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Single nucleotide polymorphism and metabolism

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https://www.readbyqxmd.com/read/28530680/the-effect-of-glucose-dependent-insulinotropic-polypeptide-gip-variants-on-visceral-fat-accumulation-in-han-chinese-populations
#1
T Wang, X Ma, T Tang, K Higuchi, D Peng, R Zhang, M Chen, J Yan, S Wang, D Yan, Z He, F Jiang, Y Bao, W Jia, K Ishida, C Hu
OBJECTIVES: We aim to validate the effects of glucose-dependent insulinotropic polypeptide (GIP) on fat distribution and glucose metabolism in Han Chinese populations. METHODS: We genotyped six tag single-nucleotide polymorphisms (SNPs) of GIP and four tag SNPs of glucose-dependent insulinotropic polypeptide receptor (GIPR) among 2884 community-based individuals from Han Chinese populations. Linear analysis was applied to test the associations of these variants with visceral fat area (VFA) and subcutaneous fat area (SFA) quantified by magnetic resonance imaging as well as glucose-related traits...
May 22, 2017: Nutrition & Diabetes
https://www.readbyqxmd.com/read/28527015/a-genome-wide-association-study-identifies-the-genomic-region-associated-with-shell-color-in-yesso-scallop-patinopecten-yessoensis
#2
Liang Zhao, Yangping Li, Yajuan Li, Jiachen Yu, Huan Liao, Shuyue Wang, Jia Lv, Jun Liang, Xiaoting Huang, Zhenmin Bao
The shell color polymorphism widely exists in economic shellfish, which not only results in a better visual perception but also shows great value as an economic trait for breeding. Small numbers of reddish-orange shell Yesso scallops, Patinopecten yessoensis, were found in cultured populations compared to the brown majority. In this study, a genome-wide association study was conducted to understand the genetic basis of shell color. Sixty-six 2b-RAD libraries with equal numbers of reddish-orange and brown shell individuals were constructed and sequenced using the Illumina HiSeq 2000 platform...
May 19, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28526279/an-emerging-role-for-mitochondrial-dynamics-in-schizophrenia
#3
REVIEW
Kyle H Flippo, Stefan Strack
Abnormal brain development has long been thought to contribute to the pathophysiology of schizophrenia. Impaired dendritic arborization, synaptogenesis, and long term potentiation and memory have been demonstrated in animal models of schizophrenia. In addition to aberrant nervous system development, altered brain metabolism and mitochondrial function has long been observed in schizophrenic patients. Single nucleotide polymorphisms in the mitochondrial genome as well as impaired mitochondrial function have both been associated with increased risk for developing schizophrenia...
May 16, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28525288/inference-of-the-genetic-polymorphisms-of-cyp2d6-in-six-subtribes-of-the-malaysian-orang-asli-from-whole-genome-sequencing-data
#4
Choo Yee Yu, Geik Yong Ang, Vinothini Subramaniam, Richard Johari James, Aminuddin Ahmad, Thuhairah Abdul Rahman, Fadzilah Mohd Nor, Syahrul Azlin Shaari, Lay Kek Teh, Mohd Zaki Salleh
AIMS: CYP2D6 is one of the major enzymes in the cytochrome P450 monooxygenase system. It metabolizes ∼25% of prescribed drugs and hence, the genetic diversity of CYP2D6 gene has continued to be of great interest to the medical and pharmaceutical industries. This study aims to perform a systematic analysis of the CYP2D6 gene in six subtribes of the Malaysian Orang Asli. METHODS: Genomic DNAs were extracted from the blood samples followed by whole-genome sequencing...
May 19, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28524801/association-of-ugt2b7-ugt1a9-abcg2-and-il23r-polymorphisms-with-rejection-risk-in-kidney-transplant-patients
#5
Heloísa Lizotti Cilião, Rossana Batista Oliveira Camargo-Godoy, Marilesia Ferreira de Souza, Mariana Bisarro Dos Reis, Lorena Iastrenski, Vinicius Daher Alvares Delfino, Silvia Regina Rogatto, Ilce Mara de Syllos Cólus
Despite advances in testing compatibility between donor and recipient, graft rejection remains a current concern. Single-nucleotide polymorphisms (SNPs) that codify altered enzymes of metabolism, drug transport, and the immune system may contribute to graft rejection in transplant patients. This study examined the association between SNPs present in genes of these processes and occurrence of graft rejection episodes in 246 kidney transplant patients, 35% of which were diagnosed with rejection. Genotype-gene expression associations were also assessed...
