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https://www.readbyqxmd.com/read/28931559/variation-in-position-effect-variegation-within-a-natural-population
#1
Keegan J P Kelsey, Andrew G Clark
Changes in chromatin state may drive changes in gene expression, and it is of growing interest to understand the population genetic forces that drive differences in chromatin state. Here, we use the phenomenon of position effect variegation (PEV), a well-studied proxy for chromatin state, to survey variation in PEV among a naturally derived population. Further, we explore the genetic architecture of natural variation in factors that modify PEV. While previous mutation screens have identified over 150 suppressors and enhancers of PEV, it remains unknown to what extent allelic variation in these modifiers mediate inter-individual variation in PEV...
September 20, 2017: Genetics
https://www.readbyqxmd.com/read/28923848/body-shape-and-coloration-of-silkworm-larvae-are-influenced-by-a-novel-cuticular-protein
#2
Gao Xiong, Xiaoling Tong, Tingting Gai, Chunlin Li, Liang Qiao, Antónia Monteiro, Hai Hu, Minjin Han, Xin Ding, Songyuan Wu, Zhonghuai Xiang, Cheng Lu, Fangyin Dai
The genetic basis of body shape and coloration patterns on caterpillars is often assumed to be regulated separately, but it is possible that common molecules affect both types of trait simultaneously. Here we examine the genetic basis of a spontaneous cuticle defect in silkworm, where larvae exhibit a bamboo-like body shape and also decreased pigmentation. We performed linkage mapping and mutation screening to determine the gene product that affects body shape and coloration simultaneously. In these mutant larvae we identified a null mutation in BmorCPH24, a gene encoding a cuticular protein with low complexity sequence...
September 18, 2017: Genetics
https://www.readbyqxmd.com/read/28912344/parasex-generates-phenotypic-diversity-de-novo-and-impacts-drug-resistance-and-virulence-in-candida-albicans
#3
Matthew P Hirakawa, Darius E Chyou, Denis Huang, Aaron R Slan, Richard J Bennett
Candida albicans is a diploid fungus that is a frequent cause of mucosal and systemic infections in humans. This species exhibits an unusual parasexual cycle in which mating produces tetraploid cells that undergo a non-meiotic program of concerted chromosome loss to return to a diploid or aneuploid state. In this work, we used a multipronged approach to examine the capacity of parasex to generate diversity in C. albicans First, we compared the phenotypic properties of 32 genotyped progeny and observed wide-ranging differences in fitness, filamentation, biofilm formation and virulence...
September 14, 2017: Genetics
https://www.readbyqxmd.com/read/28912343/diversification-of-transcriptional-regulation-determines-subfunctionalization-of-paralogous-branched-chain-aminotransferases-in-the-yeast-saccharomyces-cerevisiae
#4
James González, Geovani López, Stefany Argueta, Ximena Escalera-Fanjul, Mohamed El Hafidi, Carlos Campero-Basaldua, Joseph Strauss, Lina Riego-Ruiz, Alicia González
Saccharomyces cerevisiae harbors BAT1 and BAT2 paralogous genes encoding branched chain aminotransferases (BCATs), showing opposed expression profiles and physiological role. Accordingly, in primary nitrogen sources such as glutamine, BAT1 expression is induced, supporting Bat1-dependent valine-isoleucine-leucine (VIL) biosynthesis, while BAT2 expression is repressed. Conversely, in the presence of VIL as sole nitrogen source, BAT1 expression is hindered while that of BAT2 is activated resulting in Bat2-dependent VIL catabolism...
September 14, 2017: Genetics
https://www.readbyqxmd.com/read/28912342/a-powerful-variant-set-association-test-based-on-chi-square-distribution
#5
Zhongxue Chen, Tong Lin, Kai Wang
Detecting the association between a set of variants and a given phenotype has attracted a large amount of attention in the scientific community, although it is a difficult task. Recently, several related statistical approaches have been proposed in the literature; powerful statistical tests are still highly desired and yet to be developed in this area. In this paper, we propose a powerful test, which combines information from each individual single nucleotide polymorphism (SNP) based on principal component analysis without relying on the eigenvalues associated with the principal components...
