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https://www.readbyqxmd.com/read/28749367/genome-wide-association-study-of-susceptibility-to-particulate-matter-associated-qt-prolongation
#1
Rahul Gondalia, Christy L Avery, Melanie D Napier, Raúl Méndez-Giráldez, James D Stewart, Colleen M Sitlani, Yun Li, Kirk C Wilhelmsen, Qing Duan, Jeffrey Roach, Kari E North, Alexander P Reiner, Zhu-Ming Zhang, Lesley F Tinker, Jeff D Yanosky, Duanping Liao, Eric A Whitsel
BACKGROUND: Ambient particulate matter (PM) air pollution exposure has been associated with increases in QT interval duration (QT). However, innate susceptibility to PM-associated QT prolongation has not been characterized. OBJECTIVE: To characterize genetic susceptibility to PM-associated QT prolongation in a multi-racial/ethnic, genome-wide association study (GWAS). METHODS: Using repeated electrocardiograms (1986-2004), longitudinal data on in diameter (), and generalized estimating equations methods adapted for low-prevalence exposure, we estimated approximately interactions among nine Women's Health Initiative clinical trials and Atherosclerosis Risk in Communities Study subpopulations (), then combined subpopulation-specific results in a fixed-effects, inverse variance-weighted meta-analysis...
June 8, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28749036/advantages-of-rna-seq-compared-to-rna-microarrays-for-transcriptome-profiling-of-anterior-cruciate-ligament-tears
#2
Muhammad Farooq Rai, Eric D Tycksen, Linda J Sandell, Robert H Brophy
Microarrays and RNA-seq are at the forefront of high throughput transcriptome analyses. Since these methodologies are based on different principles there are concerns about the concordance of data between the two techniques. The concordance of RNA-seq and microarrays for genome-wide analysis of differential gene expression has not been rigorously assessed in clinically derived ligament tissues. To demonstrate the concordance between RNA-seq and microarrays and to assess potential benefits of RNA-seq over microarrays, we assessed differences in transcript expression in anterior cruciate ligament (ACL) tissues based on time-from-injury...
July 27, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/28748911/a-novel-and-quick-pcr-based-method-to-genotype-mice-with-a-leptin-receptor-mutation-db-db-mice
#3
Bao-Yu Peng, Qiang Wang, Yan-Hong Luo, Jian-Feng He, Tao Tan, Hua Zhu
db/db mice is one of most widely used animal models in studying the cellular and molecular mechanisms of metabolic disorders, such as diabetes, hyperlipidemia, and obesity. The mice carry spontaneous point mutations in the gene encoding the leptin receptor, leading to leptin receptor inactivation. Since homozygous db/db mice are sterile, the maintenance of db/db mice requires breeding between heterozygous pairs, which makes genotyping essential for the identification of offspring. The aim of this study was to develop a quick and highly repeatable method for genotyping db/db mice, which comprised only three simple steps: Genomic DNA is extracted from either tail tips or ear notches via alkaline lysis (∼20 min); Samples are then subjected to tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) using specially designed and validated primer sets (∼1...
July 27, 2017: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/28748565/evaluating-mechanisms-of-diversification-in-a-guineo-congolian-tropical-forest-frog-using-demographic-model-selection
#4
Daniel M Portik, Adam D Leaché, Danielle Rivera, Michael F Barej, Marius Burger, Mareike Hirschfeld, Mark-Oliver Rödel, David C Blackburn, Matthew K Fujita
The accumulation of biodiversity in tropical forests can occur through multiple allopatric and parapatric models of diversification, including forest refugia, riverine barriers, and ecological gradients. Considerable debate surrounds the major diversification process, particularly in the West African Lower Guinea forests, which contain a complex geographic arrangement of topographic features and historical refugia. We used genomic data to investigate alternative mechanisms of diversification in the Gaboon forest frog, Scotobleps gabonicus, by first identifying population structure and then performing demographic model selection and spatially explicit analyses...
July 27, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28748394/association-mapping-analysis-of-fiber-yield-and-quality-traits-in-upland-cotton-gossypium-hirsutum-l
#5
Mulugeta Seyoum Ademe, Shoupu He, Zhaoe Pan, Junling Sun, Qinglian Wang, Hongde Qin, Jinhai Liu, Hui Liu, Jun Yang, Dongyong Xu, Jinlong Yang, Zhiying Ma, Jinbiao Zhang, Zhikun Li, Zhongmin Cai, Xuelin Zhang, Xin Zhang, Aifen Huang, Xianda Yi, Guanyin Zhou, Lin Li, Haiyong Zhu, Baoyin Pang, Liru Wang, Yinhua Jia, Xiongming Du
Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fiber quality genes are the prime concern of researchers in cotton breeding. Association mapping offers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fiber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China...
