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Comparative genomics

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https://www.readbyqxmd.com/read/28214915/evaluation-of-the-gard-assay-in-a-blind-cosmetics-europe-study
#1
Henrik Johansson, Robin Gradin, Andy Forreryd, Maria Agemark, Kathrin Zeller, Angelica Johansson, Olivia Larne, Erwin van Vliet, Carl Borrebaeck, Malin Lindstedt
Chemical hypersensitivity is an immunological response towards foreign substances, commonly referred to as sensitizers, which gives rise primarily to the clinical symptoms known as allergic contact dermatitis. For the purpose of mitigating risks associated with consumer products, chemicals are screened for sensitizing effects. Historically, such predictive screenings have been performed using animal models. However, due to industrial and regulatory demand, animal models for the purpose of sensitization assessment are being replaced by animal-free testing methods, a global trend that is spreading across industries and market segments...
February 17, 2017: ALTEX
https://www.readbyqxmd.com/read/28214888/analysis-of-long-non-coding-rna-expression-of-lymphatic-endothelial-cells-in-response-to-type-2-diabetes
#2
Min Qi, Qiuhong Zhou, Weiqi Zeng, Minxue Shen, Xiaomin Liu, Chang Luo, Jing Long, Wangqing Chen, Jianglin Zhang, Siyu Yan
BACKGROUND: Recent evidence has indicated that long non-coding RNA (lncRNA) is involved in the pathogenesis of type 2 diabetes, but nothing is known about lncRNA expression changes of lymphatic endothelial cells in response to type 2 diabetes. METHODS: The GSE38396 dataset was downloaded from the Gene Expression Omnibus database and the probe sets of Human Gnome U133 Plus2.0 microarray were annotated for lncRNA. Differentially expressed lncRNAs between diabetic and non-diabetic lymphatic endothelial cells were calculated...
January 27, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28214713/comparative-analysis-of-metagenomes-of-italian-top-soil-improvers
#3
Federica Gigliucci, Gianfranco Brambilla, Rosangela Tozzoli, Valeria Michelacci, Stefano Morabito
Biosolids originating from Municipal Waste Water Treatment Plants are proposed as top soil improvers (TSI) for their beneficial input of organic carbon on agriculture lands. Their use to amend soil is controversial, as it may lead to the presence of emerging hazards of anthropogenic or animal origin in the environment devoted to food production. In this study, we used a shotgun metagenomics sequencing as a tool to perform a characterization of the hazards related with the TSIs. The samples showed the presence of many virulence genes associated to different diarrheagenic E...
February 16, 2017: Environmental Research
https://www.readbyqxmd.com/read/28214693/genomic-prediction-for-beef-fatty-acid-profile-in-nellore-cattle
#4
Hermenegildo Lucas Justino Chiaia, Elisa Peripoli, Rafael Medeiros de Oliveira Silva, Carolyn Aboujaoude, Fabiele Loise Braga Feitosa, Marcos Vinicius Antunes de Lemos, Mariana Piatto Berton, Bianca Ferreira Olivieri, Rafael Espigolan, Rafael Lara Tonussi, Daniel Gustavo Mansan Gordo, Tiago Bresolin, Ana Fabrícia Braga Magalhães, Gerardo Alves Fernandes Júnior, Lúcia Galvão de Albuquerque, Henrique Nunes de Oliveira, Joyce de Jesus Mangini Furlan, Adrielle Mathias Ferrinho, Lenise Freitas Mueller, Humberto Tonhati, Angélica Simone Cravo Pereira, Fernando Baldi
The objective of this study was to compare SNP-BLUP, BayesCπ, BayesC and Bayesian Lasso methodologies to predict the direct genomic value for saturated, monounsaturated, and polyunsaturated fatty acid profile, omega 3 and 6 in the Longissimus thoracis muscle of Nellore cattle finished in feedlot. A total of 963 Nellore bulls with phenotype for fatty acid profiles, were genotyped using the Illumina BovineHD BeadChip (Illumina, San Diego, CA) with 777,962 SNP. The predictive ability was evaluated using cross validation...
February 9, 2017: Meat Science
https://www.readbyqxmd.com/read/28214377/reciprocal-translocation-of-small-numbers-of-inbred-individuals-rescues-immunogenetic-diversity
#5
Catherine E Grueber, Jolene T Sutton, Sol Heber, James V Briskie, Ian G Jamieson, Bruce C Robertson
Genetic rescue can reduce inbreeding depression and increase fitness of small populations, even when the donor populations are highly inbred. In a recent experiment involving two inbred island populations of the South Island robin, Petroica australis, reciprocal translocations improved microsatellite diversity and individual fitness. While microsatellite loci may reflect patterns of genome-wide diversity, they generally do not indicate the specific genetic regions responsible for increased fitness. We tested the effectiveness of this reciprocal translocation for rescuing diversity of two immunogenetic regions: toll-like receptor (TLR) and major histocompatibility complex (MHC) genes...
