# bib

id: cord-297760-uzzuoy9v
author: Naito, Yuki
title: siVirus: web-based antiviral siRNA design software for highly divergent viral sequences
date: 2006-07-01
extension: .txt
mime: text/plain
words: 1143
sentence: 48
flesch: 49
cache: cache/cord-297760-uzzuoy9v.txt
txt: txt/cord-297760-uzzuoy9v.txt
summary:
  However, designing functional siRNAs that target viral sequences is problematic because of their extraordinarily high genetic diversity. Highly conserved siRNA sequences are selected based on their degree of conservation, defined as the proportion of viral sequences that are targeted by the corresponding siRNA, with complete matches (i.e. 21/21 matches).


id: cord-291070-y0wf456f
author: Zhang, Guang Lan
date: 2005-07-01
extension: .txt
mime: text/plain
words: 2674
sentence: 98
flesch: 48
cache: cache/cord-291070-y0wf456f.txt
txt: txt/cord-291070-y0wf456f.txt
title:
  PRED(BALB/c): a system for the prediction of peptide binding to H2(d) molecules, a haplotype of the BALB/c mouse

summary:
  Although the majority of H2 d class II binding peptides are 12-20 amino acids long, their binding cores are 9 amino acids long (22, 23) . In our previous work, an artificial neural network method and hidden Markov models were applied to the prediction of human leukocyte antigens (HLAs) binding peptides (24, 25) , where more training data were available.


id: cord-000159-8y8ho2x5
author: Bekaert, Michaël
title: Recode-2: new design, new search tools, and many more genes
date: 2009-09-25
extension: .txt
mime: text/plain
words: 2626
sentence: 74
flesch: 25
cache: cache/cord-000159-8y8ho2x5.txt
txt: txt/cord-000159-8y8ho2x5.txt
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.


id: cord-000293-pc4x5e24
author: Yu, Chien-Hung
title: Stimulation of ribosomal frameshifting by antisense LNA
date: 2010-08-06
extension: .txt
mime: text/plain
words: 3906
sentence: 134
flesch: 40
cache: cache/cord-000293-pc4x5e24.txt
txt: txt/cord-000293-pc4x5e24.txt
summary:
  To demonstrate that the enhanced effect of LNA oligonucleotides is a general feature we designed another construct (SF462) in which the target sequence was replaced by an unrelated sequence ( Figure 4 ). However, the excellent affinity of LNA oligonucleotides could be a double-edged sword in certain cases.


id: cord-002366-t94aufs3
author: Aurrecoechea, Cristina
title: EuPathDB: the eukaryotic pathogen genomics database resource
date: 2017-01-04
extension: .txt
mime: text/plain
words: 3784
sentence: 153
flesch: 40
cache: cache/cord-002366-t94aufs3.txt
txt: txt/cord-002366-t94aufs3.txt
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.


id: cord-048327-xgwbl8em
author: Henderson, Clark M.
title: Antisense-induced ribosomal frameshifting
date: 2006-08-18
extension: .txt
mime: text/plain
words: 4342
sentence: 140
flesch: 37
cache: cache/cord-048327-xgwbl8em.txt
txt: txt/cord-048327-xgwbl8em.txt
summary:
  Similarly, for +1 frameshift sites, the identity of the codons in the P-and A-sites of the ribosome is critical for efficient frameshifting. However, visual examination of upstream codons does not reveal an obvious À1 or +1 frameshift site.


id: cord-000482-wifs97yy
author: Yu, Chien-Hung
title: Stem–loop structures can effectively substitute for an RNA pseudoknot in −1 ribosomal frameshifting
date: 2011-07-29
extension: .txt
mime: text/plain
words: 4794
sentence: 163
flesch: 47
cache: cache/cord-000482-wifs97yy.txt
txt: txt/cord-000482-wifs97yy.txt
summary:
  Frameshifting efficiency was calculated by dividing the ratio of Renilla luciferase (RL) over Firefly luciferase (FL) activity of the mutant by the RL/ FL ratio of the in-frame control, multiplied by 100. Next, we investigated the role of stem length on frameshifting efficiency.


id: cord-000010-prsvv6l9
author: Qin, Jian
title: Studying copy number variations using a nanofluidic platform
date: 2008-08-18
extension: .txt
mime: text/plain
words: 4997
sentence: 188
flesch: 44
cache: cache/cord-000010-prsvv6l9.txt
txt: txt/cord-000010-prsvv6l9.txt
summary:
  DNA Amplification: Current Technologies and Applications Mathematical analysis of copy number variation in a DNA sample using digital PCR on a nanofluidic device Real-time reverse transcriptionpolymerase chain reaction assay for SARS-associated coronavirus Structure and transcription of a human gene for H1 RNA, the RNA component of human RNase P The effect of cytochrome P450 metabolism on drug response, interactions, and adverse effects Overview of enzymes of drug metabolism The clinical role of genetic polymorphisms in drug-metabolizing enzymes Individualized drug therapy The prevalence and clinical relevance of cytochrome P450 polymorphisms Pharmacogenetics and adverse drug reactions CYP2D6 polymorphisms and the impact on tamoxifen therapy Clinical implications of CYP2D6 genetic polymorphism during treatment with antipsychotic drugs Deletion of the entire cytochrome P450 CYP2D6 gene as a cause of impaired drug metabolism in poor metabolizers of the debrisoquine/sparteine polymorphism Ultrarapid metabolizers of debrisoquine: characterization and PCR-based detection of alleles with duplication of the CYP2D6 gene CYP2D6 genotyping strategy based on gene copy number determination by TaqMan real-time PCR Determination of cytochrome P450 2D6 (CYP2D6) gene copy number by real-time quantitative PCR Pharmacogenetic screening of the gene deletion and duplications of CYP2D6 The human debrisoquine 4-hydroxylase (CYP2D) locus: sequence and identification of the polymorphic CYP2D6 gene, a related gene, and a pseudogene Ultrarapid drug metabolism: PCR-based detection of CYP2D6 gene duplication Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene Studies of the HER-2/neu proto-oncogene in human breast and ovarian cancer Detection and quantitation of HER-2/neu gene amplification in human breast cancer archival material using fluorescence in situ hybridization Prognostic and predictive value of HER2/neu oncogene in breast cancer ERBB2 oncogene in human breast cancer and its clinical significance Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2 Ongoing adjuvant trials with trastuzumab in breast cancer Trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer ) 2-year follow-up of trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer: a randomised controlled trial Prognostic and predictive value of HER2/neu oncogene in breast cancer HER2 testing: a review of detection methodologies and their clinical performance Recent duplication, domain accretion and the dynamic mutation of the human genome Detection of large-scale variation in the human genome Large-scale copy number polymorphism in the human genome Segmental duplications and copy-number variation in the human genome Structural variation in the human genome Challenges and standards in integrating surveys of structural variation Autosomal-dominant microtia linked to five tandem copies of a copy-number-variable region at chromosome 4p16 A comprehensive analysis of common copynumber variations in the human genome New perspectives for the elucidation of genetic disorders Genomic rearrangements and sporadic disease Global variation in copy number in the human genome Methods and strategies for analyzing copy number variation using DNA microarrays Challenges and standards in integrating surveys of structural variation CYP2D6 genotyping strategy based on gene copy number determination by TaqMan real-time PCR Determination of cytochrome P450 2D6 (CYP2D6) gene copy number by real-time quantitative PCR Pharmacogenetic screening of the gene deletion and duplications of CYP2D6 HER-2/neu gene copy number quantified by real-time PCR: comparison of gene amplification, heterozygosity, and immunohistochemical status in breast cancer tissue Reliability and discriminant validity of HER2 gene quantification and chromosome 17 aneusomy analysis by real-time PCR in primary breast cancer Digital PCR for the molecular detection of fetal chromosomal aneuploidy Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene We have evaluated the digital array's performance using a model system, to show that this technology is exquisitely sensitive, capable of differentiating as little as a 15% difference in gene copy number (or between 6 and 7 copies of a target gene).


id: cord-048345-m56agj4z
author: Reddy, Timothy E.
date: 2007-01-03
extension: .txt
mime: text/plain
words: 5461
sentence: 232
flesch: 35
cache: cache/cord-048345-m56agj4z.txt
txt: txt/cord-048345-m56agj4z.txt
title:
  Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABA(A) receptor subunit genes

summary:
  We began by evaluating the stability of binding site predictions via repeated runs of Gibbs sampling. We introduce a simple strategy that dramatically improves robustness and accuracy of computational binding site prediction.


