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Single nucleotide polymorphism and metabolism

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https://www.readbyqxmd.com/read/28086804/comparative-analysis-of-the-root-transcriptomes-of-cultivated-sweetpotato-ipomoea-batatas-l-lam-and-its-wild-ancestor-ipomoea-trifida-kunth-g-don
#1
Sathish K Ponniah, Jyothi Thimmapuram, Ketaki Bhide, Venu Kal Kalavacharla, Muthusamy Manoharan
BACKGROUND: The complex process of formation of storage roots (SRs) from adventitious roots affects sweetpotato yield. Identifying the genes that are uniquely expressed in the SR forming cultivated species, Ipomoea batatas (Ib), and its immediate ancestral species, Ipomoea trifida (It), which does not form SRs, may provide insights into the molecular mechanisms underlying SR formation in sweetpotato. RESULTS: Illumina paired-end sequencing generated ~208 and ~200 million reads for Ib and It, respectively...
January 13, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28086798/genome-wide-association-analysis-of-seedling-traits-in-diverse-sorghum-germplasm-under-thermal-stress
#2
Ratan Chopra, Gloria Burow, John J Burke, Nicholas Gladman, Zhanguo Xin
BACKGROUND: Climate variability due to fluctuation in temperature is a worldwide concern that imperils crop production. The need to understand how the germplasm variation in major crops can be utilized to aid in discovering and developing breeding lines that can withstand and adapt to temperature fluctuations is more necessary than ever. Here, we analyzed the genetic variation associated with responses to thermal stresses in a sorghum association panel (SAP) representing major races and working groups to identify single nucleotide polymorphisms (SNPs) that are associated with resilience to temperature stress in a major cereal crop...
January 13, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28069032/glucocorticoid-receptor-gene-polymorphisms-in-hereditary-angioedema-with-c1-inhibitor-deficiency
#3
Zsuzsanna Zotter, Zsolt Nagy, Attila Patócs, Dorottya Csuka, Nóra Veszeli, Kinga Viktória Kőhalmi, Henriette Farkas
BACKGROUND: Hereditary angioedema caused by C1-inhibitor deficiency (C1-INH-HAE) is a rare, autosomal dominant disorder. C1-INH-HAE is characterized by edema-formation, which may occur in response to stress. The individual's response to stress stimuli is partly genetically determined. Activation of the hypothalamic-pituitary-adrenal axis results in the release of cortisol. In turn, the secreted gluco- and mineralocorticoids affect the metabolism, as well as the cardiovascular and immune systems...
January 10, 2017: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/28059470/levels-of-heavy-metals-and-their-binding-protein-metallothionein-in-type-2-diabetics-with-kidney-disease
#4
Martina Raudenska, Veronika Dvorakova, Lukas Pacal, Katarina Chalasova, Monika Kratochvilova, Jaromir Gumulec, Branislav Ruttkay-Nedecky, Ondrej Zitka, Katerina Kankova, Vojtech Adam, Michal Masarik
Hyperglycemia, a major metabolic disturbance present in diabetes, promotes oxidative stress. Activation of antioxidant defense is an important mechanism to prevent cell damage. Levels of heavy metals and their binding proteins can contribute to oxidative stress. Antiradical capacity and levels of metallothionein (MT), metals (zinc and copper), and selected antioxidants (bilirubin, cysteine, and glutathione) were determined in 70 type 2 diabetes mellitus (T2DM) subjects and 80 healthy subjects of Caucasian origin...
