item: #1 of 194 id: cord-000012-p56v8wi1 author: Bigot, Yves title: Molecular evidence for the evolution of ichnoviruses from ascoviruses by symbiogenesis date: 2008-09-18 words: 6431 flesch: 40 summary: Since parasitoid wasps are able to vector different viruses [44, 45] , this second scenario opens the exciting possibility that virus genes involved in the ichnovirus biology might correspond to a gene patchwork resulting from transfers from viruses belonging to different NCLDV and non-NCLVD families. Indeed, they match an evolutionary scenario of endosymbiogenesis during which, from a single integration event of symbiotic virus genome, viral genes were lost and/or translocated from the provirus to other chromosomal regions (Fig. 5 ). keywords: ascovirus; dna; dpav4; evolution; genes; genomes; gfiv; host; ichnovirus; origin; particles; proteins; viruses; wasp cache: cord-000012-p56v8wi1.txt plain text: cord-000012-p56v8wi1.txt item: #2 of 194 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 cache: cord-000159-8y8ho2x5.txt plain text: cord-000159-8y8ho2x5.txt item: #3 of 194 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 cache: cord-000248-zueoyesj.txt plain text: cord-000248-zueoyesj.txt item: #4 of 194 id: cord-000402-unr44dvp author: Yoo, Hyun Jung title: Gene Expression Profile during Chondrogenesis in Human Bone Marrow derived Mesenchymal Stem Cells using a cDNA Microarray date: 2011-06-20 words: 3189 flesch: 37 summary: The role of peroxiredoxin-1 in cell differentiation and proliferation suggests that it has a possible role in growth and development. HSF-2 plays an important role in FGF-2 stimulated osteoclast formation, and HSF-2 deficiency was found to modulate gene expression in stromal/ preosteoblast cells and affect osteoclastogenesis in the bone microenvironment (18) . keywords: bone; cells; chondrogenesis; differentiation; expression; genes; human; microarray; mscs cache: cord-000402-unr44dvp.txt plain text: cord-000402-unr44dvp.txt item: #5 of 194 id: cord-000492-ec5qzurk author: Devaney, James title: Clinical Review: Gene-based therapies for ALI/ARDS: where are we now? date: 2011-06-20 words: 6021 flesch: 34 summary: Antibodies that bind antigens selectively expressed on the pulmonary endothelial surface can be complexed to gene vectors to facilitate selective targeting following intravenous administration + ,K + -ATPase rescues endotoxin-induced lung injury Interleukin-10 gene transfer: prevention of multiple organ injury in a murine cecal ligation and puncture model of sepsis Nonviral gene delivery with indoleamine 2,3-dioxygenase targeting pulmonary endothelium protects against ischemia-reperfusion injury Silencing of Fas, but not caspase-8, in lung epithelial cells ameliorates pulmonary apoptosis, infl ammation, and neutrophil infl ux after hemorrhagic shock and sepsis Caveolin-1 siRNA increases the pulmonary microvascular and alveolar epithelial permeability in rats Interleukin-10 delivery via mesenchymal stem cells: a novel gene therapy approach to prevent lung ischemia-reperfusion injury Bone marrow stem cells expressing keratinocyte growth factor via an inducible lentivirus protects against bleomycin-induced pulmonary fi brosis Cell-based gene transfer of vascular endothelial growth factor attenuates monocrotaline-induced pulmonary hypertension Microvascular regeneration in established pulmonary hypertension by angiogenic gene transfer Tetracycline-inducible transgene expression mediated by a single AAV vector Effi cient transfection of non-proliferating human airway epithelial cells with a synthetic vector system Tailoring the AAV vector capsid for gene therapy Artifi cial evolution with adeno-associated viral libraries Analysis and optimization of the cationic lipid component of a lipid/ peptide vector formulation for enhanced transfection in vitro and in vivo Stabilized integrin-targeting ternary LPD (lipopolyplex) vectors for gene delivery designed to disassemble within the target cell CpG-free plasmids confer reduced infl ammation and sustained pulmonary gene expression Toll-like receptor expression reveals CpG DNA as a unique microbial stimulus for plasmacytoid dendritic cells which synergizes with CD40 ligand to induce high amounts of IL-12 Targeting type II and Clara cells for adenovirus-mediated gene transfer using the surfactant protein B promoter Development of lentiviral vectors with regulated respiratory epithelial expression in vivo Expression of CFTR from a ciliated cell-specifi c promoter is ineff ective at correcting nasal potential diff erence in CF mice A human epithelium-specifi c vector optimized in rat pneumocytes for lung gene therapy Tight control of gene expression in mammalian cells by tetracycline-responsive promoters Use of a new generation reverse tetracycline transactivator system for quantitative control of conditional gene expression in the murine lung Construction of an rtTA2(s)-m2/ tts(kid)-based transcription regulatory switch that displays no basal activity, good inducibility, and high responsiveness to doxycycline in mice and non-human primates Adenoviral vector transfection into the pulmonary epithelium after cecal ligation and puncture in rats Ubiquitination of both adeno-associated virus type 2 and 5 capsid proteins aff ects the transduction effi ciency of recombinant vectors GP130-STAT3 regulates epithelial cell migration and is required for repair of the bronchiolar epithelium Spatial and temporal expression of surfactant proteins in hyperoxia-induced neonatal rat lung injury Intrapulmonary TNF gene therapy reverses sepsis-induced suppression of lung antibacterial host defense Clinical Review: Gene-based therapies for ALI/ARDS: where are we now? keywords: ali; approaches; ards; cell; expression; gene; injury; lung; pulmonary; specifi; therapy; transfer; vectors cache: cord-000492-ec5qzurk.txt plain text: cord-000492-ec5qzurk.txt item: #6 of 194 id: cord-000580-dcid9emx author: Sällman Almén, Markus title: The Dispanins: A Novel Gene Family of Ancient Origin That Contains 14 Human Members date: 2012-02-20 words: 4665 flesch: 44 summary: The DSPA/IFITM subfamily is the most numerous and the mouse and human genes are all clustered in a consecutive manner on chromosome six and eleven, respectively. Establishing a rigid nomenclature based on evolutionary information and structural features of the predicted proteins facilitates prediction of the functional role of these genes that often have only have been studied in large gene or transcription consortia. keywords: analysis; dispanins; family; figure; genes; human; ifitm; proteins; sequences; subfamilies; subfamily cache: cord-000580-dcid9emx.txt plain text: cord-000580-dcid9emx.txt item: #7 of 194 id: cord-001060-9g8rwsm1 author: Arruebo, Manuel title: Assessment of the Evolution of Cancer Treatment Therapies date: 2011-08-12 words: 10518 flesch: 30 summary: An example of a retroviral vector in cancer gene therapy is Rexin-G£, currently in clinical trials for advanced pancreatic, metastatic breast cancer, osteosarcoma and soft tissue sarcoma The combined thermal and gene therapy treatment significantly arrested tumor growth in nude mice, which encouraged the refinement of this type of cancer gene therapy, which was then successfully tested in preclinical studies [129] . keywords: agents; antibodies; antibody; cancer; cells; chemotherapy; delivery; drugs; gene; human; hyperthermia; mabs; mice; monoclonal; nanoparticles; targeting; therapeutic; therapies; therapy; treatment; trials; tumor; use; vectors cache: cord-001060-9g8rwsm1.txt plain text: cord-001060-9g8rwsm1.txt item: #8 of 194 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 cache: cord-001541-5d64esp4.txt plain text: cord-001541-5d64esp4.txt item: #9 of 194 id: cord-001858-nmi39n6h author: Petriccione, Milena title: Reference gene selection for normalization of RT-qPCR gene expression data from Actinidia deliciosa leaves infected with Pseudomonas syringae pv. actinidiae date: 2015-11-19 words: 5577 flesch: 42 summary: Reference genes selection and normalization of oxidative stress responsive genes upon different temperature stress conditions in Hypericum perforatum L Reference gene selection for quantitative real-time PCR analysis in virus infected cells: SARS corona virus,Yellow fever virus, Human Herpesvirus-6, Camelpox virus and Cytomegalovirus infections Biphasic haustorial differentiation of coffee rust (Hemileia vastatrix race II) associated with defence responses in resistant and susceptible coffee cultivars Validation of reference genes for RT-qPCR normalization in common bean during biotic and abiotic stresses Reference gene selection for qPCR gene expression analysis of rust-infected wheat Validation of reference genes for gene expression studies in virus-infected Nicotiana benthamiana using quantitative real-time PCR Assessment of reference gene stability influenced by extremely divergent disease symptoms in Solanum lycopersicum L Reactive oxygen and oxidative stress tolerance in plant pathogenic Pseudomonas The antioxidant systems vis à vis reactive oxygen species during plant-pathogen interaction Selected reactive oxygen species and antioxidant enzymes in common bean after Pseudomonas syringae pv. phaseolicola and Botrytis cinerea infection Identification of Pseudomonas syringae pv. actinidiae as causal agent of bacterial canker of yellow kiwifruit (Actinidia chinensis Planchon) in Central Italy Molecular and phenotypic features of Pseudomonas syringae pv. actinidiae isolated during recent epidemics of bacterial canker of yellow kiwifruit (Actinidia chinensis) in central Italy Isolation of total RNA from tissues rich in polyphenols and polysaccharides of mangrove plants Guideline to reference gene selection for quantitative real-time PCR Analysis of relative gene expression data using real-time quantitative PCR and the 2 −ΔΔCt method This work was financed by the Regione Campania Programme under the grant agreement UR.CO. seedlings using serial analysis of gene expression (SAGE) Selection and validation of reference genes for quantitative gene expression studies by real-time PCR in eggplant (Solanum melongena L) Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera Selection of reference genes for expression studies in Cicer arietinum L.: analysis of cyp81E3 gene expression against Ascochyta rabiei Normalisation of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations Analysis of qPCR reference gene stability determination methods and a practical approach for efficiency calculation on a turbot (Scophthalmus maximus) gonad dataset Identification and validation of reference genes for normalization of transcripts from virus-infected Arabidopsis thaliana Reference gene selection for quantitative real-time PCR normalization in Caragana intermedia under different abiotic stress conditions The choice of reference genes for assessing gene expression in sugarcane under salinity and drought stresses Identification of a novel reference gene for apple transcriptional profiling under postharvest conditions keywords: analysis; deliciosa; dose; expression; gapdh; genes; leaves; normalization; pcr; reference; rgs; time cache: cord-001858-nmi39n6h.txt plain text: cord-001858-nmi39n6h.txt item: #10 of 194 id: cord-001921-73esrper author: Lin, Cheng-Yung title: Zebrafish and Medaka: new model organisms for modern biomedical research date: 2016-01-28 words: 7754 flesch: 36 summary: Light and dark-Red fish, blue fish and Glow-in-dark fish Modification of bacterial artificial chromosomes through chi-stimulated homologous recombination and its application in zebrafish transgenesis Artificial chromosome transgenesis reveals longdistance negative regulation of rag1 in zebrafish Multiple upstream modules regulate zebrafish myf5 expression Use of the GAL4-UAS technique for targeted gene expression in zebrafish UDP-glucose dehydrogenase required for cardiac valve formation in zebrafish Activation of Notch signaling pathway precedes heart regeneration in zebrafish K-ATPase is essential for embryonic heart development in the zebrafish The embryonic vertebrate heart tube is a dynamic suction pump Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences Zebrafish cardiac development requires a conserved secondary heart field Tbx1 is required for second heart field proliferation in zebrafish Novel regulatory sequence − 82/-62 functions as a key element to drive the somite-specificity of zebrafish myf-5 Foxd3 mediates zebrafish myf5 expression during early somitogenesis FoxD5 mediates anterior-posterior polarity through upstream modulator Fgf signaling during zebrafish somitogenesis Inactivation of zebrafish mrf4 leads to myofibril misalignment and motor axon growth disorganization Novel cis-element in intron 1 represses somite expression of zebrafish myf-5 MicroRNA-3906 regulates fast muscle differentiation through modulating the target gene homer-1b in zebrafish embryos Novel intronic microRNA represses zebrafish myf5 promoter activity through silencing dickkopf-3 gene Zebrafish Dkk3a protein regulates the activity of myf5 promoter through interaction with membrane receptor integrin α6b dickkopf-3-related gene regulates the expression of zebrafish myf5 gene through phosphorylated p38a-dependent Smad4 activity Myogenic regulatory factors Myf5 and Myod function distinctly during craniofacial myogenesis of zebrafish The transcription factor Six1a plays an essential role in the craniofacial myogenesis of zebrafish Normal function of Myf5 during gastrulation is required for pharyngeal arch cartilage development in zebrafish embryos Differential requirements for myogenic regulatory factors distinguish medial and lateral somitic, cranial and fin muscle fibre populations Retina-specific ciselements and binding nuclear proteins of carp rhodopsin gene Egr1 gene knockdown affects embryonic ocular development in zebrafish The embryonic expression patterns and the knockdown phenotypes of zebrafish ADP-ribosylation factor-like 6 interacting protein gene Arl6ip1 plays a role in proliferation during zebrafish retinogenesis Zebrafish arl6ip1 is required for neural crest development during embryogenesis Ras-related nuclear protein is required for late developmental stages of retinal cells in zebrafish eyes Transgenic zebrafish model to study translational control mediated by upstream open reading frame of human chop gene A parsimonious model for gene regulation by miRNAs Gene silencing by microRNAs: contributions of translational repression and mRNA decay Regulation of mRNA translation and stability by microRNAs MicroRNAs: target recognition and regulatory functions microRNA target predictions in animals Labeled microRNA pull-down assay system: an experimental approach for high-throughput identification of microRNAtarget mRNAs miR-1 and miR-206 regulate angiogenesis by modulating VegfA expression in zebrafish MiR-1 and miR-206 target different genes to have opposing roles during angiogenesis in zebrafish embryos Concise review: new frontiers in microRNA-based tissue regeneration Administration of microRNA-210 promotes spinal cord regeneration in mice Regulation of neonatal and adult mammalian heart regeneration by the miR-15 family Integrated analyses of zebrafish miRNA and mRNA expression profiles identify miR-29b and miR-223 as potential regulators of optic nerve regeneration Transplantation and in vivo imaging of multilineage engraftment in zebrafish bloodless mutants Hematopoiesis: an evolving paradigm for stem cell biology Transcriptional regulation of hematopoietic stem cell development in zebrafish Mutantspecific gene programs in the zebrafish Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis Prostaglandin E2 enhances human cord blood stem cell xenotransplants and shows long-term safety in preclinical nonhuman primate transplant models From Zebrafish to human: modular medical models Amiodarone induces overexpression of similar to versican b to repress the EGFR/Gsk3b/Snail signaling axis during cardiac valve formation of zebrafish embryos Cancer metastasis and EGFR signaling is suppressed by Amiodarone-induced Versican V2 In vivo recording of adult zebrafish electrocardiogram and assessment of drug-induced QT prolongation Zebrafish model for human long QT syndrome In-vitro recording of adult zebrafish heart electrocardiogram -a platform for pharmacological testing Liver development and cancer formation in zebrafish Zebrafish as a cancer model Zebrafish modelling of leukaemias Catch of the day: zebrafish as a human cancer model Zebrafish as a cancer model system A keratin 18 transgenic zebrafish Tg(k18(2.9):RFP) treated with inorganic arsenite reveals visible overproliferation of epithelial cells BRAF mutations are sufficient to promote nevi formation and cooperate with p53 in the genesis of melanoma The pathogenesis of cancer metastasis: the 'seed and soil' hypothesis revisited Zebrafish xenotransplantation as a tool for in vivo cancer study Metastatic behaviour of primary human tumours in a zebrafish xenotransplantation model Calpain 2 is required for the invasion of glioblastoma cells in the zebrafish brain microenvironment Distinct contributions of angiogenesis and vascular co-option during the initiation of primary microtumors and micrometastases Visualizing extravasation dynamics of metastatic tumor cells A novel zebrafish xenotransplantation model for study of glioma stem cell invasion Quantitative phenotyping-based in vivo chemical screening in a zebrafish model of leukemia stem cell xenotransplantation Zebrafish-based systems pharmacology of cancer metastasis Discovering chemical modifiers of oncogene-regulated hematopoietic differentiation STK-1, the human homolog of Flk-2/Flt-3, is selectively expressed in CD34+ human bone marrow cells and is involved in the proliferation of early progenitor/ stem cells Functions of flt3 in zebrafish hematopoiesis and its relevance to human acute myeloid leukemia Cancer-associated metabolite 2-hydroxyglutarate accumulates in acute myelogenous leukemia with isocitrate dehydrogenase 1 and 2 mutations Regulation of cancer cell metabolism Functions of idh1 and its mutation in the regulation of developmental hematopoiesis in zebrafish Inducible and repressable oncogene-addicted hepatocellular carcinoma in Tet-on xmrk transgenic zebrafish An inducible kras (V12) transgenic zebrafish model for liver tumorigenesis and chemical drug screening A transgenic zebrafish liver tumor model with inducible Myc expression reveals conserved Myc signatures with mammalian liver tumors Xmrk, kras and myc transgenic zebrafish liver cancer models share molecular signatures with subsets of human hepatocellular carcinoma Gaining translational momentum: more zebrafish models for neuroscience research Zebrafish as an emerging model for studying complex brain disorders Zebrafish models for translational neuroscience research: from tank to bedside Zebrafish models of major depressive disorders Threedimensional neurophenotyping of adult zebrafish behavior Aquatic blues: modeling depression and antidepressant action in zebrafish Social modulation of brain monoamine levels in zebrafish Can zebrafish learn spatial tasks? keywords: cancer; cells; development; embryos; example; expression; gene; heart; human; line; mir-1; mir-206; model; myf5; promoter; transgenic; vegfaa; zebrafish cache: cord-001921-73esrper.txt plain text: cord-001921-73esrper.txt item: #11 of 194 id: cord-002142-tdgu9sr9 author: Reniere, Michelle L. title: An In Vivo Selection Identifies Listeria monocytogenes Genes Required to Sense the Intracellular Environment and Activate Virulence Factor Expression date: 2016-07-14 words: 9592 flesch: 42 summary: The environmental cues that lead to temporal and spatial control of L. monocytogenes virulence gene expression are poorly understood. PrfA is a cAMP receptor protein (Crp) family transcriptional regulator that is absolutely essential for L. monocytogenes virulence gene expression and pathogenesis keywords: acta; activation; bacteria; cells; expression; fig; glutathione; growth; host; infection; intracellular; listeria; monocytogenes; mutants; plaque; prfa; virulence; yjbh cache: cord-002142-tdgu9sr9.txt plain text: cord-002142-tdgu9sr9.txt item: #12 of 194 id: cord-002366-t94aufs3 author: Aurrecoechea, Cristina title: EuPathDB: the eukaryotic pathogen genomics database resource date: 2017-01-04 words: 3784 flesch: 40 summary: The Galaxy toolshed contains many tools for data analysis. The workspace is accessed through the 'Analyze My Experiment' (Figure 2A ) tab on the home page of any EuPathDB resource and can be used to upload your own data e.g. RNA-seq reads, compose and run preconfigured or custom workflows ( Figure 2B and C), retrieve your results, visualize them in EuPathDB ( Figure 2D ), and share workflows and data analysis results with colleagues. keywords: analysis; data; database; eupathdb; figure; gene; genome; host; search; sets; transcript cache: cord-002366-t94aufs3.txt plain text: cord-002366-t94aufs3.txt item: #13 of 194 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 cache: cord-003044-9uqa39j9.txt plain text: cord-003044-9uqa39j9.txt item: #14 of 194 id: cord-003196-fdb6az0v author: Casalino-Matsuda, S. Marina title: Hypercapnia Alters Expression of Immune Response, Nucleosome Assembly and Lipid Metabolism Genes in Differentiated Human Bronchial Epithelial Cells date: 2018-09-10 words: 4666 flesch: 28 summary: Gene expression was assessed on Affymetrix microarrays, and subjected to gene ontology analysis for biological process and cluster-network representation. These changes in gene expression indicate the potential for hypercapnia to impact bronchial epithelial cell function in ways that may contribute to poor clinical outcomes in patients with severe acute or advanced chronic lung diseases. GO biological process-associated gene clusters targeted by hypercapnia. keywords: airway; analysis; assembly; cells; disease; expression; genes; histone; human; hypercapnia; lung; nhbe; nucleosome; tlr4 cache: cord-003196-fdb6az0v.txt plain text: cord-003196-fdb6az0v.txt item: #15 of 194 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 cache: cord-003254-yiqdsf9z.txt plain text: cord-003254-yiqdsf9z.txt item: #16 of 194 id: cord-003387-82573enr author: Nam, Gyu-Hwi title: Gene expression profiles alteration after infection of virus, bacteria, and parasite in the Olive flounder (Paralichthys olivaceus) date: 2018-12-24 words: 5180 flesch: 34 summary: A lot of studies reported earlier were focused on gene expression analysis of single pathogen and specifically defined the expression pattern of limited genes [32] [33] Fish physiology and biochemistry Gonadal transcriptome analysis of male and female olive flounder (Paralichthys olivaceus) De Novo assembly of the Japanese flounder (Paralichthys olivaceus) spleen transcriptome to identify putative genes involved in immunity Differentially expressed genes after viral haemorrhagic septicaemia virus infection in olive flounder (Paralichthys olivaceus) cDNA microarray analysis of viral hemorrhagic septicemia infected olive flounder, Paralichthys olivaceus: immune gene expression at different water temperature Transcriptional analysis of olive flounder lectins in response to VHSV infection Immune response of olive flounder (Paralichthys olivaceus) infected with the myxosporean parasite Kudoa septempunctata Cloning and Expression Analysis of Cathepsin D in the Olive Flounder Paralichthys olivaceus Distribution of marine birnavirus in cultured olive flounder Paralichthys olivaceus in Korea keywords: analysis; degs; expression; fish; flounder; genes; immune; infection; olivaceus; olive; paralichthys; pathogens; transcriptome; virus cache: cord-003387-82573enr.txt plain text: cord-003387-82573enr.txt item: #17 of 194 id: cord-003514-yyzbv7ys author: Arslan, Mehboob title: Dynamic Expression of Interferon Lambda Regulated Genes in Primary Fibroblasts and Immune Organs of the Chicken date: 2019-02-14 words: 6092 flesch: 40 summary: The antiviral effector IFITM3 disrupts intracellular cholesterol homeostasis to block viral entry Marek's disease virus-induced immunosuppression: Array analysis of chicken immune response gene expression profiling Cloning, expression and functional characterization of chicken CCR6 and its ligand CCL20 Unique chemotactic response profile and specific expression of chemokine receptors CCR4 and CCR8 by CD4+ CD25+ regulatory T cells Identification, mapping, and phylogenetic analysis of three novel chicken CC chemokines Unique features of chicken Toll-like receptors Expression of the avian-specific toll-like receptor 15 in chicken heterophils is mediated by gram-negative and gram-positive bacteria, but not TLR agonists Diacylated lipopeptide from Mycoplasma synoviae mediates TLR15 induced innate immune responses IFN-λ: A new spotlight in innate immunity against influenza virus infection Differential responses of innate immunity triggered by different subtypes of influenza a viruses in human and avian hosts Type III interferon gene expression in response to influenza virus infection in chicken and duck embryonic fibroblasts Distinct roles of type I and type III interferons in intestinal immunity to homologous and heterologous rotavirus infections Interferon-λ and interleukin 22 act synergistically for the induction of interferon-stimulated genes and control of rotavirus infection Interferons and viral infections Innate immune sensing of DNA viruses Neuronal activity-dependent local activation of dendritic unfolded protein response promotes expression of brain-derived neurotrophic factor in cell soma Considering their vital role in immune pathways, cytokine gene expression is widely employed as an indicator for the immune response. keywords: avian; cells; chicken; chifn; expression; figure; genes; ifns; immune; pathway; response; type; virus cache: cord-003514-yyzbv7ys.txt plain text: cord-003514-yyzbv7ys.txt item: #18 of 194 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 cache: cord-003898-y6zpvw84.txt plain text: cord-003898-y6zpvw84.txt item: #19 of 194 id: cord-003900-5p4ektzv author: Bai, Hao title: Allele-Specific Expression of CD4(+) T Cells in Response to Marek’s Disease Virus Infection date: 2019-09-17 words: 6858 flesch: 51 summary: [12] found that SNPs in ASE genes account for more than 83% of the additive genetic variation of genetic resistance to MD, demonstrating that most of the genes exhibiting ASE are strong candidates for studying MD resistance. The top diseases and disorder clusters, including inflammatory response, immunological disease, hematological disease, cancer, and To identify potential GO terms and pathways, a list of significant ASE genes (FDR < 0.05) was firstly submitted to DAVID (version 6.7) for biological processing and pathway enrichment. keywords: analysis; ase; cell; disease; genes; infection; mdv; non; pathway; snps; table cache: cord-003900-5p4ektzv.txt plain text: cord-003900-5p4ektzv.txt item: #20 of 194 id: cord-004222-z4butywi author: Joyce, Collin title: Comparisons of the antibody repertoires of a humanized rodent and humans by high throughput sequencing date: 2020-01-24 words: 3724 flesch: 38 summary: Robust estimates of overall immune-repertoire diversity from high-throughput measurements on samples Complete humanization of the mouse immunoglobulin loci enables efficient therapeutic antibody discovery Mechanisms that shape human antibody repertoire development in mice transgenic for human ig H and L chain loci Tissue-specific expressed antibody variable gene repertoires Intrinsic bias and public rearrangements in the human immunoglobulin Vλ light chain repertoire Immunoglobulin light chain gene rearrangements, receptor editing and the development of a Self-Tolerant antibody repertoire Microbial symbionts regulate the primary ig repertoire B cell superantigens in the human intestinal microbiota High frequency of shared clonotypes in human B cell receptor repertoires Moderated estimation of fold change and dispersion for RNA-seq data with DESeq. S4a-c) were found to be very similar to the observed data Columns are antibody repertoires and rows are gene segments. keywords: animal; antibody; chain; fig; gene; heavy; human; omnirat; repertoire; usage cache: cord-004222-z4butywi.txt plain text: cord-004222-z4butywi.txt item: #21 of 194 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 cache: cord-004879-pgyzluwp.txt plain text: cord-004879-pgyzluwp.txt item: #22 of 194 id: cord-004893-28mrzvsc author: Pavesi, Angelo title: On the Informational Content of Overlapping Genes in Prokaryotic and Eukaryotic Viruses date: 1997 words: 3788 flesch: 34 summary: Comparison of amino acid composition revealed an increased frequency of amino acid residues with a high level of degeneracy (arginine, leucine, and serine) in the proteins encoded by overlapping genes; this peculiar feature of overlapping genes can be viewed as a way with which they may expand their coding ability and gain new, specialized functions. In this language, overlapping genes represent an unusual pattern, as two, or exceptionally three, out-of-phase reading frames may lie in a single nucleotide sequence. keywords: acid; codon; genes; nonoverlapping; overlapping; regions; value cache: cord-004893-28mrzvsc.txt plain text: cord-004893-28mrzvsc.txt item: #23 of 194 id: cord-005089-jwcmmfdw author: Zhao, Yin-He title: Extended expression of B-class MADS-box genes in the paleoherb Asarum caudigerum date: 2009-11-11 words: 5303 flesch: 