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G3: Genes—Genomes—Genetics

Wayne Hemphill, Osvaldo Rivera, Matthew Talbert
Obesity has been shown to increase risk for cardiovascular disease and type-2 diabetes. In addition, it has been implicated in aggravation of neurological conditions such as Alzheimer's. In the model organism Drosophila melanogaster, a physiological state mimicking diet-induced obesity can be induced by subjecting fruit flies to a solid medium disproportionately higher in sugar than protein or that has been supplemented with a rich source of saturated fat. These flies can exhibit increased circulating glucose levels, increased triglyceride content, insulin-like peptide resistance, and behavior indicative of neurological decline...
November 15, 2017: G3: Genes—Genomes—Genetics
Benjamin L Rambo-Martin, Jennifer G Mulle, David J Cutler, Lora J H Bean, Tracie C Rosser, Kenneth J Dooley, Clifford Cua, George Capone, Cheryl L Maslen, Roger H Reeves, Stephanie L Sherman, Michael E Zwick
One in five people with Down syndrome (DS) are born with an atrioventricular septal defect (AVSD), an incidence 2,000 times higher than in the euploid population. The genetic loci that contribute to this risk are poorly understood. In this study, we tested two hypotheses: 1) individuals with DS carrying chromosome 21 copy number variants (CNVs) that interrupt exons may be protected from AVSD, because these CNVs return AVSD susceptibility loci back to disomy, and 2) individuals with DS carrying chromosome 21 genes spanned by microduplications are at greater risk for AVSD because these microduplications boost the dosage of AVSD susceptibility loci beyond a tolerable threshold...
November 15, 2017: G3: Genes—Genomes—Genetics
Shashi N Goonetilleke, Timothy J March, Michelle G Wirthensohn, Pere Arús, Amanda R Walker, Diane E Mather
In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond [Prunus dulcis (Mill.) D.A. Webb], application of a double pseudo-testcross mapping approach to the F1 progeny of a bi-parental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping-by-sequencing to discover and map single-nucleotide polymorphisms in the almond cultivars 'Nonpareil' and 'Lauranne'...
November 15, 2017: G3: Genes—Genomes—Genetics
Jadiel A Wasson, Onur Birol, David J Katz
Genomically imprinted loci are expressed mono-allelically dependent upon the parent of origin. Their regulation not only illuminates how chromatin regulates gene expression but also how chromatin can be reprogrammed every generation. Because of their distinct parent of origin regulation, analysis of imprinted loci can be difficult. Single nucleotide polymorphisms (SNPs) are required to accurately assess these elements allele-specifically. However, publicly available SNP databases lack robust verification, making analysis of imprinting difficult...
November 14, 2017: G3: Genes—Genomes—Genetics
Amy Sirr, Adrian C Scott, Gareth A Cromie, Catherine L Ludlow, Vida Ahyong, Trey S Morgan, Teresa Gilbert, Aimée M Dudley
Despite their ubiquitous use in laboratory strains, naturally occurring loss-of-function mutations in genes encoding core metabolic enzymes are relatively rare in wild isolates of Saccharomyces cerevisiae Here, we identify a naturally occurring serine auxotrophy in a sake brewing strain from Japan. Through a cross with a honey wine (white tecc) brewing strain from Ethiopia, we map the minimal medium growth defect to SER1, which encodes 3-phosphoserine aminotransferase and is orthologous to the human disease gene, PSAT1 To investigate the impact of this polymorphism under conditions of abundant external nutrients, we examine growth in rich medium alone or with additional stresses, including the drugs caffeine and rapamycin and relatively high concentrations of copper, salt, and ethanol...
November 14, 2017: G3: Genes—Genomes—Genetics
S E Eynard, P Croiseau, D Laloë, S Fritz, M P L Calus, G Restoux
Genomic selection is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, genomic selection allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study we propose a modification of the reference population composition to mitigate diversity loss...
November 13, 2017: G3: Genes—Genomes—Genetics
R Crystal Chaw, Matthew Collin, Marjorie Wimmer, Kara-Leigh Helmrick, Cheryl Y Hayashi
Spiders swath their eggs with silk to protect developing embryos and hatchlings. Egg case silks, like other fibrous spider silks, are primarily composed of proteins called spidroins (spidroin = spider-fibroin). Silks, and thus spidroins, are important throughout the lives of spiders, yet the evolution of spidroin genes has been relatively understudied. Spidroin genes are notoriously difficult to sequence because they are typically very long (10 or more kilobases of coding sequence) and highly repetitive. Here, we investigate the evolution of spider silk genes through long-read sequencing of BAC clones...
