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https://www.readbyqxmd.com/read/28545403/long-lasting-effect-of-obesity-on-skeletal-muscle-transcriptome
#1
Ilhem Messaoudi, Mithila Handu, Maham Rais, Suhas Sureshchandra, Byung S Park, Suzanne S Fei, Hollis Wright, Ashley E White, Ruhee Jain, Judy L Cameron, Kerri M Winters-Stone, Oleg Varlamov
BACKGROUND: Reduced physical activity and increased intake of calorically-dense diets are the main risk factors for obesity, glucose intolerance, and type 2 diabetes. Chronic overnutrition and hyperglycemia can alter gene expression, contributing to long-term obesity complications. While caloric restriction can reduce obesity and glucose intolerance, it is currently unknown whether it can effectively reprogram transcriptome to a pre-obesity level. The present study addressed this question by the preliminary examination of the transcriptional dynamics in skeletal muscle after exposure to overnutrition and following caloric restriction...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28540426/genetic-analysis-of-heterogeneous-sub-clones-in-recombinant-chinese-hamster-ovary-cells
#2
Kaiming Chen, Dong Li, Hongwen Li, Bing Li, Jie Li, Lei Huang, Renhao Li, Xiaoqing Xu, Lingxiao Jiang, Cizhong Jiang, Hua Gu, Jianmin Fang
Chinese hamster ovary (CHO) cells have been widely used for production of recombinant proteins and therapeutic antibodies. However, owing to the instability and heterogeneity of CHO cells, the development of stable and high-expression recombinant CHO cell lines is often time-consuming. To investigate the mechanisms associated with heterogeneity in protein productivity, we performed transcriptome analysis on the subclones derived from a stable parental CHO clone. Two high-expression subclones and one low-expression subclone were selected based on their similar genomic background and subjected to RNA-seq analysis...
May 24, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28534435/genome-editing-technologies-and-patent-landscape-overview
#3
Fairouz Benahmed-Miniuk, Mat Kresz, Jitendra K Kanaujiya, Christopher D Southgate
Unlike with zinc finger nuclease and transcriptional activator-like effector nuclease DNA modification technologies that rely on lead proteins, developed through expensive and time-consuming processes, the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system has rapidly emerged as the most promising gene-editing technology to date for the modification of any selected DNA sequence. CRISPR is receiving tremendous fanfare due, in part, to its potential to provide a means to fundamentally alter medical genetics and especially cancer medicine...
May 23, 2017: Pharmaceutical Patent Analyst
https://www.readbyqxmd.com/read/28534238/a-fast-algorithm-for-bayesian-multi-locus-model-in-genome-wide-association-studies
#4
Weiwei Duan, Yang Zhao, Yongyue Wei, Sheng Yang, Jianling Bai, Sipeng Shen, Mulong Du, Lihong Huang, Zhibin Hu, Feng Chen
Genome-wide association studies (GWAS) have identified a large amount of single-nucleotide polymorphisms (SNPs) associated with complex traits. A recently developed linear mixed model for estimating heritability by simultaneously fitting all SNPs suggests that common variants can explain a substantial fraction of heritability, which hints at the low power of single variant analysis typically used in GWAS. Consequently, many multi-locus shrinkage models have been proposed under a Bayesian framework. However, most use Markov Chain Monte Carlo (MCMC) algorithm, which are time-consuming and challenging to apply to GWAS data...
May 22, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28529714/recent-advances-in-predicting-gene-disease-associations
#5
REVIEW
Kenneth Opap, Nicola Mulder
Deciphering gene-disease association is a crucial step in designing therapeutic strategies against diseases. There are experimental methods for identifying gene-disease associations, such as genome-wide association studies and linkage analysis, but these can be expensive and time consuming. As a result, various in silico methods for predicting associations from these and other data have been developed using different approaches. In this article, we review some of the recent approaches to the computational prediction of gene-disease association...
