keyword
MENU ▼
Read by QxMD icon Read
search

Epistasis

keyword
https://www.readbyqxmd.com/read/28207813/interacting-networks-of-resistance-virulence-and-core-machinery-genes-identified-by-genome-wide-epistasis-analysis
#1
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
#2
Jianzhi Zhang
No abstract text is available yet for this article.
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28203149/gene-gene-environment-interactions-of-serotonin-transporter-monoamine-oxidase-a-and-childhood-maltreatment-predict-aggressive-behavior-in-chinese-adolescents
#3
Yun Zhang, Qing-Sen Ming, Jin-Yao Yi, Xiang Wang, Qiao-Lian Chai, Shu-Qiao Yao
Gene-environment interactions that moderate aggressive behavior have been identified independently in the serotonin transporter (5-HTT) gene and monoamine oxidase A gene (MAOA). The aim of the present study was to investigate epistasis interactions between MAOA-variable number tandem repeat (VNTR), 5-HTTlinked polymorphism (LPR) and child abuse and the effects of these on aggressive tendencies in a group of otherwise healthy adolescents. A group of 546 Chinese male adolescents completed the Child Trauma Questionnaire and Youth self-report of the Child Behavior Checklist...
2017: Frontiers in Behavioral Neuroscience
https://www.readbyqxmd.com/read/28201714/stability-mediated-epistasis-restricts-accessible-mutational-pathways-in-the-functional-evolution-of-avian-hemoglobin
#4
Amit Kumar, Chandrasekhar Natarajan, Hideaki Moriyama, Christopher C Witt, Roy E Weber, Angela Fago, Jay F Storz
No abstract text is available yet for this article.
February 13, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28192196/quantification-of-various-app-mrna-isoforms-and-epistasis-in-lesch-nyhan-disease
#5
Khue Vu Nguyen, William L Nyhan
The present work is the development of a simple and specific kinetic method based on RT-PCR technique coupled with direct sequencing for quantification of various amyloid precursor protein-mRNA isoforms (APP-mRNA isoforms) in biological samples, especially for identifying the most abundant one that may decisive for the normal status or disease risk. Application of this kinetic method to the Lesch-Nyhan disease (LND) was performed and results indicated an epistasis between mutated hypoxanthine phosphoribosyltransferase1 (HPRT1) and APP genes...
February 9, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28188227/the-hla-b27-peptidome-in-vivo-in-spondyloarthritis-susceptible-hla-b27-transgenic-rats-and-the-effect-of-erap1-deletion
#6
Eilon Barnea, Dganit Melamed Kadosh, Yael Haimovich, Nimman Satumtira, Martha L Dorris, Mylinh T Nguyen, Robert E Hammer, Tri M Tran, Robert A Colbert, Joel D Taurog, Arie Admon
HLA-B27 is a class I major histocompatibility (MHC-I) allele that confers susceptibility to the rheumatic disease ankylosing spondylitis (AS) by an unknown mechanism. ERAP1 is an aminopeptidase that trims peptides in the endoplasmic reticulum for binding to MHC-I molecules. ERAP1 shows genetic epistasis with HLA-B27 in conferring susceptibility to AS. Male HLA-B27 transgenic rats develop arthritis and serve as an animal model of AS, whereas female B27 transgenic rats remain healthy. We used large-scale quantitative mass-spectrometry to identify over 15,000 unique HLA-B27 peptide ligands, isolated after immunoaffinity purification of the B27 molecules from the spleens of HLA-B27 transgenic rats...
February 10, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28186227/oncosimulr-genetic-simulation-with-arbitrary-epistasis-and-mutator-genes-in-asexual-populations
#7
Ramon Diaz-Uriarte
No abstract text is available yet for this article.
February 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28186191/the-combination-of-the-functionalities-of-feedback-circuits-is-determinant-for-the-attractors-number-and-size-in-pathway-like-boolean-networks
#8
Eugenio Azpeitia, Stalin Muñoz, Daniel González-Tokman, Mariana Esther Martínez-Sánchez, Nathan Weinstein, Aurélien Naldi, Elena R Álvarez-Buylla, David A Rosenblueth, Luis Mendoza
Molecular regulation was initially assumed to follow both a unidirectional and a hierarchical organization forming pathways. Regulatory processes, however, form highly interlinked networks with non-hierarchical and non-unidirectional structures that contain statistically overrepresented circuits or motifs. Here, we analyze the behavior of pathways containing non-unidirectional (i.e. bidirectional) and non-hierarchical interactions that create motifs. In comparison with unidirectional and hierarchical pathways, our pathways have a high diversity of behaviors, characterized by the size and number of attractors...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28185903/the-thermodynamics-of-protein-aggregation-reactions-may-underpin-the-enhanced-metabolic-efficiency-associated-with-heterosis-some-balancing-selection-and-the-evolution-of-ploidy-levels
#9
REVIEW
B R Ginn
Identifying the physical basis of heterosis (or "hybrid vigor") has remained elusive despite over a hundred years of research on the subject. The three main theories of heterosis are dominance theory, overdominance theory, and epistasis theory. Kacser and Burns (1981) identified the molecular basis of dominance, which has greatly enhanced our understanding of its importance to heterosis. This paper aims to explain how overdominance, and some features of epistasis, can similarly emerge from the molecular dynamics of proteins...
