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https://www.readbyqxmd.com/read/28446001/a-post-genome-wide-association-study-validating-the-association-of-the-glycophorin-c-gene-with-serum-hemoglobin-level-in-pig
#1
Yang Liu, Zhengzheng Hu, Chen Yang, Shiwei Wang, Wenwen Wang, Qin Zhang
OBJECTIVE: This study aimed to validate the statistical evidence from the genome-wide association study (GWAS) as true-positive and to better understand the effects of the glycophorin C (GYPC) gene on serum hemoglobin traits. METHODS: Our initial GWAS revealed the presence of two single nucleotide polymorphisms (SNPs) (ASGA0069038 and ALGA0084612) for the hemoglobin concentration trait (HGB) in the 2.48 Mb region of SSC15. From this target region, GYPC was selected as a promising gene that associated with serum HGB traits in pigs...
May 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28445979/the-impacts-of-single-nucleotide-polymorphisms-in-genes-of-cell-cycle-and-nf-kb-pathways-on-the-efficacy-and-acute-toxicities-of-radiotherapy-in-patients-with-nasopharyngeal-carcinoma
#2
Chengxian Guo, Yuling Huang, Jingjing Yu, Lijuan Liu, Xiaochang Gong, Min Huang, Chunling Jiang, Yulu Liao, Lihua Huang, Guoping Yang, Jingao Li
Radiotherapy is one of the primary choices for the treatment of nasopharyngeal carcinoma (NPC) and may result in severe radiotoxicities on normal tissues. Single nucleotide polymorphisms (SNPs) in genes of cell cycle and NF-κB pathways have been linked with the prognoses of various cancers. The aim of this study was to explore whether SNPs of genes involved in cell cycle and NF-κB pathways are associated with responses to radiotherapy in NPC patients. We selected 3 SNPs in cell cycle pathway and 5 SNPs in NF-κB pathway and genotyped them in 154 NPC patients treated with radiotherapy...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445963/genetic-polymorphisms-of-bcl-2-promoter-in-cancer-susceptibility-and-prognosis-a-meta-analysis
#3
Zhongqiang Yao, Binhui Yang, Zhongqiu Liu, Wei Li, Qihua He, Xingchun Peng
Bcl-2 is critical for tumorigenesis. However, previous studies on the association of Bcl-2 promoter polymorphisms with predisposition to different cancer types are somewhat contradictory. Therefore, we performed this meta-analysis regarding the relationship between Bcl-2 promoter single nucleotide polymorphisms (SNPs) and cancer susceptibility and prognosis. Up to August 2016, 32 original publications were identified covering two Bcl-2 promoter SNPs (rs2279115 and rs1801018). Our results showed statistically significant association between rs2279115 and cancer susceptibility and prognosis in all four genetic models but not in rs1801018...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445942/mmp-3-and-mmp-8-single-nucleotide-polymorphisms-are-related-to-alcohol-induced-osteonecrosis-of-the-femoral-head-in-chinese-males
#4
Junyu Chen, Wanlin Liu, Yuju Cao, Xiyang Zhang, Yongchang Guo, Yong Zhu, Jian Li, Jieli Du, Tianbo Jin, Guoqiang Wang, Jianzhong Wang
Our study investigated the association between MMP-3 and MMP-8 single-nucleotide polymorphisms (SNPs) and alcohol-induced osteonecrosis of the femoral head (ONFH) in 695 Chinese males (299 cases and 396 control subjects). The minor allele of MMP-3 rs650108 was associated with a 0.78-fold decrease in alcohol-induced ONFH risk in the allelic model (95% CI = 0.63-0.97, P = 0.026). In the genetic model adjusted for age, rs650108 was associated with decreased risk of alcohol-induced ONFH in the dominant model (OR = 0...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445878/differential-allelic-expression-of-htr1b-in-suicide-victims-genetic-and-epigenetic-effect-of-the-cis-acting-variants
#5
Ali Bani-Fatemi, Aaron Howe, Clement Zai, James L Kennedy, John Vincent, John Strauss, Albert Wong, Vincenzo De Luca
OBJECTIVES: In the present study, we tested the allelic imbalance of the C861G single nucleotide polymorphism (SNP) of HTR1B in the frontal cortex of suicide victims. METHODS: The study was conducted using 3 sets of samples. First, C861G allele-specific mRNA levels in the frontal cortex were compared between suicide (n = 13) and nonsuicide controls (n = 13) from the Stanley Medical Research postmortem brain collection. Second, we tested common variants in the HTR1B promoter for linkage disequilibrium (LD) with the C861G variant in an unrelated sample of suicide attempters (SA; n = 38) and non-SA (NSA; n = 42)...
