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María Muñoz-Amatriaín, Hamid Mirebrahim, Pei Xu, Steve I Wanamaker, MingCheng Luo, Hind Alhakami, Matthew Alpert, Ibrahim Atokple, Benoit Joseph Batieno, Ousmane Boukar, Serdar Bozdag, Ndiaga Cisse, Issa Drabo, Jeffrey D Ehlers, Andrew Farmer, Christian Fatokun, Yong Q Gu, Yi-Ning Guo, Bao-Lam Huynh, Scott A Jackson, Francis Kusi, Cynthia T Lawley, Mitchell R Lucas, Yaqin Ma, Michael P Timko, Jiajie Wu, Frank You, Philip A Roberts, Stefano Lonardi, Timothy J Close
Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4,355 BACs...
October 24, 2016: Plant Journal: for Cell and Molecular Biology
Sergey V Malov, Alexey Antonik, Minzhong Tang, Alexandre Berred, Yi Zeng, Stephen J O'Brien
A new approach for statistical association signal identification is developed in this paper. We consider a strategy for nonprecise signal identification by extending the well-known signal detection and signal identification methods applicable to the multiple testing problem. Collection of statistical instruments under the presented approach is much broader than under the traditional signal identification methods, allowing more efficient signal discovery. Further assessments of maximal value and average statistics in signal discovery are improved...
October 24, 2016: Biometrical Journal. Biometrische Zeitschrift
José Alcaraz-Quiles, Esther Titos, Mireia Casulleras, Marco Pavesi, Cristina López-Vicario, Bibiana Rius, Aritz Lopategi, Andrea de Gottardi, Ivo Graziadei, Henning Gronbaek, Pere Ginès, Mauro Bernardi, Vicente Arroyo, Joan Clària
: Acute-on-chronic liver failure (ACLF) in cirrhosis is an increasingly recognized syndrome characterized by acute decompensation, organ failure(s) and high short-term mortality. Recent findings suggest that an over-exuberant systemic inflammation plays a primary role in ACLF progression. In this study, we examined whether genetic factors shape systemic immune responses in patients with decompensated cirrhosis. Six single nucleotide polymorphisms (SNPs) in inflammation-related genes (IL-1β: rs1143623, IL-1ra: rs4251961, IL-10: rs1800871, SOCS3: rs4969170, NOD2: rs3135500 and CMKLR1: rs1878022) were genotyped in 279 cirrhotic patients with (n=178) and without (n=101) ACLF from the CANONIC study of the CLIF consortium...
October 24, 2016: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
Ebrahiem M Babiker, Tyler Gordon, Shiaoman Chao, Matthew N Rouse, Maricelis Acevedo, Gina Brown-Guedira, Ruth Wanyera, John Michael Bonman
Wheat landrace PI 177906 has seedling resistance to stem rust caused by Puccinia graminis f. sp. tritici races TTKSK, TTKST, and BCCBC and field resistance to the Ug99 race group. Parents, 140 recombinant inbred lines, and 138 double haploid (DH) lines were evaluated for seedling resistance to races TTKSK and BCCBC. Parents and the DH population were evaluated for field resistance to Ug99 in Kenya. The 90K wheat SNP genotyping platform was used to genotype the parents and populations. Goodness-of-fit tests indicated that two dominant genes in PI 177906 conditioned seedling resistance to TTKSK...
October 24, 2016: Phytopathology
Yanwen Wang, Yongfeng Yang, Yihan Zhu, Li Li, Fei Chen, Li Zhang
CONTEXT: Polymorphisms of IL-32 related closely to tumoregenesis. MATERIALS AND METHODS: Two IL-32 polymorphisms (rs12934561 and rs28372698) and mRNA expression were conducted by SNP genotype assay and real-time PCR in 423 lung cancer patients and 437 controls. RESULTS: T allele of rs28372698 associated significantly with poor prognosis in moderate and well differentiation lung cancer patients. TT genotype of rs12934561 related closely to poor survival status in squamous carcinoma...
October 24, 2016: Biomarkers: Biochemical Indicators of Exposure, Response, and Susceptibility to Chemicals
Rahul A Bharadwaj, Andrew E Jaffe, Qiang Chen, Amy Deep-Soboslay, Aaron L Goldman, Michelle I Mighdoll, John A Cotoia, Anna C Brandtjen, JooHeon Shin, Thomas M Hyde, Venkata S Mattay, Daniel R Weinberger, Joel E Kleinman
Posttraumatic stress disorder (PTSD) follows exposure to a traumatic event in susceptible individuals. Recently, genome-wide association studies have identified a number of genetic sequence variants that are associated with the risk of developing PTSD. To follow up on identifying the molecular mechanisms of these risk variants, we performed genotype to RNA sequencing-derived quantitative expression (whole gene, exon, and exon junction levels) analysis in the dorsolateral prefrontal cortex (DLPFC) of normal postmortem human brains...