May 19, 2017: Journal of Toxicology and Environmental Health. Part A
https://www.readbyqxmd.com/read/28524154/an-analysis-of-the-polymorphisms-of-the-glut1-gene-in-urothelial-cell-carcinomas-of-the-bladder-and-its-correlation-with-p53-ki67-and-glut1-expressions
#6
C Xu, X Yang, Y Wang, N Ding, R Han, Y Sun, Y Wang
Frequencies of two glucose transporter 1 (GLUT1) single-nucleotide polymorphisms (SNPs) (XbaI G>T and HaeIII T>C) were studied with urothelial cell carcinomas of the bladder (UCC) and 204 normal persons. And the expression of the p53, Ki67 and GLUT1 was assayed by immunohistochemistry. The frequency of the TT genotype and T allele of the XbaI G>T SNP was decreased in the patients with UCC. The frequency of the CC genotype and C allele of the HaeIII T>C SNP was decreased in the patients with UCC...
May 19, 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28522317/the-association-between-cytochrome-p450-3a-progesterone-receptor-polymorphisms-plasma-17-ohpc-concentrations-and-spontaneous-preterm-birth
#7
Martha L Bustos, Steve N Caritis, Kathleen A Jablonski, Uma M Reddy, Yoram Sorokin, John M Thorp, Michael W Varner, Ronald J Wapner, Jay D Iams, Marshall W Carpenter, Alan M Peaceman, Brian M Mercer, Anthony Sciscione, Dwight J Rouse, Susan M Ramin
BACKGROUND: Infants born before 37 weeks' gestation are of public health concern since complications associated with preterm birth are the leading cause of mortality in children under 5 years of age and a major cause of morbidity and lifelong disability. The administration of 17-hydroxyprogesterone caproate (17-OHPC) reduces preterm birth by 33% in women with history spontaneous preterm birth (SPTB). We demonstrated previously that plasma concentrations of 17-OHPC vary widely among pregnant women and that women with 17-OHPC plasma concentrations in the lowest quartile had SPTB rates of 40% vs rates of 25% in those women with higher concentrations...
May 15, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28521758/genome-wide-association-study-for-feed-efficiency-and-growth-traits-in-u-s-beef-cattle
#8
Christopher M Seabury, David L Oldeschulte, Mahdi Saatchi, Jonathan E Beever, Jared E Decker, Yvette A Halley, Eric K Bhattarai, Maral Molaei, Harvey C Freetly, Stephanie L Hansen, Helen Yampara-Iquise, Kristen A Johnson, Monty S Kerley, JaeWoo Kim, Daniel D Loy, Elisa Marques, Holly L Neibergs, Robert D Schnabel, Daniel W Shike, Matthew L Spangler, Robert L Weaber, Dorian J Garrick, Jeremy F Taylor
BACKGROUND: Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28515913/promoter-polymorphisms-of-the-vascular-endothelial-growth-factor-gene-are-associated-with-metabolic-syndrome-susceptibility-in-koreans
#9
Young Ree Kim, Seung-Ho Hong
Vascular endothelial growth factor (VEGF) is a potent regulator of angiogenesis. Patients with metabolic syndrome (MetS) have elevated plasma VEGF levels. The aim of the present study was to investigate the association between promoter polymorphisms (the -2578C>A and -1154G>A) of the VEGF gene and MetS susceptibility. A total of 640 subjects were enrolled in the study including 320 patients with MetS and 320 healthy controls. Genotyping of the VEGF single nucleotide polymorphisms was performed by polymerase chain reaction-restriction fragment length polymorphism analysis...
May 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28513222/the-contribution-of-cyp2c-gene-subfamily-involved-in-epoxygenase-pathway-of-arachidonic-acids-metabolism-to-hypertension-susceptibility-in-russian-population
#10
Alexey Polonikov, Marina Bykanova, Irina Ponomarenko, Svetlana Sirotina, Anna Bocharova, Kseniya Vagaytseva, Vadim Stepanov, Mikhail Churnosov, Olga Bushueva, Maria Solodilova, Yaroslav Shvetsov, Vladimir Ivanov
Numerous studies demonstrated an importance of cytochrome P-450 epoxygenase pathway of arachidonic acids metabolism for the pathogenesis of essential hypertension (EH). The present study was designed to investigate whether common single-nucleotide polymorphisms (SNP) of CYP2C gene subfamily such as CYP2C8 (rs7909236 and rs1934953), CYP2C9 (rs9332242), and CYP2C19 (rs4244285) are associated with susceptibility to EH in Russian population. A total of 816 unrelated Russian individuals comprising 425 EH patients and 391 normotensive controls were included into the study...
