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https://www.readbyqxmd.com/read/28444412/biochemical-and-genetic-analyses-of-n-metabolism-in-maize-testcross-seedlings-1-leaves
#1
Ignacio Trucillo Silva, Hari Kishan R Abbaraju, Lynne P Fallis, Hongjun Liu, Michael Lee, Kanwarpal S Dhugga
Aside from the identification of 32 QTL for N metabolism in the seedling leaves of a maize testcross population, alanine aminotransferase was found to be a central enzyme in N assimilation. Excessive application of nitrogen (N) fertilizer to grow commercial crops like maize is a cause of concern because of the runoff of excess N into streams and rivers. Breeding maize with improved N use efficiency (NUE) would reduce environmental pollution as well as input costs for the farmers. An understanding of the genetics underlying N metabolism is key to breeding for NUE...
April 25, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28426760/regulation-of-proteinaceous-effector-expression-in-phytopathogenic-fungi
#2
REVIEW
Kar-Chun Tan, Richard P Oliver
Effectors are molecules used by microbial pathogens to facilitate infection via effector-triggered susceptibility or tissue necrosis in their host. Much research has been focussed on the identification and elucidating the function of fungal effectors during plant pathogenesis. By comparison, knowledge of how phytopathogenic fungi regulate the expression of effector genes has been lagging. Several recent studies have illustrated the role of various transcription factors, chromosome-based control, effector epistasis, and mobilisation of endosomes within the fungal hyphae in regulating effector expression and virulence on the host plant...
April 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28422646/coordinated-control-of-terminal-differentiation-and-restriction-of-cellular-plasticity
#3
Tulsi Patel, Oliver Hobert
The acquisition of a specific cellular identity is usually paralleled by a restriction of cellular plasticity. Whether and how these two processes are coordinated is poorly understood. Transcription factors called terminal selectors activate identity-specific effector genes during neuronal differentiation to define the structural and functional properties of a neuron. To study restriction of plasticity, we ectopically expressed C. elegans CHE-1, a terminal selector of ASE sensory neuron identity. In undifferentiated cells, ectopic expression of CHE-1 results in activation of ASE neuron type-specific effector genes...
April 19, 2017: ELife
https://www.readbyqxmd.com/read/28419606/stratified-polygenic-risk-prediction-model-with-application-to-cagi-bipolar-disorder-sequencing-data
#4
Maggie Haitian Wang, Billy Chang, Rui Sun, Inchi Hu, Xiaoxuan Xia, William Ka Kei Wu, Ka Chun Chong, Benny Chung-Ying Zee
Genetic data consists of a wide range of marker types, including common, low frequency, and rare variants. Multiple genetic markers and their interactions play central roles in the heritability of complex disease. In this study, we propose an algorithm that uses a stratified variable selection design by genetic architectures and interaction effects, achieved by a data-set adaptive W-test. The polygenic sets in all strata were integrated to form a classification rule. The algorithm was applied to the Critical Assessment of Genome Interpretation 4 bipolar challenge sequencing data...
April 17, 2017: Human Mutation
https://www.readbyqxmd.com/read/28419091/multidrug-resistant-bacteria-compensate-for-the-epistasis-between-resistances
#5
Jorge Moura de Sousa, Roberto Balbontín, Paulo Durão, Isabel Gordo
Mutations conferring resistance to antibiotics are typically costly in the absence of the drug, but bacteria can reduce this cost by acquiring compensatory mutations. Thus, the rate of acquisition of compensatory mutations and their effects are key for the maintenance and dissemination of antibiotic resistances. While compensation for single resistances has been extensively studied, compensatory evolution of multiresistant bacteria remains unexplored. Importantly, since resistance mutations often interact epistatically, compensation of multiresistant bacteria may significantly differ from that of single-resistant strains...
April 2017: PLoS Biology
https://www.readbyqxmd.com/read/28414087/quantifying-the-potential-and-flux-landscapes-of-multi-locus-evolution
#6
Li Xu, Jin Wang
Exploration of multi-locus evolution is critically important for understanding evolutionary dynamics. Recombination and epistasis lead to complex evolutionary dynamics. Quantifying the stability and function of such multi-locus evolutionary systems globally is a long-standing challenge for evolutionary biologists. The conventional Wright, Fisher and quasi-linkage equilibrium (QLE) theories can only be applied to highly restricted, simplified and special evolutionary scenarios. In this study, we developed a non-equilibrium potential and flux landscape theory to explore the multi-locus evolution beyond Wright, Fisher and the QLE...
