and virulence of an original US porcine epidemic diarrhea virus PC22A strain Avian influenza virus transmission to mammals Resolution of the cellular proteome of the nucleocapsid protein from a highly pathogenic isolate of porcine reproductive and respiratory syndrome virus identifies PARP-1 as a cellular target whose interaction is critical for virus biology USDA licenses first vaccine for porcine epidemic diarrhea.
    keywords: cells; coronavirus; culture; diarrhea; epidemic; icpedv; orf3; pc22a; pedv; pigs; porcine; protein; rfp; strain; transmission; virus
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        item: #1260 of 1349
          id: cord-348777-pk9y6vfp
      author: Ding, Cheng
       title: Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study
        date: 2020-09-28
       words: 3620
      flesch: 40
     summary: This study aims to investigate the association between corticosteroid therapy and the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance among patients with mild COVID-19. Corticosteroid therapy in patients with mild COVID-19 was not associated with the duration of SARS-CoV-2 clearance, suggesting that the use of corticosteroids may not be beneficial for patients with mild COVID-19 and should be prudently recommended in clinical practice.
    keywords: clearance; coronavirus; corticosteroid; covid-19; patients; rna; sars; therapy
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        item: #1261 of 1349
          id: cord-348799-qu4zin3o
      author: Wu, Nannan
       title: The interferon stimulated gene 20 protein (ISG20) is an innate defense antiviral factor that discriminates self versus non-self translation
        date: 2019-10-10
       words: 11434
      flesch: 42
     summary: B) Control cells were analyzed by confocal microscopy with the endogenous P bodies markers TNRC6A and DDX6 (ISG20-expressing cells and a portion of the overlay of control cells depicted here are presented in Fig 5A) . Translationcompetent mRNA generated in vitro were transfected in ISG20 expressing cells, prior to cell lysis one hour afterwards and analyses by RT-qPCR or luciferase assays.
    keywords: bodies; cells; control; dna; expression; fig; gfp; hek293; hours; isg20; luciferase; mrnas; non; protein; rna; self; t cells; translation; virus; vsv
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        item: #1262 of 1349
          id: cord-348815-lthz75oc
      author: Kurreck, Jens
       title: RNA Interference: From Basic Research to Therapeutic Applications
        date: 2009-01-19
       words: 14125
      flesch: 51
     summary: AAVs are attractive vectors for gene transfer, since they efficiently transduce target cells and are nonpathogenic for humans. In this way the siRNAs are preferentially taken up by the liver, and proof of principle was demonstrated in practice by the knockdown of target genes in this target organ.
    keywords: activity; antisense; cells; delivery; effects; example; expression; figure; gene; mirna; nucleotides; protein; rnai; shrna; silencing; sirnas; strand; target; target gene; target rna; vectors; virus
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        item: #1263 of 1349
          id: cord-348860-zaimorg0
      author: Ratra, Ruchi
       title: Functional genomics as a tool in virus research
        date: 2008-06-01
       words: 3382
      flesch: 34
     summary: Besides targeting specifi c viral genes, the host genes essential for the viral cycle may serve as antiviral targets based on the fact that viruses employ several strategies to alter host gene expression. The expression of viral genes: EBNA1, EBNA2, EBNA3A, EBNA3B, LMP1, and LMP2A were found to be correlated among themselves and inversely correlated with the expression of a large subset of host genes, such as multiple MHC class I HLA genes involved in regulating immune response via antigen presentation.
    keywords: analysis; dna; expression; gene; genome; genomics; microarray; rna; virus; viruses
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        item: #1264 of 1349
          id: cord-349011-kxhpdvri
      author: Grandvaux, Nathalie
       title: CSV2018: The 2nd Symposium of the Canadian Society for Virology
        date: 2019-01-18
       words: 8846
      flesch: 37
     summary: Traditionally, flow cytometry has been a very useful approach to study virus infection on a single-cell basis, but viruses themselves have been too small to analyze due to the 0.5 µm resolution of most instruments. Dr. Noyce discussed the technical challenges associated with using synthetic biology as a tool to build new viruses, as well as biosafety and ethical considerations.
    keywords: antiviral; cas; cells; crispr; dalhousie; genome; host; human; infection; nuclear; pandemic; receptors; research; rna; science; session; studies; university; vaccine; virus; viruses
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        item: #1265 of 1349
          id: cord-349042-u9svz7pf
      author: Li, Jifen
       title: The successes and future prospects of the linear antisense RNA amplification methodology
        date: 2018-03-29
       words: 5020
      flesch: 33
     summary: Primary cell culture of live neurosurgically resected aged adult human brain cells and single cell transcriptomics Serotonergic neuron regulation informed by in vivo single-cell transcriptomics CEL-seq: single-cell RNA-seq by multiplexed linear amplification Assessing characteristics of RNA amplification methods for single cell RNA sequencing Single-cell whole-genome analyses by linear amplification via transposon insertion (LIANTI) Expression monitoring by hybridization to high-density oligonucleotide arrays Dopamine receptor subtypes colocalize in rat striatonigral neurons Embryonic neuronal markers in tuberous sclerosis: single-cell molecular pathology Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA Advantages of mRNA amplification for microarray analysis Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types On the nature and differential distribution of mRNAs in hippocampal neurites: implications for neuronal functioning Molecular characterization of the dendritic growth cone: regulated mRNA transport and local protein synthesis Cytoplasmic intron sequence-retaining transcripts can be dendritically targeted via ID element retrotransposons Highfidelity mRNA amplification for gene profiling Prospective molecular profiling of melanoma metastases suggests classifiers of immune responsiveness Human transcriptome array for high-throughput clinical studies CEL-Seq2: sensitive highly-multiplexed single-cell RNA-seq Single-cell barcoding and sequencing using droplet microfluidics Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells Amplified expression profiling of platelet transcriptome reveals changes in arginine metabolic pathways in patients with sickle cell disease Given the flexibility of the technique and the ability of different aRNA reporting methods to barcode different chemicals, it is reasonable to presume that linear RNA amplification will continue to be used as a foundation for new technologies, providing deeper understanding of the multiple components and processes of cells and systems that contribute to their function.
    keywords: amplification; analysis; arna; cdna; cell; detection; linear; polymerase; promoter; rna; sequencing
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        item: #1266 of 1349
          id: cord-349249-jwvz1ux2
      author: Singh, Gagandeep
       title: A Minimally Replicative Vaccine Protects Vaccinated Piglets Against Challenge With the Porcine Epidemic Diarrhea Virus
        date: 2019-10-22
       words: 6560
      flesch: 39
     summary: The objective of this study was to evaluate the heat and RNAse treated PEDV vaccine for its safety, immunogenicity and ability to reduce viremia in a weanling piglet model, with the ultimate goal of developing a process which can potentially reduce lead vaccine development time, is safe and be easily applied to newly emerging strains. At DPC 3 and 7, challenge viral RNA was not detected in any of the pigs vaccinated with the heat and RNAse treated PEDV vaccine (Figure 4) , while 4 of the 6 pigs administered the irradiated vaccine were positive by RT-qPCR on DPC3.
    keywords: challenge; diarrhea; epidemic; heat; pedv; piglets; pigs; porcine; protein; rnase; spike; vaccine; virus
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        item: #1267 of 1349
          id: cord-349341-ap5n6ijl
      author: Kopek, Benjamin G
       title: Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-Induced Mini-Organelle
        date: 2007-08-14
       words: 8597
      flesch: 38
     summary: BMV and FHV differ in many important respects including that BMV encodes a much larger complement of RNA replication proteins [15, 19] . A revealed by fluorescence resonance energy transfer Colloidal gold: Principles, methods and applications From proteomic inventory to architecture Double-tilt electron tomography Molecular requirements for actin-based lamella formation in Drosophila S2 cells Nodaviruses of insects Areas, volumes, packing and protein structure Structure of the reovirus core at 3.6 Å resolution Retroviridae: The retroviruses and their replication Orthomyxoviridae: The viruses and their replication Symmetry, flexibility and permeability in the structure of yeast retrotransposon virus-like particles Implications of lipid microdomains for membrane curvature, budding and fission Vesicle formation at the plasma membrane and trans-Golgi network: The same but different Interferons and other cytokines Double-stranded RNA as a template for gene silencing Ultrastructure and origin of cytplasmic multivesicular bodies induced by carnation Italian ringspot virus Packaging and release of the viral genome Particle polymorphism caused by deletion of a peptide molecular switch in a quasiequivalent icosahedral virus Flock House virus subgenomic RNA3 is replicated and its replication correlates with transactivation of RNA2 Identification of sequences in brome mosaic virus replicase protein 1a that mediate association with endoplasmic reticulum membranes Interactions between the structural domains of the RNA replication proteins of plant-infecting RNA viruses Analysis of the interaction of viral RNA replication proteins by using the yeast two-hybrid assay Quantitative analysis of the hepatitis C virus replication complex Formation of the poliovirus replication complex requires coupled viral translation, vesicle production, and viral RNA synthesis Reversible dissociation of the poliovirus replication complex: functions and interactions of its components in viral RNA synthesis Drosophila cells in culture Electron microscopy methods and protocols Synaptic vesicle populations in saccular hair cells reconstructed by electron tomography Three-dimensional analysis of mouse rod and cone mitochondrial cristae architecture: bioenergetic and functional implications Dual-axis tomography: An approach with alignment methods that preserve resolution Transform-based backprojection for volume reconstruction of large format electron microscope tilt series Electron tomography of large, multicomponent biological structures Electron tomography of mitochondria after the arrest of protein import associated with Tom19 depletion We thank Randall Massey and Benjamin August of the University of Wisconsin Medical School Electron Microscopy Facility for assistance with electron microscopy; Priscilla Van Wynsberghe and Billy Dye for helpful discussions; Dan Lautenschlager, Steve Lamont, and Jean Yves-Sgro for computer assistance; and Johan den Boon for critical reading of the manuscript.
    keywords: cells; complex; drosophila; electron; fhv; figure; labeling; membrane; protein; replication; rna; rna replication; spherules; virus; viruses; þ)rna
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        item: #1268 of 1349
          id: cord-349358-leicos9j
      author: Ketzinel‐Gilad, Mali
       title: RNA interference for antiviral therapy
        date: 2006-06-16
       words: 12748
      flesch: 38
     summary: siRNAs targeting the SARS-CoV RNA polymerase gene inhibited viral RNA replication, protein synthesis and reduced the viral cytopathic effects on Vero cells [36] . A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1 RNA interference of HIV replication Lentivirus-mediated RNA interference of DC-SIGN expression inhibits human immunodeficiency virus transmission from dendritic cells to T cells Modulating HIV-1 replication by RNA interference directed against human transcription elongation factor SPT5 Inhibition of respiratory viruses by nasally administered siRNA The promise of siRNAs for the treatment of influenza Inhibition of coxsackievirus B3 replication by small interfering RNAs requires perfect sequence match in the central region of the viral positive strand Inhibition of SARS-CoV replication by siRNA Actively replicating West Nile virus is resistant to cytoplasmic delivery of siRNA Use of RNA interference to prevent lethal murine West Nile virus infection An siRNA-based microbicide protects mice from lethal herpes simplex virus 2 infection Small interfering RNA inhibits hepatitis B virus replication in mice Short interfering RNA-directed inhibition of hepatitis B virus replication Inhibition of HBV replication by siRNA in a stable HBV-producing cell line Inhibition of hepatitis B virus expression and replication by RNA interference Inhibition of hepatitis B virus in mice by RNA interference Effective inhibition of HBV replication in vivo by anti-HBx short hairpin RNAs Knock-down of hepatitis B virus X protein reduces the tumorigenicity of hepatocellular carcinoma cells Genomic analysis of anti-hepatitis B virus (HBV) activity by small interfering RNA and lamivudine in stable HBV-producing cells Small hairpin RNAs efficiently inhibit hepatitis C IRES-mediated gene expression in human tissue culture cells and a mouse model Inhibition of hepatitis C virus translation and subgenomic replication by siRNAs directed against highly conserved HCV sequence and cellular HCV cofactors Lentiviral delivery of short hairpin RNAs protects CD4 T cells from multiple clades and primary isolates of HIV HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome Evidence that HIV-1 encodes an siRNA and a suppressor of RNA silencing HIV-1 nef suppression by virally encoded microRNA Regulation of human immunodeficiency virus 1 transcription by nef microRNA Lentiviral siRNAs targeting multiple highly conserved RNA sequences of human immunodeficiency virus type 1 Identification of cellular deoxyhypusine synthase as a novel target for antiretroviral therapy Computational design of antiviral RNA interference strategies that resist human immunodeficiency virus escape RNAi induction and activation in mammalian muscle cells where Dicer and eIF2C translation initiation factors are barely expressed RNA silencing as a plant immune system against viruses Induction and suppression of RNA silencing by an animal virus Nucleic acid-based immune system: the antiviral potential of mammalian RNA silencing Adenosine kinase inhibition and suppression of RNA silencing by geminivirus AL2 and L2 proteins Effects and side-effects of viral RNA silencing suppressors on short RNAs The coat protein of turnip crinkle virus suppresses posttranscriptional gene silencing at an early initiation step A viral protein inhibits the long range signaling activity of the gene silencing signal A viral protein suppresses RNA silencing and binds silencing-generated, 21-to 25-nucleotide double-stranded RNAs Virus-encoded suppressor of posttranscriptional gene silencing targets a maintenance step in the silencing pathway P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction Suppression of posttranscriptional gene silencing by a plant viral protein localized in the nucleus Interferon antagonist proteins of influenza and vaccinia viruses are suppressors of RNA silencing A virus-encoded inhibitor that blocks RNA interference in mammalian cells Adenovirus VA1 noncoding RNA can inhibit small interfering RNA and MicroRNA biogenesis Suppression of RNA interference by adenovirus virus-associated RNA Human immunodeficiency virus type 1 escapes from RNA interferencemediated inhibition Human immunodeficiency virus type 1 escape from RNA interference Hepatitis C virus replicons escape RNA interference induced by a short interfering RNA directed against the NS5b coding region Inhibition of hepatitis B virus gene expression by single and dual small interfering RNA treatment Expression profiling reveals off-target gene regulation by RNAi Activation of the interferon system by short-interfering RNAs Cationic liposome-mediated delivery of siRNAs in adult mice Small interfering RNAs mediate sequence-independent gene suppression and induce immune activation by signaling through toll-like receptor 3 Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA A system for stable expression of short interfering RNAs in mammalian cells Determinants of interferon-stimulated gene induction by RNAi vectors An enhanced U6 promoter for synthesis of short hairpin RNA Short hairpin type of dsRNAs that are controlled by tRNA(Val) promoter significantly induce RNAimediated gene silencing in the cytoplasm of human cells Promoter choice affects the potency of HIV-1 specific RNA interference Development and application of siRNA expression vector Conditional suppression of cellular genes: lentivirus vector-mediated drug-inducible RNA interference Short-term cytotoxic effects and longterm instability of RNAi delivered using lentiviral vectors Efficient delivery of siRNA for inhibition of gene expression in postnatal mice RNA interference in mammalian cells by chemically-modified RNA RNA interference targeting Fas protects mice from fulminant hepatitis In vivo activity of nuclease-resistant siRNAs Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate siRNA function in RNAi: a chemical modification analysis Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference Challenges for RNAi in vivo Activity of stabilized short interfering RNA in a mouse model of hepatitis B virus replication siRNA relieves chronic neuropathic pain Potent and persistent in vivo anti-HBV activity of chemically modified siRNAs Inhibition of influenza virus production in virus-infected mice by RNA interference Protection against lethal influenza virus challenge by RNA interference in vivo Atelocollagenmediated synthetic small interfering RNA delivery for effective gene silencing in vitro and in vivo Intravenous RNA interference gene therapy targeting the human epidermal growth factor receptor prolongs survival in intracranial brain cancer Recombinant viral capsids as an efficient vehicle of oligonucleotide delivery into cells Adenovirus vectormediated doxycycline-inducible RNA interference Conditionally replicating adenoviruses expressing short hairpin RNAs silence the expression of a target gene in cancer cells Inducible, reversible, and stable RNA interference in mammalian cells Cre-lox-regulated conditional RNA interference from transgenes CRE recombinase-inducible RNA interference mediated by lentiviral vectors Lentiviral vector-mediated delivery of short hairpin RNA results in persistent knockdown of gene expression in mouse brain RNAi suppresses polyglutamine-induced neurodegeneration in a model of spinocerebellar ataxia First Parkinson gene therapy trial launches Optimization of an siRNA-expression system with an improved hairpin and its significant suppressive effects in mammalian cells Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide Antisense oligonucleotides: promise and reality LNA: a versatile tool for therapeutics and genomics Rational siRNA design for RNA interference Asymmetry in the assembly of the RNAi enzyme complex Functional siRNAs and miRNAs exhibit strand bias Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNAdependent RNA polymerase Silencing SARS-CoV Spike protein expression in cultured cells by RNA interference Using siRNA in prophylactic and therapeutic regimens against SARS coronavirus in Rhesus macaque RNA interference targeting VP1 inhibits foot-and-mouth disease virus replication in BHK-21 cells and suckling mice Small interfering RNA molecules as potential anti-human rhinovirus agents: in vitro potency, specificity, and mechanism Susceptibility of human hepatitis delta virus RNAs to small interfering RNA action RNA interference against enterovirus 71 infection Inhibition of porcine endogenous retroviruses by RNA interference: increasing the safety of xenotransplantation Enhanced gene silencing of HIV-1 specific siRNA using microRNA designed hairpins Expression of small hairpin RNA by lentivirus-based vector confers efficient and stable gene-suppression of HIV-1 on human cells including primary non-dividing cells Inhibition of HIV-1 by lentiviral vector-transduced siRNAs in T lymphocytes differentiated in SCID-hu mice and CD34+ progenitor cellderived macrophages Efficient gene transfer of HIV-1-specific short hairpin RNA into human lymphocytic cells using recombinant adeno-associated virus vectors Inhibition of virus production in JC virus-infected cells by postinfection RNA interference Inhibition of the Epstein-Barr virus lytic cycle by Zta-targeted RNA interference Selective inhibition of hepatitis B virus replication by RNA interference Clearance of hepatitis B virus from the liver of transgenic mice by short hairpin RNAs Short interfering RNA-mediated inhibition of herpes simplex virus type 1 gene expression and function during infection of human keratinocytes
    keywords: cells; delivery; effect; expression; gene; hcv; hepatitis; hiv; human; infection; inhibition; interference; replication; rna; rna interference; rnai; silencing; sirna; specific; targeting; virus; viruses; vitro
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        item: #1269 of 1349
          id: cord-349417-vn7q8wc4
      author: Ziebuhr, John
       title: The Coronavirus Replicase: Insights into a Sophisticated Enzyme Machinery
        date: 2006
       words: 3389
      flesch: 33
     summary: A detailed sequence analysis by Gorbalenya, Snijder and colleagues of the SARS-CoV genome revealed that the enzymology of coronavirus RNA synthesis may be significantly more complex than previously thought. It will be of particular interest to identify those proteins that are involved in the specific mechanisms of coronavirus RNA synthesis, such as the production of a nested set of subgenome-length RNAs and the replication of RNA genomes of unprecedented size.
