keyword
MENU ▼
Read by QxMD icon Read
search

nonsynonymous substitution

keyword
https://www.readbyqxmd.com/read/29029187/evidence-for-the-selective-basis-of-transition-to-transversion-substitution-bias-in-two-rna-viruses
#1
Daniel M Lyons, Adam S Lauring
The substitution rates of transitions are higher than expected by chance relative to those of transversions. Many have argued that selection disfavors transversions, as nonsynonymous transversions are less likely to conserve biochemical properties of the original amino acid. Only recently has it become feasible to directly test this selective hypothesis by comparing the fitness effects of a large number of transition and transversion mutations. For example, a recent study of six viruses and one beta-lactamase gene did not find evidence supporting the selective hypothesis...
September 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29020740/positive-and-relaxed-selection-associated-with-flight-evolution-and-loss-in-insect-transcriptomes
#2
T Fatima Mitterboeck, Shanlin Liu, Sarah J Adamowicz, Jinzhong Fu, Rui Zhang, Wenhui Song, Karen Meusemann, Xin Zhou
The evolution of powered flight is a major innovation that has facilitated the success of insects. Previously, studies of birds, bats, and insects have detected molecular signatures of differing selection regimes in energy-related genes associated with flight evolution and/or loss. Here, using DNA sequences from more than 1000 nuclear and mitochondrial protein-coding genes obtained from insect transcriptomes, we conduct a broader exploration of which gene categories display positive and relaxed selection at the origin of flight as well as with multiple independent losses of flight...
October 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28969795/legume-isoflavone-synthase-genes-have-evolved-by-whole-genome-and-local-duplications-yielding-transcriptionally-active-paralogs
#3
Dorota Narożna, Michał Książkiewicz, Łucja Przysiecka, Joanna Króliczak, Bogdan Wolko, Barbara Naganowska, Cezary J Mądrzak
Isoflavone synthase (IFS) is the key enzyme of isoflavonoid biosynthesis. IFS genes were identified in numerous species, although their evolutionary patterns have not yet been reconstructed. To address this issue, we performed structural and functional genomic analysis. Narrow leafed lupin, Lupinus angustifolius L., was used as a reference species for the genus, because it has the most developed molecular tools available. Nuclear genome BAC library clones carrying IFS homologs were localized by linkage mapping and fluorescence in situ hybridization in three chromosome pairs...
November 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28938601/mutation-profile-based-methods-for-understanding-selection-forces-in-cancer-somatic-mutations-a-comparative-analysis
#4
Zhan Zhou, Yangyun Zou, Gangbiao Liu, Jingqi Zhou, Jingcheng Wu, Shimin Zhao, Zhixi Su, Xun Gu
Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes (CN /CS ) and normal populations (pN /pS ). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28892166/clinical-patterns-associated-with-the-concurrent-detection-of-anti-hbs-and-hbv-dna
#5
Olympia E Anastasiou, Marek Widera, Johannes Korth, Helenie Kefalakes, Antonios Katsounas, Gudrun Hilgard, Guido Gerken, Ali Canbay, Sandra Ciesek, Jens Verheyen
Simultaneous detection of anti-HBs and HBV DNA is a rare serological combination and has been described in acute and chronic HBV infection. To scrutinize viral and clinical patterns associated with concurrent detection of anti-HBs and HBV DNA. Simultaneous detection of anti-HBs and HBV DNA was observed in 64/1444 (4.4%) patients treated for HBV infection at the University Hospital of Essen from 2006 to 2016 (8 with acute, 20 with reactivated, and 36 chronic HBV infection). Clinical data and laboratory parameters were analyzed...
