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Clément Niel, Christine Sinoquet, Christian Dina, Ghislain Rocheleau
Motivation: Large scale genome-wide association studies (GWAS) are tools of choice for discovering associations between genotypes and phenotypes. To date, many studies rely on univariate statistical tests for association between the phenotype and each assayed single nucleotide polymorphism (SNP). However, interaction between SNPs, namely epistasis, must be considered when tackling the complexity of underlying biological mechanisms. Epistasis analysis at large scale entails a prohibitive computational burden when addressing the detection of more than two interacting SNPs...
March 14, 2018: Bioinformatics
Ignacio Trucillo Silva, Hari Kishan R Abbaraju, Lynne P Fallis, Hongjun Liu, Michael Lee, Kanwarpal S Dhugga
Intracellular factors differentially affected enzyme activities of N assimilation in the roots of maize testcrosses where alanine aminotransferase and glutamate synthase were the main enzymes regulating the levels of glutamate. N is a key macronutrient for plant growth and development. Breeding maize with improved efficiency in N use could help reduce environmental contamination as well as increase profitability for the farmers. Quantitative trait loci (QTL) mapping of traits related to N metabolism in the root tissue was undertaken in a maize testcross mapping population grown in hydroponic cultures...
March 14, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
David Angeles-Albores, Carmie Puckett Robinson, Brian A Williams, Barbara J Wold, Paul W Sternberg
RNA-sequencing (RNA-seq) is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Also, quantifying and interpreting epistatic effects using expression profiles remains a challenge. We developed a single coefficient to quantify transcriptome-wide epistasis that reflects the underlying interactions and which can be interpreted intuitively. To demonstrate our approach, we sequenced four single and two double mutants of Caenorhabditis elegans From these mutants, we reconstructed the known hypoxia pathway...
March 12, 2018: Proceedings of the National Academy of Sciences of the United States of America
John F Wolters, Guillaume Charron, Alec Gaspary, Christian R Landry, Anthony C Fiumera, Heather L Fiumera
Genetic variation in mitochondrial DNA (mtDNA) provides adaptive potential although the underlying genetic architecture of fitness components within mtDNAs is not known. To dissect functional variation within mtDNAs, we first identified naturally occurring mtDNAs that conferred high or low fitness in Saccharomyces cerevisiae by comparing growth in strains containing identical nuclear genotypes but different mtDNAs. During respiratory growth under temperature and oxidative stress conditions, mitotype effects were largely independent of nuclear genotypes even in the presence of mitonuclear interactions...
March 12, 2018: Genetics
Niloufar Javanrouh, Maryam S Daneshpour, Ali Reza Soltanian, Leili Tapak
INTRODUCTION: Obesity is a serious health problem that leads to low quality of life and early mortality. To the purpose of prevention and gene therapy for such a worldwide disease, genome wide association study is a powerful tool for finding SNPs associated with increased risk of obesity. To conduct an association analysis, kernel machine regression is a generalized regression method, has an advantage of considering the epistasis effects as well as the correlation between individuals due to unknown factors...
March 7, 2018: Gene
Ansley Grimes Stanfill, Athena Starlard-Davenport
Most common disorders affecting human health are not attributable to simple Mendelian (single-gene) inheritance patterns. Rather, the risk of developing a complex disease is often the result of interactions across genes, whereby one gene modifies the phenotype of another gene. These types of interactions can occur between two or more genes and are referred to as epistasis. There are five major types of epistatic interactions, but in human genetics, additive epistasis is most often discussed and includes both positive and negative subtypes...
January 1, 2018: Biological Research for Nursing
Jia Wen, Andrew Quitadamo, Benika Hall, Xinghua Shi
BACKGROUND: Colon cancer is a leading cause of worldwide cancer death. It has become clear that microRNAs (miRNAs) play a role in the progress of colon cancer and understanding the effect of miRNAs on tumorigenesis could lead to better prognosis and improved treatment. However, most studies have focused on studying differentially expressed miRNAs between tumor and non-tumor samples or between stages in tumor tissue. Limited work has conducted to study the interactions or epistasis between miRNAs and how the epistasis brings about effect on tumor progression...
