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G3: Genes—Genomes—Genetics

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https://www.readbyqxmd.com/read/28325813/aging-effects-of-caenorhabditis-elegans-ryanodine-receptor-variants-corresponding-to-human-myopathic-mutations
#1
Katie Nicoll Baines, Célia Ferreira, Philip M Hopkins, Marie-Anne Shaw, Ian A Hope
Delaying the decline in skeletal muscle function will be critical to better maintenance of an active life-style in old age. The skeletal muscle ryanodine receptor, the major intracellular membrane channel through which calcium ions pass to elicit muscle contraction, is central to calcium ion balance, and is hypothesized to be a significant factor for age-related decline in muscle function. The nematode Caenorhabditis elegans is a key model system for the study of human aging and strains with modified C. elegans ryanodine receptors corresponding to human myopathic variants linked with malignant hyperthermia and related conditions were generated...
March 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28325812/thecellmap-org-a-web-accessible-database-for-visualizing-and-mining-the-global-yeast-genetic-interaction-network
#2
Matej Usaj, Yizhao Tan, Wen Wang, Benjamin VanderSluis, Albert Zou, Chad L Myers, Michael Costanzo, Brenda Andrews, Charles Boone
Providing access to quantitative genomic data is key to ensure large-scale data validation and promote new discoveries. TheCellMap.org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae In particular, TheCellMap.org allows users to easily access, visualize, explore and functionally annotate genetic interactions, or to extract and reorganize sub-networks, using data-driven network layouts in an intuitive and interactive manner...
March 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28315832/modulating-crossover-frequency-and-interference-for-obligate-crossovers-in-saccharomyces-cerevisiae-meiosis
#3
Parijat Chakraborty, Ajith V Pankajam, Gen Lin, Abhishek Dutta, Krishnaprasad G Nandanan, Manu M Tekkedil, Akira Shinohara, Lars M Steinmetz, Nishant K Thazath
Meiotic crossover frequencies show wide variation among organisms. But most organisms maintain at least one crossover per homolog pair (obligate crossover). In Saccharomyces cerevisiae, previous studies have shown crossover frequencies are reduced in the mismatch repair related mutant mlh3Δ and enhanced in a meiotic checkpoint mutant pch2Δ by up to two-fold at specific chromosomal loci, but both mutants maintain high spore viability. We analyzed meiotic recombination events genome-wide in mlh3Δ, pch2Δ and mlh3Δ pch2Δ mutants to test the effect of variation in crossover frequency on obligate crossovers...
March 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28315831/evaluating-methods-of-updating-training-data-in-long-term-genomewide-selection
#4
Jeffrey L Neyhart, Tyler Tiede, Aaron J Lorenz, Kevin P Smith
Genomewide selection is hailed for its ability to facilitate greater genetic gains per unit time. Over breeding cycles, the requisite linkage disequilibrium (LD) between quantitative trait loci (QTL) and markers is expected to change as a result of recombination, selection, and drift, leading to a decay in prediction accuracy. Previous research has identified the need to update the training population using data that may capture new LD generated over breeding cycles, however optimal methods of updating have not been explored...
March 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28315830/paternal-induction-of-hybrid-dysgenesis-in-drosophila-melanogaster-is-weakly-correlated-with-both-p-element-and-hobo-element-dosage
#5
Satyam P Srivastav, Erin S Kelleher
Transposable elements (TEs) are virtually ubiquitous components of genomes, yet they often impose significant fitness consequences on their hosts. In addition to producing specific deleterious mutations by insertional inactivation, TEs also impose general fitness costs by inducing DNA damage and participating in ectopic recombination. These latter fitness costs are often assumed to be dosage-dependent, with stronger effects occurring in the presence of higher TE copy numbers. We test this assumption in Drosophila melanogaster by considering the relationship between the copy number of two active DNA transposons, P-element and hobo element, and the incidence of hybrid dysgenesis, a sterility syndrome associated with transposon activity in the germline...
March 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28292787/extensive-copy-number-variation-in-fermentation-related-genes-among-saccharomyces-cerevisiae-wine-strains
#6
Jacob Steenwyk, Antonis Rokas
Due to the importance of Saccharomyces cerevisiae in wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences of S...
March 14, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28258114/dynamic-notch-signaling-specifies-each-cell-fate-in-drosophila-spermathecal-lineage
#7
Wei Shen, Jianjun Sun
Spermathecae are glandular organs in insect female reproductive tract and play essential roles for insect reproduction; however, the molecular mechanism involved in their development is largely unknown. Drosophila spermathecae consist of class-III secretory units, in which each secretory cell discharges its products to the central lumen through an end-apparatus and a canal. Secretory unit formation in Drosophila spermathecae utilizes a fixed cell lineage, in which each secretory unit precursor (SUP) divides to produce one pIIb cell and one pIIa cell...
