Academic literature on the topic 'Non-synonymous substitutions'
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Journal articles on the topic "Non-synonymous substitutions"
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Stenger, Drake C., Brock A. Young, and Roy French. "Random mutagenesis of wheat streak mosaic virus HC-Pro: non-infectious interfering mutations in a gene dispensable for systemic infection of plants." Journal of General Virology 87, no. 9 (September 1, 2006): 2741–47. http://dx.doi.org/10.1099/vir.0.81933-0.
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Mutations within the HC-Pro coding region of Wheat streak mosaic virus (WSMV) were introduced by misincorporation during PCR and evaluated for phenotype within the context of an infectious clone. Nine synonymous substitutions and 15 of 25 non-synonymous substitutions had no phenotypic effect. Four non-synonymous substitutions, including one that reverted consistently to wild type, resulted in attenuated systemic infection. Six non-synonymous substitutions and one nonsense substitution abolished systemic infectivity. Mutants bearing the GUS reporter gene were evaluated for the ability to establish primary infection foci. All attenuated mutants and two systemic infection-deficient mutants produced localized regions of GUS expression on inoculated leaves 3 days post-inoculation. In vitro assays revealed that mutants able to establish infection foci retained HC-Pro proteinase activity. Among mutants unable to establish infection foci, HC-Pro proteinase activity was retained, reduced or absent. As a complete HC-Pro deletion mutant can infect plants systemically, certain substitutions in this dispensable gene probably prevented infection of WSMV via interference.
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Socha, W., J. Rola, and J. F. Żmudziński. "Variability of non-structural proteins of equine arteritis virus during persistent infection of the stallion." Polish Journal of Veterinary Sciences 18, no. 2 (June 1, 2015): 255–59. http://dx.doi.org/10.1515/pjvs-2015-0033.
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AbstractThe genetic stability of ORF1a encoding non-structural proteins nsp1, nsp2, nsp3 and nsp4 of equine arteritis virus (EAV) has been analysed for nearly seven years in a persistently infected stallion of the Malopolska breed. Between November 2004 and June 2011, 11 semen samples were collected. Viral RNA extracted from semen of this carrier stallion was amplified, sequenced and compared with the sequences of the other known strains of EAV. Sequence analysis of ORF1a showed 84 synonymous and 16 non-synonymous mutations. The most variable part of ORF1a was the region encoding nsp2 protein with 13 non-synonymous substitutions. The degree of amino acid identity between isolates ranged from 98.91 to 100%. Only single non-synonymous mutations were detected in nsp1 (one substitution) and nsp4 (two substitutions). The most stable was nsp3 in which no amino acid substitutions were observed during the whole period of observation.
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dos Reis, Mario. "How to calculate the non-synonymous to synonymous rate ratio of protein-coding genes under the Fisher–Wright mutation–selection framework." Biology Letters 11, no. 4 (April 2015): 20141031. http://dx.doi.org/10.1098/rsbl.2014.1031.
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First principles of population genetics are used to obtain formulae relating the non-synonymous to synonymous substitution rate ratio to the selection coefficients acting at codon sites in protein-coding genes. Two theoretical cases are discussed and two examples from real data (a chloroplast gene and a virus polymerase) are given. The formulae give much insight into the dynamics of non-synonymous substitutions and may inform the development of methods to detect adaptive evolution.
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Woolfit, Megan. "Effective population size and the rate and pattern of nucleotide substitutions." Biology Letters 5, no. 3 (April 8, 2009): 417–20. http://dx.doi.org/10.1098/rsbl.2009.0155.
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Both the overall rate of nucleotide substitution and the relative proportions of synonymous and non-synonymous substitutions are predicted to vary between species that differ in effective population size ( N e ). Our understanding of the genetic processes underlying these lineage-specific differences in molecular evolution is still developing. Empirical analyses indicate that variation in substitution rates and patterns caused by differences in N e is often substantial, however, and must be accounted for in analyses of molecular evolution.