    keywords: activities; coronavirus; helicases; pro; protease; replication; rna; sars
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        item: #1270 of 1349
          id: cord-349623-dw5o9i59
      author: Miranda, José P.
       title: Analytical and Clinical Validation for RT-qPCR Detection of SARS-CoV-2 Without RNA Extraction
        date: 2020-10-15
       words: 3819
      flesch: 39
     summary: Optimal selected conditions for direct protocol were: thermal shock at 70°C for 10 min, loading 3.5 ul in the RT-qPCR. Methods: Optimal direct protocol was selected by comparing RT-qPCR performance under a set of thermal (65, 70, and 95° for 5, 10, and 30 min) and amplification conditions (3 or 3.5 uL loading volume; 2 commercial RT-qPCR kits with a limit of detection below 10 copies/reaction) in nasopharyngeal swabs stored at 4°C in sterile Weise's buffer pH 7.2.
    keywords: protocol; qpcr; rna; samples; sars; standard
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        item: #1271 of 1349
          id: cord-349672-2kt7xw8i
      author: Dasgupta, Tumpa
       title: Mechanism of Type IA Topoisomerases
        date: 2020-10-17
       words: 8546
      flesch: 48
     summary: Answers about involvement of the carboxyl-terminal domain in DNA topoisomerase I-mediated catalysis The Zn(II) DNA Topoisomerase I Is Part of a High-Affinity DNA Binding Domain Expression and DNA-binding properties of the 14K carboxyl terminal fragment of Escherichia coli DNA topoisomerase
    keywords: coli topoisomerase; dna; domains; e. coli; rna; rna topoisomerase; strand; terminal; topoisomerase; type; type ia
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        item: #1272 of 1349
          id: cord-349684-2tioh80m
      author: Pezzotti, Giuseppe
       title: Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride
        date: 2020-06-20
       words: 5401
      flesch: 43
     summary: Dermatol Res Pract An Overview of Copper Toxicity Relevance to Public Health Silicon Nitride and Related Materials Orthopedic Applications of Silicon Nitride Ceramics Bioactive Silicon Nitride: A New Therapeutic Material for Situ Spectroscopic Screening of Osteosarcoma Living Cells on Stoichiometry-Modulated Silicon Nitride Bioceramic Surfaces Silicon Nitride: A Synthetic Mineral for Vertebrate Biology Human Osteoblasts Grow Transitional Si/N Apatite in Quickly Osteointegrated Si3N4 Cervical Insert Decreased Bacteria Activity on Si3N4 Surfaces Compared with PEEK or Titanium Anti-Infective and Osteointegration Properties of Silicon Nitride, Poly (Ether Ether Ketone), and Titanium Implants A Spontaneous Solid-State NO Donor to Fight Antibiotic Resistant Bacteria. These investigators also showed rapid HuCoV-229E inactivation (within a few minutes) for simulated fingertip contamination on Cu surfaces.
    keywords: aln; cells; cov-2; fig; inactivation; min; nitride; rna; sars; si3n4; silicon; surface; tmprss2; virus
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        item: #1273 of 1349
          id: cord-349762-f5no10eq
      author: Nagura-Ikeda, Mayu
       title: Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription–Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19
        date: 2020-08-24
       words: 4286
      flesch: 45
     summary: The C T value of target 2 in the cobas SARS-CoV-2 test was significantly lower in saliva samples that tested positive by the RAT than in samples that tested negative (25.4 Ϯ 1.8 versus 30.8 Ϯ 2.7, respectively; P Ͻ 0.001) (Fig. 2B) . Among these 61 early-phase patients, saliva samples were taken from 37 of them within 6 days of symptom onset (Table S1 ).
    keywords: covid-19; patients; qpcr; rna; saliva; sars; specimens; test
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        item: #1274 of 1349
          id: cord-349839-s32d3di2
      author: Westhof, Eric
       title: RNA pseudoknots
        date: 1992-06-30
       words: 3431
      flesch: 53
     summary: At the functional level, there is evidence that the realm of functions encompassed by RNA pseudoknots extends from the control of translation in prokaryotes, retroviruses and coronaviruses to the control of catalytic activity in ribozymes and the control of replication in some plant viruses. In an important piece of work, Pleij and his collaborators [2] demonstrated that because of the special geometry of RNA helices, it is possible for the two helical stems in the pseudoknot to be co-axially stacked.
    keywords: base; groove; helix; pseudoknot; rna; structure; trna
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        item: #1275 of 1349
          id: cord-350019-4nlbu54e
      author: Robinson, Elektra K.
       title: The how and why of lncRNA function: An innate immune perspective()
        date: 2019-09-02
       words: 13184
      flesch: 37
     summary: Immunobiology of long noncoding RNAs Cell composition analysis of bulk genomics using single-cell data Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling Digital cell quantification identifies global immune cell dynamics during influenza infection Chromatin state dynamics during blood formation HHS Public Access, Science (80-. ) At the time we had no idea that these genes would represent the largest family of RNA genes produced in the genome.
    keywords: activation; analysis; associated; cell; coding; conservation; disease; expression; function; gene; genome; human; lncrna; modifications; mouse; noncoding; protein; regulation; rna; rnas; sequence; sequencing; specific; structure; studies; study; transcription
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        item: #1276 of 1349
          id: cord-350040-e8q7wq0h
      author: Aronin, N
       title: Target selectivity in mRNA silencing
        date: 2006-02-16
       words: 6617
      flesch: 51
     summary: The complexity of siRNA design is that small changes in siRNA:mRNA complementarity can have profound effects on RNAi effectiveness; mismatches might have few consequences or, as shown above, improve silencing by strand selection. In theory, changes in sequence of the siRNA can improve single nucleotide dependent RNAi, with little effect on RISC endonuclease activity.
    keywords: activity; ago; end; guide; guide strand; mrna; nucleotide; risc; rnai; silencing; sirna; strand; target
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        item: #1277 of 1349
          id: cord-350083-kldu8q8x
      author: Oany, Arafat Rahman
       title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach
        date: 2015-08-08
       words: 5025
      flesch: 41
     summary: Though at present, most of the vaccines are based on B cell immunity; vaccines based on T cell epitope have been encouraged recently. Thus, vaccination based on T cell epitope is a unique approach to obtain strong immune response against infectious agents, such as, viruses (Klein et al. 2005) .
    keywords: analysis; cell; ebola; epitope; et al; mhc; prediction; protein; rna; sequence; vaccine; virus
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        item: #1278 of 1349
          id: cord-350189-2su7oqbz
      author: Elmén, Joacim
       title: Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality
        date: 2005-01-14
       words: 5430
      flesch: 43
     summary: Briefly, siLNA5 has LNA modifications at the 3 0 ends and exhibits a duplex stability similar to the unmodified siRNA1 (T m = 69.7 C for siLNA5 and 70.5 C for siRNA1) whereas siLNA7 has six additional duplex stabilizing sense strand modifications at base-paired positions which increases its T m to >90 C. As shown in Figure 1a and b, unmodified siRNA (siRNA1) was markedly degraded after 6 h during which it produces a smear of faster migrating species. Introduction of LNA modifications in the 3 0 overhangs in either or both strands of the firefly siRNA revealed no loss of inhibitory effect (siLNA1-3).
    keywords: activity; antisense; cells; end; firefly; lna; luciferase; modifications; sense; sirna; strand; target
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        item: #1279 of 1349
          id: cord-350286-n7ylgqfu
      author: Giri, Rajanish
       title: When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses
        date: 2020-04-03
       words: 15857
      flesch: 51
     summary: Evaluation of intrinsic disorder in non-structural proteins of Bat CoV. Table 7 : Predicted MoRF residues in Human SARS proteins. Supplementary Table 10 : Predicted nucleotide-binding residues in Human SARS proteins.
    keywords: analysis; bat cov; binding; coronavirus; cov; cov-2; disorder; domain; figure; human; mean; protein; regions; residues; rna; sars; sars cov; sequence; structure; syndrome; table; terminal; viral; viruses
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        item: #1280 of 1349
          id: cord-350342-j4p8235a
      author: Brocato, Rebecca L.
       title: Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2-Infected Syrian Hamsters
        date: 2020-10-27
       words: 5290
      flesch: 44
     summary: RAG2 KO hamster infection with SARS-CoV-2 results in a lethal model. Disease was prolonged in transiently immunosuppressed hamsters and was uniformly lethal in RAG2 KO hamsters.
    keywords: animals; cov-2; cyp; disease; fig; hamsters; rag2; rna; sars; viral; virus; weight
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        item: #1281 of 1349
          id: cord-350533-fp1ctpax
      author: Tchesnokov, Egor P.
       title: Independent inhibition of the polymerase and deubiquitinase activities of the Crimean-Congo Hemorrhagic Fever Virus full-length L-protein
        date: 2020-06-04
       words: 6066
      flesch: 46
     summary: Recent advances in understanding Crimean-Congo hemorrhagic fever virus Crimean-Congo hemorrhagic fever and expansion from endemic regions Crimean-Congo haemorrhagic fever in travellers: A systematic review The WHO R&D Blueprint: 2018 review of emerging infectious diseases requiring urgent research and development efforts Biochemical Evaluation of the Inhibition Properties of Favipiravir and 2'-C-Methyl-Cytidine Triphosphates against Human and Mouse Norovirus RNA Polymerases The ambiguous base-pairing and high substrate efficiency of T-705 (Favipiravir) Ribofuranosyl 5'-triphosphate towards influenza A virus polymerase Mechanism of action of T-705 against influenza virus Japanese Surveillance Systems and Treatment for Influenza The broad-spectrum antiviral ribonucleoside ribavirin is an RNA virus mutagen Crimean-Congo hemorrhagic fever virusencoded ovarian tumor protease activity is dispensable for virus RNA polymerase function Favipiravir (T-705) but not ribavirin is effective against two distinct strains of Crimean-Congo hemorrhagic fever virus in mice Evaluation of antiviral efficacy of ribavirin, arbidol, and T-705 (favipiravir) in a mouse model for Crimean-Congo hemorrhagic fever Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase The efficacy of ribavirin in the treatment of Crimean-Congo hemorrhagic fever in Eastern Black Sea region in Turkey Identification of 2'-deoxy-2'-fluorocytidine as a potent inhibitor of Crimean-Congo hemorrhagic fever virus replication using a recombinant fluorescent reporter virus Inhibition of the subgenomic hepatitis C virus replicon in huh-7 cells by 2'-deoxy-2'-fluorocytidine Bunyaviridae RdRps: structure, motifs, and RNA synthesis machinery Transcription and replication mechanisms of Bunyaviridae and Arenaviridae L proteins Structural insight into cap-snatching and RNA synthesis by influenza polymerase Structure of influenza A polymerase bound to the viral RNA promoter Structural Insights into Bunyavirus Replication and Its Regulation by the vRNA Promoter A virus-like particle system identifies the endonuclease domain of Crimean-Congo hemorrhagic fever virus Biochemical and structural studies reveal differences and commonalities among cap-snatching endonucleases from segmented negative-strand RNA viruses Structure of a functional cap-binding domain in Rift Valley fever virus L protein Structural basis for the removal of ubiquitin and interferon-stimulated gene 15 by a viral ovarian tumor domaincontaining protease Crimean-Congo Hemorrhagic Fever Virus Suppresses Innate Immune Responses via a Ubiquitin and ISG15 Specific Protease Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants Stable Occupancy of the Crimean-Congo Hemorrhagic Fever Virus-Encoded Deubiquitinase Blocks Viral Infection Baculovirus expression system for heterologous multiprotein complexes MultiBac: multigene baculovirus-based eukaryotic protein complex production Recombinant RNA-Dependent RNA Polymerase Complex of Ebola Virus Mechanism of Inhibition of Ebola Virus RNA-Dependent RNA Polymerase by Remdesivir Structure-function relationships among RNA-dependent RNA polymerases The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus RNA ligands activate the Machupo virus polymerase and guide promoter usage Molecular Basis for the Selective Inhibition of Respiratory Syncytial Virus RNA Polymerase by 2'-Fluoro-4'-Chloromethyl-Cytidine Triphosphate Hepatitis C virus RNA-dependent RNA polymerase (NS5B) as a mediator of the antiviral activity of ribavirin Deubiquitinase function of arterivirus papain-like protease 2 suppresses the innate immune response in infected host cells Assembly of a functional Machupo virus polymerase complex Towards a structural understanding of RNA synthesis by negative strand RNA viral polymerases Viral replication. Both drugs show a broad spectrum of activities against RNA viruses, including CCHFV
    keywords: activity; cchfv; ctp; dub; fig; length; otu; protein; rdrp; rna; synthesis; virus
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        item: #1282 of 1349
          id: cord-350600-73q8mve4
      author: Myint, S.
       title: Detection of human coronavirus 229E in nasal washings using RNA:RNA hybridization
        date: 2005-12-09
       words: 2000
      flesch: 56
     summary: Three of the seven volunteers suffered a cold, and all three volunteers had detectable coronavirus RNA in their nasal washings. Nucleic acid hybridization is shown to be a sensitive technique for the diagnosis of HCV 229E infections.
    keywords: hcv; rna; virus; volunteers; washings
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        item: #1283 of 1349
          id: cord-350640-sz6xj5o3
      author: Menzel, Nicolas
       title: MAP-Kinase Regulated Cytosolic Phospholipase A2 Activity Is Essential for Production of Infectious Hepatitis C Virus Particles
        date: 2012-07-26
       words: 10138
      flesch: 44
     summary: It is possible that the active, phosphorylated PLA2G4A enzyme has a relatively long half-life which may preclude reduction of the active enzyme to a level that limits HCV infectious particle production under these experimental conditions. Interestingly, U0126 did not measurably impede RNA replication and only affected HCV particle production when added in serum-free medium.
    keywords: activity; apoe; cells; core; figure; hcv; jc1; lipid; particles; pla2g4a; presence; production; protein; py-2; replication; rna; specific; virus
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        item: #1284 of 1349
          id: cord-350697-u032yk0z
      author: Roy, Anupam
       title: Can concomitant use of zinc and curcumin with other immunity‐boosting nutraceuticals be the arsenal against COVID‐19?