49 summary: The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression The ABC model and its applicability to basal angiosperms MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0 Development of floral organ identity: stories from the MADS house A short history of MADS-box genes in plants The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools From floral induction to floral shape Evolution of class B floral homeotic proteins: Obligate heterodimerization originated from homodimerization On the origin of class B floral homeotic genes: Functional substitution and dominant inhibition in Arabidopsis by expression of an orthologue from the gymnosperm Gnetum A geraniol-synthase gene from Cinnamomum tenuipilum Expressed sequence tags (ESTs) and phylogenetic analysis of floral genes from a paleoherb species, Asarum caudigerum ) They proposed a 'fading borders' model of floral gene expression in these basal angiosperms, and Kim et al. keywords: box; caudigerum; class; et al; expression; genes; leaves; mads; whorl cache: cord-005089-jwcmmfdw.txt plain text: cord-005089-jwcmmfdw.txt item: #24 of 194 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 cache: cord-005147-mvoq9vln.txt plain text: cord-005147-mvoq9vln.txt item: #25 of 194 id: cord-005216-potmzdfs author: Sun, Dong title: Bioinformatics Analysis of Genes and Pathways of CD11b(+)/Ly6C(intermediate) Macrophages after Renal Ischemia-Reperfusion Injury date: 2018-03-15 words: 3311 flesch: 43 summary: Gene expression analysis was performed on an Affymetrix Mouse Genome 430 2.0 Array platform (Affymetrix, USA) for which the transcription profile GSE75808 from the Gene Expression Omnibus (GEO) database, an open-access functional genomics data repository was downloaded. Incidence, outcomes, and risk factors of community-acquired and hospital-acquired acute kidney injury: A Retrospective Cohort Study Identifying acute kidney injury in the community--a novel informatics approach Netrin-1 regulates the inflammatory response of neutrophils and macrophages, and suppresses ischemic acute kidney injury by inhibiting COX-2-mediated PGE2 production Long-term outcome of severe acute kidney injury survivors followed by nephrologists in a developing country Recognition and management of acute kidney injury in the International Society of Nephrology 0by25 Global Snapshot: a multinational cross-sectional study Small interfering RNA targeting TNF-alpha gene significantly attenuates renal ischemia-reperfusion injury in mice Double-negative alphabeta T cells are early responders to AKI and are found in human kidney Vascular-resident CD169-positive monocytes and macrophages control neutrophil accumulation in the kidney with ischemia-reperfusion injury MicroRNA 26a modulates regulatory T cells expansion and attenuates renal ischemia-reperfusion injury GM-CSF promotes macrophage alternative activation after renal ischemia/reperfusion injury Distinct macrophage phenotypes contribute to kidney injury and repair Macrophage-mediated injury and repair after ischemic kidney injury Renal F4/80+ CD11c+ mononuclear phagocytes display phenotypic and functional characteristics of macrophages in health and in adriamycin nephropathy Differential Ly6C expression after renal ischemia-reperfusion identifies unique macrophage populations Role of galectin-3 in classical and alternative macrophage activation in the liver following acetaminophen intoxication Improved normalization of systematic biases affecting ion current measurements in label-free proteomics data Time-series analysis in imatinib-resistant chronic myeloid leukemia K562-cells under different drug treatments Differential gene expression profiling analysis in workers occupationally exposed to benzene FunRich: An open access standalone functional enrichment and interaction network analysis tool Proteomic Differences between Developmental Stages of Toxoplasma gondii Revealed by iTRAQ-Based Quantitative Transcriptome analysis of chicken kidney tissues following coronavirus avian infectious bronchitis virus infection cytoHubba: identifying hub objects and sub-networks from complex interactome Effects of beta-catenin on differentially expressed genes in multiple myeloma MIF inhibits monocytic movement through a non-canonical receptor and disruption of temporal Rho GTPase activities in U-937 cells Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo SV40 small T antigen and PP2A phosphatase in cell transformation Ppp2ca knockout in mice spermatogenesis Protein phosphatase 2A is a negative regulator of IL-2 production in patients with systemic lupus erythematosus Cutting edge: mechanisms of IL-2-dependent maintenance of functional regulatory T cells Protein phosphatase 2A Calpha is involved in osteoclastogenesis by regulating RANKL and OPG expression in osteoblasts Restoration of PPP2CA expression reverses epithelial-to-mesenchymal transition and suppresses prostate tumour growth and metastasis in an orthotopic mouse model Loss of tumor suppressor RPL5/RPL11 does not induce cell cycle arrest but impedes proliferation due to reduced ribosome content and translation capacity Ribosomal proteins L11 and L5 activate TAp73 by overcoming MDM2 inhibition The ribosomal protein gene RPL5 is a haploinsufficient tumor suppressor in multiple cancer types ACA small nucleolar RNA pseudouridylation pockets bind substrate RNA to form three-way junctions that position the target U for modification Cb-f5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX/ACA-motif snoRNPs and constitute a common bipartite structure Nhp2p and Nop10p are essential for the function of H/ACA snoRNPs Expression of the human homologue of the small nucleolar RNA-binding protein NHP2 gene during monocytic differentiation of U937 cells Structure of the Shq1-Cbf5-Nop10-Gar1 complex and implications for H/ACA RNP biogenesis and dyskeratosis congenita keywords: /ly6c; analysis; cd11b; cells; expression; genes; int; iri; macrophages cache: cord-005216-potmzdfs.txt plain text: cord-005216-potmzdfs.txt item: #26 of 194 id: cord-005432-mqyvpepo author: Ma, Z title: Redirecting adenovirus to pulmonary endothelium by cationic liposomes date: 2002-02-22 words: 3992 flesch: 44 summary: The improvement in pulmonary gene transfer was associated with a decrease in the level of gene expression in the liver. The improvement in pulmonary gene transfer was associated with a decrease in the level of gene expression in the liver. keywords: cationic; expression; gene; liposomes; lung; transfer; vectors cache: cord-005432-mqyvpepo.txt plain text: cord-005432-mqyvpepo.txt item: #27 of 194 id: cord-005476-q6o5239w author: Griesenbach, U title: Gene therapy for cystic fibrosis: an example for lung gene therapy date: 2004-09-29 words: 5913 flesch: 36 summary: The cells of the pulmonary airways The Molecular and Metabolic Basis of Inherited Disease Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA Non-invasive liposome-mediated gene delivery can correct the ion transport defect in cystic fibrosis mutant mice Correction of the cystic fibrosis defect in vitro by retrovirus-mediated gene transfer Expression of the cystic fibrosis gene in adult human lung Immunological hurdles to lung gene therapy Delivery of gene transfer vectors to lung: obstacles and the role of adjunct techniques for airway administration Barriers to and new approaches for gene therapy and gene delivery in cystic fibrosis Retargeting the coxsackievirus and adenovirus receptor to the apical surface of polarized epithelial cells reveals the glycocalyx as a barrier to adenovirus-mediated gene transfer Role of alveolar macrophages in rapid elimination of adenovirus vectors administered to the epithelial surface of the respiratory tract Aerosol delivery of a beta-galactosidase adenoviral vector to the lungs of rodents Adenovirus-mediated persistent cystic fibrosis transmembrane conductance regulator expression in mouse airway epithelium Safety of local delivery of low-and intermediate-dose adenovirus gene transfer vectors to individuals with a spectrum of morbid conditions Aerosol and lobar administration of a recombinant adenovirus to individuals with cystic fibrosis. Initial results for lung gene transfer are encouraging and demonstrate that the transfection efficiency of naked DNA can be enhanced in the presence of electrical fields 49 (and Ian Pringle, personal communication). keywords: administration; airway; cells; cftr; cystic; expression; fibrosis; gene; lung; therapy; transfection; transfer cache: cord-005476-q6o5239w.txt plain text: cord-005476-q6o5239w.txt item: #28 of 194 id: cord-006230-xta38e7j author: None title: Deutsche Gesellschaft für Experimentelle und Klinische Pharmakologie und Toxikologie e.V. date: 2012-02-22 words: 136000 flesch: 40 summary: In in-vitro studies on rat and canine mast cells and human mast cell leukemia cells HMC1.2 BZ at micromolar concentrations inhibited mediator release which appeared to be related to an inhibition of the intracellular cAMP pathway. Previous work showed that mouse cells lacking the immediate-early gene c-fos are hypersensitive to ultraviolet (UVC) light. keywords: acid; activation; activity; acute; addition; adducts; agonist; aim; analysis; animals; anti; apoptosis; approach; assay; assessment; binding; blood; brain; calcium; camp; cancer; cancer cells; cardiac; cell line; cells; cellular; cgmp; changes; channels; chronic; clinical; complex; compounds; concentration; conclusion; conditions; contrast; control; current; damage; data; days; death; decrease; deficient; development; differences; differentiation; disease; dna; dose; drug; e.g.; effects; endothelial; enzyme; evidence; experiments; exposure; expression; factor; failure; family; fibroblasts; findings; fold; food; formation; function; für; g protein; gene; gene expression; germany; glucose; growth; health; heart; human; hypertrophy; increase; induction; inflammation; inhibition; inhibitors; institut; insulin; interaction; intracellular; kidney; kinase; leads; levels; like; line; liver; loss; low; lung; macrophages; mechanisms; membrane; methods; mice; model; mouse; mrna; muscle cells; mutations; nanoparticles; ndpk; non; novel; number; pain; pathway; patients; pcr; pharmakologie; phosphorylation; plasma; potential; presence; present; pressure; primary; processes; production; products; proliferation; promoter; properties; protein; protein expression; pulmonary; rats; receptor; reduced; regulation; release; response; results; risk; rkip; role; ros; samples; selective; signaling; site; skin; smooth; specific; stimulation; stress; studies; study; substances; subunits; synthesis; system; t cells; target; test; tested; therapy; time; tissue; toxicity; toxikologie; toxin; transcription; transport; treatment; tumor; tumor cells; type; universität; uptake; values; vascular; vitro; vivo; water cache: cord-006230-xta38e7j.txt plain text: cord-006230-xta38e7j.txt item: #29 of 194 id: cord-007259-vj9tv3or author: Guo, Feng-Biao title: Accurate prediction of human essential genes using only nucleotide composition and association information date: 2017-06-15 words: 5671 flesch: 46 summary: Three groups recently identified essential genes in human cancer cell lines using wet experiments and it provided wonderful opportunity to accomplish our idea. Catalogs of essential genes on a whole-genome scale, determined using wet-lab methods, are available for a large number of prokaryotic and eukaryotic organisms which are provided in DEG and OGEE databases (Chen et al., 2012; Luo et al., 2014) . keywords: curve; features; genes; human; interval cache: cord-007259-vj9tv3or.txt plain text: cord-007259-vj9tv3or.txt item: #30 of 194 id: cord-007390-3txwm6wr author: Hu, Yu‐Chen title: Baculovirus Vectors for Gene Therapy date: 2006-09-22 words: 9841 flesch: 27 summary: To date, there is no direct evidence showing that spontaneous integration of baculoviral DNA occurs in the absence of an antibiotic resistance gene and selective pressure, but extensive studies examining the state and fate of introduced viral DNA are necessary to further prove the safety of baculovirus gene therapy vectors. Baculovirus ETL promoter acts as a shuttle promoter between insect cells and mammalian cells Overexpression of promyelocytic leukemia protein precludes the dispersal of ND10 structures and has no effect on accumulation of infectious herpes simplex virus 1 or its proteins Trends in the development of baculovirus expression vectors Latest development in viral vectors for gene therapy Baculovirus-mediated gene transfer into pancreatic islet cells Liposome-induced activation of the classical complement pathway does not require immunoglobulin Gene therapy death prompts review of adenovirus vector Baculovirus entry into human hepatoma cells Efficient delivery and regulable expression of hepatitis C virus full-length and minigenome constructs in hepatocyte-derived cell lines using baculovirus vectors Chromosomal integration of transduced recombinant baculovirus DNA in mammalian cells Baculoviral display of functional scFv and synthetic IgG-binding domains Induction of apoptosis in rabbit kidney cell under high-level expression of bovine herpesvirus 1 U(s)ORF8 product RNA interference mediated in human primary cells via recombinant baculoviral vectors Specific binding of baculoviruses displaying gp64 fusion proteins to mammalian cells Expression and trafficking of fluorescent viral membrane proteins in baculovirustransduced BHK cells Hybrid cytomegalovirus enhancer H-1 promoter-based plasmid and baculovirus vectors mediate effective RNA interference Site-specific integration in mammalian cells mediated by a new hybrid baculovirus-adeno-associated virus vector Hepatocyte-specific gene expression by baculovirus pseudotyped with vesicular stomatitis virus envelope glycoprotein Baculovirus and insect cell gene expression-review of baculovirus biotechnology Titration of K-ATP channel expression in mammalian cells utilizing recombinant baculovirus transduction In vivo gene transfer in mouse skeletal muscle mediated by baculovirus vectors Autographa californica baculoviruses with large genomic deletions are rapidly generated in infected insect cells Evaluation of baculovirus expression vectors with enhanced stability in continuous cascaded insect-cell bioreactors Activation of the complement system by synthetic DNA complexes: A potential barrier for intravenous gene delivery Generation of recombinant influenza virus using baculovirus delivery vector Rapid expression of recombinant proteins in modified CHO cells using the baculovirus system Enhanced gene delivery by avidin-displaying baculovirus Improvement in nuclear entry and transgene expression of baculoviruses by disintegration of microtubules in human hepatocytes Gene transfer into hepatocytes and human liver tissue by baculovirus vectors Efficient transduction of neural cells in vitro and in vivo by a baculovirusderived vector Efficient gene transfer into various mammalian cells, including non-hepatic cells, by baculovirus vectors Production of human beta interferon in insect cells infected with a baculovirus expression vector A novel method using baculovirusmediated gene transfer for production of recombinant adeno-associated virus vectors Combination treatment for osteosarcoma with baculoviral vector mediated gene therapy (p53) and keywords: baculovirus; cells; complement; delivery; dna; efficiency; envelope; et al; expression; gene; gp64; human; mammalian; promoter; protein; therapy; transduction; transfer; transgene; vectors; vivo cache: cord-007390-3txwm6wr.txt plain text: cord-007390-3txwm6wr.txt item: #31 of 194 id: cord-007708-hr4smx24 author: van Kampen, Antoine H. C. title: Taking Bioinformatics to Systems Medicine date: 2015-08-13 words: 8773 flesch: 27 summary: Early approaches for network inference (also called reverse engineering ) used only gene expression data to reconstruct gene networks. This showed that the intrinsic subtypes (basal, luminal A and B, HER2) that had previously been determined using gene expression data only could be largely confi rmed in an integrated analysis of a large number of breast tumors. keywords: analysis; approaches; bioinformatics; biological; data; databases; disease; example; expression; gene; human; information; integration; medicine; molecular; networks; omics; protein; systems cache: cord-007708-hr4smx24.txt plain text: cord-007708-hr4smx24.txt item: #32 of 194 id: cord-007760-it9wach2 author: Jiao, Long R. title: Suicide Gene Therapy in Liver Tumors date: 2004 words: 7123 flesch: 47 summary: To safeguard the development of human gene therapy for clinical application, various countries have now established regulatory bodies for gene therapy to ensure safety and benefit for humankind. Furthermore, sampling of treated tissues will require minimal additional morbidity for study patients. keywords: adenovirus; cancer; cells; dose; gene; injection; liver; patients; study; therapy; treatment; tumor cache: cord-007760-it9wach2.txt plain text: cord-007760-it9wach2.txt item: #33 of 194 id: cord-008777-i2reanan author: None title: ECB12: 12th European Congess on Biotechnology date: 2005-07-19 words: 151661 flesch: 40 summary: During the process development for protein production, short time to market and the demand for cheap processes dominate today's process development. Interdependence of the impact of methanol and oxygen supply on protein production with recombinant Pichia pastoris N.K. Khatri, F. Hoffmann Martin-Luther-University Halle-Wittenberg, Institute for Biotechnology, Halle D-06120, Germany. keywords: acid; acid production; activities; activity; addition; adsorption; affinity; aim; alternative; amino; analysis; animal; ankara; antibody; application; applied; approach; assay; bacillus; bacteria; batch; bed; binding; biology; biomass; bioreactor; biosynthesis; biotechnology; capacity; carbon; case; cell; cell growth; cerevisiae; changes; chemical; chitosan; chromatography; coli; column; complex; composition; compounds; concentration; conditions; control; conversion; cost; cultivation; culture; data; days; degradation; denmark; department; design; development; differences; different; disease; dna; e.g.; effect; efficiency; energy; engineering; environmental; enzymatic; enzyme; enzyme activity; enzyme production; ethanol; ethanol production; experiments; expression; extract; factors; fed; fermentation; fermentation process; flow; flux; food; formation; function; gel; gene; gene expression; genome; glucose; group; growth; health; high; host; human; hydrolysis; identification; increase; induction; industrial; industry; influence; institute; interest; intracellular; knowledge; laboratory; level; limited; line; lipase; liquid; mail; mass; maximum; media; medium; metabolic; metabolites; method; microbial; microorganisms; milk; model; molecular; molecules; natural; network; new; niger; nitrogen; non; novel; number; oil; operation; optimization; order; oxygen; parameters; pathway; pcr; peptide; performance; phase; phosphate; plant; plasmid; potential; presence; present; procedure; process; processes; produce; production; production process; productivity; products; project; properties; protein; protein expression; protein production; purification; quality; range; rate; reaction; recombinant; regulation; removal; research; response; resulting; results; role; samples; scale; science; screening; separation; sequence; signal; source; species; specific; stability; state; step; strains; stress; structure; studies; study; substrate; sucrose; sugar; surface; synthesis; system; target; technical; technique; temperature; therapy; time; total; transfer; treatment; turkey; type; university; use; value; vitro; water; weight; work; yeast; yield cache: cord-008777-i2reanan.txt plain text: cord-008777-i2reanan.txt item: #34 of 194 id: cord-009664-kb9fnbgy author: None title: Oral presentations date: 2014-12-24 words: 71226 flesch: 44 summary: Resistance to penicillin, clindamycin and tetracycline fluctuated over time at~75%, 4−8% and 2−10% respectively. The median expected power was 10.0% (IQR, 7.2−13.6%) for a risk ratio for mortality of 0.85 between the compared groups; 14.7% (IQR, 10.6−21.8%) for a risk ratio of 0.80; and 7.9% (IQR, 6.3−10.2%) for a reduction in mortality from 30% to 25%. keywords: age; analysis; antibiotic; assay; associated; aureus; bacterial; blood; cases; cause; cdi; cells; clinical; common; community; conclusion; control; countries; culture; data; days; detection; diagnosis; different; difficile; disease; dna; drug; efflux; europe; expression; factors; gene; group; high; hospital; human; identification; incidence; increase; infections; influenza; isolates; laboratory; levels; like; methods; microbiology; model; mortality; mrsa; n =; negative; new; non; number; objectives; pathogens; patients; pcr; period; plasmid; pneumoniae; population; positive; potential; presence; present; prevalence; pvl; range; rate; resistance; resistance genes; response; results; risk; role; samples; screening; sensitivity; sequence; species; specimens; spread; strains; studies; study; susceptibility; system; testing; therapy; time; total; treatment; type; use; virus; years cache: cord-009664-kb9fnbgy.txt plain text: cord-009664-kb9fnbgy.txt item: #35 of 194 id: cord-010038-0m2f0eh4 author: Caspi, Jonathan title: Distribution of split DnaE inteins in cyanobacteria date: 2003-11-11 words: 4634 flesch: 51 summary: An alternative method for removal of split intein genes is to acquire a surrogate gene to replace the product of the split genes. Inteins are present in a variety of protein genes from diverse bacteria and archaea and in several eukaryotes. keywords: cyanobacteria; dnae; genes; intein; parts; protein; sequences; species; split cache: cord-010038-0m2f0eh4.txt plain text: cord-010038-0m2f0eh4.txt item: #36 of 194 id: cord-010278-loey5xq9 author: Huh, Changgoo title: Structural organization, expression and chromosomal mapping of the mouse cystatin-C-encoding gene (Cst3) date: 1995-01-23 words: 2850 flesch: 53 summary: There is evidence that induction of gene expression by TGF-13 is mediated by transcription factor AP-1. In this paper, we report the structural organization and expression of the mouse Cst3 gene, compare its regulatory elements with that of other Cst genes and map the Cst3 gene in the mouse. keywords: cst3; cystatin; gene; mouse; region; sequence cache: cord-010278-loey5xq9.txt plain text: cord-010278-loey5xq9.txt item: #37 of 194 id: cord-011630-lfm34fsw author: Li, Yan title: Epigenetic inheritance of circadian period in clonal cells date: 2020-05-27 words: 5704 flesch: 36 summary: Interestingly, we found that depletion of DNMT1 and DNMT3A had opposite effects on circadian period, suggesting non-redundant roles in circadian gene regulation. key: cord-011630-lfm34fsw authors: Li, Yan; Shan, Yongli; Kilaru, Gokhul Krishna; Berto, Stefano; Wang, Guang-Zhong; Cox, Kimberly H; Yoo, Seung-Hee; Yang, Shuzhang; Konopka, Genevieve; Takahashi, Joseph S title: Epigenetic inheritance of circadian period in clonal cells date: 2020-05-27 journal: nan DOI: 10.7554/elife.54186 sha: doc_id: 11630 cord_uid: lfm34fsw Circadian oscillations are generated via transcriptional-translational negative feedback loops. keywords: analysis; cell; clock; data; dna; et al; expression; figure; genes; knockdown; lines; methylation; period; periodicity cache: cord-011630-lfm34fsw.txt plain text: cord-011630-lfm34fsw.txt item: #38 of 194 id: cord-012035-rhpfpku9 author: Zhong, Hui-hai title: TRAIL-based gene delivery and therapeutic strategies date: 2019-08-23 words: 8766 flesch: 35 summary: Codelivery of pTRAIL and monensin using dualtargeting and stimuli-responsive self-assembling nanocomposites TRAIL and chemotherapeutic drugs in cancer therapy Evaluation of efficiency of modified polypropylenimine (PPI) with alkyl chains as non-viral vectors used in co-delivery of doxorubicin and TRAIL plasmid In vivo treatment of tumors using host-guest conjugated nanoparticles functionalized with doxorubicin and therapeutic gene pTRAIL Plasmid pORF-hTRAIL and doxorubicin co-delivery targeting to tumor using peptide-conjugated polyamidoamine dendrimer Gene and doxorubicin codelivery system for targeting therapy of glioma Choline-derivate-modified nanoparticles for brain-targeting gene delivery Choline transporter-targeting and codelivery system for glioma therapy Co-delivery of pEGFP-hTRAIL and paclitaxel to brain glioma mediated by an angiopep-conjugated liposome Candoxin, a novel toxin from Bungarus candidus, is a reversible antagonist of muscle (alphabetagammadelta) but a poorly reversible antagonist of neuronal alpha 7 nicotinic acetylcholine receptors Co-delivery of TRAIL gene enhances the anti-glioblastoma effect of paclitaxel in vitro and in vivo MSC-delivered soluble TRAIL and paclitaxel as novel combinatory treatment for pancreatic adenocarcinoma In vitro and in vivo growth inhibition of drug-resistant ovarian carcinoma cells using a combination of cisplatin and a TRAIL-encoding retrovirus Is TRAIL the holy grail of cancer therapy? SAHA (vorinostat) facilitates functional polymer-based gene transfection via upregulation of ROS and synergizes with TRAIL gene delivery for cancer therapy Histone deacetylase inhibitor panobinostat potentiates the anti-cancer effects of mesenchymal stem cell-based sTRAIL gene therapy against malignant glioma Synergistic antitumor effects of CDK inhibitor SNS032 and an oncolytic adenovirus coexpressing TRAIL and Smac in pancreatic cancer Combination of AAV-TRAIL with miR-221-Zip therapeutic strategy overcomes the resistance to TRAIL induced apoptosis in liver cancer Competing interests: The authors declare no competing interests. DR5 is the highest affinity receptor Structural determinants of DISC function: new insights into death receptor-mediated apoptosis signalling Getting TRAIL back on track for cancer therapy Preclinical studies to predict the disposition of Apo2L/tumor necrosis factor-related apoptosisinducing ligand in humans: characterization of in vivo efficacy, pharmacokinetics, and safety Unexpected hepatotoxicity in a phase I study of TAS266, a novel tetravalent agonistic Nanobody(R) targeting the DR5 receptor Phase I dose-escalation study of recombinant human Apo2L/TRAIL, a dual proapoptotic receptor agonist, in patients with advanced cancer Phase 1b study of dulanermin (recombinant human Apo2L/TRAIL) in combination with paclitaxel, carboplatin, and bevacizumab in patients with advanced non-squamous nonsmall-cell lung cancer Trailing TRAIL resistance: novel targets for TRAIL sensitization in cancer cells TRAIL and apoptosis induction by TNF-family death receptors Nanocarriers for TRAIL delivery: driving TRAIL back on track for cancer therapy Antitumor activity and bystander effects of the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) gene Membrane-bound Fas ligand only is essential for Fas-induced apoptosis Liposomes decorated with Apo2L/TRAIL overcome chemoresistance of human hematologic tumor cells Polymers for gene delivery across length scales Overcoming gene-delivery hurdles: physiological considerations for nonviral vectors Adenoviralmediated transfer of the TNF-related apoptosis-inducing ligand/Apo-2 ligand gene induces tumor cell apoptosis Efficacy of combining ING4 and TRAIL genes in cancer-targeting gene virotherapy strategy: first evidence in preclinical hepatocellular carcinoma Non-viral vectors for gene-based therapy Design and development of polymers for gene delivery Nonviral vectors for gene delivery Barriers to nonviral gene delivery Progress in developing cationic vectors for non-viral systemic gene therapy against cancer A versatile vector for gene and oligonucleotide transfer into cells in culture and in vivo: polyethylenimine Toxicity of cationic lipids and cationic polymers in gene delivery New path to treating pancreatic cancer: TRAIL gene delivery targeting the fibroblast-enriched tumor microenvironment The use of myristic acid as a ligand of polyethylenimine/DNA nanoparticles for targeted gene therapy of glioblastoma A mannosylated PEI-CPP hybrid for TRAIL gene targeting delivery for colorectal cancer therapy Poly-gamma-glutamic acid-based GGT-targeting and surface camouflage strategy for improving cervical cancer gene therapy Co-delivery of gambogic acid and TRAIL plasmid by hyaluronic acid grafted PEI-PLGA nanoparticles for the treatment of triple negative breast cancer Biodegradable poly(amine-co-ester) terpolymers for targeted gene delivery Nano-structural effects on gene transfection: large, botryoid-shaped nanoparticles enhance DNA delivery via macropinocytosis and effective dissociation Polymeric nanoparticle-based delivery of TRAIL DNA for cancer-specific killing Esterase-activated chargereversal polymer for fibroblast-exempt cancer gene therapy Enzyme-responsive charge-reversal polymer-mediated effective gene therapy for intraperitoneal tumors Sandwich-type Au-PEI/DNA/PEI-Dexa nanocomplex for nucleus-targeted gene delivery in vitro and in vivo Nanoparticlemediated target delivery of TRAIL as gene therapy for glioblastoma Antitumor effect of human TRAIL on adenoid cystic carcinoma using magnetic nanoparticle-mediated gene expression Discovery of dendrimers and dendritic polymers: a brief historical perspective Dual targeting effect of Angiopep-2-modified, DNA-loaded nanoparticles for glioma Therapeutic efficacy of intravenously administered transferrin-conjugated dendriplexes on prostate carcinomas Regression of prostate tumors after intravenous administration of lactoferrinbearing polypropylenimine dendriplexes encoding TNF-alpha, TRAIL, and interleukin-12 A self-assembled coumarin-anchored dendrimer for efficient gene delivery and light-responsive drug delivery Triazine-modified dendrimer for efficient TRAIL gene therapy in osteosarcoma Modified PAMAM vehicles for effective TRAIL gene delivery to colon adenocarcinoma: in vitro and in vivo evaluation Peptide-guided gene delivery Development of a genetically engineered biomimetic vector for targeted gene transfer to breast cancer cells Intratracheal administration of a nanoparticle-based therapy with the angiotensin II type 2 receptor gene attenuates lung cancer growth PTEN and TRAIL genes loaded zein nanoparticles as potential therapy for hepatocellular carcinoma Advancing nonviral gene delivery: lipid-and surfactant-based nanoparticle design strategies A novel cationic lipid with intrinsic antitumor activity to facilitate gene therapy of TRAIL DNA Targeting tumor-associated fibroblasts for therapeutic delivery in desmoplastic tumors A multifunctional nanocarrier for efficient TRAIL-based gene therapy against hepatocellular carcinoma with desmoplasia in mice core-shell nanoparticles-based gene delivery for treatment of aggressive melanoma Multifunctional nucleus-targeting nanoparticles with ultra-high gene transfection efficiency for in vivo gene therapy Minimal criteria for defining multipotent mesenchymal stromal cells Human bone marrow and adipose tissue mesenchymal stem cells: a user's guide Mesenchymal stem/stromal cells as a delivery platform in cell and gene therapies How do mesenchymal stromal cells exert their therapeutic benefit? keywords: apoptosis; cancer; cells; combination; death; delivery; dr5; gene; mscs; pei; receptor; resistance; targeting; therapy; trail; transfection; treatment; tumor; vectors cache: cord-012035-rhpfpku9.txt plain text: cord-012035-rhpfpku9.txt item: #39 of 194 id: cord-012542-rsqon0w0 author: Abbas, Mostafa title: Machine learning based refined differential gene expression analysis of pediatric sepsis date: 2020-08-28 words: 4577 flesch: 44 summary: Recent advances in high-throughput transcriptomic technology have created opportunities for precision critical care medicine by enabling fast and clinically feasible profiling of gene expressions within few hours. [19] where the authors had reported four sets of sepsis marker genes with only few genes in common. keywords: analysis; auc; degs; expression; feature; genes; models; pediatric; selection; sepsis cache: cord-012542-rsqon0w0.txt plain text: cord-012542-rsqon0w0.txt item: #40 of 194 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 cache: cord-013171-wgn529rc.txt plain text: cord-013171-wgn529rc.txt item: #41 of 194 id: cord-014368-4nasrbs6 author: None title: Gene Chip for Viral Discovery date: 2003-11-17 words: 10009 flesch: 47 summary: This finding has important practical implications for spinal-cord patients-if different cells can perform the same functions, then surgeons have far more flexibility in how and where they can introduce electrodes or other functional enhancements into the brain. Presenting results from a series of long-term studies in monkeys, they demonstrate that the same set of brain cells can control two distinct movements, the reaching and grasping of a robotic arm. keywords: biology; brain; cell; control; development; dna; expression; function; genes; genome; growth; motor; pathways; proteins; receptor; researchers; sequence; signaling; system; text cache: cord-014368-4nasrbs6.txt plain text: cord-014368-4nasrbs6.txt item: #42 of 194 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 cache: cord-014462-11ggaqf1.txt plain text: cord-014462-11ggaqf1.txt item: #43 of 194 id: cord-014597-66vd2mdu author: None title: Abstracts from the 25th European Society for Animal Cell Technology Meeting: Cell Technologies for Innovative Therapies: Lausanne, Switzerland. 