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Genome variation

Raquel Matoso Silva, Filomena Adega, Helena J Kjöllerström, Kim Labuschagne, Antoinette Kotze, Carlos Fernandes, Raquel Chaves, Maria do Mar Oom
Genets (Genetta) are a genus of African mammalian carnivorans with 14 currently recognized species, although taxonomic uncertainties remain, particularly regarding the number of species within the large-spotted genet complex. This study presents the first banded karyotype and molecular cytogenetic analysis of a genetically identified panther genet, Genetta maculata, the most common and widespread taxon of the large-spotted genet complex, with a wide distribution in sub-Saharan Africa. Sampled in Gauteng Province, South Africa, it could be assigned to the subspecies G...
October 27, 2016: Cytogenetic and Genome Research
Ved Prakash Kumar, Anupam Shrivastwa, Parag Nigam, Dhyanendra Kumar, Surendra Prakash Goyal
Swamp deer (Rucervus duvaucelii) is an endemic, Scheduled I species under the Wildlife (Protection) Act 1972, India. According to variations in antler size, it has been classified into three subspecies, namely Western (R. duvaucelii duvaucelii), Central (R. duvaucelii branderi), and Eastern (R. duvaucelii ranjitsinhii). For planning effective ex situ and in situ conservation of a wide-ranging species in different bioclimatic regions and in wildlife forensic, the use of genetic characterization in defining morpho/ecotypes has been suggested because of the geographic clines and reproductive isolation...
October 26, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Jonathan B Puritz, John R Gold, David S Portnoy
Conservation and management of exploited species depends on accurate knowledge of how genetic variation is partitioned across a fishery, especially as it relates to recruitment. Using double-digest restriction-site associated DNA sequencing, we surveyed variation in 7,382 single nucleotide polymorphisms (SNPs) in red snapper (Lutjanus campechanus) young-of-the-year (YOY) sampled at six localities and in adults sampled at two localities in the northern Gulf of Mexico. Significant genetic heterogeneity was detected between the two adult samples, separated by ~600 km, and at spatial scales less than five kilometers among samples of  YOY...
October 26, 2016: Scientific Reports
Changlin Liu, Fazhen Zhao, Jingping Yan, Chunsheng Liu, Siwei Liu, Siqing Chen
Golden cuttlefish Sepia esculenta Hoyle is an economically important cephalopod species. However, artificial hatching is currently challenged by low survival rate of larvae due to abnormal embryonic development. Dissecting the genetic foundation and regulatory mechanisms in embryonic development requires genomic background knowledge. Therefore, we carried out a transcriptome sequencing on Sepia embryos and larvae via mRNA-Seq. 32,597,241 raw reads were filtered and assembled into 98,615 unigenes (N50 length at 911 bp) which were annotated in NR database, GO and KEGG databases respectively...
October 22, 2016: International Journal of Molecular Sciences
Núria Rovira-Graells, Sara Aguilera-Simón, Elisabet Tintó-Font, Alfred Cortés
The growth phenotype of asexual blood stage malaria parasites can influence their virulence and also their ability to survive and achieve transmission to the next host, but there are few methods available to characterise parasite growth parameters in detail. We developed a new assay to measure growth rates at different starting parasitaemias in a 96-well format and applied it to characterise the growth of Plasmodium falciparum lines 3D7-A and 3D7-B, previously shown to have different invasion rates and to use different invasion pathways...
2016: PloS One
Luciano Rogério Braatz de Andrade, Roberto Fritsche Neto, Ítalo Stefanine Correia Granato, Gustavo César Sant'Ana, Pedro Patric Pinho Morais, Aluízio Borém
A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection...
2016: PloS One
G E B Wright, B Carleton, M R Hayden, C J D Ross
Differences in response to medications have a strong genetic component. By leveraging publically available data, the spectrum of such genomic variation can be investigated extensively. Pharmacogenomic variation was extracted from the 1000 Genomes Project Phase 3 data (2504 individuals, 26 global populations). A total of 12 084 genetic variants were found in 120 pharmacogenes, with the majority (90.0%) classified as rare variants (global minor allele frequency <0.5%), with 52.9% being singletons. Common variation clustered individuals into continental super-populations and 23 pharmacogenes contained highly differentiated variants (FST>0...
October 25, 2016: Pharmacogenomics Journal
Aung Kyaw Lwin, Edoardo Bertolini, Mario Enrico Pè, Andrea Zuccolo
Transposable elements (TEs) are the most abundant genetic material for almost all eukaryotic genomes. Their effects on the host genomes range from an extensive size variation to the regulation of gene expression, altering gene function and creating new genes. Because of TEs pivotal contribute to the host genome structure and regulation, their identification and characterization provide a wealth of useful data for gaining an in-depth understanding of host genome functioning. The giant reed (Arundo donax) is a perennial rhizomatous C3 grass, octadecaploid, with an estimated nuclear genome size of 2744 Mbp...
