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https://www.readbyqxmd.com/read/29150427/delayed-encounter-of-parental-genomes-can-lead-to-aneuploidy-in-saccharomyces%C3%A2-cerevisiae
#1
Alan Michael Tartakoff, David Dulce, Elizabeth Landis
We have investigated an extreme deviation from the norm of genome unification that occurs during mating in the yeast, Saccharomyces cerevisiae This deviation is encountered when yeast that carry a mutation of the spindle pole body protein, Kar1, are mated with wildtype cells. In this case, nuclear fusion is delayed and the genotypes of a fraction of zygotic progeny suggest that chromosomes have "transferred" between the parental nuclei in zygotes. This classic yet bizarre occurrence is routinely used to generate aneuploid (disomic) yeast...
November 17, 2017: Genetics
https://www.readbyqxmd.com/read/29146582/elucidation-of-the-two-h3k36me3-histone-methyltransferases-set2-and-ash1-in-fusarium-fujikuroi-unravels-their-different-chromosomal-targets-and-a-major-impact-of-ash1-on-genome-stability
#2
Slavica Janevska, Leonie Baumann, Christian M K Sieber, Martin Münsterkötter, Jonas Ulrich, Jörg Kämper, Ulrich Güldener, Bettina Tudzynski
In this work, we present a comprehensive analysis of the H3K36 histone methyltransferases Set2 and Ash1 in the filamentous ascomycete Fusarium fujikuroi In Saccharomyces cerevisiae, one single methyltransferase, Set2, confers all H3K36 methylation, while there are two members of the Set2 family in filamentous fungi, and even more H3K36 methyltransferases in higher eukaryotes. Whereas the yeast Set2 homolog has been analyzed in fungi previously, the second member of the Set2 family, designated Ash1, has not been described for any filamentous fungus...
November 16, 2017: Genetics
https://www.readbyqxmd.com/read/29141909/local-fitness-landscapes-predict-yeast-evolutionary-dynamics-in-directionally-changing-environments
#3
Florien A Gorter, Mark G M Aarts, Bas J Zwaan, J Arjan G M de Visser
The fitness landscape is a concept that is widely used for understanding and predicting evolutionary adaptation. The topography of the fitness landscape depends critically on the environment, with potentially far-reaching consequences for evolution under changing conditions. However, few studies have assessed directly how empirical fitness landscapes change across conditions, or validated the predicted consequences of such change. We previously evolved replicate yeast populations in the presence of either gradually increasing or constant high concentrations of the heavy metals cadmium (Cd), nickel (Ni), and zinc (Zn), and analysed their phenotypic and genomic changes...
November 15, 2017: Genetics
https://www.readbyqxmd.com/read/29141908/two-distinct-regulatory-mechanisms-of-transcriptional-initiation-in-response-to-nutrient-signaling
#4
Jannatul Ferdoush, Rwik Sen, Amala Kaja, Priyanka Barman, Sukesh R Bhaumik
SAGA (Spt-Ada-Gcn5-Acetyltransferase) and TFIID (transcription factor IID) have been previously shown to facilitate the PIC (pre-initiation complex) formation at the promoters of two distinct sets of genes. Here, we demonstrate that TFIID and SAGA differentially participate in stimulation of the PIC formation (and hence transcriptional initiation) at the promoter of PHO84, a gene for high affinity inorganic phosphate (Pi) transporter for crucial cellular functions, in response to nutrient signaling. We show that transcriptional initiation of PHO84 occurs predominantly in the TFIID-dependent manner in the absence of Pi in the growth medium...
November 15, 2017: Genetics
https://www.readbyqxmd.com/read/29138255/complex-history-and-differentiation-patterns-of-the-t-haplotype-a-mouse-meiotic-driver
#5
Reka K Kelemen, Beatriz Vicoso
The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history...