September 11, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28859098/a-comparative-transcriptomic-analysis-reveals-the-core-genetic-components-of-salt-and-osmotic-stress-responses-in-braya-humilis
#6
Pengshan Zhao, Lirong Wang, Xin Zhao, Guoxiong Chen, Xiao-Fei Ma
Braya humilis is a member of the Euclidieae tribe within the family Brassicaceae. This species exhibits a broad range of adaptations to different climatic zones and latitudes as it has a distribution that ranges from northern Asia to the arctic-alpine regions of northern North America. In China, B. humilis is mainly found on the Qinghai-Tibetan Plateau (QTP) and in adjacent arid regions. In this study, we sequenced a sample from an arid region adjacent to the QTP using the Illumina platform generating a total of 46,485 highly accurate unigenes, of which 78...
2017: PloS One
https://www.readbyqxmd.com/read/28844906/selection-originating-from-protein-stability-foldability-relationships-between-protein-folding-free-energy-sequence-ensemble-and-fitness
#7
Sanzo Miyazawa
Assuming that mutation and fixation processes are reversible Markov processes, we prove that the equilibrium ensemble of sequences obeys a Boltzmann distribution with exp(4Nem(1-1/(2N))), where m is Malthusian fitness and Ne and N are effective and actual population sizes. On the other hand, the probability distribution of sequences with maximum entropy that satisfies a given amino acid composition at each site and a given pairwise amino acid frequency at each site pair is a Boltzmann distribution with exp(-ψN), where the evolutionary statistical energy ψN is represented as the sum of one body (h) (compositional) and pairwise (J) (covariational) interactions over all sites and site pairs...
August 24, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28842611/evidence-based-tailoring-of-bioinformatics-approaches-to-optimize-methods-that-predict-the-effects-of-nonsynonymous-amino-acid-substitutions-in-glucokinase
#8
Daniela Šimčíková, Lucie Kocková, Kateřina Vackářová, Miroslav Těšínský, Petr Heneberg
Computational methods that allow predicting the effects of nonsynonymous substitutions are an integral part of exome studies. Here, we validated and improved their specificity by performing a comprehensive bioinformatics analysis combined with experimental and clinical data on a model of glucokinase (GCK): 8835 putative variations, including 515 disease-associated variations from 1596 families with diagnoses of monogenic diabetes (GCK-MODY) or persistent hyperinsulinemic hypoglycemia of infancy (PHHI), and 126 variations with available or newly reported (19 variations) data on enzyme kinetics...
August 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28812016/syntool-a-novel-region-based-intolerance-score-to-single-nucleotide-substitution-for-synonymous-mutations-predictions-based-on-123-136-individuals
#9
Tongda Zhang, Yiran Wu, Zhangzhang Lan, Quan Shi, Ying Yang, Jian Guo
BACKGROUND: Synonymous mutation is the single nucleotide change that does not cause an amino acid change but can affect the rate and efficiency of translation. So recent increase in our knowledge has revealed a substantial contribution of synonymous mutations to human disease risk and other complex traits. Nevertheless, there are still rarely synonymous mutation prediction methods. METHODS: Nonsynonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28811315/quantitative-whole-genome-sequencing-of-circulating-tumor-cells-enables-personalized-combination-therapy-of-metastatic-cancer
#10
Natali Gulbahce, Mark Jesus M Magbanua, Robert Chin, Misha R Agarwal, Xuhao Luo, Jia Liu, Daniel M Hayden, Qing Mao, Serban Ciotlos, Zhenyu Li, Yanxiang Chen, Xingpeng Chen, Yuxiang Li, Rebecca Yu Zhang, Katharine Lee, Rick Tearle, Emily Park, Snezana Drmanac, Hope S Rugo, John W Park, Radoje Drmanac, Brock A Peters
Much effort has been dedicated to developing circulating tumor cells (CTC) as a noninvasive cancer biopsy, but with limited success as yet. In this study, we combine a method for isolation of highly pure CTCs using immunomagnetic enrichment/fluorescence-activated cell sorting with advanced whole genome sequencing (WGS), based on long fragment read technology, to illustrate the utility of an accurate, comprehensive, phased, and quantitative genomic analysis platform for CTCs. Whole genomes of 34 CTCs from a patient with metastatic breast cancer were analyzed as 3,072 barcoded subgenomic compartments of long DNA...
