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Nucleotide performance

Qiang Xu, Yang Shi, Ting Yu, Xuewen Xu, Yali Yan, Xiaohua Qi, Xuehao Chen
Cucumber is an economically important vegetable crop worldwide. Powdery mildew (PM) is one of the most severe diseases that can affect cucumber crops. There have been several research efforts to isolate PM resistance genes for breeding PM-resistant cucumber. In the present study, we used a chromosome segment substitution line, SSL508-28, which carried PM resistance genes from the donor parent, JIN5-508, through twelve generations of backcrossing with a PM-susceptible inbred line, D8. We performed whole-genome resequencing of SSL508-28 and D8 to identify single nucleotide polymorphisms (SNPs), and insertions and deletions (indels)...
2016: PloS One
Karina Beatriz Acosta, Melina Noelia Lorenzini Campos, Susana Beatriz Etcheverry, Pedro Dario Zapata
The α6β4 integrin is composed of the α6 and β4 subunits that are encoded by the ITGα6 and the ITGβ4 genes, respectively. The α6β4 main function is to intervene in lamination and epithelia integrity maintenance by cell-matrix interactions. This integrin appears to have importance in breast cancer malignancy, as well as other epithelial carcinomas. The aim of this work was to investigate the potential role of ITGα6 (A380T) and ITGβ4 (R1281W) genetic variations in breast cancer susceptibility, in a female population from the northeast region of Argentina (Misiones)...
October 18, 2016: International Journal of Molecular Sciences
Inderjeet Kaur, Mohammad Zeeshan, Ekta Saini, Abhinav Kaushik, Asif Mohmmed, Dinesh Gupta, Pawan Malhotra
Post-transcriptional and post-translational modifications play a major role in Plasmodium life cycle regulation. Lysine methylation of histone proteins is well documented in several organisms, however in recent years lysine methylation of proteins outside histone code is emerging out as an important post-translational modification (PTM). In the present study we have performed global analysis of lysine methylation of proteins in asexual blood stages of Plasmodium falciparum development. We immunoprecipitated stage specific Plasmodium lysates using anti-methyl lysine specific antibodies that immunostained the asexual blood stage parasites...
October 20, 2016: Scientific Reports
Bao-Zhu Yang, Shizhong Han, Henry R Kranzler, Abraham A Palmer, Joel Gelernter
Sex influences risk for opioid dependence (OD). We hypothesized that sex might interact with genetic loci that influence the risk for OD. Therefore we performed an analysis to identify sex-specific genomic susceptibility regions for OD using linkage. Over 6,000 single nucleotide polymorphism (SNP) markers were genotyped for 1,758 African- and European-American (AA and EA) individuals from 739 families, ascertained via affected sib-pairs with OD and/or cocaine dependence. Autosomewide non-parametric linkage scans, stratified by sex and population, were performed...
October 20, 2016: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
Igor Florez-Sarasa, Ko Noguchi, Wagner Araujo, Ana Garcia-Nogales, Alisdair R Fernie, Jaume Flexas, Miquel Ribas-Carbo
The cyclic electron flow around photosystem I (CEF-PSI) increases ATP/NADPH production in the chloroplast acting as an energy balance mechanism. Higher export of reducing power from the chloroplast in CEF-PSI mutants has been correlated with higher mitochondrial alternative oxidase (AOX) capacity and protein amount under high light (HL) conditions. However, in vivo measurements of AOX activity are still required to confirm the exact role of AOX on dissipating the excess of reductant power from the chloroplast...
October 19, 2016: Plant Physiology
Hai Du, Feng Ran, Hong-Li Dong, Jing Wen, Jia-Na Li, Zhe Liang
Cytochrome P450 93 family (CYP93) belonging to the cytochrome P450 superfamily plays important roles in diverse plant processes. However, no previous studies have investigated the evolution and expression of the members of this family. In this study, we performed comprehensive genome-wide analysis to identify CYP93 genes in 60 green plants. In all, 214 CYP93 proteins were identified; they were specifically found in flowering plants and could be classified into ten subfamilies-CYP93A-K, with the last two being identified first...
2016: PloS One
B Ślaska, L Grzybowska-Szatkowska, M Bugno-Poniewierska, A Gurgul, A Śmiech, D Różańska, J Dudka
The aim of the study was to identify polymorphisms and mutations in the mitochondrial ND4 gene and to analyse the associations between the occurrence of molecular changes in mtDNA and phenotypic traits in tumours in German Shepherd dogs. Fifty samples obtained from blood and tumour tissues of German Shepherd dogs with diagnosed tumours were analysed. DNA extraction, amplification, and sequencing of the mtDNA ND4 gene, and bioinformatics, statistical, and in silico protein coding SNP analyses were performed...