2017: F1000Research
https://www.readbyqxmd.com/read/28529330/dietary-medium-chain-saturated-fatty-acids-induce-gene-expression-of-energy-metabolism-related-pathways-in-adipose-tissue-of-abdominally-obese-subjects
#6
J C Matualatupauw, M Bohl, S Gregersen, K Hermansen, L A Afman
BACKGROUND: Dietary medium-chain saturated fatty acids (MC-SFAs) have been shown to reduce total body fat. Previously, we showed that MC-SFAs prevent body fat accumulation, despite weight gain. Here, we aim to explore potential molecular mechanisms underlying the protective effect of MC-SFAs on body fat gain. METHODS: The DairyHealth study examined the long-term effects of milk protein and milk fat with a low or high content of MC-SFA. In this 12 week, randomized, double-blind, diet intervention study, participants consumed 60 g milk protein (whey or casein) and 63 g milk fat (high MC-SFA or low MC-SFA) daily in a 2 by 2 factorial design...
May 22, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/28525650/detection-of-damage-on-single-or-double-stranded-dna-in-a-population-exposed-to-arsenic-in-drinking-water
#7
J Jiménez-Villarreal, D I Rivas-Armendariz, C P Pineda-Belmontes, N D Betancourt-Martínez, M A Macías-Corral, A J Guerra-Alanis, M S Niño-Castañeda, J Morán-Martínez
Different studies have suggested an association between arsenic (As) exposure and damage to single-stranded DNA by reactive oxygen species derived from the biotransformation of arsenic. The single strand damages are converted to double strand damage upon interaction with ultraviolet radiation. Analysis of genomic integrity is important for assessing the genotoxicity caused by environmental pollutants. In this study, we compared the concentration of As in drinking water, nutritional status, lifestyle variables, and the level of genotoxicity in an exposed population and a control group...
May 18, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28516483/capabilities-and-limitations-of-dgge-for-the-analysis-of-hydrocarbonoclastic-prokaryotic-communities-directly-in-environmental-samples
#8
Dina M Al-Mailem, Mayada K Kansour, Samir S Radwan
Prokaryotic communities in pristine and oil-contaminated desert soil, seawater, and hypersaline coastal soil were analyzed using culture-dependent and culture-independent approaches. The former technique was the dilution-plating method. For the latter, total genomic DNA was extracted and the 16S rRNA genes were amplified using a universal bacterial primer pair and primer pairs specific for Actinobacteria, Gammaproteobacteria, and Archaea. The amplicons were resolved using denaturing gradient gel electrophoresis (DGGE) and sequenced, and the sequences were compared to those in GenBank...
May 18, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28514968/further-evaluation-of-the-nwf-filter-for-the-purification-of-plasmodium-vivax-infected-erythrocytes
#9
Jiangyan Li, Zhiyong Tao, Qian Li, Awtum Brashear, Ying Wang, Hui Xia, Qiang Fang, Liwang Cui
BACKGROUND: Isolation of Plasmodium-infected red blood cells (iRBCs) from clinical blood samples is often required for experiments, such as ex vivo drug assays, in vitro invasion assays and genome sequencing. Current methods for removing white blood cells (WBCs) from malaria-infected blood are time-consuming or costly. A prototype non-woven fabric (NWF) filter was developed for the purification of iRBCs, which showed great efficiency for removing WBCs in a pilot study. Previous work was performed with prototype filters optimized for processing 5-10 mL of blood...
May 17, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28512697/utilization-of-genetic-counseling-after-direct-to-consumer-genetic-testing-findings-from-the-impact-of-personal-genomics-pgen-study
#10
Diane R Koeller, Wendy R Uhlmann, Deanna Alexis Carere, Robert C Green, J Scott Roberts
Direct-to-consumer personal genomic testing (DTC-PGT) results lead some individuals to seek genetic counseling (GC), but little is known about these consumers and why they seek GC services. We analyzed survey data pre- and post-PGT from 1026 23andMe and Pathway Genomics customers. Participants were mostly white (91%), female (60%), and of high socioeconomic status (80% college educated, 43% household income of ≥$100,000). After receiving PGT results, 43 participants (4%) made or planned to schedule an appointment with a genetic counselor; 390 (38%) would have used in-person GC had it been available...
