journal
MENU ▼
Read by QxMD icon Read
search

Genetics

journal
https://www.readbyqxmd.com/read/29773560/establishment-of-locally-adapted-mutations-under-divergent-selection
#1
Matteo Tomasini, Stephan Peischl
We study the establishment probabilities of locally adapted mutations using a multi-type branching process framework. We find a surprisingly simple and intuitive analytical approximation for the establishment probabilities in a symmetric two-deme model under the assumption of weak (positive) selection. This is the first analytical closed-form approximation for arbitrary migration rate to appear in the literature. We find that the establishment probability lies between the weak and the strong migration limits if we condition the origin of the mutation to the deme where it is advantageous...
May 17, 2018: Genetics
https://www.readbyqxmd.com/read/29773559/serrate-notch-signaling-regulates-the-size-of-the-progenitor-cell-pool-in-drosophila-imaginal-rings
#2
Sheng-An Yang, Wu-Min Deng
Drosophila imaginal rings are larval tissues composed of progenitor cells that are essential for the formation of adult foreguts, hindguts and salivary glands. Specified from subsets of ectoderm in the embryo, imaginal ring cells are kept quiescent until mid-second larval instar, and undergo rapid proliferation during the third instar to attain adequate numbers of cells that will replace apoptotic larval tissues for adult organ formation. Here we show that Notch signaling is activated in all three imaginal rings from middle embryonic stage to early pupal stage and that Notch signaling positively controls cell proliferation in all three imaginal rings during the third larval instar...
May 17, 2018: Genetics
https://www.readbyqxmd.com/read/29769284/dynamic-copy-number-evolution-of-x-and-y-linked-ampliconic-genes-in-human-populations
#3
Elise A Lucotte, Laurits Skov, Jacob Malte Jensen, Moisès Coll Macià, Kasper Munch, Mikkel H Schierup
Ampliconic genes are multicopy, in majority found on sex-chromosomes and enriched for testis-expressed genes. While ampliconic genes have been associated with the emergence of hybrid incompatibilities, we know little about their copy number distribution and their turnover in human populations. Here we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read-depth on modified X and Y chromosome targets containing only one repetition of each ampliconic gene...
May 16, 2018: Genetics
https://www.readbyqxmd.com/read/29769283/-hermes-transposon-mutagenesis-shows-ure3-prion-pathology-prevented-by-a-ubiquitin-targeting-protein-evidence-for-carbon-nitrogen-assimilation-cross-talk-and-a-second-function-for-ure2p-in-saccharomyces-cerevisiae
#4
Herman K Edskes, Maryam Mukhamedova, Bouke K Edskes, Reed B Wickner
[URE3] is an amyloid-based prion of Ure2p, a regulator of nitrogen catabolism. While most variants of the [URE3] prion are toxic, mild variants that only slightly slow growth are more widely studied. The existence of several anti-prion systems suggests that some components may be protecting cells from potential detrimental effects of mild [URE3] variants. Our extensive Hermes transposon mutagenesis showed that disruption of YLR352W dramatically slows growth of [URE3-1] strains. Ylr352wp is an F-box protein, directing selection of substrates for ubiquitination by a cullin-containing E-3 ligase...
May 16, 2018: Genetics
https://www.readbyqxmd.com/read/29769282/inferring-the-probability-of-the-derived-versus-the-ancestral-allelic-state-at-a-polymorphic-site
#5
Peter D Keightley, Benjamin C Jackson
It is known that the allele ancestral to the variation at a polymorphic site cannot be assigned with certainty, and that the most frequently used method to assign the ancestral state - maximum parsimony - is prone to misinference. Estimates of counts of sites that have a certain number of copies of the derived allele in a sample (the unfolded site frequency spectrum, uSFS) made by parsimony are therefore also biased. We previously developed a maximum likelihood method to estimate the uSFS for a focal species using information from two outgroups while assuming simple models of nucleotide substitution...
