keyword
MENU ▼
Read by QxMD icon Read
search

haploid

keyword
https://www.readbyqxmd.com/read/29216822/bayesian-estimation-of-scaled-mutation-rate-under-the-coalescent-a-sequential-monte-carlo-approach
#1
Oyetunji E Ogundijo, Xiaodong Wang
BACKGROUND: Samples of molecular sequence data of a locus obtained from random individuals in a population are often related by an unknown genealogy. More importantly, population genetics parameters, for instance, the scaled population mutation rate Θ=4N e μ for diploids or Θ=2N e μ for haploids (where N e is the effective population size and μ is the mutation rate per site per generation), which explains some of the evolutionary history and past qualities of the population that the samples are obtained from, is of significant interest...
December 8, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29212471/investigation-on-the-differentiation-of-two-ustilago-esculenta-strains-implications-of-a-relationship-with-the-host-phenotypes-appearing-in-the-fields
#2
Yafen Zhang, Qianchao Cao, Peng Hu, Haifeng Cui, Xiaoping Yu, Zihong Ye
BACKGROUND: Ustilago esculenta, a pathogenic basidiomycete fungus, infects Zizania latifolia to form edible galls named Jiaobai in China. The distinct growth conditions of U. esculenta induced Z. latifolia to form three different phenotypes, named male Jiaobai, grey Jiaobai and white Jiaobai. The aim of this study is to characterize the genetic and morphological differences that distinguish the two U. esculenta strains. RESULTS: In this study, sexually compatible haploid sporidia UeT14/UeT55 from grey Jiaobai (T strains) and UeMT10/UeMT46 from white Jiaobai (MT strains) were isolated...
December 6, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/29201554/linking-y-chromosomal-short-tandem-repeat-loci-to-human-male-impulsive-aggression
#3
Chun Yang, Huajie Ba, Yin Cao, Guoying Dong, Shuyou Zhang, Zhiqin Gao, Hanqing Zhao, Xianju Zhou
Introduction: Men are more susceptible to impulsive behavior than women. Epidemiological studies revealed that the impulsive aggressive behavior is affected by genetic factors, and the male-specific Y chromosome plays an important role in this behavior. In this study, we investigated the association between the impulsive aggressive behavior and Y-chromosomal short tandem repeats (Y-STRs) loci. Methods: The collected biologic samples from 271 offenders with impulsive aggressive behavior and 492 healthy individuals without impulsive aggressive behavior were amplified by PowerPlexRY23 PCR System and the resultant products were separated by electrophoresis and further genotyped...
November 2017: Brain and Behavior
https://www.readbyqxmd.com/read/29201033/cell-based-phenotyping-reveals-qtl-for-membrane-potential-maintenance-associated-with-hypoxia-and-salinity-stress-tolerance-in-barley
#4
Muhammad B Gill, Fanrong Zeng, Lana Shabala, Guoping Zhang, Yun Fan, Sergey Shabala, Meixue Zhou
Waterlogging and salinity are two major abiotic stresses that hamper crop production world-wide resulting in multibillion losses. Plant abiotic stress tolerance is conferred by many interrelated mechanisms. Amongst these, the cell's ability to maintain membrane potential (MP) is considered to be amongst the most crucial traits, a positive relationship between the ability of plants to maintain highly negative MP and its tolerance to both salinity and waterlogging stress. However, no attempts have been made to identify quantitative trait loci (QTL) conferring this trait...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29200436/genomic-selection-of-crossing-partners-on-basis-of-the-expected-mean-and-variance-of-their-derived-lines
#5
Tanja Osthushenrich, Matthias Frisch, Eva Herzog
In a line or a hybrid breeding program superior lines are selected from a breeding pool as parental lines for the next breeding cycle. From a cross of two parental lines, new lines are derived by single-seed descent (SSD) or doubled haploid (DH) technology. However, not all possible crosses between the parental lines can be carried out due to limited resources. Our objectives were to present formulas to characterize a cross by the mean and variance of the genotypic values of the lines derived from the cross, and to apply the formulas to predict means and variances of flowering time traits in recombinant inbred line families of a publicly available data set in maize...
