keyword
MENU ▼
Read by QxMD icon Read
search

haploid

keyword
https://www.readbyqxmd.com/read/27903530/near-haploid-and-low-hypodiploid-acute-lymphoblastic-leukemia-two-distinct-subtypes-but-consistently-poor-prognosis
#1
Setareh Safavi, Kajsa Paulsson
Hypodiploidy <40 chromosomes is an uncommon genetic feature of acute lymphoblastic leukemia (ALL) in both children and adults. It has long been clear by cytogenetic analyses, and recently confirmed by mutational profiling, that these cases may be further subdivided into two subtypes: near-haploid ALL with 24-30 chromosomes and low hypodiploid ALL with 31-39 chromosomes. Both groups are associated with a very poor prognosis and these patients are among those who could benefit most from novel treatments.
November 30, 2016: Blood
https://www.readbyqxmd.com/read/27902803/alphasim-software-for-breeding-program-simulation
#2
Anne-Michelle Faux, Gregor Gorjanc, R Chris Gaynor, Mara Battagin, Stefan M Edwards, David L Wilson, Sarah J Hearne, Serap Gonen, John M Hickey
This paper describes AlphaSim, a software package for simulating plant and animal breeding programs. AlphaSim enables the simulation of multiple aspects of breeding programs with a high degree of flexibility. AlphaSim simulates breeding programs in a series of steps: (i) simulate haplotype sequences and pedigree; (ii) drop haplotypes into the base generation of the pedigree and select single-nucleotide polymorphism (SNP) and quantitative trait nucleotide (QTN); (iii) assign QTN effects, calculate genetic values, and simulate phenotypes; (iv) drop haplotypes into the burn-in generations; and (v) perform selection and simulate new generations...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27900399/quantitative-trait-loci-mapping-of-heat-tolerance-in-broccoli-brassica-oleracea-var-italica-using-genotyping-by-sequencing
#3
Sandra E Branham, Zachary J Stansell, David M Couillard, Mark W Farnham
Five quantitative trait loci and one epistatic interaction were associated with heat tolerance in a doubled haploid population of broccoli evaluated in three summer field trials. Predicted rising global temperatures due to climate change have generated a demand for crops that are resistant to yield and quality losses from heat stress. Broccoli (Brassica oleracea var. italica) is a cool weather crop with high temperatures during production decreasing both head quality and yield. Breeding for heat tolerance in broccoli has potential to both expand viable production areas and extend the growing season but breeding efficiency is constrained by limited genetic information...
November 29, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27898767/genotyping-by-sequencing-on-pooled-samples-and-its-use-in-measuring-segregation-bias-during-the-course-of-androgenesis-in-barley
#4
Sébastien Bélanger, Patricio Esteves, Isabelle Clermont, Martine Jean, François Belzile
Estimation of allelic frequencies is often required in breeding but genotyping many individuals at many loci can be expensive. We have developed a genotyping-by-sequencing (GBS) approach for estimating allelic frequencies on pooled samples (Pool-GBS) and used it to examine segregation distortion in doubled haploid (DH) populations of barley ( L.). In the first phase, we genotyped each line individually and exploited these data to explore a strategy to call single nucleotide polymorphisms (SNPs) on pooled reads...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27898766/genomic-regions-influencing-seminal-root-traits-in-barley
#5
Hannah Robinson, Lee Hickey, Cecile Richard, Emma Mace, Alison Kelly, Andrew Borrell, Jerome Franckowiak, Glen Fox
Water availability is a major limiting factor for crop production, making drought adaptation and its many component traits a desirable attribute of plant cultivars. Previous studies in cereal crops indicate that root traits expressed at early plant developmental stages, such as seminal root angle and root number, are associated with water extraction at different depths. Here, we conducted the first study to map seminal root traits in barley ( L.). Using a recently developed high-throughput phenotyping method, a panel of 30 barley genotypes and a doubled-haploid (DH) population (ND24260 × 'Flagship') comprising 330 lines genotyped with diversity array technology (DArT) markers were evaluated for seminal root angle (deviation from vertical) and root number under controlled environmental conditions...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27895927/expansion-mosaicism-and-interruption-mechanisms-of-the-cag-repeat-mutation-in-spinocerebellar-ataxia-type-1
#6
REVIEW
Cara Kraus-Perrotta, Sarita Lagalwar
Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant neurodegenerative disorder that primarily affects the cerebellum and brainstem. The genetic mutation is an expansion of CAG trinucleotide repeats within the coding region of the ataxin-1 gene, characterizing SCA1 as a polyglutamine expansion disease like Huntington's. As with most polyglutamine expansion diseases, SCA1 follows the rules of genetic anticipation: the larger the expansion, the earlier and more rapid the symptoms. Unlike the majority of polyglutamine expansion diseases, the presence of histidine interruptions within the polyglutamine tract of ataxin-1 protein can prevent or mitigate disease...
