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nonsynonymous substitution

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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...
July 24, 2017: Virology
https://www.readbyqxmd.com/read/28747543/mutation-profile-based-methods-for-understanding-selection-forces-in-cancer-somatic-mutations-a-comparative-analysis
#7
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
#8
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...
July 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28733421/differentially-regulated-orthologs-in-sorghum-and-the-subgenomes-of-maize
#9
Yang Zhang, Daniel W Ngu, Daniel Carvalho, Zhikai Liang, Yumou Qiu, Rebecca Roston, James 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...
July 21, 2017: Plant Cell
https://www.readbyqxmd.com/read/28732465/genome-wide-signals-of-positive-selection-in-strongylocentrotid-sea-urchins
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28690785/rates-and-relations-of-mitochondrial-genome-evolution-across-the-echinoidea-with-special-focus-on-the-superfamily-odontophora
#13
Áki Jarl Láruson
In order to better characterize the placement of genus Tripneustes, as a representative of the Toxopneustidae family within the broader sea urchin mitochondrial (MT) phylogeny, the complete MT genome of Tripneustes gratilla was generated and compared with all published echinoid MT genomes currently available on NCBI GenBank. The MT genome phylogeny supports the existence of the superfamily Odontophora (consisting of the families Strongylocentrotidae, Echinometridae, and Toxopneustidae). A relaxed molecular-clock time calibration suggests a split between the three key Odontophore MT lineages occurred during the late Eocene/Oligocene...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28671612/mutations-in-cancer-cause-gain-of-cysteine-histidine-and-tryptophan-at-the-expense-of-a-net-loss-of-arginine-on-the-proteome-level
#14
Viktoriia Tsuber, Yunus Kadamov, Lars Brautigam, Ulrika Warpman Berglund, Thomas Helleday
Accumulation of somatic mutations is critical for the transition of a normal cell to become cancerous. Mutations cause amino acid substitutions that change properties of proteins. However, it has not been studied as to what extent the composition and accordingly chemical properties of the cell proteome is altered as a result of the increased mutation load in cancer. Here, we analyzed data on amino acid substitutions caused by mutations in about 2000 protein coding genes from the Cancer Cell Line Encyclopedia that contains information on nucleotide and amino acid alterations in 782 cancer cell lines, and validated the analysis with information on amino acid substitutions for the same set of proteins in the Catalogue of Somatic Mutations in Cancer (COSMIC; v78) in circa 18,000 tumor samples...
July 3, 2017: Biomolecules
https://www.readbyqxmd.com/read/28665990/molecular-evolutionary-analysis-of-a-gender-limited-mid-ortholog-from-the-homothallic-species-volvox-africanus-with-male-and-monoecious-spheroids
#15
Kayoko Yamamoto, Hiroko Kawai-Toyooka, Takashi Hamaji, Yuki Tsuchikane, Toshiyuki Mori, Fumio Takahashi, Hiroyuki Sekimoto, Patrick J Ferris, Hisayoshi Nozaki
Volvox is a very interesting oogamous organism that exhibits various types of sexuality and/or sexual spheroids depending upon species or strains. However, molecular bases of such sexual reproduction characteristics have not been studied in this genus. In the model species V. carteri, an ortholog of the minus mating type-determining or minus dominance gene (MID) of isogamous Chlamydomonas reinhardtii is male-specific and determines the sperm formation. Male and female genders are genetically determined (heterothallism) in V...
2017: PloS One
https://www.readbyqxmd.com/read/28654758/looking-into-a-whale-s-heart-investigating-a-genetic-basis-for-cardiomyopathy-in-a-non-model-species
#16
Amélia Viricel, Patricia E Rosel
Understanding the pathogenesis of complex diseases can benefit from multi-species comparative studies. Yet these studies rarely include natural populations of non-model species. Here, we focused on the cause of a heart muscle disease, cardiomyopathy (CM), affecting multiple mammalian species including humans, cats, dogs, and certain species of whales. Mutations in genes coding for sarcomeric proteins have been identified as a leading cause for CM in humans, and some were also revealed to be responsible for CM in cats...
June 27, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28642160/a-novel-missense-variant-gln220arg-of-gnb4-encoding-guanine-nucleotide-binding-protein-subunit-beta-4-in-a-japanese-family-with-autosomal-dominant-motor-and-sensory-neuropathy
#17
Shiroh Miura, Takuya Morikawa, Ryuta Fujioka, Kazuhito Noda, Kengo Kosaka, Takayuki Taniwaki, Hiroki Shibata
Dominant intermediate Charcot-Marie-Tooth disease F (CMTDIF) is an autosomal dominant hereditary form of Charcot-Marie-Tooth disease (CMT) caused by variations in the guanine nucleotide-binding protein, subunit beta-4 gene (GNB4). We examined two Japanese familial cases with CMT. Case 1 was a 49-year-old male whose chief complaint was slowly progressive gait disturbance and limb dysesthesia that appeared at the age of 47. On neurological examination, he showed hyporeflexia or areflexia, distal limb muscle weakness, and distal sensory impairment with lower dominancy...
June 19, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28630112/rapid-evolution-of-ovarian-biased-genes-in-the-yellow-fever-mosquito-aedes-aegypti
#18
Carrie A Whittle, Cassandra G Extavour
Males and females exhibit highly dimorphic phenotypes, particularly in their gonads, which is believed to be driven largely by differential gene expression. Typically, the protein sequences of genes upregulated in males, or male-biased genes, evolve rapidly as compared to female-biased and unbiased genes. To date, the specific study of gonad-biased genes remains uncommon in metazoans. Here, we identified and studied a total of 2927, 2013, and 4449 coding sequences (CDS) with ovary-biased, testis-biased, and unbiased expression, respectively, in the yellow fever mosquito Aedes aegypti The results showed that ovary-biased and unbiased CDS had higher nonsynonymous to synonymous substitution rates (dN/dS) and lower optimal codon usage (those codons that promote efficient translation) than testis-biased genes...
August 2017: Genetics
https://www.readbyqxmd.com/read/28616179/prediction-of-harmful-variants-on-mitochondrial-genes-test-of-habitat-dependent-and-demographic-effects-in-a-euryhaline-fish
#19
Anti Vasemägi, Janne Sulku, Matthieu Bruneaux, Olaf Thalmann, Hannu Mäkinen, Mikhail Ozerov
Both effective population size and life history may influence the efficacy of purifying selection, but it remains unclear if the environment affects the accumulation of weakly deleterious nonsynonymous polymorphisms. We hypothesize that the reduced energetic cost of osmoregulation in brackish water habitat may cause relaxation of selective constraints at mitochondrial oxidative phosphorylation (OXPHOS) genes. To test this hypothesis, we analyzed 57 complete mitochondrial genomes of Pungitius pungitius collected from brackish and freshwater habitats...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28604700/excess-of-non-conservative-amino-acid-changes-in-marine-bacterioplankton-lineages-with-reduced-genomes
#20
Haiwei Luo, Yongjie Huang, Ramunas Stepanauskas, Jijun Tang
Surface ocean waters are dominated by planktonic bacterial lineages with highly reduced genomes. The best examples are the cyanobacterial genus Prochlorococcus, the alphaproteobacterial clade SAR11 and the gammaproteobacterial clade SAR86, which together represent over 50% of the cells in surface oceans. Several studies have identified signatures of selection on these lineages in today's ocean and have postulated selection as the primary force throughout their evolutionary history. However, massive loss of genomic DNA in these lineages often occurred in the distant past, and the selective pressures underlying these ancient events have not been assessed...
June 12, 2017: Nature Microbiology
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