April 27, 2017: Neuropsychobiology
https://www.readbyqxmd.com/read/28445866/association-of-genetic-polymorphisms-in-il-1r1-and-il-1r2-genes-with-iga-nephropathy-in-the-han-chinese-population
#6
Maowei Xie, Daofa Zhang, Yin Zhang, Xiaohong Yang, Yan Su, Yanni Wang, Haiyang Huang, Hui Han, Wenning Li, Keying Fu, Huiluan Su, Wentan Xu, Jiali Wei
AIM: IgA nephropathy (IgAN) is the major cause of end-stage renal disease(ESRD) in Asia and its pathogenesis is influenced by both genetic and environmental factors. Single nucleotide polymorphisms (SNPs) in IL1R1 and IL-1R2 may be associated with susceptibility to IgAN. In this study, we study the association between genetic variants of IL-1R1 and IL-1R2 and IgA nephropathy risk in the Chinese Han population. RESULT: In the allelic model analysis, the rs10490571 and rs3917225 were associated with a 1...
April 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445865/associations-between-lmo1-gene-polymorphisms-and-wilms-tumor-susceptibility
#7
Guo-Chang Liu, Zhen-Jian Zhuo, Shi-Bo Zhu, Jinhong Zhu, Wei Jia, Zhang Zhao, Jin-Hua Hu, Jing He, Feng-Hua Wang, Wen Fu
Wilms' tumor is the most common childhood renal malignancy. A genome-wide association study identified LIM domain only 1 (LMO1) as having oncogenic potential. We examined the associations between LMO1 gene polymorphisms and susceptibility to Wilms' tumor. In this hospital-based, case-control study, we recruited 145 children with Wilms' tumor and 531 cancer-free children. Four polymorphisms (rs110419 A>G, rs4758051 G>A, rs10840002 A>G and rs204938 A>G) were genotyped using Taqman methodology. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to measure the associations between selected polymorphisms and Wilms' tumor susceptibility...
April 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445614/two-common-human-cldn5-alleles-encode-different-open-reading-frames-but-produce-one-protein-isoform
#8
Ronald M Cornely, Barbara Schlingmann, Whitney S Shepherd, Joshua D Chandler, David C Neujahr, Michael Koval
Claudins provide tight junction barrier selectivity. The human CLDN5 gene contains a high-frequency single-nucleotide polymorphism (rs885985), where the G allele codes for glutamine (Q) and the A allele codes for an amber stop codon. Thus, these different CLDN5 alleles define nested open reading frames (ORFs) encoding claudin-5 proteins that are 303 or 218 amino acids in length. Interestingly, human claudin-16 and claudin-23 also have long ORFs. The long form of claudin-5 contrasts with the majority of claudin-5 proteins in the National Center for Biotechnology Information protein database, which are less than 220 amino acids in length...
April 26, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28445597/taller-height-as-a-risk-factor-for-venous-thromboembolism-a-mendelian-randomization-meta-analysis
#9
N S Roetker, S M Armasu, J S Pankow, P L Lutsey, W Tang, M A Rosenberg, T M Palmer, R F MacLehose, S R Heckbert, M Cushman, M de Andrade, A R Folsom
BACKGROUND: Taller height is associated with greater risk of venous thromboembolism (VTE). OBJECTIVES: We used instrumental variable (IV) techniques (Mendelian randomization) to further explore this relationship METHODS: Participants of European ancestry were included from two cohort studies [Atherosclerosis Risk in Communities (ARIC) study and Cardiovascular Health Study (CHS)] and one case-control study [Mayo Clinic VTE Study (Mayo)]. We created two weighted genetic risk scores (GRS) for height; the full GRS included 668 single nucleotide polymorphisms (SNPs) from a previously published meta-analysis and the restricted GRS included a subset of 362 SNPs not associated with weight independently of height...
April 26, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28445587/cb1-receptors-downregulate-a-camp-epac2-plc-pathway-to-silence-the-nerve-terminals-of-cerebellar-granule-cells
#10
Beatris Alonso, David Bartolomé-Martín, José Javier Ferrero, Jorge Ramírez-Franco, Magdalena Torres, José Sánchez-Prieto
Cannabinoid receptors mediate short-term retrograde inhibition of neurotransmitter release, as well as long-term depression of synaptic transmission at excitatory synapses. The responses of individual nerve terminals in VGLUT1-pHluorin transfected cerebellar granule cells to cannabinoids have shown that prolonged activation of cannabinoid type 1 receptors (CB1Rs) silences a subpopulation of previously active synaptic boutons. Adopting a combined pharmacological and genetic approach to study the molecular mechanisms of CB1R-induced silencing, we found that adenylyl cyclase inhibition decreases cAMP levels while it increases the number of silent synaptic boutons and occludes the induction of further silencing by the cannabinoid agonist HU-210...
