scholarly journals KaKs_calculator 3.0: Calculating selective pressure on coding and non-coding sequences

2022 ◽  
Author(s):  
Zhang Zhang
Keyword(s):  
Selective Pressure ◽  
Coding Sequences

Regulation of the Arf tumor suppressor in Eμ-Myc transgenic mice: longitudinal study of Myc-induced lymphomagenesis

Blood ◽  
2006 ◽  
Vol 109 (2) ◽  
pp. 792-794 ◽  
Author(s):  
David Bertwistle ◽  
Charles J. Sherr
Keyword(s):  
Tumor Suppressor ◽  
Fluorescent Protein ◽  
Selective Pressure ◽  
Wild Type Allele ◽  
Wild Type ◽  
Coding Sequences ◽  
Cycle Arrest ◽  
Induced Tumors ◽  
Low Levels ◽  
Green Fluorescent

Abstract Lymphomagenesis in Eμ-Myc mice is opposed by the Arf tumor suppressor, whose inactivation compromises p53 function and accelerates disease. Finding nascent Eμ-Myc–induced tumors in which p19Arf causes cell-cycle arrest or apoptosis is problematic, since such cells will be eliminated until Arf or p53 function is lost. Knock-in mice expressing a green fluorescent protein (GFP) in lieu of Arf coding sequences allow analysis of Arfpromoter regulation uncoupled from p19Arf action. Prior to frank lymphoma development, unexpectedly low levels of Eμ-Myc–induced p19Arf or GFP were expressed. However, as lymphomas arose in Arf+/GFP heterozygotes, additional oncogenic events synergized with Eμ-Myc to further induce the functionally null Arf-Gfp allele. Concomitant up-regulation of p19Arf was not observed; instead, the wild-type allele was inactivated. We infer that very low levels of Arf are tumor suppressive, and that further induction provides the selective pressure for the emergence of tumors that have inactivated the gene.

scholarly journals KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences

2021 ◽  
Author(s):  
Zhang Zhang
Keyword(s):  
Substitution Rate ◽  
Nucleotide Substitution ◽  
Selective Pressure ◽  
Synonymous Substitution ◽  
Nucleotide Substitution Rate ◽  
Synonymous Substitution Rate ◽  
Coding Sequences ◽  
Genome Wide ◽  
Genome Scale ◽  
Genome Wide Scan

KaKs_Calculator 3.0 is an updated toolkit that is capable for calculating selective pressure on both coding and non-coding sequences. Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as non-coding nucleotide substitution rate normalized by synonymous substitution rate of adjacent coding sequences. As testified on empirical data, it shows effectiveness to detect the strength and mode of selection operated on molecular sequences, accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at whole genome scale. The package of KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001.

scholarly journals Structure of cDNA clones coding for human type II procollagen. The α 1(II) chain is more similar to the α 1(I) chain than two other α chains of fibrillar collagens

1989 ◽  
Vol 262 (2) ◽  
pp. 521-528 ◽  
Author(s):  
C T Baldwin ◽  
A M Reginato ◽  
C Smith ◽  
S A Jimenez ◽  
D J Prockop
Keyword(s):  
Amino Acid ◽  
Selective Pressure ◽  
Cdna Clones ◽  
Type I ◽  
Type Ii ◽  
Coding Sequences ◽  
Type Iii ◽  
Human Type ◽  
Fibrillar Collagens ◽  
Triple Helical Domain

Overlapping cDNA clones were isolated for human type II procollagen. Nucleotide sequencing of the clones provided over 2.5 kb of new coding sequences for the human pro alpha 1(II) gene and the first complete amino acid sequence of type II procollagen from any species. Comparison with published data for cDNA clones covering the entire lengths of the human type I and type III procollagens made it possible to compare in detail the coding sequences and primary structures of the three most abundant human fibrillar collagens. The results indicated that the marked preference in the third base codons for glycine, proline and alanine previously seen in other fibrillar collagens was maintained in type II procollagen. The domains of the pro alpha 1(II) chain are about the same size as the same domains of the pro alpha chains of type I and type III procollagens. However, the major triple-helical domain is 15 amino acid residues less than the triple-helical domain of type III procollagen. Comparison of hydropathy profiles indicated that the alpha chain domain of type II procollagen is more similar to the alpha chain domain of the pro alpha 1(I) chain than to the pro alpha 2(I) chain or the pro alpha 1(III) chain. The results therefore suggest that selective pressure in the evolution of the pro alpha 1(II) and pro alpha 1(I) genes is more similar than the selective pressure in the evolution of the pro alpha 2(I) and pro alpha 1(III) genes.

scholarly journals VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

2017 ◽  
Vol 3 ◽  
pp. e118 ◽  
Author(s):  
Andrew E. Webb ◽  
Thomas A. Walsh ◽  
Mary J. O’Connell
Keyword(s):  
Phylogenetic Trees ◽  
Large Scale ◽  
Selective Pressure ◽  
Gene Families ◽  
Pressure Variation ◽  
Phylogeny Reconstruction ◽  
Protein Coding ◽  
Coding Sequences ◽  
A Genome ◽  
Pressure Analysis

