Relevant bibliographies by topics / RNA Sequence Analysis

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'RNA Sequence Analysis'

Author: Grafiati
Published: 4 June 2021
Last updated: 30 July 2024

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Journal articles on the topic "RNA Sequence Analysis"

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Tessier, Laurence, Olivier Côté, and Dorothee Bienzle. "Sequence variant analysis of RNA sequences in severe equine asthma." PeerJ 6 (October 11, 2018): e5759. http://dx.doi.org/10.7717/peerj.5759.

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Background Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-Seq to call gene sequence variants, and to identify sequence variants of potential relevance to the pathogenesis of asthma. Methods RNA-Seq data were generated from endobronchial biopsies collected from six asthmatic and seven non-asthmatic horses before and after challenge (26 samples total). Sequences were aligned to the equine genome with Spliced Transcripts Alignment to Reference software. Read preparation for sequence variant calling was performed with Picard tools and Genome Analysis Toolkit (GATK). Sequence variants were called and filtered using GATK and Ensembl Variant Effect Predictor (VEP) tools, and two RNA-Seq predicted sequence variants were investigated with both PCR and Sanger sequencing. Supplementary analysis of novel sequence variant selection with VEP was based on a score of <0.01 predicted with Sorting Intolerant from Tolerant software, missense nature, location within the protein coding sequence and presence in all asthmatic individuals. For select variants, effect on protein function was assessed with Polymorphism Phenotyping 2 and screening for non-acceptable polymorphism 2 software. Sequences were aligned and 3D protein structures predicted with Geneious software. Difference in allele frequency between the groups was assessed using a Pearson’s Chi-squared test with Yates’ continuity correction, and difference in genotype frequency was calculated using the Fisher’s exact test for count data. Results RNA-Seq variant calling and filtering correctly identified substitution variants in PACRG and RTTN. Sanger sequencing confirmed that the PACRG substitution was appropriately identified in all 26 samples while the RTTN substitution was identified correctly in 24 of 26 samples. These variants of uncertain significance had substitutions that were predicted to result in loss of function and to be non-neutral. Amino acid substitutions projected no change of hydrophobicity and isoelectric point in PACRG, and a change in both for RTTN. For PACRG, no difference in allele frequency between the two groups was detected but a higher proportion of asthmatic horses had the altered RTTN allele compared to non-asthmatic animals. Discussion RNA-Seq was sensitive and specific for calling gene sequence variants in this disease model. Even moderate coverage (<10–20 counts per million) yielded correct identification in 92% of samples, suggesting RNA-Seq may be suitable to detect sequence variants in low coverage samples. The impact of amino acid alterations in PACRG and RTTN proteins, and possible association of the sequence variants with asthma, is of uncertain significance, but their role in ciliary function may be of future interest.
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Eddy, Sean R., and Richard Durbin. "RNA sequence analysis using covariance models." Nucleic Acids Research 22, no. 11 (1994): 2079–88. http://dx.doi.org/10.1093/nar/22.11.2079.

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Zhang, Jianping, Shaolei Teng, Cuncong Zhong, Bo Wang, and Jie Wu. "Current Developments in RNA Sequence Analysis." Bioinformatics and Biology Insights 9s1 (January 2015): BBI.S39980. http://dx.doi.org/10.4137/bbi.s39980.

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Györgyey, János, Danièle Vaubert, José I. Jiménez-Zurdo, Celine Charon, Liliane Troussard, Ádám Kondorosi, and Éva Kondorosi. "Analysis of Medicago truncatula Nodule Expressed Sequence Tags." Molecular Plant-Microbe Interactions® 13, no. 1 (January 2000): 62–71. http://dx.doi.org/10.1094/mpmi.2000.13.1.62.

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Systematic sequencing of expressed sequence tags (ESTs) can give a global picture of the assembly of genes involved in the development and function of organs. Indeterminate nodules representing different stages of the developmental program are especially suited to the study of organogenesis. With the vector λHybriZAP, a cDNA library was constructed from emerging nodules of Medicago truncatula induced by Sinorhizobium meliloti. The 5′ ends of 389 cDNA clones were sequenced, then these ESTs were analyzed both by sequence homology search and by studying their expression in roots and nodules. Two hundred fifty-six ESTs exhibited significant similarities to characterized data base entries and 40 of them represented 26 nodulin genes, while 133 had no similarity to sequences with known function. Only 60 out of the 389 cDNA clones corresponded to previously submitted M. truncatula EST sequences. For 117 cDNAs, reverse Northern (RNA) hybridization with root and nodule RNA probes revealed enhanced expression in the nodule, 48 clones are likely to code for novel nodulins, 33 cDNAs are clones of already known nodulin genes, and 36 clones exhibit similarity to other characterized genes. Thus, systematic analysis of the EST sequences and their expression patterns is a powerful way to identify nodule-specific and nodulation-related genes.
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Hanif, Waqar, Hijab Fatima, Muhammad Qasim, Rana Muhammad Atif, and Muhammad Rizwan Javed. "SeqDown: An Efficient Sequence Retrieval Software and Comparative Sequence Retrieval Analysis." Current Trends in OMICS 1, no. 1 (August 2, 2021): 18–29. http://dx.doi.org/10.32350/cto.11.03.

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For any sequence analysis procedure, a single or multiple sequence must be retrieved, stored, organized. One of the most common public databases used for biological sequence retrieval is GenBank which is a comprehensive public database of nucleotide sequences. However, as the length of the sequence to be retrieved increases such as a chromosome, entire genome, scaffold, etc., the elapsed time to download the file gets even elongated due to slower bandwidth to download/retrieve the sequence.[8] In most cases, during sequence analysis, the researcher requires messenger RNA (mRNA), RNA, DNA, protein sequences of the same sequence-of-interest to work with, which consumes a substantial amount of the researcher in finding and retrieving the sequence files. An access to GenBank through JAVA HTTPS protocols is established to request and receive the sequence files associated with the input accessions. SeqDown was shown to be much efficient in terms of retrieval time of the sequences as compared to the other internet browsers and was found to be 15.27% faster than Mozilla Firefox. SeqDown also provides the feature to retrieve coding DNA sequences & protein sequences present in a single chromosome. Sequence retrieval from the most biological databases don’t have proper naming of their files and the user has to deal with the redundantly named sequence files which leads to incorrect and time-consuming analysis and can be solved with SeqDown. SeqDown is available as a free-to-download software at https://bit.ly/3cUwchz
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Matoušek, J. "Viroids: sequence variability and evolution of pathogenic RNA." Plant Protection Science 38, SI 1 - 6th Conf EFPP 2002 (January 1, 2002): 173–76. http://dx.doi.org/10.17221/10348-pps.