January 6, 2017: Journal of Biochemical and Molecular Toxicology
https://www.readbyqxmd.com/read/28056769/a-genome-wide-association-study-of-seed-composition-traits-in-wild-soybean-glycine-soja
#5
Larry J Leamy, Hengyou Zhang, Changbao Li, Charles Y Chen, Bao-Hua Song
BACKGROUND: Cultivated soybean (Glycine max) is a major agricultural crop that provides a crucial source of edible protein and oil. Decreased amounts of saturated palmitic acid and increased amounts of unsaturated oleic acid in soybean oil are considered optimal for human cardiovascular health and therefore there has considerable interest by breeders in discovering genes affecting the relative concentrations of these fatty acids. Using a genome-wide association (GWA) approach with nearly 30,000 single nucleotide polymorphisms (SNPs), we investigated the genetic basis of protein, oil and all five fatty acid levels in seeds from a sample of 570 wild soybeans (Glycine soja), the progenitor of domesticated soybean, to identify quantitative trait loci (QTLs) affecting these seed composition traits...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28052106/a-prediction-algorithm-for-drug-response-in-patients-with-mesial-temporal-lobe-epilepsy-based-on-clinical-and-genetic-information
#6
Mariana S Silva-Alves, Rodrigo Secolin, Benilton S Carvalho, Clarissa L Yasuda, Elizabeth Bilevicius, Marina K M Alvim, Renato O Santos, Claudia V Maurer-Morelli, Fernando Cendes, Iscia Lopes-Cendes
Mesial temporal lobe epilepsy is the most common form of adult epilepsy in surgical series. Currently, the only characteristic used to predict poor response to clinical treatment in this syndrome is the presence of hippocampal sclerosis. Single nucleotide polymorphisms (SNPs) located in genes encoding drug transporter and metabolism proteins could influence response to therapy. Therefore, we aimed to evaluate whether combining information from clinical variables as well as SNPs in candidate genes could improve the accuracy of predicting response to drug therapy in patients with mesial temporal lobe epilepsy...
2017: PloS One
https://www.readbyqxmd.com/read/28050888/a-new-cyp3a5-3-and-cyp3a4-22-cluster-influencing-tacrolimus-target-concentrations-a-population-approach
#7
Franc Andreu, Helena Colom, Laure Elens, Teun van Gelder, Ronald H N van Schaik, Dennis A Hesselink, Oriol Bestard, Joan Torras, Josep M Cruzado, Josep M Grinyó, Nuria Lloberas
BACKGROUND: Single nucleotide polymorphisms (SNPs) in the CYP3A5 and CYP3A4 genes have been reported to be an important cause of variability in the pharmacokinetics of tacrolimus in renal transplant patients. The aim of this study was to merge all of the new genetic information available with tacrolimus pharmacokinetics to generate a more robust population model with data from renal transplant recipients. METHODS: Tacrolimus exposure data from 304 renal transplant recipients were collected throughout the first year after transplantation and were simultaneously analyzed with a population pharmacokinetic approach using NONMEM(®) version 7...
January 3, 2017: Clinical Pharmacokinetics
https://www.readbyqxmd.com/read/28049954/no-effect-of-slco1b1-and-cyp3a4-5-polymorphisms-on-the-pharmacokinetics-and-pharmacodynamics-of-ticagrelor-in-healthy-chinese-male-subjects
#8
Mupeng Li, Yaodong Hu, Huilan Li, Zhipeng Wen, Xiaolei Hu, Daoyu Zhang, Yanjiao Zhang, Jian Xiao, Jie Tang, Xiaoping Chen
Ticagrelor is a direct-acting P2Y12 receptor antagonist. It is rapidly absorbed and partly metabolized to the active metabolite AR-C124910XX by CYP3A4 and CYP3A5. Three genetic loci (SLCO1B1, CYP3A4, and UGT2B7) were reported to affect ticagrelor pharmacokinetics. This study aimed to investigate the possible effects of SLCO1B1 and CYP3A4/5 genetic polymorphisms on the pharmacokinetics and pharmacodynamics of ticagrelor in healthy Chinese male volunteers. Eighteen healthy male volunteers who participated in pharmacogenetics study of ticagrelor were genotyped for SLCO1B1 rs113681054, SLCO1B1*5 (rs4149056), CYP3A4*1G (rs2242480), and CYP3A5*3 (rs776746)...
