journal
MENU ▼
Read by QxMD icon Read
search

Genetics

journal
https://www.readbyqxmd.com/read/28526698/improving-response-in-genomic-selection-with-a-population-based-selection-strategy-optimal-population-value-selection
#1
Matthew Goiffon, Aaron Kusmec, Lizhi Wang, Guiping Hu, Patrick Schnable
Genomic selection (GS) identifies individuals for inclusion in breeding programs based on the sum of their estimated marker effects or genomic estimated breeding values (GEBVs). Due to significant correlation between GEBVs and true breeding values, this has resulted in enhanced rates of genetic gain as compared to traditional methods of selection. Three extensions to GS, weighted genomic selection (WGS), optimal haploid value (OHV) selection, and genotype building (GB) selection have been proposed to improve long-term response and to facilitate the efficient development of doubled haploids...
May 19, 2017: Genetics
https://www.readbyqxmd.com/read/28522541/a-novel-histone-crosstalk-pathway-important-for-regulation-of-uv-induced-dna-damage-repair-in-saccharomyces-cerevisiae
#2
Anna L Boudoures, Jacob J Pfeil, Elizabeth M Steenkiste, Rachel A Hoffman, Elizabeth A Bailey, Sara E Wilkes, Sarah K Higdon, Jeffrey S Thompson
Histone post-translational modifications play vital roles in a variety of nuclear processes, including DNA repair. It has been previously shown that histone H3K79 methylation is important for the cellular response to DNA damage caused by ultraviolet (UV) radiation, with evidence that specific methylation states play distinct roles in UV repair. Here we report that H3K79 methylation is reduced in response to UV exposure in Saccharomyces cerevisiae This reduction is specific to the dimethylated state, as trimethylation levels are minimally altered by UV exposure...
May 18, 2017: Genetics
https://www.readbyqxmd.com/read/28522540/orthogonal-estimates-of-variances-for-additive-dominance-and-epistatic-effects-in-populations
#3
Z G Vitezica, A Legarra, M A Toro, L Varona
Genomic prediction methods based on multiple markers have potential to include non-additive effects in prediction and analysis of complex traits. However, most developments assume Hardy-Weinberg equilibrium (HWE). Statistical approaches for genomic selection that account for dominance and epistasis in a general context, without assuming HWE (e.g. crosses or homozygous lines), are therefore needed. Our method expands the NOIA orthogonal approach, that builds incidence matrices based on genotypic (not allelic) frequencies, to include genome-wide epistasis for an arbitrary number of interacting loci in a genomic evaluation context...
May 18, 2017: Genetics
https://www.readbyqxmd.com/read/28515212/regulation-of-wnt-signaling-at-the-neuromuscular-junction-by-the-immunoglobulin-super-family-protein-rig-3-in-caenorhabditis-elegans
#4
Pratima Pandey, Ashwani Bhardwaj, Kavita Babu
Perturbations in synaptic function could affect the normal behavior of an animal, making it important to understand the regulatory mechanisms of synaptic signaling. Previous work has shown that in Caenorhabditis elegans an immunoglobulin super-family protein, RIG-3, functions in pre-synaptic neurons to maintain normal acetylcholine receptor levels at the neuromuscular junction (NMJ). In this study we elucidate the molecular and functional mechanism of RIG-3. We demonstrate by genetic and BiFC (Bi-molecular Fluorescence Complementation) assays that pre-synaptic RIG-3 functions by directly interacting with the immunoglobulin domain of the non-conventional Wnt receptor, ROR receptor tyrosine kinase (RTK), CAM-1, that functions in post-synaptic body-wall muscles...
May 17, 2017: Genetics
https://www.readbyqxmd.com/read/28515211/functional-equivalence-of-the-sox2-and-sox3-transcription-factors-in-the-developing-mouse-brain-and-testes
#5
Fatwa Adikusuma, Daniel Pederick, Dale McAninch, James Hughes, Paul Thomas
Gene duplication provides spare genetic material that evolution can craft into new functions. Sox2 and Sox3 are evolutionarily-related genes with overlapping and unique sites of expression during embryogenesis. It is currently unclear whether SOX2 and SOX3 have identical or different functions. Here we use CRISPR/Cas9-assisted mutagenesis to perform a gene-swap, replacing the Sox3 ORF with the Sox2 ORF to investigate their functional equivalence in the brain and testes. We show that increased expression of SOX2 can functionally replace SOX3 in the development of the infundibular recess/ventral diencephalon and largely rescues pituitary gland defects that occur in Sox3 null mice...