September 14, 2017: Genetics
https://www.readbyqxmd.com/read/28912341/the-role-of-blm-helicase-in-homologous-recombination-gene-conversion-tract-length-and-recombination-between-diverged-sequences-in-drosophila
#6
Henry A Ertl, Daniel P Russo, Noori Srivastava, Joseph T Brooks, Thu N Dao, Jeannine R LaRocque
DNA double-strand breaks (DSBs) are a particularly deleterious class of DNA damage that threatens genome integrity. DSBs are repaired by three pathways: non-homologous end joining (NHEJ), homologous recombination (HR), and single-strand annealing (SSA). Drosophila melanogaster Blm (DmBlm) is the ortholog of Saccharomyces cerevisiae SGS1 and human BLM, and has been shown to suppress crossovers in mitotic cells and repair mitotic DNA gaps via HR. To further elucidate the role of DmBlm in repair of a simple DSB, and in particular recombination mechanisms, we utilized the DR-white and DR-white...
September 14, 2017: Genetics
https://www.readbyqxmd.com/read/28912340/donor-recipient-identification-in-para-and-poly-phyletic-trees-under-alternative-hiv-1-transmission-hypotheses-using-approximate-bayesian-computation
#7
Ethan O Romero-Severson, Ingo Bulla, Nick Hengartner, Inês Bártolo, Ana Abecasis, José M Azevedo-Pereira, Nuno Taveira, Thomas Leitner
Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods and the reconstruction of epidemiologic histories. To infer who-infected-whom and to compute the probability of alternative transmission scenarios, while explicitly taking phylogenetic uncertainty into account, we created an Approximate Bayesian Computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity...
September 14, 2017: Genetics
https://www.readbyqxmd.com/read/28899997/improving-disease-prediction-by-incorporating-family-disease-history-in-risk-prediction-models-with-large-scale-genetic-data
#8
Jungsoo Gim, Wonji Kim, Soo Heon Kwak, Hosik Choi, Changyi Park, Kyong Soo Park, Sunghoon Kwon, Taesung Park, Sungho Won
Despite the many successes of genome-wide association studies (GWAS), the known susceptibility variants identified by GWAS have modest effect sizes, leading to notable skepticism about the effectiveness of building a risk prediction model from large-scale genetic data. However, in contrast to genetic variants, the family history of diseases has been largely accepted as an important risk factor in clinical diagnosis and risk prediction. Nevertheless, the complicated structures of the family history of diseases have limited their application in clinical practice...
September 12, 2017: Genetics
https://www.readbyqxmd.com/read/28899996/prediction-and-subtyping-of-hypertension-from-pan-tissue-transcriptomic-and-genetic-analyses
#9
Mahashweta Basu, Mahfuza Sharmin, Avinash Das, Nishanth Ulhas Nair, Kun Wang, Joo Sang Lee, Yen-Pei Christy Chang, Eytan Ruppin, Sridhar Hannenhalli
Hypertension is a complex systemic disease involving transcriptional changes in multiple organs. Here we systematically investigate the pan-tissue transcriptional and genetic landscape of hypertension spanning dozens of tissues in hundreds of individuals. We find that in several tissues previously identified hypertension-linked genes are dysregulated and the gene expression profile is predictive of hypertension. Importantly, many expression quantitative trait loci (eQTL) SNPs associated with the population variance of the dysregulated genes are linked with blood pressure in an independent genome-wide association study, suggesting that the functional effect of hypertension-associated SNPs may be mediated through tissue-specific transcriptional dysregulation...
September 12, 2017: Genetics
https://www.readbyqxmd.com/read/28893856/distinct-and-cooperative-roles-of-amh-and%C3%A2-dmrt1-in-self-renewal-and-differentiation-of-male-germ-cells-in-zebrafish
#10
Qiaohong Lin, Jie Mei, Zhi Li, Xuemei Zhang, Li Zhou, Jian-Fang Gui
Spermatogenesis is a fundamental process in male reproductive biology, and depends on precise balance between self-renewal and differentiation of male germ cells. However, the regulative factors for controlling the balance are poorly understood. In this study, we examined the roles of amh and dmrt1 in male germ cell development by generating their mutants with Crispr/Cas9 technology in zebrafish. Amh mutant zebrafish displayed a female-biased sex ratio, and both male and female amh mutants developed hypertrophic gonads due to uncontrolled proliferation and impaired differentiation of germ cells...
