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https://www.readbyqxmd.com/read/25762239/physicochemical-evolution-and-molecular-adaptation-of-the-cetacean-osmoregulation-related-gene-ut-a2-and-implications-for-functional-studies
#1
Jingzhen Wang, Xueying Yu, Bo Hu, Jinsong Zheng, Wuhan Xiao, Yujiang Hao, Wenhua Liu, Ding Wang
Cetaceans have an enigmatic evolutionary history of re-invading aquatic habitats. One of their essential adaptabilities that has enabled this process is their homeostatic strategy adjustment. Here, we investigated the physicochemical evolution and molecular adaptation of the cetacean urea transporter UT-A2, which plays an important role in urine concentration and water homeostasis. First, we cloned UT-A2 from the freshwater Yangtze finless porpoise, after which bioinformatics analyses were conducted based on available datasets (including freshwater baiji and marine toothed and baleen whales) using MEGA, PAML, DataMonkey, TreeSAAP and Consurf...
2015: Scientific Reports
https://www.readbyqxmd.com/read/25329307/impact_s-integrated-multiprogram-platform-to-analyze-and-combine-tests-of-selection
#2
Emanuel Maldonado, Kartik Sunagar, Daniela Almeida, Vitor Vasconcelos, Agostinho Antunes
Among the major goals of research in evolutionary biology are the identification of genes targeted by natural selection and understanding how various regimes of evolution affect the fitness of an organism. In particular, adaptive evolution enables organisms to adapt to changing ecological factors such as diet, temperature, habitat, predatory pressures and prey abundance. An integrative approach is crucial for the identification of non-synonymous mutations that introduce radical changes in protein biochemistry and thus in turn influence the structure and function of proteins...
2014: PloS One
https://www.readbyqxmd.com/read/24085456/molecular-evolution-and-adaptation-of-the-mitochondrial-cytochrome-b-gene-in-the-subgenus-martes
#3
B Li, B Malyarchuk, X B He, M Derenko
Martes species represent a typical example of rapid evolutionary radiation and a recent speciation event. To identify regions of the genome that experienced adaptive evolution, which might provide clues to their functional importance and may be informative about the features that make each species unique, we sought evidence of molecular adaptation in the mitochondrial DNA (mtDNA) cytochrome b gene in the subgenus Martes. Complete sequences of the cytochrome b gene were obtained from 87 samples, including 49 sables, 28 pine martens, and 10 stone martens, and were combined with mtDNA sequences of other true martens, such as M...
2013: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/21954619/-adaptive-intraspecific-divergence-an-example-using-the-animal-cytochrome-b-gene
#4
B A Maliarchuk
The topologies of phylogenetic trees characterized by a high level of intraspecific divergence between the phylogenetic DNA groups (clades) are often explained in terms of the theory of Pleistocene refugia. To elucidate the issue of the adaptive role of intraspecific divergence, the changes in the physicochemical properties of amino acids in the course ofcladogenesis (MM01 model of the TreeSAAP 3.2 package) were analyzed in this work using as an example the nucleotide sequences of the cytochrome b gene in some species of northern animals (lemmings, redbacked voles, chipmunks, flying squirrels, ermines)...
August 2011: Genetika
https://www.readbyqxmd.com/read/21779385/rise-of-the-earliest-tetrapods-an-early-devonian-origin-from-marine-environment
#5
David George, Alain Blieck
Tetrapod fossil tracks are known from the Middle Devonian (Eifelian at ca. 397 million years ago--MYA), and their earliest bony remains from the Upper Devonian (Frasnian at 375-385 MYA). Tetrapods are now generally considered to have colonized land during the Carboniferous (i.e., after 359 MYA), which is considered to be one of the major events in the history of life. Our analysis on tetrapod evolution was performed using molecular data consisting of 13 proteins from 17 species and different paleontological data...
2011: PloS One
https://www.readbyqxmd.com/read/20223735/assessing-and-improving-the-accuracy-of-detecting-protein-adaptation-with-the-treesaap-analytical-software
#6
David A McClellan, David D Ellison
TreeSAAP has been used in a variety of protein studies for detecting adaptation in terms of the physicochemical properties involved in amino acid replacement. The accuracy of TreeSAAP was here tested using simulated protein-coding DNA data. A sampling of 1402 simulated amino acid replacements resulted in a default accuracy of 81.1%, with most properties exhibiting >90% accuracy. More than half of the false-positive results were traced to just 11 of the 180 possible single-step amino acid exchanges. Overall accuracy increased as the number of magnitude partitions used in the analysis decreased...