May 16, 2018: Genetics
https://www.readbyqxmd.com/read/29764901/the-histone-demethylase-kdm5-is-essential-for-larval-growth-in-drosophila
#6
Coralie Drelon, Helen M Belalcazar, Julie Secombe
Regulated gene expression is necessary for developmental and homeostatic processes. The KDM5 family of transcriptional regulators are histone H3 lysine 4 demethylases that can function through both demethylase-dependent and independent mechanisms. While loss and overexpression of KDM5 proteins are linked to intellectual disability and cancer, respectively, their normal developmental functions remain less characterized. Drosophila melanogaster provides an ideal system to investigate KDM5 function, as it encodes a single ortholog in contrast to the four paralogs found in mammalian cells...
May 15, 2018: Genetics
https://www.readbyqxmd.com/read/29752291/an-association-mapping-framework-to-account-for-potential-sex-difference-in-genetic-architectures
#7
Eun Yong Kang, Cue Hyunkyu Lee, Nicholas A Furlotte, Jong Wha J Joo, Emrah Kostem, Noah Zaitlen, Eleazar Eskin, Buhm Han
Over the past few years, genome-wide association studies have identified many trait-associated loci that have different effects on females and males, which increased attention to the genetic architecture differences between the sexes. The between-sex differences in genetic architectures can cause a variety of phenomena such as differences in the effect sizes at trait-associated loci, differences in the magnitudes of polygenic background effects, and differences in the phenotypic variances. However, current association testing approaches for dealing with sex, such as including sex as a covariate, cannot fully account for these phenomena and can be suboptimal in statistical power...
May 11, 2018: Genetics
https://www.readbyqxmd.com/read/29743175/genomic-model-with-correlation-between-additive-and-dominance-effects
#8
Tao Xiang, Ole Fredslund Christensen, Zulma Gladis Vitezica, Andres Legarra
Dominance genetic effects are rarely included in pedigree-based genetic evaluation. With the availability of single nucleotide polymorphism markers and the development of genomic evaluation, estimates of dominance genetic effects have become feasible using genomic best linear unbiased prediction (GBLUP). Usually, studies involving additive and dominance genetic effects ignore possible relationships between them. It has been often suggested that the magnitude of functional additive and dominance effects at the quantitative trait loci are related, but there is no existing GBLUP-like approach accounting for such correlation...
May 9, 2018: Genetics
https://www.readbyqxmd.com/read/29739818/spermiogenesis-and-male-fertility-require-the-function-of-suppressor-of-hairy-wing-in-somatic-cyst-cells-of-drosophila
#9
Tingting Duan, Pamela K Geyer
Drosophila Suppressor of Hairy-wing [Su(Hw)] protein is an example of a multivalent transcription factor. Although best known for its role in establishing the chromatin insulator of the gypsy retrotransposon, Su(Hw) functions as an activator and repressor at non- gypsy genomic sites. It remains unclear how the different regulatory activities of Su(Hw) are utilized during development. Motivated from observations of spatially restricted expression of Su(Hw) in the testis, we investigated the role of Su(Hw) in spermatogenesis to advance an understanding of its developmental contributions as an insulator, repressor and activator protein...
May 8, 2018: Genetics
https://www.readbyqxmd.com/read/29739817/comparison-of-genotypic-and-phenotypic-correlations-cheverud-s-conjecture-in-humans
#10
Sebastian M Sodini, Kathryn E Kemper, Naomi R Wray, Maciej Trzaskowski
Accurate estimation of genetic correlation requires large sample sizes and access to genetically informative data, which are not always available. Accordingly, phenotypic correlations are often assumed to reflect genotypic correlations in evolutionary biology. Cheverud's conjecture asserts that the use of phenotypic correlations as proxies for genetic correlations is appropriate. Empirical evidence of the conjecture has been found across plant and animal species, with results suggesting that there is indeed a robust relationship between the two...