February 6, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28182695/two-three-loci-control-scleral-ossicle-formation-via-epistasis-in-the-cavefish-astyanax-mexicanus
#10
Anastasia Lyon, Amanda K Powers, Joshua B Gross, Kelly E O'Quin
The sclera is the protective outer layer of the eye. In fishes, birds, and reptiles, the sclera may be reinforced with additional bony elements called scleral ossicles. Teleost fish vary in the number and size of scleral ossicles; however, the genetic mechanisms responsible for this variation remain poorly understood. In this study, we examine the inheritance of scleral ossicles in the Mexican tetra, Astyanax mexicanus, which exhibits both a cave morph and a surface fish morph. As these morphs and their hybrids collectively exhibit zero, one, and two scleral ossicles, they represent a microcosm of teleost scleral ossicle diversity...
2017: PloS One
https://www.readbyqxmd.com/read/28174757/transcriptional-regulation-by-atoh1-and-its-target-spdef-in%C3%A2-the%C3%A2-intestine
#11
Yuan-Hung Lo, Eunah Chung, Zhaohui Li, Ying-Wooi Wan, Maxime M Mahe, Min-Shan Chen, Taeko K Noah, Kristin N Bell, Hari Krishna Yalamanchili, Tiemo J Klisch, Zhandong Liu, Joo-Seop Park, Noah F Shroyer
BACKGROUND & AIMS: The transcription factor atonal homolog 1 (ATOH1) controls the fate of intestinal progenitors downstream of the Notch signaling pathway. Intestinal progenitors that escape Notch activation express high levels of ATOH1 and commit to a secretory lineage fate, implicating ATOH1 as a gatekeeper for differentiation of intestinal epithelial cells. Although some transcription factors downstream of ATOH1, such as SPDEF, have been identified to specify differentiation and maturation of specific cell types, the bona fide transcriptional targets of ATOH1 still largely are unknown...
January 2017: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28171656/epistasis-and-destabilizing-mutations-shape-gene-expression-variability-in-humans-via-distinct-modes-of-action
#12
Ence Yang, Gang Wang, Jizhou Yang, Beiyan Zhou, Yanan Tian, James J Cai
No abstract text is available yet for this article.
November 15, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/28170438/the-effective-rate-of-influenza-reassortment-is-limited-during-human-infection
#13
Ashley Sobel Leonard, Micah T McClain, Gavin J D Smith, David E Wentworth, Rebecca A Halpin, Xudong Lin, Amy Ransier, Timothy B Stockwell, Suman R Das, Anthony S Gilbert, Rob Lambkin-Williams, Geoffrey S Ginsburg, Christopher W Woods, Katia Koelle, Christopher J R Illingworth
We characterise the evolutionary dynamics of influenza infection described by viral sequence data collected from two challenge studies conducted in human hosts. Viral sequence data were collected at regular intervals from infected hosts. Changes in the sequence data observed across time show that the within-host evolution of the virus was driven by the reversion of variants acquired during previous passaging of the virus. Treatment of some patients with oseltamivir on the first day of infection did not lead to the emergence of drug resistance variants in patients...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28158988/microsatellite-polymorphisms-associated-with-human-behavioural-and-psychological-phenotypes-including-a-gene-environment-interaction
#14
Andrew T M Bagshaw, L John Horwood, David M Fergusson, Neil J Gemmell, Martin A Kennedy
BACKGROUND: The genetic and environmental influences on human personality and behaviour are a complex matter of ongoing debate. Accumulating evidence indicates that short tandem repeats (STRs) in regulatory regions are good candidates to explain heritability not accessed by genome-wide association studies. METHODS: We tested for associations between the genotypes of four selected repeats and 18 traits relating to personality, behaviour, cognitive ability and mental health in a well-studied longitudinal birth cohort (n = 458-589) using one way analysis of variance...