February 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28214373/improved-detection-of-zika-virus-rna-in-human-and-animal-specimens-by-a-novel-highly-sensitive-and-specific-real-time-rt-pcr-assay-targeting-the-5-untranslated-region-of-zika-virus
#6
Jasper Fuk-Woo Chan, Cyril Chik-Yan Yip, Kah-Meng Tee, Zheng Zhu, Jessica Oi-Ling Tsang, Kenn Ka-Heng Chik, Terance Gi-Wai Tsang, Chris Chung-Sing Chan, Vincent Kwok-Man Poon, Siddharth Sridhar, Feifei Yin, Ivan Fan-Ngai Hung, Sandy Ka-Yee Chau, Anna Jinxia Zhang, Kwok-Hung Chan, Kwok-Yung Yuen
OBJECTIVE AND METHOD: We developed and evaluated five novel real-time RT-PCR assays targeting conserved regions in the 5'-untranslated region (5'-UTR), envelope (E'), non-structural protein 2A (NS2A), NS5, and 3'-UTR of the ZIKV genome. RESULTS: The ZIKV-5'-UTR assay exhibited the lowest in-vitro limit of detection (5-10 RNA copies/reaction and 3.0×10(-1) plaque-forming units/ml). Compared to the modified version of a widely adopted RT-PCR assay targeting the ZIKV-E gene, the ZIKV-5'-UTR assay showed better sensitivity in human clinical specimens, and representative mouse specimens, including many organs which are known to be involved in human ZIKV infection but difficult to obtain in clinical settings...
February 18, 2017: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/28214224/escherichia-coli-sequence-type-73-as-a-cause-of-community-acquired-urinary-tract-infection-in-men-and-women-in-rio-de-janeiro-brazil
#7
Ana Paula de Souza da-Silva, Viviane Santos de Sousa, Natacha Martins, Rubens Clayton da Silva Dias, Raquel Regina Bonelli, Lee W Riley, Beatriz Meurer Moreira
Escherichia coli clones ST131, ST69, ST95, and ST73 are frequent causes of urinary tract infections (UTI) and bloodstream infections. Specific clones and virulence profiles of E. coli causing UTI in men has been rarely described. The aim of this study was to characterize patient and clonal characteristics of community-acquired UTI caused by E. coli in men (n=12) and women (n=127) in Rio de Janeiro, Brazil, complementing a previous work. We characterized isolates in phylogenetic groups, ERIC2-PCR and PFGE types, MLST, genome similarity and virulence gene-profiles...
February 7, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28214218/implication-of-downregulation-and-prospective-pathway-signaling-of-microrna-375-in-lung-squamous-cell-carcinoma
#8
Wen-Jie Chen, Ting-Qing Gan, Hui Qin, Su-Ning Huang, Li-Hua Yang, Ye-Ying Fang, Zu-Yun Li, Lin-Jiang Pan, Gang Chen
BACKGROUND: Lung cancer is one of the most typical cancers in the world. Altered expression profiles of microRNA-375(miR-375) are linked to many diseases including lung cancer. However, the relationship between miR-375 and lung squamous cell carcinoma (LUSC) is controversial. METHODS: We first evaluated the 23 LUSCs and the paired normal lung tissues by qRT-PCR. Then we analyzed the LUSC samples with miR-375 expression based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO)...
January 22, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28213802/high-expression-of-aspm-correlates-with-tumor-progression-and-predicts-poor-outcome-in-patients-with-prostate-cancer
#9
Jian-Jiang Xie, Yang-Jia Zhuo, Yu Zheng, Ru-Jun Mo, Ze-Zhen Liu, Bo-Wei Li, Zhi-Duan Cai, Xue-Jin Zhu, Yu-Xiang Liang, Hui-Chan He, Wei-de Zhong
PURPOSE: Abnormal spindle microtubule assembly (ASPM) gene was known to be linked with poor clinical prognosis in various tumors. However, the clinical significance of ASPM in prostate cancer (PCa) has not yet been understood. The purpose of this study was to determine the association of ASPM with tumor progression and prognosis in PCa patients. METHODS: The expression of ASPM at protein level in human PCa and non-cancerous prostate tissue was detected by immunohistochemical analysis, which was further validated by using microarray-based dataset (NCBI GEO: GSE21032 and The Cancer Genome Atlas (TCGA) dataset) at mRNA level...