2016: Cerebellum & Ataxias
https://www.readbyqxmd.com/read/27895628/nearshore-pelagic-microbial-community-abundance-affects-recruitment-success-of-giant-kelp-macrocystis-pyrifera
#7
Megan M Morris, John M Haggerty, Bhavya N Papudeshi, Alejandro A Vega, Matthew S Edwards, Elizabeth A Dinsdale
Marine microbes mediate key ecological processes in kelp forest ecosystems and interact with macroalgae. Pelagic and biofilm-associated microbes interact with macroalgal propagules at multiple stages of recruitment, yet these interactions have not been described for Macrocystis pyrifera. Here we investigate the influence of microbes from coastal environments on recruitment of giant kelp, M. pyrifera. Through repeated laboratory experiments, we tested the effects of altered pelagic microbial abundance on the settlement and development of the microscopic propagules of M...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27895111/discovery-and-genotyping-of-structural-variation-from-long-read-haploid-genome-sequence-data
#8
John Huddleston, Mark Jp Chaisson, Karyn Meltz Steinberg, Wes Warren, Kendra Hoekzema, David S Gordon, Tina A Graves-Lindsay, Katherine M Munson, Zev N Kronenberg, Laura Vives, Paul Peluso, Matthew Boitano, Chen-Shin Chin, Jonas Korlach, Richard K Wilson, Evan E Eichler
In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. Using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that >89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF >1%)...
November 28, 2016: Genome Research
https://www.readbyqxmd.com/read/27888605/natural-antisense-transcripts-are-linked-to-the-modulation-of-mitochondrial-function-and-teliospore-dormancy-in-ustilago-maydis
#9
Lauren A Ostrowski, Barry J Saville
The basidiomycete smut fungus Ustilago maydis causes common smut of corn. This disease is spread through the production of teliospores, which are thick-walled dormant structures characterized by low rates of respiration and metabolism. Teliospores are formed when the fungus grows within the plant, and the morphological steps involved in their formation have been described, but the molecular events leading to dormancy are not known. In U. maydis, natural antisense transcripts (NATs) can function to alter gene expression and many NATs have increased levels in the teliospore...
November 26, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27882129/whole-genome-resequencing-of-100-healthy-individuals-using-dna-pooling
#10
Xiaobin Wang, Weiguo Sui, Weiqing Wu, Xianliang Hou, Minglin Ou, Yueying Xiang, Yong Dai
With the advent of next-generation sequencing technology, the cost of sequencing has significantly decreased. However, sequencing costs remain high for large-scale studies. In the present study, DNA pooling was applied as a cost-effective strategy for sequencing. The sequencing results for 100 healthy individuals obtained via whole-genome resequencing and using DNA pooling are presented in the present study. In order to minimise the likelihood of systematic bias in sampling, paired-end libraries with an insert size of 500 bp were prepared for all samples and then subjected to whole-genome sequencing using four lanes for each library and resulting in at least a 30-fold haploid coverage for each sample...
November 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/27881764/zebrafish-embryonic-development-is-induced-by-carp-sperm
#11
Thomas A Delomas, Konrad Dabrowski
Haploid gynogenetic screens increase the efficiency of forward genetic screens and linkage analysis in fish. Typically, UV-irradiated zebrafish sperm is used to activate zebrafish oocytes for haploid screens. We describe the use of UV-irradiated common carp sperm to activate haploid gynogenetic zebrafish development. Carp × zebrafish hybrids are shown to have a characteristic set of features during embryonic development and exhibit functional development of several tissues (muscle, heart and nervous system)...
November 2016: Biology Letters
https://www.readbyqxmd.com/read/27880793/seed-quality-traits-can-be-predicted-with-high-accuracy-in-brassica-napus-using-genomic-data
#12
Jun Zou, Yusheng Zhao, Peifa Liu, Lei Shi, Xiaohua Wang, Meng Wang, Jinling Meng, Jochen Christoph Reif
Improving seed oil yield and quality are central targets in rapeseed (Brassica napus) breeding. The primary goal of our study was to examine and compare the potential and the limits of marker-assisted selection and genome-wide prediction of six important seed quality traits of B. napus. Our study is based on a bi-parental population comprising 202 doubled haploid lines and a diverse validation set including 117 B. napus inbred lines derived from interspecific crosses between B. rapa and B. carinata. We used phenotypic data for seed oil, protein, erucic acid, linolenic acid, stearic acid, and glucosinolate content...
2016: PloS One
https://www.readbyqxmd.com/read/27867148/generation-identification-formation-mechanism-and-application-of-plant-haploids
#13
Yin Liqin, Fu Shaohong, Yang Jin, Li Yun, Wang Jisheng, Wang Maolin
Haploids are individuals with gametophytic chromosome numbers. Homozygous doubled haploids can be quickly gained by genome doubling. Haploids and doubled haploids play an important role on crop breeding, mutant screening, gene functional analysis, cytological studies, construction of genetic population and so on, and have been a research hotspot of plants in recent years. In this review, we summarize the production means, identification, the genetic mechanism and the applications of haploids and doubled haploids...
