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https://www.readbyqxmd.com/read/28110091/genome-wide-association-analyses-reveal-the-genetic-basis-of-stigma-exsertion-in-rice
#1
Hao Zhou, Pingbo Li, Weibo Xie, Saddam Hussain, Yibo Li, Duo Xia, Hu Zhao, Shengyuan Sun, Junxiao Chen, Hong Ye, Jun Hou, Da Zhao, Guanjun Gao, Qinglu Zhang, Gongwei Wang, Xingming Lian, Jinghua Xiao, Sibin Yu, Xianghua Li, Yuqing He
Stigma exsertion, a key determinant of the rice mating system, greatly contributes to the application of heterosis in rice. As few QTLs have been fine mapped or cloned, the genetic architecture of stigma exsertion is quite unclear. We performed genome-wide association study of stigma exsertion and related traits using 6.5 million SNPs characterized in 533 diverse accessions of Oryza sativa. We identified 23 loci significantly associated with stigma exsertion and related traits, three of which were co-located with three major grain size genes GS3, GW5 and GW2...
January 18, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28109755/construction-of-agrobacterium-tumefaciens-mediated-tomato-black-ring-virus-infectious-cdna-clones
#2
Aleksandra Zarzyńska-Nowak, Inmaculada Ferriol, Bryce W Falk, Natasza Borodynko-Filas, Beata Hasiów-Jaroszewska
Tomato black ring virus (TBRV, genus Nepovirus) infects a wide range of economically important plants such as tomato, potato, tobacco and cucumber. Here, a successful construction of infectious full-length cDNA clones of the TBRV genomic RNAs (RNA1 and RNA2) is reported for the first time. The engineered constructs consisting of PCR-amplified DNAs were cloned into binary vector pJL89 immediately downstream of a double Cauliflower mosaic virus (CaMV) 35S promoter, and upstream of the Hepatitis delta virus (HDV) ribozyme and nopaline synthase terminator (NOS)...
January 18, 2017: Virus Research
https://www.readbyqxmd.com/read/28109725/6q12-and-11p14-variants-are-associated-with-postnatal-exhaled-nitric-oxide-and-respiratory-symptoms
#3
Oliver Fuchs, Olga Gorlanova, Philipp Latzin, Anne Schmidt, Maximilian Schieck, Antoaneta A Toncheva, Sven Michel, Vincent D Gaertner, Michael Kabesch, Urs Frey
BACKGROUND: Exhaled nitric oxide (eNO) is a biomarker of airway inflammation and seems to precede respiratory symptoms, such as asthma in childhood. Identifying genetic determinants of postnatal eNO may aid in unraveling the role of eNO in epithelial function or airway inflammation and disease. OBJECTIVE: To identify genetic determinants of early postnatal eNO and subsequent respiratory symptoms during the first year of life. METHODS: Within a population-based birth cohort, eNO was measured in healthy term infants aged 5 weeks during quiet tidal breathing in unsedated sleep...
January 18, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28109622/genetics-for-the-identification-of-lipid-targets-beyond-pcsk9
#4
REVIEW
Linda R Wang, Robert A Hegele
From studies of rare families to genome-wide associations in populations, understanding of human genetics has accelerated the search for new drug targets for the prevention of atherosclerotic cardiovascular disease. DNA sequencing and genome-wide analyses of DNA markers have illuminated rare as well as common variants in genes that regulate lipids and ultimately atherosclerosis risk. A recent innovative approach called Mendelian randomization can endorse specific genes and variants as causative not just for lipid disturbances, but also for clinical cardiovascular end points...
November 11, 2016: Canadian Journal of Cardiology
https://www.readbyqxmd.com/read/28109604/genome-wide-mapping-of-10-calving-and-fertility-traits-in-holstein-dairy-cattle-with-special-regard-to-chromosome-18
#5
M-P Müller, S Rothammer, D Seichter, I Russ, D Hinrichs, J Tetens, G Thaller, I Medugorac
Over the last decades, a dramatic decrease in reproductive performance has been observed in Holstein cattle and fertility problems have become the most common reason for a cow to leave the herd. The premature removal of animals with high breeding values results in both economic and breeding losses. For efficient future Holstein breeding, the identification of loci associated with low fertility is of major interest and thus constitutes the aim of this study. To reach this aim, a genome-wide combined linkage disequilibrium and linkage analysis (cLDLA) was conducted using data on the following 10 calving and fertility traits in the form of estimated breeding values: days from first service to conception of heifers and cows, nonreturn rate on d 56 of heifers and cows, days from calving to first insemination, days open, paternal and maternal calving ease, paternal and maternal stillbirth...