November 14, 2017: Genetics
https://www.readbyqxmd.com/read/29138254/estimating-realized-heritability-in-panmictic-populations
#6
Milan Lstibůrek, Václav Bittner, Gary R Hodge, Jan Picek, Trudy F C Mackay
Narrow sense heritability (h(2) ) is a key concept in quantitative genetics, as it expresses the proportion of the observed phenotypic variation that is transmissible from parents to offspring. h(2) determines the resemblance among relatives and the rate of response to artificial and natural selection. Classical methods for estimating h(2) use random samples of individuals with known relatedness, as well as response to artificial selection, when it is called realized heritability. Here, we present a method for estimating realized h(2) based on a simple assessment of a random-mating population with no artificial manipulation of the population structure, and derive standard errors of the estimates...
November 14, 2017: Genetics
https://www.readbyqxmd.com/read/29133298/functional-redundancy-of-variant-and-canonical-histone-h3-lysine-9-modification-in-drosophila
#7
Taylor J R Penke, Daniel J McKay, Brian D Strahl, A Gregory Matera, Robert J Duronio
Histone post-translational modifications (PTMs) and differential incorporation of variant and canonical histones into chromatin are central modes of epigenetic regulation. Despite similar protein sequences, histone variants are enriched for different suites of PTMs compared to their canonical counterparts. For example, variant histone H3.3 occurs primarily in transcribed regions and is enriched for "active" histone PTMs like Lys9 acetylation (H3.3K9ac), whereas the canonical histone H3 is enriched for Lys9 methylation (H3K9me), which is found in transcriptionally silent heterochromatin...
November 13, 2017: Genetics
https://www.readbyqxmd.com/read/29127264/protein-moonlighting-revealed-by-non-catalytic-phenotypes-of-yeast-enzymes
#8
Adriana Espinosa-Cantú, Diana Ascencio, Selene Herrera-Basurto, Jiewei Xu, Assen Roguev, Nevan J Krogan, Alexander DeLuna
A single gene can partake in several biological processes, and therefore gene deletions can lead to different-sometimes unexpected-phenotypes. However, it is not always clear whether such pleiotropy reflects the loss of a unique molecular activity involved in different processes or the loss of a multifunctional protein. Here, using Saccharomyces cerevisiae metabolism as a model, we systematically test the null hypothesis that enzyme phenotypes depend on a single annotated molecular function, namely their catalysis...
November 10, 2017: Genetics
https://www.readbyqxmd.com/read/29127263/coalescent-processes-with-skewed-offspring-distributions-and-non-equilibrium-demography
#9
Sebastian Matuszewski, Marcel E Hildebrandt, Guillaume Achaz, Jeffrey D Jensen
Non-equilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history...
November 10, 2017: Genetics
https://www.readbyqxmd.com/read/29127262/evidence-for-selection-by-environment-but-not-genotype-by-environment-interactions-for-fitness-related-traits-in-a-wild-mammal-population
#10
Adam Hayward, Josephine M Pemberton, Camillo Berenos, Alastair J Wilson, Jill G Pilkington, Loeske E B Kruuk
How do environmental conditions influence selection and genetic variation in wild populations? There is widespread evidence for selection-by-environment interactions (S*E), but we reviewed studies of natural populations estimating the extent of genotype-by-environment interactions (G*E) in response to natural variation in environmental conditions, and found that evidence for G*E appears to be rare within single populations in the wild. Studies estimating the simultaneous impact of environmental variation on both selection and genetic variation are especially scarce...
November 10, 2017: Genetics
https://www.readbyqxmd.com/read/29122827/fitness-costs-and-variation-in-transmission-distortion-associated-with-the-abnormal-chromosome-10-meiotic-drive-system-in-maize
#11
David M Higgins, Elizabeth G Lowry, Lisa B Kanizay, Philip W Becraft, David W Hall, R Kelly Dawe
Meiotic drive describes a process whereby selfish genetic elements are transmitted at levels greater than Mendelian expectations. Maize abnormal chromosome 10 (Ab10) encodes a meiotic drive system that exhibits strong preferential segregation through female gametes. We performed transmission assays of nine Ab10 chromosomes from landraces and teosinte lines and found a transmission advantage of 62% to 79% in heterozygotes. Despite this transmission advantage, Ab10 is present at low frequencies in natural populations, suggesting that it carries large negative fitness consequences...
