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https://www.readbyqxmd.com/read/28500993/nonsynonymous-changes-of-equine-lentivirus-receptor-1-elr1-gene-in-amino-acids-involved-in-the-interaction-with-equine-infectious-anemia-virus-eiav
#1
C M Corbi-Botto, S A Sadaba, M E Zappa, P Peral-García, S Díaz
Equine lentivirus receptor-1 (ELR1) has been characterized as the specific functional receptor that mediates equine infectious anemia virus (EIAV) entrance to horse macrophages. This receptor is tumor necrosis factor receptor superfamily member 14 (TNFRSF14). The aim of this study was to investigate the occurrence of allelic variants in the coding sequence of equine TNFRSF14 gene by screening for single-nucleotide polymorphisms (SNPs) in different equine populations. Forty seven horse samples were randomly selected from a reservoir of EIAV-seropositive and seronegative samples collected from different outbreaks and regions of Argentina...
May 2, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/28495802/a-common-nhe3-single-nucleotide-polymorphism-has-normal-function-and-sensitivity-to-regulatory-ligands
#2
Jianyi Yin, Chung-Ming Tse, Boyoung Cha, Rafiqual Sarker, Xinjun C Zhu, Anna Walentinsson, Peter J Greasley, Mark Donowitz
Na(+)/H(+) exchanger NHE3 mediates the majority of intestinal and renal electroneutral sodium absorption. Dysfunction of NHE3 is associated with a variety of diarrheal diseases. We previously reported that the NHE3 gene (SLC9A3) has more than 400 single nucleotide polymorphisms (SNPs) but few non-synonymous polymorphisms. Among the latter, one polymorphism (rs2247114-G>A), which causes a substitution from arginine to cysteine at amino acid position 799 (p.R799C), is common in Asian populations. To improve our understanding of the population distribution and potential clinical significance of the NHE3-799C variant, we investigated the frequency of this polymorphism in different ethnic groups using bioinformatics analyses, and in a cohort of Japanese patients with cardiovascular or renal disease...
May 11, 2017: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/28486573/is-a-non-synonymous-snp-in-the-hvaact1-coding-region-associated-with-acidic-soil-tolerance-in-barley
#3
Jéssica Rosset Ferreira, Bruna Franciele Faria, Moacyr Comar, Carla Andréa Delatorre, Euclydes Minella, Jorge Fernando Pereira
The barley HvAACT1 gene codes for a citrate transporter associated with tolerance to acidic soil. In this report, we describe a single nucleotide polymorphism (SNP) in the HvAACT1 coding region that was detected as T-1,198 (in genotypes with lower root growth on acidic soil) or G-1,198 (greater root growth) and resulted in a single amino acid change (L/V-172). Molecular dynamic analysis predicted that HvAACT1 proteins with L or V-172 were stable, although the substitution led to structural changes within the protein...
May 8, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28475630/genome-wide-analysis-of-the-evolution-of-senecavirus-a-from-swine-clinical-material-and-assembly-yard-environmental-samples
#4
Wanhong Xu, Kate Hole, Melissa Goolia, Bradley Pickering, Tim Salo, Oliver Lung, Charles Nfon
Senecavirus A (SVA), previously known as Seneca Valley virus, was first isolated in the United States in 2002. SVA was associated with porcine idiopathic vesicular disease in Canada and the USA in 2007 and 2012, respectively. Recent increase in SVA outbreaks resulting in neonatal mortality of piglets and/or vesicular lesions in sows in Brazil, the USA and Canada point to the necessity to study the pathogenicity and molecular epidemiology of the virus. Here, we report the analysis of the complete coding sequences of SVA from 2 clinical cases and 9 assembly yard environmental samples collected in 2015 in Canada, along with 22 previously released complete genomes in the GenBank...
2017: PloS One
https://www.readbyqxmd.com/read/28475588/widespread-position-specific-conservation-of-synonymous-rare-codons-within-coding-sequences
#5
Julie L Chaney, Aaron Steele, Rory Carmichael, Anabel Rodriguez, Alicia T Specht, Kim Ngo, Jun Li, Scott Emrich, Patricia L Clark
Synonymous rare codons are considered to be sub-optimal for gene expression because they are translated more slowly than common codons. Yet surprisingly, many protein coding sequences include large clusters of synonymous rare codons. Rare codons at the 5' terminus of coding sequences have been shown to increase translational efficiency. Although a general functional role for synonymous rare codons farther within coding sequences has not yet been established, several recent reports have identified rare-to-common synonymous codon substitutions that impair folding of the encoded protein...