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Viroids as the smallest pathogenic circular single-stranded pathogenic RNAs form populations of quasi-species, which<br />has been recently identified by thermodynamic methods like TGGE pre-selection and heteroduplex analysis. It was found<br />that replication under thermal stress led to enormously high level of viroid mutagenesis. Mostly multiple mutants having<br />non-random distribution of base changes were found. A specific “hot spots” were identified in the regions, where<br />a characteristic “pathogenicity domains” are localised in different viroids of the pospiviroidae family. Specific viroid<br />microevolution was observed upon artificial inoculation of non-host plant species. Our results suggest that viroid propagation<br />under physiological stress can be assumed as important factor, which is among others, responsible for an appearance<br />of viroid quasi-species in the nature. Evolution and new viroid patotypes could accumulate due to environmental stress<br />including various pollutants may be a potential danger for cultured plants.
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Klein, Ashwil, Lizex H. H. Husselmann, Achmat Williams, Liam Bell, Bret Cooper, Brent Ragar, and David L. Tabb. "Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies." Plants 10, no. 4 (April 14, 2021): 765. http://dx.doi.org/10.3390/plants10040765.

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While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought to determine the value of RNA-Seq experiments as a basis for establishing a set of protein sequences to represent a nonmodel organism, in this case, the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcript sequence sets with a high BUSCO completeness, though the number of transcript sequences and Trinity “genes” varied considerably among them. After six-frame translation, ProteinOrtho detected substantial numbers of orthologs among other species within the taxonomic order Lamiales. These protein sequence databases demonstrated a good identification efficiency for three different LC-MS/MS proteomics experiments, though a seed proteome showed considerable variability in the identification of peptides based on seed protein sequence inclusion. If a proteomics experiment emphasizes a particular tissue, an RNA-Seq experiment incorporating that same tissue is more likely to support a database search identification of that proteome.
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Evans, Donald, and Thomas Blumenthal. "trans Splicing of PolycistronicCaenorhabditis elegans Pre-mRNAs: Analysis of the SL2 RNA." Molecular and Cellular Biology 20, no. 18 (September 15, 2000): 6659–67. http://dx.doi.org/10.1128/mcb.20.18.6659-6667.2000.

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ABSTRACT Genes in Caenorhabditis elegans operons are transcribed as polycistronic pre-mRNAs in which downstream gene products aretrans spliced to a specialized spliced leader, SL2. SL2 is donated by a 110-nucleotide RNA, SL2 RNA, present in the cell as an Sm-bound snRNP. SL2 RNA can be conceptually folded into a phylogenetically conserved three-stem-loop secondary structure. Here we report an in vivo mutational analysis of the SL2 RNA. Some sequences can be changed without consequence, while other changes result in a substantial loss of trans splicing. Interestingly, the spliced leader itself can be dramatically altered, such that the first stem-loop cannot form, with only a relatively small loss intrans-splicing efficiency. However, the primary sequence of stem II is crucial for SL2 trans splicing. Similarly, the conserved primary sequence of the third stem-loop plays a key role intrans splicing. While mutations in stem-loop III allow snRNP formation, a single nucleotide substitution in the loop preventstrans splicing. In contrast, the analogous region of SL1 RNA is not highly conserved, and its mutation does not abrogate function. Thus, stem-loop III appears to confer a specific function to SL2 RNA. Finally, an upstream sequence, previously predicted to be a proximal sequence element, is shown to be required for SL2 RNA expression.
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Toung, J. M., M. Morley, M. Li, and V. G. Cheung. "RNA-sequence analysis of human B-cells." Genome Research 21, no. 6 (May 2, 2011): 991–98. http://dx.doi.org/10.1101/gr.116335.110.

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Cook, Jonathan P., and Malcolm A. McCrae. "Sequence analysis of the guanylyltransferase (VP3) of group A rotaviruses." Journal of General Virology 85, no. 4 (April 1, 2004): 929–32. http://dx.doi.org/10.1099/vir.0.19629-0.

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The RNA segment encoding the guanylyltransferase (VP3) from 12 group A rotavirus isolates has been sequenced following RT-PCR and molecular cloning of the full-length amplicons produced. Alignment of the derived amino acid sequences including those of the four VP3 sequences available from GenBank revealed two levels of sequence divergence. Virus isolates from humans showed greater than 94 % sequence identity, whereas those isolated from different mammalian species showed as low as 79 % sequence identity. The exceptions were avian virus isolates, which diverged ∼45 % from those of mammalian origin, and the human virus isolates DS1 and 69M, which showed much closer (over 90 %) identity to viruses of bovine origin, suggesting that these human isolates may have undergone recent reassortment events with a bovine virus. Analysis of the sequences for a putative enzymic active site has revealed that the KXTAMDXEXP and KXXGNNH motifs around amino acids 385 and 545, respectively, are conserved across both group A and C rotaviruses.
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Dissertations / Theses on the topic "RNA Sequence Analysis"

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Russell, Rodney S. "Novel RNA and protein sequences involved in dimerization and packaging of HIV-1 genomic RNA." Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=85092.

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During HIV-1 assembly, the Gag structural protein specifically encapsidates two copies of viral genomic RNA in the form of a dimer. An RNA stem-loop structure (SL1) in the 5' untranslated region, known as the dimerization initiation site (DIS), is important for dimerization and packaging of HIV-1 genomic RNA; however, the mechanisms involved are not fully understood. The major goal of this PhD study was to further understand HIV-1 RNA dimerization, and to study the role of the Gag protein in the dimerization and packaging processes. Despite the known involvement of the DIS in RNA dimerization, DIS-mutated viruses still contain significant levels of dimerized RNA, and electron microscopy studies suggest that the RNA molecules are linked at the extreme 5' end. We show here that RNA sequences on both sides of the DIS are also required for HIVA genome dimerization, suggesting that multiple RNA elements are involved. We have also examined the contribution of specific amino acids within Gag to the dimerization and packaging processes. Previous work showed that partial deletion of the DIS impacted on viral replication capacity, but could largely be corrected by compensatory point mutations within Gag. To further elucidate the mechanism(s) of these compensatory mutations, we generated DIS mutants lacking the entire SL1, or only the SL1 loop sequences, and combined these deletions with various combinations of compensatory mutations. Analysis of virion-derived RNA showed that the relevant mutant viruses contained increased levels of spliced viral RNA compared to wild type, indicating that a defect in genome packaging specificity was present. However, this defect was corrected by our compensatory mutations, and a T121 substitution in p2 was shown to be solely responsible for this activity. These results suggest that the p2 spacer peptide plays a critical role in the specific packaging of viral genomic RNA. In summary, these findings provide new insig
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O'Hanlon, Karen Ann. "Studies on the enzyme DNA-dependent RNA polymerase." Thesis, University of Reading, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.266340.

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鄭隆峰 and Lung-fung Cheng. "Modelling and sequence analysis of the collagen triple helix." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2001. http://hub.hku.hk/bib/B31969914.

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Cheng, Lung-fung. "Modelling and sequence analysis of the collagen triple helix." Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk/hkuto/record.jsp?B2373615X.

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Millar, N. S. "Molecular cloning and sequence analysis of Newcastle disease virus." Thesis, University of Newcastle Upon Tyne, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.380750.

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Coco, Joseph. "PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences." ScholarWorks@UNO, 2011. http://scholarworks.uno.edu/td/1297.