Background Large-scale molecular evolutionary analyses of protein coding sequences requires a number of preparatory inter-related steps from finding gene families, to generating alignments and phylogenetic trees and assessing selective pressure variation. Each phase of these analyses can represent significant challenges, particularly when working with entire proteomes (all protein coding sequences in a genome) from a large number of species. Methods We present VESPA, software capable of automating a selective pressure analysis using codeML in addition to the preparatory analyses and summary statistics. VESPA is written in python and Perl and is designed to run within a UNIX environment. Results We have benchmarked VESPA and our results show that the method is consistent, performs well on both large scale and smaller scale datasets, and produces results in line with previously published datasets. Discussion Large-scale gene family identification, sequence alignment, and phylogeny reconstruction are all important aspects of large-scale molecular evolutionary analyses. VESPA provides flexible software for simplifying these processes along with downstream selective pressure variation analyses. The software automatically interprets results from codeML and produces simplified summary files to assist the user in better understanding the results. VESPA may be found at the following website: http://www.mol-evol.org/VESPA.

Study of Alnus incana L. Moench fruit extract biologically active substances influence on resistance development in mls-resistant staphylococci skin isolates

2018 ◽  
Vol 22 (2) ◽  
pp. 263-266
Author(s):  
R.V. Kutsyk ◽  
O.I. Yurchyshyn
Keyword(s):  
Selective Pressure ◽  
Biological Response ◽  
Biologically Active Substances ◽  
Biologically Active ◽  
Alnus Incana ◽  
Fruit Extract ◽  
Antimicrobial Drugs ◽  
Resistance Development ◽  
Subinhibitory Concentrations ◽  
Active Substances

The emergence of microorganisms resistant strains is a natural biological response to the use of antimicrobial drugs that creates selective pressure, contributing to pathogens selection, survival and reproduction. The purpose of the investigation was to study the resistance development of staphylococci skin isolates to erythromycin and influence on it Alnus incana L. fruit extract subinhibitory concentrations. Development of resistance to erythromycin and influence on it Alnus incana L. fruit extract (extraction by 90% ethanol) subinhibitory concentrations were conducted with S epidermidis strains: sensitive and resistant to 14 and 15-membered macrolides. The study was carried out within 30 days by multiple consecutive passages of staphylococci test strains (concentration 1×107 CFU/ml) into test tubes containing broth and erythromycin ranging from 3 doubling dilutions above to doubling dilutions below the minimum inhibitory concentration. Statistical analysis of the results was carried out by one-and two-factor analysis of variance (ANOVA) and Microsoft Office Excel 2011. Rapid increase of resistance from 32 to 1024 μg/ml (F=34.2804; F> Fstand. max = 5.9874; p=0.0011) for S.epidermidis with a low level of resistance to 14 and 15-membered macrolides resistance to the erythromycine was observed. In the presence of Alnus incana L. fruit extract subinhibitory concentrations (¼ MIC), the initial MIC of erythromycin was decreased by 32 times to 1 μg/ml (F = 9.7497; F> Fstand. max = 5.9874; p = 0.0205). The sensitive strain after 30 passages did not develop resistance to erythromycin. Under the influence of erythromycin selective pressure, S.epidermidis strain with low initial level of MLS-resistance rapidly reaches a high-level resistance. Biologically active substances of the Alnus incana L. fruit extract significantly inhibit the resistance development in S. epidermidis to macrolides and eliminate it phenotypic features.

Evolution, natural history, and conservation of black-footed ferrets

2018 ◽  
Author(s):  
Dean E. Biggins ◽  
David A. Eads
Keyword(s):  
Natural History ◽  
Captive Breeding ◽  
Alpine Meadow ◽  
Selective Pressure ◽  
Canine Distemper ◽  
Prairie Dog ◽  
Management Tools ◽  
Diverse Area ◽  
Close Relatives ◽  
Remnant Population

Black-footed ferrets were reduced to a remnant population of 10 in 1985 due to diseases (plague, canine distemper), but successful captive breeding and releases have improved the prospects for ferret recovery. Comparisons between black-footed ferrets and Siberian polecats, close relatives that can interbreed and produce fertile offspring, allow the following evolutionary speculation. Predation on ferrets and polecats tends to narrow their niches and promote specialization due to requirements for escape habitats. In Asia, that influence is countered by the larger and more diverse area of steppe and alpine meadow habitats for polecats, and by plague which causes large variation in prey abundance. In North America, the selective pressure favoring specialization in ferrets on prairie dog prey and burrows had no strong counter-force before plague invaded. Plague is an immense challenge to black-footed ferret recovery, and several management tools including vaccines and vector control may be necessary to conserve the species.

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