May 5, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28466109/fine-mapping-identifies-csgcn5-encoding-a-histone-acetyltransferase-as-putative-candidate-gene-for-tendril-less1-mutation-td-1-in-cucumber
#6
Feifan Chen, Bingbing Fu, Yupeng Pan, Chaowen Zhang, Haifan Wen, Yiqun Weng, Peng Chen, Yuhong Li
Next-generation sequencing-aided map-based cloning delimited the cucumber tendril - less1 ( td - 1 ) locus into a 190.7-kb region in chromosome 6 harboring a putative, novel-function candidate gene encoding a histone acetyltransferase ( CsGCN5 ). The tendril initiated from the lateral meristem is an important and characteristic organ for the species in the Cucurbitaceae family including cucumber (Cucumis sativus L.). While the tendril has its evolutionary significance, it also poses a nuisance in cucumber cultivation under protected environments in which tendril-less cucumber has its advantages...
May 2, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28459834/genome-wide-analysis-of-rice-dehydrin-gene-family-its-evolutionary-conservedness-and-expression-pattern-in-response-to-peg-induced-dehydration-stress
#7
Giti Verma, Yogeshwar Vikram Dhar, Dipali Srivastava, Maria Kidwai, Puneet Singh Chauhan, Sumit Kumar Bag, Mehar Hasan Asif, Debasis Chakrabarty
Abiotic stresses adversely affect cellular homeostasis, impairing overall growth and development of plants. These initial stress signals activate downstream signalling processes, which, subsequently, activate stress-responsive mechanisms to re-establish homeostasis. Dehydrins (DHNs) play an important role in combating dehydration stress. Rice (Oryza sativa L.), which is a paddy crop, is susceptible to drought stress. As drought survival in rice might be viewed as a trait with strong evolutionary selection pressure, we observed DHNs in the light of domestication during the course of evolution...
2017: PloS One
https://www.readbyqxmd.com/read/28456503/novel-oxytocin-receptor-variants-in-laboring-women-requiring-high-doses-of-oxytocin
#8
Erin L Reinl, Zane A Goodwin, Nandini Raghuraman, Grace Y Lee, Erin Y Jo, Beakal M Gezahegn, Meghan K Pillai, Alison G Cahill, Cristina De Guzman Strong, Sarah K England
BACKGROUND: Although oxytocin commonly is used to augment or induce labor, it is difficult to predict its effectiveness because oxytocin dose requirements vary significantly among women. One possibility is that women requiring high or low doses of oxytocin have variations in the oxytocin receptor gene. OBJECTIVES: To identify oxytocin receptor gene variants in laboring women with low and high oxytocin dosage requirements. STUDY DESIGN: Term, nulliparous women requiring oxytocin doses of ≤4 mU/min (low-dose requiring, n = 83) or ≥20 mU/min (high-dose requiring, n = 104) for labor augmentation or induction provided consent to a postpartum blood draw as a source of genomic DNA...
April 26, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28456306/characterization-and-establishment-of-a-reference-deltamethrin-and-cypermethrin-resistant-tick-line-ivri-iv-of-rhipicephalus-boophilus-microplus
#9
Srikant Ghosh, Snehil Gupta, K G Ajith Kumar, Anil Kumar Sharma, Sachin Kumar, Gaurav Nagar, Rinesh Kumar, Souvik Paul, Ashutosh Fular, Gajanan Chigure, Abhijit Nandi, H V Manjunathachar, Aquil Mohammad, M R Verma, B C Saravanan, Debdatta Ray
The problem of ticks and tick borne diseases is a global threat and growing reports of resistance to commonly used insecticides further aggravated the condition and demands for country specific resistance monitoring tools and possible solutions of the problem. Establishment of standard reference is prerequisite for development of monitoring tools. For studying possible role of different mechanisms involved in development of resistance in Rhipicephalus (Boophilus) microplus population and to develop newer drug to manage the problem of resistance, a deltamethrin exposed and selected tick colony, referred to as IVRI-IV, was characterized using reference susceptible IVRI-I tick line as control...