2017: Biological & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28046029/genetic-variants-in-mthfr-gene-predict-%C3%A2-2-radiation-pneumonitis-in-esophageal-squamous-cell-carcinoma-patients-treated-with-thoracic-radiotherapy
#9
Yang Zhang, Zongjuan Li, Jian Zhang, Hongsheng Li, Yumei Qiao, Chengsuo Huang, Baosheng Li
Reactive oxygen species (ROS), formed as an indirect production of radiotherapy (RT), could cause DNA damage of normal tissues. Meanwhile, our body possesses the ability to restore the damage by DNA repair pathways. The imbalance between the two systems could finally result in radiation injury. Therefore, in this prospective cohort study, we explored the association of genetic variants in ROS metabolism and DNA repair pathway-related genes with radiation pneumonitis (RP). A total of 265 locally advanced esophageal squamous cell carcinoma (ESCC) patients receiving RT in Chinese Han population were enrolled...
2017: PloS One
https://www.readbyqxmd.com/read/28043790/thymidylate-synthase-gene-polymorphisms-as-important-contributors-affecting-hepatocellular-carcinoma-prognosis
#10
X Wang, X Sun, X Du, F Zhou, F Yang, J Xing, G Dong, X Guo
BACKGROUND: Thymidylate synthase (TYMS), a key rate-limiting enzyme in the folate metabolism, plays essential roles in the development of several malignancies including hepatocellular carcinoma (HCC). Nonetheless, the association of the single nucleotide polymorphisms (SNPs) in TYMS gene with the prognosis of Chinese HCC patients remains unknown. METHODS: A total of 492 HCC patients who underwent surgery treatment were included in this study. Five functional SNPs (rs2847153, rs2853533, rs502396, rs523230, and rs9967368) in TYMS gene were genotyped using the iPLEX genotyping system...
December 30, 2016: Clinics and Research in Hepatology and Gastroenterology
https://www.readbyqxmd.com/read/28043631/the-first-population-structure-and-comparative-genomics-analysis-of-mycobacterium-africanum-strains-from-ghana-reveals-higher-diversity-of-lineage-5
#11
Isaac D Otchere, Simon R Harris, Sanches L Busso, Adwoa Asante-Poku, Stephen Osei-Wusu, Kwadwo Koram, Julian Parkhill, Sebastien Gagneux, Dorothy Yeboah-Manu
OBJECTIVE/BACKGROUND: Mycobacterium africanum (MAF) remains an important TB causing pathogen in West Africa; however, little is known about its population structure and actual diversity which may have implications for diagnostics and vaccines. We carried out comparative genomics analysis of candidate Mycobacterium tuberculosis (MTB) and MAF using whole genome sequencing. METHODS: Clinical MTB complex strains (n=187) comprising L4 (n=22), L5 (n=126), and L6 (n=39) isolated over 8years from Ghana were whole genome sequenced...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28040800/identification-introgression-and-validation-of-fruit-volatile-qtls-from-a-red-fruited-wild-tomato-species
#12
José L Rambla, Aurora Medina, Asun Fernández-Del-Carmen, Walter Barrantes, Silvana Grandillo, Maria Cammareri, Gloria López-Casado, Guillermo Rodrigo, Arancha Alonso, Santiago García-Martínez, Jaime Primo, Juan J Ruiz, Rafael Fernández-Muñoz, Antonio J Monforte, Antonio Granell
Volatile organic compounds (VOCs) are major determinants of fruit flavor, a primary objective in tomato breeding. A recombinant inbred line (RIL) population consisting of 169 lines derived from a cross between Solanum lycopersicum and a red-fruited wild tomato species Solanum pimpinellifolium accession (SP) was characterized for VOCs in three different seasons. Correlation and hierarchical cluster analyses were performed on the 52 VOCs identified, providing a tool for the putative assignation of individual compounds to metabolic pathways...
