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synonymous 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/28807856/low-levels-of-genetic-diversity-associated-with-evidence-of-negative-selection-on-the-babesia-bovis-apical-membrane-antigen-1-from-parasite-populations-in-thailand
#2
Amarin Rittipornlertrak, Boondarika Nambooppha, Pacharathon Simking, Veerasak Punyapornwithaya, Saruda Tiwananthagorn, Sathaporn Jittapalapong, Yang-Tsung Chung, Nattawooti Sthitmatee
Babesia bovis, a parasite infecting cattle and buffalo, continues to spread throughout the developing world. The babesial vaccine was developed to be a sustainable alternative treatment to control the parasite. However, genetic diversity is a major obstacle for designing and developing a safe and effective vaccine. The apical membrane antigen 1 (AMA-1) is considered to be a potential vaccine candidate antigen among immunogenic genes of B. bovis. To gain a more comprehensive understanding of B. bovis AMA-1 (BbAMA-1), three B...
August 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28805451/genetic-characterisation-and-analysis-of-infectious-bronchitis-virus-isolated-from-brazilian-flocks-between-2010-and-2015
#3
Claudia Carranza, Claudete S Astolfi-Ferreira, Silvana H Santander Parra, Luis F N Nuñez, Zoltan Penzes, Jorge L Chacón, Luiz Sesti, Ruy D Chacón, Antonio J Piantino Ferreira
Infectious bronchitis virus (IBV) variants in Brazil were isolated during 2010-2015 for epidemiological and molecular analysis to characterise the different variants and perform a bioinformatic analysis to compare with sequences of variants collected over the previous 40 years. Of the 453 samples examined, 61.4% were positive for IBV and 75.9% of these were considered to have the BR-I genotype and were detected in birds of all ages distributed in all five Brazilian regions. The ratio of non-synonymous substitutions per non-synonymous site (dN) to synonymous substitutions per synonymous site (dS), i...
August 14, 2017: British Poultry Science
https://www.readbyqxmd.com/read/28794033/ancient-evolution-and-dispersion-of-human-papillomavirus-type-58-variants
#4
Zigui Chen, Wendy C S Ho, Siaw Shi Boon, Priscilla T Y Law, Martin C W Chan, Rob DeSalle, Robert D Burk, Paul K S Chan
Human papillomavirus type 58 is found in 10-18% of cervical cancers in East Asia but rather uncommon elsewhere. The distribution and oncogenic potential of HPV58 variants appear to be heterogeneous since the E7 T20I/G63S variant is more prevalent in East Asia and confers 7-9 fold higher risk for cervical precancer and cancer. However, the underlying genomic mechanisms that explain the geographic and carcinogenic diversity of HPV58 variants are still poorly understood. In this study, we used a combination of phylogenetic analyses and bioinformatics to investigate the deep evolutionary history of HPV58 complete genome variants...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28759591/genome-wide-diversity-and-differentiation-in-new-world-populations-of-the-human-malaria-parasite-plasmodium-vivax
#5
Thais C de Oliveira, Priscila T Rodrigues, Maria José Menezes, Raquel M Gonçalves-Lopes, Melissa S Bastos, Nathália F Lima, Susana Barbosa, Alexandra L Gerber, Guilherme Loss de Morais, Luisa Berná, Jody Phelan, Carlos Robello, Ana Tereza R de Vasconcelos, João Marcelo P Alves, Marcelo U Ferreira
BACKGROUND: The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax. METHODS: We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P...
July 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28758818/genetic-characterization-of-bactrocera-fruit-flies-diptera-tephritidae-from-northeastern-india-based-on-dna-barcodes
#6
Arpana Manger, G T Behere, D M Firake, Bhagawati Sharma, N A Deshmukh, P D Firake, N S Azad Thakur, S V Ngachan
The Northeastern region of India, one of the mega biodiversity hot spots has enormous potential for the production of fruits and vegetables. Fruit flies of the genus Bactrocera Macquart are important pests of fruits and vegetables, and one of the limiting factors in successful production of these commodities. The relationship among some of the species is unclear due to their high molecular and morphological similarities. Moreover, due to the significant morphological resemblance between fruit fly species, reliable identification is very difficult task...
July 31, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28747718/predicting-the-functional-consequences-of-non-synonymous-single-nucleotide-polymorphisms-in-il8-gene
#7
Tikam Chand Dakal, Deepak Kala, Gourav Dhiman, Vinod Yadav, Andrey Krokhotin, Nikolay V Dokholyan
Here we report an in-silico approach for identification, characterization and validation of deleterious non-synonymous SNPs (nsSNPs) in the interleukin-8 gene using three steps. In first step, sequence homology-based genetic analysis of a set of 50 coding SNPs associated with 41 rsIDs using SIFT (Sorting Intolerant from Tolerant) and PROVEAN (Protein Variation Effect Analyzer) identified 23 nsSNPs to be putatively damaging/deleterious in at least one of the two tools used. Subsequently, structure-homology based PolyPhen-2 (Polymorphism Phenotyping) analysis predicted 9 of 23 nsSNPs (K4T, E31A, E31K, S41Y, I55N, P59L, P59S, L70P and V88D) to be damaging...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747543/mutation-profile-based-methods-for-understanding-selection-forces-in-cancer-somatic-mutations-a-comparative-analysis
#8
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/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/28725363/bridging-two-scholarly-islands-enriches-both-coi-dna-barcodes-for-species-identification-versus-human-mitochondrial-variation-for-the-study-of-migrations-and-pathologies
#11
David S Thaler, Mark Y Stoeckle
DNA barcodes for species identification and the analysis of human mitochondrial variation have developed as independent fields even though both are based on sequences from animal mitochondria. This study finds questions within each field that can be addressed by reference to the other. DNA barcodes are based on a 648-bp segment of the mitochondrially encoded cytochrome oxidase I. From most species, this segment is the only sequence available. It is impossible to know whether it fairly represents overall mitochondrial variation...