2017: PloS One
https://www.readbyqxmd.com/read/29194476/recovery-k-mer-based-read-classification-for-y-chromosome-specific-sequencing-and-assembly
#6
Samarth Rangavittal, Robert S Harris, Monika Cechova, Marta Tomaszkiewicz, Rayan Chikhi, Kateryna D Makova, Paul Medvedev
Motivation: The haploid mammalian Y chromosome is usually under-represented in genome assemblies due to high repeat content and low depth due to its haploid nature. One strategy to ameliorate the low coverage of Y sequences is to experimentally enrich Y-specific material before assembly. Since the enrichment process is imperfect, algorithms are needed to identify putative Y-specific reads prior to downstream assembly. A strategy that uses k-mer abundances to identify such reads was used to assemble the gorilla Y (Tomaszkiewicz et al 2016)...
November 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29188194/beyond-paralogs-the-multiple-layers-of-redundancy-in-bacterial-pathogenesis
#7
Soma Ghosh, Tamara J O'Connor
Redundancy has been referred to as a state of no longer being needed or useful. Microbiologists often theorize that the only case of true redundancy in a haploid organism would be a recent gene duplication event, prior to divergence through selective pressure. However, a growing number of examples exist where an organism encodes two genes that appear to perform the same function. For example, many pathogens translocate multiple effector proteins into hosts. While disruption of individual effector genes does not result in a discernable phenotype, deleting genes in combination impairs pathogenesis: this has been described as redundancy...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29185797/u1-sndna-chromosomal-mapping-in-ten-spittlebug-species-cercopidade-auchenorrhyncha-hemiptera
#8
Allison Anjos, Andressa Paladini, Tatiane Casagrande Mariguela, Diogo Cavalcanti Cabral-de-Mello
Spittlebugs, which belong to the Cercopidae family (Auchenorrhyncha, Hemiptera), form a large group of xylem-feeding insects that are best known for causing damage to plantations and pasture grasses. The holocentric chromosomes of these insects remain poorly studied regarding to the organization of different classes of repetitive DNA. To improve chromosomal maps based on repetitive DNAs and to better understand the chromosomal organization and evolutionary dynamics of multigene families in spittlebugs, we physically mapped U1 snRNA gene with fluorescence in situ hybridization (FISH) in ten Cercopidae species belonging to three different genera...
November 29, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29179787/sperm-derived-factors-enhance-the-in-vitro-developmental-potential-of-haploid-parthenotes
#9
Ramya Nair, Shahin Aboobacker, Srinivas Mutalik, Guruprasad Kalthur, Satish Kumar Adiga
Parthenotes are characterized by poor in vitro developmental potential either due to the ploidy status or the absence of paternal factors. In the present study, we demonstrate the beneficial role of sperm-derived factors (SDF) on the in vitro development of mouse parthenotes. Mature (MII) oocytes collected from superovulated Swiss albino mice were activated using strontium chloride (SrCl2) in the presence or absence of various concentrations of SDF in M16 medium. The presence of SDF in activation medium did not have any significant influence on the activation rate...
November 28, 2017: Zygote: the Biology of Gametes and Early Embryos
https://www.readbyqxmd.com/read/29179435/genome-wide-5-hydroxymethylcytosine-patterns-in-human-spermatogenesis-are-associated-with-semen-quality
#10
Olga A Efimova, Anna A Pendina, Andrei V Tikhonov, Sergey E Parfenyev, Irina D Mekina, Evgeniia M Komarova, Mariia A Mazilina, Eugene V Daev, Olga G Chiryaeva, Ilona A Galembo, Mikhail I Krapivin, Oleg S Glotov, Irina S Stepanova, Svetlana A Shlykova, Igor Yu Kogan, Alexander M Gzgzyan, Tatyana V Kuznetzova, Vladislav S Baranov
We performed immunofluorescent analysis of DNA hydroxymethylation and methylation in human testicular spermatogenic cells from azoospermic patients and ejaculated spermatozoa from sperm donors and patients from infertile couples. In contrast to methylation which was present throughout spermatogenesis, hydroxymethylation was either high or almost undetectable in both spermatogenic cells and ejaculated spermatozoa. On testicular cytogenetic preparations, 5-hydroxymethylcytosine was undetectable in mitotic and meiotic chromosomes, and was present exclusively in interphase spermatogonia Ad and in a minor spermatid population...
