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G3: Genes—Genomes—Genetics

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https://www.readbyqxmd.com/read/28642365/phenotypic-diagnosis-of-lineage-and-differentiation-during-sake-yeast-breeding
#1
Shinsuke Ohnuki, Hiroki Okada, Anne Friedrich, Yoichiro Kanno, Tetsuya Goshima, Hirokazu Hasuda, Masaaki Inahashi, Naoto Okazaki, Hiroyasu Tamura, Ryo Nakamura, Dai Hirata, Hisashi Fukuda, Hitoshi Shimoi, Katsuhiko Kitamoto, Daisuke Watanabe, Joseph Schacherer, Takeshi Akao, Yoshikazu Ohya
Sake yeast was developed exclusively in Japan. Its diversification during breeding remains largely uncharacterized. To evaluate the breeding processes of the sake lineage, we thoroughly investigated the phenotypes and differentiation of 27 sake yeast strains using high-dimensional, single-cell morphological phenotyping. Although the genetic diversity of the sake yeast lineage is relatively low, its morphological diversity has expanded substantially compared to that of the Saccharomyces cerevisiae species as a whole...
June 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28642364/the-accuracy-and-bias-of-single-step-genomic-prediction-for-populations-under-selection
#2
Wan-Ling Hsu, Dorian J Garrick, Rohan Luigi Fernando
In single-step analyses, missing genotypes are explicitly or implicitly imputed, and this requires centering the observed genotypes, using the means of the unselected founders. If genotypes are only available on selected individuals, centering on the unselected founder mean is not straightforward. Here, computer simulation is used to study an alternative analysis that does not require centering genotypes but fits the mean μg of unselected individuals as a fixed effect. Centering the entire matrix of observed and imputed genotypes using their sample means can be done to improve numerical properties of the analysis, in addition to fitting μg...
June 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28637811/bayesian-networks-illustrate-genomic-and-residual-trait-connections-in-maize-zea-mays-l
#3
Katrin Töpner, Guilherme J M Rosa, Daniel Gianola, Chris-Carolin Schön
Relationships among traits were investigated on the genomic and residual levels using novel methodology. This included inference on these relationships via Bayesian networks and an assessment of the networks with structural equation models. The methodology employed three steps. First, a Bayesian multiple-trait Gaussian model was fitted to the data to decompose phenotypic values into their genomic and residual components. Second, genomic and residual network structures among traits were learned from estimates of these two components...
June 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28637810/mcclintock-an-integrated-pipeline-for-detecting-transposable-element-insertions-in-whole-genome-shotgun-sequencing-data
#4
Michael G Nelson, Raquel S Linheiro, Casey M Bergman
Transposable element (TE) insertions are among the most challenging type of variants to detect in genomic data because of their repetitive nature and complex mechanisms of replication. Nevertheless, the recent availability of large resequencing datasets has spurred development of many new methods to detect TE insertions in whole genome shotgun sequences. Here we report an integrated bioinformatics pipeline for the detection of TE insertions in whole genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods...
June 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28637809/rrna-pseudogenes-in-filamentous-ascomycetes-as-revealed-by-genome-data
#5
Yi Li, Rui-Heng Yang, Lan Jiang, Xiao-Di Hu, Zu-Jian Wu, Yi-Jian Yao
The nuclear ribosomal DNA (rDNA) is considered as a paradigm of concerted evolution. Components of the rDNA tandem repeats (45S) are widely used in phylogenetic studies of different organisms and the internal transcribed spacer (ITS) region is recently selected as a fungal DNA barcode. However, rRNA pseudogenes, as one kind of escape of concerted evolution, were reported in a wide range of organisms, especially in plants and animals. Moreover, large numbers of 5S rRNA pseudogenes were identified in several filamentous ascomycetes...