October 24, 2016: Molecular Genetics and Genomics: MGG
W S Hambright, Jie Deng, James M Tiedje, Ingrid Brettar, Jorge L M Rodrigues
In bacterial populations, subtle expressional differences may promote ecological specialization through the formation of distinct ecotypes. In a barrier-free habitat, this process most likely precedes population divergence and may predict speciation events. To examine this, we used four sequenced strains of the bacterium Shewanella baltica, OS155, OS185, OS195, and OS223, as models to assess transcriptional variation and ecotype formation within a prokaryotic population. All strains were isolated from different depths throughout a water column of the Baltic Sea, occupying different ecological niches characterized by various abiotic parameters...
September 2016: MSphere
Matthew J Gazzellone, Mehdi Zarrei, Christie L Burton, Susan Walker, Mohammed Uddin, S M Shaheen, Julie Coste, Rageen Rajendram, Reva J Schachter, Marlena Colasanto, Gregory L Hanna, David R Rosenberg, Noam Soreni, Kate D Fitzgerald, Christian R Marshall, Janet A Buchanan, Daniele Merico, Paul D Arnold, Stephen W Scherer
BACKGROUND: Obsessive-compulsive disorder (OCD) is a heterogeneous neuropsychiatric condition, thought to have a significant genetic component. When onset occurs in childhood, affected individuals generally exhibit different characteristics from adult-onset OCD, including higher prevalence in males and increased heritability. Since neuropsychiatric conditions are associated with copy number variations (CNVs), we considered their potential role in the etiology of OCD. METHODS: We genotyped 307 unrelated pediatric probands with idiopathic OCD (including 174 that were part of complete parent-child trios) and compared their genotypes with those of 3861 population controls, to identify rare CNVs (<0...
2016: Journal of Neurodevelopmental Disorders
Clive J Petry, Nuria Sanz Marcos, Gracielle Pimentel, M Geoffrey Hayes, Michael Nodzenski, Denise M Scholtens, Ieuan A Hughes, Carlo L Acerini, Ken K Ong, William L Lowe, David B Dunger
In addition to maternal genes and environmental exposures, variation in fetal imprinted genes could also affect maternal blood pressure during pregnancy. Our objective was to test the associations between polymorphic variants in 16 imprinted genes and maternal mean arterial blood pressures in 1160 DNA trios from 2 established birth cohorts (the Cambridge Baby Growth and Wellbeing Studies) and seek replication in 1367 Hyperglycemia and Adverse Pregnancy Outcome Study participants. Significant univariate associations, all independent of fetal sex, were observed in the Cambridge cohorts, including FAM99A rs1489945 transmitted from the mother (P=2×10(-)(4)), DLK1 rs10139403 (mother; P=9×10(-)(4)), DLK1 rs12147008 (mother; P=1×10(-)(3)), H19 rs217222 (father; P=1×10(-)(3)), SNRPN rs1453556 (father; P=1×10(-)(3)), IGF2 rs6356 (father; P=1×10(-)(3)), and NNAT rs6066671 (father; P=1×10(-)(3))...
October 24, 2016: Hypertension
Chao-Qiang Lai, Mary K Wojczynski, Laurence D Parnell, Bertha A Hidalgo, Marguerite Ryan Irvin, Stella Aslibekyan, Michael A Province, Devin M Absher, Donna K Arnett, Jose M Ordovas
Postprandial lipemia (PPL), the increased plasma triglyceride (TG) concentration after consuming a high-fat meal, is an independent risk factor for cardiovascular disease (CVD). Individual responses to a meal high in fat vary greatly, depending on genetic and lifestyle factors. However, only a few loci have been associated with TG-PPL response. Heritable epigenomic changes may be significant contributors to the unexplained inter-individual PPL variability. We conducted an epigenome-wide association study (EWAS) on 979 subjects with DNA methylation measured from CD4+ T cells, who were challenged with a high-fat meal as a part of the Genetics of Lipid Lowering Drugs and Diet Network study...
October 24, 2016: Journal of Lipid Research
John E Pool, Dylan T Braun, Justin B Lack
Drosophila melanogaster originated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we find elevated cold tolerance in three distinct geographic regions: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude...
October 24, 2016: Molecular Biology and Evolution
Cheng-Wei Wu, Andrew Deonarine, Aaron Przybysz, Kevin Strange, Keith P Choe
SKN-1/Nrf are the primary antioxidant/detoxification response transcription factors in animals and they promote health and longevity in many contexts. SKN-1/Nrf are activated by a remarkably broad-range of natural and synthetic compounds and physiological conditions. Defining the signaling mechanisms that regulate SKN-1/Nrf activation provides insights into how cells coordinate responses to stress. Nrf2 in mammals is regulated in part by the redox sensor repressor protein named Keap1. In C. elegans, the p38 MAPK cascade in the intestine activates SKN-1 during oxidative stress by promoting its nuclear accumulation...