May 17, 2017: Genetics
https://www.readbyqxmd.com/read/28512187/neutral-competition-for-drosophila-follicle-and-cyst-stem-cell-niches-requires-vesicle-trafficking-genes
#6
Matthew S Cook, Coralie Cazin, Marc Amoyel, Shinya Yamamoto, Erika Bach, Todd Nystul
The process of selecting for cellular fitness through competition plays a critical role in both development and disease. The germarium, a structure at the tip of the ovariole of a Drosophila ovary, contains two follicle stem cells (FSCs) that undergo neutral competition for the stem cell niche. Using the FSCs as a model, we performed a genetic screen through a collection of 126 mutants in essential genes on the X chromosome to identify candidates that increase or decrease competition for the FSC niche. We identified approximately 55% and 6% of the mutations screened as putative FSC hypo- or hypercompetitors, respectively...
May 16, 2017: Genetics
https://www.readbyqxmd.com/read/28512186/building-ultra-high-density-linkage-maps-based-on-efficient-filtering-of-trustable-markers
#7
Yefim I Ronin, David I Mester, Dina G Minkov, Eduard Akhunov, Abracham B Korol
The study is focused on addressing the problem of building genetic maps in the presence of ~10(3)-10(4) of markers per chromosome. We consider a spectrum of situations with intrachromosomal heterogeneity of recombination rate, different level of genotyping errors, and missing data. In the ideal scenario of the absence of errors and missing data, the majority of markers should appear as groups of co-segregating markers ("twins") representing no challenge for map construction. The central aspect of the proposed approach is to take into account the structure of the marker space, where each twin group (TG) and singleton markers are represented as points of this space...
May 16, 2017: Genetics
https://www.readbyqxmd.com/read/28512185/cap-n-collar-promotes-tissue-regeneration-by-regulating-ros-and-jnk-signaling-in-the-drosophila-wing-imaginal-disc
#8
Amanda R Brock, Mabel Seto, Rachel K Smith-Bolton
Regeneration is a complex process that requires an organism to recognize and repair tissue damage, as well as grow and pattern new tissue. Here we describe a genetic screen to identify novel regulators of regeneration. We ablated the Drosophila melanogaster larval wing primordium by inducing apoptosis in a spatially and temporally controlled manner and allowed the tissue to regenerate and repattern. To identify genes that regulate regeneration, we carried out a dominant modifier screen by assessing the amount and quality of regeneration in adult wings heterozygous for isogenic deficiencies...
May 16, 2017: Genetics
https://www.readbyqxmd.com/read/28495961/an-evolutionarily-conserved-role-of-presenilin-in-neuronal-protection-in-the-aging-drosophila-brain
#9
Jongkyun Kang, Sarah Shin, Norbert Perrimon, Jie Shen
Mutations in the Presenilin genes are the major genetic cause of Alzheimer's disease. Presenilin and Nicastrin are essential components of ╬│-secretase, a multi-subunit protease that cleaves Type I transmembrane proteins. Genetic studies in mice previously demonstrated that conditional inactivation of Presenilin or Nicastrin in excitatory neurons of the postnatal forebrain results in memory deficits, synaptic impairment and age-dependent neurodegeneration. The roles of Drosophila Presenilin (Psn) and Nicastrin (Nct) in the adult fly brain, however, are unknown...
May 11, 2017: Genetics
https://www.readbyqxmd.com/read/28495960/inferring-the-joint-demographic-history-of-multiple-populations-beyond-the-diffusion-approximation
#10
Julien Jouganous, Will Long, Aaron P Ragsdale, Simon Gravel
Understanding variation in allele frequencies across populations is a central goal of population genetics. Classical models for the distribution of allele frequencies, using forward simulation, coalescent theory, or the diffusion approximation, have been applied extensively for demographic inference, medical study design, and evolutionary studies. Here we propose a tractable model of ordinary differential equations for the evolution of allele frequencies that is closely related to the diffusion approximation but avoids many of its limitations and approximations...