14-17 May 2017 date: 2018-03-15 words: 50744 flesch: 43 summary: [3] ) -Error frequency does not invalidate use of direct observation methods for cell cloning -Single cell seen by both scientists is highly likely to be monoclonal -During method development, strategies established to control potential sources of error ( Table 1 ) Use of a contemporaneous visualisation approach, a strict control strategy, and a suitable statistical model (which takes into account potential errors) results in: -The CACC method being at least as robust as the LDC method -The CACC method being a reliable, single-step method for cloning to achieve a high P(monoclonality) The main feature of our CI-SCREEN technology is the ability to combine the advantage of cell linesthe unlimited cell supplywith the advantage of primary cellsthe physiological relevance. keywords: addition; analysis; antibodies; antibody; approach; background; batch; bioreactor; cell; cell clones; cell culture; cell density; cell growth; cell line; cho; cho cell; clones; concentration; conditions; control; cultivation; cultures; data; day; development; experiments; expression; fed; feed; fig; fold; free; gene; glucose; glycosylation; high; human; increase; integration; levels; lines; mab; media; medium; method; model; number; parameters; performance; perfusion; phase; platform; process; process development; processes; production; productivity; protein; protein production; quality; rate; results; scale; selection; specific; study; system; table; target; therapeutic; time; titer; transfection; use; vector; viability; virus cache: cord-014597-66vd2mdu.txt plain text: cord-014597-66vd2mdu.txt item: #44 of 194 id: cord-015684-q10sx1dm author: Cacabelos, Ramón title: Pharmacogenomic Biomarkers in Neuropsychiatry: The Path to Personalized Medicine in Mental Disorders date: 2009 words: 17012 flesch: 35 summary: 4th Edn Pharmacogenomics: the inherited basis for interindividual differences in drug response Pharmacogenetics and pharmacogenomics: development, science, and translation Pharmacogenomics and therapeutic prospect in dementia Pharmacogenetic basis for therapeutic optimization in Alzheimer's disease Infl uence of pharmacogenetic factors on Alzheimer's disease therapeutics Pharmacogenetic aspects of therapy with cholinesterase inhibitors: the role of CYP2D6 in Alzheimer's disease pharmacogenetics From pharmacogenetics and ecogenetics to pharmacogenomics Inheritance and drug response Pharmacogenomics-Drug disposition, drug targets, and side effects National estimates of medication use in nursing homes Medicare Current Benefi ciary Survey and the 1996 Medical Expenditure Survey Antidepressant drugs prescribing among elderly subjects: a population-based study Potentially inappropriate medication use among elderly home care patients in Europe Potentially inappropriate medication use by elderly persons in U.S. Health Maintenance Organizations The Metabolic & Molecular Bases of Inherited Disease Catalog of 680 variants among eight cytochrome P450 (CYP) genes: nine esterase genes, and two other genes in the Japanese population DNA sequence variations in a 3.7-kb noncoding sequence 5-prime of the CYP1A2 gene: implications for human population history and natural selection PM frequencies of major CYPs in Asians and Caucasians Polymorphisms of drug-metabolizing enzymes CYP2C9, CYP2C19, CYP2D6, CYP1A1, NAT2 and of P-glycoprotein in a Russian population CYP2C9 allelic variants: ethnic distribution and functional signifi cance Identifi cation and functional characterization of a new CYP2C9 variant (CYP2C9 * 5 1 ) expressed among African Americans Molecular basis of ethnic differences in drug disposition and response Isolation, sequence and genotyping of the drug metabolizer CYP2D6 gene in the Colombian population Effects of prototypical microsomal enzyme inducers on cytochrome P450 expression in cultured human hepatocytes Cytochrome P450 in the brain: a review The expression of CYP2B6, CYP2C9 and CYP2A4 genes: a tangle of networks of nuclear and steroid receptors Regulation of cytochrome P450 (CYP) genes by nuclear receptors The CYP2C19 enzyme polymorphism Cytochrome P450 2D6 variants in a Caucasian population: allele frequencies and phenotypic consequences Clinically signifi cant drug interactions with cholinesterase inhibitors: a guide for neurologists Assessment of the predictive power of genotypes for the in-vivo catalytic function of CYP2D6 in a German population Ten percent of North Spanish individuals carry duplicated or triplicated CYP2D6 genes associated with ultrarapid metabolism of debrisoquine Clinical pharmacokinetics of galantamine Impact of the CYP2D6 polymorphism on steady-state plasma concentrations and clinical outcome of donepezil in Alzheimer's disease patients Molecular pathology and pharmacogenomics in Alzheimer's disease: polygenic-related effects of multifactorial treatments on cognition, anxiety, and depression Pharmacogenomic studies with a combination therapy in Alzheimer's disease Interethnic differences in genetic polymorphisms of CYP2D6 in the U.S. population: clinical implications Donepezil use in Alzheimer disease Effects of cholinergic markers in rat brain and blood after short and prolonged administration of donepezil Treatment with MPEP and MTEP can induce gene expression related to ATP synthesis, hydrolase activity, and signaling pathways associated with mitogen-activated protein kinase (MAPK) in the frontal cortex, this constituting another potential therapeutic target in some neuropsychiatric disorders. keywords: activity; alzheimer; apoe; brain; carriers; cns; cyp2d6; dementia; disease; disorders; drug; enzymes; expression; factors; genes; genotype; infl; levels; metabolism; patients; pharmacogenomics; pms; profi; receptor; response; schizophrenia; studies; treatment; ums; variants cache: cord-015684-q10sx1dm.txt plain text: cord-015684-q10sx1dm.txt item: #45 of 194 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 cache: cord-015850-ef6svn8f.txt plain text: cord-015850-ef6svn8f.txt item: #46 of 194 id: cord-015935-r2wd1yfa author: Sokol, Deborah K. title: The Genetics of Autism date: 2011-02-10 words: 11284 flesch: 39 summary: Advances in autism genetics: On the threshold of a new neurobiology Linkage, association, and geneexpression analyses identify CNTNAP2 as an autism-susceptibility gene Memantine lowers amyloid-beta peptide levels in neuronal cultures and in APP/PS1 transgenic mice Investigation of potential gene-gene interactions between APOE and RELN contributing to autism risk Molecular genetic basis of tuberous sclerosis complex: From bench to bedside Peripheral biomarkers in autism: Secreted amyloid precursor protein-alpha as a probable key player in early diagnosis Autism as a strongly genetic disorder: Evidence from a British twin study Molecular cytogenetic analysis and resequencing of contactin associated protein-like 2 in autism spectrum disorders Examination of potential overlap in autism and language loci on chromosomes 2, 7, and 13 in two independent samples ascertained for specific language impairment A major susceptibility locus for specific language impairment is located on 13q21 Molecular Analysis of Fragile X Syndrome Therapeutic implications of the mGluR theory of fragile X mental retardation The mGluR theory of fragile X mental retardation Fragile X-associated tremor/ataxia syndrome in sisters related to X-inactivation Subset of individuals with autism spectrum disorders and extreme macrocephaly associated with germline PTEN tumour suppressor gene mutations Mutation screening of the PTEN gene in patients with autism spectrum disorders and macrocephaly Replication of autism linkage: Finemapping peak at 17q21 An autosomal genomic screen for autism An autosomal genomic screen for autism Autistic children and their first degree relatives: Relationships between serotonin and norepinephrine levels and intelligence Autism or atypical autism in maternally but not paternally derived proximal 15q duplication Autism, a brain developmental disorder: Some new pathophysiologic and genetics findings Evidence of brain overgrowth in the first year of life in autism Unusual brain growth patterns in early life in patients with autistic disorder: An MRI study Factor analysis of restricted and repetitive behaviors in autism using the autism diagnostic interview-R Neuron, know thy neighbor Correction of fragile X syndrome in mice Mutations in the gene encoding the synaptic scaffolding protein SHANK3 are associated with autism spectrum disorders Gene expression profiles in a transgenic animal model of fragile X syndrome Autism is not associated with the fragile X syndrome Mouse neurexin-1alpha deletion causes correlated electrophysiological and behavioral changes consistent with cognitive impairments High frequency of neurexin Rather than searching for autism genes, endophenotype investigations search for smaller grouping of genes that contribute to discreet phenotypes (Losh et al., 2008) . keywords: analysis; autism; brain; children; chromosome; disorder; dna; et al; families; gene; genome; individuals; language; linkage; mutation; protein; studies; study; syndrome cache: cord-015935-r2wd1yfa.txt plain text: cord-015935-r2wd1yfa.txt item: #47 of 194 id: cord-016062-h4vjkufn author: Gontier, Nathalie title: Evolutionary epistemology and the origin and evolution of language: Taking symbiogenesis seriously date: 2006 words: 12420 flesch: 45 summary: This universal symbiogenetic process can be implemented in the study of language evolution in at least three ways: in the study of language variation (Section 4); language genes (Section 5) and within the study of conceptual blending (Section 6). (3) Finally, three examples are given of how a universal symbiogenesis principle can be implemented in the study of language origins and evolution, more specifically within: (a) the study of language variation, (b) language genes and (c) conceptual blending. keywords: bacteria; cells; evolution; form; generation; genes; language; material; neo; organisms; selection; species; study; theory; view cache: cord-016062-h4vjkufn.txt plain text: cord-016062-h4vjkufn.txt item: #48 of 194 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 cache: cord-016095-jop2rx61.txt plain text: cord-016095-jop2rx61.txt item: #49 of 194 id: cord-016187-58rqc0cg author: Opal, S. M. title: The Challenge of Emerging Infections and Progressive Antibiotic Resistance date: 2006 words: 6625 flesch: 35 summary: These extrachromosomal DNA elements provide ready access to disposable yet potentially highly advantageous genes including antibiotic resistance genes from plasmids or phage particles. Antibiotic resistance genes probably arose from detoxifying enzymes or synthetic enzymes with altered substrate specifi city by critical mutations or recombination events resulting in the formation of mosaic genes with entirely new functions [30] . keywords: antibiotic; bacteria; beta; cell; dna; effl; genes; infl; new; pathogens; resistance; sequences; specifi; strains; vancomycin cache: cord-016187-58rqc0cg.txt plain text: cord-016187-58rqc0cg.txt item: #50 of 194 id: cord-016200-zfh20im0 author: Saxena, Jyoti title: Edible Vaccines date: 2013-10-22 words: 7629 flesch: 48 summary: Research in the field of edible vaccines holds immense potential for the future and every advancement made in this direction is bringing the dream of edible vaccine one step closer. Edible vaccines An edible vaccine for malaria using transgenic tomatoes of varying sizes, shapes and colors to carry different antigens Plant derived edible vaccines In vivo analysis of plastid psbA, rbcL and rpl32 UTR elements by chloroplast transformation: tobacco plastid gene expression is controlled by modulation of transcript levels and translation efficiency Control mechanisms of plastid gene expression Production of antibodies in transgenic plants Immunotherapeutic potential of antibodies produced in plants Production of biologically active human interleukin-4 in transgenic tomato and potato Transgenic plants as vaccine production systems Expression of hepatitis B surface antigen in transgenic plants Edible vaccine protects mice against Escherichia coli heat-labile enterotoxin (LT): potatoes expressing a synthetic LT-B gene Edible plant vaccines: applications for prophylactic and therapeutic molecular medicine Edible vaccines: a concept comes of age Plant biotechnology and in vitro biology in the 21st century Production of hepatitis B surface antigen in transgenic plants for oral immunization Human immune responses to a novel Norwalk virus vaccine delivered in transgenic potatoes Immunogenicity in humans of an edible vaccine for hepatitis B Oral immunization with a combination of Plasmodium yoelii merozoite surface protein 1 and 4/5 enhances protection against lethal malarial challenge keywords: antibodies; antigen; diseases; expression; gene; hepatitis; human; immune; plants; potatoes; production; protein; transgenic; vaccine; virus cache: cord-016200-zfh20im0.txt plain text: cord-016200-zfh20im0.txt item: #51 of 194 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 cache: cord-016293-pyb00pt5.txt plain text: cord-016293-pyb00pt5.txt item: #52 of 194 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 cache: cord-016313-n4ewq0pt.txt plain text: cord-016313-n4ewq0pt.txt item: #53 of 194 id: cord-016364-80l5mua2 author: Menotti-Raymond, Marilyn title: The Domestic Cat, Felis catus, as a Model of Hereditary and Infectious Disease date: 2008 words: 6926 flesch: 28 summary: The canine genome Understanding the genetics of autoimmune disease: Two loci that regulate late onset Addison's disease in Portuguese Water Dogs Canine RPGRIP1 mutation establishes cone-rod dystrophy in miniature longhaired dachshunds as a homologue of human Leber congenital amaurosis Cat domestication age An STR forensic typing system for genetic individualization of domestic cat (Felis catus) samples Tyrosinase and tyrosinase related protein 1 alleles specify domestic cat coat color phenotypes of the albino and brown loci Feline polycystic kidney disease mutation identified in PKD1 An ∼140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival A homozygous single-base deletion in MLPH causes the dilute coat color phenotype in the domestic cat Albinism in the domestic cat (Felis catus) is associated with a tyrosinase (TYR) mutation Tyrosinase mutations associated with Siamese and Burmese patterns in the domestic cat (Felis catus) Molecular diagnosis of gangliosidosis: A model of inherited diseases in pure breeds Characterization of the molecular defect in a feline model for type II GM2-gangliosidosis (Sandhoff disease) An inversion of 25 base pairs causes feline GM2 gangliosidosis variant Mutation of the GM2 activator protein in a feline model of GM2 gangliosidosis Glycogen storage disease Type IV: Inherited deficiency of branching enzyme activity in cats Glycogen storage disease Type IV in Norwegian Forest Cats: Molecular detection of carriers Characterization of the mutations causing hemophilia B in 2 domestic cats A mutation in the lipoprotein lipase gene is the molecular basis of chylomicronemia in a colony of domestic cats A cardiac myosin binding protein C mutation in the Maine Coon cat with familial hypertrophic cardiomyopathy A missense mutation in Nacetylglucosamine-1-phosphotransferase causes mucolipidosis II in domestic shorthair cats Two mutations within a feline mucopolysaccharidosis type VI colony cause three different clinical phenotypes Molecular basis of feline beta-glucuronidase deficiency: An animal model of mucopolysaccharidosis VII Deletion of the dystrophin muscle promoter in feline muscular dystrophy Mutation analysis of feline Niemann-Pick C1 disease A tyrosinase gene missense mutation in temperature-sensitive type I oculocutaneous albinism. [130] [131] [132] Historically, many of the human oncogenes that defi ne signal transduction pathways were originally discovered in the context of feline leukemia virus interaction in cat models. keywords: animal; cat; cats; disease; dog; feline; gene; genome; human; linkage; map; mapping; model; mucopolysaccharidosis; sequence; species; therapy; type; virus cache: cord-016364-80l5mua2.txt plain text: cord-016364-80l5mua2.txt item: #54 of 194 id: cord-016588-f8uvhstb author: Sintchenko, Vitali title: Informatics for Infectious Disease Research and Control date: 2009-10-03 words: 8187 flesch: 25 summary: These tools use either a statistical approach, in which the inferred model and prediction are 1 Informatics for Infectious Disease Research and Control treated as regression problems, or machine learning algorithms, in which the model is addressed as a classification problem (Sintchenko et al. 2008a) . ualberta.ca/basys/cgi/submit.pl) also support comparative analysis and the automated annotation of bacterial genomic (chromosomal and plasmid) sequences (Van Domselaar et al. 2005) . keywords: analysis; annotation; approach; bioinformatics; data; disease; dna; et al; gene; genome; genomic; host; identification; informatics; knowledge; microbial; networks; pathogen; sequence; sequencing; species; tools cache: cord-016588-f8uvhstb.txt plain text: cord-016588-f8uvhstb.txt item: #55 of 194 id: cord-016713-pw4f8asc author: Goyal, Amit K. title: Nanotechnological Approaches for Genetic Immunization date: 2013-05-24 words: 16058 flesch: 23 summary: Similarly, copolymers of a hydrophilic poly(ethylene glycol) block and a cationic poly(aminoethyl methacrylate) (PAEM) block have been used for DNA vaccine delivery. However, there are several associated concerns for the use of polymers as vaccines delivery systems such as toxicity, irritancy, allergenicity, and biodegradability. keywords: acid; adjuvant; antibody; antigen; cationic; cells; chitosan; delivery; dna; et al; expression; gene; hepatitis; human; immune; immunity; immunization; lipid; liposomes; mucosal; nanoparticles; oral; plasmid; polymers; potential; properties; protein; responses; surface; systems; targeting; transfection; vaccination; vaccine; virus cache: cord-016713-pw4f8asc.txt plain text: cord-016713-pw4f8asc.txt item: #56 of 194 id: cord-017156-ximzvqbm author: Forsdyke, Donald R. title: Chargaff’s GC rule date: 2010-05-18 words: 9183 flesch: 51 summary: This was a homostabilizing propensity allowing a gene to maintain a distinct (G+C)%, relatively uniform along its length , which would differentiate it from other genes in the same genome [38) . A species can be defined as a unit of recombination (or rather, of antirecombination with respect to other species). keywords: base; chapter; differences; differentiation; dna; g+c)%; gene; genomes; individual; isolation; loop; members; pairing; potential; recombination; selection; sequence; species; stem cache: cord-017156-ximzvqbm.txt plain text: cord-017156-ximzvqbm.txt item: #57 of 194 id: cord-017208-7oew461e author: Aurigemma, Rosemarie title: Regulatory Aspects in the Development of Gene Therapies date: 2005 words: 18332 flesch: 33 summary: S7A safety pharmacology studies for human pharmaceuticals Code of Federal Regulations, Title 21, Food and Drugs, Part 610.10, Subpart B, General biological products standards; general provisions; potency Code of Federal Regulations, Title 21, Food and Drugs, Part 610.12, Subpart B, General biological products standards Code of Federal Regulations, Title 21, Food and Drugs, Part 610.13, Subpart B, General biological products standards Code of Federal Regulations, Title 21, Food and Drugs, Part 610.14, Subpart B, General biological products standards Code of Federal Regulations, Title 21, Food and Drugs, Part 58, Good laboratory practice for nonclinical laboratory studies Current good manufacturing practice in manufacturing, processing, packing, or holding of drugs; general Code of Federal Regulations, Title 21, Food and Drugs, Part 211, Current good manufacturing practice for finished pharmaceuticals Code of Federal Regulations, Title 21, Food and Drugs, Part 312, Investigational new drug application INDs) for phase I studies of drugs, including well-characterized, therapeutic, biotechnology-derived products FDA guidance for industry: IND's for phases 2 and 3 studies of drugs, including specified therapeutic biotechnology-derived products, chemistry, manufacturing and controls content and format FDA guidance for industry: content and format of chemistry, manufacturing, and controls information and establishment description information for a vaccine or related product FDA guidance for industry for the submission of chemistry, manufacturing, and controls information for a therapeutic recombinant DNA-derived product or a monoclonal antibody product for in vivo use FDA guidance for industry: formal meetings with sponsors and applicants for PDUFA products FDA points to consider in the manufacturing and testing of monoclonal antibody products for human use FDA letter to manufacturers of biological products: recommendations regarding bovine spongiform encephalopathy (BSE) FDA Biological Response Modifiers Advisory Committee: current policy on sequence characterization of gene transfer products FDA Biological Response Modifiers Advisory Committee: adenovirus titer measurements and RCA levels FDA guidance for industry: supplemental guidance on testing for replication competent retrovirus in retroviral vector based gene therapy products and during follow-up of patients in clinical trials using retroviral vectors FDA points to consider in the characterization of cell lines used to produce biologicals FDA gene therapy patient tracking system final document FDA guidance concerning demonstration of comparability of human biological products, including therapeutic biotechnology-derived products Third national NIH gene transfer safety symposium: safety considerations in the use of AAV vectors in gene transfer clinical trials Basic principles of gene therapy: basic principles and safety considerations Preclinical animal models in gene therapy research A new animal model for human respiratory tract disease due to adenovirus Use of Aotus monkey to assess neurovirulence of replication-selective herpes vectors Herpes simplex type 1 infects and establishes latency in the brain and trigeminal ganglia during primary infection of the lip in cotton rats and mice Tropism of human adenovirus type 5-based vectors in swine and their ability to protect against transmissible gastroenteritis coronavirus Porcine toxicology studies of SCH 58500, an adenoviral vector for the p53 gene Pathogenesis of adenovirus type 5 pneumonia in cotton rats (Sigmodon hispidus) As a result, it was only natural that these animals be used to evaluate the safety of gene therapy vectors produced from HSV-1. keywords: adenovirus; administration; agent; animal; assays; cell; cgmp; development; dose; evaluation; fda; gene; gene therapy; human; preclinical; product; production; recombinant; replication; response; safety; studies; therapy; toxicity; transfer; use; vector; virus cache: cord-017208-7oew461e.txt plain text: cord-017208-7oew461e.txt item: #58 of 194 id: cord-017752-ofzm3x3a author: None title: Theories of Carcinogenesis date: 2007 words: 12300 flesch: 42 summary: According to Virchow's dictum omnis cellula e cellule cells of diseased tissues are derived from normal tissues, implying that malfunction begets disease (significantly, Virchow had been a student of Müller's, who had demonstrated in 1838 that cancer is made up of cells, not lymph; but he was of the opinion that cancer cells arose from interstitial budding elements, blastema, not from normal cells). As one possible underlying reason, the biochemist Otto von Warburg [von Warburg 1930] had suggested that the oxidative metabolism in cancer cells is replaced by glycolysis and that the excessive proliferation of cancer cells reflects their ability to metabolize independently of oxygen. keywords: analysis; breast; cancer; cancer cells; carcinogenesis; carcinoma; cause; cells; chemical; development; dna; et al; expression; gene; growth; human; leukemia; metastasis; mutations; number; progression; proteins; radiation; research; risk; sarcoma; system; theory; tissue; transformation; tumor; tumor cells; virus; viruses; years cache: cord-017752-ofzm3x3a.txt plain text: cord-017752-ofzm3x3a.txt item: #59 of 194 id: cord-017853-mgsuwft0 author: Machado, Roberto F. title: Genomics of Acute Lung Injury and Vascular Barrier Dysfunction date: 2010-06-28 words: 9206 flesch: 26 summary: This approach identified multiple genes already recognized as ALI genes (such as IL-6, AQP-1, and PAI-1), but also identified several novel genes that were not previously known to be mechanistically involved in ALI [38] . Together, these approaches identified novel ALI genes such as PBEF, chemokine receptor (CXCR-4) GADD45. keywords: acute; ali; association; barrier; candidate; cell; endothelial; expression; factor; gene; growth; injury; levels; lung; novel; patients; pbef; role; sepsis; susceptibility; vascular cache: cord-017853-mgsuwft0.txt plain text: cord-017853-mgsuwft0.txt item: #60 of 194 id: cord-017932-vmtjc8ct author: Georgiev, Vassil St. title: Genomic and Postgenomic Research date: 2009 words: 8483 flesch: 30 summary: Next, these gene predictions can be further refined by searching for nearby regulatory sites such as the ribosome-binding sites, as well as by aligning protein sequences to other species. Large-scale prepublication information on genome sequences is a unique research resource for the scientific community, and rapid and unrestricted