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population genome

Luca A Lotta, Isobel D Stewart, Stephen J Sharp, Felix R Day, Stephen Burgess, Jian'an Luan, Nicholas Bowker, Lina Cai, Chen Li, Laura B L Wittemans, Nicola D Kerrison, Kay-Tee Khaw, Mark I McCarthy, Stephen O'Rahilly, Robert A Scott, David B Savage, John R B Perry, Claudia Langenberg, Nicholas J Wareham
Importance: Pharmacological enhancers of lipoprotein lipase (LPL) are in preclinical or early clinical development for cardiovascular prevention. Studying whether these agents will reduce cardiovascular events or diabetes risk when added to existing lipid-lowering drugs would require large outcome trials. Human genetics studies can help prioritize or deprioritize these resource-demanding endeavors. Objective: To investigate the independent and combined associations of genetically determined differences in LPL-mediated lipolysis and low-density lipoprotein cholesterol (LDL-C) metabolism with risk of coronary disease and diabetes...
September 19, 2018: JAMA Cardiology
Casper K Lumby, Nuno R Nene, Christopher J R Illingworth
Transmission between hosts is a critical part of the viral lifecycle. Recent studies of viral transmission have used genome sequence data to evaluate the number of particles transmitted between hosts, and the role of selection as it operates during the transmission process. However, the interpretation of sequence data describing transmission events is a challenging task. We here present a novel and comprehensive framework for using short-read sequence data to understand viral transmission events, designed for influenza virus, but adaptable to other viral species...
October 16, 2018: PLoS Genetics
Si-Yu Zhang, Despina Tsementzi, Janet K Hatt, Aaron Bivins, Nikunj Khelurkar, Joe Brown, Sachchida Nand Tripathi, Konstantinos T Konstantinidis
Little is known about microbial communities in the Ganges River, India and how they respond to intensive anthropogenic inputs. Here we applied shotgun metagenomics sequencing to study microbial community dynamics and function in planktonic samples collected along a ~700 km river transect, including urban cities and rural settings in upstream waters, before and after the monsoon rainy season. Our results showed that 11-32% of the microbes represented terrestrial, sewage and human inputs (allochthonous). Sewage inputs significantly contributed to the higher abundance, by 13-fold of human gut microbiome (HG) associated sequences and 2-fold of antibiotic resistance genes (ARGs) in the Ganges relative to other riverine ecosystems in Europe, North and South America...
October 16, 2018: Environmental Microbiology
Gunn-Helen Moen, Marissa LeBlanc, Christine Sommer, Rashmi B Prasad, Tove Lekva, Kjersti R Normann, Elisabeth Qvigstad, Leif Groop, Kåre I Birkeland, David M Evans, Kathrine F Frøslie
OBJECTIVE: Hyperglycaemia during pregnancy increases the risk of adverse health outcomes in mother and child, but the genetic aetiology is scarcely studied. Our aims were to (1) assess the overlapping genetic aetiology between the pregnant and non-pregnant population and (2) assess the importance of genome-wide polygenic contributions to glucose traits during pregnancy, by exploring whether genetic risk scores (GRSs) for fasting glucose (FG), 2-h glucose (2hG), type 2 diabetes (T2D) and BMI in non-pregnant individuals were associated with glucose measures in pregnant women...
September 18, 2018: European Journal of Endocrinology
Zhe Zhang, Qianqian Zhang, Qian Xiao, Hao Sun, Hongding Gao, Yumei Yang, Jiucheng Chen, Zhengcao Li, Ming Xue, Peipei Ma, Hongjie Yang, Ningying Xu, Qishan Wang, Yuchun Pan
Inbreeding, which has several causes including genetic drift, population bottlenecks, mating of close relatives and selection, can leave tracts of runs of homozygosity (ROH) along genomes. Recently, decreasing performance on reproductive traits, which might have resulted from inbreeding, has been observed in Chinese pigs. In this study, 830 individuals from Western and Chinese pig breeds were genotyped using the reduced-representation sequencing method. After imputation and quality control, 60 850 high-confidence SNPs were retained for ROH detection...
October 16, 2018: Animal Genetics
Paul D Iordache, Dana Mates, Bjarni Gunnarsson, Hannes P Eggertsson, Patrick Sulem, Stefania Benonisdottir, Irma Eva Csiki, Stefan Rascu, Daniel Radavoi, Radu Ursu, Catalin Staicu, Violeta Calota, Angelica Voinoiu, Mariana Jinga, Gabriel Rosoga, Razvan Danau, Sorin Cristian Sima, Daniel Badescu, Nicoleta Suciu, Viorica Radoi, Ioan Nicolae Mates, Mihai Dobra, Camelia Nicolae, Sigrun Kristjansdottir, Jon G Jonasson, Andrei Manolescu, Gudny Arnadottir, Brynjar Jensson, Aslaug Jonasdottir, Asgeir Sigurdsson, Louise le Roux, Hrefna Johannsdottir, Thorunn Rafnar, Bjarni V Halldorsson, Viorel Jinga, Kari Stefansson
Two familial forms of colorectal cancer (CRC), Lynch syndrome (LS) and familial adenomatous polyposis (FAP), are caused by rare mutations in DNA mismatch repair genes (MLH1, MSH2, MSH6, PMS2) and the genes APC and MUTYH, respectively. No information is available on the presence of high-risk CRC mutations in the Romanian population. We performed whole-genome sequencing of 61 Romanian CRC cases with a family history of cancer and/or early onset of disease, focusing the analysis on candidate variants in the LS and FAP genes...