October 16, 2017: BMC Genomics
Shijia Zhu, Gang Fang
Motivation: For many traits, causal loci uncovered by genetic-mapping studies explain only a minority of the heritable contribution to trait variation. Multiple explanations for this 'missing heritability' have been proposed. SNP-SNP interaction (epistasis), as one of the compelling models, has been widely studied. However, the genome-wide scan of epistasis, especially for quantitative traits, poses huge computational challenges. Moreover, covariate adjustment is largely ignored in epistasis analysis due to the massive extra computational undertaking...
March 2, 2018: Bioinformatics
Kritika Gupta, Raghavan Varadarajan
Where convenient phenotypic readouts are available, saturation mutagenesis coupled to deep sequencing provides a rapid and facile method to infer sequence determinants of protein structure, stability and function. We provide brief descriptions and currently available options for the various steps involved, and mention limitations of current implementations. We also highlight recent applications such as estimating relative stabilities and affinities of protein variants, mapping epitopes, protein model discrimination and prediction of mutant phenotypes...
March 2, 2018: Current Opinion in Structural Biology
Rahul Chandnani, Changsoo Kim, Hui Guo, Tariq Shehzad, Jason G Wallace, Daohua He, Zhengsheng Zhang, Jinesh D Patel, Jeevan Adhikari, Sameer Khanal, Andrew H Paterson
In mapping populations segregating for many loci, the large amount of variation among genotypes often masks small-effect quantitative trait loci (QTL). This problem can be reduced by development of populations with fewer chromosome segments segregating. Here, we report early QTL detection in reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum L. 'Acala Maxxa' (GH) and G. barbadense L. 'Pima S6' (GB). A total of 297 BCF and BCF progeny rows-127 segregating for GB chromosome segments in GH background and 170 segregating for GH chromosome segments in GB background-were evaluated in three environments...
March 2018: Plant Genome
Helen H Tai, David De Koeyer, Mads Sønderkær, Sanne Hedegaard, Martin Lagüe, Claudia Goyer, Lana Nolan, Charlotte Davidson, Kyle Gardner, Jonathan Neilson, Jamuna Risal Paudel, Agnes Murphy, Benoit Bizimungu, Hui Ying Wang, Xingyao Xiong, Dennis Halterman, Kåre Lehmann Nielsen
Kleb. is a pathogenic fungus causing wilting, chlorosis, and early dying in potato ( L.). Genetic mapping of resistance to was done using a diploid population of potato. The major quantitative trait locus (QTL) for resistance was found on chromosome 5. The gene, controlling earliness of maturity and tuberization, was mapped within the interval. Another QTL on chromosome 9 co-localized with the wilt resistance gene marker. Epistasis analysis indicated that the loci on chromosomes 5 and 9 had a highly significant interaction, and that functioned downstream of The alleles were sequenced and found to encode StCDF1...
March 2018: Plant Genome
Charlene H Emerson, Christopher R Lopez, Albert Ribes-Zamora, Erica J Polleys, Christopher L Williams, Lythou Yeo, Jacques E Zaneveld, Rui Chen, Alison A Bertuch
The Ku heterodimer acts centrally in non-homologous end-joining (NHEJ) of DNA double strand breaks (DSB). Saccharomyces cerevisiae Ku, like mammalian Ku, binds and recruits NHEJ factors to DSB ends. Consequently, NHEJ is virtually absent in yeast Ku null ( yku 70Δ or yku80Δ ) strains. Previously, we unexpectedly observed imprecise NHEJ proficiency in a yeast Ku mutant with impaired DNA end-binding (DEB). However, how DEB impairment supported imprecise NHEJ was unknown. Here, we found imprecise NHEJ proficiency to be a feature of a panel of DEB-impaired Ku mutants and that DEB impairment resulted in a deficiency in precise NHEJ...
March 2, 2018: Genetics
C Robert Cloninger, Igor Zwir
There is fundamental doubt about whether the natural unit of measurement for temperament and personality corresponds to single traits or to multi-trait profiles that describe the functioning of a whole person. Biogenetic researchers of temperament usually assume they need to focus on individual traits that differ between individuals. Recent research indicates that a shift of emphasis to understand processes within the individual is crucial for identifying the natural building blocks of temperament. Evolution and development operate on adaptation of whole organisms or persons, not on individual traits or categories...