December 30, 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28030618/whole-genome-resequencing-of-holstein-bulls-for-indel-discovery-and-identification-of-genes-associated-with-milk-composition-traits-in-dairy-cattle
#13
Jianping Jiang, Yahui Gao, Yali Hou, Wenhui Li, Shengli Zhang, Qin Zhang, Dongxiao Sun
The use of whole-genome resequencing to obtain more information on genetic variation could produce a range of benefits for the dairy cattle industry, especially with regard to increasing milk production and improving milk composition. In this study, we sequenced the genomes of eight Holstein bulls from four half- or full-sib families, with high and low estimated breeding values (EBVs) of milk protein percentage and fat percentage at an average effective depth of 10×, using Illumina sequencing. Over 0.9 million nonredundant short insertions and deletions (indels) [1-49 base pairs (bp)] were obtained...
2016: PloS One
https://www.readbyqxmd.com/read/28030534/single-nucleotide-polymorphism-of-cyp3a5-impacts-the-exposure-to-tacrolimus-in-pediatric-renal-transplant-recipients-a-pharmacogenetic-substudy-of-the-twist-trial
#14
Heiko Billing, Britta Höcker, Alexander Fichtner, Rita van Damme-Lombaerts, Styrbjorn Friman, Jenö Jaray, Karel Vondrak, Eniko Sarvary, Luca Dello Strologo, Michael Oellerich, Nicolas von Ahsen, Burkhard Tönshoff
BACKGROUND: The pharmacokinetics (PK) of tacrolimus (TAC) and mycophenolic acid (MPA) are highly variable. An impact of single-nucleotide polymorphisms (SNPs) of the genes coding for enzymes and transporters involved in the PK of TAC and/or MPA is intuitively conceivable. Accordingly, we sought to analyze the influence of different SNPs on TAC and MPA exposure in pediatric renal transplant recipients. METHODS: A subpopulation of 37 patients (median age: 12.8 years, range 2...
November 24, 2016: Therapeutic Drug Monitoring
https://www.readbyqxmd.com/read/28028006/identification-and-analysis-of-the-human-sex-biased-genes
#15
Sisi Guo, Yuan Zhou, Pan Zeng, Guoheng Xu, Guoqing Wang, Qinghua Cui
Tremendous differences between human sexes are universally observed. Therefore, identifying and analyzing the sex-biased genes are becoming basically important for uncovering the mystery of sex differences and personalized medicine. Here, we presented a computational method to identify sex-biased genes from public gene expression databases. We obtained 1407 female-biased genes (FGs) and 1096 male-biased genes (MGs) across 14 different tissues. Bioinformatics analysis revealed that compared with MGs, FGs have higher evolutionary rate, higher single-nucleotide polymorphism density, less homologous gene numbers and smaller phyletic age...
December 27, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28025170/instability-of-c154y-variant-of-aldo-keto-reductase-1c3
#16
Satoshi Endo, Sayaka Takada, Ryo P Honda, Kathrin Müller, Jochen H Weishaupt, Peter M Andersen, Albert C Ludolph, Yuji O Kamatari, Toshiyuki Matsunaga, Kazuo Kuwata, Ossama El-Kabbani, Akira Ikari
Aldo-keto reductase (AKR) 1C3 is a cytosolic enzyme that metabolizes steroids, prostaglandins, toxic aldehydes and drugs. Recently, some nonsynonymous single nucleotide polymorphisms of AKR1C3 have been suggested to impact steroid and drug metabolism. In this study, we examined the effects of C154Y and L159V variants of AKR1C3 on stability and function of the enzyme. Both variants had been detected in patients with the neurodegenerative disease amyotrophic lateral sclerosis. Recombinant wild-type (WT), C154Y and L159V enzymes were similar in specific activity, but C154Y displayed much lower thermostability than WT and L159V...