July 26, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28748134/genomic-characterization-reconfirms-the-taxonomic-status-of-lactobacillus-parakefiri
#6
Yasuhiro Tanizawa, Hisami Kobayashi, Eli Kaminuma, Mitsuo Sakamoto, Moriya Ohkuma, Yasukazu Nakamura, Masanori Arita, Masanori Tohno
Whole-genome sequencing was performed for Lactobacillus parakefiri JCM 8573(T) to confirm its hitherto controversial taxonomic position. Here, we report its first reliable reference genome. Genome-wide metrics, such as average nucleotide identity and digital DNA-DNA hybridization, and phylogenomic analysis based on multiple genes supported its taxonomic status as a distinct species in the genus Lactobacillus. The availability of a reliable genome sequence will aid future investigations on the industrial applications of L...
2017: Bioscience of Microbiota, Food and Health
https://www.readbyqxmd.com/read/28747922/identification-of-major-quantitative-trait-loci-for-seed-oil-content-in-soybeans-by-combining-linkage-and-genome-wide-association-mapping
#7
Yongce Cao, Shuguang Li, Zili Wang, Fangguo Chang, Jiejie Kong, Junyi Gai, Tuanjie Zhao
Soybean oil is the most widely produced vegetable oil in the world and its content in soybean seed is an important quality trait in breeding programs. More than 100 quantitative trait loci (QTLs) for soybean oil content have been identified. However, most of them are genotype specific and/or environment sensitive. Here, we used both a linkage and association mapping methodology to dissect the genetic basis of seed oil content of Chinese soybean cultivars in various environments in the Jiang-Huai River Valley...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28747766/dna-methylation-signatures-of-chronic-alcohol-dependence-in-purified-cd3-t-cells-of-patients-undergoing-alcohol-treatment
#8
Christof Brückmann, Sumaiya A Islam, Julia L MacIsaac, Alexander M Morin, Kathrin N Karle, Adriana Di Santo, Richard Wüst, Immanuel Lang, Anil Batra, Michael S Kobor, Vanessa Nieratschker
Several studies have shown an association of alcohol dependence with DNA methylation (DNAm), suggesting that environmentally-induced changes on epigenomic variation may play an important role in alcohol dependence. In the present study, we analysed genome-wide DNAm profiles of purified CD3(+) T-cells from pre- and post-treatment alcohol dependent patients, as well as closely matched healthy controls. We identified 59 differentially methylated CpG sites comparing patients prior to treatment with healthy controls and were able to confirm 8 of those sites in additional analyses for differentially methylated regions...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747748/the-epigenetic-landscape-of-promoter-genome-wide-analysis-in-breast-cancer
#9
Seher Karsli-Ceppioglu, Aslihan Dagdemir, Gaëlle Judes, André Lebert, Frédérique Penault-Llorca, Yves-Jean Bignon, Dominique Bernard-Gallon
Breast cancer is a heterogeneous disease due to its clinico-pathological features and response to therapy. The classification of breast tumors based on their hormone receptor status and pathologic features. Post-translational histone modifications come into prominence for regulation of gene expression in cancer pathogenesis. Here, we analyzed dysregulation of H3K9ac and H3K27me3-enriched subtype-specific genes using ChIP-on-chip assay in breast cancer tumors and matched normal tissue samples. Breast cancer tumors were classified according to St Gallen Consensus 2013...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747736/association-of-ubash3a-gene-polymorphism-and-atopic-dermatitis-in-the-chinese-han-population
#10
Y Li, H Cheng, F-L Xiao, B Liang, F-S Zhou, P Li, X-D Zheng, L-D Sun, S Yang, X-J Zhang
Genome-wide association studies have revealed a large number of genetic-risk loci for many autoimmune diseases. One clear finding emerging from the published genetic studies of autoimmunity is that different autoimmune diseases share susceptibility loci. Recent evidence has demonstrated that UBASH3A gene was associated with multiple autoimmune diseases. The aim of this study was to explore the association between UBASH3A single-nucleotide polymorphisms (SNPs) and atopic dermatitis (AD) in a Chinese Han population...