May 2017: Pesticide Biochemistry and Physiology
https://www.readbyqxmd.com/read/28454448/gnaq-mutation-r183q-as-a-potential-cause-of-familial-sturge-weber-syndrome-a-case-report
#10
Zhengyi Huang, Yuchi Li, Zengxia Zhao, Jun Hu, Xiaoxin Tong, Xuhui Chen, Shuyun Liu, Xiaonan Xu, Yongjun Tao, Tingting Wang, Xin Cheng, Yangyang Dai, Yaoting Gui, Jun Wu
Sturge-Weber syndrome (SWS) is a rare neurocutaneous disorder whose etiology remains unclear. To investigate the genetic contribution underlying this disease, the genetic variants of a 4-generation family with a history of SWS was analyzed in the present study. SWS was diagnosed in 3 of the family members (II-1, III-11 and IV-6). Sanger sequencing was performed to identify mutations in G protein subunit αq (GNAQ) and RAS p21 protein activator 1 exons in the 3 patients with SWS and other unaffected family members...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28431152/insights-into-the-existence-of-isomeric-plastomes-in-cupressoideae-cupressaceae
#11
Xiao-Jian Qu, Chung-Shien Wu, Shu-Miaw Chaw, Ting-Shuang Yi
The cypress family (Cupressaceae) possesses highly rearranged plastomes that lack a pair of large inverted repeats typically found in land plants. A few cypress species have been reported to contain isomeric plastomes, but whether the existence of isomeric plastomes is ubiquitous in the family remains to be investigated with a broader taxon sampling. In this study, we sequenced the complete plastomes of ten species in Cupressoideae, the largest cypress subfamily. Cupressoideae showed relatively accelerated rates of substitutions at both nonsynonymous and synonymous sites as compared with other subfamilies of Cupressaceae...
April 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28423875/adaptive-selection-at-agouti-gene-inferred-breed-specific-selection-signature-within-the-indigenous-goat-populations
#12
Hafiz Ishfaq Ahmad, Guiqiong Liu, Xunping Jiang, Chenhui Liu, Xu Fangzheng, Yuqing Chong, Nabeel Ijaz, Huang Huarong
Objective: The aim of this study was to calculate selection signatures at possible loci leading to population differentiation, as well as pattern of selection of agouti gene within the local goat breeds and its correlation among other animal species to reveal molecular evolution. Methods: The high Fst outlier method corresponding to Fst distribution was used to identify the loci subject to positive selection. According to the empirical distribution of Fst estimates, we selected the SNPs having high Fst outlier corresponded to the upper 1% of the distribution as the loci under selection...
April 19, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28420808/sequence-variations-in-estrogen-receptor-1-and-2-genes-and-their-association-with-egg-production-traits-in-chinese-dagu-chickens
#13
Xiaotian Niu, Thobela Louis Tyasi, Ning Qin, Dehui Liu, Hongyan Zhu, Xiaoxia Chen, Fengwei Zhang, Shuguo Yuan, Rifu Xu
Estrogen receptors α (ESR1) and β (ESR2) play central roles in folliculogenesis, and therefore in reproductive biology. In the present study, two single nucleotide polymorphisms (SNPs) were identified in the ESR1 and ESR2 genes using PCR-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing. One of the identified SNPs, a T1101C transition located within exon 4 of the ESR1 gene, was significantly associated with hen-housed egg production (HHEP) at 30, 43, 57 and 66 weeks of age (P<0.05), and egg weight (EW) at 30 weeks (P<0...
April 15, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28419109/polymorphisms-in-the-selectin-gene-cluster-are-associated-with-fertility-and-survival-time-in-a-population-of-holstein-friesian-cows
#14
Xing Chen, Shujun Zhang, Zhangrui Cheng, Jessica S Cooke, Dirk Werling, D Claire Wathes, Geoffrey E Pollott
Selectins are adhesion molecules, which mediate attachment between leucocytes and endothelium. They aid extravasation of leucocytes from blood into inflamed tissue during the mammary gland's response to infection. Selectins are also involved in attachment of the conceptus to the endometrium and subsequent placental development. Poor fertility and udder health are major causes for culling dairy cows. The three identified bovine selectin genes SELP, SELL and SELE are located in a gene cluster. SELP is the most polymorphic of these genes...
2017: PloS One
https://www.readbyqxmd.com/read/28414099/molecular-evolution-of-the-plastid-genome-during-diversification-of-the-cotton-genus
#15
Zhiwen Chen, Corrinne E Grover, Pengbo Li, Yumei Wang, Hushuai Nie, Yanpeng Zhao, Meiyan Wang, Fang Liu, Zhongli Zhou, Xingxing Wang, Xiaoyan Cai, Kunbo Wang, Jonathan F Wendel, Jinping Hua
Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and one tetraploid genomic group, namely AD. To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome duringdiversification, chloroplast genomes (cpDNA) from 6 D-genome and 2 G-genome species of Gossypium (G. armourianum D2-1, G. harknessii D2-2, G. davidsonii D3-d, G. klotzschianum D3-k, G. aridum D4, G. trilobum D8, and G. australe G2, G. nelsonii G3) were newly reported here...