April 19, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Joshua V Troll, M Kristina Hamilton, Melissa L Abel, Julia Ganz, Jennifer M Bates, W Zac Stephens, Ellie Melancon, Michiel van der Vaart, Annemarie H Meijer, Martin Distel, Judith S Eisen, Karen Guillemin
Resident microbes promote many aspects of host development, although the mechanisms by which microbiota influence host tissues remain unclear. We showed previously that the microbiota is required for allocation of appropriate numbers of secretory cells in the zebrafish intestinal epithelium. Because Notch signaling is crucial for secretory fate determination, we conducted epistasis experiments to establish whether the microbiota modulates host Notch signaling. We also investigated whether innate immune signaling transduces microbiota cues via the Myd88 adaptor protein...
February 23, 2018: Development
Jianzhong Yu, Duojia Pan
Genetic studies in Drosophila have been instrumental in characterizing the Hippo pathway, which converges on the co-activator Yorkie to regulate target gene transcription. A routinely used strategy to interrogate upstream regulators of Yorkie involves the examination of selected Hippo target genes upon loss or gain of function of a suspected pathway regulator. A caveat with this strategy is that aberrant expression of a given Hippo target per se does not distinguish whether it is caused by changes in Yorkie or Yorkie-independent inputs converging on the same target gene...
February 21, 2018: Development
Ali H Ziyab, Jenny Hankinson, Susan Ewart, Eric Schauberger, Kamilla Kopec-Harding, Hongmei Zhang, Adnan Custovic, Hasan Arshad, Angela Simpson, Wilfried J Karmaus
Immune-specific genes as well as genes responsible for the formation and integrity of the epidermal barrier have been implicated in the pathogeneses of allergic sensitization. This study sought to determine whether an epistatic effect (gene-gene interaction) between genetic variants within interleukin 4 receptor (IL4R) and filaggrin (FLG) genes predispose to the development of allergic sensitization. Data from two birth cohort studies were analyzed, namely the Isle of Wight (IOW; n = 1,456) and the Manchester Asthma and Allergy Study (MAAS; n = 1,058)...
February 19, 2018: Scientific Reports
Zifeng Yang, Lingling Jin, Haitao Zhu, Shaokui Wang, Guiquan Zhang, Guifu Liu
Heading date directly determines the planting districts and seasons, and thus plays an important role for producing and introducing of varieties. Limited to the materials and methodologies, analysis of epistasis still presents an obvious challenge. This thesis estimated effectively four types of epistatic components among dual QTLs on heading date based on eight single segment substitution lines (SSSLs) in rice. The results confirmed that they carried truly with heading date QTLs. Eleven pairs of QTLs were with 50...
February 15, 2018: Scientific Reports
Paulo Durão, Roberto Balbontín, Isabel Gordo
Antibiotics target essential cellular functions but bacteria can become resistant by acquiring either exogenous resistance genes or chromosomal mutations. Resistance mutations typically occur in genes encoding essential functions; these mutations are therefore generally detrimental in the absence of drugs. However, bacteria can reduce this handicap by acquiring additional mutations, known as compensatory mutations. Genetic interactions (epistasis) either with the background or between resistances (in multiresistant bacteria) dramatically affect the fitness cost of antibiotic resistance and its compensation, therefore shaping dissemination of antibiotic resistance mutations...
February 10, 2018: Trends in Microbiology
Gang Chen, Wen-da Xue, Jun Zhu
Elucidation of the systems biology foundation underlying the effect of Fangji, which are multi-herbal traditional Chinese medicine (TCM) formulas, is one of the major aims in the field. The numerous bioactive ingredients of a Fangji deal with the multiple targets of a complex disease, which is influenced by a number of genes and their interactions with the environment. Genome-wide association study (GWAS) is an unbiased approach for dissecting the genetic variants underlying complex diseases and individual response to a given treatment...
February 8, 2018: Acta Pharmacologica Sinica
Michael Hook, Suheeta Roy, Evan G Williams, Maroun Bou Sleiman, Khyobeni Mozhui, James F Nelson, Lu Lu, Johan Auwerx, Robert W Williams
Aging is a complex and highly variable process. Heritability of longevity among humans and other species is low, and this finding has given rise to the idea that it may be futile to search for DNA variants that modulate aging. We argue that the problem in mapping longevity genes is mainly one of low power and the genetic and environmental complexity of aging. In this review we highlight progress made in mapping genes and molecular networks associated with longevity, paying special attention to work in mice and humans...
February 2, 2018: Biochimica et Biophysica Acta
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