March 3, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28258113/a-whole-transcriptome-approach-to-evaluating-reference-genes-for-quantitative-gene-expression-studies-a-case-study-in-mimulus
#8
Kimmy A Stanton, Patrick P Edger, Joshua R Puzey, Taliesin Kinser, Philip Cheng, Daniel M Vernon, Nancy R Forsthoefel, Arielle M Cooley
While qPCR is widely recognized as among the most accurate of methods for quantifying gene expression, it is highly dependent on the use of reliable, stably expressed reference genes. With the increased availability of high-throughput methods for measuring gene expression, whole transcriptome approaches may be increasingly utilized for reference gene selection and validation. In this study, RNA-seq was used to identify a set of novel qPCR reference genes and also to evaluate a panel of traditional "housekeeping" reference genes in two species of the evolutionary model plant genus Mimulus More broadly, the methods proposed in this study can be used to harness the power of transcriptomes to identify appropriate reference genes for qPCR in any study organism, including emerging and non-model systems...
March 3, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28258112/pnp4a-is-the-causal-gene-of-the-medaka-iridophore-mutant-guanineless
#9
Tetsuaki Kimura, Yusuke Takehana, Kiyoshi Naruse
See-through medaka lines are suitable for observing internal organs throughout life. They were bred by crossing multiple color mutants. However, some of the causal genes for these mutants have not been identified. The medaka has four pigment cell types: black melanophores, yellow xanthophores, white leucophores, and silvery iridophores. The causal genes of melanophore, xanthophore, and leucophore mutants have been elucidated, but the causal gene for the iridophore mutant remains unknown. Here, we describe the iridophore mutant, guanineless (gu), which exhibits a strong reduction in visible iridophores throughout its larval to adult stages...
March 3, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28258111/automated-phenotyping-indicates-pupal-size-in-drosophila-is-a-highly-heritable-trait-with-an-apparent-polygenic-basis
#10
R Guy Reeves, Diethard Tautz
The intense focus on studying human height has done more than any other genetic analysis to advance our understanding of the heritability of highly complex phenotypes. Here we describe in detail the properties of a previously unexplored trait in Drosophila melanogaster that shares many salient properties with human height. The total length of the pupal case varies between 2.8 and 3.9mm among natural variants and we report that it is among the most heritable traits reported in this species. We have developed a simple semi-automatic phenotyping system with which a single operator can reliably score >5000 individuals in a day...
March 3, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28258110/planar-cell-polarity-effector-fritz-interacts-with-dishevelled-and-has-multiple-functions-in-regulating-pcp
#11
Ying Wang, Victor F Naturale, Paul N Adler
The Planar cell Polarity Effector (PPE) genes inturned, fuzzy and fritz are downstream components in the frizzled/starry night signaling pathway, and their function is instructed by upstream Planar Cell Polarity (PCP) core genes such as frizzled and disheveled PPE proteins accumulate asymmetrically in wing cells and function in a protein complex mediated by direct interactions between In and Frtz and In and Fy. How the PCP proteins instruct the accumulation of PPE protein is unknown. We found a likely direct interaction between Dishevelled and Fritz and Dishevelled and Fuzzy that could play a role in this...
March 3, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28250016/construction-of-a-high-density-american-cranberry-vaccinium-macrocarpon-ait-composite-map-using-genotyping-by-sequencing-for-multi-pedigree-linkage-mapping
#12
Brandon Schlautman, Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Massimo Iorizzo, James Polashock, Edward Grygleski, Nicholi Vorsa, Juan Zalapa
The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three inter-related cranberry full-sib populations...
March 1, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28250015/genotype-imputation-to-improve-the-cost-efficiency-of-genomic-selection-in-farmed-atlantic-salmon
#13
Hsin-Yuan Tsai, Oswald Matika, Stefan McKinnon Edwards, Roberto Antolín-Sánchez, Alastair Hamilton, Derrick R Guy, Alan E Tinch, Karim Gharbi, Michael J Stear, John B Taggart, James E Bron, John M Hickey, Ross D Houston
Genomic selection uses genome-wide marker information to predict breeding values for traits of economic interest, and is more accurate than pedigree-based methods. The development of high density SNP arrays for Atlantic salmon has enabled genomic selection in selective breeding programmes, alongside high-resolution association mapping of the genetic basis of complex traits. However, in sibling testing schemes typical of salmon breeding programmes, trait records are available on many thousands of fish with close relationships to the selection candidates...
