journal
MENU ▼
Read by QxMD icon Read
search

G3: Genes—Genomes—Genetics

journal
https://www.readbyqxmd.com/read/27913636/the-effect-of-temperature-on-drosophila-hybrid-fitness
#1
Charles J J Miller, Daniel R Matute
Mechanisms of reproductive isolation inhibit gene flow between species and can be broadly sorted into two categories: prezygotic and postzygotic. While comparative studies suggest that prezygotic barriers tend to evolve first, postzygotic barriers are crucial for maintaining species boundaries and impeding gene flow that might otherwise cause incipient species to merge. Most, but not all, postzygotic barriers result from genetic incompatibilities between two or more loci from different species, and occur due to divergent evolution in allopatry...
December 2, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27913635/screening-and-analysis-of-janelia-flylight-project-enhancer-gal4-strains-identifies-multiple-gene-enhancers-active-during-hematopoiesis-in-normal-and-wasp-challenged-drosophila-larvae
#2
Tsuyoshi Tokusumi, Yumiko Tokusumi, Mark S Brahier, Victoria Lam, Jessica R Stoller-Conrad, Paul T Kroeger, Robert A Schulz
A GFP expression screen has been conducted on greater than one thousand Janelia FlyLight Project enhancer-Gal4 lines to identify transcriptional enhancers active in the larval hematopoietic system. A total of 190 enhancers associated with 87 distinct genes showed activity in cells of the third instar larval lymph gland and hemolymph. That is, gene enhancers were active in cells of the lymph gland posterior signaling center (PSC), medullary zone (MZ), and/or cortical zone (CZ), while certain of the transcriptional control regions were active in circulating hemocytes...
December 2, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27913634/comparative-analysis-highlights-variable-genome-content-of-wheat-rusts-and-divergence-of-the-mating-loci
#3
Christina A Cuomo, Guus Bakkeren, Hala Badr Khalil, Vinay Panwar, David Joly, Rob Linning, Sharadha Sakthikumar, Xiao Song, Xian Adiconis, Lin Fan, Jonathan M Goldberg, Joshua Z Levin, Sarah Young, Qiandong Zeng, Yehoshua Anikster, Myron Bruce, Meinan Wang, Chuntao Yin, Brent McCallum, Les J Szabo, Scot Hulbert, Xiaming Chen, John P Fellers
Three members of the Puccinia genus, P. triticina (Pt), P. striiformis f.sp. tritici (Pst), and P. graminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi and basidiomycetes, and to identify genes of significance for infection...
December 2, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27903632/genomic-prediction-with-pedigree-and-genotype-%C3%A3-environment-interaction-in-spring-wheat-grown-in-south-and-west-asia-north-africa-and-mexico
#4
Sivakumar Sukumaran, Jose Crossa, Diego Jarquin, Marta Lopes, Mathew P Reynolds
Developing genomic selection (GS) models is an important step in applying GS to accelerate the rate of genetic gain in grain yield in plant breeding. In this study, seven genomic prediction models under two cross-validation scenarios were tested on 287 advanced elite spring wheat lines phenotyped for grain yield (GY), thousand-grain weight (GW), grain number (GN), and thermal time for flowering (TTF) in 18 international environments (year-location combinations) in major wheat producing countries in 2010 and 2011...
November 30, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27903631/genomics-of-compensatory-adaptation-in-experimental-populations-of-aspergillus-nidulans
#5
Jeremy R Dettman, Nicolas Rodrigue, Sijmen E Schoustra, Rees Kassen
Knowledge of the number and nature of genetic changes responsible for adaptation is essential for understanding and predicting evolutionary trajectories. Here, we study the genomic basis of compensatory adaptation to the fitness cost of fungicide resistance in experimentally evolved strains of the filamentous fungus Aspergillus nidulans The original selection experiment tracked the fitness recovery of lines founded by an ancestral strain that was resistant to fludioxonil, but paid a fitness cost in the absence of the fungicide...