October 24, 2016: Journal of Neuroscience Research
Hillary T Graham, Daniel M Rotroff, Skylar W Marvel, John B Buse, Tammy M Havener, Alyson G Wilson, Michael J Wagner, Alison A Motsinger-Reif
Given the high costs of conducting a drug-response trial, researchers are now aiming to use retrospective analyses to conduct genome-wide association studies (GWAS) to identify underlying genetic contributions to drug-response variation. To prevent confounding results from a GWAS to investigate drug response, it is necessary to account for concomitant medications, defined as any medication taken concurrently with the primary medication being investigated. We use data from the Action to Control Cardiovascular Disease (ACCORD) trial in order to implement a novel scoring procedure for incorporating concomitant medication information into a linear regression model in preparation for GWAS...
2016: Frontiers in Genetics
Handan Tan, Bolin Deng, Hongsong Yu, Yi Yang, Lin Ding, Qi Zhang, Jieying Qin, Aize Kijlstra, Rui Chen, Peizeng Yang
Interleukin-1 (IL-1) and the IL-1 receptor (IL-1R) family play an important role in the pathogenesis of inflammatory diseases. This study aimed to investigate the association between single nucleotide polymorphisms (SNP) of IL-1 and IL-1R family genes with Vogt-Koyanagi-Harada (VKH) and Behcet's disease (BD) in Han Chinese. The case-control study was divided into two stages and included 419 VKH cases, 1063 BD cases and 1872 healthy controls. The MassARRAY platform (Sequenom), iPLEX Gold Assay and TaqMan SNP assays were used to score genotypes of 24 SNPs...
October 24, 2016: Scientific Reports
Tatiana V Tatarinova, Evgeny Chekalin, Yuri Nikolsky, Sergey Bruskin, Dmitry Chebotarov, Kenneth L McNally, Nickolai Alexandrov
We analyzed functionality and relative distribution of genetic variants across the complete Oryza sativa genome, using the 40 million single nucleotide polymorphisms (SNPs) dataset from the 3,000 Rice Genomes Project (, the largest and highest density SNP collection for any higher plant. We have shown that the DNA-binding transcription factors (TFs) are the most conserved group of genes, whereas kinases and membrane-localized transporters are the most variable ones. TFs may be conserved because they belong to some of the most connected regulatory hubs that modulate transcription of vast downstream gene networks, whereas signaling kinases and transporters need to adapt rapidly to changing environmental conditions...
October 24, 2016: Scientific Reports
Zhongfeng Li, Lingxue Jiang, Yansong Ma, Zhongyan Wei, Huilong Hong, Zhangxiong Liu, Jinhui Lei, Ying Liu, Rongxia Guan, Yong Guo, Longguo Jin, Lijuan Zhang, Yinghui Li, Yulong Ren, Wei He, Ming Liu, Nang Myint Phyu Sin Htwe, Lin Liu, Bingfu Guo, Jian Song, Bing Tan, Guifeng Liu, Maiquan Li, Xianli Zhang, Bo Liu, Xuehui Shi, Sining Han, Sunan Hua, Fulai Zhou, Lili Yu, Yanfei Li, Shuang Wang, Jun Wang, Ruzhen Chang, Lijuan Qiu
Mutagenized populations have provided important materials for introducing variation and identifying gene function in plants. In this study, an ethyl methanesulfonate (EMS) -induced soybean (Glycine max) population, consisting of 21,600 independent M2 lines, was developed. Over one thousand M4 (5) families, with diverse abnormal phenotypes for seed composition, seed shape, plant morphology, and maturity that are stably expressed across different environments and generations were identified. Phenotypic analysis of the population led to the identification of a yellow pigmentation mutant, gyl, that displayed significantly decreased chlorophyll (Chl) content and abnormal chloroplast development...
October 24, 2016: Journal of Integrative Plant Biology
Fangyuan Yin, Yuanyuan Ji, Jing Zhang, Hao Guo, Xin Huang, Jianghua Lai, Shuguang Wei
Previous studies suggested that the 5-hydroxytryptamine receptor 3B (HTR3B) is involved in heroin dependence by modulating dopamine (DA) release in the reward pathway and that the genetic polymorphisms in HTR3B play plausible role in modulating the risk of developing heroin addiction. To identify markers that contribute to the genetic susceptibility to heroin dependence, we examined the potential associations between heroin dependence and 7 single nucleotide polymorphisms (SNPs) of the HTR3B gene using multiplex SNaPshot technology in a Chinese Han population...
October 20, 2016: Neuroscience Letters
C Bickel, R B Schnabel, E Zengin, E Lubos, H Rupprecht, K Lackner, C Proust, D Tregouet, S Blankenberg, D Westermann, C Sinning
BACKGROUND AND AIMS: Whether single nucleotide polymorphisms (SNPs) of homocysteine metabolism enzymes influence the rate of cardiovascular (CV) events in coronary artery disease (CAD) patients remains controversial. METHODS AND RESULTS: In this analysis, 1126 subjects from the AtheroGene study with CAD and 332 control subjects without known CAD were included. The following SNPs were investigated: methylentetrahydrofolate reductase (MTHFR-C667T), methionin synthetase (MS-D919G), and cystathionin beta synthetase (CBS-I278T)...
September 17, 2016: Nutrition, Metabolism, and Cardiovascular Diseases: NMCD
Melody Caramins, Nicole Chia, Stephen Mulligan
No abstract text is available yet for this article.