October 16, 2018: Journal of Cellular and Molecular Medicine
Alireza Shokouhifar, Nasrin Askari, Shaghayegh Yazdani, Jalil Fallah Mehrabadi
BACKGROUND: Schizophrenia, schizoaffective disorder, and bipolar illness are common psychological disorders with high heritability and variable phenotypes. The disrupted in schizophrenia 1 ( DISC1) gene, on chromosome 1q42, has an essential role in neurite outgrowth and cell signaling. The purpose of this study was to investigate the association of three single-nucleotide polymorphisms (SNPs; rs6675281, rs2255340, and rs2738864) with schizophrenia disorder. These three SNPs were chosen as they had been used in most of the previous studies...
October 15, 2018: Journal of Cellular Biochemistry
Nicolas Yelle, David Bakhshinyan, Chitra Venugopal, Sheila K Singh
From stem cells, to the cancer stem cell hypothesis and intratumoral heterogeneity, the following introductory chapter on brain tumor stem cells explores the history of normal and cancerous stem cells, and their implication in the current model of brain tumor development. The origins of stem cells date back to the 1960s, when they were first described as cells capable of self-renewal, extensive proliferation, and differentiation. Since then, many advances have been made and adult stem cells are now known to be present in a very wide variety of tissues...
2019: Methods in Molecular Biology
Iris I de Winter, Tamar Qurkhuli, Nanine de Groot, Annemiek J M de Vos-Rouweler, Pim van Hooft, Ignas M A Heitkönig, Herbert H T Prins, Ronald E Bontrop, Gaby G M Doxiadis
The major histocompatibility complex (MHC) is a highly polymorphic and polygenic genomic region that plays a crucial role in immune-related diseases. Given the need for comparative studies on the variability of immunologically important genes among wild populations and species, we investigated the allelic variation of MHC class II DRB among three congeneric true lemur species: the red-fronted lemur (Eulemur rufifrons), red-bellied lemur (Eulemur rubriventer), and black lemur (Eulemur macaco). We noninvasively collected hair and faecal samples from these species across different regions in Madagascar...
October 15, 2018: Immunogenetics
Sara Karimkhani, Vahid Chaleshi, Hedieh Balaii, Peyman Tarban, Mahyar Nourian, Shiva Irani, Shabnam Shahrokh, Hamid Asadzadeh Aghdaei, Amir Houshang Mohammad Alizadeh, Mohsen Norouzinia, Mohammad Reza Zali
Background: Inflammatory bowel diseases (IBDs), which include ulcerative colitis (UC) and Crohn's disease (CD), are inflammatory disorders that affect the gastrointestinal tract. A combination of inflammatory cytokines has an important role in IBD development. Genome-wide association studies have shown that polymorphisms in the interleukin-23R gene ( IL-23R ) increase susceptibility to IBD. The aim of this study was to investigate the IL-23R 3' UTR SNP to determine a potential association between genotype distribution and IBD...
October 2018: Reports of Biochemistry & Molecular Biology
Moses Koobotse, Jeff Holly, Claire Perks
Within populations carrying the same genetic predisposition, the penetrance of BRCA1 mutations has increased over time. Although linked to changes in lifestyle factors associated with energy metabolism, these observations cannot be explained by the established role of BRCA1 in DNA repair alone. We manipulated BRCA1 expression using tetracycline in the UBR60-bcl2 cell line (which has an inducible, tetracycline-regulated BRCA1 expression) and siRNA in oestrogen receptor(ER)-positive MCF7 and T47D breast cancer cells...
September 11, 2018: Oncotarget
Lorenz K Fuchs, Glyn Jenkins, Dylan W Phillips
As the human population grows and continues to encroach on the natural environment, organisms that form part of such ecosystems are becoming increasingly exposed to exogenous anthropogenic factors capable of changing their meiotic landscape. Meiotic recombination generates much of the genetic variation in sexually reproducing species and is known to be a highly conserved pathway. Environmental stresses, such as variations in temperature, have long been known to change the pattern of recombination in both model and crop plants, but there are other factors capable of causing genome damage, infertility and meiotic abnormalities...
2018: Frontiers in Plant Science
Marie-Line Joffret, Patsy M Polston, Richter Razafindratsimandresy, Maël Bessaud, Jean-Michel Heraud, Francis Delpeyroux
Human enteroviruses (EV) consist of more than 100 serotypes classified within four species for enteroviruses (EV-A to -D) and three species for rhinoviruses, which have been implicated in a variety of human illnesses. Being able to simultaneously amplify the whole genome and identify enteroviruses in samples is important for studying the viral diversity in different geographical regions and populations. It also provides knowledge about the evolution of these viruses. Therefore, we developed a rapid, sensitive method to detect and genetically classify all human enteroviruses in mixtures...