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Llopart, Ana, and Montserrat Aguadé. "Synonymous Rates at the RpII215 Gene of Drosophila: Variation Among Species and Across the Coding Region." Genetics 152, no. 1 (May 1, 1999): 269–80. http://dx.doi.org/10.1093/genetics/152.1.269.
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Abstract The region encompassing the RpII215 gene that encodes the largest component of the RNA polymerase II complex (1889 amino acids) has been sequenced in Drosophila subobscura, D. madeirensis, D. guanche, and D. pseudoobscura. Nonsynonymous divergence estimates (Ka) indicate that this gene has a very low rate of amino acid replacements. Given its low Ka and constitutive expression, synonymous substitution rates are, however, unexpectedly high. Sequence comparisons have allowed the molecular clock hypothesis to be tested. D. guanche is an insular species and it is therefore expected to have a reduced effective size relative to D. subobscura. The significantly higher rate of synonymous substitutions detected in the D. guanche lineage could be explained if synonymous mutations behave as nearly neutral. Significant departure from the molecular clock hypothesis for synonymous and nonsynonymous substitutions was detected when comparing the D. subobscura, D. pseudoobscura, and D. melanogaster lineages. Codon bias and synonymous divergence between D. subobscura and D. melanogaster were negatively correlated across the RpII215 coding region, which indicates that selection coefficients for synonymous mutations vary across the gene. The C-terminal domain (CTD) of the RpII215 protein is structurally and functionally differentiated from the rest of the protein. Synonymous substitution rates were significantly different in both regions, which strongly indicates that synonymous mutations in the CTD and in the non-CTD regions are under detectably different selection coefficients.
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Kils-Hütten, Laurens, Rémi Cheynier, Simon Wain-Hobson, and Andreas Meyerhans. "Phylogenetic reconstruction of intrapatient evolution of human immunodeficiency virus type 1: predominance of drift and purifying selection." Journal of General Virology 82, no. 7 (July 1, 2001): 1621–27. http://dx.doi.org/10.1099/0022-1317-82-7-1621.
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The intra-host evolution of 73 human immunodeficiency virus type 1 quasispecies was analysed by split decomposition analysis. Non-synonymous and synonymous nucleotide substitutions were counted along the shortest path connecting all sequences and compared with the numbers expected under the assumption of a random model of mutation. For the majority of substitutions, drift and negative selection seemed to prevail.
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Belinky, Frida, Ishan Ganguly, Eugenia Poliakov, Vyacheslav Yurchenko, and Igor B. Rogozin. "Analysis of Stop Codons within Prokaryotic Protein-Coding Genes Suggests Frequent Readthrough Events." International Journal of Molecular Sciences 22, no. 4 (February 14, 2021): 1876. http://dx.doi.org/10.3390/ijms22041876.
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Nonsense mutations turn a coding (sense) codon into an in-frame stop codon that is assumed to result in a truncated protein product. Thus, nonsense substitutions are the hallmark of pseudogenes and are used to identify them. Here we show that in-frame stop codons within bacterial protein-coding genes are widespread. Their evolutionary conservation suggests that many of them are not pseudogenes, since they maintain dN/dS values (ratios of substitution rates at non-synonymous and synonymous sites) significantly lower than 1 (this is a signature of purifying selection in protein-coding regions). We also found that double substitutions in codons—where an intermediate step is a nonsense substitution—show a higher rate of evolution compared to null models, indicating that a stop codon was introduced and then changed back to sense via positive selection. This further supports the notion that nonsense substitutions in bacteria are relatively common and do not necessarily cause pseudogenization. In-frame stop codons may be an important mechanism of regulation: Such codons are likely to cause a substantial decrease of protein expression levels.