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RNA-Sequencing (RNA-Seq) has become one of the most widely used techniques to interrogate the transcriptome of an organism since the advent of next generation sequencing technologies [1]. A plethora of tools have been developed to analyze and visualize the transcriptome data from RNA-Seq experiments, solving the problem of mapping reads back to the host organism's genome [2] [3]. This allows for analysis of most reads produced by the experiments, but these tools typically discard reads that do not match well with the reference genome. This additional information could reveal important insight into the experiment and possible contributing factors to the condition under consideration. We introduce PARSES, a pipeline constructed from existing sequence analysis tools, which allows the user to interrogate RNA-Sequencing experiments for possible biological contamination or the presence of exogenous sequences that may shed light on other factors influencing an organism's condition.
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Giorgini, Flaviano. "Functional analysis of the murine sequence-specific RNA binding protein MSY4 /." Thesis, Connect to this title online; UW restricted, 2002. http://hdl.handle.net/1773/10293.

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Mohamed, Maizan. "Sequence analysis of the small (s) RNA segment of viruses in the genus Orthobunyavirus." Thesis, St Andrews, 2007. http://hdl.handle.net/10023/434.

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Fortino, Vittorio. "Sequence analysis in bioinformatics: methodological and practical aspects." Doctoral thesis, Universita degli studi di Salerno, 2013. http://hdl.handle.net/10556/985.

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2011 - 2012
My PhD research activities has focused on the development of new computational methods for biological sequence analyses. To overcome an intrinsic problem to protein sequence analysis, whose aim was to infer homologies in large biological protein databases with short queries, I developed a statistical framework BLAST-based to detect distant homologies conserved in transmembrane domains of different bacterial membrane proteins. Using this framework, transmembrane protein domains of all Salmonella spp. have been screened and more than five thousands of significant homologies have been identified. My results show that the proposed framework detects distant homologies that, because of their conservation in distinct bacterial membrane proteins, could represent ancient signatures about the existence of primeval genetic elements (or mini-genes) coding for short polypeptides that formed, through a primitive assembly process, more complex genes. Further, my statistical framework lays the foundation for new bioinformatics tools to detect homologies domain-oriented, or in other words, the ability to find statistically significant homologies in specific target-domains. The second problem that I faced deals with the analysis of transcripts obtained with RNA-Seq data. I developed a novel computational method that combines transcript borders, obtained from mapped RNA-Seq reads, with sequence features based operon predictions to accurately infer operons in prokaryotic genomes. Since the transcriptome of an organism is dynamic and condition dependent, the RNA-Seq mapped reads are used to determine a set of confirmed or predicted operons and from it specific transcriptomic features are extracted and combined with standard genomic features to train and validate three operon classification models (Random Forests - RFs, Neural Networks – NNs, and Support Vector Machines - SVMs). These classifiers have been exploited to refine the operon map annotated by DOOR, one of the most used database of prokaryotic operons. This method proved that the integration of genomic and transcriptomic features improve the accuracy of operon predictions, and that it is possible to predict the existence of potential new operons. An inherent limitation of using RNA-Seq to improve operon structure predictions is that it can be not applied to genes not expressed under the condition studied. I evaluated my approach on different RNA-Seq based transcriptome profiles of Histophilus somni and Porphyromonas gingivalis. These transcriptome profiles were obtained using the standard RNA-Seq or the strand-specific RNA-Seq method. My experimental results demonstrate that the three classifiers achieved accurate operon maps including reliable predictions of new operons. [edited by author]
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Wang, Suyue. "Characterization of a Human 28S Ribosomal RNA Retropseudogene and Other Repetitive DNA Sequence Elements Isolated from a Human X Chromosome-Specific Library." Thesis, University of North Texas, 1994. https://digital.library.unt.edu/ark:/67531/metadc278083/.

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Three genomic clones encompassing human DNA segments (designated LhX-3, LhX-4, and LhX5) were isolated from an X chromosome-specific library and subjected to analysis by physical mapping and DNA sequencing. It was found that these three clones are very rich in repetitive DNA sequence elements and retropseudogenes.
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Books on the topic "RNA Sequence Analysis"

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Peter, Bugert, ed. DNA and RNA profiling in human blood: Methods and protocols. New York, NY: Humana Press, 2009.

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author, Tuimala Jarno, Somervuo Panu author, Huss Mikael author, and Wong Garry author, eds. RNA-seq data analysis: A practical approach. Boca Raton: CRC Press, Taylor & Francis Group, 2015.

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Przykorska, Anna. Analiza przestrzennej struktury kwasów rybonukleinowych za pomocą nukleaz pochodzenia roślinnego. Warszawa: Fundacja, Rozwój SGGW, 1996.

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J, Howe C., and Ward E. S, eds. Nucleic acids sequencing: A practical approach. Oxford: IRL Press, 1989.

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Rederstorff, Mathieu. Small non-coding RNAs: Methods and protocols. New York: Humana Press, 2015.

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Warwick, Simon. Analysis of ribosmal RNA sequence from actinomcyetes and production of probes for commercially important strains. London: University of East London, 1996.

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Scholin, Christopher Alan. Analysis of toxic and non-toxic Alexandrium (Dinophyceae) species using ribosomal RNA gene sequences. Woods Hole, Mass: Woods Hole Oceanographic Institution, 1993.

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T, Kho Alvin, and Butte Atul J, eds. Microarrays for an integrative genomics. Cambridge, Mass: MIT Press, 2003.

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1949-, Müller S. C., ed. Synthetic peptides as antigens. Amsterdam: Elsevier, 1999.

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Bioinformatics. New York: John Wiley & Sons, Ltd., 2007.

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Book chapters on the topic "RNA Sequence Analysis"

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Zuker, Michael. "Prediction of RNA Secondary Structure by Energy Minimization." In Computer Analysis of Sequence Data, 267–94. Totowa, NJ: Humana Press, 1994. http://dx.doi.org/10.1385/0-89603-276-0:267.

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Backofen, Rolf. "RNA-Sequence-Structure Properties and Selenocysteine Insertion." In Advances in Intelligent Data Analysis, 187–97. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/3-540-44816-0_19.

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Wittmann-Liebold, Brigitte. "Structure Analysis of the Topography and Molecular Organization of Protein-RNA Complexes as Revealed in Ribosomes." In Methods in Protein Sequence Analysis, 289–306. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4899-1603-7_38.

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Cruz, Cristina, and Jonathan Houseley. "Protocols for Northern Analysis of Exosome Substrates and Other Noncoding RNAs." In Methods in Molecular Biology, 83–103. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9822-7_5.

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AbstractOver the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing methods provide unsurpassed insights into ncRNA distribution and expression, detailed information on structure and processing are harder to extract from sequence data. In contrast, northern blotting methods provide uniquely detailed insights into complex RNA populations but are rarely employed outside specialist RNA research groups. Such techniques are generally considered difficult for nonspecialists, which is unfortunate as substantial technical advances in the past few decades have solved the major challenges. Here we present simple, reproducible and highly robust protocols for separating glyoxylated RNA on agarose gels and heat denatured RNA on polyacrylamide–urea gels using standard laboratory electrophoresis equipment. We also provide reliable transfer and hybridization protocols that do not require optimization for most applications. Together, these should allow any molecular biology lab to elucidate the structure and processing of ncRNAs of interest.
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Ramsey, Stephen A. "A Method for Cross-Species Visualization and Analysis of RNA-Sequence Data." In Methods in Molecular Biology, 291–305. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7456-6_14.

