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https://www.readbyqxmd.com/read/28070124/an-endophenotype-approach-to-the-genetics-of-alcohol-dependence-a-genome-wide-association-study-of-fast-beta-eeg-in-families-of-african-ancestry
#1
J L Meyers, J Zhang, J C Wang, J Su, S I Kuo, M Kapoor, L Wetherill, S Bertelsen, D Lai, J E Salvatore, C Kamarajan, D Chorlian, A Agrawal, L Almasy, L Bauer, K K Bucholz, G Chan, V Hesselbrock, L Koganti, J Kramer, S Kuperman, N Manz, A Pandey, M Seay, D Scott, R E Taylor, D M Dick, H J Edenberg, A Goate, T Foroud, B Porjesz
Fast beta (20-28 Hz) electroencephalogram (EEG) oscillatory activity may be a useful endophenotype for studying the genetics of disorders characterized by neural hyperexcitability, including substance use disorders (SUDs). However, the genetic underpinnings of fast beta EEG have not previously been studied in a population of African-American ancestry (AA). In a sample of 2382 AA individuals from 482 families drawn from the Collaborative Study on the Genetics of Alcoholism (COGA), we performed a genome-wide association study (GWAS) on resting-state fast beta EEG power...
January 10, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28069037/health-and-genetic-ancestry-testing-time-to-bridge-the-gap
#2
Andrew Smart, Deborah A Bolnick, Richard Tutton
BACKGROUND: It is becoming increasingly difficult to keep information about genetic ancestry separate from information about health, and consumers of genetic ancestry tests are becoming more aware of the potential health risks associated with particular ancestral lineages. Because some of the proposed associations have received little attention from oversight agencies and professional genetic associations, scientific developments are currently outpacing governance regimes for consumer genetic testing...
January 9, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28068660/direct-to-consumer-genetic-testing-user-motivations-decision-making-and-perceived-utility-of-results
#3
J Scott Roberts, Michele C Gornick, Deanna Alexis Carere, Wendy R Uhlmann, Mack T Ruffin, Robert C Green
BACKGROUND/AIMS: To describe the interests, decision making, and responses of consumers of direct-to-consumer personal genomic testing (DTC-PGT) services. METHODS: Prior to 2013 regulatory restrictions on DTC-PGT services, 1,648 consumers from 2 leading companies completed Web surveys before and after receiving test results. RESULTS: Prior to testing, DTC-PGT consumers were as interested in ancestry (74% very interested) and trait information (72%) as they were in disease risks (72%)...
January 10, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28065918/exploiting-next-generation-sequencing-to-solve-the-haplotyping-puzzle-in-polyploids-a-simulation-study
#4
Ehsan Motazedi, Richard Finkers, Chris Maliepaard, Dick de Ridder
Haplotypes are the units of inheritance in an organism, and many genetic analyses depend on their precise determination. Methods for haplotyping single individuals use the phasing information available in next-generation sequencing reads, by matching overlapping single-nucleotide polymorphisms while penalizing post hoc nucleotide corrections made. Haplotyping diploids is relatively easy, but the complexity of the problem increases drastically for polyploid genomes, which are found in both model organisms and in economically relevant plant and animal species...
January 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28057061/congenital-infection-with-atypical-porcine-pestivirus-appv-is-associated-with-disease-and-viral-persistence
#5
Lukas Schwarz, Christiane Riedel, Sandra Högler, Leonie J Sinn, Thomas Voglmayr, Bettina Wöchtl, Nora Dinhopl, Barbara Rebel-Bauder, Herbert Weissenböck, Andrea Ladinig, Till Rümenapf, Benjamin Lamp
In 2013, several Austrian piglet-producing farms recorded outbreaks of action-related repetitive myoclonia in newborn piglets ("shaking piglets"). Malnutrition was seen in numerous piglets as a complication of this tremor syndrome. Overall piglet mortality was increased and the number of weaned piglets per sow decreased by more than 10% due to this outbreak. Histological examination of the CNS of affected piglets revealed moderate hypomyelination of the white substance in cerebellum and spinal cord. We detected a recently discovered pestivirus, termed atypical porcine pestivirus (APPV) in all these cases by RT-PCR...