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Lehad, Arezki, Ilhem Selmi, Meriem Louanchi, Mouni Aitouada, and Naima Mahfoudhi. "Survey and Genetic Diversity of Grapevine Leafroll Associated Virus 2 in Algeria." International Journal of Phytopathology 4, no. 1 (May 2, 2015): 35–42. http://dx.doi.org/10.33687/phytopath.004.01.1074.
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Vineyards in western and center regions of Algeria were surveyed for the Grapevine leafroll-associated virus 2 (GLRaV-2). Analyses by DAS-ELISA and Reverse Transcription Polymerase Chain Reaction (RT-PCR) reveal 15, 8% prevalence. The genetic diversity of the GLRaV-2 population was studied by phylogenetic analyses of the HSP70h gene region of seven samples sequenced in this study and other sequences downloaded from GenBank. Results reveal segregation of the GLRav-2 population into six distinct groups. An estimation of the ratio of non-synonymous substitutions per non-synonymous site to synonymous substitutions per synonymous site indicated that HSP70h gene evolve under positive selection. Similarity plot constructed with representative sequence from each group confirmed previous results. All Algerian isolates belong to group PN. As far as we know, this is the first characterization of GLRaV-2 isolates from Algeria.
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Yakubu, Abdulmojeed, Adebowale Salako, Donato de, and Ikhide Imumorin. "Application of computational algorithms to assess the functionality of non-synonymous substitutions in MHC DRB gene of Nigerian goats." Genetika 49, no. 1 (2017): 63–76. http://dx.doi.org/10.2298/gensr1701063y.
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The Major Histocompatibility Complex (MHC) contains highly variable multi-gene families, which play a key role in the adaptive immune response within vertebrates. Among the Capra MHC class II genes, the expressed DRB locus is highly polymorphic, particularly in exon 2, which encodes the antigen-binding site. Models of variable non-synonymous/synonymous rate ratios among sites may provide important insights into functional constraints at different amino acid sites and may be used to detect sites under positive selection. Many non-synonymous single nucleotide polymorphisms (nsSNPs) at the DRB locus in goats are suspected to impact protein function. This study, therefore, aimed at comparing the efficiency of six computational approaches to predict the likelihood of a particular non-synonymous (amino acid change) coding SNP to cause a functional impact on the protein. This involved the use of PANTHER, SNAP, SIFT, PolyPhen-2, PROVEAN and nsSNPAnalyzer bioinformatics analytical tools in detecting harmful and beneficial effects at H57G, Y89R, V104D and Y112I substitutions in the peptide binding region of the DRB gene of Nigerian goats. The results from PANTHER analysis revealed that H57G, Y89R and Y112I substitutions (Pdeleterious= 0.113, 0.204 and 0.472, respectively) were beneficial; while that of V104D was deleterious (Pdeleterious= 0.756), an indication that it was non-neutral. As regards the SNAP approach, H57G and Y89R substitutions were returned neutral with expected accuracy of 53 and 69%, respectively while V104D and Y112I substitutions were harmful. H57G and Y89R substitutions were also found harmless in the SIFT analysis. However, only H57G (PROVEAN) and V104D (nsSNPAnalyzer) amino acid substitutions were found to be beneficial. Interestingly, the predicted 3D structures of both native and mutant DRB protein appeared similar as validated by Ramachandran plots. The consensus reached by PANTHER, SNAP, SIFT and PolyPhen-2 approaches on the neutrality especially of H57G (PROVEAN inclusive) and Y89R amino acid substitutions may be used in search of disease resistant genotypes at the DRB locus of Nigerian goats.
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Moaeen-Ud-Din, M., G. Bilal, and James Reecy. "Evolution of hypothalamus-pituitary growth axis among fish, amphibian, birds and mammals." Genetika 47, no. 2 (2015): 665–77. http://dx.doi.org/10.2298/gensr1502665m.