August 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28801606/linkage-mapping-aided-by-de-novo-genome-and-transcriptome-assembly-in-portunus-trituberculatus-applications-in-growth-related-qtl-and-gene-identification
#11
Jianjian Lv, Baoquan Gao, Ping Liu, Jian Li, Xianliang Meng
A high-resolution genetic linkage map is an essential tool for decoding genetics and genomics in non-model organisms. In this study, a linkage map was constructed for the swimming crab (Portunus trituberculatus) with 10,963 markers; as far as we know, this number of markers has never been achieved in any other crustacean. The linkage map covered 98.85% of the whole genome with a mean marker interval of 0.51 cM. The de novo assembly based on genome and transcriptome sequencing data enabled 2,378 explicit annotated markers to be anchored to the map...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28799241/functional-characterization-of-carboxylesterase-gene-mutations-involved-in-aphis-gossypii-resistance-to-organophosphate-insecticides
#12
Y-H Gong, G-M Ai, M Li, X-Y Shi, Q-Y Diao, X-W Gao
Carboxylesterases (CarEs) play an important role in detoxifying insecticides in insects. Over-expression and structural modification of CarEs have been implicated in the development of organophosphate (OP) insecticide resistance in insects. A previous study identified four nonsynonymous mutations (resulting in four amino acid residue substitutions) in the open reading frame of the carboxylesterase gene of resistant cotton aphids compared to the omethoate susceptible strain, which has possibly influenced the development of resistance to omethoate (a systemic OP insecticide)...
August 11, 2017: Insect Molecular Biology
https://www.readbyqxmd.com/read/28759647/connectivity-in-gene-coexpression-networks-negatively-correlates-with-rates-of-molecular-evolution-in-flowering-plants
#13
Rishi R Masalia, Adam J Bewick, John M Burke
Gene coexpression networks are a useful tool for summarizing transcriptomic data and providing insight into patterns of gene regulation in a variety of species. Though there has been considerable interest in studying the evolution of network topology across species, less attention has been paid to the relationship between network position and patterns of molecular evolution. Here, we generated coexpression networks from publicly available expression data for seven flowering plant taxa (Arabidopsis thaliana, Glycine max, Oryza sativa, Populus spp...
2017: PloS One
https://www.readbyqxmd.com/read/28750321/modeling-the-evolution-of-siv-sooty-mangabey-progenitor-virus-towards-hiv-2-using-humanized-mice
#14
Kimberly Schmitt, Dipu Mohan Kumar, James Curlin, Leila Remling-Mulder, Mark Stenglein, Shelby O'Connor, Preston Marx, Ramesh Akkina
HIV-2 is thought to have originated from an SIV progenitor native to sooty mangabeys. To model the initial human transmission and understand the sequential viral evolution, humanized mice were infected with SIVsm and serially passaged for five generations. Productive infection was seen by week 3 during the initial challenge followed by chronic viremia and gradual CD4(+) T cell decline. Viral loads increased by the 5th generation resulting in more rapid CD4(+) T cell decline. Genetic analysis revealed several amino acid substitutions that were nonsynonymous and fixed in multiple hu-mice across each of the 5 generations in the nef, env and rev regions...
October 2017: Virology
https://www.readbyqxmd.com/read/28747543/mutation-profile-based-methods-for-understanding-selection-forces-in-cancer-somatic-mutations-a-comparative-analysis
#15
Zhan Zhou, Yangyun Zou, Gangbiao Liu, Jingqi Zhou, Jingcheng Wu, Shimin Zhao, Zhixi Su, Xun Gu
Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes (CN/CS) and normal populations (pN/pS). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels...