January 6, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28054563/joint-qtl-mapping-and-gene-expression-analysis-identify-positional-candidate-genes-influencing-pork-quality-traits
#6
Rayner González-Prendes, Raquel Quintanilla, Angela Cánovas, Arianna Manunza, Tainã Figueiredo Cardoso, Jordi Jordana, José Luis Noguera, Ramona N Pena, Marcel Amills
Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (~104 Mb), SSC5 (~15 Mb) and SSC13 (~137 Mb), while several additional regions were significantly associated with meat quality traits at the chromosome-wide level...
January 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28048816/mo-de-207b-05-predicting-gene-mutations-in-renal-cell-carcinoma-based-on-ct-imaging-features-validation-using-tcga-tcia-datasets
#7
X Chen, Z Zhou, K Thomas, J Wang
PURPOSE: The goal of this work is to investigate the use of contrast enhanced computed tomographic (CT) features for the prediction of mutations of BAP1, PBRM1, and VHL genes in renal cell carcinoma (RCC). METHODS: For this study, we used two patient databases with renal cell carcinoma (RCC). The first one consisted of 33 patients from our institution (UT Southwestern Medical Center, UTSW). The second one consisted of 24 patients from the Cancer Imaging Archive (TCIA), where each patient is connected by a unique identi?er to the tissue samples from the Cancer Genome Atlas (TCGA)...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046027/genome-wide-association-study-reveals-four-loci-for-lipid-ratios-in-the-korean-population-and-the-constitutional-subgroup
#8
Taehyeung Kim, Ah Yeon Park, Younghwa Baek, Seongwon Cha
Circulating lipid ratios are considered predictors of cardiovascular risks and metabolic syndrome, which cause coronary heart diseases. One constitutional type of Korean medicine prone to weight accumulation, the Tae-Eum type, predisposes the consumers to metabolic syndrome, hypertension, diabetes mellitus, etc. Here, we aimed to identify genetic variants for lipid ratios using a genome-wide association study (GWAS) and followed replication analysis in Koreans and constitutional subgroups. GWASs in 5,292 individuals of the Korean Genome and Epidemiology Study and replication analyses in 2,567 subjects of the Korea medicine Data Center were performed to identify genetic variants associated with triglyceride (TG) to HDL cholesterol (HDLC), LDL cholesterol (LDLC) to HDLC, and non-HDLC to HDLC ratios...
2017: PloS One
https://www.readbyqxmd.com/read/28039138/an-effective-counterselection-system-for-listeria-monocytogenes-and-its-use-to-characterize-10403s-strain-monocin-genomic-region
#9
Tal Argov, Lev Rabinovich, Nadejda Sigal, Anat A Herskovits
Construction of Listeria monocytogenes mutants by allelic exchange has been laborious and time consuming due to lack of proficient selection markers for the final recombination event. That is, a marker conveying substance sensitivity to the bacteria bearing it, enabling the exclusion of merodiploids and selection for plasmid loss. In order to address this issue, we engineered a counterselection marker based on a mutated phenylalanyl-tRNA synthetase gene (pheS*). This mutation renders the phenylalanine-binding site of the enzyme more promiscuous and allows the binding of the toxic p-chloro-phenylalanine analog (p-Cl-phe) as a substrate...
December 30, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28038787/using-the-crispr-cas9-system-to-understand-neuropeptide-biology-and-regulation
#10
REVIEW
Elizabeth A Hay, Christopher Knowles, Andreas Kolb, Alasdair MacKenzie
Neuropeptides and their receptors play a role in physiological responses such as appetite, stress and inflammatory pain. With neuropeptides having such diverse and important physiological roles, knocking-out the genes encoding them, their receptors, parts of their regulatory sequences, or reproducing disease associated polymorphic variants are important steps in studying neuropeptides and how they may contribute to disease. Previously, knock-outs were generated using methods such as targeted homologous recombination in embryonic stem cells but this method is costly and time-consuming...