May 11, 2017: Genetics
https://www.readbyqxmd.com/read/28495959/potential-nematode-alarm-pheromone-induces-acute-avoidance-in-caenorhabditis-elegans
#11
Ying Zhou, Mario Loeza-Cabrera, Zheng Liu, Boanerges Aleman-Meza, Julie K Nguyen, Sang-Kyu Jung, Yuna Choi, Qingyao Shou, Rebecca A Butcher, Weiwei Zhong
It is crucial for animal survival to detect dangers such as predators. A good indicator of dangers is injury of conspecifics. Here we show that fluids released from injured conspecifics invoke acute avoidance in both free-living and parasitic nematodes. Caenorhabditis elegans avoids extracts from closely related nematode species but not fruit fly larvae. The worm extracts have no impact on animal lifespan, suggesting that the worm extract may function as an alarm instead of inflict physical harm. Avoidance of the worm extract requires the function of a cGMP signaling pathway that includes the cGMP-gated channel TAX-2/TAX-4 in the amphid sensory neurons ASI and ASK...
May 11, 2017: Genetics
https://www.readbyqxmd.com/read/28495958/maternal-torso-like-coordinates-tissue-folding-during-drosophila-gastrulation
#12
Travis K Johnson, Karyn A Moore, James C Whisstock, Coral G Warr
The rapid and orderly folding of epithelial tissue during developmental processes such as gastrulation requires the precise coordination of changes in cell shape. Here, we report that the perforin-like protein Torso-like (Tsl), the key extracellular determinant for Drosophila embryonic terminal patterning, also functions to control epithelial morphogenesis. We find that tsl null mutants display a ventral cuticular hole phenotype that is independent of the loss of terminal structures, and arises as a consequence of mesoderm invagination defects...
May 11, 2017: Genetics
https://www.readbyqxmd.com/read/28495957/resolving-the-complex-genetic-basis-of-phenotypic-variation-and-variability-of-cellular-growth
#13
Naomi Ziv, Bentley M Shuster, Mark L Siegal, David Gresham
In all organisms, many traits vary continuously between individuals. Explaining the genetic basis of quantitative trait variation requires comprehensively accounting for genetic and non-genetic factors as well as their interactions. The growth of microbial cells can be characterized by a lag duration, an exponential growth phase and a stationary phase. Parameters that characterize these growth phases can vary among genotypes (phenotypic variation), environmental conditions (phenotypic plasticity) and among isogenic cells in a given environment (phenotypic variability)...
May 11, 2017: Genetics
https://www.readbyqxmd.com/read/28495956/sharing-of-genes-and-pathways-across-complex-phenotypes-a-multilevel-genome-wide-analysis
#14
Hongsheng Gui, Johnny S Kwan, Pak C Sham, Stacey S Cherny, Miaoxin Li
Evidence from genome-wide association studies (GWAS) suggest that pleiotropic effects on human complex phenotypes are very common. Recently an atlas of genetic correlations among complex phenotypes has broadened our understanding of human diseases and traits. Here we examine genetic overlap, from a gene-centric perspective, among the same 24 phenotypes previously investigated for genetic correlations. After adopting the multilevel pipeline (freely available at http://grass.cgs.hku.hk/limx/kgg/) that includes intragenic single nucleotide polymorphisms (SNPs), genes and gene-sets to estimate genetic similarities across phenotypes, large amount of sharing for several biologically related phenotypes is confirmed...
May 11, 2017: Genetics
https://www.readbyqxmd.com/read/28476869/mathematical-constraints-on-fst-biallelic-markers-in-arbitrarily-many-populations
#15
Nicolas Alcala, Noah A Rosenberg
FST is one of the most widely used statistics in population genetics. Recent mathematical studies have identified constraints that challenge interpretations of FST as a measure with potential to range from 0 for genetically similar populations to 1 for divergent populations. We generalize results obtained for population pairs to arbitrarily many populations, characterizing the mathematical relationship between FST , the frequency M of the more frequent allele at a polymorphic biallelic marker, and the number of subpopulations K...