May 8, 2018: Genetics
https://www.readbyqxmd.com/read/29735720/calcineurin-regulatory-subunit-calcium-binding-domains-differentially-contribute-to-calcineurin-signaling-in-saccharomyces-cerevisiae
#11
Sean Connolly, Devona Quasi-Woode, Laura Waldron, Christian Eberly, Kerri Waters, Eric M Muller, Tami J Kingsbury
The protein phosphatase calcineurin is central to Ca2+ signaling pathways from yeast to humans. Full activation of calcineurin requires Ca2+ binding to the regulatory subunit CNB, comprised of four Ca2+ -binding EF hand domains, and recruitment of Ca2+ -calmodulin. Here we report the consequences of disrupting Ca2+ binding to individual Cnb1 EF hand domains on calcineurin function in Saccharomyces cerevisiae Calcineurin activity was monitored via quantitation of the calcineurin-dependent reporter gene, CDRE -lacZ, and calcineurin-dependent growth under conditions of environmental stress...
May 7, 2018: Genetics
https://www.readbyqxmd.com/read/29728367/integration-of-enhancer-promoter-interactions-with-gwas-summary-results-identifies-novel-schizophrenia-associated-genes-and-pathways
#12
Chong Wu, Wei Pan
It remains challenging to boost statistical power of GWAS to identify more risk variants or loci that can account for "missing heritability". Furthermore, since most identified variants are not in gene coding regions, a biological interpretation of their function largely lacks. On the other hand, recent biotechnological advances have made it feasible to experimentally measure the three-dimensional organization of the genome, including enhancer-promoter interactions in high resolutions. Due to the well known critical roles of enhancer-promoter interactions in regulating gene expression programs, such data have been applied to link GWAS risk variants to their putative target genes, gaining insights into underlying biological mechanisms...
May 4, 2018: Genetics
https://www.readbyqxmd.com/read/29724862/rapid-phenotypic-and-genotypic-diversification-after-exposure-to-the-oral-host-niche-in-candida-albicans
#13
Anja Forche, Gareth Cromie, Aleeza C Gerstein, Norma V Solis, Tippapha Pisithkul, Waracharee Srifa, Eric Jeffery, Darren Abbey, Scott G Filler, Aimée M Dudley, Judith Berman
In vitro studies suggest that stress may generate random standing variation, and that different cellular and ploidy states may evolve more rapidly under stress. Yet this idea has not been tested with pathogenic fungi growing within their host niche in vivo Here, we analyzed the generation of both genotypic and phenotypic diversity during exposure of Candida albicans to the mouse oral cavity. Ploidy, aneuploidy, loss of heterozygosity (LOH) and recombination were determined using flow cytometry and ddRADseq...
May 3, 2018: Genetics
https://www.readbyqxmd.com/read/29724861/high-amplitude-circadian-rhythms-in-drosophila-driven-by-calcineurin-mediated-post-translational-control-of-sarah
#14
Sin Ho Kweon, Jongbin Lee, Chunghun Lim, Joonho Choe
Post-translational control is a crucial mechanism for circadian timekeeping. Evolutionarily conserved kinases and phosphatases have been implicated in circadian phosphorylation and degradation of clock-relevant proteins, which sustain high-amplitude rhythms with 24 hr periodicity in animal behaviors and physiology. Here, we report a novel clock function of the heterodimeric Ca2+ /calmodulin-dependent phosphatase calcineurin and its regulator sarah ( sra ) in Drosophila Genomic deletion of the sra locus dampened circadian locomotor activity rhythms in free-running constant dark after entrainment in light-dark cycles...
May 3, 2018: Genetics
https://www.readbyqxmd.com/read/29716955/evolutionary-pathways-for-the-generation-of-new-self-incompatibility-haplotypes-in-a-non-self-recognition-system
#15
Katarína Boďová, Tadeas Priklopil, David L Field, Nicholas H Barton, Melinda Pickup
Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification...