October 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/29176825/the-effect-of-spatial-randomness-on-the-average-fixation-time-of-mutants
#11
Suzan Farhang-Sardroodi, Amirhossein H Darooneh, Moladad Nikbakht, Natalia L Komarova, Mohammad Kohandel
The mean conditional fixation time of a mutant is an important measure of stochastic population dynamics, widely studied in ecology and evolution. Here, we investigate the effect of spatial randomness on the mean conditional fixation time of mutants in a constant population of cells, N. Specifically, we assume that fitness values of wild type cells and mutants at different locations come from given probability distributions and do not change in time. We study spatial arrangements of cells on regular graphs with different degrees, from the circle to the complete graph, and vary assumptions on the fitness probability distributions...
November 27, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29176810/flip-flop-mating-type-switching-in-the-methylotrophic-yeast-ogataea-polymorpha-is-regulated-by-an-efg1-rme1-ste12-pathway
#12
Sara J Hanson, Kevin P Byrne, Kenneth H Wolfe
In haploid cells of Ogataea (Hansenula) polymorpha an environmental signal, nitrogen starvation, induces a reversible change in the structure of a chromosome. This process, mating-type switching, inverts a 19-kb DNA region to place either MATa or MATα genes under centromeric repression of transcription, depending on the orientation of the region. Here, we investigated the genetic pathway that controls switching. We characterized the transcriptomes of haploid and diploid O. polymorpha by RNAseq in rich and nitrogen-deficient media, and found that there are no constitutively a-specific or α-specific genes other than the MAT genes themselves...
November 27, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29163576/quantitative-trait-loci-and-maternal-effects-affecting-the-strong-grain-dormancy-of-wild-barley-hordeum-vulgare-ssp-spontaneum
#13
Shingo Nakamura, Mohammad Pourkheirandish, Hiromi Morishige, Mohammad Sameri, Kazuhiro Sato, Takao Komatsuda
Wild barley (Hordeum vulgare ssp. spontaneum) has strong grain dormancy, a trait that may enhance its survival in non-cultivated environments; by contrast, cultivated barley (Hordeum vulgare ssp. vulgare) has weaker dormancy, allowing uniform germination in cultivation. Malting barley cultivars have been bred for especially weak dormancy to optimize their use in malt production. Here, we analyzed the genetic mechanism of this difference in seed dormancy, using recombinant inbred lines (RILs) derived from a cross between the wild barley accession 'H602' and the malting barley cultivar 'Kanto Nakate Gold (KNG)'...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163459/crispr-cas9-system-as-a-valuable-genome-editing-tool-for-wine-yeasts-with-application-to-decrease-urea-production
#14
Ileana Vigentini, Marinella Gebbia, Alessandra Belotti, Roberto Foschino, Frederick P Roth
An extensive repertoire of molecular tools is available for genetic analysis in laboratory strains of S. cerevisiae. Although this has widely contributed to the interpretation of gene functionality within haploid laboratory isolates, the genetics of metabolism in commercially-relevant polyploid yeast strains is still poorly understood. Genetic engineering in industrial yeasts is undergoing major changes due to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) engineering approaches...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29158290/a-comparative-proteome-profile-of-female-mouse-gonads-suggests-a-tight-link-between-the-electron-transport-chain-and-meiosis-initiation
#15
Cong Shen, Mingrui Li, Pan Zhang, Yueshuai Guo, Hao Zhang, Bo Zheng, Hui Teng, Tao Zhou, Xuejiang Guo, Ran Huo
Generation of haploid gametes by meiosis is a unique property of germ cells and is critical for sexual reproduction. Leaving mitosis and entering meiosis is a key step in germ cell development. Several inducers or intrinsic genes are known to be important for meiotic initiation, but the regulation of meiotic initiation, especially at the protein level, is still not well understood. We constructed a comparative proteome profile of female mouse fetal gonads at specific time points (11.5, 12.5, and 13.5 days post coitum), spanning a critical window for initiation of meiosis in female germ cells...
