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population genomics

Christian Rellstab, Stefan Zoller, Lorenz Walthert, Isabelle Lesur, Andrea R Pluess, René Graf, Catherine Bodénès, Christoph Sperisen, Antoine Kremer, Felix Gugerli
Testing how populations are locally adapted and predicting their response to their future environment is of key importance in view of climate change. Landscape genomics is a powerful approach to investigate genes and environmental factors involved in local adaptation. In a pooled amplicon sequencing approach of 94 genes in 71 populations, we tested if >3'500 single nucleotide polymorphisms (SNPs) in the three most common oak species in Switzerland (Quercus petraea, Q. pubescens, Q. robur) show an association with abiotic factors related to local topography, historical climate, and soil characteristics...
October 19, 2016: Molecular Ecology
R Rebecca Love, Aaron M Steele, Mamadou B Coulibaly, Sékou F Traore, Scott J Emrich, Michael C Fontaine, Nora J Besansky
The molecular mechanisms and genetic architecture that facilitate adaptive radiation of lineages remain elusive. Polymorphic chromosomal inversions, due to their recombination-reducing effect, are proposed instruments of ecotypic differentiation. Here we study an ecologically diversifying lineage of An. gambiae, known as the Bamako chromosomal form based on its unique complement of three chromosomal inversions, to explore the impact of these inversions on ecotypic differentiation. We used pooled and individual genome sequencing of Bamako, typical (non-Bamako) An...
October 19, 2016: Molecular Ecology
Xin-Yong Zhang, Qi Wan, Dong-Ya Zhu
BACKGROUND Recent studies demonstrated that polymorphisms in the PDE4D gene were associated with several processes involved in the occurrence of ischemic stroke (IS). The association between specific PDE4D single-nucleotide polymorphism 56 (SNP56) and IS risk was initially identified via genome-wide association studies (GWAS), although the GWAS in different populations produced inconclusive results. Thus, we performed a meta-analysis to better explain the association between PDE4D SNP56 and IS risk. MATERIAL AND METHODS A literature search was conducted using PubMed, Embase, and Web of Science up to June 1, 2015...
October 19, 2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Yoonjin Shin, Yangha Kim
The aim of this study was to investigate the association of CD36, a class B scavenger receptor, rs6969989 polymorphism with the serum lipid profiles in Korean women, together with their modulation by oily fish consumption. Subjects were participants from the Korean Genome Epidemiology Study (KoGES), which was initiated in 2001 as a large-scale. A total of 4,210 women aged 39 to 70 were included in this study. Data were collected using self-administered questionnaires, anthropometric measurements, and blood chemical analysis...
September 2016: Preventive Nutrition and Food Science
Michael V Lombardo, Meng-Chuan Lai, Bonnie Auyeung, Rosemary J Holt, Carrie Allison, Paula Smith, Bhismadev Chakrabarti, Amber N V Ruigrok, John Suckling, Edward T Bullmore, Christine Ecker, Michael C Craig, Declan G M Murphy, Francesca Happé, Simon Baron-Cohen
Individuals affected by autism spectrum conditions (ASC) are considerably heterogeneous. Novel approaches are needed to parse this heterogeneity to enhance precision in clinical and translational research. Applying a clustering approach taken from genomics and systems biology on two large independent cognitive datasets of adults with and without ASC (n = 694; n = 249), we find replicable evidence for 5 discrete ASC subgroups that are highly differentiated in item-level performance on an explicit mentalizing task tapping ability to read complex emotion and mental states from the eye region of the face (Reading the Mind in the Eyes Test; RMET)...
October 18, 2016: Scientific Reports
Paul J Planet, Apurva Narechania, Liang Chen, Barun Mathema, Sam Boundy, Gordon Archer, Barry Kreiswirth
A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions...
October 14, 2016: Trends in Microbiology
Hua Jing, Jun-Xia Zhu, Hui-Fu Wang, Wei Zhang, Zhan-Jie Zheng, Ling-Li Kong, Chen-Chen Tan, Zi-Xuan Wang, Lin Tan, Lan Tan
Inositol polyphosphate-5-phosphatase (INPP5D) was reported to be associated with Alzheimer's disease (AD) through modulating the inflammatory process and immune response. A recent genome-wide association study discovered a new locus single nucleotide polymorphism (SNP, rs35349669) of INPP5D which was significantly associated with susceptibility to late-onset Alzheimer's disease (LOAD) in Caucasians. In this study, we investigated the relations between the INPP5D polymorphism rs35349669 and LOAD in Han Chinese population comprising 984 LOAD cases and 1352 healthy controls being matched for age and gender...
