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Epistasis

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https://www.readbyqxmd.com/read/28340352/human-epistatic-interaction-controls-il7r-splicing-and-increases-multiple-sclerosis-risk
#1
Gaddiel Galarza-Muñoz, Farren B S Briggs, Irina Evsyukova, Geraldine Schott-Lerner, Edward M Kennedy, Tinashe Nyanhete, Liuyang Wang, Laura Bergamaschi, Steven G Widen, Georgia D Tomaras, Dennis C Ko, Shelton S Bradrick, Lisa F Barcellos, Simon G Gregory, Mariano A Garcia-Blanco
Multiple sclerosis (MS) is an autoimmune disorder where T cells attack neurons in the central nervous system (CNS) leading to demyelination and neurological deficits. A driver of increased MS risk is the soluble form of the interleukin-7 receptor alpha chain gene (sIL7R) produced by alternative splicing of IL7R exon 6. Here, we identified the RNA helicase DDX39B as a potent activator of this exon and consequently a repressor of sIL7R, and we found strong genetic association of DDX39B with MS risk. Indeed, we showed that a genetic variant in the 5' UTR of DDX39B reduces translation of DDX39B mRNAs and increases MS risk...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28334077/a-powerful-and-efficient-two-stage-method-for-detecting-gene-to-gene-interactions-in-gwas
#2
Jakub Pecanka, Marianne A Jonker, Zoltan Bochdanovits, Aad W Van Der Vaart
For over a decade functional gene-to-gene interaction (epistasis) has been suspected to be a determinant in the "missing heritability" of complex traits. However, searching for epistasis on the genome-wide scale has been challenging due to the prohibitively large number of tests which result in a serious loss of statistical power as well as computational challenges. In this article, we propose a two-stage method applicable to existing case-control data sets, which aims to lessen both of these problems by pre-assessing whether a candidate pair of genetic loci is involved in epistasis before it is actually tested for interaction with respect to a complex phenotype...
February 6, 2017: Biostatistics
https://www.readbyqxmd.com/read/28325749/the-nca-1-and-nca-2-ion-channels-function-downstream-of-gq-and-rho-to-regulate-locomotion-in-caenorhabditis-elegans
#3
Irini Topalidou, Pin-An Chen, Kirsten Cooper, Shigeki Watanabe, Erik M Jorgensen, Michael Ailion
The heterotrimeric G protein Gq positively regulates neuronal activity and synaptic transmission. Previously, the Rho guanine nucleotide exchange factor Trio was identified as a direct effector of Gq that acts in parallel to the canonical Gq effector phospholipase C. Here we examine how Trio and Rho act to stimulate neuronal activity downstream of Gq in the nematode Caenorhabditis elegans Through two forward genetic screens, we identify the cation channels NCA-1 and NCA-2, orthologs of mammalian NALCN, as downstream targets of the Gq/Rho pathway...
March 21, 2017: Genetics
https://www.readbyqxmd.com/read/28322827/structural-divergence-of-essential-triad-ribbon-synapse-proteins-among-placental-mammals-implications-for-preclinical-trials-in-photoreceptor-transplantation-therapy
#4
Christopher R J Laver, Joanne A Matsubara
As photoreceptor transplantation rapidly moves closer to the clinic, verifying graft efficacy in animal models may have unforeseen xenogeneic barriers. Although photoreceptor transplants have most convincingly exhibited functional synaptogenesis in conspecific studies, such evidence (while ruling out false-positives due to: viral graft labeling, fusion/cytosolic transfer, or neuroprotection) has not yet been shown for discordant xenografts. From this, a fundamental question should be raised: is useful xenosynaptogenesis likely between human photoreceptors and mouse retina? The triad ribbon synapse (TRS) that would normally form is unique and contains trans-synaptic proteins essential to its formation and function...
