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Registros recuperados: 9
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Adaptive evolution of the vertebrate skeletal muscle sodium channel Genet. Mol. Biol.
Lu,Jian; Zheng,Jianzhou; Xu,Qinggang; Chen,Keping; Zhang,Chiyu.
Tetrodotoxin (TTX) is a highly potent neurotoxin that blocks the action potential by selectively binding to voltage-gated sodium channels (Na v). The skeletal muscle Na v (Na v1.4) channels in most pufferfish species and certain North American garter snakes are resistant to TTX, whereas in most mammals they are TTX-sensitive. It still remains unclear as to whether the difference in this sensitivity among the various vertebrate species can be associated with adaptive evolution. In this study, we investigated the adaptive evolution of the vertebrate Na v1.4 channels. By means of the CODEML program of the PAML 4.3 package, the lineages of both garter snakes and pufferfishes were denoted to be under positive selection. The positively selected sites identified...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Skeletal muscle voltage-gated Na (Na v1.4) channel; Tetrodotoxin (TTX); Positive selection; Pufferfish; Garter snake.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000200026
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Evolution of DNMT2 in drosophilids: Evidence for positive and purifying selection and insights into new protein (pathways) interactions Genet. Mol. Biol.
Vieira,Gilberto Cavalheiro; D’Ávila,Marícia Fantinel; Zanini,Rebeca; Deprá,Maríndia; da Silva Valente,Vera Lúcia.
Abstract The DNA methyltransferase 2 (DNMT2) protein is the most conserved member of the DNA methyltransferase family. Nevertheless, its substrate specificity is still controversial and elusive. The genomic role and determinants of DNA methylation are poorly understood in invertebrates, and several mechanisms and associations are suggested. In Drosophila, the only known DNMT gene is Dnmt2. Here we present our findings from a wide search for Dnmt2 homologs in 68 species of Drosophilidae. We investigated its molecular evolution, and in our phylogenetic analyses the main clades of Drosophilidae species were recovered. We tested whether the Dnmt2 has evolved neutrally or under positive selection along the subgenera Drosophila and Sophophora and investigated...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Drosophila; Dnmt2; Positive selection; Epigenetic; Positive-destabilizing selection.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000200215
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Homo sapiens, Homo neanderthalensis and the Denisova specimen: new insights on their evolutionary histories using whole-genome comparisons Genet. Mol. Biol.
Paixão-Côrtes,Vanessa Rodrigues; Viscardi,Lucas Henrique; Salzano,Francisco Mauro; Hünemeier,Tábita; Bortolini,Maria Cátira.
After a brief review of the most recent findings in the study of human evolution, an extensive comparison of the complete genomes of our nearest relative, the chimpanzee (Pan troglodytes), of extant Homo sapiens, archaic Homo neanderthalensis and the Denisova specimen were made. The focus was on non-synonymous mutations, which consequently had an impact on protein levels and these changes were classified according to degree of effect. A total of 10,447 non-synonymous substitutions were found in which the derived allele is fixed or nearly fixed in humans as compared to chimpanzee. Their most frequent location was on chromosome 21. Their presence was then searched in the two archaic genomes. Mutations in 381 genes would imply radical amino acid changes, with...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Human evolution; Comparative genomics; Positive selection; Neanderthal; Denisova.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000600003
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Molecular evolution and functional divergence of alcohol dehydrogenases in animals, fungi and plants Genet. Mol. Biol.
Thompson,Claudia E.; Freitas,Loreta B.; Salzano,Francisco M..
Abstract Alcohol dehydrogenases belong to the large superfamily of medium-chain dehydrogenases/reductases, which occur throughout the biological world and are involved with many important metabolic routes. We considered the phylogeny of 190 ADH sequences of animals, fungi, and plants. Non-class III Caenorhabditis elegans ADHs were seen closely related to tetrameric fungal ADHs. ADH3 forms a sister group to amphibian, reptilian, avian and mammalian non-class III ADHs. In fishes, two main forms are identified: ADH1 and ADH3, whereas in amphibians there is a new ADH form (ADH8). ADH2 is found in Mammalia and Aves, and they formed a monophyletic group. Additionally, mammalian ADH4 seems to result from an ADH1 duplication, while in Fungi, ADH formed clusters...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Glycolytic proteins; Molecular evolution; Alcohol dehydrogenase; Functional diversification; Positive selection.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000200341
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Molecular evolution of the ent-kaurenoic acid oxidase gene in Oryzeae Genet. Mol. Biol.
Yang,Yanhua; Chen,Keping.