April 26, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28445522/revealing-phenotype-associated-functional-differences-by-genome-wide-scan-of-ancient-haplotype-blocks
#11
Ritsuko Onuki, Rui Yamaguchi, Tetsuo Shibuya, Minoru Kanehisa, Susumu Goto
Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data...
2017: PloS One
https://www.readbyqxmd.com/read/28445510/whole-genome-re-sequencing-to-identify-suppressor-mutations-of-mutant-and-foreign-escherichia-coli-ftsz
#12
Kiani A J Arkus Gardner, Masaki Osawa, Harold P Erickson
FtsZ is an essential protein for bacterial cell division, where it forms the cytoskeletal scaffold and may generate the constriction force. We have found previously that some mutant and foreign FtsZ that do not complement an ftsZ null can function for cell division in E. coli upon acquisition of a suppressor mutation somewhere in the genome. We have now identified, via whole genome re-sequencing, single nucleotide polymorphisms in 11 different suppressor strains. Most of the mutations are in genes of various metabolic pathways, which may modulate cell division indirectly...
2017: PloS One
https://www.readbyqxmd.com/read/28445507/various-mutations-compensate-for-a-deleterious-lacz%C3%AE-insert-in-the-replication-enhancer-of-m13-bacteriophage
#13
Emily M Zygiel, Karen A Noren, Marta A Adamkiewicz, Richard J Aprile, Heather K Bowditch, Christine L Carroll, Maria Abigail S Cerezo, Adelle M Dagher, Courtney R Hebert, Lauren E Hebert, Gloria M Mahame, Stephanie C Milne, Kelly M Silvestri, Sara E Sutherland, Alexandria M Sylvia, Caitlyn N Taveira, David J VanValkenburgh, Christopher J Noren, Marilena Fitzsimons Hall
M13 and other members of the Ff class of filamentous bacteriophages have been extensively employed in myriad applications. The Ph.D. series of phage-displayed peptide libraries were constructed from the M13-based vector M13KE. As a direct descendent of M13mp19, M13KE contains the lacZα insert in the intergenic region between genes IV and II, where it interrupts the replication enhancer of the (+) strand origin. Phage carrying this 816-nucleotide insert are viable, but propagate in E. coli at a reduced rate compared to wild-type M13 phage, presumably due to a replication defect caused by the insert...
2017: PloS One
https://www.readbyqxmd.com/read/28445416/structure-function-model-for-kissing-loop-interactions-that-initiate-dimerization-of-ty1-rna
#14
Eric R Gamache, Jung H Doh, Justin Ritz, Alain Laederach, Stanislav Bellaousov, David H Mathews, M Joan Curcio
The genomic RNA of the retrotransposon Ty1 is packaged as a dimer into virus-like particles. The 5' terminus of Ty1 RNA harbors cis-acting sequences required for translation initiation, packaging and initiation of reverse transcription (TIPIRT). To identify RNA motifs involved in dimerization and packaging, a structural model of the TIPIRT domain in vitro was developed from single-nucleotide resolution RNA structural data. In general agreement with previous models, the first 326 nucleotides of Ty1 RNA form a pseudoknot with a 7-bp stem (S1), a 1-nucleotide interhelical loop and an 8-bp stem (S2) that delineate two long, structured loops...
April 26, 2017: Viruses
https://www.readbyqxmd.com/read/28445188/tpmt-comt-and-acyp2-genetic-variants-in-paediatric-cancer-patients-with-cisplatin-induced-ototoxicity
#15
Signe Thiesen, Peng Yin, Andrea L Jorgensen, Jieying E Zhang, Valentina Manzo, Laurence McEvoy, Christopher Barton, Susan Picton, Simon Bailey, Penelope Brock, Harish Vyas, David Walker, Guy Makin, Srinivas Bandi, Barry Pizer, Daniel B Hawcutt, Munir Pirmohamed
OBJECTIVES: Cisplatin ototoxicity affects 42-88% of treated children. Catechol-O-methyltransferase (COMT), thiopurine methyltransferase (TPMT) and AYCP2 genetic variants have been associated with ototoxicity, but the findings have been contradictory. The aims of the study were as follows: (a) to investigate these associations in a carefully phenotyped cohort of UK children and (b) to perform a systematic review and meta-analysis. METHODS: We recruited 149 children from seven UK centres using a retrospective cohort study design...