December 23, 2016: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28008453/association-of-vdbp-and-cyp2r1-gene-polymorphisms-with-vitamin-d-status-in-women-with-polycystic-ovarian-syndrome-a-north-indian-study
#17
Deepa Haldar, Nitin Agrawal, Seema Patel, Pankaj Ramrao Kambale, Kanchan Arora, Aditi Sharma, Manish Tripathi, Aruna Batra, Bhaskar C Kabi
PURPOSE: Polycystic ovarian syndrome (PCOS) is the most common endocrine abnormality among women of reproductive age and is usually associated with oligo-ovulation/anovulation, obesity, and insulin resistance. Hypovitaminosis D may also be a primary factor in the initiation and development of PCOS. However, little is known about the role of genetic variation in vitamin D metabolism in PCOS aetiology. Therefore, we studied the genetic polymorphisms of CYP2R1 and vitamin D binding protein (VDBP) in an Indian population...
December 23, 2016: European Journal of Nutrition
https://www.readbyqxmd.com/read/28007948/genome-metabolite-associations-revealed-low-heritability-high-genetic-complexity-and-causal-relations-for-leaf-metabolites-in-winter-wheat-triticum-aestivum
#18
Andrea Matros, Guozheng Liu, Anja Hartmann, Yong Jiang, Yusheng Zhao, Huange Wang, Erhard Ebmeyer, Viktor Korzun, Ralf Schachschneider, Ebrahim Kazman, Johannes Schacht, Friedrich Longin, Jochen Christoph Reif, Hans-Peter Mock
We investigated associations between the metabolic phenotype, consisting of quantitative data of 76 metabolites from 135 contrasting winter wheat (Triticum aestivum) lines, and 17 372 single nucleotide polymorphism (SNP) markers. Metabolite profiles were generated from flag leaves of plants from three different environments, with average repeatabilities of 0.5-0.6. The average heritability of 0.25 was unaffected by the heading date. Correlations among metabolites reflected their functional grouping, highlighting the strict coordination of various routes of the citric acid cycle...
December 22, 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28005968/common-snp-rs6564851-in-the-bco1-gene-affects-the-circulating-levels-of-%C3%AE-carotene-and-the-daily-intake-of-carotenoids-in-healthy-japanese-women
#19
Suemi Yabuta, Masanori Urata, Roseline Yap Wai Kun, Motofumi Masaki, Yoshihiro Shidoji
The circulating levels of β-carotene are modulated not only by sex, but also by autosomal gene variations and fruit intake. The aim of this study was to investigate the interactions between β-carotene metabolism-related gene single nucleotide polymorphisms (SNPs; genetic factors) and nutrient intake (environmental factors) relating to their effects on circulating β-carotene. The serum concentrations of β-carotene and the habitual food intake of 92 healthy Japanese adults were examined. All subjects were genotyped for three common SNPs: rs6564851 in the β-carotene 15,15'-oxygenase 1 (BCO1) gene, rs2278986 in the scavenger receptor class B member 1 (SCARB1) gene and rs362090 in the intestine-specific homeobox (ISX) gene...
2016: PloS One
https://www.readbyqxmd.com/read/28002816/associations-of-serum-osteocalcin-and-polymorphisms-of-the-osteocalcin-gene-with-bone-mineral-density-in-postmenopausal-and-elderly-chinese-women
#20
Xiao-Ya Zhang, Jin-Wei He, Wen-Zhen Fu, Yu-Juan Liu, Zhen-Lin Zhang
BACKGROUND: The aims of this study were: (1) to evaluate the association of serum osteocalcin with bone mineral density (BMD) and markers of bone metabolism in postmenopausal and elderly Chinese women, and (2) to observe the relationships of single-nucleotide polymorphisms (SNPs) in and around the osteocalcin gene with osteocalcin and BMD. METHODS: A cross-sectional study was conducted with 725 postmenopausal Chinese women. Five SNPs (rs1543294, rs1800247, rs759330, rs2842880, and rs933489) of the osteocalcin gene were genotyped...
December 22, 2016: Journal of Nutrigenetics and Nutrigenomics
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