October 2016: Ecology and Evolution
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
#12
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/28711653/highly-conserved-intragenic-hsv-2-sequences-results-from-next-generation-sequencing-of-hsv-2-ul-and-us-regions-from-genital-swabs-collected-from-3-continents
#13
Christine Johnston, Amalia Magaret, Pavitra Roychoudhury, Alexander L Greninger, Anqi Cheng, Kurt Diem, Matthew P Fitzgibbon, Meei-Li Huang, Stacy Selke, Jairam R Lingappa, Connie Celum, Keith R Jerome, Anna Wald, David M Koelle
INTRODUCTION: Understanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines. METHODS: Genital lesion swabs containing ≥ 10(7)log10 copies HSV DNA collected from Africa, the USA, and South America underwent next-generation sequencing, followed by K-mer based filtering and de novo genomic assembly. Sites of heterogeneity within coding regions in unique long and unique short (UL_US) regions were identified...
July 13, 2017: Virology
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
#14
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/28696392/comparative-transcriptome-analysis-reveals-adaptive-evolution-of-notopterygium-incisum-and-notopterygium-franchetii-two-high-alpine-herbal-species-endemic-to-china
#15
Yun Jia, Mi-Li Liu, Ming Yue, Zhe Zhao, Gui-Fang Zhao, Zhong-Hu Li
The extreme conditions (e.g., cold, low oxygen, and strong ultraviolet radiation) of the high mountains provide an ideal natural laboratory for studies on speciation and the adaptive evolution of organisms. Up to now, few genome/transcriptome-based studies have been carried out on how plants adapt to conditions at extremely high altitudes. Notopterygium incisum and Notopterygium franchetii (Notopterygium, Apiaceae) are two endangered high-alpine herbal plants endemic to China. To explore the molecular genetic mechanisms of adaptation to high altitudes, we performed high-throughput RNA sequencing (RNA-seq) to characterize the transcriptomes of the two species...
July 11, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28690785/rates-and-relations-of-mitochondrial-genome-evolution-across-the-echinoidea-with-special-focus-on-the-superfamily-odontophora
#16
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/28690071/plasmodium-vivax-rhomboid-like-protease-1-gene-diversity-in-thailand
#17
Touchchapol Mataradchakul, Chairat Uthaipibull, Francois Nosten, Joel Vega-Rodriguez, Marcelo Jacobs-Lorena, Usa Lek-Uthai
BACKGROUND: Plasmodium vivax infection remains a major public health problem, especially along the Thailand border regions. We examined the genetic diversity of this parasite by analyzing single-nucleotide polymorphisms (SNPs) of the P. vivax rhomboid-like protease 1 gene (Pvrom1) in parasites collected from western (Tak province, Thai-Myanmar border) and eastern (Chanthaburi province, Thai-Cambodia border) regions. METHODS: Data were collected by a cross-sectional survey, consisting of 47 and 45 P...
July 6, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28687708/germline-loss-of-function-mutations-in-ephb4-cause-a-second-form-of-capillary-malformation-arteriovenous-malformation-cm-avm2-deregulating-ras-mapk-signaling
#18
Mustapha Amyere, Nicole Revencu, Raphaël Helaers, Eleonore Pairet, Eulalia Baselga, Maria R Cordisco, Wendy K Chung, Josée Dubois, Jean-Philippe Lacour, Loreto Martorell, Juliette Mazereeuw-Hautier, Reed E Pyeritz, David J Amor, Annouk Bisdorff, Francine Blei, Hannah Bombei, Anne Dompmartin, David G Brooks, Juliette Dupont, Maria A González-Enseñat, Ilona J Frieden, Marion Gérard, Malin Kvarnung, Andrea Kwan Hanson-Kahn, Louanne Hudgins, Christine Léauté-Labrèze, Catherine McCuaig, Denise Metry, Philippe Parent, Carle Paul, Florence Petit, Alice Phan, Isabelle Quéré, Aicha Salhi, Anne M Turner, Pierre Vabres, Asuncion Vicente, Orli Wargon, Shoji Watanabe, Lisa Weibel, Ashley Wilson, Marcia Willing, John B Mulliken, Laurence M Boon, Miikka Vikkula
Background -Most AVMs are localized and occur sporadically; however they also can be multifocal in autosomal dominant disorders, such as Hereditary Hemorrhagic Telangiectasia (HHT) and Capillary Malformation-Arteriovenous Malformation (CM-AVM). Previously, we identified RASA1 mutations in 50% of patients with CM-AVM. Herein we studied non-RASA1 patients to further elucidate the pathogenicity of CMs and AVMs. Methods -We conducted a genome-wide linkage study on a CM-AVM family. Whole exome sequencing was also performed on 9 unrelated CM-AVM families...
July 7, 2017: Circulation
https://www.readbyqxmd.com/read/28669524/from-genetic-variability-to-phenotypic-expression-of-blood-group-systems
#19
L Raud, C Férec, Y Fichou
More than 300 red blood cell (RBC) antigens belonging to 36 blood group systems have been officially reported in humans by the International Society of Blood Transfusion (ISBT). Phenotypic variability is directly linked to the expression of the 41 blood group genes. The Rh blood group system, which is composed of 54 antigens, is the most complex and polymorphic system. Many rare genetic variants within the RH (RHD and RHCE) genes, involving various mutational mechanisms (single-nucleotide substitutions, short insertions/deletions, rearrangements, large deletions), have been reported in the literature and reference databases...
June 29, 2017: Transfusion Clinique et Biologique: Journal de la Société Française de Transfusion Sanguine
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
#20
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
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