sharing of microbial genome sequence data is essential for advancing research on infectious agents responsible for human disease. keywords: analysis; centers; coli; data; diseases; genes; genome; genomic; host; human; influenza; microbial; niaid; proteins; research; sequence; sequencing cache: cord-017932-vmtjc8ct.txt plain text: cord-017932-vmtjc8ct.txt item: #61 of 194 id: cord-018145-kssjdn8y author: Niemann, Heiner title: Transgenic Farm Animals: Current Status and Perspectives for Agriculture and Biomedicine date: 2009 words: 9168 flesch: 28 summary: Although the efficiency of transgenic animal production by microinjection technology is low, many animals with agriculturally important transgenic traits were produced. Transgenic animal production for biomedical applications has found broad acceptance. keywords: animals; cattle; cells; et al; expression; farm; gene; generation; gland; human; mice; milk; pigs; porcine; production; protein; recombinant; sheep; stem; technology; transfer; transgenic cache: cord-018145-kssjdn8y.txt plain text: cord-018145-kssjdn8y.txt item: #62 of 194 id: cord-018526-rz7id5mt author: Braun, Serge title: Non-viral Vector for Muscle-Mediated Gene Therapy date: 2018-12-14 words: 5186 flesch: 27 summary: Nevertheless, muscle gene therapy using systemic administration of non-viral vectors retains major hurdles that need to be overcome before any human applications. The efficiency of plasmid gene transfer into skeletal muscle (and other tissues) by direct injection is low (~1% of cell nuclei) and remains confined at the injection site (along the needle track) across species keywords: delivery; dna; expression; gene; limb; muscle; phase; plasmid; safety; therapy; trial; vaccine; vectors cache: cord-018526-rz7id5mt.txt plain text: cord-018526-rz7id5mt.txt item: #63 of 194 id: cord-018647-bveks6t1 author: Butnariu, Monica title: Plant Nanobionics: Application of Nanobiosensors in Plant Biology date: 2019-10-01 words: 16819 flesch: 37 summary: A series of new genes for resistance to insect attack, transferable to plants (genes encoding δ-endotoxin production from B. thuringiensis) has been discovered; genes for the synthesis of enzymes or enzyme inhibitors; plant genes encoding the synthesis of specific lectins; genes that cause induction of synthesis of plant compounds such as phytoalexins. Given the practical significance of plant resistance to harmful insects, research has been extended to other plant species, producing eggplant plants resistant to the attack of Coleoptera, broccoli with resistance to certain lepidopteran species, maize with resistance to B. fusca, etc., as well as a number of advances in leguminous plants. keywords: analyte; binding; concentration; detection; electrochemical; electrode; enzyme; et al; genes; groups; host; interaction; membrane; molecules; nbss; optical; oxygen; plants; proteins; reaction; receptors; recognition; redox; resistance; response; signal; species; surface; transducer; use cache: cord-018647-bveks6t1.txt plain text: cord-018647-bveks6t1.txt item: #64 of 194 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 cache: cord-018798-yzxy9ogf.txt plain text: cord-018798-yzxy9ogf.txt item: #65 of 194 id: cord-018924-wo42j0ps author: Nettelbeck, Dirk M. title: Bispecific Antibodies and Gene Therapy date: 2011-07-01 words: 6921 flesch: 24 summary: Right panels: Bispecific antibodies can be either a tool for targeting gene transfer vectors to specific cell types (1) or gene transfer can be exploited as a tool for antibody therapy by antibody gene transfer and subsequent synthesis of the antibody in the patient (2) Singer and Verma (2008) cassettes are inserted either into circular plasmids, which might be further packaged by non-viral vectors, or into genomes of replication-deficient viral vectors ( into hematopoietic stem cells for treatment of inherited immunodeficiencies (Kohn 2010) . For genetic antibody delivery antibody genes, which can be engineered to match specific purposes, are incorporated into gene transfer vectors. keywords: adapter; antibodies; antibody; binding; bispecific; cells; gene; targeting; therapy; transfer; vectors; vivo cache: cord-018924-wo42j0ps.txt plain text: cord-018924-wo42j0ps.txt item: #66 of 194 id: cord-019050-a9datsoo author: Ambrogi, Federico title: Bioinformatics and Nanotechnologies: Nanomedicine date: 2014 words: 8853 flesch: 23 summary: Now, scientists can obtain a genome-wide perspective of cancer gene expression useful to discover novel cancer biomarkers for more accurate diagnosis and prognosis, and monitoring of treatment effectiveness. Current applications involve high-throughput analysis of gene expression data and for multiplexed molecular profiling of intact cells and tissue specimens. keywords: analysis; approaches; biomarkers; breast; cancer; cells; data; detection; development; discovery; disease; expression; gene; level; methods; microarray; research; studies; tumor cache: cord-019050-a9datsoo.txt plain text: cord-019050-a9datsoo.txt item: #67 of 194 id: cord-020101-5rib7pe8 author: None title: Cumulative Author Index for 2008 date: 2008-11-17 words: 2143 flesch: -170 summary: Murine leukemia virus reverse transcriptase: Structural comparison with HIV-1 reverse transcriptase The GPRLQPY motif located at the carboxy-terminal of the spike protein induces antibodies that neutralize Porcine epidemic diarrhea virus Detection of ovine herpesvirus 2 major capsid gene transcripts as an indicator of virus replication in shedding sheep and clinically affected animals Genetic characterization of equine influenza viruses isolated in Italy between A new living cell-based assay system for monitoring genome-length hepatitis C virus RNA replication Unraveling the puzzle of human anellovirus infections by comparison with avian infections with the chicken anemia virus The contribution of feathers in the spread of chicken anemia virus Cloning and subcellular localization of the phosphoprotein and nucleocapsid proteins of Potato yellow dwarf virus, type species of the genus Nucleorhabdovirus The p26 gene of the Autographa californica nucleopolyhedrovirus: Timing of transcription, and cellular localization and dimerization of product Complete genomic sequence of turkey coronavirus Recombinant L and P protein complex of Rinderpest virus catalyses mRNA synthesis in vitro Molecular divergence of Grapevine virus A (GVA) variants associated with Shiraz disease in South Africa Sequence analysis of a reovirus isolated from the winter moth Operophtera brumata (Lepidoptera: Geometridae) and its parasitoid wasp Phobocampe tempestiva (Hymenoptera: Ichneumonidae SARS coronavirus replicase proteins in pathogenesis Virus-induced gene silencing in Medicago truncatula and Lathyrus odorata Evaluating the 3C-like protease activity of SARS-Coronavirus: Recommendations for standardized assays for drug discovery HBx modulates iron regulatory protein 1-mediated iron metabolism via reactive oxygen species Pathogenetic mechanisms of severe acute respiratory syndrome Detection of a novel circovirus in mute swans (Cygnus olor) by using nested broadspectrum PCR Chimaeric HIV-1 subtype C Gag molecules with large in-frame C-terminal polypeptide fusions form virus-like particles Cross-species recombination in the haemagglutinin gene of canine distemper virus Sapovirus-like particles derived from polyprotein Cauliflower mosaic virus gene VI product N-terminus contains regions involved in resistance-breakage, self-association and interactions with movement protein Adenovirus vector induced innate immune responses: Impact upon efficacy and toxicity in gene therapy and vaccine applications Interfering with cellular signaling pathways enhances sensitization to combined sodium butyrate and GCV treatment in EBV-positive tumor cells Evidence for recombination between PCV2a and PCV2b in the field Retroviral reverse transcriptases (other than those of HIV-1 and murine leukemia virus): A comparison of their molecular and biochemical properties Mitochondrial plasmids of sugar beet amplified via rolling circle method detected during curtovirus screening Appearance of intratypic recombination of enterovirus 71 in Taiwan from The circulation of subgenogroups B5 and C5 of enterovirus 71 in Taiwan from In vitro replication of Bamboo mosaic virus satellite Characterization of the interaction of domain III of the envelope protein of dengue virus with putative receptors from CHO cells Intrahost evolution of envelope glycoprotein and OrfA sequences after experimental infection of cats with a molecular clone and a biological isolate of feline immunodeficiency virus The SARS-Coronavirus PLnc domain of nsp3 as a replication/ transcription scaffolding protein Limited compatibility between the RNA polymerase components of influenza virus type A and B Serotype-specificity of recombinant fusion proteins containing domain III of dengue virus Very virulent infectious bursal disease virus isolated from wild birds in Korea: Epidemiological implications Genetic analysis and evaluation of the reassortment of influenza B viruses isolated in Taiwan during the Enhanced immune responses of mice inoculated recombinant adenoviruses expressing GP5 by fusion with GP3 and/or GP4 of PRRS virus Effect of antiviral treatment and host susceptibility on positive selection in hepatitis C virus Novel HIV-1 reverse transcriptase inhibitors Synthesis of recombinant human parainfluenza virus 1 and 3 nucleocapsid proteins in yeast Saccharomyces cerevisiae Evolutionary analyses of European H1N2 swine influenza keywords: analysis; cell; gene; hepatitis c; infection; molecular; murine leukemia; protein; replication; transcriptase; type; virus; virus replication cache: cord-020101-5rib7pe8.txt plain text: cord-020101-5rib7pe8.txt item: #68 of 194 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 cache: cord-020969-lh2ergpm.txt plain text: cord-020969-lh2ergpm.txt item: #69 of 194 id: cord-021063-4y8m33ea author: Hug, Peter title: Chapter 18 The advantages of liposome-based gene therapy: A comparison of viral versus liposome-based gene delivery date: 2007-09-02 words: 6271 flesch: 46 summary: Some general characteristics of the viruses currently being developed as gene therapy vectors are presented in Table 2 . Wild-type retroviruses are contained within a lipid membrane and have two identical copies of an RNA genome. Adenoviruses that are being considered for use as gene therapy vectors have had substantial parts of their genome removed, rendering them unable to replicate except in specially developed cell lines (i.e., packaging cell lines) that express the removed proteins (Kozarsky and Wilson, 1993) . keywords: cells; dna; gene; gene therapy; liposomes; proteins; therapy; vectors; virus cache: cord-021063-4y8m33ea.txt plain text: cord-021063-4y8m33ea.txt item: #70 of 194 id: cord-022177-j0qcjbxg author: Markl, Jürgen title: Genome date: 2018-10-12 words: 3471 flesch: 42 summary: Die Genome anderer Katzenarten, beispielsweise von Löwe, Schneeleopard und Hauskatze, waren bereits sequenziert worden, das des Tigers allerdings noch nicht. Die Retrotransposons umfassen drei Gruppen, entsprechend der Art der repetitiven Sequenzen, die sie enthalten: lange endständige Wiederholun- Die Genome der Eukaryoten enthalten deutlich mehr Gene als die der Prokaryoten. keywords: als; auch; auf; bei; das; dem; den; der; des; die; diese; dna; durch; ein; eine; für; gene; genome; ist; können; man; menschen; mit; nicht; sequenzen; sequenzierung; sich; sie; sind; und; von; werden; wie cache: cord-022177-j0qcjbxg.txt plain text: cord-022177-j0qcjbxg.txt item: #71 of 194 id: cord-022178-4oh02tlr author: Markl, Jürgen title: Evolution von Genen und Genomen date: 2018-10-12 words: 3865 flesch: 54 summary: Das war die Geburtsstunde der Anwendungen der in vitro-Evolution (Evolution im Reagenzglas). Seit 1945 haben spezielle Impfprogramme gegen Grippeviren dazu beigetragen, die Anzahl und Schwere der Grippefälle in Grenzen zu halten. keywords: als; auf; bei; das; den; der; des; die; diese; dna; durch; einer; evolution; für; gene; haben; kopien; können; mit; nicht; oder; organismen; sich; sie; t t; und; veränderungen; von; werden; wie; zahl cache: cord-022178-4oh02tlr.txt plain text: cord-022178-4oh02tlr.txt item: #72 of 194 id: cord-022226-qxp0gfp3 author: Meager, Anthony title: Interferons Alpha, Beta, and Omega date: 2007-09-02 words: 16407 flesch: 30 summary: This extensive family of IFNA genes are tandemly arranged on the short-arm of chromosome 9 (9p23) and span a region of approximately 400 kb (Owerbach et al., 1981; Shows et al., 1982; Slate et al., 1982; Ullrich et al., 1982) . virally-induced normal fibroblasts and other tissue cell types, e.g., epithelial cells (Meager et al., 1979; Stewart, 1979) keywords: activity; amino; binding; cells; chromosome; et al; expression; factor; gene; human; ifn; ifn-[3; ifna; ifnb; ifns; inducible; induction; interferon; kinase; leukocyte; maeyer; mouse; protein; receptor; recombinant; sequence; structure; subtypes; transcription; treatment; virus cache: cord-022226-qxp0gfp3.txt plain text: cord-022226-qxp0gfp3.txt item: #73 of 194 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 cache: cord-022940-atbjwpo5.txt plain text: cord-022940-atbjwpo5.txt item: #74 of 194 id: cord-023055-ntbvmssh author: None title: Immunogenicity date: 2004-02-19 words: 64788 flesch: 56 summary: o present fragments of that antigen very efficiently t o T cells. 10. carrier (KLH) primed T cells were transferred in the presence or absence of antigen into irradiated, K-allotype distinct adoptive host. keywords: ability; activity; amino; analysis; antibodies; antibody; antigen; b cells; binding; c e; c r; c t; cd3; cd4; cd8; cell activation; cell antigen; cell clones; cell epitopes; cell line; cell proliferation; cell receptor; cell response; cell surface; cells; chain; class; ctl; cytotoxic t; data; e l; e n; e s; epitopes; expression; f e; f t; gene; h e; hla; human; induced; l l; l s; l t; l y; levels; lines; mab; mhc; mice; molecules; monoclonal; mouse; mrna; murine; murine t; n g; n s; n t; non; o l; o n; p e; p l; p t; peptide; presence; present; production; proliferation; protein; r e; r l; recognition; region; residues; response; results; s c; s p; s s; sequence; specific; spleen cells; studies; t antigen; t cell; t e; t h; t helper; t lymphocytes; t o; t r; t s; t t; t u; t y; tcr; u l; w e cache: cord-023055-ntbvmssh.txt plain text: cord-023055-ntbvmssh.txt item: #75 of 194 id: cord-023605-zibwrv76 author: None title: Genetics and biotechnology of Bacilli: A.T. Ganesan and J.A. Hoch (Eds.): (Proceedings of the Second International Conference on the Genetics and Biotechnology of Bacilli, Stanford University, Stanford, CA, July 6–8, 1983) Academic Press Inc., Orlando, FL, 1984, xviii + 421 pp. ($41.50) ISBN 0-12-274 60-9 date: 2003-01-16 words: 673 flesch: 15 summary: Genetics: chromosome mobilization and genomic organization in Pseudomonas degradative plasmids in Pseudomonas; gene cloning and manipulation in Pseudomonas; cloning of Pseudomonas genes in Escherichia coli. Sol Spiegehnan's obituary; molecular basis of gene expression (D.D. Brown). keywords: cell; gene; leukemia; pseudomonas; retroviruses cache: cord-023605-zibwrv76.txt plain text: cord-023605-zibwrv76.txt item: #76 of 194 id: cord-023647-dlqs8ay9 author: None title: Sequences and topology date: 2003-03-21 words: 4522 flesch: 38 summary: A 32-kDa Llpo~ortin from Human Mononuclear Cells Appears to be Identical with the Placental Inhibitor of Blood Coagulation Distinct Fercedoxins from Rhodobacter-Capsulstus -Complete Amino Acid Sequences and Molecular Evolution N~ptide Sequence Analysis and Molecular Cloning Reveal Two Calcium Pump Isoforms in the Human Erythrocyte Membgane Cloning and Characterization of a Novel Member of the Cytochrome-P450 Subfamily IVA in Rat Prostate A Directiy Repeated Sequence in the ~-Globin Promoter Resulates Transcription in Murine Efythroleukemla Cells Isolation and Chamcterizatinn of the Alkane-Inducibie NADPH-Cytochrome-P-450 Olf, idoreductsse Gene from Candida-Tropicalls -Identification of Invarlant Residues Wlthin Slmilmr Amino Acid Sequences of Direr'sent Flavoproteins Protein Klnase-C Inhibitor Proteins -Purification from Sheep Brain and Sequence Similarity to Lipocortins and 14-3-3 MCI~ AVEmL~ B& Sequence Homology Between Purple Acid Phosphatases and Phusphoprotein Pho*phatsses --are Phesphoprotcin Phosphatatms Metalloproteins Collt~|nln~ Oil~-bridged Dinuclcar Metal Centers Negative Regulation of the Human ~-Globin Ca~ne by Transcriptional Interference: Role of an Mu Repetitive ~lement Amino Acid Sequence of Chicken Catisequestrin Deduced from C DNA -Comp~rison of Caisequestrin and Aspartactin Caisequestrin, an Intesccilular Calciumbinding Protein of Skeletal Muscle Sarcoplssmic Reticulm, Is HomoloKous to ~, a Putstive latminin-binding Protein of the Exteac¢llular Matr~ BOvSm~ ]Prote~ C Inhihl.gog with Structugll and Fun~ HotDoIO~OU~ ]~-.gtl~ to Hum~zn The 188 ltilm0omal RNA ~-quence of the S~t Anemone Anemom~s ssdcmta and Its Evolutionary INtuition Amomqg Other Eukaryotes Inferred b'om S~l,.m.~ Comlmrttmas of a Heat Shock G~ae in Two Nematorl~ The l~'/O Multtgene Family of Ok~hag of CDNA ~ for the ~ Omin of Human Complement Component ca~bi~una Protein, seqaenoe Homolo~ with thc a C~t~:~a~h Proc Natl Acad S¢t USA1990 Highly Conserved Core Domain and Unique N Terminus with Presumptive Regulatory Moti~ in a Hmman TATA Factor (l'lql~) keywords: acid; amino; amino acid; analysis; cell; conserved; dna; domain; evolution; factor; family; gene; homology; human; member; new; novel; protein; rna; sequence; similarity; structure; virus; yeast cache: cord-023647-dlqs8ay9.txt plain text: cord-023647-dlqs8ay9.txt item: #77 of 194 id: cord-023928-9a1w174h author: Thomas, Neal J. title: Genetic Predisposition to Critical Illness in the Pediatric Intensive Care Unit date: 2011-12-16 words: 12261 flesch: 40 summary: It is unlikely as there are no reports of associations between surfactant protein gene polymorphisms and outcomes from pulmonary disease. As will be discussed below, genetic variations that infl uence the activity or level of the protein in several of these candidate genes have been examined in gene association studies in patients with ALI. keywords: adults; ali; coding; disease; expression; gene; infl; levels; polymorphisms; protein; response; risk; sepsis; studies; uence; variations cache: cord-023928-9a1w174h.txt plain text: cord-023928-9a1w174h.txt item: #78 of 194 id: cord-024290-8z6us7v4 author: Allen, Edward E. title: Time Series Adjustment Enhancement of Hierarchical Modeling of Arabidopsis Thaliana Gene Interactions date: 2020-02-01 words: 3236 flesch: 47 summary: key: cord-024290-8z6us7v4 authors: Allen, Edward E.; Farrell, John; Harkey, Alexandria F.; John, David J.; Muday, Gloria; Norris, James L.; Wu, Bo title: Time Series Adjustment Enhancement of Hierarchical Modeling of Arabidopsis Thaliana Gene Interactions date: 2020-02-01 journal: Algorithms for Computational Biology DOI: 10.1007/978-3-030-42266-0_11 sha: doc_id: 24290 cord_uid: 8z6us7v4 Network models of gene interactions, using time course gene transcript abundance data, are computationally created using a genetic algorithm designed to incorporate hierarchical Bayesian methods with time series adjustments. Using the transcript abundance data for 26 Arabidopsis thaliana genes stimulated by ACC, gene interaction models for a next state with and without time series adjustment were computationally created, shown in Fig. keywords: data; gene; modeling; series; time cache: cord-024290-8z6us7v4.txt plain text: cord-024290-8z6us7v4.txt item: #79 of 194 id: cord-028721-x6f26ahr author: Nistal, Manuel title: Non-neoplastic diseases of the testis date: 2020-06-22 words: 78262 flesch: 36 summary: 1116 Other tumors reported in patients with Klinefelter's syndrome (lymphoma, leukemia, bronchogenic carcinoma, urothelial carcinoma of the bladder, adrenal carcinoma, prostatic adenocarcinoma, testicular Leydig cell tumor, and epidermoid cyst) do not appear to have a higher incidence than in the general population. Sertoli cell-only syndrome with immature Sertoli cells Sertoli cells in adult testes with this variant of Sertoli cell-only syndrome have an immature prepubertal appearance with pseudostratifi cation. keywords: absence; adrenal; adult; age; albuginea; androgen; anomalies; atrophy; azoospermia; bilateral; cases; cause; cell hyperplasia; cell tumor; chromosome; ciency; cord; cryptorchidism; cystic; defi; development; diagnosis; disease; epididymis; epithelium; failure; fi ndings; fig; form; fsh; gene; germ cells; gonadal; hormone; human; hyperplasia; hypogonadism; incidence; infertility; klinefelter; levels; leydig cells; low; male; maturation; men; mutation; müllerian; normal; number; obstruction; orchitis; patients; present; puberty; receptor; report; rete testis; sertoli cells; serum; sex; spermatids; spermatogenesis; spermatogonia; spermatozoa; studies; study; syndrome; testes syndrome; testicular; testicular atrophy; testicular biopsy; testicular cancer; testicular descent; testicular dysgenesis; testicular function; testicular germ; testicular lesions; testicular microlithiasis; testicular parenchyma; testicular torsion; testicular tumor; testis; testis testicular; testosterone; tissue; treatment; tubular; tubules; tunica; type cache: cord-028721-x6f26ahr.txt plain text: cord-028721-x6f26ahr.txt item: #80 of 194 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 cache: cord-033692-txfuuu7d.txt plain text: cord-033692-txfuuu7d.txt item: #81 of 194 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 cache: cord-048322-5eqdrd52.txt plain text: cord-048322-5eqdrd52.txt item: #82 of 194 id: cord-102219-d3gkfo7s author: Perzel Mandell, Kira A. title: Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex date: 2019-10-30 words: 5039 flesch: 41 summary: Previously, many studies of brain DNA methylation have used the Illumina Infinium® HumanMethylation450 BeadChip (450k) and more recent Infinium MethylationEPIC (850k) microarray technologies. This corresponds to 30x coverage of the human genome as extra reads were generated to account for the addition of PhiX. Data Processing: The raw WGBS data was processed using FastQC to control for quality of reads 12 , Trim Galore to trim reads and remove adapter content 13 , Arioc for alignment to the GRCh38.p12 genome (obtained from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.27_GRCh38.p12/GC A_000001405.27_GRCh38.p12_assembly_structure/Primary_Assembly/assembled_chromoso mes/) 14 , duplicate alignments were removed with SAMBLASTER 15 , and the Bismark methylation extractor to extract methylation data from the sequencing data 16 . keywords: age; brain; cpgs; data; development; dmrs; dnam; gene; methylation; sex; sites cache: cord-102219-d3gkfo7s.txt plain text: cord-102219-d3gkfo7s.txt item: #83 of 194 id: cord-102729-b1q7gbd6 author: Mickael, Alexandra title: Asip (Agouti-signaling protein) aggression gene regulate auditory processing genes in mice date: 2020-06-12 words: 4437 flesch: 45 summary: These observation indicates that hearing could regulating aggression behavior. We examined whether aggression behavior could be caused by social stress. keywords: aggression; analysis; asip; behavior; cells; genes; hearing; melanocortin; mice; model; receptors; role; startle cache: cord-102729-b1q7gbd6.txt plain text: cord-102729-b1q7gbd6.txt item: #84 of 194 id: cord-102935-cx3elpb8 author: Hassani-Pak, Keywan title: KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species date: 2020-04-24 words: 2175 flesch: 45 summary: Evidence View is a ranked list of query related 121 evidence terms and enrichment scores along with linked genes. Here we report the main design principles behind KnetMiner and provide use cases for mining public datasets to identify unknown links between traits such grain colour and pre-harvest sprouting in Triticum aestivum, as well as, an evidence-based approach to identify candidate genes under an Arabidopsis thaliana petal size QTL. keywords: evidence; gene; information; knetminer; knowledge; search cache: cord-102935-cx3elpb8.txt plain text: cord-102935-cx3elpb8.txt item: #85 of 194 id: cord-103150-e9q8e62v author: Mishra, Shreya title: Improving gene-network inference with graph-wavelets and making insights about ageing associated regulatory changes in lungs date: 2020-11-04 words: 8220 flesch: 50 summary: An integrative approach for causal gene identification and gene regulatory pathway inference Singlecell transcriptomics unveils gene regulatory network plasticity Chemogenomic profiling of Plasmodium falciparum as a tool to aid antimalarial drug discovery Supervised, semi-supervised and unsupervised inference of gene regulatory networks Reverse engineering cellular networks Evaluating measures of association for single-cell transcriptomics Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data SCENIC: single-cell regulatory network inference and clustering SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression Noise in gene expression: origins, consequences, and control, Science Comparative assessment of differential network analysis methods Murine single-cell RNA-seq reveals cellidentity-and tissue-specific trajectories of aging Wisdom of crowds for robust gene network inference GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods Enhancing experimental signals in single-cell RNA-sequencing data using graph signal processing Comparative Analysis of Single-Cell RNA Sequencing Methods A gene regulatory network in mouse embryonic stem cells Recovering Gene Interactions from Single-Cell Data Using Data Diffusion An accurate and robust imputation method scImpute for single-cell RNA-seq data Single-cell RNA-seq denoising using a deep count autoencoder SAVER: gene expression recovery for singlecell RNA sequencing A random matrix theory approach to denoise single-cell data Missing value estimation methods for DNA microarrays Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool Histamine stimulation of surfactant secretion from rat type II pneumocytes Aging impairs VEGF-mediated, androgen-dependent regulation of angiogenesis Dysfunction of pulmonary surfactant mediated by phospholipid oxidation is cholesterol-dependent Age-Dependent Changes in the Pulmonary Renin-Angiotensin System Are Associated With Severity of Lung Injury in a Model of Acute Lung Injury in Rats MAPK and JAK-STAT signaling pathways are involved in the oxidative stress-induced decrease in expression of surfactant protein genes Transcription factor Etv5 is essential for the maintenance of alveolar type II cells, Proceedings of the National Academy of Sciences of the United States of Targeted deletion of Jun/AP-1 in alveolar epithelial cells causes progressive emphysema and worsens cigarette smoke-induced lung inflammation Androgen receptor and androgen-dependent gene expression in lung The Metabolic Signature of Macrophage Responses Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19 Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2 JAK-STAT pathway activation in COPD, The European Androgen hazards with COVID-19 The H1 histamine receptor regulates allergic lung responses Late Breaking Abstract -Evaluation of the JNK inhibitor, CC-90001, in a phase 1b pulmonary fibrosis trial Androgen-deprivation therapies for prostate cancer and risk of infection by SARS-CoV-2: a population-based study (N = 4532) For filtering in the Fourier domain, we used Chebyshev-filter for gene expression profile. keywords: at2; cells; data; denoising; expression; gene; graph; inference; lung; methods; network; noise; profiles; seq; wavelet cache: cord-103150-e9q8e62v.txt plain text: cord-103150-e9q8e62v.txt item: #86 of 194 id: cord-103465-6udhvl9n author: Schierding, William title: Low tolerance for transcriptional variation at cohesin genes is accompanied by functional links to disease-relevant pathways date: 2020-04-13 words: 6456 flesch: 34 summary: Results 140 genetic variants with regulatory potential are associated with cohesin loci Mitotic cohesin genes (SMC1A, SMC3, STAG1, STAG2, and RAD21), meiotic cohesin genes (SMC1B, STAG3, REC8, and RAD21L1), cohesin support genes (WAPL, NIPBL, PDS5A, PDS5B, and MAU2) and CTCF were investigated to determine if they contain non-coding genetic variants (SNPs) that make contact in 3D with genes and therefore could directly affect gene expression (GWAS-attributed and eQTL-attributed; Table 1, Table S1 ). key: cord-103465-6udhvl9n authors: Schierding, William; Horsfield, Julia; O’Sullivan, Justin title: Low tolerance for transcriptional variation at cohesin genes is accompanied by functional links to disease-relevant pathways date: 2020-04-13 journal: bioRxiv DOI: 10.1101/2020.04.11.037358 sha: doc_id: 103465 cord_uid: 6udhvl9n Variants in DNA regulatory elements can alter the regulation of distant genes through spatial-regulatory connections. keywords: analysis; cohesin; connections; disease; eqtl; expression; genes; gwas; human; intolerant; lof; table; variants cache: cord-103465-6udhvl9n.txt plain text: cord-103465-6udhvl9n.txt item: #87 of 194 id: cord-103505-9adtbwp2 author: Hale, A. T. title: The genetic architecture of human infectious diseases and pathogen-induced cellular phenotypes date: 2020-07-21 words: 1409 flesch: 14 summary: Nat Commun 8, 599. known genetic associations and discovery of new genetic disorders Pathogen culture and virology data linked