May 17, 2017: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/28511181/1-cmdb-a-curated-database-of-genomic-variations-of-the-one-carbon-metabolism-pathway
#11
Manoj K Bhat, Veerendra P Gadekar, Aditya Jain, Bobby Paul, Padmalatha S Rai, Kapaettu Satyamoorthy
BACKGROUND: The one-carbon metabolism pathway is vital in maintaining tissue homeostasis by driving the critical reactions of folate and methionine cycles. A myriad of genetic and epigenetic events mark the rate of reactions in a tissue-specific manner. Integration of these to predict and provide personalized health management requires robust computational tools that can process multiomics data. The DNA sequences that may determine the chain of biological events and the endpoint reactions within one-carbon metabolism genes remain to be comprehensively recorded...
May 17, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28500484/association-of-folate-metabolism-gene-polymorphisms-and-haplotype-combination-with-pulmonary-embolism-risk-in-chinese-han-population
#12
Xin Li, Ling Weng, Baihe Han, Yingnan Dai, Li Cha, Shujun Yan, Enze Jin
In this study, we aimed to investigate the association of four single nucleotide polymorphisms (SNPs) (MTHFR 677 C > T, MTHFR 1298 A > C, MTR 2756 A > G and MTRR 66 A > G), gene-gene interaction and haplotype combination with pulmonary embolism (PE) risk based on Chinese Han population. Logistic regression was performed to investigate association between four SNPs within folate metabolism gene and PE risk, and GMDR model was used to investigate the additional gene-gene interactions among the four SNPs...
May 12, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28497838/effect-of-bche-single-nucleotide-polymorphisms-on-lipid-metabolism-markers-in-women
#13
Jéssica de Oliveira, Luciane Viater Tureck, Willian Dos Santos, Louise Farah Saliba, Caroline Schovanz Schenknecht, Débora Scaraboto, Ricardo Lehtonen R Souza, Lupe Furtado-Alle
Butyrylcholinesterase (BChE) activity and polymorphisms in its encoding gene had previously been associated with metabolic traits of obesity. This study investigated the association of three single nucleotide polymorphisms (SNPs) in the BCHE gene: -116G > A (rs1126680), 1615GA (rs1803274), 1914A < G (rs3495), with obesity and lipid metabolism markers, body mass index (BMI), total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C), triglyceride (TG) levels, and BChE enzymatic activity in obese (BMI≥30/n = 226) and non-obese women (BMI < 25/n = 81)...
May 11, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28496949/the-effect-of-interactions-of-single-nucleotide-polymorphisms-of-apoa1-apoc3-with-food-group-intakes-on-the-risk-of-metabolic-syndrome
#14
Firoozeh Hosseini-Esfahani, Parvin Mirmiran, Maryam S Daneshpour, Azadeh Mottaghi, Fereidoun Azizi
BACKGROUND: The aim of this study was to examine the interaction of dietary food groups and genetic variants of APOA1/APOC3, relative to Metabolic Syndrome (MetS) risk in adults. METHODS: In this matched nested case-control study, 414 MetS subjects and 414 controls were selected from among participants of Tehran Lipid and Glucose Study. Dietary intake was assessed with the use of a valid and reliable semi-quantitative food frequency questionnaire. Single Nucleotide Polymorphisms (SNPs), APOA1 (rs670, -75G>A and rs5069, +83C>T/APOC3 rs5128 C3238>G) were genotyped by the conventional polymerase chain reaction and restriction fragment length polymorphism...
April 2017: Avicenna Journal of Medical Biotechnology
https://www.readbyqxmd.com/read/28494655/significant-locus-and-metabolic-genetic-correlations-revealed-in-genome-wide-association-study-of-anorexia-nervosa
#15
Laramie Duncan, Zeynep Yilmaz, Helena Gaspar, Raymond Walters, Jackie Goldstein, Verneri Anttila, Brendan Bulik-Sullivan, Stephan Ripke, Laura Thornton, Anke Hinney, Mark Daly, Patrick F Sullivan, Eleftheria Zeggini, Gerome Breen, Cynthia M Bulik
OBJECTIVE: The authors conducted a genome-wide association study of anorexia nervosa and calculated genetic correlations with a series of psychiatric, educational, and metabolic phenotypes. METHOD: Following uniform quality control and imputation procedures using the 1000 Genomes Project (phase 3) in 12 case-control cohorts comprising 3,495 anorexia nervosa cases and 10,982 controls, the authors performed standard association analysis followed by a meta-analysis across cohorts...