April 30, 2018: Genetics
https://www.readbyqxmd.com/read/29695490/acetylation-dependent-recruitment-of-the-fact-complex-and-its-role-in-regulating-pol-ii-occupancy-genome-wide-in-saccharomyces-cerevisiae
#16
Rakesh Pathak, Priyanka Singh, Sudha Ananthakrishnan, Sarah Adamczyk, Olivia Schimmel, Chhabi K Govind
Histone chaperones, chromatin remodelers, and histone modifying complexes play a critical role in alleviating the nucleosomal barrier for DNA-dependent processes. Here, we have examined the role of two highly conserved yeast ( Saccharomyces cerevisiae ) histone chaperones, FACT and Spt6, in regulating transcription. We show that the H3 tail contributes to the recruitment of FACT to coding sequences in a manner dependent on acetylation. We found that deleting a H3 HAT Gcn5 or mutating lysines on the H3 tail impairs FACT recruitment at ADH1 and ARG1 genes...
April 25, 2018: Genetics
https://www.readbyqxmd.com/read/29692350/the-evolution-of-polymorphic-hybrid-incompatibilities-in-house-mice
#17
Erica L Larson, Dan Vanderpool, Brice A J Sarver, Colin Callahan, Sara Keeble, Lorraine P Provencio, Michael D Kessler, Vanessa Stewart, Erin Nordquist, Matthew D Dean, Jeffrey M Good
Resolving the mechanistic and genetic bases of reproductive barriers between species is essential to understanding the evolutionary forces that shape speciation. Intrinsic hybrid incompatibilities are often treated as fixed between species, yet there can be considerable variation in the strength of reproductive isolation between populations. The extent and causes of this variation remain poorly understood in most systems. We investigated the genetic basis of variable hybrid male sterility (HMS) between two recently diverged subspecies of house mice, Mus musculus domesticus and M...
April 24, 2018: Genetics
https://www.readbyqxmd.com/read/29678830/regulation-of-cell-to-cell-communication-and-cell-wall-integrity-by-a-network-of-map-kinase-pathways-and-transcription-factors-in-neurospora-crassa
#18
Monika S Fischer, Vincent W Wu, Ji E Lee, Ronan C O'Malley, N Louise Glass
Maintenance of cell integrity and cell-to-cell communication are fundamental biological processes. Filamentous fungi, such as Neurospora crassa , depend on communication to locate compatible cells, coordinate cell fusion, and establish a robust hyphal network. Two MAP-Kinase pathways are essential for communication and cell fusion in N. crassa ; the Cell Wall Integrity/MAK-1 pathway and the MAK-2 (signal response) pathway. Previous studies have demonstrated several points of cross talk between the MAK-1 and MAK-2 pathways, which is likely necessary for coordinating chemotropic growth toward an extracellular signal, and then mediating cell fusion...
April 20, 2018: Genetics
https://www.readbyqxmd.com/read/29674520/improved-use-of-small-reference-panels-for-conditional-and-joint-analysis-with-gwas-summary-statistics
#19
Yangqing Deng, Wei Pan
Due to issues of practicality and confidentiality of genomic data-sharing on a large scale, typically only meta- or mega-analyzed GWAS summary data, not individual-level data, are publicly available. Re-analyses of such GWAS summary data for a wide range of applications have become more and more common and useful, which often require the use of an external reference panel with individual-level genotypic data to infer linkage disequilibrium (LD) among genetic variants. However, with a small sample size in only hundreds, as for the most popular 1000 Genomes Project European sample, estimation errors for LD are not negligible, leading to often dramatically increased numbers of false positives in subsequent analyses of GWAS summary data...
April 19, 2018: Genetics
https://www.readbyqxmd.com/read/29674519/discovery-of-lineage-specific-genome-change-in-rice-through-analysis-of-resequencing-data
#20
Robert A Arthur, Jeffrey L Bennetzen
Genome comparisons provide information on the nature of genetic change, but such comparisons are challenged to differentiate the importance of the actual sequence change processes relative to the role of selection. This problem can be overcome by identifying changes that have not yet had the time to undergo millions of years of natural selection. We describe a strategy to discover accession-specific changes in the rice genome using an abundant resource routinely provided for many genome analyses, resequencing data...
April 19, 2018: Genetics
journal
journal
23713
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"