        date: 2020-06-02
       words: 1111
      flesch: 37
     summary: This leads to direct antiviral actions of metallothionein against an array of viruses by sequestering Zn away from viral metalloproteins or by acting as Zn chaperones and facilitating antiviral signaling indirectly (Read et al., 2019) . Zn supplementation can also make a positive contribution to chloroquine and other antiviral treatments applied today.
    keywords: curcumin; immunity; zinc
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        item: #1285 of 1349
          id: cord-350747-5t5xthk6
      author: Gmyl, A. P.
       title: Diverse Mechanisms of RNA Recombination
        date: 2005
       words: 8188
      flesch: 36
     summary: Studies of crosses between a normal horse serum-resistant mutant and several guanidine-resistant mutants of the same strain Evidence of genetic recombination in foot-and-mouth disease virus A genetic map of poliovirus temperature-sensitive mutants Biochemical evidence for intertypic genetic recombination of polioviruses Intertypic recombination in poliovirus: Genetic and biochemical studies Multiple sites of recombination within the RNA genome of foot-and-mouth disease virus Analysis of oligonucleotide maps as a method for identifying intertypic recombination in poliovirus The primary structure of crossover region in the genome of two intertypic polyovirus recombinants The primary structure of crossover regions of intertypic poliovirus recombinants: A model of recombination between RNA genomes The mechanism of RNA recombination in poliovirus Genetics of picornaviruses Recombination between RNA genomes RNA recombination in animal and plant viruses Recombination and other genomic rearrangements in picornaviruses Evolutionary aspects of recombination in RNA viruses Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA virus New insights into the mechanisms of RNA recombination How RNA viruses exchange their genetic material Heterologous recombination in the doublestranded RNA bacteriophage phi 6 Recombination in bacteriophage Qβ its satellite RNAs: It was believed until recently that the only possible mechanism of RNA recombination is replicative template switching, with synthesis of a complementary strand starting on one viral RNA molecule and being completed on another.
    keywords: cell; fragments; genome; mechanism; nonreplicative; poliovirus; recombination; rna; rna recombination; rnas; splicing; template; trans; virus; viruses
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        item: #1286 of 1349
          id: cord-350762-rh4zbehk
      author: Hutcheson, Jessica M.
       title: Delayed Newcastle disease virus replication using RNA interference to target the nucleoprotein
        date: 2015-06-04
       words: 4310
      flesch: 44
     summary: Taken together, these results suggest that DF-1 cells transduced with pLV-miR-NP are capably of decreasing the amount of NDV viral replication following in vitro viral challenge with a velogenic strain of NDV. Upon infection with NDV, DF-1 cells constitutively expressing the NP miRNA construct had improved cell survival up to 48 h post infection (h.p.i) and decreased viral yield up to 24 h.p.i.
    keywords: cat; cells; df-1; disease; expression; mir; mirna; ndv; newcastle; protein; virus
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        item: #1287 of 1349
          id: cord-350836-1enteev7
      author: Brisse, Morgan
       title: Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5
        date: 2019-07-17
       words: 16397
      flesch: 23
     summary: Front Immunol Molecular mechanisms of Dicer: endonuclease and enzymatic activity The RIG-I-like receptor LGP2 inhibits Dicer-dependent processing of long double-stranded RNA and blocks RNA interference in mammalian cells Virus sensor RIG-I represses RNA interference by interacting with TRBP through LGP2 in mammalian cells LGP2: positive about viral sensing MDA5 and LGP2: accomplices and antagonists of antiviral signal transduction Negative regulators of the RIG-I-like receptor signaling pathway Tissue-based map of the human proteome Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I Structural basis for dsRNA recognition, filament formation, and antiviral signal activation by MDA5 Molecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I Parts, assembly and operation of the RIG-I family of motors The RNA helicase RIG-I has an essential function in doublestranded RNA-induced innate antiviral responses The C-terminal regulatory domain is the RNA 5'-triphosphate sensor of RIG-I 5 ′ -Triphosphate RNA is the ligand for RIG-I RIG-I-mediated antiviral responses to single-stranded RNA bearing 5'-Phosphates Nonself RNA-sensing mechanism of RIG-I helicase and activation of antiviral immune responses Cytosolic viral sensor RIG-I is a 5'-Triphosphate-dependent translocase on doublestranded RNA The structural basis of 5' triphosphate double-stranded RNA recognition by RIG-I C-terminal domain RIG-I detects viral genomic RNA during negative-strand RNA virus infection Structural and functional insights into 5'-ppp RNA pattern recognition by the innate immune receptor RIG-I The thermodynamic basis for viral RNA detection by the RIG-I innate immune sensor RIG-I ATPase activity and discrimination of self-RNA versus non-self-RNA Length-dependent recognition of doublestranded ribonucleic acids by retinoic acid -inducible gene-I and melanoma differentiation -associated gene 5 Activation of MDA5 requires higher-order RNA structures generated during virus infection MDA5 detects the double-stranded RNA replicative form in picornavirusinfected cells Visualisation of direct interaction of MDA5 and the dsRNA replicative intermediate form of positive strand RNA viruses A structure-based model of RIG-I activation Toward a crystal-clear view of the viral RNA sensing and response by RIG-I-like receptors Pattern recognition and signaling mechanisms of RIG-I and MDA5 Antiviral RNA recognition and assembly by RLR family innate immune sensors Post-translational control of intracellular pathogen sensing pathways Essential role of the N-terminal domain in the regulation of RIG-I ATPase activity Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA Structural and biochemical studies of RIG-I antiviral signaling Negative role of RIG-I serine 8 phosphorylation in the regulation of interferon-beta production Conventional protein kinase C-α (PKC-α) and PKC-β negatively regulate RIG-I antiviral signal transduction Phosphorylation of RIG-I by casein kinase II inhibits its antiviral response RIOK3-mediated phosphorylation of MDA5 interferes with its assembly and attenuates the innate immune response Dephosphorylation of the RNA sensors RIG-I and MDA5 by the phosphatase PP1 is essential for innate immune signaling Antagonism of the phosphatase PP1 by the measles virus V protein is required for innate immune escape of MDA5 HDAC6 regulates cellular viral RNA sensing by deacetylation of RIG-I The mechanism of ATP-dependent RNA unwinding by DEAD box proteins Mechanisms of RIG-I-like receptor activation and manipulation by viral pathogens The catcher in the RIG-I Viral RNA detection by RIG-I-like receptors MDA5 cooperatively forms dimers and ATP-sensitive filaments upon binding double-stranded RNA Riplet/RNF135, a RING finger protein, ubiquitinates RIG-I to promote interferon-beta induction during the early phase of viral infection REUL is a novel E3 ubiquitin ligase and stimulator of retinoic-acid-inducible gene-I A distinct role of Riplet-mediated K63-Linked polyubiquitination of the RIG-I repressor domain in human antiviral innate immune responses Ubiquitindependent and -independent roles of E3 ligase RIPLET in innate immunity TRIM25 RINGfinger ) RIG-I uses an ATPase-powered translocation-throttling mechanism for kinetic proofreading of RNAs and oligomerization Filament assemblies in foreign nucleic acid sensors IPS-1, an adaptor triggering RIG-I-and Mda5-mediated type I interferon induction VISA is an adapter protein required for virus-triggered IFN-β signaling Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-κB and IRF3 A common polymorphism in the caspase recruitment domain of RIG-I modifies the innate immune response of human dendritic cells Defective interfering particles with covalently linked [+/-]RNA induce interferon Structure and dynamics of the second CARD of human RIG-I provide mechanistic insights into regulation of RIG-I activation Pattern recognition receptors and inflammation Mitochondria in innate immunity Viral targeting of DEAD box protein 3 reveals its role in TBK1/IKKepsilon-mediated IRF activation Blockade of interferon beta, but not interferon alpha, signaling controls persistent viral infection The effects of dendritic cell hypersensitivity on persistent viral infection A role for neutrophils in viral respiratory disease.
    keywords: activation; antiviral; binding; card; cells; domain; dsrna; expression; helicase; host; immunity; infection; interferon; like; mavs; mda5; mechanisms; protein; recognition; response; rig; rna; signaling; trim25; type; ubiquitination; virus
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        item: #1288 of 1349
          id: cord-350906-ew04zzh6
      author: Khambhati, Khushal
       title: Current progress in CRISPR‐based diagnostic platforms
        date: 2018-10-26
       words: 2269
      flesch: 43
     summary: In SHERLOCK, the target sequence is amplified with recombinase polymerase amplification for DNA detection (RPA) or reverse transcriptase-recombinase polymerase amplification for RNA detection (RT-RPA), an isothermal, nucleic acid amplification technique that eliminates the use of thermal cycler. Tropical infectious diseases: diagnostics for the developing world Evaluating novel diagnostics in an outbreak setting: lessons learned from Ebola List of blueprint priority diseases Nucleic acid detection with CRISPR-Cas13a/C2c2 A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity Biology and applications of CRISPR systems: harnessing nature's toolbox for genome engineering Recent advances in CRISPR-Cas9 genome editing technology for biological and biomedical investigations Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system Expanding the genetic editing tool kit: ZFNs, TALENs, and CRISPR-Cas9 Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6 Field-deployable viral diagnostics using CRISPR-Cas13 Bacterial physiology: it's never too late for CRISPR RNases Lateral flow assays: principles, designs and labels Novel diagnostic technologies for clinical and frontline use: advanced diagnostics based on molecular markers and analysis technologies has been improving diagnosis across a wide range of diseases The authors declare that there are no conflicts of interest.
    keywords: crispr; detection; molecule; rna; sherlock; target
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        item: #1289 of 1349
          id: cord-351115-dy81dtnk
      author: Wang, Chen
       title: Identification of evolutionarily stable sites across the SARS-CoV-2 proteome
        date: 2020-10-20
       words: 6145
      flesch: 39
     summary: Overall, these results show that predicted ET drug sites can recover experimentally tested drug binding pockets and suggest new sites that can be targeted in computational docking approaches. In addition, because these sites are conserved across multiple coronavirus genera, these predicted ET drug sites are anticipated to be relevant for identifying inhibitors of SARS-CoV-2 as well as more distantly related coronaviruses.
    keywords: coronavirus; cov-2; covid-19; cross; drug; epitopes; information; protein; rankings; sars; sequence; sites; structure
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        item: #1290 of 1349
          id: cord-351365-dc9t3vh3
      author: Todt, Daniel
       title: Mutagenic Effects of Ribavirin on Hepatitis E Virus—Viral Extinction versus Selection of Fitness-Enhancing Mutations
        date: 2016-10-13
       words: 6337
      flesch: 36
     summary: From Error Catastrophe to Lethal Defection Counteracting quasispecies adaptability: Extinction of a ribavirin-resistant virus mutant by an alternative mutagenic treatment Potential benefits of sequential inhibitor-mutagen treatments of RNA virus infections Antiviral Strategies Based on Lethal Mutagenesis and Error Threshold Pegylated interferon-alpha for treating chronic hepatitis E virus infection after liver transplantation Treatment of chronic hepatitis E in liver transplant recipients with pegylated interferon alpha-2b Antiviral Activities of Different Interferon Types and Subtypes against Hepatitis E Virus Replication Disparity of basal and therapeutically activated interferon signalling in constraining hepatitis E virus infection Viral hepatitis during pregnancy Incidence and severity of viral hepatitis in pregnancy Following an overview of RNA viruses treated with RBV in clinics and a summary of the different antiviral modes of action of this drug, we focus on the mutagenic effect of RBV on HEV intrahost populations, and how HEV is able to overcome lethal mutagenesis.
    keywords: antiviral; effect; hcv; hepatitis; hev; infection; rbv; replication; ribavirin; rna; treatment; virus; viruses
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        item: #1291 of 1349
          id: cord-351377-xorj8tnz
      author: Kao, Chi-Fei
       title: The Characterization of Immunoprotection Induced by a cDNA Clone Derived from the Attenuated Taiwan Porcine Epidemic Diarrhea Virus Pintung 52 Strain
        date: 2018-10-04
       words: 5964
      flesch: 41
     summary: Swine enteric coronavirus disease: A review of 4 years with porcine epidemic diarrhoea virus and porcine deltacoronavirus in the United States and Canada Lactogenic immunity and vaccines for porcine epidemic diarrhea virus (PEDV): Historical and current concepts Porcine epidemic diarrhea virus: An emerging and re-emerging epizootic swine virus Experimental infection of a US spike-insertion deletion porcine epidemic diarrhea virus in conventional nursing piglets and cross-protection to the original US PEDV infection Previous infection of sows with a mild strain of porcine epidemic diarrhea virus confers protection against infection with a severe Evaluation of serological cross-reactivity and cross-neutralization between the United States porcine epidemic diarrhea virus prototype and S-INDEL-variant strains Evaluation of the efficacy of a commercial inactivated genogroup 2b-based porcine epidemic diarrhea virus (PEDV) vaccine and experimental live genogroup 1b exposure against 2b challenge Bioinformatics insight into the spike glycoprotein gene of field porcine epidemic diarrhea strains during 2011-2013 in Guangdong, China Distinct characteristics and complex evolution of PEDV strains Evaluation and Comparison of the Pathogenicity and Host Immune Responses Induced by a G2b Taiwan Porcine Epidemic Diarrhea Virus (Strain Pintung 52) and Its Highly Cell-Culture Passaged Strain in Conventional 5-Week-Old Pigs Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin Manipulation of the porcine epidemic diarrhea virus genome using targeted RNA recombination Genetic manipulation of porcine epidemic diarrhoea virus recovered from a full-length infectious cDNA clone Characterization of a pathogenic full-length cDNA clone of a virulent porcine epidemic diarrhea virus strain AH2012/12 in China Development of the full-length cDNA clones of two porcine epidemic diarrhea disease virus isolates with different virulence Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A Strategy for systematic assembly of large RNA and DNA genomes: transmissible gastroenteritis virus model An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol Efficacy of heat-labile enterotoxin B subunit-adjuvanted parenteral porcine epidemic diarrhea virus trimeric spike subunit vaccine in piglets Ribavirin-resistant variants of foot-and-mouth disease virus: the effect of restricted quasispecies diversity on viral virulence Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population Viral quasispecies Quasispecies Theory in Virology Virus-based vectors for gene expression in mammalian cells Coronaviruses as vectors: Stability of foreign gene expression Recombination in large RNA viruses: Coronaviruses. A new coronavirus-like particle associated with diarrhea in swine Genome organization of porcine epidemic diarrhoea virus New variants of porcine epidemic diarrhea virus, China Pathology of US Porcine Epidemic Diarrhea Virus Strain PC21A in Gnotobiotic Pigs Phylogenetic Analysis of the Spike (S) Gene of the New Variants of Porcine Epidemic Diarrhoea Virus in Taiwan
    keywords: cdna; cells; diarrhea; epidemic; figure; group; p96; pedvpt; piglets; porcine; titer; vero; virus
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        item: #1292 of 1349
          id: cord-351482-hzh5tyoo
      author: Peng, Xinxia
       title: Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection
        date: 2011-11-15
       words: 7714
      flesch: 40
     summary: small RNA loci to the corresponding expression ratios that we calculated for the overlapping miRNA precursors on the basis of the reads directly mapped to annotated precursor sequences. Also, we observed length distributions of small RNA loci overlapping an-notated small RNA loci that were similar to those of small RNA loci with no overlap (Fig. 3a) , indicating that our identified loci were indeed producing small RNAs.
    keywords: analysis; annotated; expression; infection; influenza; loci; mirnas; mouse; reads; rnas; samples; sars; small; virus
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        item: #1293 of 1349
          id: cord-351489-tzmev77c
      author: Yuan, Shuofeng
       title: Broad-Spectrum Host-Based Antivirals Targeting the Interferon and Lipogenesis Pathways as Potential Treatment Options for the Pandemic Coronavirus Disease 2019 (COVID-19)
        date: 2020-06-10
       words: 5058
      flesch: 27
     summary: The most prominent reduction in viral N antigen expression was observed in cells treated with Avonex, Rebif, Betaferon, and AM580, which achieved similar degree To quantify the anti-SARS-CoV-2 activity of the identified antiviral agents in the primary screening and the viral N antigen expression assay, SARS-CoV-2 viral load reduction assay by qRT-PCR was conducted to determine the SARS-CoV-2 RNA copies released in the cell culture supernatant with or without antiviral agent treatment. As To quantify the anti-SARS-CoV-2 activity of the identified antiviral agents in the primary screening and the viral N antigen expression assay, SARS-CoV-2 viral load reduction assay by qRT-PCR was conducted to determine the SARS-CoV-2 RNA copies released in the cell culture supernatant with or without antiviral agent treatment.