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O’Connell, Catherine D., and Maurice Cohen. "ERV3, A Full-Length Human Endogenous Provirus: Sequence Analysis and Evolutionary Relationships." In RNA Tumor Viruses, Oncogenes, Human Cancer and AIDS: On the Frontiers of Understanding, 108–15. Boston, MA: Springer US, 1985. http://dx.doi.org/10.1007/978-1-4613-2583-3_9.

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Teubl, Fabian, Katrin Schwank, Uli Ohmayer, Joachim Griesenbeck, Herbert Tschochner, and Philipp Milkereit. "Tethered MNase Structure Probing as Versatile Technique for Analyzing RNPs Using Tagging Cassettes for Homologous Recombination in Saccharomyces cerevisiae." In Ribosome Biogenesis, 127–45. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_8.

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AbstractMicrococcal nuclease (MNase) originating from Staphylococcus aureus is a calcium dependent ribo- and desoxyribonuclease which has endo- and exonucleolytic activity of low sequence preference. MNase is widely used to analyze nucleosome positions in chromatin by probing the enzyme’s DNA accessibility in limited digestion reactions. Probing reactions can be performed in a global way by addition of exogenous MNase, or locally by “chromatin endogenous cleavage” (ChEC) reactions using MNasefusion proteins. The latter approach has recently been adopted for the analysis of local RNA environments of MNasefusion proteins which are incorporated in vivo at specific sites of ribonucleoprotein (RNP) complexes. In this case, ex vivo activation of MNase by addition of calcium leads to RNA cleavages in proximity to the tethered anchor protein thus providing information about the folding state of its RNA environment.Here, we describe a set of plasmids that can be used as template for PCR-based MNase tagging of genes by homologous recombination in S. cerevisiae. The templates enable both N- and C-terminal tagging with MNase in combination with linker regions of different lengths and properties. In addition, an affinity tag is included in the recombination cassettes which can be used for purification of the particle of interest before or after induction of MNase cleavages in the surrounding RNA or DNA. A step-by-step protocol is provided for tagging of a gene of interest, followed by affinity purification of the resulting fusion protein together with associated RNA and subsequent induction of local MNase cleavages.
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Jabeen, Almas, Nadeem Ahmad, and Khalid Raza. "Differential Expression Analysis of ZIKV Infected Human RNA Sequence Reveals Potential Genetic Biomarkers." In Bioinformatics and Biomedical Engineering, 283–94. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-17938-0_26.

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Loh, Yong-Hwee Eddie, and Li Shen. "Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot." In Methods in Molecular Biology, 371–83. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3572-7_18.

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Stock, David W., Kirk D. Moberg, Linda R. Maxson, and Gregory S. Whitt. "A phylogenetic analysis of the 18S ribosomal RNA sequence of the coelacanth Latimeria chalumnae." In Developments in environmental biology of fishes, 99–118. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-3194-0_6.

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Conference papers on the topic "RNA Sequence Analysis"

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Benslimane, Fatiha M., Hebah Al Khatib, Dana Albatesh, Ola Al-Jamal, Sonia Boughattas, Asmaa A. Althani, and Hadi M. Yassine. "Nanopore Sequencing SARS-CoV-2 Genome in Qatar." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0289.

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Background: The current pandemic, COVID-19, is cause by an RNA Coronavirus that was recently identified as SARS-CoV-2. RNA viruses tend to have a high mutation rate; the rate is around a million times greater than that of their hosts. The mutagenic potential of the virus depends on many factors, including the fidelity of nucleic acid-replicating viral enzymes, such as SARSCoV-2 RNA dependent RNA polymerase (RdRp). The rate of mutation drives viral evolution and genome variability, consequently allowing viruses to escape the immunity of the host and develop resistance to drugs. Therefore, the characterization of SARS-CoV-2 variants might lead to implement better therapeutics treatments, vaccines design and identify new diagnostics approaches. Aim: The aim of this study was to establish a fast sequencing method to identify SARS-CoV-2 mutations in Qatar. This will help to assess if there are new viral variants that are spreading in country. Methods: RNA was isolated from samples collected from Qatar COVID-19 positive patients. The Artic Network V3 primer scheme and Oxford Nanopore ligation sequencing kit were used to prepare the sequencing libraries. Libraries were loaded on to R9.4.1 flow cells and ran on a GridION. Bioinformatics analysis was done following the Artic Network SARA-CoV-2 bioinformatics tools. Results: Genome coverage of sequenced samples was >80% and the depth was average at 200x. The coverage was highly dependable on sample viral load; samples of CT value lower than 30 resulted in better sequence coverage. The sequenced genomes were deposited in GISAID and were mainly clustering with genomes deposited from the UK. Sequences were compared to Illumina and sanger sequences and they showed compatible results. Conclusion: The use of ONT to sequence SARA-CoV-2 is a quick, affordable, and reliable technique to determine viral mutation. Using this technique, the first sequences from Qatar were deposited in to GISAID. Up to date, 700 genomes have been sequenced from Qatari samples.
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Carolan, Brendan J., Jacqueline Salit, Neil R. Hackett, Larsson Omberg, Juan Rodriguez-Flores, Renat Shaykhiev, Jason Mezey, and Ronald G. Crystal. "Rna Sequence Analysis Identifies Novel Low-Level Expressed Smoking-Responsive Genes In Human Alveolar Macrophages." In American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado. American Thoracic Society, 2011. http://dx.doi.org/10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a5686.

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Lopez, J. A., D. W. Chung, K. Fujikawa, F. S. Hagen, T. Papavannopoulou, and G. J. Roth. "MOLECULAR CLONING OF HUMAN PLATELET GLYCOPROTEIN Ib." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642927.

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Glycoprotein Ib (GPIb) mediates von Willebrand factor-dependent platelet adhesion and participates in the resulting platelet activation process. In the present investigation, the primary structure of human platelet GPIb was studied. GPIb and its proteolytic fragment glycocalicin were purified to near homogeneity from human platelets by affinity chromatography using wheat germ agglutinin and anti-GPIb monoclonal antibody (D. Nugent, University of Washington) coupled to Sepharose. GPIba chain, β chain, and glycocalicin were isolated, reduced and carboxymethylated, and then fragmented by trypsin and S. aureus V8 protease. Peptides were isolated by HPLC and subjected to amino acid sequence analysis. Approximately 200 amino acid residues were identified. Affinity purified rabbit antibodies directed against the a chain, the ft chain, and glycocalicin were prepared and shown to be monospecific by Western blot analysis. Total RNA was prepared from human erythroleukemia cells grown in the presence of phorbol acetate. Poly(A)+ RNA was selected and used to prepare a cDNA library in λgt11. The library was screened with [125]I-labeled polyclonal antibody to glycocalicin. The clone with the largest cDNA insert was sequenced and shown to code for amino acid sequences corresponding to those determined by Edman degradation of glycocalicin. The predicted amino acid sequence contains at least six tandem repeats of 24 amino acids that are highly homologous with 13 repeats present in leucine rich α2 glycoprotein of human plasma. Another region in the protein contains a second repeat rich in threonine and serine, which shows some homology to a 9 amino acid repeat in the connecting region of human factor V. This region is probably the major site of attachment of clusters of O-linked carbohydrate in GPIbα. These results indicate that human platelet glycoprotein Ibα has a multi-domain structure composed of a number of repetitive sequences. Supported in part by grants from the American Heart Association, Robert Wood Johnson Foundation, Veterans Administration, and National Institutes of Health.
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Muramatsu, Tomoki, Kousuke Tanimoto, and Johji Inazawa. "Abstract 1992: Exploring target genes of eukaryotic initiation factor 5A in cancer using RNA sequence analysis." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-1992.