January 18, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28109590/phenotypic-genetic-and-single-nucleotide-polymorphism-marker-associations-between-calf-diseases-and-subsequent-performance-and-disease-occurrences-of-first-lactation-german-holstein-cows
#6
M Mahmoud, T Yin, K Brügemann, S König
A total of 31,396 females born from 2010 to 2013 in 43 large-scale Holstein-Friesian herds were phenotyped for calf and cow disease traits using a veterinarian diagnosis key. Calf diseases were general disease status (cGDS), calf diarrhea (cDIA), and calf respiratory disease (cRD) recorded from birth to 2 mo of age. Incidences were 0.48 for cGDS, 0.28 for cRD, and 0.21 for cDIA. Cow disease trait recording focused on the early period directly after calving in first parity, including the interval from 10 d before calving to 200 d in lactation...
January 18, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28109325/studying-hematopoiesis-using-single-cell-technologies
#7
REVIEW
Fang Ye, Wentao Huang, Guoji Guo
Hematopoiesis is probably the best-understood stem cell differentiation system; hematopoietic stem cell (HSC) transplantation represents the most widely used regenerative therapy. The classical view of lineage hierarchy in hematopoiesis is built on cell type definition system by a group of cell surface markers. However, the traditional model is facing increasing challenges, as many classical cell types are proved to be heterogeneous. Recently, the developments of new technologies allow genome, transcriptome, proteome, and epigenome analysis at the single-cell level...
January 21, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28108933/modelling-genome-wide-topological-associating-domains-in-mouse-embryonic-stem-cells
#8
REVIEW
Y Zhan, L Giorgetti, G Tiana
Chromosome conformation capture (3C)-based techniques such as chromosome conformation capture carbon copy (5C) and Hi-C revealed that the folding of mammalian chromosomes is highly hierarchical. A fundamental structural unit in the hierarchy is represented by topologically associating domains (TADs), sub-megabase regions of the genome within which the chromatin fibre preferentially interacts. 3C-based methods provide the mean contact probabilities between chromosomal loci, averaged over a large number of cells, and do not give immediate access to the single-cell conformations of the chromatin fibre...
January 20, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28108698/genome-wide-analysis-of-fatty-acid-desaturation-and-its-response-to-temperature
#9
Guillaume Menard, Jose Martin Moreno, Fiona Bryant, Olaya Munoz-Azcarate, Amélie A Kelly, Keywan Hassani-Pak, Smita Kurup, Peter J Eastmond
Plants modify the polyunsaturated fatty acid content of their membrane and storage lipids in order to adapt to changes in temperature. In developing seeds this response is largely controlled by the activities of the microsomal ω-6 and ω-3 fatty acid desaturases, FAD2 and FAD3. Although temperature-regulation of desaturation has been studied at the molecular and biochemical level, the genetic control of this trait is poorly understood. Here we have characterised the response of Arabidopsis thaliana seed lipids to variation in ambient temperature and found that heat inhibits both ω-6 and ω-3 desaturation in phosphatidylcholine, leading to a proportional change in triacylglycerol composition...