id: cord-000532-e18licyc
author: Tholstrup, Jesper
title: mRNA pseudoknot structures can act as ribosomal roadblocks
date: 2011-09-08
extension: .txt
mime: text/plain
words: 5814
sentence: 203
flesch: 49
cache: cache/cord-000532-e18licyc.txt
txt: txt/cord-000532-e18licyc.txt
summary:
  The ribosome uses two active mechanisms to unwind messenger RNA during translation Codon usage determines the translation rate in Escherichia coli Ribosomal movement impeded at a pseudoknot required for frameshifting Ribosomal pausing during translation of an RNA pseudoknot Ribosomal pausing at a frameshifter RNA pseudoknot is sensitive to reading phase but shows little correlation with frameshift efficiency Torsional restraint: a new twist on frameshifting pseudoknots Divergent stalling sequences sense and control cellular physiology Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting Characterization of the Mechanical Unfolding of RNA Pseudoknots Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an RNA pseudoknot Achieving a golden mean: mechanisms by which coronaviruses ensure synthesis of the correct stoichiometric ratios of viral proteins The role of RNA pseudoknot stem 1 length in the promotion of efficient -1 ribosomal frameshifting Evidence for an RNA pseudoknot loop-helix interaction essential for efficient-1 ribosomal frameshifting Culture medium for enterobacteria pknotsRG: key: cord-000532-e18licyc authors: Tholstrup, Jesper; Oddershede, Lene B.; Sørensen, Michael A. title: mRNA pseudoknot structures can act as ribosomal roadblocks date: 2011-09-08 journal: Nucleic Acids Res DOI: 10.1093/nar/gkr686 sha: doc_id: 532 cord_uid: e18licyc Several viruses utilize programmed ribosomal frameshifting mediated by mRNA pseudoknots in combination with a slippery sequence to produce a well defined stochiometric ratio of the upstream encoded to the downstream-encoded protein.


id: cord-001502-omq0becw
author: Shabanpoor, Fazel
date: 2015-01-09
extension: .txt
mime: text/plain
words: 6429
sentence: 207
flesch: 43
cache: cache/cord-001502-omq0becw.txt
txt: txt/cord-001502-omq0becw.txt
title:
  Bi-specific splice-switching PMO oligonucleotides conjugated via a single peptide active in a mouse model of Duchenne muscular dystrophy

summary:
  Instead of the use of a cocktail of P-PMOs and with the need in mind to minimize toxicity, we sought to develop proof-of-concept for use of bi-specific PMO SSOs that could simultaneously target two different exons in different genes rather than in the same gene. Based on the potential success of this approach, we sought to simultaneously target both the dystrophin and the myostatin pathway as a molecular model to evaluate the efficacy of using bi-specific PMO compounds.


id: cord-001824-7c37elh6
author: Tükenmez, Hasan
title: The role of wobble uridine modifications in +1 translational frameshifting in eukaryotes
date: 2015-10-30
extension: .txt
mime: text/plain
words: 7176
sentence: 229
flesch: 50
cache: cache/cord-001824-7c37elh6.txt
txt: txt/cord-001824-7c37elh6.txt
summary:
  complex influences telomeric gene silencing and DNA damage response by its role in wobble uridine tRNA modification The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivo Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications Improved method for high efficiency transformation of intact yeast cells Methods in yeast genetics An in vivo dual-luciferase assay system for studying translational recoding in the yeast Saccharomyces cerevisiae Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site Studies on polynucleotides, lxviii the primary structure of yeast phenylalanine transfer RNA 2009: compilation of tRNA sequences and tRNA genes Translational termination comes of age An early step in wobble uridine tRNA modification requires the Elongator complex Novel methyltransferase for modified uridine residues at the wobble position of tRNA is a 15-kDa zinc finger protein essential for the activity of two tRNA and one protein methyltransferases in yeast


id: cord-262076-b5u5hp2r
author: Liu, Ying Poi
title: Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron
date: 2008-03-16
extension: .txt
mime: text/plain
words: 6911
sentence: 266
flesch: 46
cache: cache/cord-262076-b5u5hp2r.txt
txt: txt/cord-262076-b5u5hp2r.txt
summary:
  We therefore selected the 19-nt inhibitors for the construction of antiviral miRNA polycistrons. HIV-1 sequences are blue, mature wild-type miRNA sequences are red, pre-miRNA sequences are black, Watson-Crick base pairs are shown with dashes and GU wobbles with dots.


id: cord-000363-cbzd8ybv
author: Belew, Ashton T.
date: 2010-11-24
extension: .txt
mime: text/plain
words: 6326
sentence: 232
flesch: 44
cache: cache/cord-000363-cbzd8ybv.txt
txt: txt/cord-000363-cbzd8ybv.txt
title:
  Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast

summary:
  As a control, six S. cerevisiae genes lacking predicted À1 RF signals were selected (PGK1, HHT1, TEF2, MIC14, CMD1 and GRX1), orthologs from the six other yeast species identified, and these were in turn queried for the presence of putative À1 RF signals. Importantly, the control experiment showed that putative À1 RF signals were not detected in any of the orthologs of six S. cerevisiae genes that themselves were not predicted to contain À1 RF signals.


id: cord-007041-rloey02j
author: Harel, Noam
title: Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations
date: 2019-12-16
extension: .txt
mime: text/plain
words: 7128
sentence: 265
flesch: 45
cache: cache/cord-007041-rloey02j.txt
txt: txt/cord-007041-rloey02j.txt
summary:
  In microbes, such diversity is generated in particular by high mutation rates, which may generate both nucleotide substitutions as well as point insertions or deletions (indels) (1) . We devised a method called AssociVar that detects the real variants in the data, based on the following properties: (a) the method searches for the strongest non-random associations, (b) the method takes into account that pairs of proximal positions (i.e. up to 15 bases apart) that have high associations between them are likely false positives induced by the MinION machine itself, (c) in order to make the different positions comparable, the method normalizes the distribution of chi square scores per position, essentially searching for outliers from all the associations of a given po-sition, (d) the method also takes into account that because proximal positions are highly associated, a position next to a real mutation may be associated with other real mutations due to transitivity.


id: cord-302368-uhhtvdif
author: Longhini, Andrew P.
date: 2016-04-07
extension: .txt
mime: text/plain
words: 6557
sentence: 210
flesch: 38
cache: cache/cord-302368-uhhtvdif.txt
txt: txt/cord-302368-uhhtvdif.txt
title:
  Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations

summary:
  Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression Widespread genetic switches and toxicity resistance proteins for fluoride Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy Three-state mechanism couples ligand and temperature sensing in riboswitches The 3 untranslated region of pea enation mosaic virus contains two T-shaped, ribosome-binding, cap-independent translation enhancers Identification of a Minimal Region of the HIV-1 5-Leader Required for RNA Dimerization, NC Binding, and Packaging Flipping of the Ribosomal A-Site Adenines Provides a Basis for tRNA Selection Visualizing transient low-populated structures of RNA Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR Time-resolved structural studies of protein reaction dynamics: A smorgasbord of X-ray approaches Alternate-site isotopic labeling of ribonucleotides for NMR studies of ribose conformational dynamics in RNA Selective 13 C labeling of nucleotides for large RNA NMR spectroscopy using an E. coli strain disabled in the TCA cycle Selective 13 C labeling of nucleotides for large RNA NMR spectroscopy using an E. coli strain disabled in the TCA cycle Three-dimensional heteronuclear NMR studies of RNA Preparation of 13 C and 15 N labelled RNAs for heteronuclear multi-dimensional NMR studies Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA Structure of HCVIRES domain II determined by NMR NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus Solution structure of tRNA(Val) from refinement of homology model against residual dipolar coupling and SAXS data Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3 ' UTR of turnip crinkle virus Structure of the yeast U2/U6 snRNA complex A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure Structure of the HIV-1 RNA packaging signal Key labeling technologies to tackle sizeable problems in RNA structural biology These nucleotides are suitable for use in three key aspects of RNA NMR structural biology: assignment, structural and dynamics measurements.