2018: Frontiers in Microbiology
Juliana D Siqueira, Maria Gloria Dominguez-Bello, Monica Contreras, Orlana Lander, Hortensia Caballero-Arias, Deng Xutao, Oscar Noya-Alarcon, Eric Delwart
The number of viruses circulating in small isolated human populations may be reduced by viral extinctions and rare introductions. Here we used viral metagenomics to characterize the eukaryotic virome in feces from healthy children from a large urban center and from three Amerindian villages with minimal outside contact. Numerous human enteric viruses, mainly from the Picornaviridae and Caliciviridae families, were sequenced from each of the sites. Multiple children from the same villages shed closely related viruses reflecting frequent transmission clusters...
October 15, 2018: Nature Communications
Federica Palma, Gerardo Manfreda, Mickael Silva, Antonio Parisi, Dillon O R Barker, Eduardo N Taboada, Frédérique Pasquali, Mirko Rossi
Salmonella enterica ser. Typhimurium monophasic variant 4,[5],12:i:- has been associated with food-borne epidemics worldwide and swine appeared to be the main reservoir in most of the countries of isolation. However, the monomorphic nature of this serovar has, so far, hindered identification of the source due to expansion of clonal lineages in multiple hosts and food producing systems. Since geographically structured genetic signals can shape bacterial populations, identification of biogeographical markers in S...
October 15, 2018: Scientific Reports
Alexander I Young, Fabian L Wauthier, Peter Donnelly
Identification of genetic variants with effects on trait variability can provide insights into the biological mechanisms that control variation and can identify potential interactions. We propose a two-degree-of-freedom test for jointly testing mean and variance effects to identify such variants. We implement the test in a linear mixed model, for which we provide an efficient algorithm and software. To focus on biologically interesting settings, we develop a test for dispersion effects, that is, variance effects not driven solely by mean effects when the trait distribution is non-normal...
October 15, 2018: Nature Genetics
Alice Wegener, Els M Broens, Aldert Zomer, Mirlin Spaninks, Jaap A Wagenaar, Birgitta Duim
Staphylococcus pseudintermedius is an important pathogen in dogs. Since 2004, methicillin- resistant S. pseudintermedius (MRSP) isolates, often multidrug resistant, have been observed in dogs in the Netherlands. This study aims to link the observed resistance phenotypes in canine MRSP to genotypic antimicrobial resistance markers, and to study the phylogeny of MRSP by genomic comparisons. The genomes of fifty clinical isolates of MRSP from dogs from the Netherlands were sequenced. The resistance genes were identified, and for twenty one different antimicrobials their presence and sequence were associated with the resistance phenotypes...
November 2018: Veterinary Microbiology
Alan D Kaye, Thomas Mahakian, Aaron J Kaye, Andrew A Pham, Brendon M Hart, Sonja Gennuso, Elyse M Cornett, Rodney A Gabriel, Richard D Urman
The study of how individual genetic differences, known as polymorphisms, change the pharmacokinetics and pharmacodynamics of drugs is called pharmacogenomics. As the field of pharmacogenetics grows and continues to identify genetic polymorphisms, it is promising that the unmet need in this patient population may soon be addressed with personalized drug therapy based on the patient's genetic composition. Although encouraging, pharmacogenomic testing is underutilized in the United States and is often not covered by insurance companies...
June 2018: Best Practice & Research. Clinical Anaesthesiology
Marco Dinis, Khaled Merabet, Fernando Martínez-Freiría, Sebastian Steinfartz, Miguel Vences, James D Burgon, Kathryn R Elmer, David Donaire, Arlo Hinckley, Soumia Fahd, Ulrich Joger, Adnane Fawzi, Tahar Slimani, Guillermo Velo-Antón
North Africa is a climatically and topographically complex region with unique biotic assemblages resulting from the combination of multiple biogeographic realms. Here, we assess the role of climate in promoting intra-specific diversification in a Palearctic relict, the North African fire salamander, Salamandra algira, using a combination of phylogenetic and population genetic analyses, paleoclimatic modelling and niche overlap tests. We used mitochondrial DNA (Cyt-b), 9838 ddRADseq loci, and 14 microsatellite loci to characterize patterns of genetic diversity and population structure...
October 12, 2018: Molecular Phylogenetics and Evolution
Min Jung Kwun, Marco R Oggioni, Megan De Ste Croix, Stephen D Bentley, Nicholas J Croucher
Phase-variation of Type I restriction-modification systems can rapidly alter the sequence motifs they target, diversifying both the epigenetic patterns and endonuclease activity within clonally descended populations. Here, we characterize the Streptococcus pneumoniae SpnIV phase-variable Type I RMS, encoded by the translocating variable restriction (tvr) locus, to identify its target motifs, mechanism and regulation of phase variation, and effects on exchange of sequence through transformation. The specificity-determining hsdS genes were shuffled through a recombinase-mediated excision-reintegration mechanism involving circular intermediate molecules, guided by two types of direct repeat...
October 13, 2018: Nucleic Acids Research
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