November 20, 2016: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/27866168/fixation-probability-in-a-haploid-diploid-population
#14
Kazuhiro Bessho, Sarah P Otto
Classical population genetic theory generally assumes either a fully haploid or fully diploid life cycle. However, many organisms exhibit more complex life cycles, with both free-living haploid and diploid stages. Here we ask what the probability of fixation is for selected alleles in organisms with haploid-diploid life cycles. We develop a genetic model that considers the population dynamics using both the Moran model and Wright-Fisher model. Applying a branching process approximation, we obtain an accurate fixation probability assuming that the population is large and the net effect of the mutation is beneficial...
November 18, 2016: Genetics
https://www.readbyqxmd.com/read/27861615/doubled-haploid-cudh2107-as-a-reference-for-bulb-onion-allium-cepa-l-research-development-of-a-transcriptome-catalogue-and-identification-of-transcripts-associated-with-male-fertility
#15
Jiffinvir S Khosa, Robyn Lee, Sophia Bräuning, Janice Lord, Meeghan Pither-Joyce, John McCallum, Richard C Macknight
Researchers working on model plants have derived great benefit from developing genomic and genetic resources using 'reference' genotypes. Onion has a large and highly heterozygous genome making the sharing of germplasm and analysis of sequencing data complicated. To simplify the discovery and analysis of genes underlying important onion traits, we are promoting the use of the homozygous double haploid line 'CUDH2107' by the onion research community. In the present investigation, we performed transcriptome sequencing on vegetative and reproductive tissues of CUDH2107 to develop a multi-organ reference transcriptome catalogue...
2016: PloS One
https://www.readbyqxmd.com/read/27859032/evolution-of-haploid-diploid-life-cycles-when-haploid-and-diploid-fitnesses-are-not-equal
#16
Michael F Scott, Marie Rescan
Many organisms spend a significant portion of their life cycle as haploids and as diploids (a haploid-diploid life cycle). However, the evolutionary processes that could maintain this sort of life cycle are unclear. Most previous models of ploidy evolution have assumed that the fitness effects of new mutations are equal in haploids and homozygous diploids, however, this equivalency is not supported by empirical data. With different mutational effects, the overall (intrinsic) fitness of a haploid would not be equal to that of a diploid after a series of substitution events...
November 12, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27857452/embryonic-development-and-a-quantitative-model-of-programmed-dna-elimination-in-mesocyclops-edax-s-a-forbes-1891-copepoda-cyclopoida
#17
Michelle K Clower, Ashton S Holub, Rebecca T Smith, Grace A Wyngaard
The highly programmed fragmentation of chromosomes and elimination of large amounts of nuclear DNA from the presomatic cell lineages (i.e., chromatin diminution), occurs in the embryos of the freshwater zooplankton Mesocyclops edax (S. A. Forbes, 1891) (Crustacea: Copepoda). The somatic genome is reorganized and reduced to a size five times smaller even though the germline genome remains intact. We present the first comprehensive, quantitative model of DNA content throughout embryogenesis in a copepod that possesses embryonic DNA elimination...
2016: Journal of Crustacean Biology
https://www.readbyqxmd.com/read/27853577/chemical-communication-is-not-sufficient-to-explain-reproductive-inhibition-in-the-bumblebee-bombus-impatiens
#18
Mario Padilla, Etya Amsalem, Naomi Altman, Abraham Hefetz, Christina M Grozinger
Reproductive division of labour is a hallmark of eusociality, but disentangling the underlying proximate mechanisms can be challenging. In bumblebees, workers isolated from the queen can activate their ovaries and lay haploid, male eggs. We investigated if volatile, contact, visual or behavioural cues produced by the queen or brood mediate reproductive dominance in Bombus impatiens. Exposure to queen-produced volatiles, brood-produced volatiles and direct contact with pupae did not reduce worker ovary activation; only direct contact with the queen could reduce ovary activation...
October 2016: Royal Society Open Science
https://www.readbyqxmd.com/read/27843115/de-novo-transcriptome-analysis-of-the-red-seaweed-gracilaria-chilensis-and-identification-of-linkers-associated-with-phycobilisomes
#19
María Alejandra Vorphal, Cristian Gallardo-Escárate, Valentina Valenzuela-Muñoz, Jorge Dagnino-Leone, José Aleikar Vásquez, José Martínez-Oyanedel, Marta Bunster
This work reports the results of the Illumina RNA-Seq of a wild population of female haploid plants of Gracilaria chilensis (Bird et al., 1986) (Rhodophyta, Gigartinalis). Most transcripts were de novo assembled in 12,331 contigs with an average length of 1756bp, showing that 96.64% of the sequences were annotated with known proteins. In particular, the identification of linker proteins of phycobilisomes (PBS) is reported. Linker proteins have primary been identified in cyanobacteria but the information available about them in eukaryotic red alga is not complete, and this is the first report in G...
November 11, 2016: Marine Genomics
https://www.readbyqxmd.com/read/27836908/dissecting-gene-expression-changes-accompanying-a-ploidy-based-phenotypic-switch
#20
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
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"