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Al Khatib, Hebah A., Fatiha M. Benslimane, Israa El Bashir, Asmaa A. Al Thani, and Hadi M. Yassine. "Within-Host Diversity of SARS-Cov-2 in COVID-19 Patients with Variable Disease Severities." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0280.

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Background: The ongoing pandemic of SARS-COV-2 has already infected more than eight million people worldwide. The majority of COVID-19 patients are either asymptomatic or have mild symptoms. Yet, about 15% of the cases experience severe complications and require intensive care. Factors determining disease severity are not yet fully characterized. Aim: Here, we investigated the within-host virus diversity in COVID-19 patients with different clinical manifestations. Methods: We compared SARS-COV-2 genetic diversity in 19 mild and 27 severe cases. Viral RNA was extracted from nasopharyngeal samples and sequenced using Illumina MiSeq platform. This was followed by deep-sequencing analyses of SARS-CoV-2 genomes at both consensus and sub-consensus sequence levels. Results: Consensus sequences of all viruses were very similar, showing more than 99·8% sequence identity regardless of the disease severity. However, the sub-consensus analysis revealed significant differences in within-host diversity between mild and severe cases. Patients with severe symptoms exhibited a significantly (p-value 0.001) higher number of variants in coding and non-coding regions compared to mild cases. Analysis also revealed higher prevalence of some variants among severe cases. Most importantly, severe cases exhibited significantly higher within-host diversity (mean= 13) compared to mild cases (mean=6). Further, higher within-host diversity was observed in patients above the age of 60 compared to the younger age group. Conclusion: These observations provided evidence that within-host diversity might play a role in the development of severe disease outcomes in COVID19 patients; however, further investigations is required to elucidate this association.
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Mumby, S., V. Elyasigomari, C. K. Hui, F. Perros, A. Hautefort, M. Humbert, J. Wort, and I. M. Adcock. "Evidence for Endothelial Barrier Dysfunction, Vascular Permeability and Altered Matrix Degradation in PAH Pathogenesis Using RNA-Sequence Analysis." In American Thoracic Society 2019 International Conference, May 17-22, 2019 - Dallas, TX. American Thoracic Society, 2019. http://dx.doi.org/10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a7194.

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Zheng, Ying, and Wilson S. Meng. "Polycation Coated Polymeric Particles as Vehicles of RNA Delivery Into Immune Cells." In ASME 2010 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. ASMEDC, 2010. http://dx.doi.org/10.1115/smasis2010-3714.

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The purpose of this work is to develop a carrier system for delivering RNA molecules aimed to downregulate specific functions in T cells. In many forms of cancer, T cells that express the protein Forkhead Box P3 (Foxp3) are associated with cancer progression. These cells can be identified by CD4 and CD25, molecules express on the cell surface. Studies have shown that downregulation of Foxp3 can increase the ability of other immune cells to destroy tumors. A class of RNA molecules, commonly referred to as “siRNA”, bind to and degrade specific messenger RNA (mRNA) in a sequence-dependent manner such that expression of the encoded protein is terminated. Because mRNA molecules are located inside cells, a carrier system is required to facilitate the uptake of siRNA, which does not passively diffuse through the plasma membrane. To this end, nanosized polymeric particles coated with the polycation, ornithinex10-histidinex6 (or O10H6) were used to adsorb siRNA that bind to the mRNA encoding Foxp3. The RNA-loaded particles are spherical and uniform in size (normally distributed, polydispersity index = 0.072). Loading of RNA to the particles was confirmed using gel electrophoresis. RNA complexed with the particles are protected from serum destabilization: 83.1% of RNA were recovered compared to 36.1% in RNA that were not associated with the particles. Association with the particles increased the uptake of the RNA in mouse T cells from 3.2±0.2% (free RNA) to 20.1±3.9%. Specifically, uptake of the RNA in T cells that express CD4 increased from 2.7±0.2% to 27.1±1.3% when particles were employed. These differences are statistically significant in three experiments conducted (p &lt; 0.01). Internalization of the RNA into T cells was confirmed using confocal imaging. Flow cytometric analysis showed that the particle-complexed RNA reduced the percentage of T cells that express both CD4 and CD25 in mice carrying tumors from 24.0% when free RNA molecules were used to 13.5%. In these cells, the level of Foxp3 mRNA was reduced by 30%. In conclusion, the particles facilitate the uptake of siRNA molecules into a population of T cells that is known to promote cancer growth.
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Kralj, Sebastjan, Milan Hodošček, Marko Jukić, and Urban Bren. "A comprehensive in silico protocol for fast automated mutagenesis and binding affinity scoring of protein-ligand complexes." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.674k.

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Protein-protein interactions (PPI) are critical for cellular functions, host-pathogen dynamics and are crucial with drug design efforts. The interaction of proteins is dependent on the amino acid sequence of a protein as it determines its binding affinity to various molecules, including drugs, DNA, RNA, and proteins. Polymorphisms, natural DNA variations, affect PPIs by altering protein structure and stability. Computational chemistry is vital for the prediction of ligand-protein interactions through techniques such as docking and molecular dynamics and can elucidate the changes in energy associated with such mutations. We present a user-friendly protocol that uses the INTE command of CHARMM to predict the effects of mutations on PPIs. This command-line tool automates mutation analysis and interaction energy estimation, is applicable to different ligand types (protein, DNA, RNA, ion, small molecule) and provides various other features. The energy values yield absolute and normalized heat maps that allow rapid identification of stabilizing and destabilizing mutations. Our protocol forms the basis for automated programs that facilitate studies of binding-altering mutations in host-pathogen, protein-protein, and drug-target interactions.
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Liu, Chung Y., Dominic Chung, Earl Davie, and Leonard Chess. "FORMER STUDIES OF FIBRINOGEN NEW YORK I : ANALYSIS OF HE GENUINIC C DISORDER for the deletion OF MINO ACID SEQUENCE 9-72 OF THE Bβ CHAIN." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644697.