November 30, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27903630/genetic-causes-of-phenotypic-adaptation-to-the-second-fermentation-of-sparkling-wines-in-saccharomyces-cerevisiae
#6
Maria Martí-Raga, Emilien Peltier, Albert Mas, Gemma Beltran, Philippe Marullo
Hybridization is known to improve complex traits due to heterosis and phenotypic robustness. However, these phenomena have been rarely explained at the molecular level. Here, the genetic determinism of Saccharomyces cerevisiae fermentation performance was investigated using a QTL-mapping approach on an F1-progeny population. Three main QTLs were detected, with positive alleles coming from both parental strains. The heterosis effect found in the hybrid was partially explained by three loci showing pseudo-overdominance and dominance effect...
November 30, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27866151/genotyping-by-sequencing-based-investigation-of-the-genetic-architecture-responsible-for-a-7-fold-increase-in-soybean-seed-stearic-acid
#7
Crystal B Heim, Jason D Gillman
Soybean oil is highly unsaturated but oxidatively unstable, rendering it non-ideal for food applications. Until recently, the majority of soybean oil underwent partial chemical hydrogenation, which produces trans fats as an unavoidable consequence. Dietary intake of trans fats and most saturated fats are conclusively linked to negative impacts on cholesterol levels and cardiovascular health. Two major soybean oil breeding targets are : 1) to reduce or eliminate the need for chemical hydrogenation, and 2) to replace the functional properties of partially hydrogenated soybean oil...
November 18, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27866150/crispr-cas9-induced-double-strand-break-repair-in-arabidopsis-non-homologous-end-joining-mutants
#8
Hexi Shen, Gary D Strunks, Bart J P M Klemann, Paul J J Hooykaas, Sylvia de Pater
Double-strand breaks (DSBs) are one of the most harmful DNA lesions. Cells utilize two main pathways for DSB repair: homologous recombination (HR) and non-homologous end-joining (NHEJ). NHEJ can be subdivided into the KU-dependent classical NHEJ (c-NHEJ) and the more error-prone KU-independent backup-NHEJ (b-NHEJ) pathways, involving the poly (ADP-ribose) polymerases (PARPs). However, in absence of these factors, cells still seem able to adequately maintain genome integrity, suggesting the presence of other b-NHEJ repair factors or pathways independent from KU and PARPs...
November 18, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27866149/correlations-of-genotype-with-climate-parameters-suggest-caenorhabditis-elegans-niche-adaptations
#9
Kathryn S Evans, Yuehui Zhao, Shannon C Brady, Lijiang Long, Patrick T McGrath, Erik C Andersen
Species inhabit a variety of environmental niches, and the adaptation to a particular niche is often controlled by genetic factors, including gene-by-environment interactions. The genes that vary in order to regulate the ability to colonize a niche are often difficult to identify, especially in the context of complex ecological systems and in experimentally uncontrolled natural environments. Quantitative genetic approaches provide an opportunity to investigate correlations between genetic factors and environmental parameters that might define a niche...
November 18, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27866148/identification-of-genes-mediating-drosophila-follicle-cell-progenitor-differentiation-by-screening-for-modifiers-of-gal4-uas-variegation
#10
Ming-Chia Lee, Andrew D Skora, Allan C Spradling
The Drosophila melanogaster ovarian follicle cell lineage provides a powerful system for investigating how epigenetic changes contribute to differentiation. Downstream from an epithelial stem cell, follicle progenitors undergo nine mitotic cell cycles before transitioning to the endocycle and initiating differentiation. During their proliferative phase, follicle progenitors experience Lsd1-dependent changes in epigenetic stability that can be monitored using GAL4::UAS variegation. Eventually, follicle progenitors acquire competence to respond to Delta, a Notch ligand present in the environment, which signals them to cease division and initiate differentiation...
November 18, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27856697/caenorhabditis-elegans-daf-2-as-a-model-for-human-insulin-receptoropathies
#11
David A Bulger, Tetsunari Fukushige, Sijung Yun, Robert K Semple, John A Hanover, Michael W Krause
Human exome sequencing has dramatically increased the rate of identification of diseaseassociated polymorphisms. However, examining the functional consequences of those variants has created an analytic bottleneck. Insulin-like signaling in Caenorhabditis elegans has long provided a model to assess consequences of human insulin signaling mutations, but this has not been evaluated in the context of current genetic tools. We have exploited strains derived from the Million Mutation Project and gene editing to explore further the evolutionary relationships and conservation between the human and C...