March 18, 2017: Experimental Eye Research
https://www.readbyqxmd.com/read/28322202/genetic-epistasis-regulates-amyloid-deposition-in-resilient-aging
#5
Daniel Felsky, Jishu Xu, Lori Chibnik, Julie Schneider, Jo Knight, James L Kennedy, David A Bennett, Philip L De Jager, Aristotle N Voineskos
INTRODUCTION: The brain-derived neurotrophic factor (BDNF) interacts with important genetic Alzheimer's disease (AD) risk factors. Specifically, variants within the SORL1 gene determine BDNF's ability to reduce amyloid β (Aβ) in vitro. We sought to test whether functional BDNF variation interacts with SORL1 genotypes to influence expression and downstream AD-related processes in humans. METHODS: We analyzed postmortem brain RNA sequencing and neuropathological data for 441 subjects from the Religious Orders Study/Memory and Aging Project and molecular and structural neuroimaging data for 1285 subjects from the Alzheimer's Disease Neuroimaging Initiative...
March 16, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28295769/hill-robertson-interference-maintained-by-red-queen-dynamics-favours-the-evolution-of-sex
#6
Jack da Silva, James D Galbraith
Although it is well established theoretically that selective interference among mutations (Hill-Robertson interference) favours meiotic recombination, genome-wide mean rates of mutation and strengths of selection appear too low to support this as the mechanism favouring recombination in nature. A possible solution to this discrepancy between theory and observation is that selection is at least intermittently very strong due to the antagonistic coevolution between a host and its parasites. The Red Queen theory posits that such coevolution generates fitness epistasis among loci, which generates negative linkage disequilibrium among beneficial mutations, which in turn favours recombination...
March 15, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28289197/toll-pathway-is-required-for-wound-induced-expression-of-barrier-repair-genes-in-the-drosophila-epidermis
#7
Amalia Capilla, Dmitry Karachentsev, Rachel A Patterson, Anita Hermann, Michelle T Juarez, William McGinnis
The epidermis serves as a protective barrier in animals. After epidermal injury, barrier repair requires activation of many wound response genes in epidermal cells surrounding wound sites. Two such genes in Drosophila encode the enzymes dopa decarboxylase (Ddc) and tyrosine hydroxylase (ple). In this paper we explore the involvement of the Toll/NF-κB pathway in the localized activation of wound repair genes around epidermal breaks. Robust activation of wound-induced transcription from ple and Ddc requires Toll pathway components ranging from the extracellular ligand Spätzle to the Dif transcription factor...
March 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28283832/genetic-and-phenotypic-dissection-of-1q43q44-microdeletion-syndrome-and-neurodevelopmental-phenotypes-associated-with-mutations-in-zbtb18-and-hnrnpu
#8
Christel Depienne, Caroline Nava, Boris Keren, Solveig Heide, Agnès Rastetter, Sandrine Passemard, Sandra Chantot-Bastaraud, Marie-Laure Moutard, Pankaj B Agrawal, Grace VanNoy, Joan M Stoler, David J Amor, Thierry Billette de Villemeur, Diane Doummar, Caroline Alby, Valérie Cormier-Daire, Catherine Garel, Pauline Marzin, Sophie Scheidecker, Anne de Saint-Martin, Edouard Hirsch, Christian Korff, Armand Bottani, Laurence Faivre, Alain Verloes, Christine Orzechowski, Lydie Burglen, Bruno Leheup, Joelle Roume, Joris Andrieux, Frenny Sheth, Chaitanya Datar, Michael J Parker, Laurent Pasquier, Sylvie Odent, Sophie Naudion, Marie-Ange Delrue, Cédric Le Caignec, Marie Vincent, Bertrand Isidor, Florence Renaldo, Fiona Stewart, Annick Toutain, Udo Koehler, Birgit Häckl, Celina von Stülpnagel, Gerhard Kluger, Rikke S Møller, Deb Pal, Tord Jonson, Maria Soller, Nienke E Verbeek, Mieke M van Haelst, Carolien de Kovel, Bobby Koeleman, Glen Monroe, Gijs van Haaften, Tania Attié-Bitach, Lucile Boutaud, Delphine Héron, Cyril Mignot
Subtelomeric 1q43q44 microdeletions cause a syndrome associating intellectual disability, microcephaly, seizures and anomalies of the corpus callosum. Despite several previous studies assessing genotype-phenotype correlations, the contribution of genes located in this region to the specific features of this syndrome remains uncertain. Among those, three genes, AKT3, HNRNPU and ZBTB18 are highly expressed in the brain and point mutations in these genes have been recently identified in children with neurodevelopmental phenotypes...