September 11, 2017: Genetics
https://www.readbyqxmd.com/read/28893855/mitigating-mitochondrial-genome-erosion-without-recombination
#11
Arunas L Radzvilavicius, Hanna Kokko, Joshua R Christie
Mitochondria are ATP-producing organelles of bacterial ancestry that played a key role in the origin and early evolution of complex eukaryotic cells. Most modern eukaryotes transmit mitochondrial genes uniparentally, often without recombination among genetically divergent organelles. While this asymmetric inheritance maintains the efficacy of purifying selection at the level of the cell, the absence of recombination could also make the genome susceptible to Muller's ratchet. How mitochondria escape this irreversible defect accumulation is a fundamental unsolved question...
September 11, 2017: Genetics
https://www.readbyqxmd.com/read/28893854/will-big-data-close-the-missing-heritability-gap
#12
Hwasoon Kim, Alexander Grueneberg, Ana I Vazquez, Stephen Hsu, Gustavo de Los Campos
Despite the important discoveries reported by Genome-Wide Association studies, for most traits and diseases the prediction R-squared (R-sq.) achieved with genetic scores remains considerably lower than the trait heritability. Modern biobanks will soon deliver unprecedentedly large biomedical data sets: Will the advent of Big Data close the gap between the trait heritability and the proportion of variance that can be explained by a genomic predictor? We addressed this question using Bayesian methods and a data analysis approach that produces a surface response relating prediction R-sq...
September 11, 2017: Genetics
https://www.readbyqxmd.com/read/28893853/a-powerful-framework-for-integrating-eqtl-and-gwas-summary-data
#13
Zhiyuan Xu, Chong Wu, Peng Wei, Wei Pan
Two new gene-based association analysis methods, called PrediXcan and TWAS for GWAS individual-level and summary data respectively, were recently proposed to integrate GWAS with eQTL data, alleviating two common problems in GWAS by boosting statistical power and facilitating biological interpretation of GWAS discoveries. Based on a novel reformulation of PrediXcan and TWAS, we propose a more powerful gene-based association test to integrate single set or multiple sets of eQTL data with GWAS individual-level data or summary statistics...
September 11, 2017: Genetics
https://www.readbyqxmd.com/read/28882990/extended-synaptotagmin-localizes-to-presynaptic-er-and-promotes-neurotransmission-and-synaptic-growth-in-drosophila
#14
Koto Kikuma, Xiling Li, Daniel Kim, David Sutter, Dion K Dickman
The endoplasmic reticulum (ER) is an extensive organelle in neurons with important roles at synapses including the regulation of cytosolic Ca(2+), neurotransmission, lipid metabolism, and membrane trafficking. Despite intriguing evidence for these crucial functions, how presynaptic ER influences synaptic physiology remains enigmatic. To gain insight into this question, we have generated and characterized mutations in the single Extended Synaptotagmin (Esyt) ortholog in Drosophila melanogaster Esyts are evolutionarily conserved ER proteins with Ca(2+)-sensing domains that have recently been shown to orchestrate membrane tethering and lipid exchange between the ER and plasma membrane...
September 7, 2017: Genetics
https://www.readbyqxmd.com/read/28882989/apico-basal-polarity-determinants-encoded-by-crumbs%C3%A2-genes-affect-ciliary-shaft-protein-composition-ift-movement-dynamics-and-cilia-length
#15
Khodor Hazime, Jarema J Malicki
One of the most obvious manifestations of polarity in epithelia is the subdivision of the cell surface by cell junctions into apical and baso-lateral domains. crumbs genes are among key regulators of this form of polarity. Loss of crumbs function disrupts the apical cell junction belt and crumbs overexpression expands the apical membrane size. Crumbs proteins contain a single transmembrane domain and localise to cell junction area at the apical surface of epithelia. In some tissues, they are also found in cilia...