December 3, 2016: Neuropeptides
https://www.readbyqxmd.com/read/28029645/an-ensemble-approach-for-large-scale-identification-of-protein-protein-interactions-using-the-alignments-of-multiple-sequences
#11
Lei Wang, Zhu-Hong You, Xing Chen, Jian-Qiang Li, Xin Yan, Wei Zhang, Yu-An Huang
Protein-Protein Interactions (PPI) is not only the critical component of various biological processes in cells, but also the key to understand the mechanisms leading to healthy and diseased states in organisms. However, it is time-consuming and cost-intensive to identify the interactions among proteins using biological experiments. Hence, how to develop a more efficient computational method rapidly became an attractive topic in the post-genomic era. In this paper, we propose a novel method for inference of protein-protein interactions from protein amino acids sequences only...
December 22, 2016: Oncotarget
https://www.readbyqxmd.com/read/28028921/oscillospira-and-related-bacteria-from-metagenomics-species-to-metabolic-features
#12
Uri Gophna, Tom Konikoff, Henrik Bjørn Nielsen
Oscillospira is an under-studied anaerobic bacterial genus from Clostridial cluster IV that has resisted cultivation for over a decade since the first time it was observed. In recent years its 16S rRNA gene was identified in several human gut microbiota studies where it was often associated with interesting traits, especially leanness. However, very little is known about its metabolism or physiology. Here we use nearly complete genomes derived from shot-gun metagenomic data from the human gut to analyze Oscillospira and related bacteria...
December 28, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/28027431/from-classical-mutagenesis-to-nuclease-based-breeding-directing-natural-dna-repair-for-a-natural-end-product
#13
Michael Pacher, Holger Puchta
The production of mutants of crop plants by the use of chemical or physical genotoxins has a long tradition. These factors induce the natural DNA repair machinery to repair damages in an error-prone way. In case of radiation, multiple double strand breaks (DSBs) are induced randomly in the genome, leading in very rare cases to a desirable phenotype. In recent years the use of synthetic, site directed nucleases (SDNs), also referred to as sequence specific nucleases (SSNs), like the CRISPR/Cas system, enabled scientists to use exactly the same naturally occurring DNA repair mechanisms for the controlled induction of genomic changes at predefined sites in plant genomes...
December 27, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28027425/indel-seq-a-fast-forward-genetics-approach-for-identification-of-trait-associated-putative-candidate-genomic-regions-and-its-application-in-pigeonpea-cajanus-cajan
#14
Vikas K Singh, Aamir W Khan, Rachit K Saxena, Pallavi Sinha, Sandip M Kale, Swathi Parupalli, Vinay Kumar, Annapurna Chitikineni, V Suryanarayana, C V Sameer Kumar, Mamta Sharma, G Anuradha, K N Yamini, S Muniswamy, Rajeev K Varshney
Identification of candidate genomic regions associated with target traits using conventional mapping methods is challenging and time-consuming. In recent years, a number of single nucleotide polymorphisms (SNPs) based mapping approaches have been developed and used for identification of candidate/putative genomic regions. However, in the majority of these studies, insertion-deletion (Indel) mutations were largely ignored. For efficient use of Indels in mapping target traits, we propose Indel-seq approach, which is a combination of whole genome re-sequencing (WGRS) and bulked segregant analysis (BSA) and relies on the Indel frequencies in a given germplasm set...