November 18, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27856699/first-in-vivo-batrachochytrium-dendrobatidis-transcriptomes-reveal-mechanisms-of-host-exploitation-host-specific-gene-expression-and-expressed-genotype-shifts
#12
Amy R Ellison, Graziella V DiRenzo, Caitlin A McDonald, Karen R Lips, Kelly R Zamudio
For generalist pathogens, host species represent distinct selective environments, providing unique challenges for resource acquisition and defense from host immunity, potentially resulting in host-dependent differences in pathogen fitness. Gene expression modulation should be advantageous, responding optimally to a given host and mitigating the costs of generalism. Batrachochytrium dendrobatidis (Bd), a fungal pathogen of amphibians, shows variability in pathogenicity among isolates and within-strain virulence changes rapidly during serial passages through artificial culture...
November 16, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27856698/one-cell-doubling-evaluation-by-living-arrays-of-yeast-odelay
#13
Thurston Herricks, David J Dilworth, Fred D Mast, Song Li, Jennifer J Smith, Alexander V Ratushny, John D Aitchison
Cell growth is a complex phenotype widely used in systems biology to gauge the impact of genetic and environmental perturbations. Due to the magnitude of genome-wide studies, resolution is often sacrificed in favor of throughput, creating a demand for scalable, time-resolved, quantitative methods of growth assessment. We present ODELAY (One-cell Doubling Evaluation by Living Arrays of Yeast), an automated and scalable growth analysis platform. High measurement density and single cell resolution provide a powerful tool for large-scale multiparameter growth analysis based on the modeling of microcolony expansion on solid media...
November 16, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27856696/the-neurospora-transcription-factor-adv-1-transduces-light-signals-and-temporal-information-to-control-rhythmic-expression-of-genes-involved-in-cell-fusion
#14
Rigzin Dekhang, Cheng Wu, Kristina M Smith, Teresa M Lamb, Matthew Peterson, Erin L Bredeweg, Oneida Ibarra, Jillian M Emerson, Nirmala Karunarathna, Anna Lyubetskaya, Elham Azizi, Jennifer M Hurely, Jay C Dunlap, James E Galagan, Michael Freitag, Matthew S Sachs, Deborah Bell-Pedersen
Light and the circadian clock have a profound effect on the biology of organisms through the regulation of large sets of genes. Towards understanding how light and the circadian clock regulate gene expression, we used genome-wide approaches to identify the direct and indirect targets of the light-responsive and clock-controlled transcription factor ADV-1 in Neurospora crassa A large proportion of ADV-1 targets were found to be light and/or clock-controlled, and enriched for genes involved in development, metabolism, cell growth, and cell fusion...
November 16, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27856695/multiplex-shrna-screening-of-germ-cell-development-by-in-vivo-transfection-of-mouse-testis
#15
Nicholas R Y Ho, Abul R Usmani, Yan Yin, Liang Ma, Donald F Conrad
Spermatozoa are one of the few mammalian cells types that cannot be fully derived in vitro, severely limiting the application of modern genomic techniques to study germ cell biology. The current gold standard approach of characterizing single gene knockout mice is slow as generation of each mutant line can take 6-9 months. Here, we describe an in vivo approach to rapid functional screening of germline genes based on a new non-surgical, non-viral in vivo transfection method to deliver nucleic acids into testicular germ cells...
November 16, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27836908/dissecting-gene-expression-changes-accompanying-a-ploidy-based-phenotypic-switch
#16
Gareth A Cromie, Zhihao Tan, Michelle Hays, Eric W Jeffery, Aimee M Dudley
Aneuploidy, a state in which the chromosome number deviates from a multiple of the haploid count, significantly impacts human health. The phenotypic consequences of aneuploidy are believed to arise from gene expression changes associated with the altered copy number of genes on the aneuploid chromosomes. To dissect the mechanisms underlying altered gene expression in aneuploids, we used RNA-seq to measure transcript abundance in colonies of the haploid Saccharomyces cerevisiae strain F45 and two aneuploid derivatives harboring disomies of chromosomes XV and XVI...