    keywords: agents; assay; cells; cov-2; hydroxycholesterol; ifn; load; reduction; rna; sars; viral; virus
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        item: #1294 of 1349
          id: cord-351520-c5fi2uoh
      author: Zhong, Bo
       title: Regulation of virus-triggered type I interferon signaling by cellular and viral proteins
        date: 2010-02-01
       words: 10652
      flesch: 30
     summary: However, over-produced type I IFNs cause excessive and harmful immune effects to the host (Theofilopoulos et al., 2005) . However, the overproduction of type I IFNs can cause unwanted or excessive immune responses that may lead to allergy, necrosis, autoimmune diseases and other harmful effects (Theofilopoulos et al., 2005) .
    keywords: activation; cells; domain; et al; expression; ifn; ifns; infection; inhibits; interferon; irf3; protein; receptor; rig; rna; signaling; tbk1; toll; type; virus
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        item: #1295 of 1349
          id: cord-351548-jvl63652
      author: Juranic Lisnic, Vanda
       title: Dual Analysis of the Murine Cytomegalovirus and Host Cell Transcriptomes Reveal New Aspects of the Virus-Host Cell Interface
        date: 2013-09-26
       words: 12013
      flesch: 45
     summary: A primary caveat of RNA-Seq analysis is determining whether changes in gene transcript levels are also reflected at the protein level. Our understanding of MCMV viral genes and genomes has evolved with the technology used to study them.
    keywords: analysis; annotation; cdna; clones; cytomegalovirus; data; expression; figure; genes; genome; host; infected; infection; library; mcmv; novel; protein; region; rna; seq; study; transcripts
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        item: #1296 of 1349
          id: cord-351559-az4pgi9k
      author: Turjya, Rafeed Rahman
       title: Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection
        date: 2020-06-29
       words: 2444
      flesch: 26
     summary: There 122 are direct RNA-RNA interactions for 4 genes, and RNA-protein interactions for the rest 123 ( Figure 2 ). 777 MOV10 Is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by 778 translocation along 3' UTRs 780 Identification of novel argonaute-associated proteins APOBEC3G inhibits 783 microRNA-mediated repression of translation by interfering with the interaction between 784 MicroRNA silencing through RISC recruitment of eIF6 Virus Escape and Manipulation of Cellular 788 Nonsense-Mediated mRNA Decay Provides Antiviral Activity against RNA Viruses by Enhancing RIG-I-MAVS-Independent 791 IFN Induction Not applicable.
    keywords: cell; cov-2; genes; infection; lncrnas; protein; rna; sars
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        item: #1297 of 1349
          id: cord-351837-vasuu70k
      author: Shannon, Ashleigh
       title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis
        date: 2020-09-17
       words: 6551
      flesch: 43
     summary: Accepted: 10 August 2020; Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage RNA 3′-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex Discovery of an RNA virus 3′→5′ exoribonuclease that is critically involved in coronavirus RNA synthesis High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants Understanding the mechanism of the broad-spectrum antiviral activity of favipiravir (T-705): key role of the F1 motif of the viral polymerase Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus Remdesivir is a direct-acting antiviral that inhibits RNAdependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency Nucleoside analogues for the treatment of coronavirus infections Favipiravir as a potential countermeasure against neglected and emerging RNA viruses Determining the mutation bias of favipiravir in influenza virus using next-generation sequencing Antiviral efficacy of favipiravir against Ebola virus: a translational study in cynomolgus macaques The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent Expression, purification, and characterization of SARS coronavirus RNA polymerase One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors Structure of the RNA-dependent RNA polymerase from COVID-19 virus Structure of replicating SARS-CoV-2 polymerase Continuous and discontinuous RNA synthesis in coronaviruses Synthesis of T-705-ribonucleoside and T-705-ribonucleotide and studies of chemical stability Cell line-dependent activation and antiviral activity of T-1105, the non-fluorinated analogue of T-705 (favipiravir) Prodrugs of the phosphoribosylated forms of hydroxypyrazinecarboxamide pseudobase T-705 and its de-fluoro analogue T-1105 as potent influenza virus inhibitors T-705 (Favipiravir) induces lethal mutagenesis in influenza A H1N1 viruses in vitro Extinction of west nile virus by favipiravir through lethal mutagenesis Lethal mutagenesis of hepatitis C virus induced by favipiravir Favipiravir elicits antiviral mutagenesis during virus replication in vivo Mechanism of action of T-705 ribosyl triphosphate against influenza virus RNA polymerase The ambiguous basepairing and high substrate efficiency of T-705 (Favipiravir) Ribofuranosyl 59-triphosphate towards influenza A virus polymerase Signatures of nucleotide analog incorporation by an RNAdependent RNA polymerase revealed using high-throughput magnetic tweezers Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics Polymerase (3Dpol): assembly of stable, elongation-competent complexes by using a symmetrical primer-template substrate (sym/sub) Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase A nucleobase-binding pocket in a viral RNA-dependent RNA polymerase contributes to elongation complex stability A quantitative stopped-flow fluorescence assay for measuring polymerase elongation rates Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases Assembly, purification, and pre-steady-state kinetic analysis of active RNA-dependent RNA polymerase elongation complex Characterization of the elongation complex of dengue virus RNA polymerase: assembly, kinetics of nucleotide incorporation, and fidelity Structure-function relationships underlying the replication fidelity of viral RNA-dependent RNA polymerases Viral mutation rates A comprehensive superposition of viral polymerase structures Nonstructural proteins 7 and 8 of feline coronavirus form a 2:1 heterotrimer that exhibits primer-independent RNA polymerase activity The SARScoronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension A second, non-canonical RNA-dependent RNA polymerase in SARS Coronavirus Identification and characterization of a human coronavirus 229E nonstructural protein 8-associated RNA 3′-terminal adenylyltransferase activity Global Kinetic Explorer: a new computer program for dynamic simulation and fitting of kinetic data In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication Phylogenetically based establishment of a dengue virus panel, representing all available genotypes, as a tool in dengue drug discovery Mutations in the chikungunya virus non-structural proteins cause resistance to favipiravir (T-705), a broad-spectrum antiviral We thank Magali Gilles and Karine Alvarez for excellent technical support, as well as Prs. C. Drosten and F. Drexler for providing the SARS-CoV-2 through EVA-GLOBAL (European Union's Horizon 2020 programme, GA 871029). As with all positive strand RNA viruses, an RdRp lies at the core of the viral replication machinery and for CoVs this is the nsp12 protein.
    keywords: antiviral; complex; cov; data; elongation; favipiravir; fig; incorporation; nsp12; polymerase; rdrp; rna; sars; supplementary; t-1105; t-705; virus
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        item: #1298 of 1349
          id: cord-351854-5s03f0pp
      author: Ben-Ami, Roni
       title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection
        date: 2020-04-22
       words: 3321
      flesch: 49
     summary: As shown in Figure 1 , positive samples were readily detected, even when their individual Ct ranged between 35 and 38. Alternatively, it is possible to dynamically adapt pooling sizes, when the measured rate of positive samples is different than expected.
    keywords: medrxiv; pooling; preprint; rna; samples; sars
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        item: #1299 of 1349
          id: cord-351864-zozrj7w5
      author: Chappleboim, A.
       title: ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection
        date: 2020-08-13
       words: 5787
      flesch: 51
     summary: After pooling samples are washed once in buffer A, twice in buffer B, and can then be kept in RNA later until they are processed further. To test cross-contamination levels in the RT stage, we hybridized positive (Ct 26) and negative samples with two differently barcoded primers, pooled them, performed RT and tested the amount of cross-contamination by barcode-specific qPCR ( Figure 3A and 3B).
    keywords: beads; figure; license; medrxiv; pcr; preprint; primers; rna; samples; sequencing
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        item: #1300 of 1349
          id: cord-351920-igmb2yfe
      author: Oma, Veslemøy Sunniva
       title: Bovine coronavirus in naturally and experimentally exposed calves; viral shedding and the potential for transmission
        date: 2016-06-13
       words: 5533
      flesch: 52
     summary: General depression and cough were the signs that correlated best with shedding of BCoV RNA, while peak respiratory rate and peak rectal temperature appeared more than a week later than the peak shedding. Although the calves were shedding BCoV RNA 21 days after infection the sentinel animals were not infected.
    keywords: bcov; bovine; calves; coronavirus; day; infection; nasal; rna; samples; shedding; viral; virus
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        item: #1301 of 1349
          id: cord-352088-9k01ej6l
      author: Saiz, Juan-Carlos
       title: Vaccines against RNA Viruses
        date: 2020-08-27
       words: 2344
      flesch: 32
     summary: Artificial anti-HIV-1 immunogen comprising epitopes of broadly neutralizing antibodies 2F5, 10E8, and a peptide mimic of VRC01 discontinuous epitope Parenterally administered P24-VP8* nanoparticle vaccine conferred strong protection against rotavirus diarrhea and virus shedding in gnotobiotic pigs Hepatitis C virus vaccine: Challenges and prospects Broad protection of pigs against heterologous PRRSV strains by a GP5-mosaic DNA vaccine prime/GP5-mosaic rVaccinia (VACV) vaccine boost Significant interference with porcine epidemic diarrhea virus pandemic and classical strain replication in small-intestine epithelial cells using an shRNA expression vector A single dose of dendrimer B 2 T peptide vaccine partially protects pigs against foot-and-mouth disease virus infection MVA vectored vaccines encoding rift valley fever virus glycoproteins protect mice against lethal challenge in the absence of neutralizing antibody responses Differential immune transcriptome and modulated signalling pathways in rainbow trout infected with Viral Haemorrhagic Septicaemia Virus (VHSV) and its Derivative Non-Virion (NV) gene deleted. [6] deepen their many years of previous research with peptides as vaccine candidates against foot-and mouth disease virus (FMDV).
    keywords: pigs; response; rna; vaccines; vhsv; virus; viruses
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        item: #1302 of 1349
          id: cord-352178-irjhmxsg
      author: Saxton-Shaw, Kali D.
       title: O'nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3
        date: 2013-01-24
       words: 5960
      flesch: 44
     summary: The use of chimeric Venezuelan equine encephalitis viruses as an approach for the molecular identification of natural virulence determinants Structural and nonstructural protein genome regions of eastern equine encephalitis virus are determinants of interferon sensitivity and murine virulence Vector infection determinants of Venezuelan equine encephalitis virus reside within the E2 envelope glycoprotein Determinants of vector specificity of o'nyong nyong and chikungunya viruses in Anopheles and Aedes mosquitoes Intracellular immunization of mosquito cells to LaCrosse virus using a recombinant Sindbis virus vector Manual for Mosquito Rearing and Experimental Techniques Virulence variation among isolates of western equine encephalitis virus in an outbred mouse model Lineage replacement accompanying duplication and rapid fixation of an RNA element in the nsP3 gene in a species of alphavirus Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences Evolutionary conservation of histone macroH2A subtypes and domains Functions of alphavirus nonstructural proteins in RNA replication Amino acid mutations in the replicase protein nsP3 of Semliki Forest virus cumulatively affect neurovirulence Deletion and duplication mutations in the C-terminal nonconserved region of Sindbis virus nsP3: effects on phosphorylation and on virus replication in vertebrate and invertebrate cells SH3 Domain-Mediated Recruitment of Host Cell Amphiphysins by Alphavirus nsP3 Promotes Viral RNA Replication Deletions in the hypervariable domain of the nsP3 gene attenuate Semliki Forest virus virulence In vitro synthesis of infectious venezuelan equine encephalitis virus RNA from a cDNA clone: analysis of a viable deletion mutant Semliki Forest virusspecific non-structural protein nsP3 is a phosphoprotein Phosphorylation of Sindbis virus nsP3 in vivo and in vitro Elimination of phosphorylation sites of Semliki Forest virus replicase protein nsP3 Phosphorylation site analysis of Semliki forest virus nonstructural protein 3 Deletion mapping of Sindbis virus DI RNAs derived from cDNAs defines the sequences essential for replication and packaging Mutagenesis of the 39 nontranslated region of Sindbis virus RNA The 39 untranslated region of sindbis virus represses deadenylation of viral transcripts in mosquito and Mammalian cells We would like to thank Andrea Peterson for maintaining the An. gambiae, G3 colony used in this study. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%.
    keywords: chikv; chimeric; gambiae; genome; infection; mosquito; nsp3; onnv; rates; region; replication; virus; viruses
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        item: #1303 of 1349
          id: cord-352200-i05h8csb
      author: Xu, Yi
       title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus
        date: 2012-04-27
       words: 5289
      flesch: 41
     summary: During this time, non-viruliferous WBPH, as the control group, were treated identically. Biology and epidemiology of rice virus Southern rice blackstreaked dwarf virus: A new proposed Fijivirus species in the family Reoviridae Molecular characterization of segments S7 to S10 of a southern rice black-streaked dwarf virus isolate from maize in northern China A black-streaked dwarf disease on rice in China is caused by a novel fijivirus Virus taxonomy: classification and nomenclature of viruses.
    keywords: analysis; expression; figure; genes; infection; pathway; proteasome; protein; rice; rna; srbsdv; table; unigenes; virus; viruses; wbph
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        item: #1304 of 1349
          id: cord-352361-jh31omg2
      author: Nobach, Daniel
       title: No evidence for European bats serving as reservoir for Borna disease virus 1 or other known mammalian orthobornaviruses
        date: 2020-01-30
       words: 3760
      flesch: 37
     summary: Spiking of bat RNA with serial dilutions of various orthobornavirus-RNA demonstrated the detection limit of 5000 orthobornavirus copies in 660 ng RNA. Although the bicolored white-toothed shrew has been identified as indigenous reservoir of BoDV-1, other potential reservoirs or animal carriers are still unknown so that further investigations of small mammals including bat species are urgently needed.
    keywords: bats; bodv-1; control; disease; orthobornavirus; rna; species; virus; viruses
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        item: #1305 of 1349
          id: cord-352379-q5inrxcm
      author: Lai, Michael M. C.
       title: SARS virus: The beginning of the unraveling of a new coronavirus
        date: 2003-10-17
       words: 7005
      flesch: 45
     summary: key: cord-352379-q5inrxcm authors: Lai, Michael M. C. title: SARS virus: The beginning of the unraveling of a new coronavirus date: 2003-10-17 journal: J Biomed Sci DOI: 10.1007/bf02256318 sha: doc_id: 352379 cord_uid: q5inrxcm Severe acute respiratory syndrome (SARS) virus caused a severe outbreak in several regions of the world in 2003. The comparative studies of other coronaviruses offer insights into the understanding of SARS virus.