June 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28634244/simple-expression-domains-are-regulated-by-discrete-crms-during-drosophila-oogenesis
#6
Nicole T Revaitis, Robert A Marmion, Maira Farhat, Vesile Ekiz, Wei Wang, Nir Yakoby
Eggshell patterning has been extensively studied in Drosophila melanogaster However, the cis-regulatory modules (CRMs), which control spatiotemporal expression of these patterns, are vastly unexplored. The FlyLight collection contains over 7,000 intergenic and intronic DNA fragments that, if containing CRMs, can drive the transcription factor GAL4. We cross-listed the 84 genes known to be expressed during D. melanogaster oogenesis with the ~1200 listed genes of the FlyLight collection, and found 22 common genes that are represented by 281 FlyLight fly lines...
June 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28630104/evidence-for-adaptive-introgression-of-disease-resistance-genes-among-closely-related-arabidopsis-species
#7
Jesper Bechsgaard, Tove Hedegaard Jorgensen, Mikkel Heide Schierup
The generation and maintenance of functional variation in the pathogen defense system of plants is central to the constant evolutionary battle between hosts and parasites. If a species is susceptible to a given pathogen, hybridisation and subsequent introgression of a resistance allele from a related species can potentially be an important source of new immunity and is therefore expected to be selected for in a process referred to as adaptive introgression. Here we survey sequence variation in ten resistance (R) genes and compare with 37 reference genes in natural populations of the two closely related and interfertile species Arabidopsis lyrata and A...
June 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28624774/sex-and-genetic-background-influence-superoxide-dismutase-csod-related-phenotypic-variation-in-drosophila-melanogaster
#8
Courtney E Lessel, Tony L Parkes, Joel Dickinson, Thomas J S Merritt
Mutations often have drastically different effects in different genetic backgrounds; understanding a gene's biological function then requires an understanding of its interaction with genetic diversity. The antioxidant enzyme cytosolic superoxide dismutase, cSOD, catalyzes the dismutation of the superoxide radical, a molecule that can induce oxidative stress if its concentration exceeds cellular control. Accordingly, Drosophila melanogaster lacking functional cSOD exhibit a suite of phenotypes including decreased longevity, hypersensitivity to oxidative stress, impaired locomotion, and reduced NADP(H) enzyme activity in males...
June 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28626004/sex-chromosome-evolution-heterochiasmy-and-physiological-qtl-in-the-salmonid-brook-charr-salvelinus-fontinalis
#9
Ben J G Sutherland, Ciro Rico, Céline Audet, Louis Bernatchez
Whole genome duplication can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into non-recombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i...
June 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28626003/transcriptional-complexity-and-distinct-expression-patterns-of-auts2-paralogs-in-danio-rerio
#10
Igor Kondrychyn, Lena Robra, Vatsala Thirumalai
Several genes that have been implicated in autism spectrum disorders are large and have multiple transcripts. Neurons are especially enriched with longer transcripts compared to non-neural cell types. The human autism susceptibility candidate 2 (AUTS2) gene is ~1.2 Mb long and is implicated in a number of neurological disorders including autism, intellectual disability, addiction and developmental delay. Recent studies show AUTS2 to be important for activation of transcription of neural specific genes, neuronal migration and neurite outgrowth...
June 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28620088/the-r148-3-gene-modulates-caenorhabditis-elegans-lifespan-and-fat-metabolism
#11
Catherine Roy-Bellavance, Jennifer M Grants, Stéphanie Miard, Kayoung Lee, Évelyne Rondeau, Chantal Guillemette, Martin J Simard, Stefan Taubert, Frédéric Picard
Despite many advances, the molecular links between energy metabolism and longevity are not well understood. Here, we have used the nematode model Caenorhabditis elegans to study the role of the yet uncharacterized gene R148.3 in fat accumulation and lifespan. In wild-type worms, a R148.3p::GFP reporter showed enhanced expression throughout life in the pharynx, in neurons, and in muscles. Functionally, a protein fusing a predicted 22 aa N-terminal signal sequence (SS) of R148.3 to mCherry displayed robust accumulation in coelomyocytes, indicating that R148...