2010: International Journal of Bioinformatics Research and Applications
https://www.readbyqxmd.com/read/20162021/phylogenetics-applied-to-genotype-phenotype-association-and-selection-analyses-with-sequence-data-from-angptl4-in-humans
#7
Taylor J Maxwell, Matthew L Bendall, Jeffrey Staples, Todd Jarvis, Keith A Crandall
Genotype/phenotype association analyses (Treescan) with plasma lipid levels and functional site prediction methods (TreeSAAP and PolyPhen) were performed using sequence data for ANGPTL4 from 3,551 patients in the Dallas Heart Study. Biological assays of rare variants in phenotypic tails and results from a Treescan analysis were used as "known" variants to assess the site prediction abilities of PolyPhen and TreeSAAP. The E40K variant in European Americans and the R278Q variant in African Americans were significantly associated with multiple lipid phenotypes...
2010: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/19503808/evolutionary-pressure-on-mitochondrial-cytochrome-b-is-consistent-with-a-role-of-cytbi7t-affecting-longevity-during-caloric-restriction
#8
Wesley A Beckstead, Mark T W Ebbert, Mark J Rowe, David A McClellan
BACKGROUND: Metabolism of energy nutrients by the mitochondrial electron transport chain (ETC) is implicated in the aging process. Polymorphisms in core ETC proteins may have an effect on longevity. Here we investigate the cytochrome b (cytb) polymorphism at amino acid 7 (cytbI7T) that distinguishes human mitochondrial haplogroup H from haplogroup U. PRINCIPAL FINDINGS: We compared longevity of individuals in these two haplogroups during historical extremes of caloric intake...
2009: PloS One
https://www.readbyqxmd.com/read/18048316/evolutionary-selective-pressure-on-three-mitochondrial-snps-is-consistent-with-their-influence-on-metabolic-efficiency-in-pima-indians
#9
Srikar Chamala, Wesley A Beckstead, Mark J Rowe, David A McClellan
We investigated whether the effect of evolutionary selection on three recent Single Nucleotide Polymorphisms (SNPs) in the mitochondrial sub-haplogroups of Pima Indians is consistent with their effects on metabolic efficiency. The mitochondrial SNPs impact metabolic rate and respiratory quotient, and may be adaptations to caloric restriction in a desert habitat. Using TreeSAAP software, we examined evolutionary selection in 107 mammalian species at these SNPs, characterising the biochemical shifts produced by the amino acid substitutions...
2007: International Journal of Bioinformatics Research and Applications
https://www.readbyqxmd.com/read/18048313/pharmacogenomics-analysing-snps-in-the-cyp2d6-gene-using-amino-acid-properties
#10
Mark T W Ebbert, Wesley A Beckstead, Timothy D O'Connor, Mark J Clement, David A McClellan
The CYP2D6 gene is responsible for metabolising a large portion of the commonly prescribed drugs. Because of its importance, various approaches have been taken to analyse CYP2D6 and Single Nucleotide Polymorphisms (SNPs) throughout its sequence. This study introduces a novel method to analyse the effects of SNPs on encoded protein complexes by focusing on the biochemical properties of each non-synonymous substitution using the program TreeSAAP. Our results show four SNPs in CYP2D6 that exhibit radical changes in amino acid properties which may cause a lack of functionality in the CYP2D6 gene and contribute to a person's inability to metabolise specific drugs...
2007: International Journal of Bioinformatics Research and Applications
https://www.readbyqxmd.com/read/15509727/physicochemical-evolution-and-molecular-adaptation-of-the-cetacean-and-artiodactyl-cytochrome-b-proteins
#11
D A McClellan, E J Palfreyman, M J Smith, J L Moss, R G Christensen, J K Sailsbery
Cetaceans have most likely experienced metabolic shifts since evolutionarily diverging from their terrestrial ancestors, shifts that may be reflected in the proteins such as cytochrome b that are responsible for metabolic efficiency. However, accepted statistical methods for detecting molecular adaptation are largely biased against even moderately conservative proteins because the primary criterion involves a comparison of nonsynonymous and synonymous substitution rates (dN/dS); they do not allow for the possibility that adaptation may come in the form of very few amino acid changes...
March 2005: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/12651734/treesaap-selection-on-amino-acid-properties-using-phylogenetic-trees
#12
Steve Woolley, Justin Johnson, Matthew J Smith, Keith A Crandall, David A McClellan
The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during cladogenesis, and performs goodness-of-fit and categorical statistical tests.
March 22, 2003: Bioinformatics
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