to whole-genome genetic information 1017 These data identify specific molecular mechanisms across ID traits with critical 239 regulatory roles (e.g., protein modifications) in host response among the ID-associated genes. keywords: association; genes; genome; human; traits cache: cord-103505-9adtbwp2.txt plain text: cord-103505-9adtbwp2.txt item: #88 of 194 id: cord-104073-vsa5y7ip author: Warner, Emily F. title: Cross kingdom analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets to ameliorate fungal pathogenicity? date: 2020-09-23 words: 3225 flesch: 45 summary: As expected, there was a positive correlation between GC content 230 and PQS frequency amongst all the fungal species analysed (r=0.5290; p<0.0001; Figure 3A ). The Mucoromycota and Basidiomycota displayed high PQS frequencies relative to GC 220 content (459 and 340 PQS/GC%, respectively; Figure 2C and G). keywords: drug; figure; fungal; genes; kbp; pqs; quadruplex cache: cord-104073-vsa5y7ip.txt plain text: cord-104073-vsa5y7ip.txt item: #89 of 194 id: cord-252147-bvtchcbt author: Domingo-Espín, Joan title: Engineered Biological Entities for Drug Delivery and Gene Therapy: Protein Nanoparticles date: 2011-11-15 words: 17227 flesch: 30 summary: The main biological production systems for protein drugs are described below. Finally, some successful examples of protein nanoparticles on the market will be described in addition to protein products currently in clinical trials and under preclinical research in order to envision which type of protein nanoparticles will be available soon on the market. keywords: binding; cancer; cell; complex; delivery; design; dna; drug; drug delivery; expression; gene; gene delivery; human; interactions; molecules; nanoparticles; nuclear; particles; peptides; production; properties; protein; receptor; self; specific; system; targeting; therapy; transfer; tumor; use; vector; virus; vivo; vlps cache: cord-252147-bvtchcbt.txt plain text: cord-252147-bvtchcbt.txt item: #90 of 194 id: cord-252536-gfx4cq03 author: Bieniossek, Christoph title: MultiBac: expanding the research toolbox for multiprotein complexes date: 2011-12-07 words: 7133 flesch: 36 summary: Protein complexes composed of many subunits carry out most essential processes in cells and, therefore, have become the focus of intense research. Notwithstanding, our molecular understanding of the very large number of protein complexes in the cell remains limited to a handful of examples for which detailed nearatomic structures are known. keywords: baculovirus; cells; complexes; dna; eukaryotic; expression; gene; genome; head; insect; loxp; multibac; multigene; production; protein; structure; system cache: cord-252536-gfx4cq03.txt plain text: cord-252536-gfx4cq03.txt item: #91 of 194 id: cord-252781-06hs9pit author: Lai, Wing-Fu title: Cyclodextrins in non-viral gene delivery date: 2013-10-05 words: 6617 flesch: 38 summary: Over the years, substantial efforts have been undertaken to investigate the possible use of CDs in drug delivery and controlled drug release, yet the potential of CDs in gene delivery has received comparatively less discussion in the literature. In this article, we will first discuss the properties of CDs for gene delivery, followed by a synopsis of the use of CDs in development and modification of non-viral gene carriers. keywords: cds; cells; conjugate; cyclodextrin; delivery; dendrimer; dna; drug; efficiency; gene; pei; polymer; transfection; transfer cache: cord-252781-06hs9pit.txt plain text: cord-252781-06hs9pit.txt item: #92 of 194 id: cord-252859-zir02q69 author: Chung, T. Philip title: Molecular Diagnostics in Sepsis: From Bedside to Bench date: 2006-09-11 words: 5746 flesch: 41 summary: Using mouse spleen samples for gene expression analysis, we were able to classify the samples as CLP or Sham with 96.0% accuracy, estimated using cross-validation. Because the clinical use of gene expression analysis using splenic tissue is severely limited, we explored next the use of circulating blood for class prediction in our mouse models. keywords: analysis; blood; clp; data; expression; gene; human; inflammation; mouse; patients; samples; sepsis; spleen cache: cord-252859-zir02q69.txt plain text: cord-252859-zir02q69.txt item: #93 of 194 id: cord-253450-k7p510p4 author: keha, Abi title: Prevalence of a novel bovine coronavirus strain with a recombinant hemagglutinin/esterase gene in dairy calves in China date: 2019-05-31 words: 3540 flesch: 39 summary: In this study, compared with other BCoV S genes, we found that nine out of 13 of our sequences and 13 Chinese BCoV sequences (one strain from cattle and 12 strains from Yaks), which clustered on a large independent branch of the phylogenetic tree, each had an identical aa variant (N1192Y) in the S2 subunit. The primary role of BCoV N protein is to package the viral genome into long, flexible, helical ribonucleoprotein (RNP) complexes, protect the genome and ensure its timely replication and reliable transmission, as well as playing a role in viral transcription and translation (Hurst, Ye, Goebel, Jayaraman, & Masters, 2010) . keywords: bcov; coronavirus; genes; protein; recombination; sequences; strains cache: cord-253450-k7p510p4.txt plain text: cord-253450-k7p510p4.txt item: #94 of 194 id: cord-253973-zr28uujh author: Maccoux, Lindsey J title: Identification of new reference genes for the normalisation of canine osteoarthritic joint tissue transcripts from microarray data date: 2007-07-25 words: 5359 flesch: 40 summary: Reference gene expression stability and ranking was compared using three different mathematical algorithms. Therefore a ubiquitous reference gene suitable for normalisation of gene expression of all experiments probably does not exist, but the identification of new reference genes to improve in reference gene stability is important to reduce error in RT-qPCR experiments. keywords: bestkeeper; data; expression; genes; genorm; microarray; normfinder; reference; stability; tissues cache: cord-253973-zr28uujh.txt plain text: cord-253973-zr28uujh.txt item: #95 of 194 id: cord-256837-100ir651 author: Smith, Steven B. title: Identification of Common Biological Pathways and Drug Targets Across Multiple Respiratory Viruses Based on Human Host Gene Expression Analysis date: 2012-03-14 words: 8455 flesch: 33 summary: In particular, resistance to different classes of antiviral drugs is becoming more clinically prevalent in respiratory virus infections as seen with RSV and FLU treated with the antiviral drugs palivizumab [7] , and oseltamivir Therefore, more study is needed specifically on the role of caspase and tubulin in host response to respiratory virus infection. keywords: analysis; cells; comparison; datasets; drug; expression; factor; figure; gene; group; host; human; infection; parkin; pathways; protein; response; signaling; table; treatment; viruses cache: cord-256837-100ir651.txt plain text: cord-256837-100ir651.txt item: #96 of 194 id: cord-257843-nj2707mv author: Mariani, Thomas J title: Association of Dynamic Changes in the CD4 T-Cell Transcriptome With Disease Severity During Primary Respiratory Syncytial Virus Infection in Young Infants date: 2017-08-17 words: 4588 flesch: 37 summary: Because CD4 T cells are critical in the development of adaptive immunity following infection and also influence the degree of inflammation, we sought to investigate gene expression patterns using high-throughput RNA sequencing (RNA-seq) of isolated CD4 T cells in healthy full-term infants aged <10 months at the time of primary RSV infection by comparing infants with mild and severe clinical disease. Because CD4 T cells are important in the early adaptive immune response to RSV and are associated with the degree of inflammation during infection, we chose to investigate gene expression patterns in isolated CD4 T cells from infants with primary RSV infection of differing severity during their first year of life. keywords: cd4; cell; disease; expression; genes; infants; rsv; severity; virus cache: cord-257843-nj2707mv.txt plain text: cord-257843-nj2707mv.txt item: #97 of 194 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 cache: cord-258035-2tk7maqk.txt plain text: cord-258035-2tk7maqk.txt item: #98 of 194 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 cache: cord-260345-ugd8kkor.txt plain text: cord-260345-ugd8kkor.txt item: #99 of 194 id: cord-260496-s2ba7uy3 author: Moncany, Maurice L.J. title: Identification of conserved lentiviral sequences as landmarks of genomic flexibility date: 2006-08-08 words: 5998 flesch: 48 summary: A likelihood method for the detection of selection and recombination using nucleotide sequences In vivo characteristics of human immunodeficiency virus type 1 intersubtype recombination: determination of hot spots and correlation with sequence similarity A novel exploratory method for visual recombination detection Scanning the database for recombinant HIV-1 genomes Characterization of a highly replicative intergroup M/O human immunodeficiency virus type 1 recombinant isolated from a Cameroonian patient Sequence variability of the integrase protein from a diverse collection of HIV type 1 isolates representing several subtypes High prevalence of diverse forms of HIV-1 intersubtype recombinants in Central Myanmar: geographical hot spot of extensive recombination Development and application of a highthroughput HIV type-1 genotyping assay to identify CRF02_AG in West/West Central Africa Stepwise detection of recombination breakpoints in sequence alignments Sequencing and comparison of yeast species to identify genes and regulatory elements Genetic characterization of the nef gene from human immunodeficiency virus type 1 group M strains representing genetic subtypes A Precise mapping of recombination breakpoints suggests a common parent of two BC recombinant HIV type 1 strains circulating in China Genotypic and phenotypic analysis of HIV type 1 primary isolates from western Cameroon Human immunodeficiency virus type 1 recombination: rate, fidelity, and putative hot spots V118I substitution in the reverse transcriptase gene of HIV type 1 CRF02_AG strains infecting drug-naive individuals in Cameroon HIV type-1 circulating recombinant form CRF09_cpx from west Africa combines subtypes A, F, G, and may share ancestors with CRF02_AG and Z321 Isolation and characterization of a fulllength molecular DNA clone of Ghanaian HIV type 1 intersubtype A/G recombinant CRF02_AG, which is replication competent in a restricted host range Emergence of new forms of human immunodeficiency virus type 1 intersubtype recombinants in central Myanmar Independent introduction of transmissible F/D recombinant HIV-1 from Africa into Belgium and The Netherlands Mother-to-child HIV type-1 transmission in Argentina: BF recombinants have predominated in infected children since the mid-1980s Identification of Ugandan HIV type-1 variants with unique patterns of recombination in pol involving subtypes A and D Evolution and diversity of HIV-1 in Africa -a review Prevalence and origin of HIV-1 group M subtypes among patients attending a Belgian hospital in 1999 Dual human immunodeficiency virus type 1 infection and recombination in a dually exposed transfusion recipient. keywords: cls; clss; gag; gene; genomes; hiv; pol; recombination; sequences; type; viruses cache: cord-260496-s2ba7uy3.txt plain text: cord-260496-s2ba7uy3.txt item: #100 of 194 id: cord-260793-bb4h255w author: Brann, David H. title: Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia date: 2020-05-18 words: 12011 flesch: 46 summary: medRxiv A primer on viral-associated olfactory loss in the era of COVID-19 Sudden and Complete Olfactory Loss Function as a Possible Symptom of COVID-19 European Patients with mild-to-moderate Coronavirus Disease SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Efficient replication of severe acute respiratory syndrome coronavirus in mouse cells is limited by murine angiotensin-converting enzyme 2 A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury Cleavage and activation of the severe acute respiratory syndrome coronavirus spike protein by human airway trypsin-like protease Influenza and SARS-coronavirus activating proteases TMPRSS2 and HAT are expressed at multiple sites in human respiratory and gastrointestinal tracts Middle East respiratory syndrome coronavirus and bat coronavirus HKU9 both can utilize GRP78 for attachment onto host cells The Laboratory Mouse Comparative anatomy, physiology, and function of the upper respiratory tract Phagocytic cells in the rat olfactory epithelium after bulbectomy Supporting cells as phagocytes in the olfactory epithelium after bulbectomy Ionic conductances in sustentacular cells of the mouse olfactory epithelium Novel role of cystic fibrosis transmembrane conductance regulator in maintaining adult mouse olfactory neuronal homeostasis Olfactory epithelium: Cells, clinical disorders, and insights from an adult stem cell niche Stem and progenitor cells of the mammalian olfactory epithelium: Taking poietic license Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes A single-cell atlas of the human healthy airways A cellular census of human lungs identifies novel cell states in health and in asthma A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans Single-cell analysis of olfactory neurogenesis and differentiation in adult humans SARS-CoV-2 Entry Genes Are Most Highly Expressed in Nasal Goblet and Ciliated Cells within Human Airways Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq Deep Sequencing of the Murine Olfactory Receptor Neuron Transcriptome Dnmt3a Regulates Global Gene Expression in Olfactory Sensory Neurons and Enables Odorant-Induced Transcription Molecular Architecture of the Mouse Nervous System Pericytes and Neurovascular Function in the Healthy and Diseased Brain Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. If humans also exhibit a similar relationship between mRNA and protein (a reasonable possibility given the precise match in olfactory cell types that express CoV-2 cell entry genes between the two species), then ACE2 protein is likely to be broadly expressed in human dorsal sustentacular cells. keywords: ace2; bulb; cell types; cells; cov-2; data; dataset; entry; epithelium; expression; figure; genes; human; infection; mice; mouse; neurons; olfactory; osns; respiratory; seq; sustentacular; tmprss2; types; wom cache: cord-260793-bb4h255w.txt plain text: cord-260793-bb4h255w.txt item: #101 of 194 id: cord-263470-vmqvropy author: Rukavtsova, E. B. title: Tissue specific expression of hepatitis B virus surface antigen in transgenic plant cells and tissue culture date: 2007 words: 2912 flesch: 50 summary: Mechanical leaf wounding for induction of HBsAg gene expression. The immunoassay was carried out to study the expression profile of the surface antigen HBsAg in obtained plants. keywords: antigen; expression; gene; hbsag; plants; promoter; surface; transgenic cache: cord-263470-vmqvropy.txt plain text: cord-263470-vmqvropy.txt item: #102 of 194 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 cache: cord-264746-gfn312aa.txt plain text: cord-264746-gfn312aa.txt item: #103 of 194 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 cache: cord-264884-ydkigome.txt plain text: cord-264884-ydkigome.txt item: #104 of 194 id: cord-264996-og3sg0qw author: Howell, Gareth J. title: Cell Biology of Membrane Trafficking in Human Disease date: 2006-09-17 words: 20376 flesch: 29 summary: Sorting of proteins from donor to target membranes involves the recognition of cytoplasmic sequences in membrane proteins by clathrin-associated AP complexes. However, their exact role in the internalization of membrane proteins and soluble protein ligands is controversial. keywords: actin; apparatus; binding; caveolae; caveolin-1; cell; clathrin; complex; copii; degradation; disease; endocytosis; endoplasmic; endosome; et al; expression; factor; formation; function; fusion; gene; golgi; intracellular; lysosomal; lysosomes; membrane; mutations; novel; number; pathway; patients; plasma; plasma membrane; protein; receptor; reticulum; role; secretory; snare; sorting; specific; syndrome; target; tgn; transport; traycking; type; vesicles; virus cache: cord-264996-og3sg0qw.txt plain text: cord-264996-og3sg0qw.txt item: #105 of 194 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 cache: cord-266521-vovas81d.txt plain text: cord-266521-vovas81d.txt item: #106 of 194 id: cord-266617-z8uecyl6 author: Pavesi, Angelo title: Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation date: 2019-04-03 words: 6694 flesch: 41 summary: Overlapping genes can undergo “symmetric evolution” (similar selection pressures on the two proteins) or “asymmetric evolution” (significantly different selection pressures on the two proteins). These findings suggest that overlapping genes, besides to increase the coding ability of viruses, are also a source of selective protein adaptation. keywords: acid; amino; asymmetric; et al; evolution; frame; genes; overlapping; protein; substitutions cache: cord-266617-z8uecyl6.txt plain text: cord-266617-z8uecyl6.txt item: #107 of 194 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 cache: cord-267475-6f4h3cck.txt plain text: cord-267475-6f4h3cck.txt item: #108 of 194 id: cord-267733-fuz8r3vj author: Al Ali, Sally title: Use of Reporter Genes in the Generation of Vaccinia Virus-Derived Vectors date: 2016-05-21 words: 7989 flesch: 38 summary: Viruses Poxvirus host cell entry Comparative analysis of viral gene expression programs during poxvirus infection: A transcriptional map of the vaccinia and monkeypox genomes Vaccinia virus morphogenesis and dissemination Vaccinia virus infection & temporal analysis of virus gene expression: Part 1 Exploring vaccinia virus as a tool for large-scale recombinant protein expression Evaluation of production parameters with the vaccinia virus expression system using microcarrier attached HeLa cells Cis-and trans-acting elements involved in reactivation of vaccinia virus early transcription Recombinant vaccines and the development of new vaccine strategies. This reporter gene system has been widely used in transgenic plants, and it has also been successfully used in mammalian cells for VACV recombinant virus selection keywords: cell; expression; gene; genome; insertion; protein; recombinant; reporter; selection; vaccines; vaccinia; vacv; vectors; virus; viruses cache: cord-267733-fuz8r3vj.txt plain text: cord-267733-fuz8r3vj.txt item: #109 of 194 id: cord-268098-71g1w1mc author: Beckman, M. F. title: Comorbidities and Susceptibility to COVID-19: A Generalized Gene Set Meta-Analysis Approach date: 2020-09-15 words: 4204 flesch: 44 summary: Significant genes had high levels of association with each pathway. For the VEP matched gene STRINGv11.0 analysis, there were four distinct biological groupings recognized within the mapped network based on the closeness of protein interactions (Figure 2b ). keywords: analysis; author; comorbidities; funder; genes; medrxiv; pathways; perpetuity; preprint; protein; review cache: cord-268098-71g1w1mc.txt plain text: cord-268098-71g1w1mc.txt item: #110 of 194 id: cord-269352-0o3mryu1 author: Dhama, K. title: DNA vaccines and their applications in veterinary practice: current perspectives date: 2008-04-19 words: 6863 flesch: 29 summary: Salient features of DNA vaccines and strategies to improve vaccine efficacy DNA vaccines, generated using plasmids, include a gene encoding target antigen under the transcriptional control of an effective viral/eukaryotic promoter, along with a polyadenylation signal sequence (poly-A) and a bacterial origin of replication ( Fig. 1 ) (Gurunathan et al. 2000) . Sichuan Da Xue Xue Bao Yi Xue Ban Use of attenuated bacteria as delivery vectors for DNA vaccines Immunization of bovines using a DNA vaccine prepared from the Jaboticabal strain of Anaplasma marginale Bm86 antigen induces a protective immune response against Boophilus microplus following DNA and protein vaccination in sheep Immunity and disease resistance strategies in poultry: current and future prospects DNA vaccines and prevention of infectious diseases in bovines: A Review In ovo vaccination with the Eimeria tenella EtMIC2 gene induces protective immunity against coccidiosis Construction of recombinant plasmid with VP1 genes against Asia I FMDV and elementary analysis of its immunological activity CpG motif in ATCGAT hexamer improves DNA-vaccine efficiency against lethal Pseudorabies virus infection in pigs Humoral immune responses to DNA vaccines expressing secreted, membrane bound and non-secreted forms of the Taenia ovis 45W antigen The application of nucleic acid vaccines in veterinary medicine Priming of cytotoxic T lymphocytes by DNA vaccines: requirement for professional antigen-presenting cells and evidence for antigen transfer from myocytes Prime-boost immunization with DNA followed by a recombinant vaccinia virus expressing P50 induced protective immunity against Babesia gibsoni infection in dogs Potency of an experimental DNA vaccine against Aujeszky's disease in pigs Stable and long-lasting immune response in horses after DNA vaccination against equine arteritis virus Development of novel strategies to control foot-and-mouth disease: marker vaccines and antivirals Induction of protection against porcine cysticercosis in growing pigs by DNA vaccination Induction of immune responses in cattle with a DNA vaccine encoding glycoprotein C of bovine herpesvirus-1 Cloning of canine parvovirus VP2 gene and its use as DNA vaccine in dogs Immunogenicity of a recombinant plasmid DNA containing glycoprotein gene of rabies virus CVS A DNA vaccine that encodes rabies virus glycoprotein lacking transmembrane domain enhances antibody response but not protection Induction of immune response in mice with a DNA vaccine encoding outer membrane protein (omp31) of Brucella melitensis 16M DNA vaccines: immunology, application, and optimization Comparison of the immunological memory after DNA vaccination and protein vaccination against anthrax in sheep West Nile virus vaccines On the use of DNA vaccines for the prophylaxis of mycobacterial diseases A tumor reducing factor extracted by phenol from papillomatous tissue of cotton tail rabbits Hemagglutinin (H) gene of canine distemper virus cloned in pTargeT mammalian expression vector induces neutralizing antibody response in dogs Nucleic acid immunization protects dogs against challenge with virulent canine parvovirus Novel chitosan derivative nanoparticles enhance the immunogenicity of a DNA vaccine encoding hepatitis B virus core antigen in mice DNA prime followed by protein boost enhances neutralization and Th1 type immunity against FMDV Strategies for inducing protection against avian influenza A virus subtypes with DNA vaccines CpG motifs in bacterial DNA and their immune effects Nucleic acid vaccination of Brucella abortus ribosomal L7/L12 gene elicits immune response Generation of reassortant influenza vaccines by reverse genetics that allows utilization of a DIVA (Differentiating Infected from Vaccinated Animals) strategy for the control of avian influenza Oral DNA vaccination with polyprotein gene of IBDV delivered by attenuated Salmonella elicits protective immune response in chickens A Semliki Forest virus replicon vectored DNA vaccine expressing the E2 glycoprotein of classical swine fever virus protects pigs from lethal challenge Priming with DNA encoding E2 and boosting with E2 protein formulated with CpG oligodeoxynucleotides induces strong immune responses and protection from Bovine viral diarrhea virus in cattle DNA vaccines: a review DNA vaccines: recent developments and future possibilities Suppository-mediated DNA immunization induces mucosal immunity against bovine herpesvirus-1 in cattle Improved protection from velogenic Newcastle disease virus challenge following multiple immunizations with plasmid DNA encoding for F and HN genes Antibody responses to DNA vaccination of horses using the influenza virus hemagglutinin gene Approaches to enhance the efficacy of DNA vaccines Modulation of immune responses to bovine herpesvirus-1 in cattle by immunization with a DNA vaccine encoding glycoprotein D as a fusion protein with bovine CD154 Adjuvant effects of ILl beta, IL-2, IL-8, 1L-15, IFN-alpha, IFN-gamma TGF-beta and lymphotactin in DNA vaccination against Eimeria acervulina Use of DNA and recombinant canarypox viral vectors for equine herpes virus vaccination Efficacy of particle-based DNA delivery for vaccination of sheep against FMDV DNA vaccination against bovine viral diarrhoea virus induces humoral and cellular responses in cattle with evidence for protection against viral challenge DNA immunization of dairy cows with the clumping factor A of Staphylococcus aureus DNA vaccination against influenza viruses: a review with emphasis on equine and swine influenza DNA vaccination in avian Virus neutralizing antibody response in mice and dogs with a bicistronic DNA vaccine encoding rabies virus glycoprotein and canine parvovirus VP2 Electric pulses applied prior to intramuscular DNA vaccination greatly improve the vaccine immunogenicity Development of rabies DNA vaccine using a recombinant plasmid Brucella abortus: immunity, vaccines and prevention strategies based on nucleic acids Immune response in mice and cattle after immunization with a B. microplus DNA vaccine containing bm86 gene Protection of kids against C. parvum infection after immunization of dams with CP15-DNA Immunization with DNA vaccines encoding different mycobacterial antigens elicits a Th1 type immune response in lambs and protects against Mycobacterium avium subspecies paratuberculosis infection Development of DNA vaccine against chicken anemia virus simultaneously using it's VP1 and VP2 proteins The carboxyl-terminal 120-residue polypeptide of IB virus nucleocapsid induces CTLs and protects chickens from acute infection Recent developments in veterinary vaccinology DNA Fragment Encoding Human IL-1β 163-171 Peptide Enhances the Immune Responses Elicited in Mice by DNA Vaccine against Foot-and-Mouth Disease DNA vaccines: future strategies and relevance to intracellular pathogens Laboratory and field evaluation of Schistosoma japonicum DNA vaccines in sheep and water buffalo in China CD virus DNA vaccination induces humoral and cellular immunity and protects against a lethal intracerebral challenge DNA vaccines and adjuvants DNA immunization with a bovine rotavirus VP4 gene induces a Th1-like immune response in mice DNA vaccine using M. bovis Ag85B antigen induces partial protection against experimental infection in BALB/c mice Enhancing DNA vaccine potency by modifying the properties of antigen-presenting cells DNA vaccines: recent technological and clinical advances Effect of vaccination route and composition of DNA vaccine on the induction of protective immunity against psuedorabies infection in pigs Immune response to vaccines based upon the VapA protein of the horse pathogen, Rhodococcus equi, in a murine model Protection of turkeys against C. psittaci challenge by parenteral and mucosal inoculations and the effect of turkey interferon-gamma on genetic immunization Enhanced immunogenicity of microparticulated multiepitope DNA vaccine encoding T and B cell epitopes of foot and mouth disease virus in mice Immunomodulatory effect of plasmids co-expressing cytokines in classical swine fever virus subunit gp55/E2-DNA vaccination Direct gene transfer into mouse muscle in vivo A DNA vaccine against FMD elicits an immune response in swine which is enhanced by co-administration with interleukin-2. keywords: antigen; disease; dna; encoding; et al; gene; immunity; immunization; infection; plasmid; protection; protein; responses; vaccination; vaccines; virus cache: cord-269352-0o3mryu1.txt plain text: cord-269352-0o3mryu1.txt item: #111 of 194 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 cache: cord-272378-umvi0veu.txt plain text: cord-272378-umvi0veu.txt item: #112 of 194 id: cord-273347-eyxc4rt0 author: Mohammadinejad, Reza title: In vivo gene delivery mediated by non-viral vectors for cancer therapy date: 2020-07-04 words: 7799 flesch: 18 summary: There are J o u r n a l P r e -p r o o f several studies demonstrating that the p53 mediated gene therapy for breast cancer treatment is an efficient approach in cancer gene therapy (204, 205) . Moreover, gene delivery is accounted as a hopeful strategy for brain cancer treatment. keywords: brain; breast; cancer; cas9; cells; delivery; dna; drug; gene; lung; nanoparticles; novel; plasmid; prostate; sirna; systems; targeting; therapy; treatment; tumor; vivo cache: cord-273347-eyxc4rt0.txt plain text: cord-273347-eyxc4rt0.txt item: #113 of 194 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 cache: cord-273609-whm2ce4u.txt plain text: cord-273609-whm2ce4u.txt item: #114 of 194 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 cache: cord-273910-fna7s9te.txt plain text: cord-273910-fna7s9te.txt item: #115 of 194 id: cord-274241-biqbsggu author: Shaw, Timothy I. title: Transcriptome Sequencing and Annotation for the Jamaican Fruit Bat (Artibeus jamaicensis) date: 2012-11-15 words: 6004 flesch: 48 summary: Human and mouse genomes were used as references to estimate the distribution of bat contigs within known gene transcripts. Horse and human were identified as the top two species with best BLAST hits for bat contigs ( Figure 2 ). keywords: analysis; artibeus; bats; contigs; fruit; genes; genome; human; immune; mouse; sequences; species; transcriptome; tree; virus cache: cord-274241-biqbsggu.txt plain text: cord-274241-biqbsggu.txt item: #116 of 194 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 cache: cord-275720-kf9m4zho.txt plain text: cord-275720-kf9m4zho.txt item: #117 of 194 id: cord-277491-q18b88lm author: Cao, Ying-Li title: Identification and Characterization of Three Novel Small Interference RNAs That Effectively Down-Regulate the Isolated Nucleocapsid Gene Expression of SARS Coronavirus date: 2011-02-11 words: 4010 flesch: 46 summary: Similarly, si-N863, which targeted at the 3' half of N gene, also dramatically inhibited N protein expression by about four-fold when the molar ratio of si-N863: N reached 6:1 (Figure 5a and 5b) . Therefore, N gene has long been thought an ideal target for the design of small interference RNA (siRNA). keywords: coronavirus; cov; expression; gene; protein; sars; sequence; sirna cache: cord-277491-q18b88lm.txt plain text: cord-277491-q18b88lm.txt item: #118 of 194 id: cord-278136-ol2buwld author: Gonzales, Natalia M. title: 29th International Mammalian Genome Conference meeting report date: 2016-05-02 words: 4689 flesch: 31 summary: Alterations to the Seok et al. (2013) analysis included comparing genes that exist in both mouse and human, not just human disease genes that lack rodent homologs. The impact of mouse models on precision oncology was showcased by Carol Bult (O-01; The Jackson Laboratory), who discussed how patient-derived xenograft models can provide a platform for testing therapeutic options to guide treatments for breast and other cancers (Fig. 2) . keywords: analysis; cell; data; disease; expression; gene; genetics; genome; human; institute; meeting; models; mouse; research; riken; session; university cache: cord-278136-ol2buwld.txt plain text: cord-278136-ol2buwld.txt item: #119 of 194 id: cord-279781-5ldpz9m9 author: Chen, Chi-Yuan title: Baculovirus as a gene delivery vector: Recent understandings of molecular alterations in transduced cells and latest applications date: 2011-04-28 words: 13147 flesch: 19 summary: Baculovirus neither replicates inside the transduced cells nor integrates its DNA into host chromosomes in the absence of selective pressure (Chen et al., 2011a; Merrihew et al., 2001) , hence easing the safety concerns. al., , 2011 Lucifora et al., 2008; McCormick et al., 2002; Nakowitsch et al., 2006; Zheng et al., 2010) , virus-like particle production (Chen et al., 2005; Matsuo et al., 2006; Wang et al., 2005) , eucaryotic protein display (Ernst et al., 2006, Grabherr and Ernst, 2010) , vaccine development Madhan et al., 2010; keywords: antigen; baculovirus; bmscs; bone; cells; delivery; display; envelope; et al; expression; gene; gp64; human; ifn; immunity; influenza; insect; mice; production; promoter; protein; recombinant; responses; specific; stem; surface; therapy; transduction; vaccine; vector cache: cord-279781-5ldpz9m9.txt plain text: cord-279781-5ldpz9m9.txt item: #120 of 194 id: cord-280691-nzc8ir0n author: Guo, Sun-Wei title: China’s “Gene War of the Century” and Its Aftermath: The Contest Goes On date: 2013-08-30 words: 12491 flesch: 47 summary: Association studies identify disease genes by finding the significant gene frequency differentials between a group of unrelated healthy individuals and another group of unrelated people with the disease of interest. They quickly reached a consensus and soon made it public: (1) China's genetic resources should not be pilfered by foreigners; (2) Chinese scientists should immediately grasp the opportunity to find disease genes and patent them; (3) We should educate the people, and raise the awareness and importance of protection of our genetic resources; (4) We welcome all international collaborations based on fairness and mutual benefits; (5) Through various avenues, the Chinese scientists should be vocal about certain views deemed to be harmful to China's genetic research (Xiao et al. 1997) . keywords: anhui; china; chinese; disease; dna; gene; gene war; genetic; genome; government; harvard; human; medical; people; population; projects; research; resources; samples; science; scientists; war cache: cord-280691-nzc8ir0n.txt plain text: cord-280691-nzc8ir0n.txt item: #121 of 194 id: cord-280897-el7bdkcf author: Wang, Hai-Fang title: Relationship between mRNA stability and intron presence date: 2007-03-02 words: 3041 flesch: 50 summary: The biology of intron gain and loss The evolution of spliceosomal introns: patterns, puzzles and progress The rise and falls of introns How introns influence and enhance eukaryotic gene expression Bringing the role of rnRNA decay in the control of gene expression into focus Post-transcriptional control of gene expression: a genome-wide perspective Simian virus 40 late transcripts lacking excisable intervening sequences are defective in both stability in the nucleus and transport to the cytoplasm Intronmediated enhancement of transgene expression in maize is a nuclear, gene-dependent process A quantitative analysis of intron effects on mammalian gene expression 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 Analysis of the stimulatory effect of splicing on mRNA production and utilization in mammalian cells The effect of intron location on intron-mediated enhancement of gene expression in Arabidopsis A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch-and specific clockcontrolled genes Precision and functional specificity in mRNA decay Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes A gene atlas of the mouse and human protein-encoding transcriptomes Dissecting the regulatory circuitry of a eukaryotic genome The relationship between mRNA stability and length in Saccharomyces cerevisiae Relationship between mRNA stability and length: an old question with a new twist The non-random distribution of intronless human genes across molecular function categories Molecular mechanisms regulating mRNA stability: physiological and pathological significance Induction of TSP1 gene expression by heat shock is mediated via an increase in mRNA stability Linking nuclear mRNP assembly and cytoplasmic destiny The exon junction complex is detected on CBP80-bound but not eIF4E-bound mRNA in mammalian cells: dynamics of mRNP remodeling Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination Keeping RNA and DNA apart during transcription Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability mRNA processing and genomic instability Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation RNA lost in translation Post-transcriptional gene silencing by siRNAs and miRNAs Splicing enhances translation in mammalian cells: an additional function of the exon junction complex We thank Jie Guo and Da-Yong Zhang for suggestion. Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2006.12.184 sha: doc_id: 280897 cord_uid: el7bdkcf Abstract Introns were found to enhance almost every steps of gene expression except increasing mRNA stability. keywords: decay; genes; human; intron; mrna; stability cache: cord-280897-el7bdkcf.txt plain text: cord-280897-el7bdkcf.txt item: #122 of 194 id: cord-280924-g6062fwk author: Hachim, Mahmood Yaseen title: Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells date: 2020-06-10 words: 2857 flesch: 31 summary: Interestingly valproic acid, carbon nanotubes, nickel, and tert-butylhydroperoxide were shown to upregulate IFITM3 expression while pirinixic acid, acetaminophen, and Ethinyl estradiol decreased such an expression ( Table 5) . IFITM3 polymorphisms have been linked with hospitalization and mortality during influenza virus infection (29) . keywords: acid; cells; cov-2; covid-19; genes; ifitm3; infected; sars cache: cord-280924-g6062fwk.txt plain text: cord-280924-g6062fwk.txt item: #123 of 194 id: cord-282968-kjvvoveq author: Qu, Renjun title: Selection of reference genes for the quantitative real-time PCR normalization of gene expression in Isatis indigotica fortune date: 2019-03-25 words: 6295 flesch: 42 summary: Choose BMC and benefit from: sweetpotato cultivars subjected to abiotic stress conditions Genomewide identification and testing of superior reference genes for transcript normalization in Arabidopsis Identification and validation of reference genes and their impact on normalized gene expression studies across cultivated and wild cicer species Reliable reference genes for normalization of gene expression in cucumber grown under different nitrogen nutrition Selection of reference genes for diurnal and developmental time-course real-time PCR expression analyses in lettuce Comparison of the response of ion distribution in the tissues and cells of the succulent plants Aloe vera and Salicornia europaea to saline stress Selection of suitable reference genes for qRT-PCR normalization during leaf development and hormonal stimuli in tea plant (Camellia sinensis) Identification of stable reference genes for quantitative PCR in koalas Analysis of relative gene expression data using real-time quantitative PCR and the 2 −ΔΔCT method Not applicable. key: cord-282968-kjvvoveq authors: Qu, Renjun; Miao, Yujing; Cui, Yingjing; Cao, Yiwen; Zhou, Ying; Tang, Xiaoqing; Yang, Jie; Wang, Fangquan title: Selection of reference genes for the quantitative real-time PCR normalization of gene expression in Isatis indigotica fortune date: 2019-03-25 journal: BMC Mol Biol DOI: 10.1186/s12867-019-0126-y sha: doc_id: 282968 cord_uid: kjvvoveq BACKGROUND: keywords: analysis; expression; genes; indigotica; mub; normalization; pcr; reference; reference genes; results; samples; stress; tissues cache: cord-282968-kjvvoveq.txt plain text: cord-282968-kjvvoveq.txt item: #124 of 194 id: cord-284015-vvtv492b author: Nikaido, Masato title: Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera date: 2020-09-23 words: 8601 flesch: 43 summary: RepbaseSubmitter and censor Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences Repbase update, a database of repetitive elements in eukaryotic genomes PAML 4: a program package for phylogenetic analysis by maximum likelihood The PyMOL molecular graphics system A genomic approach to examine the complex evolution of laurasiatherian mammals A molecular phylogeny for bats illuminates biogeography and the fossil record Characterization of the mitochondrial genome of Rousettus leschenaulti Dynamics of genome size evolution in birds and mammals Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring, and morphological innovation Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome 5S rRNA-derived and tRNA-derived SINEs in fruit bats Origin of avian genome size and structure in non-avian dinosaurs Palaeogenomics of pterosaurs and the evolution of small genome size in flying vertebrates Loss of LINE-1 activity in the megabats Reviving the dead: history and reactivation of an extinct L1 Viral encounters with 2 0 ,5 0 -oligoadenylate synthetase and RNase L during the interferon antiviral response RNase L restricts the mobility of engineered retrotransposons in cultured human cells Restricting retrotransposons: a review LINE-mediated retrotransposition of marked Alu sequences The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals A cluster of olfactory receptor genes linked to frugivory in bats Genomic and genetic evidence for the loss of umami taste in bats Extreme variability among mammalian V1R gene families Prenatal development supports a single origin of laryngeal echolocation in bats Evolution of the sweet taste receptor gene Tas1r2 in bats Frequent expansions of the bitter taste receptor gene repertoire during evolution of mammals in the Euarchontoglires clade Formyl peptide receptor-like proteins are a novel family of vomeronasal chemosensors Adaptive evolution of formyl peptide receptors in mammals Molecular organization of vomeronasal chemoreception From genes to social communication: molecular sensing by the vomeronasal organ Evolution of V1R pheromone receptor genes in vertebrates: diversity and commonality Widespread losses of vomeronasal signal transduction in bats Trpc2 pseudogenization dynamics in bats reveal ancestral vomeronasal signaling, then pervasive loss A single pheromone receptor gene conserved across 400 million years of vertebrate evolution Inactivation of ancV1R as a predictive signature for the loss of vomeronasal system in mammals Vomeronasal organ in bats and primates: extremes of structural variability and its phylogenetic implications Expressed vomeronasal type-1 receptors (V1rs) in bats uncover conserved sequences underlying social chemical signaling A novel family of putative pheromone receptors in mammals with a topographically organized and sexually dimorphic distribution A multigene family encoding a diverse array of putative pheromone receptors in mammals The male mouse pheromone ESP1 enhances female sexual receptive behaviour through a specific vomeronasal receptor Sexual rejection via a vomeronasal receptor-triggered limbic circuit First evidence for functional vomeronasal 2 receptor genes in primates Comparative genomic analysis identifies an evolutionary shift of vomeronasal receptor gene repertoires in the vertebrate transition from water to land A renaissance in trace amines inspired by a novel gpcr family A second class of chemosensory receptors in the olfactory epithelium Trace amine-associated receptors: ligands, neural circuits, and behaviors Molecular evolution and functional divergence of trace amine-associated receptors MHC-dependent mate choice is linked to a trace-amine-associated receptor gene in a mammal WebGestalt, a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit Pangolin genomes and the evolution of mammalian scales and immunity Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins Adaptive evolution in the glucose transporter 4 gene Slc2a4 in Old World fruit bats (family: pteropodidae) It is possible that megabats re-allocated the diversity in chemosensory receptor genes as a sensory trade-off, given that megabats have experienced the secondary loss of echolocation ability, which is one of the most specialized senses in bats. keywords: analyses; evolution; fig; fruit; fruit bat; genes; genome; mammals; megabats; microbats; receptor; rousette; sequences; species; supplementary; taars; table; tes cache: cord-284015-vvtv492b.txt plain text: cord-284015-vvtv492b.txt item: #125 of 194 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 cache: cord-284933-flbibrcm.txt plain text: cord-284933-flbibrcm.txt item: #126 of 194 id: cord-285656-7o7ofk1e author: Dawson, Harry D. title: The porcine translational research database: a manually curated, genomics and proteomics-based research resource date: 2017-08-22 words: 5701 flesch: 44 summary: This database is the largest manually curated database for any single veterinary species and is unique among porcine gene databases in regard to linking gene expression to gene function, identifying related gene pathways, and connecting data with other porcine gene databases. These sequences represent 6 Zebrafish genes (LOC100003615, LOC447815, LOC108179932, LOC108183883, LOC108183971, and LOC103910681) and are annotated as porcine genes by Ensembl build 10.2 (ENSSSCG00000006223) and NCBI genomes (LOC100739857). keywords: build; database; ensembl; expression; genes; genome; human; mouse; ncbi; pig; pigs; porcine; protein; sequences; species cache: cord-285656-7o7ofk1e.txt plain text: cord-285656-7o7ofk1e.txt item: #127 of 194 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 cache: cord-287396-18p171nr.txt plain text: cord-287396-18p171nr.txt item: #128 of 194 id: cord-289033-vfh3op6a author: Algammal, Abdelazeem M. title: Genes Encoding the Virulence and the Antimicrobial Resistance in Enterotoxigenic and Shiga-toxigenic E. coli Isolated from Diarrheic Calves date: 2020-06-10 words: 4897 flesch: 43 summary: The multidrug resistance (MDR) is common in E. coli and primarily associated with several genes like; bla-TEM, blaCTX (β-lactamase genes), sul1 (sulfonamide resistance gene), and aadB (aminoglycoside resistance gene) This study was aimed at determining the prevalence of STEC and ETEC incriminated in calf diarrhea, with special reference to the Shiga-toxins genes (stx1 and stx2) and enterotoxins genes (lt and sta) that govern their pathogenesis, as well as the virulence genes; eaeA and f41, and the screening of their antimicrobial resistance profiles and antimicrobial resistance genes; aadB, sul1, and bla-TEM. keywords: calves; coli; e. coli; genes; prevalence; resistance; shiga; strains; virulence cache: cord-289033-vfh3op6a.txt plain text: cord-289033-vfh3op6a.txt item: #129 of 194 id: cord-290282-oxyzndsj author: Ortego, Javier title: Transmissible gastroenteritis coronavirus gene 7 is not essential but influences in vivo virus replication and virulence date: 2003-03-30 words: 4324 flesch: 45 summary: rTGEV in which gene 7 expression was abrogated (rTGEV-Δ7) were recovered from cDNA constructs, indicating that TGEV gene 7 was a nonessential gene for virus replication. The 3Ј end of the majority of TGEV genes overlaps with the 5Ј terminus of the next gene (Enjuanes et al., 2000b) , complicating insertion of heterologous genes into the viral genome and deletion of different genes to determine whether they are essential. keywords: gene; pbac; restriction; tgev; virus; viruses cache: cord-290282-oxyzndsj.txt plain text: cord-290282-oxyzndsj.txt item: #130 of 194 id: cord-290861-5bxvenue author: Ashwell, M. title: Characterization of gene expression in naturally occurring feline degenerative joint disease-associated pain date: 2018-11-19 words: 4912 flesch: 43 summary: At least three other studies have identified suitable gene expression housekeeping genes in various feline tissues. Expression of an investigator-selected set of pain signaling genes (including ASIC3, ATF3, COX2, CX3CL1, NAV1.7, NAV1.8, NAV1.9, NGF, NK1R, TNFα, TRKA) in lumbar spinal cord dorsal horn and lumbar dorsal root ganglia tissues from clinically healthy cats and cats with DJD were studied using quantitative RT-PCR (qPCR). keywords: cats; djd; drg; expression; feline; genes; pain; reference; samples; spinal cache: cord-290861-5bxvenue.txt plain text: cord-290861-5bxvenue.txt item: #131 of 194 id: cord-291349-tq2n4mx3 author: Smith, Kevin R title: Gene transfer in higher animals: theoretical considerations and key concepts date: 2002-10-09 words: 12239 flesch: 39 summary: Thus, alternative viruses have been explored as potential agents for somatic cell gene therapy. Thus, microinjection is fundamentally unsuitable for in vivo somatic cell gene therapy. keywords: animals; cells; dna; eggs; electroporation; et al; expression; gene; germline; integration; liposomes; mammalian; mice; microinjection; mouse; targeting; therapy; transfer; transgene; transgenesis; vectors cache: cord-291349-tq2n4mx3.txt plain text: cord-291349-tq2n4mx3.txt item: #132 of 194 id: cord-291719-1ku6cmwj author: Hajjo, Rima title: A Systems Biology Workflow for Drug and Vaccine Repurposing: Identifying Small-Molecule BCG Mimics to Reduce or Prevent COVID-19 Mortality date: 2020-10-06 words: 6506 flesch: 27 summary: Our analysis demonstrates that BCG vaccine affects the production and maturation of naïve T cells resulting in enhanced, long-lasting trained innate immune responses that can provide protection against novel viruses. A consensus gene signature for BCG vaccine was derived from gene expression profiles in peripheral blood mononuclear cells (PBMCs) in response to a BCG challenge test reported by Matsumiya et al (76) , GSE58636 dataset on NCBI Gene Expression Omnibus (GEO) (27) . keywords: bcg; cells; cgs; cov-2; covid-19; effects; expression; gene; network; protein; response; sars; study; vaccination; vaccine cache: cord-291719-1ku6cmwj.txt plain text: cord-291719-1ku6cmwj.txt item: #133 of 194 id: cord-292004-9rpoll7y author: Mitchell, Hugh D. title: The Role of EGFR in Influenza Pathogenicity: Multiple Network-Based Approaches to Identify a Key Regulator of Non-lethal Infections date: 2019-09-20 words: 8365 flesch: 36 summary: Our results show that by using association networks, bottleneck genes that lack hub characteristics can be used to predict a gene’s involvement in influenza virus pathogenicity. Our results show that by using association networks, bottleneck genes that lack hub characteristics can be used to predict a gene's involvement in influenza virus pathogenicity. keywords: bottlenecks; data; day; egfr; et al; expression; figure; genes; infection; influenza; mice; network; pathogenicity; virus cache: cord-292004-9rpoll7y.txt plain text: cord-292004-9rpoll7y.txt item: #134 of 194 id: cord-294725-wyrg0nq8 author: Bourdon, Julie A. title: Gene expression profiling to identify potentially relevant disease outcomes and support human health risk assessment for carbon black nanoparticle exposure date: 2013-01-07 words: 6422 flesch: 31 summary: Meta-analysis using CBNP gene expression profiles in mouse ranked 473 canonical pathways and 21,277 genes present in at least one of the studies on select models of pulmonary fibrosis and lung injury (identified in NextBio disease correlation profiles). In order for gene expression data to become accepted for routine use in HHRA, it is necessary to demonstrate that mRNA/protein expression profiles can effectively predict the modes of action and biological outcomes of exposure at relevant doses, and to confirm that these data can be used to strengthen the foundation for HHRA and regulatory decisions. keywords: analysis; cbnp; data; disease; exposure; expression; gene; human; lung; mice; models; pathways; profiles cache: cord-294725-wyrg0nq8.txt plain text: cord-294725-wyrg0nq8.txt item: #135 of 194 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 cache: cord-295019-8tf8ah6g.txt plain text: cord-295019-8tf8ah6g.txt item: #136 of 194 id: cord-295307-zrtixzgu author: Delgado-Chaves, Fernando M. title: Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks date: 2020-07-21 words: 10178 flesch: 46 summary: For this reason, the use of gene networks may well encourage therapy-associated research in the context of the coronavirus pandemic, orchestrating experimental scrutiny and reducing costs. Within this framework, gene networks (GN) have become an important tool in the modeling and analysis of biological processes from gene expression data [5] . keywords: analyses; cases; control; deg; expression; figure; gene; infection; liver; ly6e; networks; p.i; q q; response; samples; spleen cache: cord-295307-zrtixzgu.txt plain text: cord-295307-zrtixzgu.txt item: #137 of 194 id: cord-296979-8r851j4t author: Zhong, Ying title: Host genes regulate transcription of sperm-introduced hepatitis B virus genes in embryo date: 2017-10-31 words: 6777 flesch: 44 summary: Finally, we silenced the target genes and a control gene by RNA interference (RNAi) to detect effects of the silencing of these genes on transcriptional level of HBV genes to determine whether host genes participate in regulation of HBV gene transcription. The transcription levels of HBV genes between the test and control groups are significantly different (P < 0.05), which suggested that in the test group the target genes have been silenced by RNAi and participated in transcriptional regulation of HBV genes, causing the change of HBV gene transcription levels. keywords: cell; control; embryos; expression; genes; group; hbv; hepatitis; human; pcr; sperm; target; test; transcription; virus cache: cord-296979-8r851j4t.txt plain text: cord-296979-8r851j4t.txt item: #138 of 194 id: cord-298131-zolwjl9u author: Xiao, Shuqi title: Understanding PRRSV Infection in Porcine Lung Based on Genome-Wide Transcriptome Response Identified by Deep Sequencing date: 2010-06-29 words: 9366 flesch: 34 summary: Data were presented as fold changes in gene expression normalized to the HPRT1 gene and relative to the C sample. Despite such limitations, our DGE study offers a broad, system-wide window into molecular processes that regulate gene expression and also provides new leads for functional studies of candidate genes involved in host-virus interaction, as illustrated in this paper. keywords: abundance; analysis; cells; expression; figure; genes; host; infected; infection; lungs; number; pigs; porcine; prrsv; response; syndrome; tags; transcript; viral; virus cache: cord-298131-zolwjl9u.txt plain text: cord-298131-zolwjl9u.txt item: #139 of 194 id: cord-301218-zsp5sh9o author: Weeraratna, Ashani T. title: Gene Expression Profiling: From Microarrays to Medicine date: 2004 words: 6390 flesch: 25 summary: An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae Cluster analysis and display of genome-wide expression patterns Molecular classification of cutaneous malignant melanoma by gene expression profiling Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation Systematic determination of genetic network architecture Analysis of large-scale gene expression data Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring The main biological determinants of tumor line taxonomy elucidated by a principal component analysis of microarray data Knowledge-based analysis of microarray gene expression data by using support vector machines Support vector machine classification and validation of cancer tissue samples using microarray expression data Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks Using Bayesian networks to analyze expression data Bayesian hierarchical model for identifying changes in gene expression from microarray experiments Development of a prostate cDNA microarray and statistical gene expression analysis package Identifying and quantifying sources of variation in microarray data using high-density cDNA membrane arrays Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations Standards for microarray data Minimum information about a microarray experiment (MIAME) toward standards for microarray data Roses AD: Pharmacogenetics and the practice of medicine The use of single-nucleotide polymorphism maps in pharmacogenomics Haplotype variation and linkage disequilibrium in 313 human genes A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms The SNP consortium: Clearly, gene expression analysis remains a work in progress. keywords: analysis; arrays; cancer; cdna; cells; data; disease; expression; gene; human; microarray; profiling; rna; snp; studies; technology cache: cord-301218-zsp5sh9o.txt plain text: cord-301218-zsp5sh9o.txt item: #140 of 194 id: cord-301546-yck1t3pp author: Kozaki, Toshinori title: Comparison of two acetylcholinesterase gene cDNAs of the lesser mealworm, Alphitobius diaperinus, in insecticide susceptible and resistant strains date: 2007-12-28 words: 2508 flesch: 42 summary: Despite the diversity and economic importance of Coleoptera, Ace genes have been reported from only two beetles: Leptinotarsa decemlineata (Say) (Zhu et al., 1996) and Tribolium castaneum (http://www.hgsc.bcm.tmc/edu/projects/ tribolium/). The nucleotide and deduced amino acid sequences of AdAce1 (Drosophila Ace orthologous) keywords: ace; beetles; diaperinus; drosophila; gene; resistance cache: cord-301546-yck1t3pp.txt plain text: cord-301546-yck1t3pp.txt item: #141 of 194 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 cache: cord-302047-vv5gpldi.txt plain text: cord-302047-vv5gpldi.txt item: #142 of 194 id: cord-303132-m3j1dekj author: Smith, S. E. title: Chicken Interferon-Inducible Transmembrane Protein 3 Restricts Influenza Viruses and Lyssaviruses In Vitro date: 2013-12-17 words: 5206 flesch: 41 summary: (26) have undertaken a comprehensive analysis of IFITM genes across a broad range of chordates. Here we have resolved the entire antiviral IFITM locus on chromosome 5 of the chicken genome, expanding the number of IFITM genes to 4 in this locus, and confirmed that the locus is flanked by the genes ATHL1 and B4GALNT4 (9) . keywords: analysis; cells; chicken; chifitm3; expression; gene; human; ifitm; infection; influenza; proteins; virus; viruses cache: cord-303132-m3j1dekj.txt plain text: cord-303132-m3j1dekj.txt item: #143 of 194 id: cord-303939-7knzjnyr author: Hu, Fang title: Identification of a metabolic gene panel to predict the prognosis of myelodysplastic syndrome date: 2020-04-26 words: 2284 flesch: 30 summary: Si-liang Chen https://orcid.org/0000-0002-4095-5974 The genetic basis of phenotypic heterogeneity in myelodysplastic syndromes Myelodysplastic syndromes Clinical implications of genetic mutations in myelodysplastic syndrome Immunologic aspects of hypoplastic myelodysplastic syndrome Revised international prognostic scoring system for myelodysplastic syndromes Myelodysplastic syndromes, version 2.2017, NCCN clinical practice guidelines in oncology Use of newer prognostic indices for patients with myelodysplastic syndromes in the low and intermediate-1 risk categories: a population-based study Transplantation of a myelodysplastic syndrome by a long-term repopulating hematopoietic cell Characterization and targeting of malignant stem cells in patients with advanced myelodysplastic syndromes Inhibition of amino acid metabolism selectively targets human leukemia stem cells Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia BCL-2 inhibition targets oxidative phosphorylation and selectively eradicates quiescent human leukemia stem cells Evaluation of bone marrow microenvironment could change how myelodysplastic syndromes are diagnosed and treated Protective mitochondrial transfer from bone marrow stromal cells to acute myeloid leukemic cells during