id: cord-000125-uvf5qzfd
author: Kenworthy, Rachael
date: 2009-09-03
extension: .txt
mime: text/plain
words: 6664
sentence: 215
flesch: 43
cache: cache/cord-000125-uvf5qzfd.txt
txt: txt/cord-000125-uvf5qzfd.txt
title:
  Short-hairpin RNAs delivered by lentiviral vector transduction trigger RIG-I-mediated IFN activation

summary:
  Moreover, activation of IRF-3 ( Figure 1E ) and IFN promoters ( Figure 1F ) in 293FT cells, which do not contain a functional TLR3 signaling pathway (42) , indicates that TLR3 plays a negligible role, if any, in IFN induction by sh-B971. These results demonstrate that sh-B971 is a potent activator of IRF-3 and IRF-7, master regulators of IFN expression in human cells.


id: cord-275859-ix8du1er
author: Mouzakis, Kathryn D.
date: 2012-12-15
extension: .txt
mime: text/plain
words: 6740
sentence: 234
flesch: 42
cache: cache/cord-275859-ix8du1er.txt
txt: txt/cord-275859-ix8du1er.txt
title:
  HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome

summary:
  key: cord-275859-ix8du1er authors: Mouzakis, Kathryn D.; Lang, Andrew L.; Vander Meulen, Kirk A.; Easterday, Preston D.; Butcher, Samuel E. title: HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome date: 2012-12-15 journal: Nucleic Acids Res DOI: 10.1093/nar/gks1254 sha: doc_id: 275859 cord_uid: ix8du1er The sequence of the frameshift site stemloop was varied to dissect the relative contributions of local and overall RNA stability on HIV-1 frameshift efficiency.


id: cord-275232-0sg0hv9w
author: Yeung, Siu-Wai
title: A DNA biochip for on-the-spot multiplexed pathogen identification
date: 2006-09-25
extension: .txt
mime: text/plain
words: 3243
sentence: 133
flesch: 36
cache: cache/cord-275232-0sg0hv9w.txt
txt: txt/cord-275232-0sg0hv9w.txt
summary:
  Miniaturised nucleic acid analysis Microfabricated systems for nucleic acid analysis DNA-based bioanalytical microsystems for handheld device applications Electrochemical DNA sensors Electrochemical nucleic acid biosensors Nanomaterial-based electrochemical biosensors Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection Microfabricated PCR-electrochemical device for simultaneous DNA amplification and detection An integrated nanoliter DNA analysis device Effects of gold nanoparticle and electrode surface properties on electrocatalytic silver deposition for electrochemical DNA hybridization detection Preparation of a DNA matrix via an electrochemically directed copolymerization of pyrrole and oligonucleotides bearing a pyrrole group Gold nanoparticle-catalyzed silver electrodeposition on an indium tin oxide electrode and its application in DNA hybridization transduction Results of the two different types of electrodes (functionalized with E.coli and B.subtilis detection capture probe) when subjected to different sample solutions. (7) successfully demonstrated a fully integrated biochip for cell isolation and lysis, target amplification, as well as electrochemical amplicon detection.


id: cord-269150-d1sgnxc0
author: Tan, Yong Wah
date: 2012-02-22
extension: .txt
mime: text/plain
words: 6997
sentence: 214
flesch: 41
cache: cache/cord-269150-d1sgnxc0.txt
txt: txt/cord-269150-d1sgnxc0.txt
title:
  Binding of the 5′-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription

summary:
  Western blot analysis also noted a reduction in the expression of viral structural genes, between 50% and 90% reduction for S and N proteins, with a reduction between 40% and 80% of MADP1 protein ( Figure 5B ). key: cord-269150-d1sgnxc0 authors: Tan, Yong Wah; Hong, Wanjin; Liu, Ding Xiang title: Binding of the 5′-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription date: 2012-02-22 journal: Nucleic Acids Res DOI: 10.1093/nar/gks165 sha: doc_id: 269150 cord_uid: d1sgnxc0 Coronaviruses RNA synthesis occurs in the cytoplasm and is regulated by host cell proteins.


id: cord-000271-812uc4w7
author: Chen, Zhiqi
title: Alternative splicing of CD200 is regulated by an exonic splicing enhancer and SF2/ASF
date: 2010-06-17
extension: .txt
mime: text/plain
words: 6967
sentence: 254
flesch: 49
cache: cache/cord-000271-812uc4w7.txt
txt: txt/cord-000271-812uc4w7.txt
summary:
  This expression pattern is the reverse of that seen for endogenous CD200 expression in SK-N cells, in which the predominant expression is of full-length CD200. Increased expression of SF2/ASF was detected in lungs of A/J mice 12 h postinfection, whereas no increase of SF2/ASF in C57BL/6J mice even 36 h postinfection, suggesting that the role of virus on host CD200 expression is mediated by SF2/ASF.


id: cord-048222-1pq6dkl5
author: Imbeaud, Sandrine
date: 2005-03-30
extension: .txt
mime: text/plain
words: 7009
sentence: 240
flesch: 41
cache: cache/cord-048222-1pq6dkl5.txt
txt: txt/cord-048222-1pq6dkl5.txt
title:
  Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces

summary:
  The relevance of the RNA quality metrics for assessment of gene expression differences was tested by Q-PCR, revealing a significant decline of the relative expression of genes in RNA samples of disparate quality, while samples of similar, even poor integrity were found highly comparable. It requires only a very small amount of RNA sample (as low as 200 pg), the use of a size standard during electrophoresis allows the estimation of sizes of RNA bands and the measurement appears relatively unaffected by contaminants.


id: cord-002494-qm9urt2w
author: Blank, Maximilian F.
title: SIRT7-dependent deacetylation of CDK9 activates RNA polymerase II transcription
date: 2017-03-17
extension: .txt
mime: text/plain
words: 6841
sentence: 263
flesch: 43
cache: cache/cord-002494-qm9urt2w.txt
txt: txt/cord-002494-qm9urt2w.txt
summary:
  The N-terminal part of SIRT7 binds to RNA and mediates RNA-dependent interactions with SIRT7 target proteins. not interact with SIRT7, did not deacetylate CDK9 in vitro, underscoring the importance of the N-terminus for SIRT7 function (Supplementary Figures S3C and S3D) .


id: cord-000435-2u49b7xo
author: Firth, Andrew E.
title: Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element
date: 2011-04-27
extension: .txt
mime: text/plain
words: 7281
sentence: 208
flesch: 37
cache: cache/cord-000435-2u49b7xo.txt
txt: txt/cord-000435-2u49b7xo.txt
summary:
  Sequence alignments of coding sequences containing RT stop codons were generated for a number of RNA virus taxa and the degree of conservation at synonymous sites was analyzed as described in the 'Materials and Methods' section. In terms of 5 0 stimulatory motifs, adenines at the À1 and À2 nucleotide positions have been shown to positively modulate RT in yeast and are a feature common to many virus RT sites, notably in the tobamoviruses, poleroviruses and luteoviruses (38) .


id: cord-263645-wupre5uj
author: Morgan, Brittany S
title: Insights into the development of chemical probes for RNA
date: 2018-09-19
extension: .txt
mime: text/plain
words: 7113
sentence: 218
flesch: 31
cache: cache/cord-263645-wupre5uj.txt
txt: txt/cord-263645-wupre5uj.txt
summary:
  We discuss the applicability of current tools to identify and evaluate RNA-targeted chemical probes, suggest criteria to assess the quality of RNA chemical probes and targets, and propose areas where new tools are particularly needed. A virus RNA promoter for up-regulating the translation of Antiamyloidogenic Secretase, a Disintegrin and Metalloproteinase 10 (ADAM10), by binding to the G-quadruplex-forming sequence in the 5 untranslated region (UTR) of its mRNA Studying a drug-like, RNA-focused small molecule library identifies compounds that inhibit RNA toxicity in Myotonic Dystrophy Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways Chemical correction of pre-mRNA splicing defects associated with sequestration of muscleblind-like 1 protein by expanded r(CAG)-containing transcripts Structure-based design of an RNA-binding p-terphenylene scaffold that inhibits HIV-1 Rev protein function Targeting RNA-protein interactions within the Human Immunodeficiency Virus Type 1 lifecycle A small molecule that represses translation of G-quadruplex-containing mRNA Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones Development of small molecules with a noncanonical binding mode to HIV-1 Trans Activation Response (TAR) RNA


id: cord-000294-2g471tb4
author: Rhodin, Michael H. J.
title: A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding
date: 2010-08-12
extension: .txt
mime: text/plain
words: 8182
sentence: 280
flesch: 49
cache: cache/cord-000294-2g471tb4.txt
txt: txt/cord-000294-2g471tb4.txt
summary:
  Thus, the structural changes observed are indicative of changes in the full 'dynamic potential' of the ribosome as opposed to conformations locked in by e.g. occupation of binding sites by tRNAs or ribosome-associated factors. Ribosomal protein L11 of Saccharomyces cerevisiae is an essential, highly conserved component of the 60S subunit (in bacteria and archaea, the homologous protein is named L5; the yeast nomenclature is used throughout this text to minimize confusion).