July 27, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28747667/rna-sequencing-reveals-resistance-of-tlr4-ligand-activated-microglial-cells-to-inflammation-mediated-by-the-selective-jumonji-h3k27-demethylase-inhibitor
#11
Amitabh Das, Sarder Arifuzzaman, Taeho Yoon, Sun Hwa Kim, Jin Choul Chai, Young Seek Lee, Kyoung Hwa Jung, Young Gyu Chai
Persistent microglial activation is associated with the production and secretion of various pro-inflammatory genes, cytokines and chemokines, which may initiate or amplify neurodegenerative diseases. A novel synthetic histone 3 lysine 27 (H3K27) demethylase JMJD3 inhibitor, GSK-J4, was proven to exert immunosuppressive activities in macrophages. However, a genome-wide search for GSK-J4 molecular targets has not been undertaken in microglia. To study the immuno-modulatory effects of GSK-J4 at the transcriptomic level, triplicate RNA sequencing and quantitative real-time PCR analyses were performed with resting, GSK-J4-, LPS- and LPS + GSK-J4-challenged primary microglial (PM) and BV-2 microglial cells...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747644/active-nuclear-transcriptome-analysis-reveals-inflammasome-dependent-mechanism-for-early-neutrophil-response-to-mycobacterium-marinum
#12
Amy Kenyon, Daria Gavriouchkina, Jernej Zorman, Giorgio Napolitani, Vincenzo Cerundolo, Tatjana Sauka-Spengler
The mechanisms governing neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilise biotagging, a novel genome-wide profiling approach based on cell type-specific in vivo biotinylation in zebrafish to analyse the initial response of neutrophils to Mycobacterium marinum, a close genetic relative of M. tuberculosis used to model tuberculosis. Differential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, NLRC3 ortholog (wu: fb15h11) and il1β...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747472/disentangling-sources-of-variation-in-ssu-rdna-sequences-from-single-cell-analyses-of-ciliates-impact-of-copy-number-variation-and-experimental-error
#13
Chundi Wang, Tengteng Zhang, Yurui Wang, Laura A Katz, Feng Gao, Weibo Song
Small subunit ribosomal DNA (SSU rDNA) is widely used for phylogenetic inference, barcoding and other taxonomy-based analyses. Recent studies indicate that SSU rDNA of ciliates may have a high level of sequence variation within a single cell, which impacts the interpretation of rDNA-based surveys. However, sequence variation can come from a variety of sources including experimental errors, especially the mutations generated by DNA polymerase in PCR. In the present study, we explore the impact of four DNA polymerases on sequence variation and find that low-fidelity polymerases exaggerate the estimates of single-cell sequence variation...
July 26, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28747387/molecular-characteristics-of-the-kcnj5-mutated-aldosterone-producing-adenomas
#14
Masanori Murakami, Takanobu Yoshimoto, Kazuhiko Nakabayashi, Yujiro Nakano, Takahiro Fukaishi, Kyoichiro Tsuchiya, Isao Minami, Ryotaro Bouchi, Kohji Okamura, Yasuhisa Fujii, Koshi Hashimoto, Ken-Ichiro Hata, Kazunori Kihara, Yoshihiro Ogawa
The pathophysiology of aldosterone-producing adenomas (APAs) has been investigated via genetic approaches and the pathogenic significance of a series of somatic mutations, including KCNJ5, has been uncovered. However, how the mutational status of an APA is associated with its molecular characteristics, including its transcriptome and methylome, has not been fully understood. This study was undertaken to explore the molecular characteristics of APAs, specifically focusing on APAs with KCNJ5 mutations as opposed to those without KCNJ5 mutations, by comparing their transcriptome and methylome status...
July 26, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28747381/rapid-evolution-of-female-biased-genes-among-four-species-of-anopheles-malaria-mosquitoes
#15
Francesco Papa, Nikolai Windbichler, Robert M Waterhouse, Alessia Cagnetti, Rocco D'Amato, Tania Persampieri, Mara K N Lawniczak, Tony Nolan, Philippos A Papathanos
Understanding how phenotypic differences between males and females arise from the sex-biased expression of nearly identical genomes can reveal important insights into the biology and evolution of a species. Among Anopheles mosquito species, these phenotypic differences include vectorial capacity, as it is only females that blood feed and thus transmit human malaria. Here, we use RNA-seq data from multiple tissues of four vector species spanning the Anopheles phylogeny to explore the genomic and evolutionary properties of sex-biased genes...
