The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during cladogenesis, performs goodness-of-fit categorical statistical tests.

Cetaceans have most likely experienced metabolic shifts since evolutionarily diverging from their terrestrial ancestors, that may be reflected in the proteins such as cytochrome b are responsible for efficiency. However, accepted statistical methods detecting molecular adaptation largely biased against even moderately conservative because primary criterion involves a comparison of nonsynonymous and synonymous substitution rates (dN/dS); they do not allow possibility come form very few amino...

The unwitting inclusion of convergent characters in phylogenetic estimates poses a serious problem for efforts to recover phylogeny. Convergence is not inscrutable, however, particularly when one group tracks phylogeny and another set adaptive history. In such cases, may be correlated with or few functional anatomical units readily identifiable by using comparative methods. Stifftail ducks (Oxyurinae) offer opportunity study character evolution function the context reconstruction....

We evaluated the effects of selection on molecular evolution functional domains mammalian cytochrome b gene as it relates to physicochemical properties shown correlate with rates amino acid replacement. Two groups mammals were considered: pocket gophers rodent family Geomyidae, and cetaceans ungulates monophyletic taxon Cetartiodactyla. Several characteristics common both mammal groups. The matrix domain reflected region's relative lack function. Goodness fit neutral expectations indicated...

Investigations of opsin evolution outside vertebrate systems have long been focused on insect visual pigments, whereas other groups received little attention. Furthermore, few studies explicitly investigated the selective influences across all currently characterized arthropod opsins. In this study, we contribute to knowledge crustacean opsins by sequencing 1 gene each from 6 previously uncharacterized species (Euphausia superba, Homarus gammarus, Archaeomysis grebnitzkii, Holmesimysis...

ABSTRACT Seventy-two full genomes corresponding to nine mammalian (67 strains) and two avian (5 polyomavirus species were analyzed using maximum likelihood Bayesian methods of phylogenetic inference. Our fully resolved well-supported (bootstrap proportions > 90%; posterior probabilities = 1.0) trees separate the bird polyomaviruses (avian goose hemorrhagic polyomavirus) from polyomaviruses, which supports idea spitting genus into subgenera. Such a split is also consistent with different...

Abstract Motivation: Multiple sequence alignments (MSAs) are at the heart of bioinformatics analysis. Recently, a number multiple protein alignment benchmarks (i.e. BAliBASE, OXBench, PREFAB and SMART) have been released to evaluate new existing MSA applications. These databases well received by researchers help quantitatively programs on sequences. Unfortunately, analogous DNA not available, making evaluation difficult for Results: This work presents first known that (1) comprised...

We use a multigene data set (the mitochondrial locus and nine nuclear gene regions) to test phylogenetic relationships in the South American "lava lizards" (genus Microlophus) describe strategy for aligning noncoding sequences that accounts differences tempo class of mutational events. focus on seven introns vary size frequency multibase length mutations (i.e., indels) present manual alignment incorporates insertions deletions (indels) each intron. Our method is based mechanistic...

TreeSAAP has been used in a variety of protein studies for detecting adaptation terms the physicochemical properties involved amino acid replacement. The accuracy was here tested using simulated protein-coding DNA data. A sampling 1402 replacements resulted default 81.1%, with most exhibiting >90% accuracy. More than half false-positive results were traced to just 11 180 possible single-step exchanges. Overall increased as number magnitude partitions analysis decreased. Sliding window size...

Metabolism of energy nutrients by the mitochondrial electron transport chain (ETC) is implicated in aging process. Polymorphisms core ETC proteins may have an effect on longevity. Here we investigate cytochrome b (cytb) polymorphism at amino acid 7 (cytbI7T) that distinguishes human haplogroup H from U.We compared longevity individuals these two haplogroups during historical extremes caloric intake. Haplogroup exhibits significantly increased restriction to U (p = 0.02) while abundance they...

Quinoa (Chenopodium quinoa Willd.) is a food crop cultivated by subsistence farmers and commercial growers on the high Andean plateau, primarily in Bolivia, Peru, Chile. Present interest due to its tolerance of harsh environments nutritional value. It thought that seed storage proteins quinoa, particularly 11S globulins 2S albumins, are responsible for relatively protein content ideal amino acid balance seed. Here we report genomic cDNA sequences two genes representing orthologous loci from...

To determine the association between health literacy, communication habits and colorectal cancer (CRC) screening among low-income patients.Survey responses of patients who received financial assistance for colonoscopy 2011 2014 at a family medicine residency clinic were analyzed using multivariate logistic regression (n = 456). There two dependent variables: (1) previous CRC (2) adherence. Our independent variables interest literacy habits.Over two-thirds (67.13%) respondents had not been...

<h3>Background:</h3> An inadequate supply of physicians who perform colonoscopies contributes to suboptimal screening rates, especially among the underserved. This shortage could be reduced if primary care colonoscopies. purpose this article is report quality indicators from colonoscopy procedures performed by family medicine as part a colorectal cancer prevention program targeting uninsured, low-income individuals. <h3>Methods:</h3> A grant-funded was implemented increase access affordable...

Two human papillomavirus (HPV) vaccines are available and can prevent 98% of HPV 16 18 infections. This study aimed to explore determinants 1) vaccine awareness among a cohort low-income women participating in cancer prevention program Central Texas compare them United States residents; 2) healthcare providers' discussion female residents the States. Bivariate multivariable analysis using survey data (n = 359) collected between 2014 2016 Texas, Health Information Nutrition Survey (HINTS)...

Amino acid property methods have repeatedly proven more sensitive than nucleotide-based methods, especially to the subtle influences of selection on Single Nucleotide Polymorphisms (SNPs). The purpose this study is evaluate effects population sampling and sliding window size sensitivity one amino based method by assessing drug resistant SNPs from HIV-1 gag-pol gene. analysis most produced positive results. There was not a trend in terms properties affected often, but results sampling.

Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths weaknesses, no one approach provides clear picture how natural selection works at the molecular level. The purpose this work to present simple new method that uses quantitative amino acid properties identify characterize directional in proteins. Inferred replacements are viewed through prism single physicochemical property...