May 5, 2017: Genetics
https://www.readbyqxmd.com/read/28476868/a-new-method-reverse-yeast-two-hybrid-array-rytha-identifies-mutants-that-dissociate-the-physical-interaction-between-elg1-and-slx5
#16
Ifat Lev, Keren Shemesh, Marina Volpe, Soumitra Sau, Nelly Levinton, Maya Molco, Shivani Singh, Batia Liefshitz, Shay Ben Aroya, Martin Kupiec
The vast majority of processes within the cell are carried out by proteins working in conjunction. The Yeast Two Hybrid (Y2H) methodology allows the detection of physical interactions between any two interacting proteins. Here we describe a novel systematic genetic methodology: "Reverse Yeast Two Hybrid Array (RYTHA)," that allows the identification of proteins required for modulating the physical interaction between two given proteins. Our assay starts with a yeast strain in which the physical interaction of interest can be detected by growth on media lacking histidine, in the context of the Yeast Two Hybrid (Y2H) methodology...
May 5, 2017: Genetics
https://www.readbyqxmd.com/read/28476867/regulatory-mechanisms-of-metamorphic-neuronal-remodeling-revealed-through-a-genome-wide-modifier-screen-in-drosophila-melanogaster
#17
Dahong Chen, Tingting Gu, Tom N Pham, Montgomery J Zachary, Randall S Hewes
During development, neuronal remodeling shapes neuronal connections to establish fully mature and functional nervous systems. Our previous studies have shown that the RNA binding factor alan shepard (shep) is an important regulator of neuronal remodeling during metamorphosis in Drosophila melanogaster, and loss of shep leads to smaller soma size and fewer neurites in a stage-dependent manner. To shed light on the mechanisms by which shep regulates neuronal remodeling, we conducted a genetic modifier screen for suppressors of shep-dependent wing expansion defects and cellular morphological defects in a set of peptidergic neurons, the bursicon neurons, that promote post-eclosion wing expansion...
May 5, 2017: Genetics
https://www.readbyqxmd.com/read/28476866/selection-to-increase-expression-not-sequence-diversity-precedes-gene-family-origin-and-expansion-in-rattlesnake-venom
#18
Mark J Margres, Alyssa T Bigelow, Emily Moriarty Lemmon, Alan R Lemmon, Darin R Rokyta
Gene duplication is the primary mechanism leading to new genes and phenotypic novelty, but the proximate evolutionary processes underlying gene family origin, maintenance, and expansion are poorly understood. Although sub- and neofunctionalization provide clear long-term advantages, selection does not act with foresight, and unless a redundant gene copy provides an immediate fitness advantage, the copy will most likely be lost. Many models for the evolution of genes immediately following duplication have been proposed, but the robustness and applicability of these models is unclear because of the lack of data at the population-level...
May 5, 2017: Genetics
https://www.readbyqxmd.com/read/28476865/accounting-for-sampling-error-in-genetic-eigenvalues-using-random-matrix-theory
#19
Jacqueline L Sztepanacz, Mark W Blows
The distribution of genetic variance in multivariate phenotypes is characterized by the empirical spectral distribution of the eigenvalues of the genetic covariance matrix. Empirical estimates of genetic eigenvalues from random effects linear models are known to be over-dispersed by sampling error, where large eigenvalues are biased upwards, and small eigenvalues are biased downwards. The overdispersion of the leading eigenvalues of sample covariance matrices have been demonstrated to conform to the Tracy-Widom (TW) distribution...
May 5, 2017: Genetics
https://www.readbyqxmd.com/read/28468910/the-sos-and-rpos-regulons-contribute-to-bacterial-cell-robustness-to-genotoxic-stress-by-synergistically-regulating-dna-polymerase-pol-ii
#20
Tanja Dapa, S├ębastien Fleurier, Marie-Florence Bredeche, Ivan Matic
Mitomycin C (MMC) is a genotoxic agent that induces DNA cross-links, DNA alkylation, and the production of reactive oxygen species (ROS). MMC induces the SOS response and RpoS regulons in Escherichia coli SOS-encoded functions are required for DNA repair, whereas the RpoS regulon is typically induced by metabolic stresses that slow growth. Thus, induction of the RpoS regulon by MMC may be coincidental, because DNA damage slows growth; alternatively, the RpoS regulon may be an adaptive response contributing to cell survival...
May 3, 2017: 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"