October 13, 2016: Oncotarget
Zachery R Reichert, Maha Hussain
The development of metastatic castration-resistant prostate cancer (mCRPC) signals the terminal disease phase. The preceding hormone-dependent disease setting is effectively managed with androgen deprivation therapy. This foundation of treatment has a high rate of biochemical and clinical response and meaningful clinical benefit but is finite in duration as most cancers will progress to castration resistance. Historically, treatment for mCRPC entailed androgen receptor (AR) inhibitors (nilutamide, flutamide, bicalutamide), nonspecific steroidal biosynthesis inhibitors (ketoconazole, itraconazole), steroids (prednisone, diethylstilbesterol, dexamethasone), or palliative chemotherapy (mitoxantrone, estramustine), but none of these strategies impacted survival...
September 2016: Cancer Journal
Paul M Hime, Scott Hotaling, Richard E Grewelle, Eric M O'Neill, S Randal Voss, H Bradley Shaffer, David W Weisrock
Perhaps the most important recent advance in species delimitation has been the development of model-based approaches to objectively diagnose species diversity from genetic data. Additionally, the growing accessibility of next-generation sequence datasets provides powerful insights into genome-wide patterns of divergence during speciation. However, applying complex models to large datasets is time consuming and computationally costly, requiring careful consideration of the influence of both individual and population sampling, as well as the number and informativeness of loci on species delimitation conclusions...
October 17, 2016: Molecular Ecology
Zhijiao Song, Miaomiao Zhang, Fagen Li, Qijie Weng, Chanpin Zhou, Mei Li, Jie Li, Huanhua Huang, Xiaoyong Mo, Siming Gan
Identification of loci or genes under natural selection is important for both understanding the genetic basis of local adaptation and practical applications, and genome scans provide a powerful means for such identification purposes. In this study, genome-wide simple sequence repeats markers (SSRs) were used to scan for molecular footprints of divergent selection in Eucalyptus grandis, a hardwood species occurring widely in costal areas from 32° S to 16° S in Australia. High population diversity levels and weak population structure were detected with putatively neutral genomic SSRs...
October 17, 2016: Scientific Reports
Billie A Gould, Yani Chen, David B Lowry
The early stages of speciation are often characterized by the formation of partially reproductively isolated ecotypes, which evolve as a byproduct of divergent selective forces that are endemic to different habitats. Identifying the genomic regions, genes, and ultimately functional polymorphisms that are involved in the processes of ecotype formation is inherently challenging, as there are likely to be many different loci involved in the process. To localize candidate regions of the genome contributing to ecotype formation, we conducted whole genome pooled-sequencing (pool-seq) with 47 coastal perennial and 50 inland annual populations of the yellow monkeyflower, Mimulus guttatus...
October 16, 2016: Molecular Ecology
Nídia Cangi, Jonathan L Gordon, Laure Bournez, Valérie Pinarello, Rosalie Aprelon, Karine Huber, Thierry Lefrançois, Luís Neves, Damien F Meyer, Nathalie Vachiéry
The disease, Heartwater, caused by the Anaplasmataceae E. ruminantium, represents a major problem for tropical livestock and wild ruminants. Up to now, no effective vaccine has been available due to a limited cross protection of vaccinal strains on field strains and a high genetic diversity of Ehrlichia ruminantium within geographical locations. To address this issue, we inferred the genetic diversity and population structure of 194 E. ruminantium isolates circulating worldwide using Multilocus Sequence Typing based on lipA, lipB, secY, sodB, and sucA genes...
2016: Frontiers in Cellular and Infection Microbiology
Lixia Li, Yujie Luo, Biyun Chen, Kun Xu, Fugui Zhang, Hao Li, Qian Huang, Xin Xiao, Tianyao Zhang, Jihong Hu, Feng Li, Xiaoming Wu
Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. However, the yield and quality of rapeseed were largely decreased by clubroot (Plasmodiophora brassicae Woronin). Therefore, it is of great importance for screening more resistant germplasms or genes and improving the resistance to P. brassicae in rapeseed breeding. In this study, a massive resistant identification for a natural global population was conducted in two environments with race/pathotype 4 of P. brassicae which was the most predominant in China, and a wide range of phenotypic variation was found in the population...
2016: Frontiers in Plant Science
Dung VAN Nguyen, Junko Suzuki, Shohei Minami, Kenzo Yonemitsu, Nao Nagata, Ryusei Kuwata, Hiroshi Shimoda, Chien Kim Vu, Thuy Quoc Truong, Ken Maeda
Canine distemper virus (CDV) is one of the most serious pathogens found in many species of carnivores, including domestic dogs. In this study, hemagglutinin (H) genes were detected in five domestic Vietnamese dogs with diarrhea, and two CDVs were successfully isolated from dogs positive for H genes. The complete genome of one isolate, CDV/dog/HCM/33/140816, was determined. Phylogenetic analysis showed that all Vietnamese CDVs belonged to the Asia-1 genotype. In addition, the H proteins of Vietnamese CDV strains were the most homologous to those of Chinese CDVs (98...