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Fibrinogens New York I and la (NY-I and NY-la) have been purified from blood plasma samples of a^ sister and a brother in a white family with thrombotic tendency. Both are heterozygous and contain both thrombin-clottable fibrinogen with two normal Bβ-chains and thrombin-nonclottable fibrinogen with two abnormal Bβ chains. The abnormal β-chains result- fran deletions of ammo acid residues 9-72, which are encoded exactly by exon II of the gene. To study the genomic disorder for this deletion, gencmic DNAs were isolated respectively from leukocytes of NY-la, NY-Ib (a nonaffected brother), and four normal individuals outside the NY-I family, and analysed in Southern blotting experiments with a human gencmic DNA probe containing exons I-V. Digestion of various DNAs were performed with two different restriction enzymes, and these digestions were analyzed respectively by agrose electroptoresis.Digestion with Hind III reveals 3 cleavage sites (one site in intron A near exon II)witn formation of two fragments of equal size (2 bands : 3.1kb and 3.1 kb) in normal, NY-la and NY-Id, but an extra fragment (one band = 6.0 kb) in NY-Ia.Digestion with Pvu II reveals 3 cleavage sites (one site in exonII) with formation of two fragments (2 bands : 7.5 kb and 2.9kb)m normal, NY-Ia and NY-Ib, but an extra fragment (one band - 5.7 kb) in NY-Ia. These results show that one Hind III and one Pvu II cleavage sites which are present in the normal allele are absent in the abnormal allele of NY-Ia. Thus, these studies indicate that generic disorder is associated with the patient (NY-Ia) with a thrombotic tendency, and further suggest that the genomic defect in the aonormal allele is near the junction of intron A and exon II. A possible mechanism for this genomic disorder is due to that an inverse double crossover have taken place in a region covering this junction, resulting in m abnormal RNA-splicing site in this junction. Thus, exon II is eliminated with intron A during RNA processing and absent in the abnormal rnRNA. Accordingly, the β(9-72) amino acid sequence disappears from one abnromal β-chains.
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Cool, D. E., and R. T. A. MacGillivray. "CHARACTERIZATION OF THe HUMAN FACTOR XII GENE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642800.

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Surface activation of the plasma systems involved with coagulation, fibrinolysis, renin formation and kinin generation involves factor XII (Hageman factor). This protein is a 76,000 dalton glycoprotein which circulates in plasma as an inactive form of a serine protease. A human liver cDNA coding for factor XII was used to screen a human genomic phage library. Two overlapping clones were isolated, XHXII27 and XHXII76, and contain the entire gene for human factor XII. The gene is 13.5 Kbp in length and consists of 14 exons and 13 introns. The transcriptional start site of the mRNA was determined using S1 mapping and primer extension analysis. The results indicate that the 5′ untranslated end of the mRNA has a leader sequence of 47 bp and is not interrupted by an intron in the gene. DNA sequence analysis of the region upstream of the transcriptional start site does not contain TATA or CAAT sequences, which are often found in other genes transcribed by RNA polymerase II. The positions of the introns in the coding sequence separate the protein into domains which are homologous to similar regions found in fibronectin and tissue-type plasminogen activator. Furthermore, wherever protein homologies are found, the positions of the introns in the triplet codon occur in the same reading frame as in the tissue-type plasminogen activator, urokinase plasminogen activator and factor XII genes. The intron/exon organization of the factor XII gene is different to the organization of other coagulation genes such as prothrombin, factor IX and factor X. Therefore, factor XII appears to have evolved as a member of the plasminogen activator family of genes rather than as a member of the clotting factor gene family.
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Reports on the topic "RNA Sequence Analysis"

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Fox, George E., and Timmothy Haselman. Comparative Sequence Analysis of Structural RNA. Fort Belvoir, VA: Defense Technical Information Center, January 1991. http://dx.doi.org/10.21236/ada232340.

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Liao, Jianhua, Jingting Liu, Baoqing Liu, Chunyan Meng, and Peiwen Yuan. Effect of OIP5-AS1 on clinicopathological characteristics and prognosis of cancer patients: a meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, October 2022. http://dx.doi.org/10.37766/inplasy2022.10.0118.

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Review question / Objective: According to recent studies, long non-coding RNA (lncRNAs) i.e., OPA-interacting protein 5 antisense RNA 1 (OIP5-AS1) has an important role in various carcinomas. However, its role in the cancer is contradictory. Therefore, we aimed to evaluate the link between OIP5-AS1 and cancer patients' clinicopathological characteristics and prognosis to better understand OIP5-AS1's role in cancer. Condition being studied: Reported studies have revealed that long non-coding RNA (lncRNAs) are considerably involved in crucial physiological events in several carcinomas, it can inhibit or promote the occurrence and development of tumors by changing the sequence and spatial structure, modulating epigenetic, regulating the expression level and interacting with binding proteins. However, the mechanism of cancer regulation via lncRNAs was incompletely understood. Hence, clarifying the application value of lncRNAs in preclinical and clinical disease diagnosis and treatment was therefore the prime objective in the field of cancer research at the time.
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Vakharia, Vikram, Shoshana Arad, Yonathan Zohar, Yacob Weinstein, Shamila Yusuff, and Arun Ammayappan. Development of Fish Edible Vaccines on the Yeast and Redmicroalgae Platforms. United States Department of Agriculture, February 2013. http://dx.doi.org/10.32747/2013.7699839.bard.

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Betanodaviruses are causative agents of viral nervous necrosis (VNN), a devastating disease of cultured marine fish worldwide. Betanodavirus (BTN) genome is composed of two single-stranded, positive-sense RNA molecules. The larger genomic segment, RNA1 (3.1 kb), encodes the RNA-dependent RNA polymerase, while the smaller genomic segment, RNA 2 (1.4kb), encodes the coat protein. This structural protein is the host-protective antigen of VNN which assembles to form virus-like particles (VLPs). BTNs are classified into four genotypes, designated red-spotted grouper nervous necrosis virus (RGNNV), barfin flounder nervous necrosis virus (BFNNV), tiger puffer nervous necrosis virus (TPNNV), and striped jack nervous necrosis virus (SJNNV), based on phylogenetic analysis of the coat protein sequences. RGNNV type is quite important as it has a broad host-range, infecting warm-water fish species. At present, there is no commercial vaccine available to prevent VNN in fish. The general goal of this research was to develop oral fish vaccines in yeast and red microalgae (Porphyridium sp.) against the RGNNV genotype. To achieve this, we planned to clone and sequence the coat protein gene of RGNNV, express the coat protein gene of RGNNV in yeast and red microalgae and evaluate the immune response in fish fed with recombinantVLPs antigens produced in yeast and algae. The collaboration between the Israeli group and the US group, having wide experience in red microalgae biochemistry, molecular genetics and large-scale cultivation, and the development of viral vaccines and eukaryotic protein expression systems, respectively, was synergistic to produce a vaccine for fish that would be cost-effective and efficacious against the betanodavirus infection.
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Mawassi, Munir, and Valerian Dolja. Role of RNA Silencing Suppression in the Pathogenicity and Host Specificity of the Grapevine Virus A. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592114.bard.