July 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28739599/evolutionary-dynamics-of-male-reproductive-genes-in-the-drosophila-virilis-subgroup
#16
Yasir H Ahmed-Braimah, Robert L Unckless, Andrew G Clark
Postcopulatory sexual selection (PCSS) is a potent evolutionary force that can drive rapid changes of reproductive genes within species, and thus has the potential to generate reproductive incompatibilities between species. Male seminal fluid proteins (SFPs) are major players in postmating interactions, and are important targets of PCSS in males. The virilis subgroup of Drosophila exhibits strong interspecific gametic incompatibilities, and can serve as a model to study the genetic basis of PCSS and gametic isolation...
September 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28733421/differentially-regulated-orthologs-in-sorghum-and-the-subgenomes-of-maize
#17
Yang Zhang, Daniel W Ngu, Daniel Carvalho, Zhikai Liang, Yumou Qiu, Rebecca L Roston, James C Schnable
Identifying interspecies changes in gene regulation, one of the two primary sources of phenotypic variation, is challenging on a genome-wide scale. The use of paired time-course data on cold-responsive gene expression in maize (Zea mays) and sorghum (Sorghum bicolor) allowed us to identify differentially regulated orthologs. While the majority of cold-responsive transcriptional regulation of conserved gene pairs is species specific, the initial transcriptional responses to cold appear to be more conserved than later responses...
August 2017: Plant Cell
https://www.readbyqxmd.com/read/28732465/genome-wide-signals-of-positive-selection-in-strongylocentrotid-sea-urchins
#18
Kord M Kober, Grant H Pogson
BACKGROUND: Comparative genomics studies investigating the signals of positive selection among groups of closely related species are still rare and limited in taxonomic breadth. Such studies show great promise in advancing our knowledge about the proportion and the identity of genes experiencing diversifying selection. However, methodological challenges have led to high levels of false positives in past studies. Here, we use the well-annotated genome of the purple sea urchin, Strongylocentrotus purpuratus, as a reference to investigate the signals of positive selection at 6520 single-copy orthologs from nine sea urchin species belonging to the family Strongylocentrotidae paying careful attention to minimizing false positives...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28717152/effects-of-population-bottleneck-and-balancing-selection-on-the-chinese-alligator-are-revealed-by-locus-specific-characterization-of-mhc-genes
#19
Teng Zhai, Hai-Qiong Yang, Rui-Can Zhang, Li-Ming Fang, Guo-Heng Zhong, Sheng-Guo Fang
Chinese alligator (Alligator sinensis) is an endangered freshwater crocodilian endemic to China, which experienced a severe bottleneck about 30 years ago. In this study, we developed locus-specific primers to investigate the polymorphism of 3 major histocompatibility complex (MHC) loci in 3 Chinese alligator populations, in combination with 6 neutral microsatellite markers as a contrast. We found the genetic trace for the bottleneck effect on the endangered Chinese alligator: the low allelic diversity (2 alleles at each locus), the low nucleotide substitution rate (no more than 0...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28711373/comparative-genomic-and-phylogenetic-analysis-of-a-toxigenic-clinical-isolate-of-corynebacterium-diphtheriae-strain-b-d-16-78-from-malaysia
#20
Kar-Wai Hong, A W Asmah Hani, C A Nurul Aina Murni, R R Pusparani, Chee Kheong Chong, Khebir Verasahib, Wan Noraini W Yusoff, Noorliza M Noordin, Kok Keng Tee, Wai-Fong Yin, Choo Yee Yu, Geik Yong Ang, Kok-Gan Chan
In this study, we report the comparative genomics and phylogenetic analysis of Corynebacterium diphtheriae strain B-D-16-78 that was isolated from a clinical specimen in 2016. The complete genome of C. diphtheriae strain B-D-16-78 was sequenced using PacBio Single Molecule, Real-Time sequencing technology and consists of a 2,474,151-bp circular chromosome with an average GC content of 53.56%. The core genome of C. diphtheriae was also deduced from a total of 74 strains with complete or draft genome sequences and the core genome-based phylogenetic analysis revealed close genetic relationship among strains that shared the same MLST allelic profile...
July 12, 2017: Infection, Genetics and Evolution
keyword
keyword
71104
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"