September 7, 2017: Genetics
https://www.readbyqxmd.com/read/28882988/autosomal-trisomy-and-triploidy-are-corrected-during-female-meiosis-in-caenorhabditis-elegans
#16
Elizabeth Vargas, Karen McNally, Jacob A Friedman, Daniel B Cortes, David Y Wang, Ian F Korf, Francis J McNally
Trisomy and triploidy, defined as the presence of a third copy of one or all chromosomes respectively, are deleterious in many species including humans. Previous studies demonstrated that C. elegans with a third copy of the X chromosome are viable and fertile. However, the extra X chromosome was shown to preferentially segregate into the first polar body during oocyte meiosis to produce a higher frequency of euploid offspring than would be generated by random segregation. Here we demonstrate that extra autosomes are preferentially eliminated by triploid C...
September 7, 2017: Genetics
https://www.readbyqxmd.com/read/28878002/combat-a-combined-association-test-for-genes-using-summary-statistics
#17
Minghui Wang, Jianfei Huang, Yiyuan Liu, Li Ma, James B Potash, Shizhong Han
Genome-wide association studies (GWAS) have been widely used for identifying common variants associated with complex diseases. Traditional analysis of GWAS typically examines one marker at a time, usually single nucleotide polymorphisms (SNPs), to identify individual variants associated with a disease. However, due to the small effect sizes of common variants, the power to detect individual risk variants is generally low. As a complementary approach to SNP-level analysis, a variety of gene-based association tests have been proposed...
September 6, 2017: Genetics
https://www.readbyqxmd.com/read/28860320/cross-species-y-chromosome-function-between-malaria-vectors-of-the-anopheles-gambiae%C3%A2-species-complex
#18
Federica Bernardini, Roberto Galizi, Mariana Wunderlich, Chrysanthi Taxiarchi, Nace Kranjc, Kyros Kyrou, Andrew Hammond, Tony Nolan, Mara N K Lawniczak, Philippos Aris Papathanos, Andrea Crisanti, Nikolai Windbichler
Y chromosome function, structure and evolution is poorly understood in many species including the Anopheles genus of mosquitoes, an emerging model system for studying speciation that also represents the major vectors of malaria. While the Anopheline Y had previously been implicated in male mating behavior, recent data from the Anopheles gambiae complex suggests that, apart from the putative primary sex-determiner, no other genes are conserved on the Y. Studying the functional basis of the evolutionary divergence of the Y chromosome in the gambiae complex is complicated by complete F1 male hybrid sterility...
August 31, 2017: Genetics
https://www.readbyqxmd.com/read/28855307/testing-two-evolutionary-theories-of-human-aging-with-dna-methylation-data
#19
Chloe Robins, Allan F McRae, Joseph E Powell, Howard W Wiener, Stella Aslibekyan, Elizabeth M Kennedy, Devin M Absher, Donna K Arnett, Grant W Montgomery, Peter M Visscher, David J Cutler, Karen N Conneely
The evolutionary theories of mutation accumulation (MA) and disposable soma (DS) provide possible explanations for the existence of human aging. To better understand the relative importance of these theories, we devised a test to identify MA- and DS-consistent sites across the genome using familial DNA methylation data. Two key characteristics of DNA methylation allowed us to do so. First, DNA methylation exhibits distinct and widespread changes with age, with numerous age-differentially-methylated sites observed across the genome...
August 30, 2017: Genetics
https://www.readbyqxmd.com/read/28851745/a-key-regulator-of-the-glycolytic-and-gluconeogenic-central-metabolic-pathways-in-sinorhizobium-meliloti
#20
George C diCenzo, Zahed Muhammed, Magne Østerås, Shelley A P O'Brien, Turlough M Finan
The order Rhizobiales contains numerous agriculturally, biotechnologically, and medically important bacteria including the rhizobia, Agrobacterium, Brucella, and Methylobacterium, among others. These organisms tend to be metabolically versatile, but there has been relatively little investigation into the regulation of their central carbon metabolic pathways. Here, RNA-seq and promoter fusion data are presented to show that the PckR protein is a key regulator of central carbon metabolism in Sinorhizobium meliloti; during growth with gluconeogenic substrates, PckR represses expression of the complete Entner-Doudoroff glycolytic pathway and induces expression of the pckA and fbaB gluconeogenic genes...
August 29, 2017: Genetics
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