November 15, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27852012/analysis-of-ribosome-associated-mrnas-in-rice-reveals-the-importance-of-transcript-size-and-gc-content-in-translation
#17
Dongyan Zhao, John P Hamilton, Michael Hardigan, Dongmei Yin, Tao He, Brieanne Vaillancourt, Mauricio Reynoso, Germain Pauluzzi, Scott Funkhouser, Yuehua Cui, Julia Bailey-Serres, Jiming Jiang, C Robin Buell, Ning Jiang
Gene expression is controlled at transcriptional and post-transcriptional levels including decoding of mRNA into polypeptides via ribosome-mediated translation. Translational regulation has been intensively studied in the model dicot plant Arabidopsis thaliana, and in this study, we assessed the translational status (proportion of steady-state mRNA associated with ribosomes) of mRNAs by Translating Ribosome Affinity Purification followed by mRNA-sequencing (TRAP-seq) in rice (Oryza sativa), a model monocot plant and the most important food crop...
November 14, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27852011/a-new-chicken-genome-assembly-provides-insight-into-avian-genome-structure
#18
Wesley C Warren, LaDeana W Hillier, Chad Tomlinson, Patrick Minx, Milinn Kremitzki, Tina Graves, Chris Markovic, Nathan Bouk, Kim D Pruitt, Francoise Thibaud-Nissen, Valerie Schneider, Tamer A Mansour, C Titus Brown, Aleksey Zimin, Rachel Hawken, Mitch Abrahamsen, Alexis B Pyrkosz, Mireille Morisson, Valerie Fillon, Alain Vignal, William Chow, Kerstin Howe, Janet E Fulton, Marcia M Miller, Peter Lovell, Claudio V Mello, Morgan Wirthlin, Andrew S Mason, Richard Kuo, David W Burt, Jerry B Dodgson, Hans H Cheng
The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3) built from combined long single molecule sequencing technology, finished BACs, and improved physical maps. In overall assembled bases, we see a gain of 183 Mb including 16.4 Mb in placed chromosomes with a corresponding gain in the percentage of intact repeat elements characterized...
November 14, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27836907/regulatory-architecture-of-gene-expression-variation-in-the-threespine-stickleback-gasterosteus-aculeatus
#19
Victoria L Pritchard, Heidi M Viitaniemi, R J Scott McCairns, Juha Merilä, Mikko Nikinmaa, Craig R Primmer, Erica H Leder
Much adaptive evolutionary change is underlain by mutational variation in regions of the genome that regulate gene expression rather than in the coding regions of the genes themselves. An understanding of the role of gene expression variation in facilitating local adaptation will be aided by an understanding of underlying regulatory networks. Here, we characterize the genetic architecture of gene expression variation in the threespine stickleback (Gasterosteus aculeatus), an important model in the study of adaptive evolution...
November 11, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27883312/time-course-analysis-of-gene-expression-during-the-saccharomyces-cerevisiae-hypoxic-response
#20
Nasrine Bendjilali, Samuel MacLeon, Gurmannat Kalra, Stephen D Willis, A K M Nawshad Hossian, Erica Avery, Olivia Wojtowicz, Mark J Hickman
Many cells experience hypoxia, or low oxygen, and respond by dramatically altering gene expression. In the yeast S. cerevisiae, genes that respond are required for many oxygen-dependent cellular processes, such as respiration, biosynthesis and redox regulation. To more fully characterize the global response to hypoxia, we exposed yeast to hypoxic conditions, extracted RNA at different times and performed RNA-seq analysis. Time-course statistical analysis revealed hundreds of genes that changed expression by up to 550-fold...
November 9, 2016: G3: Genes—Genomes—Genetics
journal
journal
43700
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"