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https://www.readbyqxmd.com/read/29229304/functional-characterization-of-the-g162r-and-d216h-genetic-variants-of-human-cyp17a1
#1
C P Capper, J Liu, L R McIntosh, J M Larios, M D Johnson, P F Hollenberg, Y Osawa, R J Auchus, J M Rae
Cytochrome P450 17A1 (CYP17A1) is a dual-function enzyme catalyzing reactions necessary for cortisol and androgen biosynthesis. CYP17A1 is a validated drug target for prostate cancer as CYP17A1 inhibition significantly reduces circulating androgens and improves survival in castration-resistant prostate cancer. Germline CYP17A1 genetic variants with altered CYP17A1 activity manifesting as various endocrinopathies are extremely rare; however, characterizing these variants provides critical insights into CYP17A1 protein structure and function...
December 8, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29228267/the-effects-of-sex-biased-gene-expression-and-x-linkage-on-rates-of-sequence-evolution-in-drosophila
#2
José Luis Campos, Keira Johnston, Brian Charlesworth
A faster rate of adaptive evolution of X-linked genes compared with autosomal genes (the faster-X effect) can be caused by the fixation of recessive or partially recessive advantageous mutations. This effect should be largest for advantageous mutations that affect only male fitness, and least for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using coding and functionally significant non-coding sequences of genes with different levels of sex-biased expression...
December 8, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29212937/experimental-adaptive-evolution-of-sivcpz-to-pandemic-hiv-1-using-a-humanized-mouse-model
#3
Kei Sato, Naoko Misawa, Junko S Takeuchi, Tomoko Kobayashi, Taisuke Izumi, Hirofumi Aso, Shumpei Nagaoka, Keisuke Yamamoto, Izumi Kimura, Yoriyuki Konno, Yusuke Nakano, Yoshio Koyanagi
HIV-1, the causative agent of AIDS, is originated from SIVcpz, the chimpanzee precursor of the human virus, approximately 100 years ago. This indicates that HIV-1 has emerged through the cross-species transmission of SIVcpz from chimpanzees to humans. However, it remains unclear how SIVcpz has evolved into pandemic HIV-1 in humans. To address this question, we inoculated three SIVcpz (MB897, EK505, and MT145), four pandemic HIV-1 (NL4-3, NLCSFV3, JRCSF and AD8) and 2 non-pandemic HIV-1 (YBF30 and DJO0131) strains...
December 6, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29203828/foxp2-variation-in-great-ape-populations-offers-insight-into-the-evolution-of-communication-skills
#4
Nicky Staes, Chet C Sherwood, Katharine Wright, Marc de Manuel, Elaine E Guevara, Tomas Marques-Bonet, Michael Krützen, Michael Massiah, William D Hopkins, John J Ely, Brenda J Bradley
The gene coding for the forkhead box protein P2 (FOXP2) is associated with human language disorders. Evolutionary changes in this gene are hypothesized to have contributed to the emergence of speech and language in the human lineage. Although FOXP2 is highly conserved across most mammals, humans differ at two functional amino acid substitutions from chimpanzees, bonobos and gorillas, with an additional fixed substitution found in orangutans. However, FOXP2 has been characterized in only a small number of apes and no publication to date has examined the degree of natural variation in large samples of unrelated great apes...
December 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29178647/comprehensive-analysis-of-mutations-in-the-mefv-gene-reveal-that-the-location-and-not-the-substitution-type-determines-symptom-severity-in-fmf
#5
Mike M Moradian, Davit Babikyan, Dion Banoian, Hasmik Hayrapetyan, Hakob Manvelyan, Nareh Avanesian, Tamara Sarkisian
BACKGROUND: Familial Mediterranean Fever (FMF) is an autoinflammatory disorder caused by mutations in the MEFV gene. These mutations appear in different populations with different frequencies and their caused symptom severities vary from mild to moderate to severe depending on the mutation type. METHODS: In this study, we analyzed the mutations that have been reported in the MEFV gene from symptomatic FMF patients and compared their frequencies in different populations from the 1000 Genome and the Exome databases, using statistical clustering...
November 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29170851/the-complete-chloroplast-genome-sequence-of-dodonaea-viscosa-comparative-and-phylogenetic-analyses
#6
Josphat K Saina, Andrew W Gichira, Zhi-Zhong Li, Guang-Wan Hu, Qing-Feng Wang, Kuo Liao
The plant chloroplast (cp) genome is a highly conserved structure which is beneficial for evolution and systematic research. Currently, numerous complete cp genome sequences have been reported due to high throughput sequencing technology. However, there is no complete chloroplast genome of genus Dodonaea that has been reported before. To better understand the molecular basis of Dodonaea viscosa chloroplast, we used Illumina sequencing technology to sequence its complete genome. The whole length of the cp genome is 159,375 base pairs (bp), with a pair of inverted repeats (IRs) of 27,099 bp separated by a large single copy (LSC) 87,204 bp, and small single copy (SSC) 17,972 bp...