April 2017: Human Genetics
https://www.readbyqxmd.com/read/28270831/genomic-prediction-of-genotypic-effects-with-epistasis-and-environment-interactions-for-yield-related-traits-of-rapeseed-brassica-napus-l
#9
Xiang Luo, Yi Ding, Linzhong Zhang, Yao Yue, John H Snyder, Chaozhi Ma, Jun Zhu
Oilseed rape (Brassica napus) is an economically important oil crop, yet the genetic architecture of its complex traits remain largely unknown. Here, genome-wide association study was conducted for eight yield-related traits to dissect the genetic architecture of additive, dominance, epistasis, and their environment interaction. Additionally, the optimal genotype combination and the breeding value of superior line, superior hybrid and existing best line in mapping population were predicted for each trait in two environments based on the predicted genotypic effects...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28268034/epistasis-in-neuropsychiatric-disorders
#10
REVIEW
Caleb Webber
The contribution of epistasis to human disease remains unclear. However, several studies have now identified epistatic interactions between common variants that increase the risk of a neuropsychiatric disorder, while there is growing evidence that genetic interactions contribute to the pathogenicity of rare, multigenic copy-number variants (CNVs) that have been observed in patients. This review discusses the current evidence for epistatic events and genetic interactions in neuropsychiatric disorders, how paradigm shifts in the phenotypic classification of patients would empower the search for epistatic effects, and how network and cellular models might be employed to further elucidate relevant epistatic interactions...
March 3, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28261193/epistasis-and-the-evolution-of-antimicrobial-resistance
#11
REVIEW
Alex Wong
The fitness effects of a mutation can depend, sometimes dramatically, on genetic background; this phenomenon is often referred to as "epistasis." Epistasis can have important practical consequences in the context of antimicrobial resistance (AMR). For example, genetic background plays an important role in determining the costs of resistance, and hence in whether resistance will persist in the absence of antibiotic pressure. Furthermore, interactions between resistance mutations can have important implications for the evolution of multi-drug resistance...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28257811/functional-interaction-of-pkca-and-pldb-regulate-aggregation-and-development-in-dictyostelium-discoideum
#12
Sean Singh, Wasima Mohamed, Annelie Aguessy, Ella Dyett, Shriraj Shah, Mohammedasad Khan, Ramamurthy Baskar, Derrick Brazill
Multicellular development in Dictyostelium discoideum involves tightly regulated signaling events controlling the entry into development, initiation of aggregation and chemotaxis, and cellular differentiation. Here we show that PkcA, a Dictyostelium discoideum Protein Kinase C-orthologue, is involved in quorum sensing and the initiation of development, as well as cAMP sensing during chemotaxis. Additionally, by epistasis analysis we provide evidence that PkcA and PldB (a Phospholipase D-orthologue) functionally interact to regulate aggregation, differentiation, and cell-cell adhesion during development...
February 28, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/28254761/the-reveille-clock-genes-inhibit-growth-of-juvenile-and-adult-plants-by-control-of-cell-size
#13
Jennifer A Gray, Akiva Shalit-Kaneh, Dalena Nhu Chu, Polly Yingshan Hsu, Stacey Harmer
The circadian clock is a complex regulatory network that enhances plant growth and fitness in a constantly changing environment. In Arabidopsis thaliana, the clock is comprised of numerous regulatory feedback loops in which REVEILLE8 (RVE8) and its homologs RVE4 and RVE6 act in a partially redundant manner to promote clock pace. Here, we report that the remaining members of the RVE8 clade, RVE3 and RVE5, play only minor roles in regulation of clock function. However, we find that RVE8 clade proteins have unexpected functions in modulation of light input to the clock and control of plant growth at multiple stages of development...