March 1, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28250014/the-pivotal-role-of-protein-phosphorylation-in-the-control-of-yeast-central-metabolism
#14
Panayotis Vlastaridis, Athanasios Papakyriakou, Anargyros Chaliotis, Efstratios Stratikos, Stephen G Oliver, Grigoris D Amoutzias
Protein phosphorylation is the most frequent eukaryotic post-translational modification and can act as either a molecular switch or rheostat for protein functions. The deliberate manipulation of protein phosphorylation has great potential for regulating specific protein functions with surgical precision, rather than the gross effects gained by the over/under-expression or complete deletion of a protein-encoding gene. In order to assess the impact of phosphorylation on central metabolism, and thus its potential for biotechnological and medical exploitation, a compendium of highly confident protein phosphorylation sites (p-sites) for the model organism Saccharomyces cerevisiae has been analyzed together with two more datasets from the fungal pathogen Candida albicans Our analysis highlights the global properties of the regulation of yeast central metabolism by protein phosphorylation, where almost half of the enzymes involved are subject to this sort of post-translational modification...
March 1, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28250013/time-variant-genetic-effects-as-a-cause-for-preterm-birth-insights-from-a-population-of-maternal-cousins-in-sweden
#15
Julius Juodakis, Jonas Bacelis, Ge Zhang, Louis J Muglia, Bo Jacobsson
Preterm delivery is the leading cause of neonatal mortality worldwide, yet its etiology remains largely unexplained. We propose that the genetic factors controlling this trait could act in a non-uniform manner during pregnancy, with each factor having a unique 'window of sensitivity.' We test this hypothesis by modeling the distribution of gestational ages observed in maternal cousins from the Swedish Medical Birth Register (n=35,541 pairs). The models were built using a time-to-event framework, with simulated genetic factors that increase the hazard of birth either uniformly across the pregnancy (constant effect) or only in particular windows (varying effect)...
March 1, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28235829/a-dense-brown-trout-salmo-trutta-linkage-map-reveals-recent-chromosomal-rearrangements-in-the-salmo-genus-and-the-impact-of-selection-on-linked-neutral-diversity
#16
Maeva Leitwein, Bruno Guinand, Juliette Pouzadoux, Erick Desmarais, Patrick Berrebi, Pierre-Alexandre Gagnaire
High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socio-economically important species heavily impacted by human activities. A total of 3,977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses...
February 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28235828/independent-maternal-and-fetal-genetic-effects-on-mid-gestational-circulating-levels-of-environmental-pollutants
#17
Michela Traglia, Lisa A Croen, Kristen Lyall, Gayle C Windham, Marty Kharrazi, Gerald N DeLorenze, Anthony R Torres, Lauren A Weiss
Maternal exposure to environmental pollutants could affect fetal brain development and increase autism spectrum disorder (ASD) risk in conjunction with differential genetic susceptibility. Organohalogen congeners measured in maternal mid-pregnancy blood samples have recently shown significant, but negative associations with offspring ASD outcome. We report the first large scale maternal and fetal genetic study of the mid-pregnancy serum levels of a set of 21 organohalogens in a subset of 790 genotyped women and 764 children collected in California by the Early Markers for Autism (EMA) Project...
February 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28235827/genomic-data-quality-impacts-automated-detection-of-lateral-gene-transfer-in-fungi
#18
Pierre-Yves Dupont, Murray P Cox
Lateral gene transfer (or horizontal gene transfer), an atypical mechanism of transferring genes between species, has almost become the default explanation for genes that display an unexpected composition or phylogeny. Numerous methods of detecting lateral gene transfer events all rely on two fundamental strategies: primary structure composition or gene tree/species tree comparisons. Discouragingly, the results of these different approaches rarely coincide. With the wealth of genome data now available, detection of laterally transferred genes is increasingly being attempted in large uncurated eukaryotic datasets...
February 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28235826/a-new-reference-genome-assembly-for-the-microcrustacean-daphnia-pulex
#19
Zhiqiang Ye, Sen Xu, Ken Spitze, Jana Asselman, Xiaoqian Jiang, Matthew S Ackerman, Jacqueline Lopez, Brent Harker, R Taylor Raborn, W Kelley Thomas, Jordan Ramsdell, Michael E Pfrender, Michael Lynch
Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high-quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino-acid sequence identity of 98...
February 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28235825/genome-wide-screen-reveals-sec21-mutants-of-saccharomyces-cerevisiae-are-methotrexate-resistant
#20
Lai H Wong, Stephane Flibotte, Sunita Sinha, Jennifer Chiang, Guri Giaever, Corey Nislow
Exposure of cells to small molecules and drug therapies imposes a strong selective pressure. As a result, cells rapidly acquire mutations in order to survive. These include resistant variants of the drug target as well as those that modulate drug transport and detoxification. To systematically explore how cells acquire drug resistance in an unbiased manner, rapid cost-effective approaches are required. Methotrexate, as one of the first rationally designed anticancer drug, has served as a prototypic example of such acquired resistance...
February 24, 2017: G3: Genes—Genomes—Genetics
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