id: cord-289274-3g67f8sw
author: Tosoni, Elena
date: 2015-10-15
extension: .txt
mime: text/plain
words: 8094
sentence: 252
flesch: 40
cache: cache/cord-289274-3g67f8sw.txt
txt: txt/cord-289274-3g67f8sw.txt
title:
  Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription

summary:
  In particular, a very specific band migrated with the same rate in all G4 oligonucleotide samples (arrow in Figure 1B) , thus suggesting that the same protein was able to bind all LTR G4 sequences considered. While viral proteins were well represented in the transfected extract, the EMSA determinations revealed no major difference and confirmed that cellular proteins must constitute the major players in LTR G4 binding ( Figure 1C) .


id: cord-001453-l1r416w7
author: Hou, Linlin
date: 2014-11-10
extension: .txt
mime: text/plain
words: 8382
sentence: 298
flesch: 46
cache: cache/cord-001453-l1r416w7.txt
txt: txt/cord-001453-l1r416w7.txt
title:
  Archaeal DnaG contains a conserved N-terminal RNA-binding domain and enables tailing of rRNA by the exosome

summary:
  Genes encoding archaeal DnaG proteins are found in all genome-sequenced archaea regardless of presence or absence of an exosome (2, 44) . We conclude that the NTD of S. solfataricus DnaG is a novel, conserved archaeal RNA binding domain and its K6 and Y7 residues are important for binding of RNA.


id: cord-302895-471zei5o
author: Deng, Zengqin
date: 2013-12-24
extension: .txt
mime: text/plain
words: 8489
sentence: 278
flesch: 43
cache: cache/cord-302895-471zei5o.txt
txt: txt/cord-302895-471zei5o.txt
title:
  Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase

summary:
  Previous studies identified the nsp carrying RNA helicase activity (arterivirus nsp10 and coronavirus nsp13) as one of the two most evolutionarily conserved nidovirus proteins. Therefore, our study not only provides the first insights into the structural basis for nidovirus RNA helicase function, but also creates a basis to propose a role for this protein in the posttranscriptional quality control of viral mRNAs.


id: cord-275519-98qxf6xo
author: Chun, Jong-Yoon
date: 2007-02-07
extension: .txt
mime: text/plain
words: 3293
sentence: 112
flesch: 43
cache: cache/cord-275519-98qxf6xo.txt
txt: txt/cord-275519-98qxf6xo.txt
title:
  Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene

summary:
  In addition, DPO primers detected the influenza A virus in patient 1 (lane 6), which was not detected using the conventional primer system (lane 1). DPO primers are easier to design than conventional primers.


id: cord-000881-s90geszi
author: Lang, Dorothy M.
date: 2012-12-25
extension: .txt
mime: text/plain
words: 9729
sentence: 393
flesch: 53
cache: cache/cord-000881-s90geszi.txt
txt: txt/cord-000881-s90geszi.txt
title:
  Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases

summary:
  It would be interesting to explore the possibility that interactions at the surface of the protein (e.g. protein-protein contact at surface homomorph residues) may subtly affect function buried deep beneath, within the tunnel. In total, 18 well-studied viral species with solved RNA polymerase structures and four viral species with solved DNA polymerase structures were selected for analysis.


id: cord-048478-ftlb5b95
author: Mroczek, Seweryn
title: Apoptotic signals induce specific degradation of ribosomal RNA in yeast
date: 2008-04-01
extension: .txt
mime: text/plain
words: 9819
sentence: 299
flesch: 35
cache: cache/cord-048478-ftlb5b95.txt
txt: txt/cord-048478-ftlb5b95.txt
summary:
  Nevertheless, a similar approach had been used to demonstrate that DNA damage in apoptotic yeast cells was an enzymatic process (30) . Cytochrome c release and mitochondria involvement in programmed cell death induced by acetic acid in Saccharomyces cerevisiae Production of reactive oxygen species and loss of viability in yeast mitochondrial mutants: protective effect of Bcl-xL Application of inhibitors and uncouplers for a study of oxidative phosphorylation Effects of the inhibitors azide, dicyclohexylcarbodiimide, and aurovertin on nucleotide binding to the three F1-ATPase catalytic sites measured using specific tryptophan probes The mitochondrial F0F1-ATPase proton pump is required for function of the proapoptotic protein Bax in yeast and mammalian cells Translational control in stress and apoptosis Translational control by the ER transmembrane kinase/ribonuclease IRE1 under ER stress Ribosome inactivating proteins and apoptosis Rearrangement of nuclear ribonucleoprotein (RNP)-containing structures during apoptosis and transcriptional arrest Lsm proteins are required for normal processing and stability of ribosomal RNAs Yeast programmed cell death: an intricate puzzle The transmembrane kinase Ire1p is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response Role of mitochondria in the pheromone-and amiodarone-induced programmed death of yeast Saccharomyces cerevisiae has distinct adaptive responses to both hydrogen peroxide and menadione Mitochondrial function is required for resistance to oxidative stress in the yeast Saccharomyces cerevisiae The role of respiration, reactive oxygen species and oxidative stress in mother cell-specific ageing of yeast strains defective in the RAS signalling pathway Starvation for an essential amino acid induces apoptosis and oxidative stress in yeast Cells depleted of mitochondrial DNA (rho0) yield insight into physiological mechanisms Physiological regulation of yeast cell death in multicellular colonies is triggered by ammonia Defects in N-glycosylation induce apoptosis in yeast


id: cord-001337-a3y1rfas
author: Sharma, Virag
date: 2014-07-01
extension: .txt
mime: text/plain
words: 10093
sentence: 340
flesch: 49
cache: cache/cord-001337-a3y1rfas.txt
txt: txt/cord-001337-a3y1rfas.txt
title:
  Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli

summary:
  All the protein coding gene sequences were extracted from the .ffn files (National Center for Biotechnological Information website; ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/) of these 37 accessions and merged together to make a combined genome of 169 302 sequences. Thus, presence of a lys-tRNA with a 3 UUC 5 anticodon, which should pair perfectly with the AAG codon and thus reduce frameshifting (41) , does not preclude the use of A AA.G or V VV.A AA.G frameshift motifs in IS elements from many bacterial species.


id: cord-273107-xc61osdx
author: Qureshi, Abid
date: 2014-01-01
extension: .txt
mime: text/plain
words: 2371
sentence: 100
flesch: 41
cache: cache/cord-273107-xc61osdx.txt
txt: txt/cord-273107-xc61osdx.txt
title:
  AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses

summary:
  Antiviral peptides (AVPs) are being regarded as such new promising entities to combat the viral infections. AVPs are a subset of antimicrobial peptides (AMPs) which act as the first line of defence in many organisms as innate immune response and are the hosts' defence peptides generated in response to pathogenic disease condition (8) (9) (10) .


id: cord-048370-noscodew
author: Wu, Rebecca P.
date: 2007-08-01
extension: .txt
mime: text/plain
words: 5272
sentence: 198
flesch: 49
cache: cache/cord-048370-noscodew.txt
txt: txt/cord-048370-noscodew.txt
title:
  Cell-penetrating peptides as transporters for morpholino oligomers: effects of amino acid composition on intracellular delivery and cytotoxicity

summary:
  The microscopic phase images of treated cells were visualized by a Nikon Diaphot inverted microscope (Melville, NY), captured by an Olympus digital camera and processed by the Magnafire software (Optronics, Goleta, CA). Cell uptake assay pLuc705 cells were seeded 20 h prior to treatment in 12-well plates at 100 000 cells/well.