November 9, 2017: Genetics
https://www.readbyqxmd.com/read/29113979/more-than-one-way-in-three-gln3-sequences-required-to-relieve-negative-ure2-regulation-and-support-nuclear-gln3-import-in-saccharomyces-cerevisiae
#12
Jennifer J Tate, Rajendra Rai, Terrance G Cooper
Gln3 is responsible for Nitrogen Catabolite Repression-sensitive transcriptional activation in the yeast Saccharomyces cerevisiae In nitrogen-replete medium, Gln3 is cytoplasmic and NCR-sensitive transcription is repressed. In nitrogen-limiting medium, in cells treated with TorC1 inhibitor, rapamycin or glutamine synthetase inhibitor, methionine sulfoximine (Msx), Gln3 becomes highly nuclear and NCR-sensitive transcription derepressed. Previously, nuclear Gln3 localization was concluded to be mediated by a single nuclear localization sequence, NLS1...
November 7, 2017: Genetics
https://www.readbyqxmd.com/read/29113978/additive-phenotypes-underlie-epistasis-of-fitness-effects
#13
Andrew M Sackman, Darin R Rokyta
Gene interactions, or epistasis, play a large role in determining evolutionary outcomes. The ruggedness of fitness landscapes, and thus the predictability of evolution and the accessibility of high-fitness genotypes, is determined largely by the pervasiveness of epistasis and the degree of correlation between similar genotypes. We created all possible pairings of three sets of five beneficial first-step mutations fixed during adaptive walks under three different regimes: selection on growth rate alone, on growth rate and thermal stability, and on growth rate and pH stability...
November 7, 2017: Genetics
https://www.readbyqxmd.com/read/29109180/isolation-of-aggressive-behavior-mutants-in-drosophila%C3%A2-using-a-screen-for-wing-damage
#14
Shaun M Davis, Amanda L Thomas, Lingzhi Liu, Ian M Campbell, Herman A Dierick
Aggression is a complex social behavior that is widespread in nature. To date only a limited number of genes that affect aggression have been identified, in large part because the complexity of the phenotype makes screening difficult and time consuming regardless of the species that is studied. We discovered that aggressive group-housed Drosophila melanogaster males inflict damage on each other's wings, and show that wing damage negatively affects their ability to fly and mate. Using this wing-damage phenotype, we screened males from ~1,400 chemically mutagenized strains and found ~40 mutant strains with substantial wing damage...
November 6, 2017: Genetics
https://www.readbyqxmd.com/read/29109179/why-publish-in-scientific-society-journals
#15
Mark Johnston
Publication of scientific studies is the primary product of science. But scholarly publishing is in a state of flux-some would even say dysfunction. How did we get here?
November 6, 2017: Genetics
https://www.readbyqxmd.com/read/29097405/the-evolution-of-gene-specific-transcriptional-noise-is-driven-by-selection-at-the-pathway-level
#16
Gustavo Valadares Barroso, Natasa Puzovic, Julien Y Dutheil
Biochemical reactions within individual cells result from the interactions of molecules, typically in small numbers. Consequently, the inherent stochasticity of binding and diffusion processes generate noise along the cascade that leads to the synthesis of a protein from its encoding gene. As a result, isogenic cell populations display phenotypic variability even in homogeneous environments. The extent and consequences of this stochastic gene expression have only recently been assessed on a genome-wide scale, in particular owing to the advent of single cell transcriptomics...