February 3, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28143579/method-for-generating-multiple-risky-barcodes-of-complex-diseases-using-ant-colony-algorithm
#15
Xiong Li, Wen Jiang
BACKGROUND: Susceptible barcode recognition plays an important role in the diagnosis and treatment of complex diseases. Numerous approaches have been proposed to identify risky barcodes involved in the progress of complex diseases. However, some methods only consider differences in barcode frequencies between the control and disease groups; as such, these methods may be partial or even wrong. For example, some barcodes with a high risk ratio yield a low frequency on cases or exhibit a high frequency on controls, which may unreasonable from a statistical point...
February 1, 2017: Theoretical Biology & Medical Modelling
https://www.readbyqxmd.com/read/28131836/regulation-of-a-hitchhiking-behavior-by-neuronal-insulin-and-tgf-%C3%AE-signaling-in-the-nematode-caenorhabditis-elegans
#16
Daehan Lee, Harksun Lee, Nari Kim, Daisy S Lim, Junho Lee
Free-living nematode Caenorhabditis elegans exhibits various behaviors to adapt to the fluctuating environment. When early larvae of C. elegans experience the harsh environmental condition, they develop to an alternative developmental stage called dauer, which shows nictation, a stage-specific waving behavior. Nictation enables dauers to attach to more mobile animals, which helps them disperse to other habitats beyond physical barriers. However, underlying molecular mechanisms that regulate nictation behavior are largely unknown...
January 25, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28131339/review-epistasis-and-dominance-in-the-emergence-of-catalytic-function-as-exemplified-by-the-evolution-of-plant-terpene-synthases
#17
REVIEW
Jitender Cheema, Juan A Faraldos, Paul E O'Maille
Epistasis, the interaction between mutations and the genetic background, is a pervasive force in evolution that is difficult to predict yet derives from a simple principle - biological systems are interconnected. Therefore, one effect may be intimately linked to another, hence interdependent. Untangling epistatic interactions between and within genes is a vibrant area of research. Deriving a mechanistic understanding of epistasis is a major challenge. Particularly, elucidating how epistasis can attenuate the effects of otherwise dominant mutations that control phenotypes...
February 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28128449/parallel-emergence-of-negative-epistasis-across-experimental-lineages
#18
Peter C Zee, Gregory J Velicer
Epistatic interactions can greatly impact evolutionary phenomena, particularly the process of adaptation. Here, we leverage four parallel experimentally evolved lineages to study the emergence and trajectories of epistatic interactions in the social bacterium Myxococcus xanthus. A social gene (pilA) necessary for effective group swarming on soft agar had been deleted from the common ancestor of these lineages. During selection for competitiveness at the leading edge of growing colonies, two lineages evolved qualitatively novel mechanisms for greatly increased swarming on soft agar, whereas the other two lineages evolved relatively small increases in swarming...
January 27, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28124475/genome-wide-two-locus-interaction-analysis-identifies-multiple-epistatic-snp-pairs-that-confer-risk-of-prostate-cancer-a-cross-population-study
#19
Jiawei Shen, Zhiqiang Li, Zhijian Song, Jianhua Chen, Yongyong Shi
Prostate cancer is one of the most common carcinomas among adult males. Recently, genome-wide association studies (GWAS) have identified several susceptibility genes of prostate cancer. However, these single locus results can only explain a small proportion of the genetic etiology. In order to understand how multiple genetics variants may contribute to the penetrance of prostate cancer, we conducted a genome-wide SNP-SNP interaction study in four populations, involving 5,269 cases and 5,289 controls. We exhaustively evaluated all pairs of SNP-SNP interactions for 661,658 SNPs that were consensus in all four groups, and then performed a meta-analysis to combine the results...
January 25, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28123028/c-terminal-region-truncation-of-reln-disrupts-an-interaction-with-vldlr-causing-abnormal-development-of-the-cerebral-cortex-and-hippocampus
#20
Seungshin Ha, Prem P Tripathi, Anca B Mihalas, Robert F Hevner, David R Beier
: We discovered a hypomorphic reelin (Reln) mutant with abnormal cortical lamination and no cerebellar hypoplasia. This mutant, Reln(CTRdel), carries a chemically induced splice-site mutation that truncates the C-terminal region (CTR) domain of RELN protein and displays remarkably distinct phenotypes from reeler The mutant does not have an inverted cortex, but cortical neurons overmigrate and invade the marginal zone, which are characteristics similar to a phenotype seen in the cerebral cortex of Vldlr(null) mice...
January 25, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
keyword
keyword
5224
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"