id: cord-330067-ujhgb3b0
author: Huang, Yi
title: CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes
date: 2007-10-02
extension: .txt
mime: text/plain
words: 3010
sentence: 132
flesch: 50
cache: cache/cord-330067-ujhgb3b0.txt
txt: txt/cord-330067-ujhgb3b0.txt
summary:
  During the process of coronavirus gene sequences analysis, we encountered a major problem when coronavirus gene sequences, especially those of orf1ab, were used for blast search against GenBank or any other coronavirus databases. The main goal for setting up CoVDB is to provide a convenient and efficient platform for retrieving batches of coronavirus gene sequences.


id: cord-011565-8ncgldaq
author: Elworth, R A Leo
date: 2020-06-04
extension: .txt
mime: text/plain
words: 12966
sentence: 555
flesch: 47
cache: cache/cord-011565-8ncgldaq.txt
txt: txt/cord-011565-8ncgldaq.txt
title:
  To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics

summary:
  algorithm Sliding hyperloglog: estimating cardinality in a data stream over a sliding window Using cascading Bloom filters to improve the memory usage for de Brujin graphs Fast lossless compression via cascading Bloom filters Improving Bloom filter performance on sequence data using k-mer Bloom filters An improved construction for counting Bloom filters Spectral Bloom filters Diversified RACE sampling on data streams applied to metagenomic sequence analysis Repeated And Merged Bloom Filter for Multiple Set Membership Testing (MSMT) in sub-linear time Sub-linear sequence search via a Repeated And Merged Bloom Filter (RAMBO): indexing 170 TB data in 14 hours Efficient generation of transcriptomic profiles by random composite measurements The restricted isometry property and its implications for compressed sensing A simple proof of the restricted isometry property for random matrices Adaptive compressed sensing MRI with unsupervised learning Insense: incoherent sensor selection for sparse signals A data-driven and distributed approach to sparse signal representation and recovery The sparse recovery autoencoder Learned D-AMP: principled neural network based compressive image recovery DeepCodec: adaptive sensing and recovery via deep convolutional neural networks Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection Clinical metagenomics Generating WGS trees with Mashtree Variant tolerant read mapping using min-hashing Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis BinDash, software for fast genome distance estimation on a typical personal laptop Dashing: fast and accurate genomic distances with HyperLogLog Finch: a tool adding dynamic abundance filtering to genomic MinHashing Streaming histogram sketching for rapid microbiome analytics Histosketch: fast similarity-preserving sketching of streaming histograms with concept drift kWIP: the k-mer weighted inner product, a de novo estimator of genetic similarity The khmer software package: enabling efficient nucleotide sequence analysis Locality-sensitive hashing for the edit distance Fast search of thousands of short-read sequencing experiments Improved search of large transcriptomic sequencing databases using split sequence bloom trees Ultrafast search of all deposited bacterial and viral genomic data Mash Screen: high-throughput sequence containment estimation for genome discovery Kraken: ultrafast metagenomic sequence classification using exact alignments Fast and sensitive protein alignment using DIAMOND KrakenUniq: confident and fast metagenomics classification using unique k-mer counts Improved metagenomic analysis with Kraken 2 Improving on hash-based probabilistic sequence classification using multiple spaced seeds and multi-index Bloom filters Efficient computation of spaced seeds Ganon: precise metagenomics classification against large and up-to-date sets of reference sequences DREAM-Yara: an exact read mapper for very large databases with short update time Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps A fast approximate algorithm for mapping long reads to large reference databases A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures Metagenomic binning through low-density hashing The ecologist's field guide to sequence-based identification of biodiversity A reference-free algorithm for computational normalization of shotgun sequencing data An improved filtering algorithm for big read datasets and its application to single-cell assembly WGSQuikr: fast whole-genome shotgun metagenomic classification Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing MetaPalette: a k-mer painting approach for metagenomic taxonomic profiling and quantification of novel strain variation MISSION: While ntHash can be faster than xxHash, CityHash and MurmurHash, it is only appropriate for sequence data.


id: cord-333502-3ulketgy
author: Snyder, E. E.
title: PATRIC: The VBI PathoSystems Resource Integration Center
date: 2006-11-16
extension: .txt
mime: text/plain
words: 3349
sentence: 123
flesch: 35
cache: cache/cord-333502-3ulketgy.txt
txt: txt/cord-333502-3ulketgy.txt
summary:
  The ortholog group table shows the presence or absence of reference gene list proteins for each organism in the organism category and provides links to an MSA and tree viewer and the Base-By-Base MSA editor (38) for every ortholog group. Manually curated protein sequences will be available in early 2007.


id: cord-320627-7vi6skvh
author: Horejsh, Douglas
title: A molecular beacon, bead-based assay for the detection of nucleic acids by flow cytometry
date: 2005-01-19
extension: .txt
mime: text/plain
words: 3731
sentence: 136
flesch: 42
cache: cache/cord-320627-7vi6skvh.txt
txt: txt/cord-320627-7vi6skvh.txt
summary:
  Identification of a novel coronavirus in patients with severe acute respiratory syndrome A novel coronavirus associated with severe acute respiratory syndrome Viral discovery and sequence recovery using DNA microarrays Kinetic PCR analysis: real-time monitoring of DNA amplification reactions Quantification using real-time PCR technology: applications and limitations Molecular beacons: probes that fluoresce upon hybridization Multiplex detection of single-nucleotide variations using molecular beacons Multicolor molecular beacons for allele discrimination In situ visualization of messenger RNA for basic fibroblast growth factor in living cells Real time detection of DNA.RNA hybridization in living cells Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA Multiplex detection of four pathogenic retroviruses using molecular beacons Ultrasensitive optical DNA biosensor based on surface immobilization of molecular beacon by a bridge structure Molecular beacons for DNA biosensors with micrometer to submicrometer dimensions Hybridization-based unquenching of DNA hairpins on au surfaces: prototypical ''molecular beacon'' biosensors Multiplexed, particle-based detection of DNA using flow cytometry with 3DNA dendrimers for signal amplification Real-time RT-PCR for quantitation of hepatitis C virus RNA A fiber-optic evanescent wave DNA biosensor based on novel molecular beacons Molecular-beacon-based array for sensitive DNA analysis Thermodynamic basis of the enhanced specificity of structured DNA probes Molecular beacons: novel fluorescent probes Using molecular beacons to detect single-nucleotide polymorphisms with real-time PCR Target discrimination by surface-immobilized molecular beacons designed to detect Francisella tularensis Structure-function relationships of shared-stem and conventional molecular beacons This work was supported by funding from the 'Ministero della Salute' of the Italian government, Ricerca Corrente e Finalizzata. In other applications, molecular beacon probes were designed for use as DNA biosensors by binding molecular beacons to glass beads or cover slips (13) , ultra small optical fibre probes (14) and gold surfaces (15) , allowing the specific detection of complementary sequences.


id: cord-334127-wjf8t8vp
author: Brister, J. Rodney
title: NCBI Viral Genomes Resource
date: 2015-01-28
extension: .txt
mime: text/plain
words: 3865
sentence: 120
flesch: 25
cache: cache/cord-334127-wjf8t8vp.txt
txt: txt/cord-334127-wjf8t8vp.txt
summary:
  Given the difficulty of implementing a purely well annotated representation of viral genome sequences, the viral RefSeq model has evolved into a more flexible approach that includes both reference and representative sequences. The growing cloud of viral genome sequences also poses significant barriers to the maintenance of reference genome records.


id: cord-325985-xfzhn1n1
author: Jabado, Omar J.
title: Comprehensive viral oligonucleotide probe design using conserved protein regions
date: 2007-12-13
extension: .txt
mime: text/plain
words: 4266
sentence: 173
flesch: 41
cache: cache/cord-325985-xfzhn1n1.txt
txt: txt/cord-325985-xfzhn1n1.txt
summary:
  All four subtypes were subjected to the same three step design method: identification of conserved regions, extraction of nucleotide probe sequences, and minimization of covering probes. All probe sequences were compared to the non-redundant set of viral sequences by BLASTN (37) .


id: cord-308331-55ge7kmr
author: Routh, Andrew
date: 2013-10-09
extension: .txt
mime: text/plain
words: 6026
sentence: 224
flesch: 46
cache: cache/cord-308331-55ge7kmr.txt
txt: txt/cord-308331-55ge7kmr.txt
title:
  Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data

summary:
  In addition to single recombination events, multiple recombination events within a single read are detected, as are virus-to-host recombination and insertion and substitution events. By mapping the distribution of recombination events in the genome of flock house virus, we demonstrate that this information can be used to discover de novo functional motifs located in conserved regions of the viral genome.