April 13, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28406896/inferring-modulators-of-genetic-interactions-with-epistatic-nested-effects-models
#7
Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz
Maps of genetic interactions can dissect functional redundancies in cellular networks. Gene expression profiles as high-dimensional molecular readouts of combinatorial perturbations provide a detailed view of genetic interactions, but can be hard to interpret if different gene sets respond in different ways (called mixed epistasis). Here we test the hypothesis that mixed epistasis between a gene pair can be explained by the action of a third gene that modulates the interaction. We have extended the framework of Nested Effects Models (NEMs), a type of graphical model specifically tailored to analyze high-dimensional gene perturbation data, to incorporate logical functions that describe interactions between regulators on downstream genes and proteins...
April 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28400567/genetic-dissection-of-yield-traits-in-super-hybrid-rice-xieyou9308-using-both-unconditional-and-conditional-genome-wide-association-mapping
#8
Yingxin Zhang, Liyuan Zhou, Xihong Shen, Daibo Chen, Weixun Wu, Xiaodeng Zhan, Qunen Liu, Aike Zhu, Xiangyang Lou, Haiming Xu, Shihua Cheng, Liyong Cao
With the development and application of super rice breeding, elite rice hybrids with super high-yielding potential have been widely developed in last decades in China. Xieyou9308 is one of the most famous super hybrid rice varieties. To uncover the genetic mechanism of Xieyou9308's high yield potential, a recombinant inbred line (RIL) population derived from cross of XieqingzaoB and Zhonghui9308 was re-sequenced and investigated on the grain yield (GYD) and its three component traits, number of panicles per plant (NP), number of filled grains per panicle (NFGP), and grain weight (GW)...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28388655/functional-toll-like-receptor-tlr-2-polymorphisms-in-the-susceptibility-to-inflammatory-bowel-disease
#9
Helga Paula Török, Victor Bellon, Astrid Konrad, Martin Lacher, Laurian Tonenchi, Matthias Siebeck, Stephan Brand, Enrico Narciso De Toni
BACKGROUND: The recent genome-wide association studies (GWAS) in inflammatory bowel disease (IBD) suggest significant genetic overlap with complex mycobacterial diseases like tuberculosis or leprosy. TLR variants have previously been linked to susceptibility for mycobacterial diseases. Here we investigated the contribution to IBD risk of two TLR2 polymorphisms, the low-prevalence variant Arg753Gln and the GTn microsatellite repeat polymorphism in intron 2. We studied association with disease, possible correlations with phenotype and gene-gene interactions...
2017: PloS One
https://www.readbyqxmd.com/read/28386122/epistasis-between-tifab-and-mir-146a-neighboring-genes-in-del-5q-myelodysplastic-syndrome
#10
M E Varney, K Choi, L Bolanos, S Christie, J Fang, H L Grimes, J P Maciejewski, J-I Inoue, D T Starczynowski
No abstract text is available yet for this article.
April 7, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28379570/gene-tree-discordance-does-not-explain-away-the-temporal-decline-of-convergence-in-mammalian-protein-sequence-evolution
#11
Zhengting Zou, Jianzhi Zhang
Several authors reported lower frequencies of protein sequence convergence between more distantly related evolutionary lineages and attributed this trend to epistasis, which renders the acceptable amino acids at a site more different and convergence less likely in more divergent lineages. A recent primate study, however, suggested that this trend is at least partially and potentially entirely an artifact of gene tree discordance (GTD). Here we demonstrate in a genome-wide dataset from 17 mammals that the temporal trend remains (1) upon the control of the GTD level, (2) in genes whose genealogies are concordant with the species tree, and (3) for convergent changes, which are extremely unlikely to be caused by GTD...
April 3, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28379338/cmdr-based-differential-evolution-identify-the-epistatic-interaction-in-genome-wide-association-studies
#12
Cheng-Hong Yang, Li-Yeh Chuang, Yu-Da Lin
Motivation: Detecting epistatic interactions in genome-wide association studies is a computational challenge. Such huge numbers of single nucleotide polymorphism (SNP) combinations limit the some of the powerful algorithms to be applied to detect the potential epistasis in large-scale SNP data sets. Approach: We propose a new algorithm which combines the differential evolution (DE) algorithm with a classification based multifactor-dimensionality reduction (CMDR), termed DECMDR...
April 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28362804/fishing-for-adaptive-epistasis-using-mitonuclear-interactions
#13
David M Rand
No abstract text is available yet for this article.
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28340352/human-epistatic-interaction-controls-il7r-splicing-and-increases-multiple-sclerosis-risk
#14
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
#15
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
#16
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
#17
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
#18
Daniel Felsky, Jishu Xu, Lori B Chibnik, Julie A 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 17, 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
#19
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
#20
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 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
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