    keywords: cells; coronavirus; gene; genome; group; infection; mhv; protein; recombination; rna; sars; sars virus; vaccines; virus
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        item: #1306 of 1349
          id: cord-352465-n746e8qt
      author: Wang, Fei
       title: Targeting stress granules: A novel therapeutic strategy for human diseases
        date: 2020-08-16
       words: 9163
      flesch: 35
     summary: TIA1 oxidation inhibits stress granule assembly and sensitizes cells to stress-induced apoptosis Stress granules and cell signaling: more than just a passing phase? Cap-dependent, scanning-free translation initiation mechanisms Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets Phosphorylation of Eukaryotic Translation Initiation Factor 2 Mediates Apoptosis in Response to Activation of the Double-stranded RNA-dependent Protein Kinase Stress granules: the Tao of RNA triage Regulated Translation Initiation Controls Stress-Induced Gene Expression in Mammalian Cells Kinase-mediated Phosphorylation of Eukaryotic Translation Initiation Factor 2 Inhibits Translation, Induces Stress Granule Formation, and Mediates Survival upon Arsenite Exposure Perk Is Essential for Translational Regulation and Cell Survival during the Unfolded Protein Response Stressful initiations Vinca alkaloid drugs promote stress-induced translational repression and stress granule formation Hippuristanol-A potent steroid inhibitor of eukaryotic initiation factor 4A Hydrogen peroxide induces stress granule formation independent of eIF2α phosphorylation Eukaryotic Initiation Factor 2α-independent Pathway of Stress Granule Induction by the Natural Product Pateamine A Inhibition of ribosome recruitment induces stress granule formation independently of eukaryotic initiation factor 2α phosphorylation Stress Granule Assembly Is Mediated by Prion-like Aggregation of TIA-1 The RasGAPassociated endoribonuclease G3BP assembles stress granules Unravelling the ultrastructure of stress granules and associated P-bodies in human cells Principles and Properties of Stress Granules Liquid phase condensation in cell physiology and disease Distinct stages in stress granule assembly and disassembly P bodies promote stress granule assembly in Saccharomyces cerevisiae Possible Roles in the Control of Translation and mRNA Degradation Eukaryotic stress granules are cleared by granulophagy and Cdc48/VCP function A Surveillance Function of the HSPB8-BAG3-HSP70 Chaperone Complex Ensures Stress Granule Integrity and Dynamism Stress granules: sites of mRNA triage that regulate mRNA stability and translatability Dynein and kinesin regulate stressgranule and P-body dynamics Translation inhibition and stress granules in the antiviral immune response Stress granules and neurodegeneration The involvement of stress granules in aging and aging-associated diseases Stress granule: A promising target for cancer treatment Cytoplasmic stress granules: Dynamic modulators of cell signaling and disease Differences between acute and chronic stress granules, and how these differences may impact function in human disease Selenite targets eIF4E-binding protein-1 to inhibit translation initiation and induce the assembly of non-canonical stress granules The chemotherapeutic agent bortezomib induces the formation of Formation of stress granules inhibits apoptosis by suppressing stress-responsive MAPK pathways RhoA/ROCK1 signaling regulates stress granule formation and apoptosis Inhibition of mTORC1 by astrin and stress granules prevents apoptosis in cancer cells The chemotherapeutic drug 5-fluorouracil promotes PKR-mediated apoptosis in a p53-independent manner in colon and breast cancer cells Stress Granule-Inducing Eukaryotic Translation Initiation Factor 4A Inhibitors Block Influenza A Virus Replication DHX36 enhances RIG-I signaling by facilitating PKR-mediated antiviral stress granule formation Regulation of stress granules in virus systems Mammalian Orthoreovirus Particles Induce and Are Recruited into Stress Granules at Early Times Postinfection Influenza A virus inhibits cytoplasmic stress granule formation Respiratory Syncytial Virus Induces Host RNA Stress Granules To Facilitate Viral Replication Mouse hepatitis coronavirus replication induces host translational shutoff and mRNA decay, with concomitant formation of stress granules and processing bodies Picornavirus 2A protease regulates stress granule formation to facilitate viral translation Stress granules (SG) and processing bodies (PB) in viral infections SARS-CoV-2 Nucleocapsid Protein Impairs SG Assembly by Partitioning into G3BP Condensate Nucleocapsid protein of SARS-CoV-2 phase separates into RNArich polymerase-containing condensates A SARS-CoV-2 protein interaction map reveals targets for drug repurposing The Global Phosphorylation Landscape of SARS-CoV-2 Infection Relation Between Stress Granules and Cytoplasmic Protein Aggregates Linked to Neurodegenerative Diseases Emerging small-molecule therapeutic approaches for amyotrophic lateral sclerosis and frontotemporal dementia Converging Mechanisms in ALS and FTD: Check your RNA granule aggregation A Systematic Survey Identifies Prions and Illuminates Sequence Features of Prionogenic Proteins A new subtype of frontotemporal lobar degeneration with FUS pathology TDP-43 is a component of ubiquitin-positive tau-negative inclusions in frontotemporal lobar degeneration and amyotrophic lateral sclerosis Ubiquitinated TDP-43 in Frontotemporal Lobar Degeneration and Amyotrophic Lateral Sclerosis Polyglutamine-Expanded Huntingtin Exacerbates Age-Related Disruption of Nuclear Integrity and Nucleocytoplasmic Transport Cytoplasmic protein aggregates interfere with nucleocytoplasmic transport of protein and RNA Dissecting the molecular mechanisms that impair stress granule formation in aging cells Stress granules counteract senescence by sequestration of PAI-1 DDX3X acts as a live-or-die checkpoint in stressed cells by regulating NLRP3 inflammasome Activation of the integrated stress response during T helper cell differentiation Sequestration of TRAF2 into stress granules interrupts tumor necrosis factor signaling under stress conditions Presence and function of stress granules in atrial fibrillation The Kinase Inhibitor Sorafenib Induces Cell Death through a Process Involving Induction of Endoplasmic Reticulum Stress Sorafenib, a multikinase inhibitor, induces formation of stress granules in hepatocarcinoma cells Clinical Pharmacology of 5-Fluorouracil 5-Fluorouracil affects assembly of stress granules based on RNA incorporation Proteasome inhibitors in cancer therapy Psammaplysin F increases the efficacy of bortezomib and sorafenib through regulation of stress granule formation Psammaplysin F, a New Bromotyrosine Derivative from a Sponge, Aplysinella sp Modulation of p-eIF2α cellular levels and stress granule assembly/disassembly by trehalose Structural insights into ISRIB, a memory-enhancing inhibitor of the integrated stress response Protein synthesis in eukaryotes: the growing biological relevance of cap-independent translation initiation The Unfolded Protein Response Triggers Selective mRNA Release from the Endoplasmic Reticulum The small molecule ISRIB reverses the effects of eIF2α phosphorylation on translation and stress granule assembly Nitric oxide triggers the assembly of type II stress granules linked to decreased cell viability Inactivation of the mTORC1-Eukaryotic Translation Initiation Factor 4E Pathway Alters Stress Granule Formation Role of the malonyl-CoA synthetase ACSF3 in mitochondrial metabolism Malonate induces the assembly of cytoplasmic stress granules Molecular Pathways: The eIF4F Translation Initiation Complex-New Opportunities for Cancer Treatment 15-Deoxy-∆-12,14-Prostaglandin J2 (15d-PGJ2), an Endogenous Ligand of PPAR-γ: Function and Mechanism Translational Dysregulation by Pateamine A A comparative study of small molecules targeting eIF4A Active-site inhibitors of mTOR target rapamycin-resistant outputs of mTORC1 and mTORC2 Mammalian Target of Rapamycin Inhibitor Reveals Rapamycin-resistant Functions of mTORC1 Mass Spectrometry Analysis of a Protein Kinase CK2β Subunit Interactome Isolated from Mouse Brain by Affinity Chromatography One-thousand-and-one substrates of protein kinase CK2?
    keywords: apoptosis; assembly; cancer; cells; disassembly; diseases; eif2α; formation; granules; inhibitor; initiation; mrna; phosphorylation; protein; response; sgs; stress; tdp-43; translation
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        item: #1307 of 1349
          id: cord-352664-heoj8ji8
      author: Hubbard, Amelia
       title: Field pathogenomics reveals the emergence of a diverse wheat yellow rust population
        date: 2015-02-25
       words: 9186
      flesch: 41
     summary: To assess the genetic diversity both within and between PST population clusters, all heterokaryotic and homokaryotic SNPs determined above from individual alignment of each isolate to the PST-130 reference were incorporated into a synthetic gene set for that isolate. Based on this evidence, we hypothesize that the change in PST population structure may have arisen from exotic incursions from multiple sources over recent years.
    keywords: analysis; cluster; data; field; genome; isolates; pathogen; population; pst; pst field; pst isolates; pst population; rna; samples; sequencing; sites; snp; wheat
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        item: #1308 of 1349
          id: cord-352768-16vgnq14
      author: Tang, Qingquan
       title: Application of siRNA Against SARS in the Rhesus Macaque Model
        date: 2008
       words: 4390
      flesch: 35
     summary: Observations of SCV-induced SARS-like symptoms, measurements of SCV RNA presence in the respiratory tract, microscopic inspections of lung histopathology, and immunohistochemistry sections from 21 tested macaques consistently demonstrated siRNA-mediated anti-SCV activity. The antiviral effect of interferon-against SARS-coronavirus is not mediated by MxA protein Interferonbeta and interferon-gamma synergistically inhibit the replication of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) Pegylated interferonprotects type 1 pneumocytes against SARS coronavirus infection in macaques Macaque model for severe acute respiratory syndrome Histological changes in SARS-CoV infected rhesus monkeys Virologic and serologic detection of SARS-CaV in infected rhesus monkey Recombinant modified vaccinia virus Ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies primarily targeting the receptor binding region An animal model of SARS produced by infection of Macaca mulatta with SARS coronavirus Inhibition of virus replication by RNA interference Phenotypic silencing of cytoplasmic genes using sequence-specific double-stranded short interfering RNA and its application in the reverse genetics of wild type negative-strand RNA viruses Prophylactic and therapeutic effects of small interfering RNA targeting SARS-coronavirus SARS virus inhibited by siRNA.
    keywords: coronavirus; fig; lung; macaque; model; sars; scv; sirna; sisc2; study; syndrome
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        item: #1309 of 1349
          id: cord-352814-fcl2g5wr
      author: Balboni, Andrea
       title: A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys
        date: 2011-11-22
       words: 4005
      flesch: 39
     summary: The interassay variability was tested on bat samples by testing the three samples with different viral concentrations (B1, B2, and B3) in triplicate on three different days (Table 2) . Bat samples were considered positive if the mean of three replicates was greater than the LOD.
    keywords: bat; bats; coronavirus; like; pcr; plasmid; rna; sars; standard; time
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        item: #1310 of 1349
          id: cord-352891-ljmkqdzx
      author: Parang, Keykavous
       title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E)
        date: 2020-05-17
       words: 3177
      flesch: 47
     summary: 3-azido-2,3-dideoxythymidine (AZT) Treatment of chronic hepatitis B in HIV co-infected patients Emtricitabine, a new antiretroviral agent with activity against HIV and hepatitis B virus Emtricitabine (FTC) for the treatment of HIV infection Synthesis and anti-HIV activities of phosphate triester derivatives of 3 -fluoro-2 ,3 -dideoxythymidine and 3 -azido-2 ,3 -dideoxythymidine Synthesis and biological evaluation of fatty acyl ester derivatives of 2 ,3 -didehydro-2 ,3 -dideoxythymidine Synthesis and biological evaluation of fatty acyl ester derivatives of (-)-2 ,3 -dideoxy-3 -thiacytidine Emtricitabine prodrugs with improved anti-HIV activity and cellular uptake Structure of the RNA-dependent RNA polymerase from COVID-19 virus We acknowledge ImQuest Biosciences for assistance in conducting the antiviral assays. Human Coronaviruses: A Review of Virus-Host Interactions Coronavirus 229E-related pneumonia in immunocompromised patients Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia Human coronaviruses A Rare Case of Human Coronavirus 229E Associated with Acute Respiratory Distress Syndrome in a Healthy Adult Prophylactic and therapeutic remdesivir (GS-5734) treatment in the rhesus macaque model of MERS-CoV infection Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses Compassionate Use of Remdesivir for Patients with Severe Covid-19 Coronavirus Susceptibility to the Antiviral Remdesivir (GS-5734) Is Mediated by the Viral Polymerase and the Proofreading Exoribonuclease Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019-nCoV Arguments in favour of remdesivir for treating SARS-CoV-2 infections Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase RNA-dependent DNA polymerases Anti-HIV activity of adefovir (PMEA) and PMPA in combination with antiretroviral compounds: In vitro analyses Anti-human immunodeficiency virus activity and cellular metabolism of a potential prodrug of the acyclic nucleoside phosphonate 9-R-(2-phosphonomethoxypropyl)adenine (PMPA) 2 -deoxy-4 -C-ethynyl-2-fluoroadenosine: A nucleoside reverse transcriptase inhibitor with highly potent activity against wide spectrum of HIV-1 strains, favorable toxic profiles, and stability in plasma Concise synthesis of the anti-HIV nucleoside EFdA 3 -substituted 2 ,3 -dideoxynucleoside analogues as potential anti-HIV (HTLV-III/LAV) agents Synthesis, in vitro anti-HIV activity, and biological stability of 5 -O-myristoyl analogue derivatives of 3 -fluoro-2 ,3 -dideoxythymidine (FLT) as potential bifunctional prodrugs of FLT In vitro anti-hepatitis B virus activities of 5-O-myristoyl analogue derivatives of 3-fluoro-2,3-dideoxythymidine (FLT) and
    keywords: activity; compounds; coronaviruses; hcov-229e; hiv; remdesivir; rna; sars
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        item: #1311 of 1349
          id: cord-352991-duqkpkll
      author: Waghmare, Alpana
       title: Respiratory Syncytial Virus Lower Respiratory Disease in Hematopoietic Cell Transplant Recipients: Viral RNA Detection in Blood, Antiviral Treatment, and Clinical Outcomes
        date: 2013-09-24
       words: 5113
      flesch: 40
     summary: Interestingly, our study did not show a substantial effect of lymphopenia or steroid use up to 2 mg/kg on RSV RNA detection, indicating that moderate immune suppression does not impact blood RSV RNA detection. Among these patients, BAL viral load above the median (>1.8 × 10 6 copies/mL) was associated with an increased risk of serum RSV RNA detection (HR, 1.74 [95% CI, .74-4.13], P = .21) in univariate analysis.
    keywords: day; detection; lrd; models; patients; ribavirin; rna; rsv; virus
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        item: #1312 of 1349
          id: cord-353274-wozwpvpq
      author: Borremans, B.
       title: Quantifying antibody kinetics and RNA shedding during early-phase SARS-CoV-2 infection
        date: 2020-05-20
       words: 6166
      flesch: 40
     summary: Raw antibody detection probability data are provided in Supplementary Information S1. For the estimation of seroconversion times, 270 data points from 99 individuals were used for IgG, and 240 data points from 71 individuals for IgM. Mean IgG seroconversion time is 13.3 days post symptom onset (dpo) when using ELISA-NP, and 12.6 dpo for IgM using ELISA-Spike (Figure 1a) .
    keywords: antibody; data; igg; license; medrxiv; preprint; sars; time
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        item: #1313 of 1349
          id: cord-353290-1wi1dhv6
      author: Kustin, Talia
       title: Biased mutation and selection in RNA viruses
        date: 2020-09-28
       words: 7615
      flesch: 42
     summary: One major challenge in tackling RNA viruses is the fact they are extremely genetically diverse. RNA viruses are an extremely diverse collection of entities, spanning a diverse range of hosts, morphologies, genome organizations, and genetic composition.
    keywords: bias; branches; codon; fig; genomes; host; mutation; nucleotide; rna; selection; sequences; usage; viruses
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        item: #1314 of 1349
          id: cord-353342-2n6kqyeo
      author: Corman, Victor M.