March 2, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28250185/epistatic-interactions-influence-terrestrial-marine-functional-shifts-in-cetacean-rhodopsin
#14
Sarah Z Dungan, Belinda S W Chang
Like many aquatic vertebrates, whales have blue-shifting spectral tuning substitutions in the dim-light visual pigment, rhodopsin, that are thought to increase photosensitivity in underwater environments. We have discovered that known spectral tuning substitutions also have surprising epistatic effects on another function of rhodopsin, the kinetic rates associated with light-activated intermediates. By using absorbance spectroscopy and fluorescence-based retinal release assays on heterologously expressed rhodopsin, we assessed both spectral and kinetic differences between cetaceans (killer whale) and terrestrial outgroups (hippo, bovine)...
March 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28240252/novel-quantitative-pigmentation-phenotyping-enhances-genetic-association-epistasis-and-prediction-of-human-eye-colour
#15
Andreas Wollstein, Susan Walsh, Fan Liu, Usha Chakravarthy, Mati Rahu, Johan H Seland, Gisèle Soubrane, Laura Tomazzoli, Fotis Topouzis, Johannes R Vingerling, Jesus Vioque, Stefan Böhringer, Astrid E Fletcher, Manfred Kayser
Success of genetic association and the prediction of phenotypic traits from DNA are known to depend on the accuracy of phenotype characterization, amongst other parameters. To overcome limitations in the characterization of human iris pigmentation, we introduce a fully automated approach that specifies the areal proportions proposed to represent differing pigmentation types, such as pheomelanin, eumelanin, and non-pigmented areas within the iris. We demonstrate the utility of this approach using high-resolution digital eye imagery and genotype data from 12 selected SNPs from over 3000 European samples of seven populations that are part of the EUREYE study...
February 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28238656/moonwalker-descending-neurons-mediate-visually-evoked-retreat-in-drosophila
#16
Rajyashree Sen, Ming Wu, Kristin Branson, Alice Robie, Gerald M Rubin, Barry J Dickson
Insects, like most animals, tend to steer away from imminent threats [1-7]. Drosophila melanogaster, for example, generally initiate an escape take-off in response to a looming visual stimulus, mimicking a potential predator [8]. The escape response to a visual threat is, however, flexible [9-12] and can alternatively consist of walking backward away from the perceived threat [11], which may be a more effective response to ambush predators such as nymphal praying mantids [7]. Flexibility in escape behavior may also add an element of unpredictability that makes it difficult for predators to anticipate or learn the prey's likely response [3-6]...
March 6, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28230247/digest-less-than-the-sum-of-its-parts-negative-epistasis-in-bacterial-swarming
#17
Sonia Singhal, Katrina van Raay
No abstract text is available yet for this article.
February 23, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28225073/high-mutation-rates-explain-low-population-genetic-divergence-at-copy-number-variable-loci-in-homo-sapiens
#18
Xin-Sheng Hu, Francis C Yeh, Yang Hu, Li-Ting Deng, Richard A Ennos, Xiaoyang Chen
Copy-number-variable (CNV) loci differ from single nucleotide polymorphic (SNP) sites in size, mutation rate, and mechanisms of maintenance in natural populations. It is therefore hypothesized that population genetic divergence at CNV loci will differ from that found at SNP sites. Here, we test this hypothesis by analysing 856 CNV loci from the genomes of 1184 healthy individuals from 11 HapMap populations with a wide range of ancestry. The results show that population genetic divergence at the CNV loci is generally more than three times lower than at genome-wide SNP sites...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28207813/interacting-networks-of-resistance-virulence-and-core-machinery-genes-identified-by-genome-wide-epistasis-analysis
#19
Marcin J Skwark, Nicholas J Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R Harris, Stephen B Beres, James M Musser, Julian Parkhill, Stephen D Bentley, Erik Aurell, Jukka Corander
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus)...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28207740/epistasis-analysis-goes-genome-wide
#20
Jianzhi Zhang
No abstract text is available yet for this article.
February 2017: PLoS Genetics
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