September 1, 2016: Polish Journal of Veterinary Sciences
Xin-Yong Zhang, Qi Wan, Dong-Ya Zhu
BACKGROUND Recent studies demonstrated that polymorphisms in the PDE4D gene were associated with several processes involved in the occurrence of ischemic stroke (IS). The association between specific PDE4D single-nucleotide polymorphism 56 (SNP56) and IS risk was initially identified via genome-wide association studies (GWAS), although the GWAS in different populations produced inconclusive results. Thus, we performed a meta-analysis to better explain the association between PDE4D SNP56 and IS risk. MATERIAL AND METHODS A literature search was conducted using PubMed, Embase, and Web of Science up to June 1, 2015...
October 19, 2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Ou Liu, Wuxiang Xie, Yanwen Qin, Lixin Jia, Jing Zhang, Yi Xin, Xinliang Guan, Haiyang Li, Ming Gong, Yuyong Liu, Xiaolong Wang, Jianrong Li, Feng Lan, Hongjia Zhang
Matrix metalloproteinases-2 (MMP-2) plays an important role in the pathogenesis of type A aortic dissection (AD). The aim of this study was to evaluate the association of 3 single nucleotide polymorphisms (SNPs) in the MMP-2 gene with type A AD risk and aortic diameters in patients. We performed a case-control study with 172 unrelated type A AD patients and 439 controls. Three SNPs rs11644561, rs11643630, and rs243865 were genotyped through the MassARRAY platform. Allelic associations of SNPs and SNP haplotypes with type A AD and aortic diameters in patients were evaluated...
October 2016: Medicine (Baltimore)
Suzanne Gonzalez, Jayanta Gupta, Erika Villa, Indika Mallawaarachchi, Marco Rodriguez, Mercedes Ramirez, Juan Zavala, Regina Armas, Albana Dassori, Javier Contreras, Deborah Flores, Alvaro Jerez, Alfonso Ontiveros, Humberto Nicolini, Michael Escamilla
OBJECTIVES: Recent genome-wide association studies (GWASs) have identified numerous putative genetic polymorphisms associated with bipolar disorder (BD) and/or schizophrenia (SC). We hypothesized that a portion of these polymorphisms would also be associated with BD in the Latino American population. To identify such regions, we tested previously identified genetic variants associated with BD and/or SC and ancestral haploblocks containing these single nucleotide polymorphisms (SNPs) in a sample of Latino subjects with BD...
September 2016: Bipolar Disorders
Xin-Yong Zhang, Qi Wan, Dong-Ya Zhu
BACKGROUND Recent studies demonstrated that polymorphisms in the PDE4D gene were associated with several processes involved in the occurrence of ischemic stroke (IS). The association between specific PDE4D single-nucleotide polymorphism 56 (SNP56) and IS risk was initially identified via genome-wide association studies (GWAS), although the GWAS in different populations produced inconclusive results. Thus, we performed a meta-analysis to better explain the association between PDE4D SNP56 and IS risk. MATERIAL AND METHODS A literature search was conducted using PubMed, Embase, and Web of Science up to June 1, 2015...
October 19, 2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Diego Dal Ben, Anna Marchenkova, Ajiroghene Thomas, Catia Lambertucci, Andrea Spinaci, Gabriella Marucci, Andrea Nistri, Rosaria Volpini
Blocking membrane currents evoked by the activation of purinergic P2X3 receptors localized on nociceptive neurons represents a promising strategy for the development of agents useful for the treatment of chronic pain conditions. Among compounds endowed with such antagonistic action, 2',3'-O-(2,4,6-trinitrophenyl)-ATP (TNP-ATP) is an ATP analogue, whose inhibitory activity on P2X receptors has been previously reported. Based on the results of molecular modelling studies performed with homology models of the P2X3 receptor, novel adenosine nucleotide analogues bearing cycloalkyl or arylalkyl substituents replacing the trinitrophenyl moiety of TNP-ATP were designed and synthesized...
October 18, 2016: Purinergic Signalling
Chunxiao Xu, Dan Zhou, Feixia Pan, Yi Liu, Dandan Zhang, Aifen Lin, Xiaoping Miao, Yaqin Ni, Duo Lv, Shuai Zhang, Xiaobo Li, Yimin Zhu, Maode Lai
BACKGROUND: Genes in inflammatory pathways play a pivotal role in the development of colorectal cancer. We conducted a two-stage case-control study and aimed at screening the colorectal cancer-associated genetic variations in inflammatory genes. METHODS: Twenty-three candidate variants were genotyped in 952 primary colorectal cancer cases and 875 cancer-free controls from eastern China. Promising single nucleotide polymorphisms were further genotyped in 518 cases and 554 controls from middle China...
October 18, 2016: BMC Cancer
Silvia Mahmood, Andrea Evinová, Mária Škereňová, Igor Ondrejka, Ján Lehotský
BACKGROUND: Major depressive disorder (MDD) is a main public health concern worldwide. Despite extensive investigations, the exact mechanisms responsible for MDD have not been identified. Epidermal growth factor (EGF) and insulin growth factor binding protein-3 (IGFBP-3) are involved in brain function. Tumour suppressor protein p53 is widely involved in neuronal death in response to different forms of acute insults and neurological disorders. The present study focuses on the possible associations of the single-nucleotide polymorphisms (SNP) of EGF A61G (rs4444903), IGFBP-3 C32G (rs2854746) and TP53 G72C (rs1042522) genes with MDD risk in the Slovak population...