May 16, 2017: Journal of Genetic Counseling
https://www.readbyqxmd.com/read/28512219/energetic-cost-of-building-a-virus
#11
Gita Mahmoudabadi, Ron Milo, Rob Phillips
Viruses are incapable of autonomous energy production. Although many experimental studies make it clear that viruses are parasitic entities that hijack the molecular resources of the host, a detailed estimate for the energetic cost of viral synthesis is largely lacking. To quantify the energetic cost of viruses to their hosts, we enumerated the costs associated with two very distinct but representative DNA and RNA viruses, namely, T4 and influenza. We found that, for these viruses, translation of viral proteins is the most energetically expensive process...
May 16, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28511110/determination-of-regional-relationships-among-salmonella-spp-isolated-from-retail-pork-circulating-in-the-chiang-mai-municipality-area-using-a-wgs-data-approach
#12
Prapas Patchanee, Thanaporn Eiamsam-Ang, Juntakarn Vanaseang, Phacharaporn Boonkhot, Pakpoom Tadee
Salmonella is recognized as a significant zoonotic foodborne pathogen, and pork products are involved in one-fifth of infections. Whole genome sequencing data of Salmonella isolated from retail's pork circulating in the Chiang Mai Municipality area between April 2013 and September 2014, were used to focus on genetic diversity and proven in pig-human transmission based on Multilocus Sequence Typing (MLST). Additionally, WGS data were used to investigate virulence genes, to assess the hazard or pathogenic potential transferred into the food production chain...
May 10, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28511109/sensitive-detection-of-viable-escherichia-coli-o157-h7-from-foods-using-a-luciferase-reporter-phage-phiv10lux
#13
Jinwoo Kim, Minsik Kim, Seongmi Kim, Sangryeol Ryu
Escherichia coli O157:H7, a major foodborne pathogen, is a major public health concern associated with life-threatening diseases such as hemolytic uremic syndrome. To alleviate this burden, a sensitive and rapid system is required to detect this pathogen in various kinds of foods. Herein, we propose a phage-based pathogen detection method to replace laborious and time-consuming conventional methods. We engineered an E. coli O157:H7-specific phage phiV10 to rapidly and sensitively detect this notorious pathogen...
May 5, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28508221/rapid-reverse-genetics-systems-for-rhabdoviruses-from-forward-to-reverse-and-back-again
#14
Tobias Nolden, Stefan Finke
Methods to recover recombinant negative strand RNA viruses (rNSVs) from cloned cDNAs have been significantly improved in more than two decades of NSV reverse genetics . In particular, for non-segmented negative strand RNA viruses (NNSVs ) like rhabdoviruses , time-consuming generation of reverse genetics systems by stitching PCR subfragments of genomic rhabdovirus cDNAs using ligase-based conventional cloning approaches limited the number of available recombinant virus cDNA clones. As genetic variability is considered an intrinsic feature of RNA viruses, it is thus reasonable to conclude that reverse genetics approaches to investigate natural virus functions and pathogenesis require improved systems that reflect the complexity of naturally occurring wild-type viruses, and that largely exclude adaption to cell culture conditions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28503508/carbohydrate-composition-associated-with-the-2-year-incidence-of-metabolic-syndrome-in-korean-adults
#15
Nam H Cho, Ara K Cho, Hyun Kyu Kim, Jong Bae Kim, Kyung Eun Lee, Sung Soo Kim, Yeon-Jung Kim, Hak C Jang, Inkyung Baik
The aim of this study was to investigate the association between macronutrient composition and metabolic syndrome (MetS) incidence in Korean adults. Data were obtained from a cohort of 10,030 members aged 40 to 69 years who were enrolled from the 2 cities (Ansung and Ansan) between 2001 and 2002 to participate in the Korean Genome Epidemiology Study. Of these members, 5,565 participants, who were free of MetS and reported no diagnosis of cardiovascular disease at baseline, were included in this study. MetS was defined using the criteria of the National Cholesterol Education Program-Adult Treatment Panel III and Asia-Pacific criteria for waist circumference...