November 20, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29155894/estimating-virus-effective-population-size-and-selection-without-neutral-markers
#16
Elsa Rousseau, Benoît Moury, Ludovic Mailleret, Rachid Senoussi, Alain Palloix, Vincent Simon, Sophie Valière, Frédéric Grognard, Frédéric Fabre
By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and, variant frequencies were determined by HTS in eight plants of each pepper line, at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers...
November 20, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29152028/a-fast-and-efficient-size-separation-method-for-haploid-embryonic-stem-cells
#17
Remo Freimann, Anton Wutz
Hemizygous mutations introduced in haploid genomes can directly expose a phenotype, thus facilitating gene function analysis and forward genetic screening. Recently, mammalian haploid cells could be derived from mouse, rat, monkey, and human embryos and have been applied to screens of cellular mechanisms including cell signaling, pathogen host factors, and developmental pathways. Notably, haploid cell cultures have an intrinsic tendency for diploidization and, thus, require periodic cell sorting. Here, we report a method for rapid purification of haploid mouse embryonic stem cells from mixed cell populations with high viability and yield...
September 2017: Biomicrofluidics
https://www.readbyqxmd.com/read/29150593/rapid-and-efficient-crispr-cas9-based-mating-type-switching-of-saccharomyces-cerevisiae
#18
Ze-Xiong Xie, Leslie A Mitchell, Hui-Min Liu, Bing-Zhi Li, Duo Liu, Neta Agmon, Yi Wu, Xia Li, Xiao Zhou, Bo Li, Wen-Hai Xiao, Ming-Zhu Ding, Ying Wang, Ying-Jin Yuan, Jef D Boeke
Rapid and highly efficient mating-type switching of Saccharomyces cerevisiae enables a wide variety of genetic manipulations such as the construction of strains, for instance isogenic haploid pairs of both mating-types, diploids and polyploids. We used the CRISPR/Cas9 system to generate a double-strand break (DSB) at the MAT locus, and in a single co-transformation, both haploid and diploid cells were switched to the specified mating-type at ~80% efficiency. The mating-type of strains carrying either rod or ring chromosome III were switched, including those lacking HMLα and HMRa cryptic mating loci...
November 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29150592/the-influence-of-genetic-stability-on-aspergillus-fumigatus-virulence-and-azole-resistance
#19
Thaila Fernanda Dos Reis, Lilian Pereira Silva, Patrícia Alves de Castro, Pollyne Borborema Almeida de Lima, Rafaela Andrade do Carmo, Marjorie Mendes Marini, José Franco da Silveira, Beatriz Henriques Ferreira, Fernando Rodrigues, Iran Malavazi, Gustavo H Goldman
Genetic stability is extremely important for the survival of every living organism and a very complex set of genes have evolved to cope with DNA repair upon DNA damage. Here, we investigated the Aspergillus fumigatus AtmA (Ataxia-telangiectasia mutated) and AtrA kinases and how they impact virulence and the evolution of azole resistance. We demonstrated that A. fumigatus atmA and atrA null mutants are haploid and have a discrete chromosomal polymorphism. The ΔatmA and ΔatrA strains are sensitive to several DNA damaging agents but surprisingly both strains were more resistant than the wild-type strain to paraquat, menadione, and hydrogen peroxide...
November 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29150006/genome-engineering-using-haploid-embryonic-stem-cells
#20
Takuro Horii, Izuho Hatada
Haploidy is a useful feature for the study of gene function because disruption of one allele in haploid cells, which contain only a single set of chromosomes, can cause loss-of-function phenotypes. Recent success in generating haploid embryonic stem (ES) cells from several mammalian species, including human, provides a new platform for simple genetic manipulation of the mammalian genome. The genome-editing potential of the CRISPR/Cas system is enhanced by the use of haploid ES cells. For example, CRISPR/Cas has been used for high-efficiency generation of multiple knockouts and knockins in haploid ES cells, with potential application in genome-wide screening...
2017: Progress in Molecular Biology and Translational Science
keyword
keyword
40842
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"