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Hypothalamus-pituitary growth axis (HP growth axis) regulates animal growth and development in pre-natal and post natal life governed by many factors. However, until recently, the evolutionary history of this axis among lineages is not understood. Aim of the present study was to understand the major events in evolution and evolutionary history and trend of HP growth axis. The diversity among Homo sapience, Mus musculus, Rattus norvegicus, Gallus gallus, Danio rerio and Xenopus laevis was determined for genes involved in HP growth axis in current study. Sequences of HP growth axis genes were retrieved from NCBI (http://www.ncbi.nlm.nih.gov/). Nucleotide diversity using Kimura?s two-parameter method; codon-based test of positive selection using the Nei-Gojobori; equality of evolutionary rate with Tajima's relative rate test and phylogenetic history using the RelTime method were estimated in MEGA6. Estimates of the coefficients of evolutionary differentiation based on nucleotides and amino acids substitution patterns of HP growth axis genes showed contrasting evolutionary patterns among the lineages. The results demonstrated that although these genes might have crucial functional roles in each of the species, however, their sequence divergence did not necessarily reflect similar molecular evolution among the species. Codon-based test of positive selection revealed that Human vs Mouse, Chicken vs Rat, Human vs Rat and Mouse vs Rat had similar and higher non synonymous substitutions (P > 0.05). Higher rate of non-synonymous substitutions at similar orthologs level among species indicated a similar positive selection pressure in these species. Results for relative rate test assessed with the chi-squared test showed difference on unique mutations among lineages at synonymous and non synonymous sites except Chicken vs Mouse, Human vs Mouse, Chicken vs Rat, Human vs Rat and Mouse vs Rat. This indicated that the mutagenic process that generates substitutional mutation is taking place at approximately the same rate at synonymous and non-synonymous sites these lineages. Moreover, despite of common ancestry, our results indicate a different divergent time among genes of these species. This is the first demonstration that variable rates of molecular evolution may be present within HP growth axis genes among different species. This difference could be of interest for comparative genomics analysis and physiological genes functions identification among tho comparative genomics, evolution rate, HP growth axis, positive selection se species whose HP growth axis is not explored.
Dissertations / Theses on the topic "Non-synonymous substitutions"
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Tzeng, Yun-Huei, and 曾雲輝. "Methods for Estimating Rates of Synonymous and Non-synonymous Nucleotide Substitutions and Its Application." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/11559125911569234020.
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博士國立清華大學
數學系
93
There are three chapters in this dissertation and I focus on the comparison and modification of methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions. In chapter 1, I describe the background and terminology of evolutionary change in nucleotide sequences. I also introduce the derivations of two methods for estimating the synonymous and nonsynonymous substitution rates (Ks and Ka) -- Li-Wu-Luo (1985), Li (1993) and Pamilo and Bianchi (1993). In chapter 2, I compared three frequently used methods for estimating the synonymous and nonsynonymous substitution rates (Ks and Ka) -- Li-Wu-Luo (1985), Li (1993) and Pamilo and Bianchi (1993), and Goldman and Yang (1994) as in the PAML package. These methods were evaluated and compared for their accuracies and are denoted by LWL85, LPB93, and GY94, respectively. After comparing their performance, I proposed a correction to improve the accuracies of LWL85 and LPB93 and a modification method, denoted by M-LWL85. In chapter 3, I describe the comparative analysis of the receptor-like kinase family in Arabidopsis thaliana and Rice. This is an application of estimating Ka and Ks in the comparison between different species.
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Wagner, Günter P., Kazuhiko Takahashi, Vincent Lynch, Sonja J. Prohaska, Claudia Fried, Peter F. Stadler, and Chris Amemiya. "Molecular Evolution of Duplicated Ray Finned Fish HoxA Clusters: Increased Synonymous Substitution Rate and Asymmetrical Co-divergence of Coding and Non-coding Sequences." 2005. https://ul.qucosa.de/id/qucosa%3A31898.