May 12, 2017: American Journal of Psychiatry
https://www.readbyqxmd.com/read/28488691/interaction-effect-of-pgc-1%C3%AE-rs10517030-variants-and-energy-intake-in-the-risk-of-type-2-diabetes-in-middle-aged-adults
#16
S Park, B C Kim, S Kang
BACKGROUND/OBJECTIVES: PGC-1α is an important regulatory factor for energy and glucose metabolism. Therefore, we investigated whether the PGC-1α genotype (rs10517030 and rs10212638) affects the incidence of type 2 diabetes mellitus (T2DM) and sought to explain the interactions between their variants and nutrient intake on the development of T2DM. SUBJECTS/METHODS: Subjects aged 40-65 years of both genders were from the Ansung/Ansan cohorts (8842 adults) in Korea...
May 10, 2017: European Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28487722/association-mapping-reveals-novel-genetic-loci-contributing-to-flooding-tolerance-during-germination-in-indica-rice
#17
Mengchen Zhang, Qing Lu, Wei Wu, Xiaojun Niu, Caihong Wang, Yue Feng, Qun Xu, Shan Wang, Xiaoping Yuan, Hanyong Yu, Yiping Wang, Xinghua Wei
Rice (Oryza sativa L.) is the only cereal crop that possesses the ability to germinate under flooded or other oxygen-deficient conditions. Rapid elongation of the coleoptile is a perfect response to flooding during germination, with coleoptile length differing among various rice varieties. Despite multiple studies have uncovered valuable information concerning this trait by focusing on the physiological metabolism of oxygen stress, the underlying genetic mechanism still remains unknown. In the present study, we screened coleoptile lengths of 432 indica varieties germinated in two environments (normal and flooded) and found more variation existing in flooded coleoptile length (FCL) rather than in normal coleoptile length (NCL)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28486474/vitamin-d-levels-and-susceptibility-to-asthma-elevated-immunoglobulin-e-levels-and-atopic-dermatitis-a-mendelian-randomization-study
#18
Despoina Manousaki, Lavinia Paternoster, Marie Standl, Miriam F Moffatt, Martin Farrall, Emmanuelle Bouzigon, David P Strachan, Florence Demenais, Mark Lathrop, William O C M Cookson, J Brent Richards
BACKGROUND: Low circulating vitamin D levels have been associated with risk of asthma, atopic dermatitis, and elevated total immunoglobulin E (IgE). These epidemiological associations, if true, would have public health importance, since vitamin D insufficiency is common and correctable. METHODS AND FINDINGS: We aimed to test whether genetically lowered vitamin D levels were associated with risk of asthma, atopic dermatitis, or elevated serum IgE levels, using Mendelian randomization (MR) methodology to control bias owing to confounding and reverse causation...
May 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28484228/genomic-evidence-for-local-adaptation-in-the-ovoviviparous-marine-fish-sebastiscus-marmoratus-with-a-background-of-population-homogeneity
#19
Shengyong Xu, Na Song, Linlin Zhao, Shanshan Cai, Zhiqiang Han, Tianxiang Gao
Advances in next-generation sequencing techniques have allowed for the generation of genome-wide sequence data, to gain insight into the dynamics influencing genetic structure and the local adaptation of marine fish. Here, using genotyping-by-sequencing (GBS) technique, we identified 31,119 single nucleotide polymorphisms (SNPs) for Sebastiscus marmoratus in 59 individuals from three populations in Chinese coastal waters. Based on all SNPs, there was little evidence of genetic differentiation among populations...
May 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28476773/genome-stability-in-engineered-strains-of-the-extremely-thermophilic-lignocellulose-degrading-bacterium-caldicellulosiruptor-bescii
#20
Amanda M Williams-Rhaesa, Farris L Poole, Jessica T Dinsmore, Gina L Lipscomb, Gabriel M Rubinstein, Israel M Scott, Jonathan M Conway, Laura L Lee, Piyum A Khatibi, Robert M Kelly, Michael W W Adams
Caldicellulosiruptor bescii is the most thermophilic cellulose-degrader known and is of great interest because of its ability to degrade non-pretreated plant biomass. For biotechnological applications, an efficient genetic system is required to engineer it to convert plant biomass into desired products. To date, two different genetically-tractable lineages of C. bescii strains have been generated. The first (JWCB005) is based on a random deletion within the pyrimidine biosynthesis genes pyrFA, and the second (MACB1018) is based on the targeted deletion of pyrE making use of a kanamycin resistance marker...
May 5, 2017: Applied and Environmental Microbiology
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