October 14, 2016: Journal of Veterinary Medical Science
Laura Pérez-Lago, Santiago Izco, Marta Herranz, Griselda Tudó, María Carcelén, Iñaki Comas, Olalla Sierra, Juliá González, María Jesús Ruiz-Serrano, Juan Eyene, Emilio Bouza, Darío García-de-Viedma
OBJECTIVE: Molecular epidemiology techniques in tuberculosis (TB) can identify high-risk strains that are actively transmitted. We aimed to implement a novel strategy to optimize the identification and control of MDR-TB in a specific population. METHODS: We developed a strain-specific-PCR tailored from whole-genome-sequencing (WGS) data to track a specific multidrug-resistant prevalent strain in Equatorial Guinea (EG-MDR). RESULTS: The PCR was applied prospectively on remnants of GeneXpert reaction mixtures owing to the lack of culture facilities in EG...
October 13, 2016: Clinical Microbiology and Infection
Nancy Chen, Elissa J Cosgrove, Reed Bowman, John W Fitzpatrick, Andrew G Clark
Understanding the population genetic consequences of declining population size is important for conserving the many species worldwide facing severe decline [1]. Thorough empirical studies on the impacts of population reduction at a genome-wide scale in the wild are scarce because they demand huge field and laboratory investments [1, 2]. Previous studies have demonstrated the importance of gene flow in introducing genetic variation to small populations [3], but few have documented both genetic and fitness consequences of decreased immigration through time in a natural population [4-6]...
October 6, 2016: Current Biology: CB
Ivana V Yang, Brent S Pedersen, Andrew H Liu, George T O'Connor, Dinesh Pillai, Meyer Kattan, Rana Tawil Misiak, Rebecca Gruchalla, Stanley J Szefler, Gurjit K Khurana Hershey, Carolyn Kercsmar, Adam Richards, Allen D Stevens, Christena A Kolakowski, Melanie Makhija, Christine A Sorkness, Rebecca Z Krouse, Cynthia Visness, Elizabeth J Davidson, Corinne E Hennessy, Richard J Martin, Alkis Togias, William W Busse, David A Schwartz
BACKGROUND: Given the strong environmental influence on both epigenetic marks and allergic asthma in children, the epigenetic alterations in respiratory epithelia might provide insight into allergic asthma. OBJECTIVE: We sought to identify DNA methylation and gene expression changes associated with childhood allergic persistent asthma. METHODS: We compared genomic DNA methylation patterns and gene expression in African American children with persistent atopic asthma (n = 36) versus healthy control subjects (n = 36)...
October 13, 2016: Journal of Allergy and Clinical Immunology
Najaf Amin, Nadezhda M Belonogova, Olivera Jovanova, Rutger W W Brouwer, Jeroen G J van Rooij, Mirjam C G N van den Hout, Gulnara R Svishcheva, Robert Kraaij, Irina V Zorkoltseva, Anatoly V Kirichenko, Albert Hofman, André G Uitterlinden, Wilfred F J van IJcken, Henning Tiemeier, Tatiana I Axenovich, Cornelia M van Duijn
BACKGROUND: Despite high heritability, little success was achieved in mapping genetic determinants of depression-related traits by means of genome-wide association studies. METHODS: To identify genes associated with depressive symptomology, we performed a gene-based association analysis of nonsynonymous variation captured using exome-sequencing and exome-chip genotyping in a genetically isolated population from the Netherlands (n = 1999). Finally, we reproduced our significant findings in an independent population-based cohort (n = 1604)...
August 11, 2016: Biological Psychiatry
Luca Bello, Kevin M Flanigan, Robert B Weiss, Pietro Spitali, Annemieke Aartsma-Rus, Francesco Muntoni, Irina Zaharieva, Alessandra Ferlini, Eugenio Mercuri, Sylvie Tuffery-Giraud, Mireille Claustres, Volker Straub, Hanns Lochmüller, Andrea Barp, Sara Vianello, Elena Pegoraro, Jaya Punetha, Heather Gordish-Dressman, Mamta Giri, Craig M McDonald, Eric P Hoffman
The expressivity of Mendelian diseases can be influenced by factors independent from the pathogenic mutation: in Duchenne muscular dystrophy (DMD), for instance, age at loss of ambulation (LoA) varies between individuals whose DMD mutations all abolish dystrophin expression. This suggests the existence of trans-acting variants in modifier genes. Common single nucleotide polymorphisms (SNPs) in candidate genes (SPP1, encoding osteopontin, and LTBP4, encoding latent transforming growth factor β [TGFβ]-binding protein 4) have been established as DMD modifiers...
October 12, 2016: American Journal of Human Genetics
Wenqing Fu, Sharon R Browning, Brian L Browning, Joshua M Akey
Identifying and characterizing genomic regions that are shared identical by descent (IBD) among individuals can yield insight into population history, facilitate the identification of adaptively evolving loci, and be an important tool in disease gene mapping. Although increasingly large collections of exome sequences have been generated, it is challenging to detect IBD segments in exomes, precluding many potentially informative downstream analyses. Here, we describe an approach, ExIBD, to robustly detect IBD segments in exome-sequencing data, rigorously evaluate its performance, and apply this method to high-coverage exomes from 6,515 European and African Americans...
October 6, 2016: American Journal of Human Genetics
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