id: cord-003711-l3brhmzq
author: Munnur, Deeksha
title: Reversible ADP-ribosylation of RNA
date: 2019-06-20
extension: .txt
mime: text/plain
words: 6863
sentence: 247
flesch: 46
cache: cache/cord-003711-l3brhmzq.txt
txt: txt/cord-003711-l3brhmzq.txt
summary:
  We expressed and purified full length PARP10 and tested it for RNA modification activity. For this, we analysed RNA ADP-ribosylation catalysed by PARP10 catalytic domain in the excess presence of adenosine mono-phosphate (AMP) or 5 -phosphoadenosine 3 phosphate (PAP) as potential competitors and we observed no significant change in RNA modification in presence of nucleotide analogue in excess (Supplementary Figure S1D) .


id: cord-048359-lz37rh82
author: Li, Jin
date: 2007-06-01
extension: .txt
mime: text/plain
words: 6264
sentence: 203
flesch: 39
cache: cache/cord-048359-lz37rh82.txt
txt: txt/cord-048359-lz37rh82.txt
title:
  s-RT-MELT for rapid mutation scanning using enzymatic selection and real time DNA-melting: new potential for multiplex genetic analysis

summary:
  s-RT-MELT was subsequently applied in the same manner to screen for p53 mutations in exons 5-7 from cell lines and surgical colon samples harboring sequencing-identified mutations including a single-base frameshift mutation in exon 7 (listed in Supplementary Table 2 ). Since 480% of p53 mutations in human tumors are encountered in exons 5-9 (45), the multiplex single-tube s-RT-MELT reaction could be used to identify most p53 mutations encountered in clinical tumor samples.


id: cord-321352-174q2pjw
author: Lew, Qiao Jing
title: PCAF interacts with XBP-1S and mediates XBP-1S-dependent transcription
date: 2010-09-04
extension: .txt
mime: text/plain
words: 5839
sentence: 230
flesch: 45
cache: cache/cord-321352-174q2pjw.txt
txt: txt/cord-321352-174q2pjw.txt
summary:
  The cell lysates of XBP-1S expressing cells were used for IP with an anti-PCAF antibody. PCAF was found in the immunoprecipitated complexes of XBP-1S expressing cells, but not in XBP-1U or CREB1 expressing cells ( Figure 1A ).


id: cord-003305-ya0siivm
author: Liu, Weichi
date: 2018-11-16
extension: .txt
mime: text/plain
words: 8929
sentence: 264
flesch: 41
cache: cache/cord-003305-ya0siivm.txt
txt: txt/cord-003305-ya0siivm.txt
title:
  A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase

summary:
  The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation The structure of bovine viral diarrhea virus RNA-dependent RNA polymerase and its amino-terminal domain Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5 Crystal structure of the full-length Japanese encephalitis virus NS5 reveals a conserved methyltransferase-polymerase interface Crystal structure of classical swine fever virus NS5B reveals a novel N-Terminal domain Characterization of the N-terminal domain of classical swine fever virus RNA-dependent RNA polymerase Mutational analysis of bovine viral diarrhea virus RNA-dependent RNA polymerase Site-directed mutagenesis in one day with >80% efficiency Site-directed, Ligase-Independent Mutagenesis (SLIM): a single-tube methodology approaching 100% efficiency in 4 h Processing of X-ray Diffraction Data Collected in Oscillation Mode Phaser crystallographic software Coot: model-building tools for molecular graphics PHENIX: a comprehensive Python-based system for macromolecular structure solution Crystallography & NMR system: A new software suite for macromolecular structure determination THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures Perturbation in the conserved methyltransferase-polymerase interface of flavivirus NS5 differentially affects polymerase initiation and elongation Structural and functional analysis of methylation and 5 -RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5 A novel mechanism to ensure terminal initiation by hepatitis C virus NS5B polymerase Hydrophobic and charged residues in the C-terminal arm of hepatitis C virus RNA-dependent RNA polymerase regulate initiation and elongation Characterization of soluble hepatitis C virus RNA-dependent RNA polymerase expressed in Escherichia coli Assembly, purification, and pre-steady-state kinetic analysis of active RNA-dependent RNA polymerase elongation complex Substrate complexes of hepatitis C virus RNA polymerase (HC-J4): structural evidence for nucleotide import and de-novo initiation Dali server: conservation mapping in 3D A crystal structure of the Dengue virus NS5 protein reveals a novel inter-domain interface essential for protein flexibility and virus replication Characterisation of interaction between NS3 and NS5B protein of classical swine fever virus by deletion of terminal sequences of NS5B Poliovirus RNA-dependent RNA polymerase (3Dpol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mn2+ The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent Structural insights into bunyavirus replication and its regulation by the vRNA promoter Structure of influenza A polymerase bound to the viral RNA promoter An RNA cap (nucleoside-2 -O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Structural basis for RNA replication by the hepatitis C virus polymerase Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective Coxsackievirus B3 mutator strains are attenuated in vivo Design of a genetically stable high fidelity coxsackievirus B3 polymerase that attenuates virus growth in vivo Attenuation of Foot-and-Mouth disease virus by engineered viral polymerase fidelity Structure-Function relationships underlying the replication fidelity of viral RNA-Dependent RNA polymerases Residues Arg283, Arg285, and Ile287 in the nucleotide binding pocket of bovine viral diarrhea virus NS5B RNA polymerase affect catalysis and fidelity A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity Remote site control of an active site fidelity checkpoint in a viral RNA-dependent RNA polymerase Picornaviral polymerase structure, function, and fidelity modulation Rationalizing the development of live attenuated virus vaccines Engineering attenuated virus vaccines by controlling replication fidelity


id: cord-271701-tx0lqgff
author: te Velthuis, Aartjan J.W.
date: 2011-10-29
extension: .txt
mime: text/plain
words: 7431
sentence: 236
flesch: 46
cache: cache/cord-271701-tx0lqgff.txt
txt: txt/cord-271701-tx0lqgff.txt
title:
  The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension

summary:
  Given the absence of classical RdRp A and C motifs in the nsp8 sequence (12), we screened an alignment of CoV nsp8 sequences for conserved D/ExD/E motifs. Mutagenesis of nsp8 was performed to identify residues that may contribute to the catalytic centre of the nsp(7+8) polymerase, while differently tagged nsp8 recombinant proteins were constructed to explain some striking differences with previous observations.


id: cord-320325-sjab8zsk
author: Mendez, Aaron S
date: 2018-12-14
extension: .txt
mime: text/plain
words: 6521
sentence: 236
flesch: 45
cache: cache/cord-320325-sjab8zsk.txt
txt: txt/cord-320325-sjab8zsk.txt
title:
  Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX

summary:
  Our data suggest that this is likely because the K2-31 RNA lacks the additional residues necessary for SOX binding site found in both LIMD1 and GFP. This mutant has been previously identified to block SOX cleavage in vivo (20) .


id: cord-348427-worgd0xu
author: Hatcher, Eneida L.
title: Virus Variation Resource – improved response to emergent viral outbreaks
date: 2017-01-04
extension: .txt
mime: text/plain
words: 5555
sentence: 203
flesch: 43
cache: cache/cord-348427-worgd0xu.txt
txt: txt/cord-348427-worgd0xu.txt
summary:
  When searching protein sequences, selecting 'Full-length sequences only' filter, limits retrieved sequences to those with a complete coding region as determined to the relevant reference. Here, protein reference sequences are aligned with potential translations of the query sequence.


id: cord-341154-wwq0sd2r
author: Liao, Pei-Yu
date: 2010-09-07
extension: .txt
mime: text/plain
words: 7249
sentence: 285
flesch: 52
cache: cache/cord-341154-wwq0sd2r.txt
txt: txt/cord-341154-wwq0sd2r.txt
title:
  The many paths to frameshifting: kinetic modelling and analysis of the effects of different elongation steps on programmed –1 ribosomal frameshifting

summary:
  Our kinetic model suggests three possible reaction pathways that could generate À1 frameshift proteins ( Figure 2 ). To our knowledge, this is the first kinetic model to explain the production of two types of À1 frameshift proteins through three distinct kinetic pathways.