October 2016: PLoS Genetics
Amy B Wilfert, Katherine R Chao, Madhurima Kaushal, Sanjay Jain, Sebastian Zöllner, David R Adams, Donald F Conrad
Standard techniques from genetic epidemiology are ill-suited to formally assess the significance of variants identified from a single case. We developed a statistical inference framework for identifying unusual functional variation from a single exome or genome, what we refer to as the 'n-of-one' problem. Using this approach we assessed our ability to identify the causal genotypes in over 5 million simulated cases of Mendelian disease, identifying 39% of disease genotypes as the most damaging unit in a typical exome background...
October 24, 2016: Nature Genetics
B N Keel, J W Keele, W M Snelling
Copy number variations (CNVs) are large insertions, deletions or duplications in the genome that vary between members of a species and are known to affect a wide variety of phenotypic traits. In this study, we identified CNVs in a population of bulls using low coverage next-generation sequence data. First, in order to determine a suitable strategy for CNV detection in our data, we compared the performance of three distinct CNV detection algorithms on benchmark CNV datasets and concluded that using the multiple sample read depth approach was the best method for identifying CNVs in our sequences...
October 24, 2016: Animal Genetics
Hillary T Graham, Daniel M Rotroff, Skylar W Marvel, John B Buse, Tammy M Havener, Alyson G Wilson, Michael J Wagner, Alison A Motsinger-Reif
Given the high costs of conducting a drug-response trial, researchers are now aiming to use retrospective analyses to conduct genome-wide association studies (GWAS) to identify underlying genetic contributions to drug-response variation. To prevent confounding results from a GWAS to investigate drug response, it is necessary to account for concomitant medications, defined as any medication taken concurrently with the primary medication being investigated. We use data from the Action to Control Cardiovascular Disease (ACCORD) trial in order to implement a novel scoring procedure for incorporating concomitant medication information into a linear regression model in preparation for GWAS...
2016: Frontiers in Genetics
Joanna Melonek, James D Stone, Ian Small
Hybrid seed production in rice relies on cytoplasmic male sterility (CMS) induced by specific mitochondrial proteins, whose deleterious effects are suppressed by nuclear Restorer of Fertility (RF) genes. The majority of RF proteins belong to a specific clade of the RNA-binding pentatricopeptide repeat protein family. We have characterised 'restorer-of-fertility-like' (RFL) sequences from 13 Oryza genomes and the Brachypodium distachyon genome. The majority of the RFL sequences are found in genomic clusters located at two or three chromosomal loci with only a minor proportion being present as isolated genes...
October 24, 2016: Scientific Reports
Steffen Grampp, James L Platt, Victoria Lauer, Rafik Salama, Franziska Kranz, Viviana K Neumann, Sven Wach, Christine Stöhr, Arndt Hartmann, Kai-Uwe Eckardt, Peter J Ratcliffe, David R Mole, Johannes Schödel
Clear cell renal cell carcinoma (ccRCC) is characterized by loss of function of the von Hippel-Lindau tumour suppressor (VHL) and unrestrained activation of hypoxia-inducible transcription factors (HIFs). Genetic and epigenetic determinants have an impact on HIF pathways. A recent genome-wide association study on renal cancer susceptibility identified single-nucleotide polymorphisms (SNPs) in an intergenic region located between the oncogenes MYC and PVT1. Here using assays of chromatin conformation, allele-specific chromatin immunoprecipitation and genome editing, we show that HIF binding to this regulatory element is necessary to trans-activate MYC and PVT1 expression specifically in cells of renal tubular origins...
October 24, 2016: Nature Communications
Zhongfeng Li, Lingxue Jiang, Yansong Ma, Zhongyan Wei, Huilong Hong, Zhangxiong Liu, Jinhui Lei, Ying Liu, Rongxia Guan, Yong Guo, Longguo Jin, Lijuan Zhang, Yinghui Li, Yulong Ren, Wei He, Ming Liu, Nang Myint Phyu Sin Htwe, Lin Liu, Bingfu Guo, Jian Song, Bing Tan, Guifeng Liu, Maiquan Li, Xianli Zhang, Bo Liu, Xuehui Shi, Sining Han, Sunan Hua, Fulai Zhou, Lili Yu, Yanfei Li, Shuang Wang, Jun Wang, Ruzhen Chang, Lijuan Qiu
Mutagenized populations have provided important materials for introducing variation and identifying gene function in plants. In this study, an ethyl methanesulfonate (EMS) -induced soybean (Glycine max) population, consisting of 21,600 independent M2 lines, was developed. Over one thousand M4 (5) families, with diverse abnormal phenotypes for seed composition, seed shape, plant morphology, and maturity that are stably expressed across different environments and generations were identified. Phenotypic analysis of the population led to the identification of a yellow pigmentation mutant, gyl, that displayed significantly decreased chlorophyll (Chl) content and abnormal chloroplast development...
October 24, 2016: Journal of Integrative Plant Biology
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