July 26, 2017: Genome Research
https://www.readbyqxmd.com/read/28747331/assessing-the-causal-role-of-adiposity-on-disordered-eating-in-childhood-adolescence-and-adulthood-a-mendelian-randomization-analysis
#16
Zoe E Reed, Nadia Micali, Cynthia M Bulik, George Davey Smith, Kaitlin H Wade
Background: Observational studies have shown that higher body mass index (BMI) is associated with increased risk of developing disordered eating patterns. However, the causal direction of this relation remains ambiguous.Objective: We used Mendelian randomization (MR) to infer the direction of causality between BMI and disordered eating in childhood, adolescence, and adulthood.Design: MR analyses were conducted with a genetic score as an instrumental variable for BMI to assess the causal effect of BMI at age 7 y on disordered eating patterns at age 13 y with the use of data from the Avon Longitudinal Study of Parents and Children (ALSPAC) (n = 4473)...
July 26, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28747224/regions-of-common-inter-individual-dna-methylation-differences-in-human-monocytes-genetic-basis-and-potential-function
#17
Christopher Schröder, Elsa Leitão, Stefan Wallner, Gerd Schmitz, Ludger Klein-Hitpass, Anupam Sinha, Karl-Heinz Jöckel, Stefanie Heilmann-Heimbach, Per Hoffmann, Markus M Nöthen, Michael Steffens, Peter Ebert, Sven Rahmann, Bernhard Horsthemke
BACKGROUND: There is increasing evidence for inter-individual methylation differences at CpG dinucleotides in the human genome, but the regional extent and function of these differences have not yet been studied in detail. For identifying regions of common methylation differences, we used whole genome bisulfite sequencing data of monocytes from five donors and a novel bioinformatic strategy. RESULTS: We identified 157 differentially methylated regions (DMRs) with four or more CpGs, almost none of which has been described before...
July 26, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28747171/incorporation-of-causative-quantitative-trait-nucleotides-in-single-step-gblup
#18
Breno O Fragomeni, Daniela A L Lourenco, Yukata Masuda, Andres Legarra, Ignacy Misztal
BACKGROUND: Much effort is put into identifying causative quantitative trait nucleotides (QTN) in animal breeding, empowered by the availability of dense single nucleotide polymorphism (SNP) information. Genomic selection using traditional SNP information is easily implemented for any number of genotyped individuals using single-step genomic best linear unbiased predictor (ssGBLUP) with the algorithm for proven and young (APY). Our aim was to investigate whether ssGBLUP is useful for genomic prediction when some or all QTN are known...
July 26, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28746868/ddx6-represses-aberrant-activation-of-interferon-stimulated-genes
#19
Jennifer H Lumb, Qin Li, Lauren M Popov, Siyuan Ding, Marie T Keith, Bryan D Merrill, Harry B Greenberg, Jin Billy Li, Jan E Carette
The innate immune system tightly regulates activation of interferon-stimulated genes (ISGs) to avoid inappropriate expression. Pathological ISG activation resulting from aberrant nucleic acid metabolism has been implicated in autoimmune disease; however, the mechanisms governing ISG suppression are unknown. Through a genome-wide genetic screen, we identified DEAD-box helicase 6 (DDX6) as a suppressor of ISGs. Genetic ablation of DDX6 induced global upregulation of ISGs and other immune genes. ISG upregulation proved cell intrinsic, imposing an antiviral state and making cells refractory to divergent families of RNA viruses...
July 25, 2017: Cell Reports
https://www.readbyqxmd.com/read/28746865/polycomb-responds-to-low-levels-of-transcription
#20
Georgina Berrozpe, Gene O Bryant, Katherine Warpinski, Dan Spagna, Santosh Narayan, Shivangi Shah, Mark Ptashne
How is Polycomb (Pc), a eukaryotic negative regulator of transcription, targeted to specific mammalian genes? Our genome-wide analysis of the Pc mark H3K27me3 in murine cells revealed that Pc is preferentially associated with CpG island promoters of genes that are transcribed at a low level and less so with promoters of genes that are either silent or more highly expressed. Studies of the CpG island promoter of the Kit gene demonstrate that Pc is largely absent when the gene is silent in myeloid cells, as well as when the gene is highly expressed in mast cells...
July 25, 2017: Cell Reports
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