       title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection
        date: 2016-02-15
       words: 4051
      flesch: 50
     summary: WHO/MERS/RA/15 MERS-CoV outbreak in Jeddah-a link to health care facilities An observational, laboratory-based study of outbreaks of Middle East respiratory syndrome coronavirus in Jeddah and Riyadh, Kingdom of Saudi Arabia Preliminary epidemiological assessment of MERS-CoV outbreak in South Korea The aetiology, origins, and diagnosis of severe acute respiratory syndrome Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections Infectious Middle East respiratory syndrome coronavirus excretion and serotype variability based on live virus isolates from patients in Saudi Arabia Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC Transmission of MERS-coronavirus in household contacts Presence of Middle East respiratory syndrome coronavirus antibodies in Saudi Arabia: a nationwide, cross-sectional, serological study Antibodies against MERS coronavirus in dromedary camels Middle East respiratory syndrome Respiratory tract samples, viral load, and genome fraction yield in patients with Middle East respiratory syndrome Evaluation of advanced reverse transcription-PCR assays and an alternative PCR target region for detection of severe acute respiratory syndrome-associated coronavirus Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays The epidemiology of severe acute respiratory syndrome in the 2003 Hong Kong epidemic: an analysis of all 1755 patients Detection of SARS coronavirus in patients with suspected SARS Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study Efficient replication of the novel human betacoronavirus EMC on primary human epithelium highlights its zoonotic potential Detection of SARS coronavirus in plasma by real-time RT-PCR Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome Detection of severe acute respiratory syndrome coronavirus RNA in plasma during the course of infection Multiple organ infection and the pathogenesis of SARS Chemokine up-regulation in SARS-coronavirus-infected, monocyte-derived human dendritic cells SARS-coronavirus replicates in mononuclear cells of peripheral blood (PBMCs) from SARS patients SARS-coronavirus replication in human peripheral monocytes/macrophages Acute renal impairment in coronavirusassociated severe acute respiratory syndrome Enteric involvement of severe acute respiratory syndrome-associated coronavirus infection Contact investigation of a case of human novel coronavirus infection treated in a German hospital Acknowledgments. As in SARS, kidney failure in MERS patients might well be explained by severe inflammatory reaction combined with the administration of potentially nephrotoxic drugs during intensive care
    keywords: cases; coronavirus; cov; mers; patients; rna; samples; sars; syndrome
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        item: #1315 of 1349
          id: cord-353475-dtn7h1gj
      author: Haddad, Hazem
       title: miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East
        date: 2020-08-20
       words: 1465
      flesch: 51
     summary: Many miRNA sequences that targeted Influenza viral RNA segments were linked with the activity of host miRNA-induced antiviral defense. key: cord-353475-dtn7h1gj authors: Haddad, Hazem; Walid Al-Zyoud title: miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East date: 2020-08-20 journal:
    keywords: hsa; rna
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        item: #1316 of 1349
          id: cord-353484-q7d0ysbo
      author: Liu, Xue
       title: COVID-19: Progress in diagnostics, therapy and vaccination
        date: 2020-06-19
       words: 8584
      flesch: 33
     summary: medRxiv Coronaviruses -drug discovery and therapeutic options Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro First Case of 2019 Novel Coronavirus in the United States Compassionate Use of Remdesivir for Patients with Severe Covid-19 Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial Effects of chloroquine on viral infections: an old drug against today's diseases? Efficacy of hydroxychloroquine in patients with COVID-19: results of a randomized clinical trial Breakthrough: Chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies Treating COVID-19 with Chloroquine Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial Clinical efficacy of hydroxychloroquine in patients with covid-19 pneumonia who require oxygen: observational comparative study using routine care data Hydroxychloroquine in patients with mainly mild to moderate coronavirus disease 2019: open label, randomised controlled trial Comparative efficacy and safety of second-line antiretroviral therapy for treatment of HIV/AIDS: a systematic review and network meta-analysis Optimizing use of theranostic nanoparticles as a life-saving strategy for treating COVID-19 patients Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV Role of lopinavir/ritonavir in the treatment of SARS: initial virological and clinical findings Consideration of highly active antiretroviral therapy in the prevention and treatment of severe acute respiratory syndrome Screening of an FDA-approved compound library identifies four small-molecule inhibitors of Middle East respiratory syndrome coronavirus replication in cell culture Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase A phase 1/2 trial to evaluate the pharmacokinetics, safety, and efficacy of NI-03 in patients with chronic pancreatitis: study protocol for a randomized controlled trial on the assessment of camostat treatment in chronic pancreatitis (TACTIC) Experimental drugs poised for use in Ebola outbreak Mechanism of Inhibition of Ebola Virus RNA-Dependent RNA Polymerase by Remdesivir Chloroquine is a potent inhibitor of SARS coronavirus infection and spread SARS-CoV-2: Recent Reports on Antiviral Therapies Based on Lopinavir/Ritonavir, Darunavir/Umifenovir, Hydroxychloroquine, Remdesivir, Favipiravir and Other Drugs for the Treatment of the New Coronavirus Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro Pharmacologic Treatments for Coronavirus Disease 2019 (COVID-19): A Review Experimental Treatment with Favipiravir for COVID-19: An Open-Label Control Study. Revised 18 Engineering DNA vaccines against infectious diseases Safety and immunogenicity of an anti-Middle East respiratory syndrome coronavirus DNA vaccine: a phase 1, open-label, single-arm, dose-escalation trial Immunogenicity of a DNA vaccine candidate for COVID-19 Safety, tolerability, and immunogenicity of a recombinant adenovirus type-5 vectored COVID-19 vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial ChAdOx1 nCoV-19 vaccination prevents SARS-CoV-2 pneumonia in rhesus macaques Safety of trivalent inactivated influenza vaccines in adults: background for pandemic influenza vaccine safety monitoring Inactivated poliovirus vaccine: past and present experience Safety and Immunogenicity Study of Inactivated Vaccine for Prophylaxis of SARS CoV-2 Infection (COVID-19) Novavax Initiates Phase 1/2 Clinical Trial of COVID-19 Vaccine.
    keywords: antibodies; antibody; coronavirus; cov-2; covid-19; detection; disease; human; infection; novel; patients; protein; receptor; sars; specific; treatment; trial; vaccines
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        item: #1317 of 1349
          id: cord-353524-3w970ycx
      author: Dömling, Alexander
       title: Chemistry and Biology of SARS-CoV-2
        date: 2020-05-22
       words: 3961
      flesch: 46
     summary: Several approved HIV protease inhibitors (15, 16, and 18) were previously repurposed for the treatment of SARS (Scheme 2). The reported case-fatality rate of COVID-19 is %3% and is thus rather low as compared with SARS (30% , Table 1 ).
    keywords: coronavirus; cov-2; covid-19; drug; inhibitors; potential; protease; protein; rna; sars
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        item: #1318 of 1349
          id: cord-353576-f29kmtot
      author: Maricic, T.
       title: A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2
        date: 2020-06-26
       words: 3502
      flesch: 54
     summary: (B) Correlation of Ct values between direct NEB assays and RNA extraction followed by Roche assays for mouthwash samples positive with both methods. To systematically investigate how the NEB Luna assay performs compared to RNA extraction followed by the Roche assay for mouthwash samples, we investigated 62 gargle lavages from patients that were either negative or presented with various viral loads based on previous investigations.
    keywords: individuals; license; medrxiv; preprint; samples; sars
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        item: #1319 of 1349
          id: cord-353640-giznbcpd
      author: Barza, Ruby
       title: Use of a Simplified Sample Processing step without RNA Extraction for direct SARS-CoV-2 RT-PCR Detection
        date: 2020-08-11
       words: 1206
      flesch: 37
     summary: The authors declare that there are no conflicts of interest This work received no specific grant from any funding agency J o u r n a l P r e -p r o o f Response and the President's Plan for Opening America Up Again Failing the Test -The Tragic Data Gap Undermining the U.S. Pandemic Response Access to Lifesaving Medical Resources for African Countries: COVID-19 Testing and Response, Ethics, and Politics Direct RT-qPCR detection of SARS-COV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step Development of a TaqMan® RT-PCR assay without RNA extraction step for the detection and quantification of African Chikungunya viruses Bei Resources Product Information Sheet for NR-52286 Use of reverse transcription and PCR to discriminate between infectious and non-infectious hepatitis A virus The authors would like to thank ChromaCode for providing the ChromaCode HDPCR™ SARS-CoV-2 Research Use Only (ChromaCode RUO) assay kit We found that the direct detection of SARS-CoV-2 using a 65°C heat inactivation and release step for 20minutes without RNA extraction and purification performed very well compared to the use of an automated RNA extraction instrument.
    keywords: extraction; heat; release; rna
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        item: #1320 of 1349
          id: cord-353703-u86ggw11
      author: Gao, Peng
       title: Reprogramming the unfolded protein response for replication by porcine reproductive and respiratory syndrome virus
        date: 2019-11-18
       words: 8293
      flesch: 42
     summary: This coincided with detectable viral protein expression (here assayed for N; Fig 3A and 3B ), but it occurred earlier than peak virus replication, which was at 36 hpi in MARC-145 cells ( Fig 3G) and 24 hpi in PAMs (Fig 3H) . The unfolded protein response: from stress pathway to homeostatic regulation The unfolded protein response Intracellular signaling by the unfolded protein response Signal integration in the endoplasmic reticulum unfolded protein response The Unfolded Protein Response and Cell Fate Control Dynamic interaction of BiP and ER stress transducers in the unfolded-protein response Master Regulator of the Unfolded Protein Response and Crucial Factor in Flavivirus Biology Dissociation of Kar2p/BiP from an ER sensory molecule, Ire1p, triggers the unfolded protein response in yeast Coping with stress: eIF2 kinases and translational control Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells Regulated translation initiation controls stress-induced gene expression in mammalian cells An integrated stress response regulates amino acid metabolism and resistance to oxidative stress Transcription factor ATF4 directs basal and stress-induced gene expression in the unfolded protein response and cholesterol metabolism in the liver TRB3, a novel ER stress-inducible gene, is induced via ATF4-CHOP pathway and is involved in cell death Activating transcription factor 4 In vitro reconstitution of ER-stress induced ATF6 transport in COPII vesicles The luminal domain of ATF6 senses endoplasmic reticulum (ER) stress and causes translocation of ATF6 from the ER to the Golgi Underglycosylation of ATF6 as a novel sensing mechanism for activation of the unfolded protein response ATF6 Is a Transcription Factor Specializing in the Regulation of Quality Control Proteins in the Endoplasmic Reticulum ER stress signaling by regulated splicing: IRE1/ HAC1/XBP1 Intracellular signaling from the endoplasmic reticulum to the nucleus: the unfolded protein response in yeast and mammals Decay of endoplasmic reticulum-localized mRNAs during the unfolded protein response RNA surveillance is required for endoplasmic reticulum homeostasis XBP1: a link between the unfolded protein response, lipid biosynthesis, and biogenesis of the endoplasmic reticulum The Multiple Roles of XBP1 in Regulation of Glucose and Lipid Metabolism A review of the mammalian unfolded protein response Innate Sensing of Influenza A Virus Hemagglutinin Glycoproteins by the Host Endoplasmic Reticulum (ER) Stress Pathway Triggers a Potent Antiviral Response via ER-Associated Protein Degradation Antiviral activity of an isatin derivative via induction of PERK-Nrf2-mediated suppression of cap-independent translation Roles of Endoplasmic Reticulum Stress in Immune Responses Cross talk between ER stress, oxidative stress, and inflammation in health and disease Crosstalk of ER stress-mediated autophagy and ER-phagy: Involvement of UPR and the core autophagy machinery FXR Inhibits Endoplasmic Reticulum Stress-Induced NLRP3 Inflammasome in Hepatocytes and Ameliorates Liver Injury The expanding roles of endoplasmic reticulum stress in virus replication and pathogenesis Nidovirales: a new order comprising Coronaviridae and Arteriviridae Reorganization and expansion of the nidoviral family Arteriviridae Mystery swine disease in The Netherlands: the isolation of Lelystad virus Pathogenesis and control of the Chinese highly pathogenic porcine reproductive and respiratory syndrome virus Emergence of fatal PRRSV variants: unparalleled outbreaks of atypical PRRS in China and molecular dissection of the unique hallmark Importation and Recombination Are Responsible for the Latest Emergence of Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus in China Porcine reproductive and respiratory syndrome virus: a persistent infection Genotype 2 Strains of Porcine Reproductive and Respiratory Syndrome Virus Dysregulate Alveolar Macrophage Cytokine Production via the Unfolded Protein Response The ER chaperone and signaling regulator GRP78/BiP as a monitor of endoplasmic reticulum stress Japanese encephalitis virus infection initiates endoplasmic reticulum stress and an unfolded protein response Endoplasmic reticulum stress is induced and modulated by enterovirus 71 Induction of the unfolded protein response (UPR) during Marek's disease virus (MDV) infection.
    keywords: anti; atf4; cells; control; expression; fig; grp78; infection; marc-145; protein; prrsv; replication; response; reticulum; rna; stress; upr; virus; xbp1s
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        item: #1321 of 1349
          id: cord-353810-mf753ae9
      author: Tan, Cedric Chih Shen
       title: A novel method for the capture-based purification of whole viral native RNA genomes
        date: 2019-04-08
       words: 5950
      flesch: 49
     summary: key: cord-353810-mf753ae9 authors: Tan, Cedric Chih Shen; Maurer-Stroh, Sebastian; Wan, Yue; Sessions, October Michael; de Sessions, Paola Florez title: A novel method for the capture-based purification of whole viral native RNA genomes date: 2019-04-08 journal: AMB Express DOI: 10.1186/s13568-019-0772-y sha: doc_id: 353810 cord_uid: mf753ae9 Current technologies for targeted characterization and manipulation of viral RNA primarily involve amplification or ultracentrifugation with isopycnic gradients of viral particles to decrease host RNA background. We report that this protocol was able to successfully purify viral RNA by 561- to 791-fold.
    keywords: capture; denv1; direct; host; method; pcr; post; purification; rna; sequencing; strategy; viral
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        item: #1322 of 1349
          id: cord-354003-ko45l1qv
      author: Scarpin, M Regina
       title: Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation
        date: 2020-10-15
       words: 16889
      flesch: 36
     summary: Total RNA was extracted from one set of samples in polysome buffer with cycloheximide; an aliquot of this RNA was used to build RNA-Seq libraries after protease treatment and depletion of rRNA, and the rest of the RNA was used for ribosome footprint profiling (Hsu et al., 2016; Ingolia et al., 2009) . [Hsu et al., 2011; Yu et al., 2011] ) and to orthogonal experimental approaches in Arabidopsis (e.g. cell suspension culture proteomics ), we defined a core set of bona fide TOR-sensitive phosphoproteins in Arabidopsis, including LARP1.
    keywords: activity; analysis; arabidopsis; biogenesis; cell; cytosolic; encode; et al; eukaryotic; expression; figure; file; fold; genes; growth; larp1; levels; mrnas; mutants; phosphorylation; plants; protein; regulation; ribosome; seedlings; seq; signaling; tor; torin2; transcripts; translation; treatment; type
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        item: #1323 of 1349
          id: cord-354051-ro3o27pv
      author: Peccia, J.
       title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics
        date: 2020-05-22
       words: 1245
      flesch: 43
     summary: key: cord-354051-ro3o27pv authors: Peccia, J.; Zulli, A.; Brackney, D. E.; Grubaugh, N. D.; Kaplan, E. H.; Casanovas-Massana, A.; Ko, A. I.; Malik, A. A.; Wang, D.; Wang, M.; Weinberger, D. M.; Omer, S. B. title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics date: 2020-05-22 journal: nan DOI: 10.1101/2020.05.19.20105999 sha: doc_id: 354051 cord_uid: ro3o27pv We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area. As viral shedding can occur before cases are detected, we hypothesize that the time course of SARS-CoV-2 RNA concentrations in primary sewage sludge is a leading indicator of outbreak dynamics within a community served by the treatment plant.
    keywords: concentrations; covid-19; rna; sars; sludge
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        item: #1324 of 1349
          id: cord-354096-x2skguz8
      author: Ray, Pradipta R.
       title: A pharmacological interactome between COVID-19 patient samples and human sensory neurons reveals potential drivers of neurogenic pulmonary dysfunction
        date: 2020-06-01
       words: 6357
      flesch: 32
     summary: Mouse bulk RNA-sequencing datasets were obtained from sorted neuronal cell pools from the DRG (Liang et al., 2019) and whole tissue RNA-seq from the JNC complex before and after LPS injury (Kaelberer et al., 2020) . Two other metrics help rank neuronal genes: gene expression levels in sorted mouse DRG neuron datasets (Liang et al., 2019) and in mouse DRG neuron scRNA-seq datasets (Usoskin et al., 2015) , and degree of differential expression (log fold change) in LPS based injury models of mouse airway-innervating neurons (Kaelberer et al., 2020)
    keywords: balf; cell; covid-19; data; et al; gene; interactions; lung; neurons; patients; potential; receptor; rna; samples
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        item: #1325 of 1349
          id: cord-354114-frdsct44
      author: Vogel, Liesbeth
       title: Pathogenic characteristics of persistent feline enteric coronavirus infection in cats
        date: 2010-07-23
       words: 5344
      flesch: 48
     summary: A study of naturally occurring feline coronavirus infections in kittens Use of a reverse-transcriptase polymerase chain reaction for monitoring the shedding of feline coronavirus by healthy cats Rapid and simple method for purification of nucleic acids Feline infectious peritonitis: insights into feline coronavirus pathobiogenesis and epidemiology based on genetic analysis of the viral 3c gene Replication of feline coronaviruses in peripheral blood monocytes Patterns of feline coronavirus infection and fecal shedding from cats in multiple-cat environments Detection of feline coronaviruses by culture and reverse transcriptase-polymerase chain reaction of blood samples from healthy cats and cats with clinical feline infectious peritonitis Detection of FCoV quasispecies using denaturing gradient gel electrophoresis One-tube fluorogenic reverse transcription-polymerase chain reaction for the quantitation of feline coronaviruses Live, attenuated coronavirus vaccines through the directed deletion of group-specific genes provide protection against feline infectious peritonitis Feline coronaviruses: a tale of two-faced types Detection of feline coronavirus RNA in feces, tissues, and body fluids of naturally infected cats by reverse transcriptase PCR Persistence and evolution of feline coronavirus in a closed cat-breeding colony Elimination of feline coronavirus infection from a large experimental specific pathogen-free cat breeding colony by serologic testing and isolation Characterization of monoclonal antibodies against feline infectious peritonitis virus type II and antigenic relationship between feline, porcine, and canine coronaviruses The prevalence of types I and II feline coronavirus infections in cats Natural FCoV infection: cats with FIP exhibit significantly higher viral loads than healthy infected cats Natural feline coronavirus infection: Differences in cytokine patterns in association with the outcome of infection Sites of feline coronavirus persistence in healthy cats Feline immunodeficiency virus in Switzerland: clinical aspects and epidemiology in comparison with feline leukemia virus and coronaviruses High viral loads despite absence of clinical and pathological findings in cats experimentally infected with feline coronavirus (FCoV) type I and in naturally FCoV-infected cats Infection studies in kittens, using feline infectious peritonitis virus propagated in cell culture An enteric coronavirus infection of cats and its relationship to feline infectious peritonitis Pathogenesis of feline enteric coronavirus infection A review of feline infectious peritonitis virus infection Two related strains of feline infectious peritonitis virus isolated from immunocompromised cats infected with a feline enteric coronavirus Acquisition of macrophage tropism during the pathogenesis of feline infectious peritonitis is determined by mutations in the feline coronavirus spike protein A mRNA PCR for the diagnosis of feline infectious peritonitis Intrinsic resistance of feline peritoneal macrophages to coronavirus infection correlates with in vivo virulence Feline infectious peritonitis viruses arise by mutation from endemic feline enteric coronaviruses Acknowledgements. The presence of virus in blood was tested by performing a real-time RT-PCR on whole EDTA blood of FECV UCD infected cats.