November 10, 2017: G3: Genes—Genomes—Genetics
Virginia S Muir, Audrey P Gasch, Philip Anderson
Nonsense-mediated mRNA decay (NMD) is a conserved pathway that strongly influences eukaryotic gene expression.  Inactivating or inhibiting NMD affects the abundance of a substantial fraction of the transcriptome in numerous species.  Transcripts whose abundance is altered in NMD-deficient cells may represent either direct substrates of NMD or indirect effects of inhibiting NMD.  We present a genome-wide investigation of the direct substrates of NMD in Caenorhabditis elegans  Our goals were (i) to identify mRNA substrates of NMD and (ii) to distinguish those mRNAs from others whose abundance is indirectly influenced by the absence of NMD...
November 9, 2017: G3: Genes—Genomes—Genetics
Sujal S Phadke, Calum J Maclean, Serena Y Zhao, Emmi A Mueller, Lucas A Michelotti, Kaitlyn L Norman, Anuj Kumar, Timothy Y James
Environmental opportunistic pathogens can exploit vulnerable hosts through expression of traits selected for in their natural environments. Pathogenicity is a complicated trait underpinned by multiple complex traits, such as thermotolerance, morphology, and stress response. The baker's yeast, Saccharomyces cerevisiae, is a species with broad environmental tolerance which has been increasingly reported as an opportunistic pathogen of humans. Here we leveraged the genetic resources available in yeast and a model insect species, the greater waxmoth Galleria mellonella, to provide a genome-wide analysis of pathogenicity factors...
November 9, 2017: G3: Genes—Genomes—Genetics
David W Hall, R Kelly Dawe
Autosomal drivers violate Mendel's law of segregation in that they are overrepresented in gametes of heterozygous parents. For drivers to be polymorphic within populations rather than fixing, their transmission advantage must be offset by deleterious effects on other fitness components. In this paper we develop an analytical model for the evolution of autosomal drivers that is motivated by the neocentromere drive system found in maize. In particular we model both the transmission advantage and deleterious fitness effects on seed viability, pollen viability, seed to adult survival mediated by maternal genotype, and seed to adult survival mediated by offspring genotype...
November 9, 2017: G3: Genes—Genomes—Genetics
Bianca P Hennig, Lars Velten, Ines Racke, Chelsea Szu Tu, Matthias Thoms, Vladimir Rybin, Hüseyin Besir, Kim Remans, Lars M Steinmetz
Efficient preparation of high quality sequencing libraries that represent well the biological sample is a key step for using next-generation sequencing in research. Tn5 enables fast, robust, and highly efficient processing of limited input material while scaling to the parallel processing of hundreds of samples. Here, we present a robust Tn5 transposase purification strategy based on an N-terminal His6-Sumo3 tag. We demonstrate that libraries prepared with our in-house Tn5 are of the same quality as those processed with a commercially available kit (Nextera XT), while they reduce the cost of large-scale experiments dramatically...
November 8, 2017: G3: Genes—Genomes—Genetics
Ani A Elias, Ismail Rabbi, Peter Kulakow, Jean-Luc Jannink
Cassava (Manihot esculenta Crantz) is an important staple food in sub-Saharan Africa. Breeding experiments were conducted at the International Institute of Tropical Agriculture in cassava to select elite parents. Taking into account the heterogeneity in the field while evaluating these trials can increase the accuracy in estimation of breeding values. We used an exploratory approach using the parametric spatial kernels Power, Spherical, and Gaussian to determine the best kernel for a given scenario. The spatial kernel was fit simultaneously with a genomic kernel in a genomic selection model...
November 6, 2017: G3: Genes—Genomes—Genetics
Deepika Jaiswal, Meagan Jezek, Jeremiah Quijote, Joanna Lum, Grace Choi, Rushmie Kulkarni, DoHwan Park, Erin M Green
The conserved yeast histone methyltransferase Set1 targets H3 lysine 4 (H3K4) for mono-, di- and tri-methylation and is linked to active transcription due to the euchromatic distribution of these methyl marks and the recruitment of Set1 during transcription. However, loss of Set1 results in increased expression of multiple classes of genes, including genes adjacent to telomeres and middle sporulation genes, which are repressed under normal growth conditions because they function in meiotic progression and spore formation...