December 27, 2016: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28018329/propidium-monoazide-integrated-with-qpcr-enables-the-detection-and-enumeration-of-infectious-enteric-rna-and-dna-viruses-in-clam-and-fermented-sausages
#15
Narciso M Quijada, Gislaine Fongaro, Célia R M Barardi, Marta Hernández, David Rodríguez-Lázaro
The increase of foodborne viral outbreaks highlights the need for a rapid and sensitive method for the prediction of viral infectivity in food samples. This study assesses the use of propidium monoazide (PMA) coupled with real-time PCR methods (RT-qPCR or qPCR for RNA or DNA viruses, respectively) in the determination of viral infectivity in complex animal-related food matrices. Clam and Spanish fermented sausage ("chorizo") samples were spiked with infectious and heat-inactivated human adenovirus-2 (HAdV-2) and mengovirus (vMC0)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28011748/genotoxicity-and-gene-expression-analyses-of-liver-and-lung-tissues-of-mice-treated-with-titanium-dioxide-nanoparticles
#16
Yan Li, Jian Yan, Wei Ding, Ying Chen, Lindsay M Pack, Tao Chen
Titanium dioxide nanoparticles (TiO2 NPs) are used in paints, plastics, papers, inks, foods, toothpaste, pharmaceuticals and cosmetics. However, TiO2 NPs cause inflammation, pulmonary damage, fibrosis and lung tumours in animals and are possibly carcinogenic to humans. Although there are a large number of studies on the toxicities of TiO2 NPs, the data are inconclusive and the mechanisms underlying the toxicity are not clear. In this study, we used the Comet assay to evaluate genotoxicity and whole-genome microarray technology to analyse gene expression pattern in vivo to explore the possible mechanisms for toxicity and genotoxicity of TiO2 NPs...
January 2017: Mutagenesis
https://www.readbyqxmd.com/read/28005991/drug-repositioning-for-alzheimer-s-disease-based-on-systematic-omics-data-mining
#17
Ming Zhang, Gerold Schmitt-Ulms, Christine Sato, Zhengrui Xi, Yalun Zhang, Ye Zhou, Peter St George-Hyslop, Ekaterina Rogaeva
Traditional drug development for Alzheimer's disease (AD) is costly, time consuming and burdened by a very low success rate. An alternative strategy is drug repositioning, redirecting existing drugs for another disease. The large amount of biological data accumulated to date warrants a comprehensive investigation to better understand AD pathogenesis and facilitate the process of anti-AD drug repositioning. Hence, we generated a list of anti-AD protein targets by analyzing the most recent publically available 'omics' data, including genomics, epigenomics, proteomics and metabolomics data...
2016: PloS One
https://www.readbyqxmd.com/read/28003311/unlocking-the-potential-of-orphan-legumes
#18
REVIEW
Christopher Cullis, Karl J Kunert
Orphan, or underutilized, legumes are domesticated legumes with useful properties, but with less importance than major world crops due to use and supply constraints. However, they play a significant role in many developing countries, providing food security and nutrition to consumers, as well as income to resource-poor farmers. They have been largely neglected by both researchers and industry due to their limited economic importance in the global market. Orphan legumes are better adapted than the major legume crops to extreme soil and climatic conditions, with high tolerance to abiotic environmental stresses such as drought...
December 21, 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28002826/the-capn2-capn8-locus-on-chromosome-1q-is-associated-with-variation-in-serum-alpha-carotene-concentrations
#19
Christopher R D'Adamo, Valerie J Dawson, Kathleen A Ryan, Laura M Yerges-Armstrong, Richard D Semba, Nanette I Steinle, Braxton D Mitchell, Alan R Shuldiner, Patrick F McArdle
BACKGROUND/AIMS: Alpha-carotene is a provitamin A carotenoid present in fruits and vegetables. Higher serum concentrations of α-carotene have been associated with lower risk of cancer and all-cause mortality. Previous studies have suggested that genetic variants influence serum concentrations of provitamin A carotenoids, but to date no variants have been robustly associated with serum α-carotene concentrations. The aim of this study was to identify genetic associations with serum α-carotene concentrations using the genome-wide association study (GWAS) approach...
December 22, 2016: Journal of Nutrigenetics and Nutrigenomics
https://www.readbyqxmd.com/read/27987172/exploring-plant-co-expression-and-gene-gene-interactions-with-cornet-3-0
#20
Michiel Van Bel, Frederik Coppens
Selecting and filtering a reference expression and interaction dataset when studying specific pathways and regulatory interactions can be a very time-consuming and error-prone task. In order to reduce the duplicated efforts required to amass such datasets, we have created the CORNET (CORrelation NETworks) platform which allows for easy access to a wide variety of data types: coexpression data, protein-protein interactions, regulatory interactions, and functional annotations. The CORNET platform outputs its results in either text format or through the Cytoscape framework, which is automatically launched by the CORNET website...
2017: Methods in Molecular Biology
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