June 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28620087/daily-activity-of-the-housefly-musca-domestica-is-influenced-by-temperature-independent-of-3-utr-period-gene-splicing
#12
Olga Bazalova, David Dolezel
Circadian clocks orchestrate daily activity patterns and free running periods of locomotor activity under constant conditions. While the first often depends on temperature, the latter is temperature-compensated over a physiologically relevant range. Here, we explored the locomotor activity of the temperate housefly, Musca domestica Under low temperatures, activity was centered round a major and broad afternoon peak, while high temperatures resulted in activity throughout the photophase with a mild mid-day depression, which was especially pronounced in males exposed to long photoperiods...
June 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28620086/a-genetic-screen-reveals-an-unexpected-role-for-yorkie-signaling-in-jak-stat-dependent-hematopoietic-malignancies-in-drosophila-melanogaster
#13
Abigail M Anderson, Alessandro A Bailetti, Elizabeth Rodkin, Atish De, Erika A Bach
A gain-of-function mutation in the tyrosine kinase JAK2 (JAK2(V617F) ) causes human myeloproliferative neoplasms (MPNs). These patients present with high numbers of myeloid lineage cells and have numerous complications. Since current MPN therapies are not curative, there is a need to find new regulators and targets of JAK/STAT signaling that may represent additional clinical interventions. Drosophila melanogaster offers a low complexity model to study MPNs as JAK/STAT signaling is simplified with only one JAK (Hopscotch (Hop)) and one STAT (Stat92E)...
June 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28620085/a-sine-insertion-in-atp1b2-in-belgian-shepherd-dogs-affected-by-spongy-degeneration-with-cerebellar-ataxia-sdca2
#14
Nico Mauri, Miriam Kleiter, Elisabeth Dietschi, Michael Leschnik, Sandra Högler, Michaela Wiedmer, Joëlle Dietrich, Diana Henke, Frank Steffen, Simone Schuller, Corinne Gurtner, Nadine Stokar-Regenscheit, Donal O'Toole, Thomas Bilzer, Christiane Herden, Anna Oevermann, Vidhya Jagannathan, Tosso Leeb
Spongy degeneration with cerebellar ataxia (SDCA) is a genetically heterogeneous neurodegenerative disorder with autosomal recessive inheritance in Malinois dogs, one of the four varieties of the Belgian Shepherd breed. Using a combined linkage and homozygosity mapping approach we identified a ~10.6 Mb critical interval on chromosome 5 in a Malinois family with four puppies affected by cerebellar dysfunction. Visual inspection of the 10.6 Mb interval in whole genome sequencing data from one affected puppy revealed a 227 bp SINE insertion into the ATP1B2 gene encoding the β2 subunit of the Na(+)/K(+)-ATPase holoenzyme (ATP1B2:c...
June 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28620084/multidimensional-genetic-analysis-of-repeated-seizures-in-the-hybrid-mouse-diversity-panel-reveals-a-novel-epileptogenesis-susceptibility-locus
#15
Russell J Ferland, Jason Smith, Dominick Papandrea, Jessica Gracias, Leah Hains, Sridhar B Kadiyala, Brittany O'Brien, Eun Yong Kang, Barbara S Beyer, Bruce J Herron
Epilepsy has many causes and comorbidities affecting as many as 4% of people in their lifetime. Both idiopathic and symptomatic epilepsies are highly heritable, but genetic factors are difficult to characterize among humans due to complex disease etiologies. Rodent genetic studies have been critical to the discovery of seizure susceptibility loci, including Kcnj10 mutations identified in both mouse and human cohorts. However, genetic analyses of epilepsy phenotypes in mice to date have been carried out as acute studies in seizure-naive animals or in Mendelian models of epilepsy, while humans with epilepsy have a history of recurrent seizures that also modify brain physiology...