February 17, 2017: International Urology and Nephrology
https://www.readbyqxmd.com/read/28213571/mir-146a-b-a-family-with-shared-seeds-and-different-roots
#10
Mark Paterson, Alison J Kriegel
MicroRNAs are small, non-coding, RNAs known for their powerful modulation of molecular processes, making them a major focus for studying pathological mechanisms. The human miR-146 family of microRNAs consists of two member genes - MIR146A and MIR146B These two miRNAs are located on different chromosomes and exhibit differential regulation in many cases. However, they are nearly identical in sequence and share a seed sequence, thus they are predicted to target the same set of genes. A large proportion of the miR-146 literature focuses on its role in regulating the innate immune response in the context of various pathologies by modulating two widely studied target genes in the toll-like receptor signaling cascade...
February 17, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28213570/blunted-transcriptional-response-to-skeletal-muscle-ischemia-in-rats-with-chronic-kidney-disease-potential-role-for-impaired-ischemia-induced-angiogenesis
#11
Rafael U Heiss, Fabian Fahlbusch, Johannes Jacobi, Christoph Daniel, Arif B Ekici, Nada Cordasic, Kerstin Amann, Andrea Hartner, Karl F Hilgers
Chronic kidney disease (CKD) is associated with increased cardiovascular morbidity and mortality. Previous studies indicated an impairment of ischemia-induced angiogenesis in skeletal muscle of rats with CKD. We performed a systematic comparison of early gene expression in response to ischemia in rats with or without CKD to identify potential molecular mechanisms underlying impaired angiogenesis in CKD. CKD was induced in male rats by 5/6 nephrectomy (SNX); control rats were sham operated (sham). Eight weeks later, ischemia of the right limb was induced by ligation and resection of the femoral artery...
February 17, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28213480/a-common-genetic-variant-risk-score-is-associated-with-drug-induced-qt-prolongation-and-torsade-de-pointes-risk-a-pilot-study
#12
David G Strauss, Jose Vicente, Lars Johannesen, Ksenia Blinova, Jay W Mason, Peter Weeke, Elijah R Behr, Dan M Roden, Raymond Woosley, Gulum Kosova, Michael A Rosenberg, Christopher Newton-Cheh
Background -Drug-induced QT interval prolongation, a risk factor for life-threatening ventricular arrhythmias, is a potential side effect of many marketed and withdrawn medications. The contribution of common genetic variants previously associated with baseline QT interval to drug-induced QT prolongation and arrhythmias is not known. Methods -We tested the hypothesis that a weighted combination of common genetic variants contributing to QT interval at baseline, identified through genome-wide association studies, can predict individual response to multiple QT-prolonging drugs...
February 17, 2017: Circulation
https://www.readbyqxmd.com/read/28213475/wheat-landrace-genome-diversity
#13
Luzie U Wingen, Claire West, Michelle Leverington-Waite, Sarah Collier, Simon Orford, Richard Goram, Cai-Yun Yang, Julie King, Alexandra M Allen, Amanda Burridge, Keith J Edwards, Simon Griffiths
Understanding the genomic complexity of bread wheat (Triticum aestivum L.) is a cornerstone in the quest to unravel the processes of domestication and the following adaptation of domesticated wheat to a wide variety of environments across the globe. Additionally, it is of importance for future improvement of the crop, particularly in the light of climate change. Focussing on the adaptation after domestication, a nested association mapping (NAM) panel of 60 segregating bi-parental populations were developed mainly involving landrace accessions from the core set of the Watkins hexaploid wheat collection optimized for genetic diversity (WINGEN et al...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28213165/hbvcircle-a-novel-tool-to-investigate-hepatitis-b-virus-covalently-closed-circular-dna
#14
Zhipeng Yan, Jing Zeng, Youjun Yu, Kunlun Xiang, Hui Hu, Xue Zhou, Lili Gu, Li Wang, Jie Zhao, John A T Young, Lu Gao
BACKGROUND & AIMS: Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) persists as a stable episome in infected hepatocytes and serves as a template for the transcription of all viral genes. Due to the narrow host range of HBV, the development of a robust mouse model that supports cccDNA-dependent viral replication is a key hurdle in the development of novel HBV therapeutics. This study aimed to develop a novel tool to investigate HBV cccDNA. METHODS: Through minicircle technology, HBVcircle, a recombinant cccDNA, was easily generated and extracted from a genetically engineered E...
February 14, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28213040/the-locus-of-heat-resistance-lhr-mediates-heat-resistance-in-salmonella-enterica-escherichia-coli-and-enterobacter-cloacae
#15
Ryan G Mercer, Brian D Walker, Xianqin Yang, Lynn M McMullen, Michael G Gänzle
Enterobacteriaceae comprise food spoilage organisms as well as food-borne pathogens including Escherichia coli. Heat resistance in E. coli was attributed to a genomic island called the locus of heat resistance (LHR). This genomic island is also present in several other genera of Enterobacteriaceae, but its function in the enteric pathogens Salmonella enterica and Enterobacter cloacae is unknown. This study aimed to determine the frequency of the LHR in food isolates of E. coli, and its influence on heat resistance in S...