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RNA silencing is a defense mechanism that functions against virus infection and involves sequence-specific degradation of viral RNA. Diverse RNA and DNA viruses of plants encode RNA silencing suppressors (RSSs), which, in addition to their role in viral counterdefense, were implicated in the efficient accumulation of viral RNAs, virus transport, pathogenesis, and determination of the virus host range. Despite rapidly growing understanding of the mechanisms of RNA silencing suppression, systematic analysis of the roles played by diverse RSSs in virus biology and pathology is yet to be completed. Our research was aimed at conducting such analysis for two grapevine viruses, Grapevine virus A (GVA) and Grapevine leafroll-associated virus-2 (GLRaV- 2). Our major achievements on the previous cycle of BARD funding are as follows. 1. GVA and GLRaV-2 were engineered into efficient gene expression and silencing vectors for grapevine. The efficient techniques for grapevine infection resulting in systemic expression or silencing of the recombinant genes were developed. Therefore, GVA and GLRaV-2 were rendered into powerful tools of grapevine virology and functional genomics. 2. The GVA and GLRaV-2 RSSs, p10 and p24, respectively, were identified, and their roles in viral pathogenesis were determined. In particular, we found that p10 functions in suppression and pathogenesis are genetically separable. 3. We revealed that p10 is a self-interactive protein that is targeted to the nucleus. In contrast, p24 mechanism involves binding small interfering RNAs in the cytoplasm. We have also demonstrated that p10 is relatively weak, whereas p24 is extremely strong enhancer of the viral agroinfection. 4. We found that, in addition to the dedicated RSSs, GVA and GLRaV-2 counterdefenses involve ORF1 product and leader proteases, respectively. 5. We have teamed up with Dr. Koonin and Dr. Falnes groups to study the evolution and function of the AlkB domain presents in GVA and many other plant viruses. It was demonstrated that viral AlkBs are RNA-specific demethylases thus providing critical support for the biological relevance of the novel process of AlkB-mediated RNA repair.
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Gelb, Jr., Jack, Yoram Weisman, Brian Ladman, and Rosie Meir. Identification of Avian Infectious Brochitis Virus Variant Serotypes and Subtypes by PCR Product Cycle Sequencing for the Rational Selection of Effective Vaccines. United States Department of Agriculture, December 2003. http://dx.doi.org/10.32747/2003.7586470.bard.

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Objectives 1. Determine the serotypic identities of 40 recent IBV isolates from commercial chickens raised in the USA and Israel. 2. Sequence all IBV field isolates using PCR product cycle sequencing and analyze their S 1 sequence to detennine their homology to other strains in the Genbank and EMBL databases. 3. Select vaccinal strains with the highest S 1 sequence homology to the field isolates and perform challenge of immunity studies in chickens in laboratory trials to detennine level of protection afforded by the vaccines. Background Infectious bronchitis (IB) is a common, economically important disease of the chicken. IB occurs as a respiratory form, associated with airsacculitis, condemnation, and mortality of meat-type broilers, a reproductive form responsible for egg production losses in layers and breeders, and a renal form causing high mortality in broilers and pullets. The causative agent is avian coronavirus infectious bronchitis virus (IBV). Replication of the virus' RNA genome is error-prone and mutations commonly result. A major target for mutation is the gene encoding the spike (S) envelope protein used by the virus to attach and infect the host cell. Mutations in the S gene result in antigenic changes that can lead to the emergence of variant serotypes. The S gene is able to tolerate numerous mutations without compromising the virus' ability to replicate and cause disease. An end result of the virus' "flexibility" is that many strains of IBV are capable of existing in nature. Once formed, new mutant strains, often referred to as variants, are soon subjected to immunological selection so that only the most antigenically novel variants survive in poultry populations. Many novel antigenic variant serotypes and genotypes have been isolated from commercial poultry flocks. Identification of the field isolates of IBV responsible for outbreaks is critical for selecting the appropriate strain(s) for vaccination. Reverse transcriptase polymerase chain reaction (RT-PCR) of the Sl subunit of the envelope spike glycoprotein gene has been a common method used to identify field strains, replacing other time-consuming or less precise tests. Two PCR approaches have been used for identification, restriction fragment length polymorphism (RFLP) and direct automated cycle sequence analysis of a diagnostically relevant hypervariab1e region were compared in our BARD research. Vaccination for IB, although practiced routinely in commercial flocks, is often not protective. Field isolates responsible for outbreaks may be unrelated to the strain(s) used in the vaccination program. However, vaccines may provide varying degrees of cross- protection vs. unrelated field strains so vaccination studies should be performed. Conclusions RFLP and S1 sequence analysis methods were successfully performed using the field isolates from the USA and Israel. Importantly, the S1 sequence analysis method enabled a direct comparison of the genotypes of the field strains by aligning them to sequences in public databases e.g. GenBank. Novel S1 gene sequences were identified in both USA and Israel IBVs but greater diversity was observed in the field isolates from the USA. One novel genotype, characterized in this project, Israel/720/99, is currently being considered for development as an inactivated vaccine. Vaccination with IBV strains in the US (Massachusetts, Arkansas, Delaware 072) or in Israel (Massachusetts, Holland strain) provided higher degrees of cross-protection vs. homologous than heterologous strain challenge. In many cases however, vaccination with two strains (only studies with US strains) produced reasonable cross-protection against heterologous field isolate challenge. Implications S1 sequence analysis provides numerical similarity values and phylogenetic information that can be useful, although by no means conclusive, in developing vaccine control strategies. Identification of many novel S1 genotypes of IBV in the USA is evidence that commercial flocks will be challenged today and in the future with strains unrelated to vaccines. In Israel, monitoring flocks for novel IBV field isolates should continue given the identification of Israel/720/99, and perhaps others in the future. Strains selected for vaccination of commercial flocks should induce cross- protection against unrelated genotypes. Using diverse genotypes for vaccination may result in immunity against unrelated field strains.
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Berube, Paul M., Scott M. Gifford, Bonnie Hurwitz, Bethany Jenkins, Adrian Marchetti, and Alyson E. Santoro. Roadmap Towards Communitywide Intercalibration and Standardization of Ocean Nucleic Acids ‘Omics Measurements. Woods Hole Oceanographic Institution, March 2022. http://dx.doi.org/10.1575/1912/28054.

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In January 2020, the US Ocean Carbon & Biogeochemistry (OCB) Project Office funded the Ocean Nucleic Acids 'omics Intercalibration and Standardization workshop held at the University of North Carolina in Chapel Hill. Thirty-two participants from across the US, along with guests from Canada and France, met to develop a framework for standardization and intercalibration (S&I) of ocean nucleic acid ‘omics (na’omics) approaches (i.e., amplicon sequencing, metagenomics and metatranscriptomics). During the three-day workshop, participants discussed numerous topics, including: a) sample biomass collection and nucleic acid preservation for downstream analysis, b) extraction protocols for nucleic acids, c) addition of standard reference material to nucleic acid isolation protocols, d) isolation methods unique to RNA, e) sequence library construction, and f ) integration of bioinformatic considerations. This report provides a summary of these and other topics covered during the workshop and a series of recommendations for future S&I activities for na’omics approaches.
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Lers, Amnon, and Pamela J. Green. Analysis of Small RNAs Associated with Plant Senescence. United States Department of Agriculture, March 2013. http://dx.doi.org/10.32747/2013.7593393.bard.