September 2016: Central European Journal of Public Health
Linlu Zhao, Darren M Roffey, Suzan Chen
STUDY DESIGN: Systematic review and meta-analysis. OBJECTIVE: To assess and synthesize the current evidence on the association between the rs1256120 single nucleotide polymorphism (SNP) of the estrogen receptor beta gene (ESR2) and adolescent idiopathic scoliosis (AIS). SUMMARY OF BACKGROUND DATA: Hormonal disturbance has been postulated as a potential etiological factor in the development of AIS. As estrogen receptors are important mediators of estrogen response, mutations in these genes, including rs1256120 of ESR2, have been chosen as susceptibility candidates for AIS predisposition...
October 17, 2016: Spine
Anna V Motorina, Nadezhda V Palkina, Anna V Komina, Tatiana G Ruksha, Ivan P Artyukhov, Vasily V Kozlov
The melanocortin 1 receptor is a Gs protein-coupled receptor implicated in melanogenesis regulation. The receptor gene is highly polymorphic, which accounts for the association of several of its single-nucleotide polymorphisms (SNPs) with an increased risk of melanoma. The present study aimed to evaluate the distribution of melanocortin 1 receptor gene variants R151C, R160W, and D294H within the Russian population of Eastern Siberia and its association with melanoma development. Melanoma patients (n=95) admitted to Krasnoyarsk Territorial Oncological Center and healthy controls (n=334) were enrolled in the study...
October 13, 2016: European Journal of Cancer Prevention
Woong Choi, Gyoo Yeol Jung
For the development of clinically useful genotyping methods for single nucleotide polymorphisms (SNPs), accuracy, simplicity, sensitivity, and cost-effectiveness are the most important criteria. Among the methods currently being developed for SNP genotyping technology, the ligation-dependent method is considered the simplest for clinical diagnosis. However, sensitivity is not guaranteed by the ligation reaction alone, and analysis of multiple targets is limited by the detection method. Although CE is an attractive alternative to error-prone hybridization-based detection, the multiplex assay process is complicated because of the size-based DNA separation principle...
October 18, 2016: Electrophoresis
Mahmut Asfuroglu, Busranur Cavdarli, Ozlem G Koz, Ahmet A Yarangumeli, Emine Y Ozdemir
PURPOSE: To investigate the genetic association of lysyl oxidase-like 1 (LOXL1) gene polymorphisms in patients with pseudoexfoliation (PEX) syndrome and PEX glaucoma of Turkish descent. METHODS: Three LOXL1 single nucleotide polymorphisms (SNPs) (rs1048661, rs3825942, and rs2165241) were analyzed in 109 Turkish patients (44 patients with PEX syndrome, 65 patients with PEX glaucoma) and 47 healthy subjects. RESULTS: "A" allele of SNP rs3825942 was underrepresented in control group compared with the glaucoma [odds ratio (OR)=4...
October 6, 2016: Journal of Glaucoma
Frauke Degenhardt, Andrea Dirmeier, Rocio Lopez, Sylvia Lang, Claudia Kunst, Dirk Roggenbuck, Dirk Reinhold, Silke Szymczak, Gerhard Rogler, Frank Klebl, Andre Franke, Florian Rieder
BACKGROUND: The presentation of Crohn's disease (CD) is heterogeneous and often leads to serious complications and need for surgery. We tested serum anti-zymogen granule glycoprotein 2 (GP2) antibodies, including its novel isoform alpha, for association with genetic variants, diagnosis, disease stratification, and prediction of CD courses in a combined cross-sectional and cohort study. METHODS: Serum samples of 303 CD, 108 ulcerative colitis, 72 other inflammatory gastrointestinal diseases, and 206 controls without predominant gastrointestinal diseases controls (HC) were tested for the presence of Anti-GP2 and Anti-Saccharomyces cervisiae (ASCA) by enzyme-linked immunosorbent assay...
November 2016: Inflammatory Bowel Diseases
M Maddah, S Harsini, V Ziaee, M H Moradinejad, A Rezaei, S Zoghi, M Sadr, Y Aghighi, N Rezaei
Juvenile idiopathic arthritis (JIA) is a heterogeneous autoimmune disorder of unknown origin. As proinflammatory cytokines are known to contribute towards the pathogenesis of JIA, this case-control study was performed to examine the associations of certain single nucleotide polymorphisms (SNPs) of tumour necrosis factor-α (TNF-α) gene. Fifty-three patients with JIA participated in this study as patients group and compared with 137 healthy unrelated controls. Genotyping was performed for TNF-α gene at positions -308 and -238, using polymerase chain reaction with sequence-specific primers method...
October 18, 2016: International Journal of Immunogenetics
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