June 2017: Food Microbiology
https://www.readbyqxmd.com/read/28212810/chromosomal-instability-analysis-and-regional-tumor-heterogeneity-in-colon-cancer
#16
Vincenza Barresi, Sergio Castorina, Nicolò Musso, Carmela Capizzi, Tonia Luca, Giovanna Privitera, Daniele Filippo Condorelli
Chromosomal instability (CIN) is classically defined as an increase in the rate at which numerical or structural chromosomal aberrations are acquired in a cancer cell. The number of somatic copy number abnormalities (CNAs) revealed by high resolution genomic array can be considered as a surrogate marker for CIN, but several points, related to sample processing and data analysis, need to be standardized. In this work we analyzed 51 CRC samples and matched normal mucosae by whole genome SNP arrays and compared different bioinformatics tools in order to identify broad (>25% of a chromosomal arm) and focal somatic copy number abnormalities (BCNAs and FCNAs respectively)...
January 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28212614/transcriptomic-profiling-provides-molecular-insights-into-hydrogen-peroxide-induced-adventitious-rooting-in-mung-bean-seedlings
#17
Shi-Weng Li, Yan Leng, Rui-Fang Shi
BACKGROUND: Hydrogen peroxide (H2O2) has been known to function as a signalling molecule involved in the modulation of various physiological processes in plants. H2O2 has been shown to act as a promoter during adventitious root formation in hypocotyl cuttings. In this study, RNA-Seq was performed to reveal the molecular mechanisms underlying H2O2-induced adventitious rooting. RESULTS: RNA-Seq data revealed that H2O2 treatment greatly increased the numbers of clean reads and expressed genes and abundance of gene expression relative to the water treatment...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212602/happi-2-a-comprehensive-and-high-quality-map-of-human-annotated-and-predicted-protein-interactions
#18
Jake Y Chen, Ragini Pandey, Thanh M Nguyen
BACKGROUND: Human protein-protein interaction (PPI) data is essential to network and systems biology studies. PPI data can help biochemists hypothesize how proteins form complexes by binding to each other, how extracellular signals propagate through post-translational modification of de-activated signaling molecules, and how chemical reactions are coupled by enzymes involved in a complex biological process. Our capability to develop good public database resources for human PPI data has a direct impact on the quality of future research on genome biology and medicine...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212550/plcb4-copy-gain-and-plc%C3%A3-4-overexpression-in-primary-gastrointestinal-stromal-tumors-integrative-characterization-of-a-lipid-catabolizing-enzyme-associated-with-worse-disease-free-survival
#19
Chien-Feng Li, Ting-Ting Liu, I-Chieh Chuang, Yen-Yang Chen, Fu-Min Fang, Ti-Chun Chan, Wan-Shan Li, Hsuan-Ying Huang
To explore the implications of lipid catabolism-associated genes in gastrointestinal stromal tumors, we reappraised transcriptomic and genomic datasets and identified copy-gained and differentially upregulated PLCB4 gene associated with tumor progression. On full sections, PLCB4 mRNA abundance and PLCß4 immunoexpression were validated in 70 cases. On tissue microarrays, PLCB4 gene copies and PLCß4 immunoexpression were both informative in 350 cases with KIT/PDGFRA/BRAF genotypes noted in 213. In GIST48 cell line, we stably silenced PLCB4 and YAP1 to characterize their functional effects and regulatory link...
February 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28212542/two-stage-genome-wide-association-study-identifies-a-novel-susceptibility-locus-associated-with-melanoma
#20
Katherine J Ransohoff, Wenting Wu, Hyunje G Cho, Harvind C Chahal, Yuan Lin, Hong-Ji Dai, Christopher I Amos, Jeffrey E Lee, Jean Y Tang, David A Hinds, Jiali Han, Qingyi Wei, Kavita Y Sarin
Genome-wide association studies have identified 21 susceptibility loci associated with melanoma. These loci implicate genes affecting pigmentation, nevus count, telomere maintenance, and DNA repair in melanoma risk. Here, we report the results of a two-stage genome-wide association study of melanoma. The stage 1 discovery phase consisted of 4,842 self-reported melanoma cases and 286,565 controls of European ancestry from the 23andMe research cohort and the stage 2 replication phase consisted of 1,804 melanoma cases and 1,026 controls from the University of Texas M...
February 9, 2017: Oncotarget
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