id: cord-350189-2su7oqbz
author: Elmén, Joacim
title: Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality
date: 2005-01-14
extension: .txt
mime: text/plain
words: 5430
sentence: 189
flesch: 43
cache: cache/cord-350189-2su7oqbz.txt
txt: txt/cord-350189-2su7oqbz.txt
summary:
  Briefly, siLNA5 has LNA modifications at the 3 0 ends and exhibits a duplex stability similar to the unmodified siRNA1 (T m = 69.7 C for siLNA5 and 70.5 C for siRNA1) whereas siLNA7 has six additional duplex stabilizing sense strand modifications at base-paired positions which increases its T m to >90 C. As shown in Figure 1a and b, unmodified siRNA (siRNA1) was markedly degraded after 6 h during which it produces a smear of faster migrating species. Introduction of LNA modifications in the 3 0 overhangs in either or both strands of the firefly siRNA revealed no loss of inhibitory effect (siLNA1-3).


id: cord-335377-zrbn637z
author: Ishimaru, Daniella
title: RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus
date: 2012-12-26
extension: .txt
mime: text/plain
words: 7763
sentence: 275
flesch: 45
cache: cache/cord-335377-zrbn637z.txt
txt: txt/cord-335377-zrbn637z.txt
summary:
  A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal An atypical RNA pseudoknot stimulator and an upstream attenuation signal for -1 ribosomal frameshifting of SARS coronavirus Mechanisms and enzymes involved in SARS coronavirus genome expression Comparative study of the effects of heptameric slippery site composition on -1 frameshifting among different eukaryotic systems Frameshifting RNA pseudoknots: structure and mechanism Programmed ribosomal frameshifting in decoding the SARS-CoV genome Mutational analysis of the RNA pseudoknot component of a coronavirus ribosomal frameshifting signal Ecoepidemiology and complete genome comparison of different strains of severe acute respiratory syndrome-related Rhinolophus bat coronavirus in China reveal bats as a reservoir for acute, self-limiting infection that allows recombination events A review of studies on animal reservoirs of the SARS coronavirus Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA Evidence that a kissing loop structure facilitates genomic RNA dimerisation in HIV-1 A 19-nucleotide sequence upstream of the 5 0 major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro Impact of human immunodeficiency virus type 1 RNA dimerization on viral infectivity and of stem-loop B on RNA dimerization and reverse transcription and dissociation of dimerization from packaging Dimerization of retroviral RNA genomes: an inseparable pair Genome of infectious bronchitis virus Biochemical aspects of coronavirus replication and virus-host interaction RNA structure determination by NMR NMRPipe: a multidimensional spectral processing system based on UNIX pipes University of California Absorption mode two-dimensional NOE spectroscopy of exchangeable protons in oligonucleotides Use of a water flip-back pulse in the homonuclear noesy experiment Pattern of 4-thiouridine-induced cross-linking in 16S ribosomal RNA in the Escherichia coli 30S subunit Systematic analysis of bicistronic reporter assay data Severe acute respiratory syndrome coronavirus infection of human ciliated airway epithelia: role of ciliated cells in viral spread in the conducting airways of the lungs Identification and characterization of severe acute respiratory syndrome coronavirus replicase proteins Clustal W and Clustal X version 2.0 Mfold web server for nucleic acid folding and hybridization prediction Dimerization of a pathogenic human mitochondrial tRNA Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets RNA LEGO: magnesium-dependent formation of specific RNA assemblies through kissing interactions Bipartite signal for genomic RNA dimerization in Moloney murine leukemia virus Hepatitis C virus genomic RNA dimerization is mediated via a kissing complex intermediate Kissing-loop model of HIV-1 genome dimerization: RNA pseudoknots implicated in -1


id: cord-324367-il9mz5na
author: Rodnina, Marina V
title: Translational recoding: canonical translation mechanisms reinterpreted
date: 2020-02-20
extension: .txt
mime: text/plain
words: 7415
sentence: 217
flesch: 34
cache: cache/cord-324367-il9mz5na.txt
txt: txt/cord-324367-il9mz5na.txt
summary:
  Functional translational readthrough: A systems biology perspective Translational readthrough potential of natural termination codons in eucaryotes-The impact of RNA sequence Stimulation of stop codon readthrough: frequent presence of an extended 3 RNA structural element Programmed translational readthrough generates antiangiogenic VEGF-Ax Impact of the six nucleotides downstream of the stop codon on translation termination Translational accuracy and the fitness of bacteria The evolutionary consequences of erroneous protein synthesis A molecular characterization of spontaneous frameshift mutagenesis within the trpA gene of Escherichia coli Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use Changed in translation: mRNA recoding by -1 programmed ribosomal frameshifting Recoding: expansion of decoding rules enrichesgene expression Reprogramming the genetic code: the emerging role of ribosomal frameshifting in regulating cellular gene expression New insights into the incorporation of natural suppressor tRNAs at stop codons in Saccharomyces cerevisiae Leaky UAG termination codon in tobacco mosaic virus RNA Expression of the gag-pol fusion protein of Moloney murine leukemia virus without gag protein does not induce virion formation or proteolytic processing The readthrough protein A1 is essential for the formation of viable Q beta particles Evidence of efficient stop codon readthrough in four mammalian genes Eukaryotic translational termination efficiency is influenced by the 3 nucleotides within the ribosomal mRNA channel Aminoglycoside antibiotics mediate context-dependent suppression of termination codons in a mammalian translation system Sequence specificity of aminoglycoside-induced stop condon readthrough: potential implications for treatment of Duchenne muscular dystrophy 5 contexts of Escherichia coli and human termination codons are similar The major 5 determinant in stop codon read-through involves two adjacent adenines A single UGA codon functions as a natural termination signal in the coliphage Q␤ coat protein cistron The signal for translational readthrough of a UGA codon in Sindbis virus RNA involves a single cytidine residue immediately downstream of the termination codon Sequence analysis suggests that tetra-nucleotides signal the termination of protein synthesis in eukaryotes Effects of the nucleotide 3 to an amber codon on ribosomal selection rates of suppressor tRNA and release factor-1 Translational termination efficiency in both bacteria and mammals is regulated by the base following the stop codon Translational termination efficiency in mammals is influenced by the base following the stop codon The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs UGA suppression by tRNACmCATrp occurs in diverse virus RNAs due to a limited influence of the codon context Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons Decoding mammalian Ribosome-mRNA states by translational GTPase complexes Structural basis for stop codon recognition in eukaryotes Structural basis for translation termination on the 70S ribosome Bipartite signal for read-through suppression in murine leukemia virus mRNA: an eight-nucleotide purine-rich sequence immediately downstream of the gag termination codon followed by an RNA pseudoknot Pseudoknot-dependent read-through of retroviral gag termination codons: importance of sequences in the spacer and loop 2 Evidence that a downstream pseudoknot is required for translational read-through of the Moloney murine leukemia virus gag stop codon Evidence of abundant stop codon readthrough in Drosophila and The 5 context of stop codons shows a non-random distribution of nucleotides in Escherichia coli and in humans (25) .


id: cord-319649-d6dqr03e
author: Yang, Jie
date: 2013-12-05
extension: .txt
mime: text/plain
words: 7891
sentence: 261
flesch: 43
cache: cache/cord-319649-d6dqr03e.txt
txt: txt/cord-319649-d6dqr03e.txt
title:
  A cypovirus VP5 displays the RNA chaperone-like activity that destabilizes RNA helices and accelerates strand annealing

summary:
  Our disorder prediction of CPV VP5 using PONDR VL-XT (51, 53, 54) indicates that VP5 proteins from three different types of cypoviruses-CPV-5, CPV-1 and CPV-18-contain similar distribution patterns of potentially disordered regions (data not shown), thereby suggesting that the 'entropy transfer' applies to HaCPV-5 VP5, and VP5 proteins of other CPVs may also contain RNA chaperone activity. This phenomenon is consistent with our previous observation of Ectropis obliqua picorna-like virus (EoV) nonstructural protein 2C, which also displays RNA chaperone activity (32) .


id: cord-314572-1pou702r
author: Lin, Ya-Hui
date: 2016-10-14
extension: .txt
mime: text/plain
words: 7213
sentence: 257
flesch: 40
cache: cache/cord-314572-1pou702r.txt
txt: txt/cord-314572-1pou702r.txt
title:
  Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator

summary:
  In addition, dual-luciferase based −1 PRF activity obtained from 293T cells transfected by Switch-1 containing reporter possessed a similar dosagedependent trend toward theophylline as that of the in vitro analysis, whereas cells transfected by Switch-1M1 reporter lost theophylline-dependency for −1 PRF activity ( Figure 4D ). The ligand-binding pocket of theophylline aptamer is composed of an internal-loop and an adjacent bulge with conserved key theophyllinecontact sequences distributed within the two motifs.