January 20, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28108657/risearch2-suffix-array-based-large-scale-prediction-of-rna-rna-interactions-and-sirna-off-targets
#10
Ferhat Alkan, Anne Wenzel, Oana Palasca, Peter Kerpedjiev, Anders Frost Rudebeck, Peter F Stadler, Ivo L Hofacker, Jan Gorodkin
Intermolecular interactions of ncRNAs are at the core of gene regulation events, and identifying the full map of these interactions bears crucial importance for ncRNA functional studies. It is known that RNA-RNA interactions are built up by complementary base pairings between interacting RNAs and high level of complementarity between two RNA sequences is a powerful predictor of such interactions. Here, we present RIsearch2, a large-scale RNA-RNA interaction prediction tool that enables quick localization of potential near-complementary RNA-RNA interactions between given query and target sequences...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108622/a-genome-wide-loss-of-function-screen-identifies-slc26a2-as-a-novel-mediator-of-trail-resistance
#11
Lina Dimberg, Christina G Towers, Kian Behbakht, Taylor Hotz, Jihye Kim, Susan P Fosmire, Christopher C Porter, Aik-Choon Tan, Andrew Thorburn, Heide L Ford
: TNF-related apoptosis inducing ligand (TRAIL) is a potent death-inducing ligand that mediates apoptosis through the extrinsic pathway and serves as an important endogenous tumor suppressor mechanism. Because tumor cells are often killed by TRAIL and normal cells are not, drugs that activate the TRAIL pathway have been thought to have potential clinical value. However, to date, most TRAIL-related clinical trials have largely failed due to the tumor cells having intrinsic or acquired resistance to TRAIL-induced apoptosis...
January 20, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28108586/fluctuating-selection-in-the-moran
#12
Antony M Dean, Clarence Lehman, Xiao Yi
Contrary to classical population genetics theory, experiments demonstrate that fluctuating selection can protect a haploid polymorphism in the absence of frequency dependent effects on fitness. Using forward simulations with the Moran model we confirm our analytical results showing that a fluctuating selection regime, with a mean selection coefficient of zero, promotes polymorphism. We find that increases in heterozygosity over neutral expectations are especially pronounced when fluctuations are rapid, mutation is weak, the population size is large and the variance in selection is big...
January 20, 2017: Genetics
https://www.readbyqxmd.com/read/28108585/histone-h3k4-and-h3k36-methylation-independently-recruit-the-nua3-histone-acetyltransferase-in-saccharomyces-cerevisiae
#13
Benjamin J E Martin, Kristina L McBurney, Vicki E Maltby, Kristoffer N Jensen, Julie Brind'Amour, LeAnn Howe
Histone post-translational modifications (PTMs) alter chromatin structure by promoting the interaction of chromatin-modifying complexes with nucleosomes. The majority of chromatin-modifying complexes contain multiple domains that preferentially interact with modified histones, leading to speculation that these domains function in concert to target nucleosomes with distinct combinations of histone PTMs. In S. cerevisiae, the NuA3 histone acetyltransferase complex contains three domains, the PHD finger in Yng1, the PWWP domain in Pdp3, and the YEATS domain in Taf14, which in vitro bind to H3K4 methylation, H3K36 methylation, and acetylated and crotonylated H3K9 respectively...
January 20, 2017: Genetics
https://www.readbyqxmd.com/read/28108556/confirmation-of-five-novel-susceptibility-loci-for-systemic-lupus-erythematosus-sle-and-integrated-network-analysis-of-82-sle-susceptibility-loci
#14
Julio E Molineros, Wanling Yang, Xu-Jie Zhou, Celi Sun, Yukinori Okada, Huoru Zhang, Kek Heng Chua, Yu-Lung Lau, Yuta Kochi, Akari Suzuki, Kazuhiko Yamamoto, Jianyang Ma, So-Young Bang, Hye-Soon Lee, Kwangwoo Kim, Sang-Cheol Bae, Hong Zhang, Nan Shen, Loren L Looger, Swapan K Nath
We recently identified ten novel SLE susceptibility loci in Asians and uncovered several additional suggestive loci requiring further validation. This study aimed to replicate five of these suggestive loci in a Han Chinese cohort from Hong Kong, followed by meta-analysis (11,656 cases and 23,968 controls) on previously reported Asian and European populations, and perform bioinformatic analyses on all 82 reported SLE loci to identify shared regulatory signatures. We performed a battery of analyses for these five loci, as well as joint analyses on all 82 SLE loci...