February 2016: Pathology
Sarah L Nickerson, Renate Marquis-Nicholson, Karen Claxton, Fern Ashton, Ivone U S Leong, Debra O Prosser, Jennifer M Love, Alice M George, Graham Taylor, Callum Wilson, R J McKinlay Gardner, Donald R Love
No abstract text is available yet for this article.
February 2016: Pathology
Nicole M Gatto, Kimberly C Paul, Janet S Sinsheimer, Jeff M Bronstein, Yvette Bordelon, Rebecca Rausch, Beate Ritz
We and others have suggested that vitamin D receptor gene (VDR) polymorphisms influence susceptibility for Parkinson's disease (PD), Alzheimer's disease (AD), mild cognitive impairment (MCI) or overall cognitive functioning. Here we examine VDR polymorphisms and cognitive decline in patients with PD. Non-Hispanic Caucasian PD patients (n=190) in the Parkinson Environment Gene (PEG) study were successfully genotyped for seven VDR polymorphisms. Cognitive function was assessed with the Mini-Mental State Exam (MMSE) at baseline and at a maximum of three follow-up exams...
November 15, 2016: Journal of the Neurological Sciences
Yo Niida, Hitoshi Sato, Mamoru Ozaki, Masatsune Itoh, Kanju Ikeno, Etsuko Takase
Less than 1% of the cases with Angelman syndrome (AS) are caused by chromosomal rearrangements. This category of AS is not well defined and may manifest atypical phenotypes. Here, we report a girl with AS due to der(13)t(13;15)(q14.1;q12)mat. SNP array detected the precise deletion/duplication points and the parental origin of the 15q deletion. Multicolor FISH confirmed a balanced translocation t(13;15)(q14.1;q12) in her mother. Her facial appearance showed some features of dup(13)(pter→q14). Also, she lacked the most characteristic and unique behavioral symptoms of AS, i...
October 22, 2016: Cytogenetic and Genome Research
Laila Y AlAyadhi, Jamil A Hashmi, Muhammad Iqbal, Alia M Albalawi, Mohammad I Samman, Nadra E Elamin, Shahid Bashir, Sulman Basit
Single nucleotide polymorphisms (SNP) - based genotyping using microarray platform is now frequently used to detect copy number variants (CNVs) in the human genome. Here, we report CNVs identified using Illumina HumanOmni 2.5 M oligonucleotide microarrays in 11 multiplex families with autism spectrum disorder (ASD) referred to Autism Research and Treatment Center (ART) and Madinah Maternity and Children Hospital (MMCH). Of the 11 families, 22 patients with ASD (all males) and their parents, were recruited for the present study...
October 19, 2016: Neuroscience
H Toinét Cronjé, Cornelie Nienaber-Rousseau, Lizelle Zandberg, Tinashe Chikowore, Zelda de Lange, Tertia van Zyl, Marlien Pieters
Fibrinogen and its functional aspects have been linked to cardiovascular disease. There is vast discrepancy between the heritability of fibrinogen concentrations observed in twin studies and the heritability uncovered by genome wide association studies. We postulate that some of the missing heritability might be explained by the pleiotropic and polygenic co-regulation of fibrinogen through multiple targeted genes, apart from the fibrinogen genes themselves. To this end we investigated single nucleotide polymorphisms (SNPs) in genes coding for phenotypes associated with total and γ' fibrinogen concentrations and clot properties...
October 19, 2016: Matrix Biology: Journal of the International Society for Matrix Biology
Demetris Yannopoulos, Jason A Bartos, Stephen A George, George Sideris, Sebastian Voicu, Brett Oestreich, Timothy Matsuura, Kadambari Shekar, Jennifer Rees, Tom P Aufderheide
INTRODUCTION: Sodium nitroprusside (SNP) enhanced CPR (SNPeCPR) demonstrates increased vital organ blood flow and survival in multiple porcine models. We developed a new, coronary occlusion/ischemia model of prolonged resuscitation, mimicking the majority of out-of-hospital cardiac arrests presenting with shockable rhythms. HYPOTHESIS: SNPeCPR will increase short term (4-hour) survival compared to standard 2015 Advanced Cardiac Life Support (ACLS) guidelines in an ischemic refractory ventricular fibrillation (VF), prolonged CPR model...
October 19, 2016: Resuscitation
Yahui Wu, Lixin Luo, Likai Chen, Xingxing Tao, Ming Huang, Hui Wang, Zhiqiang Chen, Wuming Xiao
Genetic analysis revealed that narrow leaf, small panicle, thin and slender stems as well as low fertility rate of an Indica rice variety were recessive traits and controlled by a single gene. Applying map-based cloning strategy, a novel narrow leaf gene, which was named nal11 was delimited to an interval of 58.3 kb between the InDel markers N10 and InD5016. There are 9 genes in the mapping interval, and only a heat shock DNAJ protein encode gene (Os07g09450) has a specific G to T SNP, which was occurred at the last base of the second exon of Os07g09450 in ZYX...
October 19, 2016: Biochemical and Biophysical Research Communications
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