chemotherapy Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/ pathways and clinical associations Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal Hallmarks of cancer: the next generation Enhanced renewal of erythroid progenitors in myelodysplastic anemia by peripheral serotonin Higher fetuin-A, lower adiponectin and free leptin levels mediate effects of excess body weight on insulin resistance and risk for myelodysplastic syndrome Identification of glucocorticoid-response genes in children with acute lymphoblastic leukemia Anti-spike IgG causes severe acute lung injury by skewing macrophage responses during acute SARS-CoV infection Distinct prognostic values of phospholipase C beta family members for non-small cell lung carcinoma Loss of Dnmt3b function upregulates the tumor modifier Ment and accelerates mouse lymphomagenesis Loss of Dnmt3b accelerates MLL-AF9 leukemia progression Prognostic and biologic significance of DNMT3B expression in older patients with cytogenetically normal primary acute myeloid leukemia Pathways of retinoid synthesis in mouse macrophages and bone marrow cells Arginine addiction in AML Arginine deprivation for ASS1-deficient mesothelioma A phase II study of arginine deiminase (ADI-PEG20) in relapsed/refractory or poor-risk acute myeloid leukemia patients Arginine deprivation using pegylated arginine deiminase has activity against primary acute myeloid leukemia cells in vivo Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors Impact of DNA amplification on gene expression patterns in breast cancer Identification of a metabolic gene panel to predict the prognosis of myelodysplastic syndrome A prognostic model was constructed by the least absolute shrinkage and selection operator (LASSO) regression analysis for MDS patients based on the identified metabolic gene panel in training cohort, followed by external validation in an independent cohort. keywords: cells; cohort; gene; mds; metabolic; patients; prognostic; risk; training cache: cord-303939-7knzjnyr.txt plain text: cord-303939-7knzjnyr.txt item: #144 of 194 id: cord-304607-td0776wj author: Paszkiewicz, Konrad H. title: Omics, Bioinformatics, and Infectious Disease Research date: 2010-12-24 words: 7023 flesch: 39 summary: In addition, 21 nonannotated regions had clear levels of transcription and should therefore be considered as genes (Passalacqua et al., 2009) . Indeed, the first bacterial genomes sequenced were those from pathogens Fraser et al., 1995; Tomb et al., 1997) , and these were preceded by many bacteriophage genomes such as bacteriophage MS2 (Fiers et al., 1976) and ϕX174 (Sanger et al., 1977) and viral genomes (Fiers et al., 1978) . keywords: analysis; assembly; bioinformatics; data; disease; et al; genes; genome; genomics; proteins; sequence; sequencing; species; vaccine cache: cord-304607-td0776wj.txt plain text: cord-304607-td0776wj.txt item: #145 of 194 id: cord-304913-qb9zeazk author: Thibivilliers, Sandra title: Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection date: 2009-04-27 words: 6690 flesch: 47 summary: Plant gene expression was similar for both race 41 and 49 during the first 48 hours of the infection process but varied significantly at the later time points (72–96 hours after inoculation) mainly due to the presence of the Avr4 gene in the race 49 leading to a hypersensitive response in the bean plants. Among these 10,581 unisequences, 10,221 were annotated as bean genes and 360 were annotated as fungal genes based on best Blast hits to the database These 360 fungal unisequences included 62 singletons and 298 contigs (Table 1) . keywords: appendiculatus; bean; cdna; ests; expression; fungal; genes; infection; library; pcr; plant; race; resistance; rust; sequences cache: cord-304913-qb9zeazk.txt plain text: cord-304913-qb9zeazk.txt item: #146 of 194 id: cord-305177-i71z2sf4 author: Neshat, Sarah Y title: Gene delivery for immunoengineering date: 2020-06-15 words: 5279 flesch: 23 summary: key: cord-305177-i71z2sf4 authors: Neshat, Sarah Y; Tzeng, Stephany Y; Green, Jordan J title: Gene delivery for immunoengineering date: 2020-06-15 journal: Curr Opin Biotechnol DOI: 10.1016/j.copbio.2020.05.008 sha: doc_id: 305177 cord_uid: i71z2sf4 A growing number of gene delivery strategies are being employed for immunoengineering in applications ranging from infectious disease prevention to cancer therapy. Non-viral methods of gene delivery, including polymeric, lipid-based, and inorganic nanoparticles as well as physical delivery techniques, have also been widely investigated. keywords: cancer; cells; delivery; dna; gene; immune; immunotherapy; lipid; mrna; nanoparticles; response; tumor; vivo cache: cord-305177-i71z2sf4.txt plain text: cord-305177-i71z2sf4.txt item: #147 of 194 id: cord-306380-msk9p1yy author: Lee, C.-W. title: Evidence of genetic diversity generated by recombination among avian coronavirus IBV date: 2000 words: 2800 flesch: 54 summary: Sequencing primers to various regions of the gene for DE072 and The relative primer positions were calculated using the ATG start site of Gene 3 as 1 for primers gene 3 and 4, and ATG start site of S1 gene as 1 for primers HVR in S1 D1466 were designed using OLIGO version 4.0 software (National Bioscience, Plymouth, MN, USA) and are available upon request. Gene 4 consisted of the M protein gene with a single ORF and a non-coding region between the 3 end of the M protein gene and gene 5. keywords: d1466; de072; gene; ibv; sequence; strains; virus cache: cord-306380-msk9p1yy.txt plain text: cord-306380-msk9p1yy.txt item: #148 of 194 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 cache: cord-306535-j26eqmxt.txt plain text: cord-306535-j26eqmxt.txt item: #149 of 194 id: cord-307202-iz1bo218 author: Shaw, Dominick title: Asthma date: 2014-05-02 words: 19202 flesch: 32 summary: The aim of asthma treatment is to improve symptoms, maintain lung function, and prevent exacerbations. Although there are several pharmacological options for asthma treatment (see Figure 28 .4), the two main classes remain bronchodilators (short-or long-acting) and corticosteroids. keywords: airway; approaches; association; asthma; cells; children; control; corticosteroid; disease; effects; exacerbations; factors; fev; function; gene; inflammation; leukotriene; lung; montelukast; patients; polymorphisms; protein; receptor; response; snps; studies; study; symptoms; therapy; treatment; use cache: cord-307202-iz1bo218.txt plain text: cord-307202-iz1bo218.txt item: #150 of 194 id: cord-307769-rjseio5s author: Sim, Winnie H title: Expression profile of genes involved in pathogenesis of pediatric Crohn's disease date: 2012-05-24 words: 4681 flesch: 33 summary: (125 fg) of each gene was used as the calibrator in every assay to allow for direct comparison of gene expression for all samples analyzed across multiple assays. The Mann-Whitney U-test was used to compare the difference in median values between gene expression in CD and non-IBD patient samples. keywords: biopsies; crohn; disease; expression; genes; human; ibd; ileal; mmp2; pathogenesis; patients; reg1a; ssh; study cache: cord-307769-rjseio5s.txt plain text: cord-307769-rjseio5s.txt item: #151 of 194 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 cache: cord-308034-9b219k0v.txt plain text: cord-308034-9b219k0v.txt item: #152 of 194 id: cord-309556-xv3413k1 author: Chow, Ryan D. title: The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2 date: 2020-04-15 words: 5772 flesch: 41 summary: Lung epithelial cells, macrophages, and Th1 cells decrease in abundance with age, whereas fibroblasts, pericytes and CD4+ Tcm cells increase in abundance with age. We showed that lung epithelial cells, macrophages, and Th1 cells decrease in abundance with age, whereas fibroblasts and pericytes increase in abundance with age. keywords: age; aging; cell; cluster; cov-2; covid-19; data; expression; factors; figure; genes; human; infection; lung; sars cache: cord-309556-xv3413k1.txt plain text: cord-309556-xv3413k1.txt item: #153 of 194 id: cord-311430-o32d3kaw author: Shahabi, Vafa title: Gene expression profiling of whole blood in ipilimumab-treated patients for identification of potential biomarkers of immune-related gastrointestinal adverse events date: 2013-03-22 words: 6486 flesch: 44 summary: Changes in gene expression over time were also characterized. Statistical inference based on this model focused on two hypothesis tests: a test of the null hypothesis that mean gene expression (averaged over time) was the same in the two GI irAE status groups, and a test of the null hypothesis that mean gene expression (averaged over GI irAE status) was the same for the three time points. keywords: baseline; cd177; expression; genes; gi irae; groups; ipilimumab; irae; mean; patients; treatment; week cache: cord-311430-o32d3kaw.txt plain text: cord-311430-o32d3kaw.txt item: #154 of 194 id: cord-312551-w4tps34p author: Razvi, Mohammad H. title: Transcriptional oncogenomic hot spots in Barrett's adenocarcinomas: Serial analysis of gene expression date: 2007-07-17 words: 5053 flesch: 37 summary: APN/CD13 is an epithelial-mesenchymal marker in skin E-cadherin expression in gastroesophageal reflux disease, Barrett's esophagus, and esophageal adenocarcinoma: An immunohistochemical and immunoblot study Evaluation of genetic patterns in different tumor areas of intermediate-grade prostatic adenocarcinomas by high-resolution genomic array analysis Targets of gene amplification and overexpression at 17q in gastric cancer Serial analysis of gene expression Analysing uncharted transcriptomes with SAGE Protein kinases and phosphatases as therapeutic targets in cancer Chromosomal clustering of a human transcriptome reveals regulatory background Sucrase-isomaltase gene expression in Barrett's esophagus and adenocarcinoma A novel method for gene expression mapping of metastatic competence in human bladder cancer Human aminopeptidase N is a receptor for human coronavirus 229E key: cord-312551-w4tps34p authors: Razvi, Mohammad H.; Peng, Dunfa; Dar, Altaf A.; Powell, Steven M.; Frierson, Henry F.; Moskaluk, Christopher A.; Washington, Kay; El‐Rifai, Wael title: Transcriptional oncogenomic hot spots in Barrett's adenocarcinomas: Serial analysis of gene expression date: 2007-07-17 journal: Genes Chromosomes Cancer DOI: 10.1002/gcc.20479 sha: doc_id: 312551 cord_uid: w4tps34p Serial analysis of gene expression (SAGE) provides quantitative and comprehensive expression profiling in a given cell population. keywords: analysis; anpep; barrett; cancer; cell; et al; expression; genes; sage; samples; tags; tumor cache: cord-312551-w4tps34p.txt plain text: cord-312551-w4tps34p.txt item: #155 of 194 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 cache: cord-313138-y485ev30.txt plain text: cord-313138-y485ev30.txt item: #156 of 194 id: cord-314503-u1y1bznk author: Jaluria, Pratik title: A perspective on microarrays: current applications, pitfalls, and potential uses date: 2007-01-25 words: 7765 flesch: 37 summary: Microcirculation The use and analysis of microarray data Microarray expression profiling: capturing a genome-wide portrait of the transcriptome Microarray expression profiling: analysis and applications From patterns to pathways: gene expression data analysis comes of age Bioinformatics in microbial biotechnology -a mini review Computational analysis of microarray data Differential gene expression in recombinant Pichia pastoris analysed by heterologous DNA microarray hybridization An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays A framework to analyze multiple time series data: a case study with Streptomyces coelicolor Design of studies using DNA microarrays Applications of microarrays in the pharmaceutical industry Methods and approaches in the analysis of gene expression data Uncovering evolutionary patterns of gene expression using microarrays Microarray analysis of gene expression during the cell cycle Biological methods for cell-cycle synchronization of mammalian cells TM4: a free, open-source system for microarray data management and analysis Comparisons and validation of statistical clustering techniques for microarray gene expression data Cluster analysis and display of genome-wide expression patterns Systematic determination of genetic network architecture Fundamentals of Biostatistics Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics Transcriptional response of Candida albicans to nitric oxide and the role of the YHB1 gene in nitrosative stress and virulence High-resolution mutation mapping reveals parallel experimental evolution in Without these considerations, it can be exceedingly difficult to ascertain valuable information from microarray data. keywords: analysis; arrays; control; data; dna; experiments; expression; genes; methods; microarray; number; researchers; samples; technology cache: cord-314503-u1y1bznk.txt plain text: cord-314503-u1y1bznk.txt item: #157 of 194 id: cord-314642-oobbdgzh author: Campbell, Allan title: The future of bacteriophage biology date: 2003 words: 5949 flesch: 48 summary: The dodecameric portal protein rotates in the protein shell of the phage, in steps of 12 °, which reel in phage DNA and are powered by ATP hydrolysis (FIG. 2) . The insertion of phage DNA into the chromosome during lysogenization is a good example. keywords: bacteria; bacteriophage; cell; dna; genes; host; lambdoid; phage; protein; recombination; repressor; site; viruses cache: cord-314642-oobbdgzh.txt plain text: cord-314642-oobbdgzh.txt item: #158 of 194 id: cord-314915-b6aqwubh author: Futas, Jan title: Natural Killer Cell Receptor Genes in Camels: Another Mammalian Model date: 2019-07-02 words: 10067 flesch: 49 summary: Based on its structure, this inhibitory type of receptor gene may be functional, similarly to pigs. This cluster was related with the cluster of camelid LILRB1 genes, while the cluster containing NCR1 gene sequences was related to the camelid LILRA2-Ig genes. keywords: camel; cell; complex; dromedarius; et al; genes; genome; genomic; killer; lrc; nkc; protein; receptor; region; sequences; species; variants cache: cord-314915-b6aqwubh.txt plain text: cord-314915-b6aqwubh.txt item: #159 of 194 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 cache: cord-315072-b28yikvj.txt plain text: cord-315072-b28yikvj.txt item: #160 of 194 id: cord-315498-gpzee1f2 author: Parkinson, N. title: Systematic review and meta-analysis identifies potential host therapeutic targets in COVID-19. date: 2020-09-01 words: 4968 flesch: 38 summary: Results from identified studies, in the form of lists of implicated host factor genes, were combined using meta-analysis by information content (MAIC), 3 an approach we previously developed to identify host genes necessary for Influenza A virus (IAV) replication. We identified limited overlap of our gene list with host genes implicated in ARDS (innate immune and inflammation genes) and Influenza A virus infection (RNA-binding and ribosome-associated genes). keywords: analysis; covid-19; data; genes; host; license; list; maic; preprint; protein; sars; studies cache: cord-315498-gpzee1f2.txt plain text: cord-315498-gpzee1f2.txt item: #161 of 194 id: cord-317779-j67vb7f3 author: Irizarry, Kristopher J. L. title: RNA sequencing demonstrates large-scale temporal dysregulation of gene expression in stimulated macrophages derived from MHC-defined chicken haplotypes date: 2017-08-28 words: 9744 flesch: 37 summary: key: cord-317779-j67vb7f3 authors: Irizarry, Kristopher J. L.; Downs, Eileen; Bryden, Randall; Clark, Jory; Griggs, Lisa; Kopulos, Renee; Boettger, Cynthia M.; Carr, Thomas J.; Keeler, Calvin L.; Collisson, Ellen; Drechsler, Yvonne title: RNA sequencing demonstrates large-scale temporal dysregulation of gene expression in stimulated macrophages derived from MHC-defined chicken haplotypes date: 2017-08-28 journal: PLoS One DOI: 10.1371/journal.pone.0179391 sha: doc_id: 317779 cord_uid: j67vb7f3 Discovering genetic biomarkers associated with disease resistance and enhanced immunity is critical to developing advanced strategies for controlling viral and bacterial infections in different species. These differences in gene expression appear to be regulated by complex epigenetic mechanisms that need further investigation. keywords: b19; b19 cells; b2 cells; birds; cells; data; day; differentiation; expression; gene expression; genes; haplotype; hours; ifnγ; macrophages; stimulation; time cache: cord-317779-j67vb7f3.txt plain text: cord-317779-j67vb7f3.txt item: #162 of 194 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 cache: cord-318576-dc5n6ni4.txt plain text: cord-318576-dc5n6ni4.txt item: #163 of 194 id: cord-319517-denczc6t author: Salipalli, Sandeep title: Recent advances in live cell imaging of hepatoma cells date: 2014-07-08 words: 9219 flesch: 41 summary: An enhanced monomeric blue fluorescent protein with the high chemical stability of the chromophore Evolutionary optimization of fluorescent proteins for intracellular FRET Fluorescent proteins from nonbioluminescent Anthozoa species A monomeric red fluorescent protein Dynamic motion of paxillin on actin filaments in living endothelial cells A guide to choosing fluorescent proteins Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein Bright monomeric red fluorescent protein with an extended fluorescence lifetime Green fluorescent protein as a marker for gene expression Aequorea green fluorescent protein: expression of the gene and fluorescence characteristics of the recombinant protein Two-photon fluorescence absorption and emission spectra of dyes relevant for cell imaging In vitro activity of fluorescent dyes against asexual blood stages of Plasmodium falciparum Antibodies for fluorescent molecular rotors ReAsH/FlAsH labeling and image analysis of tetracysteine sensor proteins in cells Specific covalent labeling of recombinant protein molecules inside live cells Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications Fluorogen-activating single-chain antibodies for imaging cell surface proteins Moreover, ELuc was tested in cell lines such as NIH/3T3 using various promoters, and it was shown that the luciferase primarily localizes in nucleus, cytosol and in peroxisomes. keywords: cell; droplets; efficiency; emission; expression; fluorescent; fluorescent protein; gene; gfp; green; imaging; lines; lipid; methods; protein; red; study; transfection; transfer; vectors cache: cord-319517-denczc6t.txt plain text: cord-319517-denczc6t.txt item: #164 of 194 id: cord-319519-mb9ofh12 author: Ding, J. title: A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes' interactions points to Neutrophil Extracellular Traps as mediators of thrombosis in COVID-19 date: 2020-07-02 words: 7253 flesch: 42 summary: HLH genes are significantly enriched within the SARS-CoV-2 host protein interactome 106 In the case of the SARS-Cov-2 pandemic, with widespread impact across the world, there 107 is an urgency that requires the adaptation of different strategies to understand COVID-19. After the method was validated, we compared the connectivity score for HLH genes 138 listed above with all genes that connect to SARS-CoV-2 proteins through our assembled protein-139 protein interaction network (Fig. 2) . keywords: cov-2; covid-19; disease; genes; hlh; license; medrxiv; nets; network; preprint; proteins; sars cache: cord-319519-mb9ofh12.txt plain text: cord-319519-mb9ofh12.txt item: #165 of 194 id: cord-320005-i30t7cvr author: Pardo, A. title: The Human Genome and Advances in Medicine: Limits and Future Prospects date: 2004-03-31 words: 4923 flesch: 45 summary: A blueprint for the genomic era Human genome sequencing Available at The genome sequence of Drosophila melanogaster Genome sequence of the rematode C. elegans: a platform for investigating biology. The identification of the different groups of genes involved in the pathogenic processes of human disease will also facilitate the discovery of new molecular targets that can eventually be used in the treatment of such diseases. keywords: chromosome; disease; dna; example; genes; genome; human; regions; sequences; sequencing cache: cord-320005-i30t7cvr.txt plain text: cord-320005-i30t7cvr.txt item: #166 of 194 id: cord-322286-2de6r1h6 author: Vandewege, Michael W title: Positive Selection and Gene Expression Analyses from Salivary Glands Reveal Discrete Adaptations within the Ecologically Diverse Bat Family Phyllostomidae date: 2020-07-22 words: 6217 flesch: 38 summary: Selection analyses among bat genes have generally been limited to few species for specific purposes (Shen et al. 2010; From the assembled transcriptomes, we performed an array of selection tests and gene expression analyses to identify signatures of adaptation. keywords: bat; bats; et al; expression; fig; genes; glands; material; online; plant; salivary; selection; species; terms; tests cache: cord-322286-2de6r1h6.txt plain text: cord-322286-2de6r1h6.txt item: #167 of 194 id: cord-322566-ye27nqj2 author: Huang, Yuxiang title: Stable Internal Reference Genes for Normalizing Real-Time Quantitative PCR in Baphicacanthus cusia under Hormonal Stimuli and UV Irradiation, and in Different Plant Organs date: 2017-05-03 words: 5813 flesch: 40 summary: Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets Role of plant hormones in plant defence responses Selection of endogenous genes for gene expression studies in Eucalyptus under biotic (Puccinia psidii) and abiotic (acibenzolar-S-methyl) stresses using RT-qPCR Selection of candidate reference genes for realtime PCR studies in lettuce under abiotic stresses Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors Evaluation of coffee reference genes for relative expression studies by quantitative real-time RT-PCR Stable internal reference genes for normalization of real-time RT-PCR in tobacco (Nicotiana tabacum) during development and abiotic stress How to do successful gene expression analysis using real-time PCR Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process Intervention effects of QRZSLXF, a Chinese medicinal herb recipe, on the DORβ-arrestin1-Bcl2 signal transduction pathway in a rat model of ulcerative colitis Selection of reliable reference genes for quantitative real-time polymerase chain reaction studies in maize grains Selection and validation of reference genes for quantitative gene expression studies by real-time PCR in eggplant (Solanum melongena L) Selection and validation of reference genes for quantitative real-time PCR in Gentiana macrophylla Arsenic disulfide induced apoptosis and concurrently promoted erythroid differentiation in cytokine-dependent myelodysplastic syndrome-progressed leukemia cell line F-36p with complex karyotype including monosomy 7 Evaluation of meisoindigo, an indirubin derivative: in vitro antileukemic activity and in vivo pharmacokinetics Careful selection of reference genes is required for reliable performance of RT-qPCR in human normal and cancer cell lines Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR Identification of three shikimate kinase genes in rice: characterization of their differential expression during panicle development and of the enzymatic activities of the encoded proteins Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice Reference genes in real-time PCR RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome Selection of reliable reference genes for gene expression analysis under abiotic stresses in the desert biomass willow, Salix psammophila Chemical studies of strobilanthes cusia Suitable reference genes for accurate gene expression analysis in parsley (Petroselinum crispum) for abiotic stresses and hormone stimuli Validation of candidate reference genes for the accurate normalization of real-time quantitative RT-PCR data in rice during seed development Natura-alpha targets forkhead box m1 and inhibits androgen-dependent and -independent prostate cancer growth and invasion Comparison of refined and crude indigo naturalis ointment in treating psoriasis: randomized, observer-blind, controlled, intrapatient trial Validation of reference genes for gene expression studies in virus-infected Nicotiana benthamiana Using quantitative real-time An indirubin derivative, indirubin-3 ′ -monoxime suppresses oral cancer tumorigenesis through the downregulation of survivin Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses Pharmacopoeia of the People's Republic of China Vol 1 Quantification of mRNA using real-time RT-PCR A new mathematical model for relative quantification in real-time RT-PCR Reference gene selection for RT-qPCR analysis of flower development in Chrysanthemum morifolium and Chrysanthemum lavandulifolium An optimized grapevine RNA isolation procedure and statistical determination of reference Reference Genes Selection in B. cusia genes for real-time RT-PCR during berry development Primer3 on the WWW for general users and for biologist programmers Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data Analyses of Catharanthus roseus and Arabidopsis thaliana WRKY transcription factors reveal involvement in jasmonate signaling The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes Research progress of chemical constituents and pharmacological activities for Baphicacanthus cusia (Nees)bremek Therapeutic efficacy of the Qing Dai in patients with intractable ulcerative colitis Selection of suitable reference genes for qPCR normalization under abiotic stresses and hormone stimuli in carrot leaves Potential utilization of NAC transcription factors to enhance abiotic stress tolerance in plants by biotechnological approach Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Abscisic Acid and abiotic stress signaling Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Twenty-five years of quantitative PCR for gene expression analysis Cloning and expression of cDNAs encoding two enzymes of the MEP pathway in Catharanthus roseus Identification of reference genes for reverse transcription quantitative real-time PCR normalization in pepper (Capsicum annuum L.) Synergistic effects of ultraviolet-B and methyl jasmonate on tanshinone biosynthesis in Salvia miltiorrhiza hairy roots Evaluation and selection of appropriate reference genes for real-time quantitative pcr analysis of gene expression in Nile Tilapia (Oreochromis niloticus) during vaccination and infection RNA-Seq: a revolutionary tool for transcriptomics Characterization of anti-leukemia components from Indigo naturalis using comprehensive two-dimensional K562/cell membrane chromatography and in silico target identification Chemical studies of Baphicacanthus cusia (Nees)Bremek. keywords: cusia; different; expression; genes; pcr; reference; reference genes; samples; stress; time cache: cord-322566-ye27nqj2.txt plain text: cord-322566-ye27nqj2.txt item: #168 of 194 id: cord-323307-nu9ib62h author: Dong, Dong title: The genomes of two bat species with long constant frequency echolocation calls date: 2016-10-26 words: 7643 flesch: 44 summary: Our result showed more visual perception genes have become pseudogenes in rhinolophoid bats, and it is reasonable to speculate that some visual perception gene may have undergone relaxed natural selection in echolocating bats. The result based on nucleotide data was in line with previous analysis that bats are a sister group to odd-toed ungulates, whereas the result based on amino acid data supported that bat bats are sister group to the Fereuungulata (Carnivores + Perissodactyla + Cetartiodactyla). keywords: bats; et al; evolution; genes; genome; hearing; horseshoe; leaf; result; rhinolophoid; sequences; species; substitutions; supplementary cache: cord-323307-nu9ib62h.txt plain text: cord-323307-nu9ib62h.txt item: #169 of 194 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 cache: cord-326719-p1ma4akz.txt plain text: cord-326719-p1ma4akz.txt item: #170 of 194 id: cord-328287-3qgzulgj author: Moni, Mohammad Ali title: Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies date: 2014-10-24 words: 10661 flesch: 39 summary: The list of disorders, disease genes, and associations between them were obtained from the Online Mendelian Inheritance in Man (OMIM) [58] , a compendium of human disease genes and phenotypes (see details in the Methods section). keywords: cancer; comorbidities; comorbidity; cov; data; disease; expression; file; genes; hiv; human; infection; network; pathways; protein; risk; sars; table cache: cord-328287-3qgzulgj.txt plain text: cord-328287-3qgzulgj.txt item: #171 of 194 id: cord-328899-kog99kk5 author: Ferrari, Stefano title: Barriers to and new approaches for gene therapy and gene delivery in cystic fibrosis date: 2002-12-05 words: 10510 flesch: 40 summary: Adv Drug Deliv Rev DOI: 10.1016/s0169-409x(02)00145-x sha: doc_id: 328899 cord_uid: kog99kk5 Clinical trials of gene therapy for cystic fibrosis suggest that current levels of gene transfer efficiency are probably too low to result in clinical benefit, largely as a result of the barriers faced by gene transfer vectors within the airways. CFTR gene transfer to patients with CF. keywords: aav; adenovirus; administration; airway; cells; cftr; cystic; delivery; dna; epithelial; expression; fibrosis; gene; gene transfer; human; lung; nuclear; surface; transfer; transgene; vectors; virus; vivo cache: cord-328899-kog99kk5.txt plain text: cord-328899-kog99kk5.txt item: #172 of 194 id: cord-329617-gzivtsho author: Lee, Albert K. title: De novo transcriptome reconstruction and annotation of the Egyptian rousette bat date: 2015-12-07 