id: cord-314877-db7tze8j
author: Chkuaseli, Tamari
title: Activation of viral transcription by stepwise largescale folding of an RNA virus genome
date: 2020-08-12
extension: .txt
mime: text/plain
words: 8613
sentence: 297
flesch: 40
cache: cache/cord-314877-db7tze8j.txt
txt: txt/cord-314877-db7tze8j.txt
summary:
  The functional RNA domain 5BSL3.2 within the NS5B coding sequence influences hepatitis C virus IRES-mediated translation A long-range RNA-RNA interaction between the 5 and 3 ends of the HCV genome A twist in the tail: SHAPE mapping of long-range interactions and structural rearrangements of RNA elements involved in HCV replication Hepatitis C virus RNA: molecular switches mediated by long-range RNA-RNA interactions? Identification of a coronavirus transcription enhancer Gene N proximal and distal RNA motifs regulate coronavirus nucleocapsid mRNA transcription Long distance RNA-RNA interactions in the coronavirus genome form high-order structures promoting discontinuous RNA synthesis during transcription Advances in the molecular biology of tombusviruses: gene expression, genome replication and recombination Tomato bushy stunt virus at 2.9 A resolution A defective interfering RNA that contains a mosaic of a plant virus genome Recognition of small interfering RNA by a viral suppressor of RNA silencing A host Ca 2+ /Mn 2+ ion pump is a factor in the emergence of viral RNA recombinants The glycolytic pyruvate kinase is recruited directly into the viral replicase complex to generate ATP for RNA synthesis Tombusvirus-host interactions: co-opted evolutionarily conserved host factors take center court Exploring the architecture of viral RNA genomes Context-influenced cap-independent translation of Tombusvirus mRNAs in vitro Tombusvirus Y-shaped translational enhancer forms a complex with eIF4F and can be functionally replaced by heterologous translational enhancers Tombusvirus recruitment of translational machinery via the 3 UTR Multifaceted regulation of translational readthrough by RNA replication elements in a tombusvirus Subgenomic mRNA transcription in Tombusviridae Uncoupling RNA virus replication from transcription via the polymerase: functional and evolutionary insights Subgenomic mRNA regulation by a distal RNA element in a (+)-strand RNA virus Effects of inactivation of the coat protein and movement genes of Tomato bushy stunt virus on early accumulation of genomic and subgenomic RNAs Long-distance base pairing in flock house virus RNA1 regulates subgenomic RNA3 synthesis and RNA2 replication Discontinuous and non-discontinuous subgenomic RNA transcription in a nidovirus The premature termination model: a possible third mechanism for subgenomic mRNA transcription in (+)-strand RNA viruses A complex network of RNA-RNA interactions controls subgenomic mRNA transcription in a tombusvirus Global organization of a positive strand RNA virus genome An RNA activator of subgenomic mRNA1 transcription in Tomato bushy stunt virus Molecular cloning and complete nucleotide sequence of carnation Italian ringspot tombusvirus genomic and defective interfering RNAs Nonhomologous RNA recombination in tombusviruses: generation and evolution of defective interfering RNAs by stepwise deletions Regulatory activity of distal and core RNA elements in tombusvirus subgenomic mRNA2 transcription Analysis of a 3 -translation enhancer in a tombusvirus: a dynamic model for RNA-RNA interactions of mRNA termini Long-range RNA-RNA interactions between distal regions of the hepatitis C virus internal ribosome entry site element RNA purification by preparative polyacrylamide gel electrophoresis in Laboratory methods in enzymology Structural analysis of RNA backbone using in-line probing in laboratory methods in enzymology In-line probing analysis of riboswitches in Post transcriptional gene regulation Denaturing gel electrophoresis for sequencing RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences Global architecture of viral RNA genomes can contribute significantly to the regulation of critical viral functions.


id: cord-319116-2ts6zpdb
author: Ruggiero, Emanuela
title: G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy
date: 2018-04-20
extension: .txt
mime: text/plain
words: 9174
sentence: 286
flesch: 33
cache: cache/cord-319116-2ts6zpdb.txt
txt: txt/cord-319116-2ts6zpdb.txt
summary:
  Mass spectrometry competition analysis revealed a stronger preference for HIV-1 G4s over HSV-1, but generally, viral G4s were preferentially bound, when compared to the telomeric G4. Since c-exNDI selectivity towards HSV-1 G4s in vitro resulted to be good but not outstanding, the marked anti-HSV-1 activity was likely due also to the massive presence of viral G4s in the cell nucleus, which was demonstrated to occur during HSV-1 replication (70) .


id: cord-009318-zt1o1bcz
author: Rolando, Justin C
date: 2020-04-17
extension: .txt
mime: text/plain
words: 13731
sentence: 498
flesch: 39
cache: cache/cord-009318-zt1o1bcz.txt
txt: txt/cord-009318-zt1o1bcz.txt
title:
  Real-time kinetics and high-resolution melt curves in single-molecule digital LAMP to differentiate and study specific and non-specific amplification

summary:
  However, elimination of non-specific amplification remains a key challenge for the optimization of LAMP assays. Here, using chlamydia DNA as a clinically relevant target and high-throughput sequencing as an analytical tool, we investigate a potential mechanism of non-specific amplification.


id: cord-304794-z2kx314h
author: Métifiot, Mathieu
title: G-quadruplexes in viruses: function and potential therapeutic applications
date: 2014-11-10
extension: .txt
mime: text/plain
words: 9130
sentence: 326
flesch: 38
cache: cache/cord-304794-z2kx314h.txt
txt: txt/cord-304794-z2kx314h.txt
summary:
  Interestingly, TAg can unwind G4 DNA structures (122, 123) ; thus, it might play a crucial role in regulating replication as well as early and late transcription. Even if a 200-bp cis-regulatory element is necessary for efficient initiation, G4 structure formation at ORIs might be the key to selecting the firing origins (67, 68) .


id: cord-337998-08tknscm
author: Sztuba-Solinska, Joanna
date: 2016-11-16
extension: .txt
mime: text/plain
words: 8292
sentence: 299
flesch: 42
cache: cache/cord-337998-08tknscm.txt
txt: txt/cord-337998-08tknscm.txt
title:
  A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8

summary:
  The NCRs of RNA virus genomes have highly conserved primary and secondary structures (4) (5) (6) (7) . Reactivity to the SHAPE reagent 1M7 for EBOV minigenome RNA is shown in Figure 4A (Supplementary Figure S2) .


id: cord-319681-kjet3e50
author: Lin, Zhaoru
date: 2012-06-28
extension: .txt
mime: text/plain
words: 8876
sentence: 266
flesch: 47
cache: cache/cord-319681-kjet3e50.txt
txt: txt/cord-319681-kjet3e50.txt
title:
  Spacer-length dependence of programmed −1 or −2 ribosomal frameshifting on a U(6)A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting

summary:
  These data suggested strongly that the +1/ À2 FS product results from À2 FS and this was confirmed by MS (for convenience, these data are presented at the end of the 'Results' section, since acquisition of sufficient trans-frame protein for MS analysis required additional knowledge obtained from experiments outlined in the following sections). Examination of known viral À1 FS sites possessing a U 6 A or A 6 C slippery sequence, however, reveals that in most cases the spacing distances seem inappropriately long for efficient À2 FS.


id: cord-284990-klsl1nzn
author: Zhang, Dapeng
date: 2011-02-08
extension: .txt
mime: text/plain
words: 13717
sentence: 430
flesch: 33
cache: cache/cord-284990-klsl1nzn.txt
txt: txt/cord-284990-klsl1nzn.txt
title:
  A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems

summary:
  Phylogenetic analysis of each group, along with the phyletic patterns, strongly suggests that SUKH domain proteins have been widely disseminated both within and across the superkingdoms via extensive lateral transfer (Supplementary Data). Firstly, across the bacterial phylogenetic tree we found numerous genomic neighborhoods that linked two or more adjacent genes encoding SUKH domain proteins.