    keywords: animals; cats; fcov; fecv; feline; infection; inoculation; rna; shedding; virus; viruses
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        item: #1326 of 1349
          id: cord-354394-zojhdnlu
      author: Wang, Wei-Kung
       title: Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early Diagnosis
        date: 2004-07-17
       words: 3981
      flesch: 47
     summary: However, a cluster of SARS cases was reported among apparently protected healthcare workers during aerosol-generating procedures performed on SARS patients (27) . However, RT-PCR performed on nasopharyngeal aspirates from SARS patients had positive rates of 32% at day 3, 50% at day 5, and 68% at day 14 (8, 14) .
    keywords: copies; cov; rna; saliva; sars; throat; wash
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        item: #1327 of 1349
          id: cord-354398-f3cg8gi1
      author: Al-Saud, Haya
       title: Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing
        date: 2020-09-20
       words: 4027
      flesch: 46
     summary: In order to start our mass testing platform, we first addressed the shortage of RNA extraction kits, which is a bottleneck in the testing capacity, at a global level. The modifica-tions of this kit were successful in extracting RNA when performed automatically using a robotic system suitable for mass extraction, which provides an alternative to commercial viral RNA extraction kits and provides a protocol to increase preparedness for future crises.
    keywords: assay; cov-2; extraction; kit; qpcr; rna; sars
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        item: #1328 of 1349
          id: cord-354407-zzxjv666
      author: Campanacci, Valérie
       title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein
        date: 2004-06-07
       words: 2344
      flesch: 53
     summary: In agreement, the CD spectrum of puri®ed Nsp9 reveals a structured protein formed by a majority of -strands (35%) and -turns (18%), but which also contains 15% -helix. The aetiologic agent of SARS is a positivestranded RNA virus belonging to the Coronaviridae family and its genome differs substantially from those of previously identi®ed coronaviruses, including two other human coronaviruses (Peiris et al., 2003; Ksiazek et al., 2003; Drosten et al., 2003; Snijder et al., 2003) .
    keywords: cov; nsp9; protein; rna; sars
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        item: #1329 of 1349
          id: cord-354465-5nqrrnqr
      author: Haslinger, Christian
       title: RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties
        date: 1999
       words: 10375
      flesch: 61
     summary: A new principle of RNA folding based on pseudoknotting Random induced subgraphs of generalized n-cubes Bio-molecular shapes and algebraic structures Generic properties of combinatory maps: Neural networks of RNA secondary structures Petersen family minors Sachs' linkless embedding conjecture Linear trees and RNA secondary structure How to search for RNA structures. Combinatorial aspects of RNA secondary structures have been studied in detail by Waterman and co-workers (Stein and Waterman, 1978; Waterman, 1978; Waterman and Smith, 1978a, b; Penner and Waterman, 1993;
    keywords: base; diagram; energy; graph; knots; neutral; number; pseudo; rna; sequences; structures; vertices
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        item: #1330 of 1349
          id: cord-354510-jlg5je0s
      author: de Carvalho, A. F.
       title: THE USE OF DENATURING SOLUTION AS COLLECTION AND TRANSPORT MEDIA TO IMPROVE SARS-COV-2 RNA DETECTION AND REDUCE INFECTION OF LABORATORY PERSONNEL
        date: 2020-06-20
       words: 4116
      flesch: 48
     summary: Here, we proposed the use of a virus-inactivating solution as part of a sample collection kit to decrease the infectious potential of the collected material without affecting the integrity of RNA samples used in diagnostic tests based on RT-qPCR. Here, we proposed the use of a virus-inactivating solution as part of a sample collection kit to decrease the infectious potential of the collected material without affecting the integrity of RNA samples used in diagnostic tests based on RT-qPCR.
    keywords: laboratory; license; n d; preprint; rna; samples
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        item: #1331 of 1349
          id: cord-354529-k8p2u7iq
      author: Wu, Yongran
       title: Patients with Prolonged Positivity of SARS-CoV-2 RNA Benefit from Convalescent Plasma Therapy: A Retrospective Study
        date: 2020-08-31
       words: 3757
      flesch: 47
     summary: Chest CT findings of early and progressive phase COVID-19 infection from a US patient Use of convalescent plasma therapy in two COVID-19 patients with acute respiratory distress syndrome in Korea A case of long-term excretion and subclinical infection with Middle East respiratory syndrome coronavirus in a healthcare worker Use of convalescent plasma therapy in SARS patients in Hong Kong Chinese National Health Commission (2020) Recently, many studies about long-term viral duration in COVID-19 patients have been published Wan et al. 2020;
    keywords: covid-19; days; group; patients; sars; therapy
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        item: #1332 of 1349
          id: cord-354536-c9v9kbw8
      author: Han, Yan-Jie
       title: Advances and challenges in the prevention and treatment of COVID-19
        date: 2020-07-09
       words: 5277
      flesch: 41
     summary: 61, 62 Chloroquine phosphate can block virus infection by up-regulating the pH of endosomes, required low for virus-cell fusion, and inhibiting glycosylation of cellular receptors. 73 Blood-derived immunotherapy based on recovered patients can be used to treat infections including measles virus, Lhasa virus, SARS coronavirus and influenza A H5N1 virus.
    keywords: coronavirus; cov; cov-2; human; infection; interferon; mers; protein; replication; sars; treatment; vitro
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        item: #1333 of 1349
          id: cord-354582-fniymnmf
      author: Ma, Zhiqian
       title: Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae
        date: 2020-06-30
       words: 8398
      flesch: 27
     summary: In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. Reverse genetics systems are highly valuable research tools for RNA virus vaccine development, which may be more efficient than conventional approaches with live attenuation through passing (forward genetics) or inactivation (Stobart and Moore, 2014) .
    keywords: acute; cdna; cells; coronavirus; cov; et al; genetics; genome; immune; mers; mhv; porcine; protein; replication; rna; sars; syndrome; type; vaccines; virulence
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        item: #1334 of 1349
          id: cord-354733-qxivrhj8
      author: Gniazdowski, V.
       title: Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity
        date: 2020-08-06
       words: 3930
      flesch: 47
     summary: 354733 cord_uid: qxivrhj8 Repeat molecular testing for SARS-CoV-2 may result in scenarios including multiple positive results, positive test results after negative tests, and repeated false negative results in symptomatic individuals. Repeat molecular testing for SARS-CoV-2 may result in scenarios including multiple positive 24 results, positive test results after negative tests, and repeated false negative results in 25 symptomatic individuals.
    keywords: license; negative; patients; preprint; results; rna; sars; virus
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        item: #1335 of 1349
          id: cord-354824-7fdcu2f0
      author: Wu, Renyi
       title: An Update on Current Therapeutic Drugs Treating COVID-19
        date: 2020-05-11
       words: 9676
      flesch: 38
     summary: Chinese Clinical Trial Registry Why tocilizumab could be an effective treatment for severe COVID-19? Evaluation of the efficacy and safety of sarilumab in hospitalized patients with COVID-19 Overview of the IL-1 family in innate inflammation and acquired immunity Personalised immunotherapy for SARS-CoV-2 (COVID-19) associated with organ dysfunction Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study Clinical characteristics of coronavirus disease 2019 in China Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan Are patients with hypertension and diabetes mellitus at increased risk for COVID-19 infection? Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus Genetic associations between genes in the renin-angiotensinaldosterone system and renal disease: a systematic review and meta-analysis Angiotensin receptor blockers as tentative SARS-CoV-2 therapeutics Effect of angiotensin-converting enzyme inhibition and angiotensin II receptor blockers on cardiac angiotensinconverting enzyme 2 A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury FDA advises patients on use of non-steroidal anti-inflammatory drugs (NSAIDs) for COVID-19 Peroxisome proliferatoractivated receptor-gamma agonists inhibit respiratory syncytial virus-induced expression of intercellular adhesion molecule-1 in human lung epithelial cells Treating viral exacerbations of chronic obstructive pulmonary disease: insights from a mouse model of cigarette smoke and H1N1 influenza infection Indomethacin has a potent antiviral activity against SARS coronavirus Colchicine-update on mechanisms of action and therapeutic uses Colchicine and the heart: pushing the envelope Inhibition of severe acute respiratory syndrome coronavirus replication by niclosamide SKP2 attenuates autophagy through Beclin1-ubiquitination and its inhibition reduces MERS-coronavirus infection An AlphaScreen®-based assay for high-throughput screening for specific inhibitors of nuclear import Ivermectin is a specific inhibitor of importin α/β-mediated nuclear import able to inhibit replication of HIV-1 and dengue virus Ivermectin is a potent inhibitor of flavivirus replication specifically targeting NS3 helicase activity: new prospects for an old drug The broad spectrum antiviral ivermectin targets the host nuclear transport importin alpha/beta1 heterodimer The FDAapproved drug ivermectin inhibits the replication of SARS-CoV-2 in vitro A screen of the NIH clinical collection small molecule library identifies potential anti-coronavirus drugs Nitazoxanide, a new drug candidate for the treatment of Middle East respiratory syndrome coronavirus Meta-analysis: convalescent blood products for Spanish influenza pneumonia: a future H5N1 treatment? Antibody-mediated regulation of cellular immunity and the inflammatory response Serum therapy revisited: animal models of infection and development of passive antibody therapy Fcmediated antibody effector functions during respiratory syncytial virus infection and disease A role for Fc function in therapeutic monoclonal antibody-mediated protection against Ebola virus A serological survey on neutralizing antibody titer of SARS convalescent sera Use of convalescent plasma therapy in SARS patients in Hong Kong Experience of using convalescent plasma for severe acute respiratory syndrome among healthcare workers in a Taiwan hospital Challenges of convalescent plasma infusion therapy in Middle East respiratory coronavirus infection: a single centre experience Deployment of convalescent plasma for the prevention and treatment of COVID-19 Treatment of 5 critically ill patients with COVID-19 with convalescent plasma Effectiveness of convalescent plasma therapy in severe COVID-19 patients Abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia Anticoagulant treatment is associated with decreased mortality in severe coronavirus disease 2019 patients with coagulopathy The 2019 coronavirus (SARS-CoV-2) surface protein (Spike) S1 receptor binding domain The potential of low molecular weight heparin to mitigate cytokine storm in severe COVID-19 patients: a retrospective clinical study Redeploying plant defences Chinese herbal medicines for the treatment of type a H1N1 influenza: a systematic review of randomized controlled trials Clinical outcomes of influenza-like illness treated with Chinese herbal medicine: an observational study Herbal medicine and pattern identification for treating COVID-19: a rapid review of guidelines Traditional Chinese medicine in the treatment of patients infected with 2019-new coronavirus (SARS-CoV-2): a review and perspective Investigating mechanism of Qingfei Dayuan granules for treatment of COVID-19 based on network pharmacology and molecular docking Study on screening potential traditional Chinese medicines against 2019-nCoV based on Mpro and PLP Chinese herbal medicine for severe acute respiratory syndrome: a systematic review and metaanalysis Traditional Chinese herbal medicine as a source of molecules with antiviral activity Can Chinese medicine be used for prevention of corona virus disease 2019 (COVID-19)? Evolving research and clinical data regarding the virologic SARS-CoV-2 suggest a potential list of repurposed drugs with appropriate pharmacological effects and therapeutic efficacies in treating COVID-19 patients.
    keywords: activity; antiviral; azithromycin; cells; clinical; coronavirus; cov-2; covid-19; disease; drugs; hydroxychloroquine; infection; influenza; lung; patients; rna; sars; study; syndrome; treatment; trial; viral
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        item: #1336 of 1349
          id: cord-354829-god79qzw
      author: Mao, Kaimin
       title: Identification of robust genetic signatures associated with lipopolysaccharide-induced acute lung injury onset and astaxanthin therapeutic effects by integrative analysis of RNA sequencing data and GEO datasets
        date: 2020-09-23
       words: 6341
      flesch: 39
     summary: Astaxanthin inhibits nitric oxide production and inflammatory gene expression by suppressing I(kappa)B kinase-dependent NF-kappaB activation Effects of astaxanthin on lipopolysaccharide-induced inflammation in vitro and in vivo Astaxanthin prevents pulmonary fibrosis by promoting myofibroblast apoptosis dependent on Drp1-mediated mitochondrial fission Astaxanthin alleviated acute lung injury by inhibiting oxidative/nitrative stress and the inflammatory response in mice Astaxanthin prevents against lipopolysaccharideinduced acute lung injury and sepsis via inhibiting activation of MAPK/NF-κB NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and metaanalysis clusterProfiler: an R package for comparing biological themes among gene clusters Inflammatory cytokines in patients with persistence of the acute respiratory distress syndrome Neutrophils in the initiation and resolution of acute pulmonary inflammation: understanding biological function and therapeutic potential Evidence for chemokine synergy during neutrophil migration in ARDS Fernández-Botrán R. Modulation of acute inflammation by targeting glycosaminoglycan-cytokine interactions Contribution of neutrophils to acute lung injury Antiinflammatory activity of a novel family of aryl ureas compounds in an endotoxin-induced airway epithelial cell injury model C-X-C motif chemokine 13 (CXCL13) is a prognostic biomarker of idiopathic pulmonary fibrosis ZBP1: innate sensor regulating cell death and inflammation Dynamic gene expression analysis in a H1N1 influenza virus mouse pneumonia model The CC chemokine ligand 2 (CCL2) mediates fibroblast survival through IL-6 Complement inhibition decreases early fibrogenic events in the lung of septic baboons The cytokine-serum amyloid achemokine network Serum amyloid A is a biomarker of severe coronavirus disease and poor prognosis Serum amyloid A3 is a high density lipoprotein-associated acute-phase protein Exosomes derived from microRNA-30b-3p-overexpressing mesenchymal stem cells protect against lipopolysaccharide-induced acute lung injury by inhibiting SAA3 Long non-coding RNA MALAT1 regulates hyperglycaemia induced inflammatory process in the endothelial cells IL-6 induced lncRNA MALAT1 enhances TNF-α expression in LPS-induced septic cardiomyocytes via activation of SAA3 Emerging functions of serum amyloid a in inflammation Suppression of lipopolysaccharide-induced inflammatory response by fragments from serum amyloid a Serum amyloid a promotes LPS clearance and suppresses LPS-induced inflammation and tissue injury Knockdown of miR-660 protects nucleus pulposus cells from TNF-a-induced apoptosis by targeting serum amyloid A1 IRF7: activation, regulation, modification and function Attenuation of interferon regulatory factor 7 activity in local infectious sites of trachea and lung for preventing the development of acute lung injury caused by influenza a virus Mir-302c mediates influenza a virus-induced IFNβ expression by targeting NF-κB inducing kinase Then, we performed a meta-analysis using NetworkAnalyst (http://www.networkanalyst.ca), which is a comprehensive web-based tool designed to perform meta-analyses of gene expression data [20] .