November 2, 2017: Genetics
https://www.readbyqxmd.com/read/29092889/a-statistically-oriented-asymmetric-localization-soal-model-for-neuronal-outgrowth-patterning-by-caenorhabditis-elegans-unc-5-unc5-and-unc-40-dcc-netrin-receptors
#17
Gerard Limerick, Xia Tang, Won Suk Lee, Ahmed Mohamed, Aseel Al-Aamiri, William G Wadsworth
Neurons extend processes that vary in number, length, and direction of outgrowth. Extracellular cues help determine outgrowth patterns. In Caenorhabditis elegans, neurons respond to the extracellular UNC-6 (netrin) cue via UNC-40 (DCC) and UNC-5 (UNC5) receptors. Previously we presented evidence that UNC-40 asymmetric localization at the plasma membrane is self-organizing and that UNC-40 can localize and mediate outgrowth at randomly selected sites. Here we provide further evidence for a statistically oriented asymmetric localization (SOAL) model in which UNC-5 receptor activity affects patterns of axon outgrowth by regulating UNC-40 asymmetric localization...
November 1, 2017: Genetics
https://www.readbyqxmd.com/read/29084817/construction-of-comprehensive-dosage-matching-core-histone-mutant-libraries-for-saccharomyces-cerevisiae
#18
Shuangying Jiang, Yan Liu, Ann Wang, Yiran Qin, Maoguo Luo, Qingyu Wu, Jef D Boeke, Junbiao Dai
Saccharomyces cerevisiae contains two genes for each core histone, which are presented as pairs under the control of a divergent promoter, i.e. HHT1-HHF1, HHT2-HHF2, HTA1-HTB1 and HTA2-HTB2HHT1-HHF1 and HHT2-HHF2 encode histone H3 and H4 with identical amino acid sequences but under the control of differently regulated promoters. Previous mutagenesis studies were carried out by deleting one pair and mutating the other one. Here we present the design and construction of three additional libraries covering HTA1-HTB1, HTA2-HTB2 and HHT1-HHF1 respectively...
October 30, 2017: Genetics
https://www.readbyqxmd.com/read/29074555/efficient-prioritization-of-multiple-causal-eqtl-variants-via-sparse-polygenic-modeling
#19
Naoki Nariai, William W Greenwald, Christopher DeBoever, He Li, Kelly A Frazer
Expression quantitative trait loci (eQTL) studies have typically used single-variant association analysis to identify genetic variants correlated with gene expression. However, this approach has several drawbacks: causal variants cannot be distinguished from non-functional variants in strong linkage disequilibrium, combined effects from multiple causal variants cannot be captured, and low-frequency (<5% MAF) eQTL variants are difficult to identify. While these issues possibly could be overcome by using sparse polygenic models which associate multiple genetic variants with gene expression simultaneously, the predictive performance of these models for eQTL studies has not been evaluated...
October 26, 2017: Genetics
https://www.readbyqxmd.com/read/29066469/polygenicity-and-epistasis-underlie-fitness-proximal-traits-in-the-caenorhabditis-elegans-multiparental-experimental-evolution-cemee-panel
#20
Luke M Noble, Ivo Chelo, Thiago Guzella, Bruno Afonso, David D Riccardi, Patrick Ammerman, Adel Dayarian, Sara Carvalho, Anna Crist, Ania Pino-Querido, Boris Shraiman, Matthew V Rockman, Henrique Teotónio
Understanding the genetic basis of complex traits remains a major challenge in biology. Polygenicity, phenotypic plasticity and epistasis contribute to phenotypic variance in ways that are rarely clear. This uncertainty can be problematic for estimating heritability, for predicting individual phenotypes from genomic data, and for parameterizing models of phenotypic evolution. Here we report an advanced recombinant inbred line (RIL) quantitative trait locus (QTL) mapping panel for the hermaphroditic nematode Caenorhabditis elegans, the C...
October 24, 2017: Genetics
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