words: 5061 flesch: 49 summary: In other bat transcriptomes, such as P. alecto and A. jamaicensis, coverage of NK cellrelated genes was more sparse than that of other mammals [32, 33] . Interestingly, bats have recently come to the forefront of zoonotic disease research with vast number of pathogens identified in a wide variety of bat species [2] . keywords: aegyptiacus; assembly; bat; bats; contigs; expression; fig; gene; host; species; transcriptome; transcripts; virus cache: cord-329617-gzivtsho.txt plain text: cord-329617-gzivtsho.txt item: #173 of 194 id: cord-331592-l44rupmi author: Wang, Tzu-Hao title: Microarray Analysis of Gene Expression of Cancer to Guide the Use of Chemotherapeutics date: 2007-09-30 words: 4556 flesch: 33 summary: Analysis of expression modules, in which functional pathways (i.e. gene modules) are used as gene modules, was proposed to extend the investigation of cancer gene expression from individual genes to biologic processes [23] . For instance, multiple important papers of breast cancer gene expression profiles [35, [48] keywords: analysis; breast; cancer; data; expression; gene; microarray; patients; profiles; signatures cache: cord-331592-l44rupmi.txt plain text: cord-331592-l44rupmi.txt item: #174 of 194 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 cache: cord-332006-if46jycd.txt plain text: cord-332006-if46jycd.txt item: #175 of 194 id: cord-335382-fk4um9nw author: Farver, Carol F. title: Molecular Basis of Pulmonary Disease date: 2012-08-10 words: 32359 flesch: 38 summary: In hyperoxia-induced cell death, hyperoxia may induce the expression of angiopoietin 2 (Ang2) in lung epithelial cells. Annual report to the nation on the status of cancer Pathology and Genetics of Tumours of the Lung, Pleura AJCC Cancer Staging Manual varying), National Cancer Institute, DCCPS, Surveillance Research Program, Cancer Statistics Branch, released Diagnosis and management of lung cancer executive summary: ACCP evidence-based clinical practice guidelines Genetics of preneoplasia: Lessons from lung cancer Allelotyping demonstrates common and distinct patterns of chromosomal loss in human lung cancer types Genome-wide allelotyping of lung cancer identifies new regions of allelic loss, differences between small cell lung cancer and non-small cell lung cancer, and loci clustering High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH Lung cancer preneoplasia Characterizing the cancer genome in lung adenocarcinoma Focus on lung cancer New molecularly targeted therapies for lung cancer High resolution chromosome 3p allelotyping of human lung cancer and preneoplastic/preinvasive bronchial epithelium reveals multiple, discontinuous sites of 3p allele loss and three regions of frequent breakpoints Genetic and molecular alterations Allelic losses at chromosome 8p21-23 are early and frequent events in the pathogenesis of lung cancer Sequential molecular abnormalities are involved in the multistage development of squamous cell lung carcinoma Hereditary cancers disclose a class of cancer genes Tobacco smoke carcinogens, DNA damage and p53 mutations in smoking-associated cancers Molecular oncogenesis of lung cancer Molecular genetics of lung cancer The P16/cyclin D1/ keywords: airways; alveolar; asthma; carcinoids; cases; cause; cell lung; cells; changes; chest; chronic; disease; epithelium; factor; features; fibrosis; figure; form; gene; human; infections; inflammatory; injury; lesions; loss; lung; lung cancer; lung disease; macrophages; mechanisms; mutations; organisms; pathogenesis; pathology; patients; pneumonia; present; proliferation; protein; pulmonary; response; result; role; sarcoidosis; studies; surfactant; tissue; tumor; type cache: cord-335382-fk4um9nw.txt plain text: cord-335382-fk4um9nw.txt item: #176 of 194 id: cord-336573-bpg1dg24 author: Greenaway, Hui Yee title: Extraction and characterization of the rhesus macaque T cell receptor β-chain genes date: 2009-06-09 words: 3733 flesch: 45 summary: Indeed, rhesus macaques have been used to study fundamental aspects of immunology, including the development and maintenance of T cell memory 4, immunodominance5 and the aging immune system6. Furthermore, rhesus macaques have been instrumental in the design and testing of vaccines against infections such as HIV19 and smallpox 16. keywords: genes; human; macaque; rhesus; rhesus macaque; sequences; tcrβ; trb cache: cord-336573-bpg1dg24.txt plain text: cord-336573-bpg1dg24.txt item: #177 of 194 id: cord-337492-o6sy4zi4 author: Baric, Ralph S. title: Next-Generation High-Throughput Functional Annotation of Microbial Genomes date: 2016-10-04 words: 3031 flesch: 28 summary: The National Institute of Allergy and Infectious Diseases (NIAID) addressed this gap by creating functional genomics centers dedicated to developing high-throughput approaches to assign gene function. In cases where gene function is experimentally assigned and validated, the information is often not broadly propagated or may not apply to another organism. keywords: approaches; data; efforts; function; genes; genomics; host; protein cache: cord-337492-o6sy4zi4.txt plain text: cord-337492-o6sy4zi4.txt item: #178 of 194 id: cord-339012-4juhmjaj author: Hou, Wei title: Rapid host response to an infection with Coronavirus. Study of transcriptional responses with Porcine Epidemic Diarrhea Virus date: 2020-07-28 words: 6784 flesch: 39 summary: Differential expressed genes (DEGs) in PEDV infected cells were compared to DEGs responding in Vero cells infected with Mammalian Orthoreovirus (MRV). A decrease in CT-values for PEDV was not observed before 6 h post inoculation (6 h.p.i), indicating that replication in PEDV infected cells started later than was observed for MRV (at 4 h.p.i). keywords: cells; coronavirus; cov-2; degs; expression; file; genes; infection; mrv; pedv; processes; response; sars; vero; virus cache: cord-339012-4juhmjaj.txt plain text: cord-339012-4juhmjaj.txt item: #179 of 194 id: cord-340125-il35gs97 author: Jayapal, Manikandan title: Genome-wide gene expression profiling of human mast cells stimulated by IgE or FcεRI-aggregation reveals a complex network of genes involved in inflammatory responses date: 2006-08-16 words: 7398 flesch: 42 summary: Mast cells in innate immunity Mast cells to the defense Mast cells in autoimmune disease Mast cells The diverse potential effector and immunoregulatory roles of mast cells in allergic disease Transcriptional response of human mast cells stimulated via the FcεRI and identification of mast cells as a source of IL-11 The receptor with high affinity for IgE Signalling through the high-affinity IgE receptor FcεRI Roles of mast cells and basophils in innate and acquired immunity Complexity and redundancy in the pathogenesis of asthma: reassessing the roles of mast cells and T cells Mast cells can amplify airway reactivity and features of chronic inflammation in an asthma model in mice An essential role of mast cells in the development of airway hyperresponsiveness in a murine asthma model Mast cells phagocytosis of FimH expressing enterobacteria Histamine-induced activation of human lung macrophages key: cord-340125-il35gs97 authors: Jayapal, Manikandan; Tay, Hwee Kee; Reghunathan, Renji; Zhi, Liang; Chow, Kah Kiong; Rauff, Mary; Melendez, Alirio J title: Genome-wide gene expression profiling of human mast cells stimulated by IgE or FcεRI-aggregation reveals a complex network of genes involved in inflammatory responses date: 2006-08-16 journal: BMC Genomics DOI: 10.1186/1471-2164-7-210 sha: doc_id: 340125 cord_uid: il35gs97 BACKGROUND: keywords: activation; aggregation; anti; cells; cytokines; expression; fcεri; genes; ige; immune; mast; mast cells; responses; role; sensitization; table cache: cord-340125-il35gs97.txt plain text: cord-340125-il35gs97.txt item: #180 of 194 id: cord-344297-qqohijqi author: Smith, Jacqueline title: The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds date: 2015-10-09 words: 5080 flesch: 46 summary: An apparently new respiratory disease in baby chicks Studies of infectious coryza of chickens with special reference to its etiology Cultivation of the virus of infectious bronchitis Coronavirus avian infectious bronchitis virus Coronavirus Replication and Interaction with Host Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism Interleukin-6 expression after infectious bronchitis virus infection in chickens Review of infectious bronchitis virus around the world Nephropathogenic avian infectious bronchitis viruses The role of phagocytic cells in enhanced susceptibility of broilers to colibacillosis after Infectious Bronchitis Virus infection Ability of Massachusetts-type infectious bronchitis virus to increase colibacillosis susceptibility in commercial broilers: a comparison between vaccine and virulent field virus Diseases of Poultry A reverse transcriptase-polymerase chain reaction survey of infectious IBV infection bronchitis virus genotypes in Western Europe from Isolation of a variant infectious bronchitis virus in Australia that further illustrates diversity among emerging strains A novel genotype of avian infectious bronchitis virus isolated in Japan in 2009 Association of the chicken MHC B haplotypes with resistance to avian coronavirus Transcriptional analysis of avian embryonic tissues following infection with avian infectious bronchitis virus Transcriptome of Local Innate and Adaptive Immunity during Early Phase of Infectious Bronchitis Viral Infection Identification of a novel coronavirus in patients with severe acute respiratory syndrome A novel coronavirus associated with severe acute respiratory syndrome Investigations into resistance of chicken lines to infection with infectious bronchitis virus Use of highly inbred chickens in research Studies on genetic resistance to Marek's disease Guide to Probe Logarithmic Intensity Error (PLIER) Estimation. Dramatic differences in gene expression of certain genes, including DDT, SRI, BLB1, HSCB, BF1, BF2, SUCLG2, MX1 and SRI, which are more highly expressed in the resistant N line Table S2 shows all 1930 DE probes) keywords: birds; bronchitis; chicken; disease; expression; genes; host; ibv; infection; line; resistance; response; virus cache: cord-344297-qqohijqi.txt plain text: cord-344297-qqohijqi.txt item: #181 of 194 id: cord-345475-ttrcmtu4 author: de Oliveira, Luisa Abruzzi title: Reference Genes for the Normalization of Gene Expression in Eucalyptus Species date: 2011-12-24 words: 9769 flesch: 41 summary: Method Reference gene selection for quantitative real-time PCR normalization in tomato subjected to nitrogen, cold, and light stress Validation of reference genes for gene expression analysis in chicory (Cichorium intybus) using quantitative real-time PCR Evaluation of reference genes for quantitative RT-PCR in Lolium perenne Growthrelated gene expression in Nicotiana tabacum mesophyll protoplasts The two ribosomal protein L23A genes are differentially transcribed in Arabidopsis thaliana Global analysis of the core cell cycle regulators of Arabidopsis identifies novel genes, reveals multiple and highly specific profiles of expression and provides a coherent model for plant cell cycle control Characterization of the structure and expression of a highly conserved ribosomal protein gene, L9, from pea Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress Identification and validation of reference genes for quantitative RT-PCR normalization in wheat Reference gene selection for quantitative real-time PCR analysis in virus infected cells: SARS corona virus, Yellow fever virus, Human Herpesvirus-6, Camelpox virus and Cytomegalovirus infections Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development Normalisation of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations A new genomic resource dedicated to wood formation in Eucalyptus Involvement of Arabidopsis thaliana ribosomal protein S27 in mRNA degradation triggered by genotoxic stress Accumulation and nuclear targeting of BnC24, a Brassica napus ribosomal protein corresponding to a mRNA accumulating in response to cold treatment Stable internal reference genes for normalization of real-time RT-PCR in tobacco (Nicotiana tabacum) during development and abiotic stress Selection of reference genes for quantitative real-time PCR expression studies in the apomictic and sexual grass Brachiaria brizantha Properties of the reverse transcription reaction in mRNA quantification Real-time quantitative RT-PCR for low-abundance transcripts in the inner ear: analysis of neurotrophic factor expression Higher-level relationships among the eucalypts are resolved by ITS-sequence data Differential expression and sequence analysis of ribosomal protein genes induced in stolon tips of potato (Solanum tuberosum L.) during the early stages of tuberization A practical approach to RT-qPCR-publishing data that conform to the MIQE guidelines Housekeeping genes as internal standards: use and limits Selection of reliable reference genes for gene expression studies in peach using real-time PCR Significance analysis of microarrays applied to the ionizing radiation response Control of cell division and transcription by cyclin-dependent kinase-activating kinases in plants Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Heat-stressdependency and developmental modulation of gene expression: the potential of house-keeping genes as internal standards in mRNA expression profiling using real-time RT-PCR Selection of appropriate reference genes for gene expression studies by quantitative real-time polymerase chain reaction in cucumber Developmental regulation of ribosomal protein L16 genes in Arabidopsis thaliana Transcription elongation factor SII Extraribosomal functions of ribosomal proteins Cloning and characterization of the 1-deoxy-D-xylulose 5-phosphate reductoisomerase gene for diterpenoid tanshinone biosynthesis in Salvia miltiorrhiza (Chinese sage) hairy roots Molecular characterization and expression of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) gene from Salvia miltiorrhiza Characterization of reference genes for quantitative real-time PCR analysis in various tissues of Salvia miltiorrhiza An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression Normalization with genes encoding ribosomal proteins but not GAPDH provides an accurate quantification of gene expressions in neuronal differentiation of PC12 cells We acknowledge M.Sc. Given the increasing interest in the functional genomics of Eucalyptus, we sought to identify and experimentally verify suitable reference genes for the normalization of gene expression associated with the flower, leaf and xylem of six species of the genus. keywords: 2010; analysis; data; et al; eucalyptus; expression; genes; grandis; microarray; normalization; qpcr; reference; stability; studies; time; tissues; xylem cache: cord-345475-ttrcmtu4.txt plain text: cord-345475-ttrcmtu4.txt item: #182 of 194 id: cord-345516-fgn7rps3 author: Miller, Laura C title: Analysis of the swine tracheobronchial lymph node transcriptomic response to infection with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus date: 2012-10-30 words: 4749 flesch: 34 summary: There are specific cellular proteins that regulate a protective immune response, for example the pro-inflammatory genes that were upregulated to a greater extent in HP-PRRSV rJXwn06 than VR-2332 when normalized to control samples as observed when comparing the pathogenicity of HP-PRRSV isolate rJXwn06 with the North American prototype strain VR-2332 PRRSV. Amplified library constructs were directly sequenced and a list of sequence transcripts and counts was generated using an RNAseq analysis pipeline to determine differential gene expression. keywords: analysis; disease; expression; genes; infection; pigs; porcine; prrsv; rjxwn06; syndrome; tbln; transcript; virus; vr-2332 cache: cord-345516-fgn7rps3.txt plain text: cord-345516-fgn7rps3.txt item: #183 of 194 id: cord-346308-9h2fk9qt author: Kaur, Rajwinder title: Microbiology of hospital wastewater date: 2020-05-01 words: 14679 flesch: 30 summary: and Enterobacteriaceae in sewage Hospital wastewater releases of carbapenem-resistance pathogens and genes in urban India Assessment of antibiotic-and disinfectant-resistant bacteria in hospital wastewater, south Ethiopia: a cross-sectional study Antibiotic susceptibilities of Enterococcus species isolated from hospital and domestic wastewater effluents in Alice, Eastern Cape Province of South Africa Beta-lactamase-producing Enterobacteriaceae in hospital effluents Insights into the relationship between antimicrobial residues and bacterial populations in a hospital-urban wastewater treatment plant system Influence of hospital wastewater discharged from University of Benin Teaching Hospital (UBTH) Multiresistance, beta-lactamaseencoding genes and bacterial diversity in hospital wastewater in Rio de Janeiro, Brazil Enumeration and characterization of antimicrobial-resistant Escherichia coli bacteria in effluent from municipal, hospital, and secondary treatment facility sources Antibiotic resistance and antibiotic resistance genes in Escherichia coli isolates from hospital wastewater in Vietnam Antibiotic resistant bacteria in hospital wastewaters and sewage treatment plants Dissemination of antibiotic resistance in methicillin-resistant Staphylococcus aureus and vancomycin-resistant S aureus strains isolated from hospital effluents Detection of antimicrobial-resistant Gram-negative bacteria in hospital effluents and in the sewage treatment station of Goiânia Brazil Antimicrobial resistance of 3 types of gram-negative bacteria isolated from hospital surfaces and the hands of health care workers Abundance of antibiotics, antibiotic resistance genes and bacterial community composition in wastewater effluents from different Romanian hospitals Vancomycin resistant enterococci: from the hospital effluent to the urban wastewater treatment plant The role of aquatic ecosystems as reservoirs of antibiotic resistance Environmental dissemination of antibiotic resistance genes and correlation to anthropogenic contamination with antibiotics Occurrence of antibiotics and antibiotic resistance genes in hospital and urban wastewaters and their impact on the receiving river Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review Levels of antibiotic resistance genes in manure, biosolids, and fertilized soil Epidemiology of resistance to antibiotics: links between animals and humans Detection of antibiotic resistance genes in source and drinking water samples from a first nation community in Canada Prevalence of antibiotic resistance in drinking water treatment and distribution systems Antimicrobial Resistance: Global Report on Surveillance, World Health Organization Society's failure to protect a precious resource: antibiotics Hospital effluents are one of several sources of metal, antibiotic resistance genes, and bacterial markers disseminated in Sub-Saharan urban rivers Identifying antimicrobial resistance genes with DNA microarrays Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940 Antibiotic resistance genes in water environment Prevalence of antibiotic resistance genes and their relationship with antibiotics in the Huangpu River and the drinking water sources Multiple drug resistance and biocide resistance in Escherichia coli environmental isolates from hospital and household settings Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes Tackling antibiotic resistance: the environmental framework Screening methods for the detection of antimicrobial resistance genes present in bacterial isolates and the microbiota Culture-based methods for detection of antibiotic resistance in agroecosystems: advantages, challenges, and gaps in knowledge Insights into antibiotic resistance through metagenomic approaches Molecular evaluation of antibiotic susceptibility: keywords: analysis; antibiotics; args; bacteria; detection; dna; environment; fungal; genes; health; hospital; host; human; hww; infections; methods; norovirus; pathogens; pcr; present; prevalence; resistance; resistance genes; rotavirus; samples; species; transfer; treatment; virus; viruses; wastewater cache: cord-346308-9h2fk9qt.txt plain text: cord-346308-9h2fk9qt.txt item: #184 of 194 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 cache: cord-347917-fmb5nyxu.txt plain text: cord-347917-fmb5nyxu.txt item: #185 of 194 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 cache: cord-348815-lthz75oc.txt plain text: cord-348815-lthz75oc.txt item: #186 of 194 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 cache: cord-350019-4nlbu54e.txt plain text: cord-350019-4nlbu54e.txt item: #187 of 194 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 cache: cord-351548-jvl63652.txt plain text: cord-351548-jvl63652.txt item: #188 of 194 id: cord-351845-bli3qm8w author: Prasad, Kartikay title: Targeting hub genes and pathways of innate immune response in COVID-19: A network biology perspective date: 2020-06-26 words: 4631 flesch: 38 summary: Network topology analyses identified 15 high-value targets of SARS CoV-2, which belongs to a subset of canonical ISGs. An Integrative Modeling Approach for Effective Drug Repurposing SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems 0: a major update to the DrugBank database for The comparative toxicogenomics database: update SARS-CoV-2 Launches a Unique Transcriptional Signature from in Vitro, Ex Vivo, and in Vivo Systems Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists Cytoscape: a software environment for integrated models of biomolecular interaction networks STITCH: interaction networks of chemicals and proteins Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources The SARS-coronavirus-host interactome: identification of cyclophilins as target for pancoronavirus inhibitors A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection Network-Guided Discovery of Influenza Virus Replication Host Factors Common Nodes of Virus-Host Interaction Revealed Through an Integrated Network Analysis A cellular census of human lungs identifies novel cell states in health and in asthma A single-cell atlas of the human healthy airways SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes SARS-CoV-2 Receptor ACE2 Is an Interferon Enrichr: a comprehensive gene set enrichment analysis web server 2016 update Interferon-stimulated genes: a complex web of host defenses Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection Interferon-inducible protein Mx1 inhibits influenza virus by interfering with functional viral ribonucleoprotein complex assembly Host genetics of severe influenza: from mouse Mx1 to human IRF7 Hepatitis E virus polymerase binds to IFIT1 to protect the viral RNA from IFIT1-mediated translation inhibition Polymorphisms of interferon-inducible genes OAS-1 and MxA associated with SARS in the Vietnamese population Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication Differential regulation of the OASL and OAS1 genes in response to viral infections Severe acute respiratory syndrome coronavirus ORF6 antagonizes STAT1 function by sequestering nuclear import factors on the rough endoplasmic reticulum/Golgi membrane Middle East respiratory syndrome coronavirus ORF4b protein inhibits type I interferon production through both cytoplasmic and nuclear targets Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species ISG15: It's Complicated Consecutive Inhibition of ISG15 Expression and ISGylation by Cytomegalovirus Regulators Innate antiviral response targets HIV-1 release by the induction of ubiquitin-like protein ISG15 ISG15 facilitates cellular antiviral response to dengue and west nile virus infection in vitro Antiviral activity of ISG15 against classical swine fever virus replication in porcine alveolar macrophages via inhibition of autophagy by ISGylating BECN1 MERS-CoV papain-like protease has deISGylating and deubiquitinating activities Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating activity of SARS-CoV papain-like protease Targeting poly(I:C) to the TLR3-independent pathway boosts effector CD8 T cell differentiation through IFN-alpha/beta Intranasal treatment with poly(I*C) protects aged mice from lethal respiratory virus infections Prophylactic and therapeutic intranasal administration with an immunomodulator, Hiltonol((R)) keywords: analysis; cov-2; covid-19; drug; genes; immune; infection; interaction; network; response; sars; virus cache: cord-351845-bli3qm8w.txt plain text: cord-351845-bli3qm8w.txt item: #189 of 194 id: cord-352190-1987sfyz author: Xia, Hongyue title: Adaptive Evolution of Feline Coronavirus Genes Based on Selection Analysis date: 2020-08-13 words: 4287 flesch: 48 summary: To amplify partial nsp12, nsp13, and nsp14 gene sequences, we designed primer pairs 1b3F and 1b1R and 1b6F and 1b6R. To amplify part of the N gene, primer pair N1 and N2 was used Of the 31 cats investigated, two suspected FIP cats and one healthy cat tested positive for FCoV. Phylogenetic analysis showed that all of the sequences from mainland China cluster together with a few sequences from the Netherlands as a distinct clade when analyzed with FCoV sequences from other countries. keywords: analysis; fcov; feline; gene; nsp12; selection; sequences; sites; type cache: cord-352190-1987sfyz.txt plain text: cord-352190-1987sfyz.txt item: #190 of 194 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 cache: cord-352200-i05h8csb.txt plain text: cord-352200-i05h8csb.txt item: #191 of 194 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 cache: cord-354829-god79qzw.txt plain text: cord-354829-god79qzw.txt item: #192 of 194 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 cache: cord-355075-ieb35upi.txt plain text: cord-355075-ieb35upi.txt item: #193 of 194 id: cord-355927-nzoiv9pj author: Lemmon, Alan R. title: The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference date: 2009-05-21 words: 9480 flesch: 45 summary: The magnitude and direction of the ambiguous data bias are a function of the number and taxonomic distribution of ambiguous characters, the strength of topological support, and whether or not the model is correctly specified. Incomplete sequences and sampling biases in these databases have led researchers to build phylogenetic data sets that have large numbers of ambiguous characters and gaps (Driskell et al. 2004) . keywords: bayesian; bias; branch; characters; data; evolution; gene; rate; sites; support; taxa cache: cord-355927-nzoiv9pj.txt plain text: cord-355927-nzoiv9pj.txt item: #194 of 194 id: cord-356197-js7l86fh author: Zhou, Ping title: Molecular Characterization of Transcriptome-wide Interactions between Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus and Porcine Alveolar Macrophages in vivo date: 2011-08-07 words: 4648 flesch: 35 summary: Seven genes (CCL2, SLC39A14, ATP6V1B2, C3, DDIT3, GLRX2 and TNF) were selected for Q-PCR assay to validate the changes in gene expression observed by microarray analysis. Genetic parameters for performance traits in commercial sows estimated before and after an outbreak of porcine reproductive and respiratory syndrome Immunohistochemical detection of porcine reproductive and respiratory syndrome virus antigen in neurovascular lesions Immunological responses of swine to porcine reproductive and respiratory syndrome virus infection Distribution of a Korean strain of porcine reproductive and respiratory syndrome virus in experimentally infected pigs, as demonstrated immunohistochemically and by in-situ hybridization The combination of PRRS virus and bacterial endotoxin as a model for multifactorial respiratory disease in pigs Understanding PRRSV infection in porcine lung based on genome-wide transcriptome response identified by deep sequencing Aberrant host immune response induced by highly virulent PRRSV identified by digital gene expression tag profiling Genome-wide transcriptional response of primary alveolar macrophages following infection with porcine reproductive and respiratory syndrome virus Effect of porcine reproductive and respiratory syndrome virus on porcine alveolar macrophage function as determined using serial analysis of gene expression (SAGE) Emergence of fatal PRRSV variants: unparalleled outbreaks of atypical PRRS in China and molecular dissection of the unique hallmark Immunogenicity of the highly pathogenic porcine reproductive and respiratory syndrome virus GP5 protein encoded by a synthetic ORF5 gene Comparative pathogenicity of nine US porcine reproductive and respiratory syndrome virus (PRRSV) isolates in a five-week-old cesarean-derived, colostrum-deprived pig model Comparison of the pathogenicity of two US porcine reproductive and respiratory syndrome virus isolates with that of the Lelystad virus Assessment of the efficacy of commercial porcine reproductive and respiratory syndrome virus (PRRSV) vaccines based on measurement of serologic response, frequency of gamma-IFN-producing cells and virological parameters of protection upon challenge Understanding Haemophilus parasuis infection in porcine spleen through a transcriptomics approach A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Cluster analysis and display of genome-wide expression patterns Database for Annotation, Visualization, and Integrated Discovery Annotation of the Affymetrix porcine keywords: analysis; dpi; expression; figure; genes; infection; lung; pams; porcine; prrsv; syndrome; table; virus cache: cord-356197-js7l86fh.txt plain text: cord-356197-js7l86fh.txt