April 25, 2017: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/28445187/the-effects-of-inherited-nudt15-polymorphisms-on-thiopurine-active-metabolites-in-japanese-children-with-acute-lymphoblastic-leukemia
#16
Takaya Moriyama, Rina Nishii, Ting-Nien Lin, Kentaro Kihira, Hidemi Toyoda, Nersting Jacob, Motohiro Kato, Katsuyoshi Koh, Hiroto Inaba, Atsushi Manabe, Kjeld Schmiegelow, Jun J Yang, Hiroki Hori
Thiopurines [e.g. mercaptopurine (MP)] are widely used as chemotherapeutic agents in the treatment of pediatric acute lymphoblastic leukemia with dose-limiting hematopoietic toxicity. Recently, germline variants in NUDT15 have been identified as a major genetic cause for MP-related bone marrow suppression, and there is increasing interest in the clinical implementation of NUDT15 genotype-guided MP dose individualization. Therefore, we sought to evaluate the effects of NUDT15 on thiopurine metabolism and identify pharmacologic markers to inform NUDT15 genotype-guided MP dosing...
April 25, 2017: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/28445147/identification-of-rs7350481-at-chromosome-11q23-3-as-a-novel-susceptibility-locus-for-metabolic-syndrome-in-japanese-individuals-by-an-exome-wide-association-study
#17
Yoshiji Yamada, Jun Sakuma, Ichiro Takeuchi, Yoshiki Yasukochi, Kimihiko Kato, Mitsutoshi Oguri, Tetsuo Fujimaki, Hideki Horibe, Masaaki Muramatsu, Motoji Sawabe, Yoshinori Fujiwara, Yu Taniguchi, Shuichi Obuchi, Hisashi Kawai, Shoji Shinkai, Seijiro Mori, Tomio Arai, Masashi Tanaka
We have performed exome-wide association studies to identify genetic variants that influence body mass index or confer susceptibility to obesity or metabolic syndrome in Japanese. The exome-wide association study for body mass index included 12,890 subjects, and those for obesity and metabolic syndrome included 12,968 subjects (3954 individuals with obesity, 9014 controls) and 6817 subjects (3998 individuals with MetS, 2819 controls), respectively. Exome-wide association studies were performed with Illumina HumanExome-12 DNA Analysis BeadChip or Infinium Exome-24 BeadChip arrays...
April 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445130/single-nucleotide-polymorphisms-in-mlh1-predict-poor-prognosis-of-hepatocellular-carcinoma-in-a-chinese-population
#18
Xiaonian Zhu, Wei Liu, Xiaoqiang Qiu, Zhigang Wang, Chao Tan, Chunhua Bei, Linyuan Qin, Yuan Ren, Shengkui Tan
Hepatocellular carcinoma (HCC) is a malignant cancer causing deleterious health effect worldwide, especially in China. So far clinical cure rate and long-term survival rate of HCC remains low. Most HCC patients after cancer resection have recurrence or metastasis within 5 years. This study aims to explore the genetic association of mutL homolog 1 (MLH1) polymorphisms with HCC risk and prognosis. Four candidate MLH1 polymorphisms, rs1800734, rs10849, rs3774343 and rs1540354 were studied from a hospital-based case-control study including 1,036 cases (HCC patients) and 1,036 controls (non-HCC patients) in Guangxi, China...
April 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28444966/correlation-between-genetic-polymorphisms-within-the-mapk1-hif-1-ho-1-signaling-pathway-and-risk-or-prognosis-of-perimenopausal-coronary-artery-disease
#19
Nan Guo, Nan Zhang, Liqiu Yan, Xufen Cao, Jiawang Wang, Yunfei Wang
BACKGROUND: Mitogen-activated protein kinase-1 (MAPK1), as well as its downstream factors of hypoxia-inducible factor-1 (HIF-1) and heme oxygenase-1 (HO-1), have been documented to be involved in modulating development of coronary artery disease (CAD). HYPOTHESIS: Genetic mutations within the MAPK1/HIF-1/HO-1 signaling pathway could alter the risk of perimenopausal CAD in Chinese patients. METHODS: Peripheral blood samples were gathered from 589 CAD patients and 860 healthy controls, and 12 potential single-nucleotide polymorphisms (SNPs) were obtained from HapMap database and previously published studies...
April 26, 2017: Clinical Cardiology
https://www.readbyqxmd.com/read/28444962/fine-scale-species-distribution-changes-in-a-mixed-oak-stand-over-two-successive-generations
#20
Laura Truffaut, Emilie Chancerel, Alexis Ducousso, Jean Luc Dupouey, Vincent Badeau, François Ehrenmann, Antoine Kremer
Large-scale tree distribution changes have received considerable attention but underlying demo-genetic mechanisms are less well documented. We used a diachronic approach to track species shifts in a mixed oak stand (Quercus petraea-Quercus robur) at a fine spatiotemporal scale. Species assignment was made using single nucleotide polymorphism (SNP) fingerprints employing clustering and parentage analysis. Mating patterns and reproductive success were assessed by parentage analysis. Plot-based inventories of soil parameters and sapling densities provided ecological and demographic information, respectively...
April 26, 2017: New Phytologist
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