    keywords: acute; ali; analysis; ards; ast; data; degs; expression; genes; group; injury; lps; lung; meta; mice; rna
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        item: #1337 of 1349
          id: cord-355075-ieb35upi
      author: Papenfuss, Anthony T
       title: The immune gene repertoire of an important viral reservoir, the Australian black flying fox
        date: 2012-06-20
       words: 8959
      flesch: 48
     summary: The GO classification demonstrates that a diverse range of genes were identified in each of our two datasets providing a broad survey of bat genes. We have also begun to identify some of the genes involved in immune responses in this species and carry out functional studies in bat cells
    keywords: alecto; antiviral; bat; bats; cells; class; contigs; datasets; genes; immune; mammals; mhc; protein; receptors; sequences; species; thymus; transcriptome; transcripts; viruses
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        item: #1338 of 1349
          id: cord-355179-wmfwl2bh
      author: Jung, Eunhye
       title: Neutralization of Acidic Intracellular Vesicles by Niclosamide Inhibits Multiple Steps of the Dengue Virus Life Cycle In Vitro
        date: 2019-06-18
       words: 5317
      flesch: 34
     summary: To rule out the possibility that virus infected cells were more sensitive to niclosamide treatment resulting in synergistic cytotoxicity compared to mock-infected cells, the percentages of live and dead cells from mock-and DENV-2 infected cultures with increasing concentrations of niclosamide were determined by FACS analysis. Dengue/dengue haemorrhagic fever: history and current status The global distribution and burden of dengue Dengue: a continuing global threat Fields Virology Zika Virus Associated with Microcephaly Zika Virus and Birth Defects-Reviewing the Evidence for Causality Rapid Spread of Zika Virus in The Americas-Implications for Public Health Preparedness for Mass Gatherings at the 2016 Brazil Olympic Games Guillain-Barre Syndrome outbreak associated with Zika virus infection in French Polynesia: a casecontrol study Guillain-Barre syndrome associated with the Zika virus outbreak in Brazil Magnetic resonance imaging findings in Guillain-Barre syndrome caused by Zika virus infection The dengue viruses NS3 protease from flavivirus as a target for designing antiviral inhibitors against dengue virus Flavivirus infection enhancement in macrophages: radioactive and biological studies on the effect of antibody on viral fate Morphogenesis of yellow fever virus 17D in infected cell cultures Dissecting the cell entry pathway of dengue virus by single-particle tracking in living cells Characterization of the early events in dengue virus cell entry by biochemical assays and single-virus tracking The entry machinery of flaviviruses Receptors and routes of dengue virus entry into the host cells Molecular basis of endosomal-membrane association for the dengue virus envelope protein The flavivirus precursor membrane-envelope protein complex: structure and maturation New insights into the immunopathology and control of dengue virus infection Structure of the immature dengue virus at low pH primes proteolytic maturation Rodenhuis-Zybert, I. & Wilschut, J. Flavivirus cell entry and membrane fusion Acidotropic amines inhibit proteolytic processing of flavivirus prM protein Fusion activity of flaviviruses: comparison of mature and immature (prM-containing) tick-borne encephalitis virions Structural changes and functional control of the tick-borne encephalitis virus glycoprotein E by the heterodimeric association with protein prM Cleavage of protein prM is necessary for infection of BHK-21 cells by tickborne encephalitis virus Functional importance of dengue virus maturation: infectious properties of immature virions pH-Dependent entry of chikungunya virus fusion into mosquito cells Proteolytic activation of tick-borne encephalitis virus by furin Amodiaquine, an antimalarial drug, inhibits dengue virus type 2 replication and infectivity Worm cure without tears.
    keywords: cells; dengue; denv; fig; niclosamide; p.i; particles; protein; replication; rna; virus
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        item: #1339 of 1349
          id: cord-355357-b6aklh44
      author: Stapleford, Kenneth A.
       title: Viral Polymerase-Helicase Complexes Regulate Replication Fidelity To Overcome Intracellular Nucleotide Depletion
        date: 2015-08-26
       words: 7683
      flesch: 37
     summary: In addition, this variant increased the fidelity of CHIKV in multiple cell types, providing a novel role for the nsP2 protein in the viral life cycle and demonstrating that other nonstructural proteins play important roles in RNA replication fidelity aside from the polymerase itself. Ribavirinresistant variants of foot-and-mouth disease virus: the effect of restricted quasispecies diversity on viral virulence Determinants of RNA-dependent RNA polymerase (in)fidelity revealed by kinetic analysis of the polymerase encoded by a foot-and-mouth disease virus mutant with reduced sensitivity to ribavirin A single mutation in poliovirus RNAdependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population Fidelity variants of RNA-dependent RNA polymerases uncover an indirect, mutagenic activity of amiloride compounds Coxsackievirus B3 mutator strains are attenuated in vivo Generation and characterization of influenza A viruses with altered polymerase fidelity Ribavirin-resistant mutants of human enterovirus 71 express a high replication fidelity phenotype during growth in cell culture Attenuation of human enterovirus 71 highreplication-fidelity variants in AG129 mice Arbovirus high fidelity variant loses fitness in mosquitoes and mice Alphavirus mutator variants present hostspecific defects and attenuation in mammalian and insect models Implications of high RNA virus mutation rates: lethal mutagenesis and the antiviral drug ribavirin Ribavirin: a drug active against many viruses with multiple effects on virus replication and propagation: molecular basis of ribavirin resistance Effect of ribavirin triphosphate on primer generation and elongation during influenza virus transcription in vitro The predominant mechanism by which ribavirin exerts its antiviral activity in vitro against flaviviruses and paramyxoviruses is mediated by inhibition of IMP dehydrogenase 5-Fluorouracil: mechanisms of action and clinical strategies Replication cycle of Chikungunya: a re-emerging arbovirus Reaction in alphavirus mRNA capping: formation of a covalent complex of nonstructural protein nsP1 with 7-methyl-GMP NTPase and 5=-RNA triphosphatase activities of Chikungunya virus nsP2 protein Mapping of Chikungunya virus interactions with host proteins identified nsP2 as a highly connected viral component Mutations conferring a noncytotoxic phenotype on Chikungunya virus replicons compromise enzymatic properties of nonstructural protein 2 The C-terminal domain of Chikungunya virus nsP2 independently governs viral RNA replication, cytopathicity, and inhibition of interferon signaling Chikungunya virus nonstructural protein 2-mediated host shut-off disables the unfolded protein response Chikungunya virus nonstructural protein 2 inhibits type I/II interferon-stimulated JAK-STAT signaling Chikungunya virus nsP3 and nsP4 interacts with HSP-90 to promote virus replication:
    keywords: activity; addition; cells; chikv; fidelity; fig; g641d; mutation; nsp2; nucleotide; replication; ribavirin; rna; variant; virus
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        item: #1340 of 1349
          id: cord-355397-y69bk5jc
      author: Caruso, Ícaro P.
       title: Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism
        date: 2020-09-06
       words: 5131
      flesch: 44
     summary: We probed dsRNAs’ Watson and Crick (WC) base-pairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, initiating melting. Our results support a 1:1 stoichiometry (N-NTD:dsRNA), matching MD simulations and raising different possibilities for N-NTD action: (i) two N-NTDs of dimeric N would act independently, increasing efficiency; (ii) two N-NTDs of dimeric N would bind to two different RNA sites, bridging distant regions of the genome; and (iii) monomeric N would be active, opening up the possibility of a regulatory dissociation event.
    keywords: complex; dsns; dsrna; dstrs; figure; melting; model; ntd; protein
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        item: #1341 of 1349
          id: cord-355477-7xd93aqv
      author: SATIJA, NAMITA
       title: The Molecular Biology of SARS Coronavirus
        date: 2007-04-23
       words: 4952
      flesch: 46
     summary: A bound to the amino-terminal domain of HIV-1 capsid The nucleocapsid protein of SARS coronavirus has a high binding affinity to the human cellular heterogeneous nuclear ribonucleoprotein A1 Crystal structure of human UP1, the domain of hnRNP A1that contains two RNA-recognition motifs The nucleocapsid protein of coronavirus mouse hepatitis virus interacts with the cellular heterogeneous nuclear ribonucleoprotein A1 in vitro and in vivo Activation of AP-1 signal transduction pathway by SARS coronavirus nucleocapsid protein The nucleocapsid protein of sars-coronavirus inhibits the activity of cyclin-CDK complex and blocks S phase progression in mammalian cells The SARS coronavirus nucleocapsid protein induces actin reorganization and apoptosis in COS-1 cells in the absence of growth factors Nuclear/nucleolar localization properties of C-terminal nucleocapsid protein of SARS coronavirus The severe acute respiratory syndrome coronavirus nucleocapsid protein is phosphorylated and localizes in the cytoplasm by 14-3-3-mediated translocation Phosphorylation of the porcine reproductive and respiratory syndrome virus nucleocapsid protein Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells Peptide domain involved in the interaction between membrane protein and nucleocapsid protein of SARS-associated coronavirus Characterization of severe acute respiratory syndrome coronavirus membrane protein Differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins S, M and E Biochemical and functional characterization of the membrane association and membrane permeabilizing activity of the severe acute respiratory syndrome coronavirus envelope protein The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells The severe acute respiratory syndrome (SARS) coronavirus 3a protein may function as a modulator of the trafficking properties of the spike protein The severe acute respiratory syndrome coronavirus 3a protein up-regulates expression of fibrinogen in lung epithelial cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells Overexpression of 7a, a protein specifically encoded by severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway Severe acute respiratory syndromeassociated coronavirus 3a protein forms an ion channel and modulates virus release Carboxyl terminus of severe acute respiratory coronavirus nucleocapsid protein: self-association analysis and nucleic acid binding characteristics Nucleocapsid amino acids 211 to 254, in particular, tetrad glutamines, are essential for the interaction between the nucleocapsid and membrane proteins of SARS-associated coronavirus Coronavirus nucleocapsid protein is an RNA chaperone A first step in understanding SARS pathogenesis Mechanisms and enzymes involved in SARS coronavirus genome expression Molecular biology of severe acute respiratory syndrome coronavirus A 193 amino acid fragment of SARS coronavirus S protein efficiently binds angiotensin converting enzyme 2 Mass spectrometric characterization of proteins from the SARS virus: a preliminary report Proteomic analysis on structural proteins of severe acute respiratory syndrome coronavirus Differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins S, M and E Structure of SARS coronavirus spike receptor-binding domain complexed with receptor Profile of antibodies to the nucleocapsid protein of the severe acute respiratory syndrome (SARS)-associated coronavirus in probable SARS patients Diagnosis of severe acute respiratory syndrome (SARS) by detection of SARS coronavirus nucleocapsid antibodies in an antigencapturing enzyme-linked immunosorbent assay Assessment of immunoreactive synthetic peptides from the structural proteins of severe acute respiratory syndrome coronavirus Mapping of antigenic sites on the nucleocapsid protein of the severe acute respiratory syndrome coronavirus Antigenic structure of transmissible gastroenteritis virus nucleoprotein Location of antibody epitopes within the mouse hepatitis virus nucleocapsid protein Localization of linear B-cell epitopes on infectious bronchitis virus nucleocapsid protein The epitope study on the SARS-CoV nucleocapsid protein Structure of the N-terminal RNAbinding domain of the SARS CoV nucleocapsid protein Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent The nucleocapsid protein of the SARS coronavirus is capable of self-association through a C-terminal 209 amino acid interaction domain Recombinant severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein forms a dimer through its C-terminal domain Nucleocapsid protein of SARS coronavirus tightly binds to human cyclophilin A Crystal structure of human cyclophilin
    keywords: cells; coronavirus; cov; covs; domain; nucleocapsid; protein; rna; sars; syndrome; terminal
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        item: #1342 of 1349
          id: cord-355499-5vj3oasa
      author: Song, Xiangjun
       title: Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7
        date: 2015-06-07
       words: 4237
      flesch: 47
     summary: In conclusion, differentially expressed miR-4331 that is caused by TGEV infection can suppress transcription of TGEV gene 7 via targeting cellular CDCA7. Overall, we observed that TGEV infection caused the change of miRNA profile and miR-4331 suppressed transcription of TGEV gene 7 via directly targeting CDCA7.
    keywords: cdca7; cells; cellular; expression; gene; infection; mir-4331; mirnas; tgev; transcription; virus
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        item: #1343 of 1349
          id: cord-355676-2y8vowbi
      author: Liu, Pinghua
       title: A Previously Unrecognized Unr Stem-Loop Structure in the Coronavirus 5’ Untranslated Region Plays a Functional role in Replication
        date: 2006
       words: 1333
      flesch: 53
     summary: Taken together, these results are consistent with a role for SL2 in MHV RNA replication and transcription. The effect of mutations in the mouse hepatitis virus 3'(+)42 protein binding element on RNA replication The UCUAAAC promoter motif is not required for highfrequency leader recombination in bovine coronavirus defective interfering RNA Predicting U-turns in ribosomal RNA with comparative sequence analysis
    keywords: loop; rna; sl2
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        item: #1344 of 1349
          id: cord-355743-vjiecd4k
      author: Ghosh, Sabyasachi
       title: Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing
        date: 2020-04-29
       words: 4834
      flesch: 58
     summary: Sample pools containing one or more positive samples were emulated by spiking with appropriate amounts of RNA fragments to simulate the viral load after pooling. While these strategies can augment testing capacities, they do not substantially improve throughput, since two rounds of testing are still needed to identify positive samples.
    keywords: license; pooling; positives; preprint; rna; samples; testing; tests; threshold
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        item: #1345 of 1349
          id: cord-355758-tk7eturq
      author: Berrio, Alejandro
       title: Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function
        date: 2020-09-22
       words: 2181
      flesch: 28
     summary: The first is Nsp4, which encodes a similarities to, but also notable differences from, that of SARS-Cov-2 (Fig 1) . In the case of Nsp4 protein, two nearly adjacent nonsynonymous substitutions at residues 380 430 and 382 occurred on the branch leading to SARS-CoV-2 ( Fig 3B) .
    keywords: coronavirus; cov-2; protein; rna; sars; selection; structure
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        item: #1346 of 1349
          id: cord-355913-fhvt1ht1
      author: Burrell, Christopher J.
       title: Virus Replication
        date: 2016-11-11
       words: 9867
      flesch: 41
     summary: The situation is quite different for RNA viruses as these are unique having genetic information coded as RNA. For RNA viruses, the regulation of transcription is, on the whole, not as complex as is the case for DNA viruses.
    keywords: acid; cell; dna; example; genes; genome; host; membrane; mrna; particles; proteins; replication; rna; rna viruses; synthesis; transcription; viruses
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        item: #1347 of 1349
          id: cord-356009-emn2w8if
      author: Roshandel, M. R.
       title: What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis
        date: 2020-10-13
       words: 4690
      flesch: 40
     summary: The Journal of infection Persistent shedding of viable SARS-CoV in urine and stool of SARS patients during the convalescent phase SARS-CoV-2 infection does not significantly cause acute renal injury: an analysis of 116 hospitalized patients with COVID-19 in a single hospital Quantitative detection and viral load analysis of SARS-CoV-2 in infected patients Viral load of SARS-CoV-2 in clinical samples. Nevertheless, a lack of concordance between the severity of disease and ICU admission rates in two groups in table 2 indicates heterogeneity of study populations among the studies.
    keywords: cov-2; covid-19; disease; medrxiv; patients; preprint; sars; shedding; studies; urine
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        item: #1348 of 1349
          id: cord-356013-pl3tmky8
      author: Brian, D. A.
       title: Coronavirus Genome Structure and Replication
        date: 2005
       words: 8406
      flesch: 37
     summary: The question of what cis-acting sequences act in coronavirus RNA replication has relevance not only for genome replication but also for poorly understood features of sgmRNA behavior. N protein, for example, binds leader sequence with high affinity (Nelson et al. 2000) , is present in a subpopulation of coronavirus RNA replication complexes (Sethna and Brian 1997;
    keywords: cis; coronavirus; et al; gene; genome; hepatitis; mhv; orf; protein; replication; rna; rnas; sequence
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        item: #1349 of 1349
          id: cord-356115-vblgotjn
      author: Sawicki, Stanley G
       title: Functional and Genetic Analysis of Coronavirus Replicase-Transcriptase Proteins
        date: 2005-12-09
       words: 10675
      flesch: 45
     summary: This allowed us to follow the activity at 40 8C of the viral RNA-dependent RNA polymerase that was made and assembled at 30 8C. At this time, Alb ts22 RNA synthesis was at its maximum rate and RNA synthesis by wt MHV-A59 and Alb 22R was declining. These proteins have been shown, or are predicted to have multiple enzymatic functions, including papain-like proteases (nsp3), adenosine diphosphate-ribose 19-phosphatase (nsp3), 3C-like cysteine proteinase (nsp5), RNA-dependent RNA polymerase (nsp12), superfamily 1 helicase (nsp13), exonuclease (nsp14), endoribonuclease (nsp15), and S-adenosylmethionine-dependent 29-O-methyl transferase (nsp16)
    keywords: a59; alb; cells; complementation; mhv; mutants; negative; replicase; rna; rna synthesis; strand; synthesis; temperature; ts6; virus
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