January 20, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28108554/genome-wide-analysis-of-lncrna-and-mrna-expression-during-differentiation-of-abdominal-preadipocytes-in-the-chicken
#15
Tao Zhang, Xiangqian Zhang, Kunpeng Han, Genxi Zhang, Jinyu Wang, Kaizhou Xie, Qian Xue
Long non-coding RNAs (lncRNAs) regulate adipogenesis and other processes associated with metabolic tissue development and function. However, little is known about the function and profile of lncRNAs during preadipocyte differentiation in the chicken (Gallus gallus). Herein, lncRNA and mRNA expression in preadipocytes at different stages of differentiation were analyzed using RNA sequencing. A total of 1,300,074,528 clean reads and 27,023 novel lncRNAs were obtained from 12 samples. The number of genes (1,336 lncRNAs and 1,759 mRNAs; 3,095 in total) differentially expressed across various stages declined as differentiation progressed...
January 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28108551/genotype-calling-from-population-genomic-sequencing-data
#16
Takahiro Maruki, Michael Lynch
Genotype calling plays important roles in population-genomic studies, which have been greatly accelerated by sequencing technologies. To take full advantage of the resultant information, we have developed maximum-likelihood (ML) methods for calling genotypes from high-throughput sequencing data. As the statistical uncertainties associated with sequencing data depend on depths of coverage, we have developed two types of genotype callers. One approach is appropriate for low-coverage sequencing data, and incorporates population-level information on genotype frequencies and error rates pre-estimated by an ML method...
January 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28108460/enhancer-remodeling-during-adaptive-bypass-to-mek-inhibition-is-attenuated-by-pharmacological-targeting-of-the-p-tefb-complex
#17
Jon S Zawistowski, Samantha M Bevill, Daniel R Goulet, Timothy J Stuhlmiller, Adriana S Beltran, Jose F Olivares-Quintero, Darshan Singh, Noah Sciaky, Joel S Parker, Naim U Rashid, Xin Chen, James S Duncan, Martin C Whittle, Steven P Angus, Sara Hanna Velarde, Brian T Golitz, Xiaping He, Charlene Santos, David B Darr, Kristalyn Gallagher, Lee M Graves, Charles M Perou, Lisa A Carey, H Shelton Earp, Gary L Johnson
Targeting the dysregulated BRaf-MEK-ERK pathway in cancer has increasingly emerged in clinical trial design. Despite clinical responses in specific cancers using inhibitors targeting BRaf and MEK, resistance develops often involving non-genomic adaptive bypass mechanisms. Inhibition of MEK1/2 by trametinib in triple negative breast cancer (TNBC) patients induced dramatic transcriptional responses, including upregulation of receptor tyrosine kinases (RTKs) comparing tumor samples before and after one week of treatment...
January 20, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28108451/gwar-robust-analysis-and-meta-analysis-of-genome-wide-association-studies
#18
Niki L Dimou, Konstantinos D Tsirigos, Arne Elofsson, Pantelis G Bagos
MOTIVATION: In the context of genome-wide association studies (GWAS), there is a variety of statistical techniques in order to conduct the analysis, but, in most cases, the underlying genetic model is usually unknown. Under these circumstances, the classical Cochran-Armitage trend test is suboptimal. Robust procedures that maximize the power and preserve the nominal type I error rate are preferable. Moreover, performing a meta-analysis using robust procedures is of great interest and has never been addressed in the past...
January 20, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108448/arnapipe-a-balanced-efficient-and-distributed-pipeline-for-processing-rna-seq-data-in-high-performance-computing-environments
#19
Arnald Alonso, Brittany N Lasseigne, Kelly Williams, Josh Nielsen, Ryne C Ramaker, Andrew A Hardigan, Bobbi Johnston, Brian S Roberts, Sara J Cooper, Sara Marsal, Richard M Myers
The wide range of RNA-seq applications and their high computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing, and sequence variant calling...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108246/engineered-cell-lines-for-fish-health-research
#20
Bertrand Collet, Catherine Collins, Katherine Lester
As fish farming continues to increase worldwide, the related research areas of fish disease and immunology are also expanding, aided by the revolution in access to genomic information and molecular technology. The genomes of most fish species of economic importance are now available and annotation based on sequence homology with characterised genomes is underway. However, while useful, functional homology is more difficult to determine, there being a lack of widely distributed and well characterised reagents such as monoclonal antibodies, traditionally used in mammalian studies, to help with confirming functions and cellular interactions of fish molecules...
January 17, 2017: Developmental and Comparative Immunology
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