April 2017: Clinical Nutrition Research
https://www.readbyqxmd.com/read/28502225/genomics-of-lactic-acid-bacteria-current-status-and-potential-applications
#16
Chongde Wu, Jun Huang, Rongqing Zhou
Lactic acid bacteria (LAB) are widely used for the production of a variety of foods and feed raw materials where they contribute to flavor and texture of the fermented products. In addition, specific LAB strains are considered as probiotic due to their health-promoting effects in consumers. Recently, the genome sequencing of LAB is booming and the increased amount of published genomics data brings unprecedented opportunity for us to reveal the important traits of LAB. This review describes the recent progress on LAB genomics and special emphasis is placed on understanding the industry-related physiological features based on genomics analysis...
August 2017: Critical Reviews in Microbiology
https://www.readbyqxmd.com/read/28499415/discrimination-of-candidate-subgenome-specific-loci-by-linkage-map-construction-with-an-s1-population-of-octoploid-strawberry-fragaria%C3%A2-%C3%A3-%C3%A2-ananassa
#17
Soichiro Nagano, Kenta Shirasawa, Hideki Hirakawa, Fumi Maeda, Masami Ishikawa, Sachiko N Isobe
BACKGROUND: The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S1 mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers...
May 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28486511/open-sharing-of-genomic-data-who-does-it-and-why
#18
Tobias Haeusermann, Bastian Greshake, Alessandro Blasimme, Darja Irdam, Martin Richards, Effy Vayena
We explored the characteristics and motivations of people who, having obtained their genetic or genomic data from Direct-To-Consumer genetic testing (DTC-GT) companies, voluntarily decide to share them on the publicly accessible web platform openSNP. The study is the first attempt to describe open data sharing activities undertaken by individuals without institutional oversight. In the paper we provide a detailed overview of the distribution of the demographic characteristics and motivations of people engaged in genetic or genomic open data sharing...
2017: PloS One
https://www.readbyqxmd.com/read/28485404/genetic-contributors-to-variation-in-alcohol-consumption-vary-by-race-ethnicity-in-a-large-multi-ethnic-genome-wide-association-study
#19
E Jorgenson, K K Thai, T J Hoffmann, L C Sakoda, M N Kvale, Y Banda, C Schaefer, N Risch, J Mertens, C Weisner, H Choquet
Alcohol consumption is a complex trait determined by both genetic and environmental factors, and is correlated with the risk of alcohol use disorders. Although a small number of genetic loci have been reported to be associated with variation in alcohol consumption, genetic factors are estimated to explain about half of the variance in alcohol consumption, suggesting that additional loci remain to be discovered. We conducted a genome-wide association study (GWAS) of alcohol consumption in the large Genetic Epidemiology Research in Adult Health and Aging (GERA) cohort, in four race/ethnicity groups: non-Hispanic whites, Hispanic/Latinos, East Asians and African Americans...
May 9, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28480303/a-one-step-pcr-based-assay-to-evaluate-the-efficiency-and-precision-of-genomic-dna-editing-tools
#20
Diego Germini, Yara Bou Saada, Tatiana Tsfasman, Kristina Osina, Chloé Robin, Nikolay Lomov, Mikhail Rubtsov, Nikolajs Sjakste, Mar Lipinski, Yegor Vassetzky
Despite rapid progress, many problems and limitations persist and limit the applicability of gene-editing techniques. Making use of meganucleases, TALENs, or CRISPR/Cas9-based tools requires an initial step of pre-screening to determine the efficiency and specificity of the designed tools. This step remains time consuming and material consuming. Here we propose a simple, cheap, reliable, time-saving, and highly sensitive method to evaluate a given gene-editing tool based on its capacity to induce chromosomal translocations when combined with a reference engineered nuclease...
June 16, 2017: Molecular Therapy. Methods & Clinical Development
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