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In this study the molecular evolution of duplicated HoxA genes in zebrafish and fugu has been investigated. All 18 duplicated HoxA genes studied have a higher non-synonymous substitution rate than the corresponding genes in either bichir or paddlefish, where these genes are not duplicated. The higher rate of evolution is not due solely to a higher non-synonymous-to-synonymous rate ratio but to an increase in both the non-synonymous as well as the synonymous substitution rate. The synonymous rate increase can be explained by a change in base composition, codon usage, or mutation rate. We found no changes in nucleotide composition or codon bias. Thus, we suggest that the HoxA genes may experience an increased mutation rate following cluster duplication. In the non-Hox nuclear gene RAG1 only an increase in non-synonymous substitutions could be detected, suggesting that the increased mutation rate is specific to duplicated Hox clusters and might be related to the structural instability of Hox clusters following duplication. The divergence among paralog genes tends to be asymmetric, with one paralog diverging faster than the other. In fugu, all b-paralogs diverge faster than the a-paralogs, while in zebrafish Hoxa-13a diverges faster. This asymmetry corresponds to the asymmetry in the divergence rate of conserved non-coding sequences, i.e., putative cis-regulatory elements. These results suggest that the 5′ HoxA genes in the same cluster belong to a co-evolutionary unit in which genes have a tendency to diverge together.
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Mitterboeck, T. Fatima. "Consequences of Insect Flight Loss for Molecular Evolutionary Rates and Diversification." Thesis, 2012. http://hdl.handle.net/10214/3679.
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This thesis investigates the molecular evolutionary and macroevolutionary consequences of flight loss in insects. Chapter 2 tests the hypothesis that flightless groups have smaller effective population sizes than related flighted groups, expected to result in a consistent pattern of increased non-synonymous to synonymous ratios in flightless lineages due to the greater effect of genetic drift in smaller populations. Chapter 3 tests the hypothesis that reduced dispersal and species-level traits such as range size associated with flightlessness increase extinction rates, which over the long term will counteract increased speciation rates in flightless lineages, leading to lower net diversification. The wide-spread loss of flight in insects has led to increased molecular evolutionary rates and is associated with decreased long-term net diversification. I demonstrate that the fundamental trait of dispersal ability has shaped two forms of diversity—molecular and species—in the largest group of animals, and that microevolutionary and macroevolutionary patterns do not necessarily mirror each other.Generously funded by NSERC with a Canada Graduate Scholarship and the Government of Ontario with an Ontario Graduate Scholarship to T. Fatima Mitterboeck; NSERC with a Discovery Grant to Dr. Sarah J. Adamowicz
Book chapters on the topic "Non-synonymous substitutions"
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Bennington, Geoffrey. "Afterword." In The Marrano Specter. Fordham University Press, 2017. http://dx.doi.org/10.5422/fordham/9780823277674.003.0010.
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“Marrano” enters into the non-finite sequence of “non-synonymous substitutions,” becoming one of the “quasi-transcendentals” (alongside trace, writing, pharmakon and the rest) that hold Derrida’s work together in its somewhat gathered dispersion, but that entail that no one of those terms (not even “quasi-transcendental”) could ever become the proper name for what Derrida is endlessly trying to write.
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Schulze-Bahr, Eric. "Basic principles of genetic disease." In ESC CardioMed, 669–71. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198784906.003.0148.
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The human genome consists of approximately 3 billion (3 × 109) base pairs of DNA (around 20,000 genes), organized as 23 chromosomes (diploid parental set), and a small mitochondrial genome (37 genes, including 13 proteins; 16,589 base pairs) of maternal origin. Most human genetic variation is natural, that is, common or rare (minor allele frequency >0.1%) and does not cause disease—apart from every true disease-causing (bona fide) mutation each individual genome harbours more than 3.5 million single nucleotide variants (including >10,000 non-synonymous changes causing amino acid substitutions) and 200–300 large structural or copy number variants (insertions/deletions, up to several thousands of base-pairs) that are non-disease-causing variations and scattered throughout coding and non-coding genomic regions.