November 23, 2017: Genetica
https://www.readbyqxmd.com/read/29155285/parasite-infection-of-specific-host-genotypes-relates-to-changes-in-prevalence-in-two-natural-populations-of-bumblebees
#7
Oliver Manlik, Regula Schmid-Hempel, Paul Schmid-Hempel
The antagonistic relationship between parasites and their hosts is strongly influenced by genotype-by-genotype interactions. Defense against parasitism is commonly studied in the context of immune system-based mechanisms and, thus, the focus in the search for candidate genes in host-parasite interactions is often on immune genes. In this study, we investigated the association between prevalence of parasite infection and host mitochondrial DNA (mtDNA) haplotypes in two natural populations of bumblebees (Bombus terrestris)...
November 16, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29151870/elevated-mitochondrial-genome-variation-after-50-generations-of-radiation-exposure-in-a-wild-rodent
#8
Robert J Baker, Benjamin Dickins, Jeffrey K Wickliffe, Faisal A A Khan, Sergey Gaschak, Kateryna D Makova, Caleb D Phillips
Currently, the effects of chronic, continuous low dose environmental irradiation on the mitochondrial genome of resident small mammals are unknown. Using the bank vole (Myodes glareolus) as a model system, we tested the hypothesis that approximately 50 generations of exposure to the Chernobyl environment has significantly altered genetic diversity of the mitochondrial genome. Using deep sequencing, we compared mitochondrial genomes from 131 individuals from reference sites with radioactive contamination comparable to that present in northern Ukraine before the 26 April 1986 meltdown, to populations where substantial fallout was deposited following the nuclear accident...
September 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/29137431/mitochondrial-dna-depletion-mitochondrial-mutations-and-high-tfam-expression-in-hepatocellular-carcinoma
#9
Lihua Qiao, Guoqing Ru, Zhuochao Mao, Chenghui Wang, Zhipeng Nie, Qiang Li, Yiyi Huang-Yang, Ling Zhu, Xiaoyang Liang, Jialing Yu, Pingping Jiang
We investigated the role of mitochondrial genetic alterations in hepatocellular carcinoma by directly comparing the mitochondrial genomes of 86 matched pairs of HCC and non-tumor liver samples. Substitutions in 637 mtDNA sites were detected, comprising 89.80% transitions and 6.60% transversions. Forty-six somatic variants, including 15 novel mutations, were identified in 40.70% of tumor tissues. Of those, 21 were located in the non-coding region and 25 in the protein-coding region. Twenty-two somatic nonsynonymous changes were identified as putative pathogenic variants, including 4 truncating mutations produced by three frameshifts (MT-ATP6 8628 insC; MT-ND5 13475 T-del, and MT-CYB 14984 insA) and 1 nonsense mutation in MT-CO3 9253 G>A...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29128519/genetic-structure-of-two-erythrocyte-binding-antigens-of-plasmodium-falciparum-reveals-a-contrasting-pattern-of-selection
#10
Pramita Chowdhury, Srikanta Sen, Sumana Datta Kanjilal, Sanghamitra Sengupta
Erythrocyte binding antigens 175 (EBA-175) and 140 (EBA-140) play key roles in erythrocyte invasion by binding to glycophorin A (GPA) and C (GPC) respectively in human malaria. Since antigenic variation in malaria endemic region is a major barrier to development of effective vaccine, we explore the nature and pattern of sequence diversity of these two vaccine candidates in Kolkata, India. Population genetic parameters based on parasite sequences representing region II of Pfeba-175 and Pfeba-140 genes were estimated using DnaSP V...
November 8, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29122469/sensitivity-of-whole-exome-sequencing-in-detecting-infantile-and-late-onset-pompe-disease
#11
Mari Mori, Gloria Haskell, Zoheb Kazi, Xiaolin Zhu, Stephanie M DeArmey, Jennifer L Goldstein, Deeksha Bali, Catherine Rehder, Elizabeth T Cirulli, Priya S Kishnani
Pompe disease is a metabolic myopathy with a wide spectrum of clinical presentation. The gold-standard diagnostic test is acid alpha-glucosidase assay on skin fibroblasts, muscle or blood. Identification of two GAA pathogenic variants in-trans is confirmatory. Optimal effectiveness of enzyme replacement therapy hinges on early diagnosis, which is challenging in late-onset form of the disease due to non-specific presentation. Next-generation sequencing-based panels effectively facilitate diagnosis, but the sensitivity of whole-exome sequencing (WES) in detecting pathogenic GAA variants remains unknown...
October 17, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/29029187/evidence-for-the-selective-basis-of-transition-to-transversion-substitution-bias-in-two-rna-viruses
#12
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
#13
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
#14
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
#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...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28892166/clinical-patterns-associated-with-the-concurrent-detection-of-anti-hbs-and-hbv-dna
#16
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
#17
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
#18
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
#19
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
#20
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
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