We surveyed the substitution patterns in the ent-kaurenoic acid oxidase (KAO) gene in 11 species of Oryzeae with an outgroup in the Ehrhartoidaea. The synonymous and non-synonymous substitution rates showed a high positive correlation with each other, but were negatively correlated with codon usage bias and GC content at third codon positions. The substitution rate was heterogenous among lineages. Likelihood-ratio tests showed that the non-synonymous/synonymous rate ratio changed significantly among lineages. Site-specific models provided no evidence for positive selection of particular amino acid sites in any codon of the KAO gene. This finding suggested that the significant rate heterogeneity among some lineages may have been caused by variability in the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Codon usage bias; Ent-kaurenoic acid oxidase (KAO); Positive selection; Rate heterogeneity; Substitution rate.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000300011
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Oxytocin and arginine vasopressin systems in the domestication process Genet. Mol. Biol.
Fam,Bibiana S.O.; Paré,Pamela; Felkl,Aline B.; Vargas-Pinilla,Pedro; Paixão-Côrtes,Vanessa R.; Viscardi,Lucas Henriques; Bortolini,Maria Cátira.
Abstract Domestication is of unquestionable importance to the technological revolution that has given rise to modern human societies. In this study, we analyzed the DNA and protein sequences of six genes of the oxytocin and arginine vasopressin systems (OXT-OXTR; AVP-AVPR1a, AVPR1b and AVPR2) in 40 placental mammals. These systems play an important role in the control of physiology and behavior. According to our analyses, neutrality does not explain the pattern of molecular evolution found in some of these genes. We observed specific sites under positive selection in AVPR1b (ω = 1.429, p = 0.001) and AVPR2 (ω= 1.49, p = 0.001), suggesting that they could be involved in behavior and physiological changes, including those related to the domestication...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Oxytocin and receptors; Vasopressin and receptors; Animal domestication; Molecular evolution; Positive selection.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000200235
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Patterns of molecular evolution in pathogenesis-related proteins Genet. Mol. Biol.
Scherer,Nicole M.; Thompson,Claudia E.; Freitas,Loreta B.; Bonatto,Sandro L.; Salzano,Francisco M..
The genes encoding 13 classes of pathogenesis-related (PR) proteins were examined for positive selection using maximum-likelihood (ML) models of codon substitution. The study involved 194 sequences from 54 species belonging to 37 genera. Although the sizes of the sequences examined varied from 237 bp for PR12 to 1,110 bp for PR7, most classes (9 out of 13) contained sequences made up of more than 400 nucleotides. Signs of positive selection were obtained for sites in PR proteins 4, 6, 8, 9 and 15 using an ML-based Bayesian method and likelihood ratio tests. These results confirm the importance of positive selection in proteins related to defense mechanisms already observed in a wide array of organisms.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Pathogenesis-related proteins; PRs; Molecular variability; Positive selection; Maximum-likelihood methods.
Ano: 2005 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572005000500001
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Positive selection, molecular recombination structure and phylogenetic reconstruction of members of the family Tombusviridae: implication in virus taxonomy Genet. Mol. Biol.
Boulila,Moncef.
A detailed study of putative recombination events and their evolution frequency in the whole genome of the currently known members of the family Tombusviridae, comprising 79 accessions retrieved from the international databases, was carried out by using the RECCO and RDP version 3.31β algorithms. The first program allowed the detection of potential recombination sites in seven out of eight virus genera (Aureusvirus, Avenavirus, Carmovirus, Dianthovirus, Necrovirus, Panicovirus, and Tombusvirus), the second program provided the same results except for genus Dianthovirus. On the other hand, both methods failed to detect recombination breakpoints in the genome of members of genus Machlomovirus. Furthermore, based on Fisher's Exact Test of Neutrality, positive...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bioinformatics; Phylogeny; Recombination; Positive selection; Tombusviridae; Sequence; Taxonomy.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000400018
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POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes. Repositório Alice
HONGO, J. A.; CASTRO, G. M. de.; CINTRA, L. C.; ZERLOTINI, A.; LOBO, F. P..
Abstract: Background: Detection of genes evolving under positive Darwinian evolution in genome-scale data is nowadays a prevailing strategy in comparative genomics studies to identify genes potentially involved in adaptation processes. Despite the large number of studies aiming to detect and contextualize such gene sets, there is virtually no software available to perform this task in a general, automatic, large-scale and reliable manner. This certainly occurs due to the computational challenges involved in this task, such as the appropriate modeling of data under analysis, the computation time to perform several of the required steps when dealing with genome-scale data and the highly error-prone nature of the sequence and alignment data structures needed...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Potion; Evolução Darwiniana; Comparative genomics; Positive selection; Gene; Fenótipo; Pesquisa; Genomics; Phylogeny; Genes; Genome.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1027912
Registros recuperados: 9
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