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Senescence is an agriculturally significant process due to its negative impact to crop yield and postharvest quality. The genetic regulatory systems controlling senescence induction and progress respond to both developmental and environmental stress signals and involve numerous gene expression changes. Knowledge about the key molecular factors which control senescence is very limited. MicroRNAs (miRNAs) are a class of small RNAs which typically function by guiding cleavage of target messenger RNAs. They have been shown to play major roles in a variety of plant processes including development, responses to environmental stresses, and senescence. The long-term goal of this work is to elucidate roles of small RNAs associated with plant senescence. The hypothesis underlying this research is that miRNA-mediated regulation makes important contributions to the senescence process in plants. Specific, original research objectives included: 1) Profiling of small RNAs from senescing plants; 2) Data Analysis and public access via a user-friendly web interface; 3) Validation of senescence-associated miRNAs and target RNAs; 4) Development of transgenic plants for functional analysis of miRNAs in Arabidopsis. Major revisions made in the research compared to the original work plan included 1) Exclusion of the planned work with tomato as recommended by the BARD review panel; 2) Performing miRNA study also in senescing Arabidopsis siliques, in addition to senescing leaves. To identify senescenceregulation of miRNAs in Arabidopsis thaliana, eight small RNA libraries were constructed and sequenced at four different stages of development and senescence from both leaves and siliques, resulting in more than 200 million genome-matched sequences. Parallel Analysis of RNA Ends (PARE) libraries, which enable the large-scale examination of miRNA-guided cleavage products, were also constructed and sequenced, resulting in over 750 million genome-matched sequences. These massive datasets lead to the identification of new miRNAs, as well as new regulation of known miRNAs and their target genes during senescence, many of which have established roles in nutrient responsiveness and cell structural integrity. In keeping with remobilization of nutrients thought to occur during senescence, many miRNAs and targets had opposite expression pattern changes between leaf and silique tissues during the progression of senescence. Taken together, these findings highlight the integral role that miRNAs may play in the remobilization of resources and alteration of cellular structure that is known to occur in senescence. Experiments were initiated for functional analysis of specific senescence-associated miRNAs and respective target genes. Transgenic Arabidopsis plants were generated in which miR408, found in this study to be significantly induced in leaf senescence, was over-expressed either constitutively or under a senescence-specific promoter. These plants are currently being characterized for any altered phenotypes. In addition T-DNA knock out mutants for various target genes identified in this research are being analyzed. This work provides insights about specific miRNAs that contribute to leaf and silique senescence. The knowledge generated may suggest new strategies to monitor and alter the progression of senescence in crops for agricultural improvement.
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Pace, Norman R. Phylogenetic Analysis of Marine Picoplankton Using Tau RNA Sequences. Fort Belvoir, VA: Defense Technical Information Center, February 1991. http://dx.doi.org/10.21236/ada254451.

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Mevarech, Moshe, Jeremy Bruenn, and Yigal Koltin. Virus Encoded Toxin of the Corn Smut Ustilago Maydis - Isolation of Receptors and Mapping Functional Domains. United States Department of Agriculture, September 1995. http://dx.doi.org/10.32747/1995.7613022.bard.

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Ustilago maydis is a fungal pathogen of maize. Some strains of U. maydis encode secreted polypeptide toxins capable of killing other susceptible strains of U. maydis. Resistance to the toxins is conferred by recessive nuclear genes. The toxins are encoded by genomic segments of resident double-strande RNA viruses. The best characterized toxin, KP6, is composed of two polypeptides, a and b, which are not covalently linked. It is encoded by P6M2 dsRNA, which has been cloned, sequenced and expressed in a variety of systems. In this study we have shown that the toxin acts on the membranes of sensitive cells and that both polypeptides are required for toxin activity. The toxin has been shown to function by creating new pores in the cell membrane and disrupting ion fluxes. The experiments performed on artificial phospholipid bilayers indicated that KP6 forms large voltage-independent, cation-selective channels. Experiments leading to the resolution of structure-function relationship of the toxin by in vitro analysis have been initiated. During the course of this research the collaboration also yielded X-ray diffracion data of the crystallized a polypeptide. The effect of the toxin on the pathogen has been shown to be receptor-mediated. A potential receptor protein, identified in membrane fractions of sensitive cells, was subjected to tryptic hydrolysis followed by amino-acid analysis. The peptides obtained were used to isolate a cDNA fragment by reverse PCR, which showed 30% sequence homology to the human HLA protein. Analysis of other toxins secreted by U. maydis, KP1 and KP4, have demonstrated that, unlike KP6, they are composed of a single polypeptide. Finally, KP6 has been expressed in transgenic tobacco plants, indicating that accurate processing by Kex2p-like activity occurs in plants as well. Using tobacco as a model system, we determined that active antifungal toxins can be synthesized and targeted to the outside of transgenic plant cells. If this methodology can be applied to other agronomically crop species, then U. maydis toxins may provide a novel means for biological control of pathogenic fungi.
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Grumet, R., J. Burger, Y. Tadmor, A. Gur, C. Barry, A. Schäffer, and M. Petreikov. Cucumis fruit surface biology: Genetic analysis of fruit exocarp features in melon (C. melo) and cucumber (C. sativus). Israel: United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134155.bard.

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The fruit surface (exocarp) is a unique tissue with multiple roles influencing fruit growth and development, disease susceptibility, crop yield, post-harvest treatments, shipping and storage quality, and food safety. Furthermore, highly visible exocarp traits are the consumer's first exposure to the fruit, serving to identify fruit type, variety, attractiveness, and market value. Cucurbit fruit, including the closely related Cucumis species, melon (C. melo) and cucumber (C. sativus), exhibit tremendous diversity for fruit surface properties that are not present in model species. In this project, we identified genetic factors influencing Cucumis fruit surface morphology with respect to important quality determinants such as exocarp and flesh color, cuticle deposition, and surface netting. We employed a combination of approaches including: genome-wide association studies (GWAS) utilizing an extensive melon population and the U.S. Plant Introduction (PI) collection for cucumber to identify genomic regions associated with natural variation in fruit surface traits; bulked segregant RNA-seq (BSR-seq) analysis of bi-parental F2:3 or RIL (recombinant inbred line) populations to genomic regions and candidate genes segregating for fruit surface traits; and comparison of syntenic genomic regions and identification of homologous candidate genes. Candidate genes were examined for sequence and/or expression differences during fruit development that correspond with phenotypic differences. Primary outcomes of the work included identification of candidate genes influencing cuticle deposition, epidermal cell structure, surface netting, and intensity of rind and flesh color. Parallel studies identified mutations within the cucumber and melon homologs of the transcription factor WIN1 (WAX INDUCER1) as a significant factor influencing these surface properties. Additional QTL (quantitative trait loci) were identified in both species, and candidate genes in melon include a novel beta-glucosidase involved in lignin production and an integral membrane protein potentially involved in cuticle metabolism. Genetic resources and biochemical approaches have been developed to study cuticle and wax deposition in both species: segregating populations of melon were developed and sequenced for bulked segregant analysis and samples collected for metabolic analysis; an isolation procedure was developed for lipid droplets from cucumber peel and metabolomic analyses have been initiated. Genetic studies in melon identified mutations in a candidate gene (APRR2), associated with light immature rind, and further indicated that this gene is also associated with color intensity of both mature rinds and flesh, making it a good target for breeding. GWAS studies utilizing the cucumber core diversity population are being performed to identify additional sources of variation for fruit surface properties, map QTL, and examine for synteny with melon. Collectively these studies identified genetic regions associated with important quality traits and contributed to our understanding of underlying biological processes associated with fruit surface development. Knowledge of genetic control of these characteristics can facilitate more efficient breeding for important fruit surface traits.
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