April 13, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28411162/insights-into-evolution-in-andean-polystichum-dryopteridaceae-from-expanded-understanding-of-the-cytosolic-phosphoglucose-isomerase-gene
#16
Brendan M Lyons, Monique A McHenry, David S Barrington
Cytosolic phosphoglucose isomerase (pgiC) is an enzyme essential to glycolysis found universally in eukaryotes, but broad understanding of variation in the gene coding for pgiC is lacking for ferns. We used a substantially expanded representation of the gene for Andean species of the fern genus Polystichum to characterize pgiC in ferns relative to angiosperms, insects, and an amoebozoan; assess the impact of selection versus neutral evolutionary processes on pgiC; and explore evolutionary relationships of selected Andean species...
April 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28397003/plastome-wide-nucleotide-substitution-rates-reveal-accelerated-rates-in-papilionoideae-and-correlations-with-genome-features-across-legume-subfamilies
#17
Erika N Schwarz, Tracey A Ruhlman, Mao-Lun Weng, Mohammad A Khiyami, Jamal S M Sabir, Nahid H Hajarah, Njud S Alharbi, Samar O Rabah, Robert K Jansen
This study represents the most comprehensive plastome-wide comparison of nucleotide substitution rates across the three subfamilies of Fabaceae: Caesalpinioideae, Mimosoideae, and Papilionoideae. Caesalpinioid and mimosoid legumes have large, unrearranged plastomes compared with papilionoids, which exhibit varying levels of rearrangement including the loss of the inverted repeat (IR) in the IR-lacking clade (IRLC). Using 71 genes common to 39 legume taxa representing all the three subfamilies, we show that papilionoids consistently have higher nucleotide substitution rates than caesalpinioids and mimosoids, and rates in the IRLC papilionoids are generally higher than those in the IR-containing papilionoids...
April 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28396254/mutpred-mutational-load-analysis-shows-mildly-deleterious-mitochondrial-dna-variants-are-not-more-prevalent-in-alzheimer-s-patients-but-may-be-under-represented-in-healthy-older-individuals
#18
Ilse S Pienaar, Neil Howell, Joanna L Elson
Mitochondrial DNA (mtDNA) association studies have been conducted for over a decade using the haplogroup (lineage) association method, but this frequently produces conflicting results. Here we analyzed complete mtDNA sequence data of Alzheimer's disease (AD) patients and aged controls, from the United Kingdom (UK) and the United States (US), using a new "mutational load" method. We calculated a pathogenicity score for each of the non-synonymous substitutions of the mtDNA sequences to produce a "total mutational load" for each sequence, and compared the mutational loads of cases and controls...
April 7, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28391525/regsnps-splicing-a-tool-for-prioritizing-synonymous-single-nucleotide-substitution
#19
Xinjun Zhang, Meng Li, Hai Lin, Xi Rao, Weixing Feng, Yuedong Yang, Matthew Mort, David N Cooper, Yue Wang, Yadong Wang, Clark Wells, Yaoqi Zhou, Yunlong Liu
While synonymous single-nucleotide variants (sSNVs) have largely been unstudied, since they do not alter protein sequence, mounting evidence suggests that they may affect RNA conformation, splicing, and the stability of nascent-mRNAs to promote various diseases. Accurately prioritizing deleterious sSNVs from a pool of neutral ones can significantly improve our ability of selecting functional genetic variants identified from various genome-sequencing projects, and, therefore, advance our understanding of disease etiology...
April 8, 2017: Human Genetics
https://www.readbyqxmd.com/read/28388287/in-silico-analysis-of-non-synonymous-single-nucleotide-polymorphisms-in-human-dazl-gene-associated-with-male-infertility
#20
Mili Nailwal, Jenabhai B Chauhan
In living systems the most frequent type of genetic mutation is the single nucleotide polymorphism (SNP). Non-synonymous SNPs (nsSNPs) or missense mutations arise in coding regions of a particular gene. nsSNPs result in a single amino acid substitution which may have effects on the structure and/or function of proteins. Spermatogenesis is a complex process where haploid spermatozoa are formed. The deleted in azoospermia like (DAZL) gene has a relationship with male infertility and dysfunction of DAZL may decrease the sperm count which leads to oligozoospermia or azoospermia...
April 7, 2017: Systems Biology in Reproductive Medicine
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