June 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28611256/a-duplicated-truncated-amh-gene-is-involved-in-male-sex-determination-in-an-old-world-silverside
#16
Dilip Kumar Bej, Kaho Miyoshi, Ricardo S Hattori, Carlos A Strüssmann, Yoji Yamamoto
A master sex-determining gene, the Y chromosome-linked anti-Müllerian hormone (amhy), has been described in two New World atheriniform species but little is known on the distribution, evolution, and function(s) of this gene in other Atheriniformes. Interestingly, amhy has been found to coexist with temperature-dependent sex determination (TSD), providing a unique opportunity to explore the interplay between genotypic and environmental sex determination. In this study, the search for an amhy homologue was extended to an Old World atheriniform, the cobaltcap silverside Hypoatherina tsurugae (Atherinidae)...
June 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28611255/a-kinome-rnai-screen-in-drosophila-identifies-novel-genes-interacting-with-lgl-apkc-and-crb-cell-polarity-genes-in-epithelial-tissues
#17
Linda M Parsons, Nicola A Grzeschik, Kasun Amaratunga, Peter Burke, Leonie M Quinn, Helena E Richardson
In both Drosophila melanogaster and mammalian systems, epithelial structure and underlying cell polarity are essential for proper tissue morphogenesis and organ growth. Cell polarity interfaces with multiple cellular processes that are regulated by the phosphorylation status of large protein networks. To gain insight into the molecular mechanisms that coordinate cell polarity with tissue growth, we screened a boutique collection of RNAi stocks targeting the kinome for their capacity to modify Drosophila 'cell polarity' eye and wing phenotypes...
June 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28611254/patterns-of-genetic-structure-and-linkage-disequilibrium-in-a-large-collection-of-pea-germplasm
#18
Mathieu Siol, Françoise Jacquin, Marianne Chabert-Martinello, Petr Smýkal, Marie-Christine Le Paslier, Grégoire Aubert, Judith Burstin
Pea (Pisum sativum, L.) is a major pulse crop used both for animal and human alimentation. Owing to its association with nitrogen-fixing bacteria, it is also a valuable component for low-input cropping systems. To evaluate the genetic diversity and the scale of linkage disequilibrium (LD) decay in pea, we genotyped a collection of 917 accessions gathering elite cultivars, landraces and wild relatives using an array of ~13,000 single nucleotide polymorphisms (SNP). Genetic diversity is broadly distributed across three groups corresponding to wild/landraces peas, winter types and spring types...
June 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28606944/cytonuclear-epistasis-controls-the-density-of-symbiont-wolbachia-pipientis-in-non-gonadal-tissues-of-mosquito-culex-quinquefasciatus
#19
Kevin J Emerson, Robert L Glaser
Wolbachia pipientis, a bacterial symbiont infecting arthropods and nematodes, is vertically transmitted through the female germline and manipulates its host's reproduction to favor infected females. Wolbachia also infects somatic tissues where it can cause non-reproductive phenotypes in its host, including resistance to viral pathogens. Wolbachia-mediated phenotypes are strongly associated with the density of Wolbachia in host tissues. Little is known, however, about how Wolbachia density is regulated in native or heterologous hosts...
June 12, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28600441/unique-allelic-eqtl-clusters-in-human-mhc-haplotypes
#20
Tze Hau Lam, Meixin Shen, Matthew Zirui Tay, Ee Chee Ren
The control of gene regulation within the MHC remains poorly understood despite several eQTL studies revealing an association of MHC gene expression with independent tag-SNPs. MHC haplotype variation may exert a greater effect on gene expression phenotype than specific single variants. To explore the effect of MHC haplotype sequence diversity on gene expression phenotypes across the MHC, we examined the MHC transcriptomic landscape at haplotype-specific resolution for three prominent MHC haplotypes (A2-B46-DR9, A33-B58-DR3, and A1-B8-DR3) derived from MHC-homozygous B-lymphoblastoid cell lines...
June 9, 2017: G3: Genes—Genomes—Genetics
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