November 4, 2017: G3: Genes—Genomes—Genetics
Osval A Montesinos-López, Abelardo Montesinos-López, José Crossa, José C Montesinos-López, David Mota-Sanchez, Fermín Estrada-Gonzalez, Jussi Gilberg, Ravi Singh, Suchismita Mondal, Philomin Juliana
In genomic-enabled prediction, the task of improving the accuracy of the prediction of lines in environments is difficult because the available information is generally sparse and usually has low correlations between traits. In current genomic selection, while researchers have a large amount of information and appropriate statistical models to process it, there is still limited computing efficiency to do so. Although statistical models are usually mathematically elegant, they are also computationally inefficient, and they are impractical for many traits, lines, environments, and years because they need to sample from huge normal multivariate distributions...
November 2, 2017: G3: Genes—Genomes—Genetics
Yu Wang, Dierck Segelke, Reiner Emmerling, Jörn Bennewitz, Robin Wellmann
The long-term performance of different selection strategies was evaluated via simulation at the example of a local cattle breed, the German Angler cattle. Different optimum contribution selection approaches to maximize genetic gain were compared to a reference scenario without selection and truncation selection. The kinships and migrant contribution were estimated from genomic data. Truncation selection achieved the highest genetic gain but decreased diversity considerably at native alleles. It also caused the highest increase in migrant contributions...
October 31, 2017: G3: Genes—Genomes—Genetics
Qi Zheng
The past few years saw a surge of novel applications of the Luria-Delbruck fluctuation assay protocol in bacterial research.  Appropriate analysis of fluctuation assay data often requires computational methods that are unavailable in the popular web tool FALCOR. This paper introduces an R packages named rSalvador to bring improvements to the field. The paper focuses on rSalvador's capabilities to alleviate three kinds of problems found in recent investigations: (i) resorting to partial plating without properly accounting for the effects of partial plating; (ii) conducting attendant fitness assays without incorporating mutants' relative fitness in subsequent data analysis; and (iii) comparing mutation rates using methods that are in general inapplicable to fluctuation assay data...
October 30, 2017: G3: Genes—Genomes—Genetics
Xuhua Xia
Two major stumbling blocks exist in high-throughput sequencing (HTS) data analysis. The first is the sheer file size typically in gigabytes when uncompressed, causing problems in storage, transmission and analysis. However, these files do not need to be so large and can be reduced without loss of information. Each HTS file, either in compressed .SRA or plain text .fastq format, contains numerous identical reads stored as separate entries. For example, among 44603541 forward reads in the SRR4011234.sra file (from a Bacillus subtilis transcriptomic study) deposited at NCBI's SRA database, one read has 497027 identical copies...
October 27, 2017: G3: Genes—Genomes—Genetics
Hugh M Robertson
The non-canonical 5' intron donor splice sites GA and GG are exceedingly rare in described eukaryotic genomes, however they are present in approximately 12% of introns in the genome of the copepod Eurytemora affinis Failure to recognize the high frequency of these donor sites compromised the modeling of genes in this newly sequenced genome, including ten conserved ionotropic glutamate receptor family genes curated herein. These introns appear to have been acquired recently, along with many additional idiosyncratic introns...
October 27, 2017: G3: Genes—Genomes—Genetics
Hao Song, Lu Qi, Tao Zhang, Hai-Yan Wang
The veined rapa whelk (Rapana venosa) is widely consumed in China. Nevertheless, it preys on oceanic bivalves, thereby reducing this resource worldwide. Its larval metamorphosis comprises transition from pelagic to benthic form, which implicates considerable physiological and structural changes and plays vital roles in its natural populations and commercial breeding. Thus, understanding the endogenous microRNAs that drive metamorphosis is of great interest. This is the first study to use high-throughput sequencing to examine the alterations in microRNA (miRNA) expression that occur during metamorphosis in a marine gastropod...
October 27, 2017: G3: Genes—Genomes—Genetics
Katarina Akhmetova, Maxim Balasov, Anton Svitin, Elena Chesnokova, Matthew Renfrow, Igor Chesnokov
Septin proteins are polymerizing GTPases that are found in most eukaryotic species. Septins are important for cytokinesis and participate in many processes involving spatial modifications of the cell cortex. In Drosophila, septin proteins Pnut, Sep1 and Sep2 form a hexameric septin complex. Here, we found that septin protein Pnut is phosphorylated during the first two hours of Drosophila embryo development. To study the effect of Pnut phosphorylation in a live organism, we created a new Drosophila pnut null mutant which allows for the analysis of Pnut mutations during embryogenesis...
October 27, 2017: G3: Genes—Genomes—Genetics
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