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Genomic selection

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https://www.readbyqxmd.com/read/29792895/pharmacogenomics-of-drug-induced-liver-injury-dili-molecular-biology-to-clinical-applications
#1
REVIEW
Kalaiyarasi Kaliyaperumal, Jane I Grove, Robin M Delahay, William J H Griffiths, Adam Duckworth, Guruprasad P Aithal
A number of drug-specific and host-related factors contribute to the development of drug-induced liver injury (DILI). Investigations focused on genetic susceptibility to DILI have advanced our understanding of the pathogenesis of this rare, yet potentially life-threatening adverse reaction. Candidate gene studies involving well-characterized patients with DILI and drug-exposed controls have identified single nucleotide polymorphisms (SNPs) affecting the metabolism and clearance of specific drugs and hence, influencing individual's susceptibility to DILI...
May 21, 2018: Journal of Hepatology
https://www.readbyqxmd.com/read/29792566/clues-to-an-evolutionary-mystery-the-genes-for-t-toxin-enabler-of-the-devastating-1970-southern-corn-leaf-blight-epidemic-are-present-in-ancestral-species-suggesting-an-ancient-origin
#2
Bradford J Condon, Candace E Elliott, Jonathan Gonzalez, Sung-Hwan Yun, Yasunori Akagi, Tyr Wiesner-Hanks, Motoichiro Kodama, Gillian Turgeon
The Southern Corn Leaf Blight epidemic of 1970 devastated fields of T-cytoplasm corn planted in monoculture throughout the eastern US. The epidemic was driven by race T, a previously unseen race of Cochliobolus heterostrophus. A second fungus, Phyllosticta zeae-maydis, with the same biological specificity, appeared coincidentally. Race T produces T-toxin, while P. zeae-maydis produces PM-toxin, both host selective polyketide toxins necessary for supervirulence. Present abundance of genome sequences offers an opportunity to tackle the evolutionary origins of T- and PM- toxin biosynthetic genes, previously thought unique to these species...
May 24, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29792377/comparative-analysis-of-probiotic-bacteria-based-on-a-new-definition-of-core-genome
#3
Maria Satti, Yasuhiro Tanizawa, Akihito Endo, Masanori Arita
The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of "core genome", core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes...
March 26, 2018: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29792307/putative-vaccine-candidates-and-drug-targets-identified-by-reverse-vaccinology-and-subtractive-genomics-approaches-to-control-haemophilus-ducreyi-the-causative-agent-of-chancroid
#4
Alissa de Sarom, Arun Kumar Jaiswal, Sandeep Tiwari, Letícia de Castro Oliveira, Debmalya Barh, Vasco Azevedo, Carlo Jose Oliveira, Siomar de Castro Soares
Chancroid is a sexually transmitted infection (STI) caused by the Gram-negative bacterium Haemophilus ducreyi The control of chancroid is difficult and the only current available treatment is antibiotic therapy; however, antibiotic resistance has been reported in endemic areas. Owing to recent outbreaks of STIs worldwide, it is important to keep searching for new treatment strategies and preventive measures. Here, we applied reverse vaccinology and subtractive genomic approaches for the in silico prediction of potential vaccine and drug targets against 28 strains of H...
May 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29792161/a-website-to-identify-shared-genes-in-saccharomyces-cerevisiae-homozygous-deletion-library-screens
#5
Mark D Temple
BACKGROUND: The homozygous yeast deletion library includes approximately 4800 diploid strains each containing one deleted non-essential gene. Hundreds of publications have arisen through experimentation using this genome-wide biological resource. As part of this work over 677 genesets have been collated from these experiments representing the phenotypic responses of the library to a diverse set of chemical and physical challenges. DESCRIPTION: A website called the Saccharomyces cerevisiae Homozygous Deletion Library Tools (ScHo DeLiTo-96) has been developed with the primary goal of browsing and identifying genes shared between these responsive phenotypes (available at yeastdb...
May 23, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29792158/landraces-of-snake-melon-an-ancient-middle-eastern-crop-reveal-extensive-morphological-and-dna-diversity-for-potential-genetic-improvement
#6
Samer Omari, Yuri Kamenir, Jennifer I C Benichou, Sarah Pariente, Hanan Sela, Rafael Perl-Treves
BACKGROUND: Snake melon (Cucumis melo var. flexuosus, "Faqqous") is a traditional and ancient vegetable in the Mediterranean area. A collection of landraces from 42 grower fields in Israel and Palestinian territories was grown and characterized in a "Common Garden" rain-fed experiment, at the morphological-horticultural and molecular level using seq-DArT markers. RESULTS: The different landraces ("populations") showed extensive variation in morphology and quantitative traits such as yield and femaleness, and clustered into four horticultural varieties...
May 23, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29791785/expressed-exome-capture-sequencing-eecseq-a-method-for-cost-effective-exome-sequencing-for-all-organisms
#7
Jonathan B Puritz, Katie E Lotterhos
Exome capture is an effective tool for surveying the genome for loci under selection. However, traditional methods require annotated genomic resources. Here, we present a method for creating cDNA probes from expressed mRNA, which are then used to enrich and capture genomic DNA for exon regions. This approach, called "EecSeq", eliminates the need for costly probe design and synthesis. We tested EecSeq in the eastern oyster, Crassostrea virginica, using a controlled exposure experiment. Four adult oysters were heat shocked at 36° C for 1 hour along with four control oysters kept at 14° C...
May 23, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29791438/identity-by-descent-analyses-for-measuring-population-dynamics-and-selection-in-recombining-pathogens
#8
Lyndal Henden, Stuart Lee, Ivo Mueller, Alyssa Barry, Melanie Bahlo
Identification of genomic regions that are identical by descent (IBD) has proven useful for human genetic studies where analyses have led to the discovery of familial relatedness and fine-mapping of disease critical regions. Unfortunately however, IBD analyses have been underutilized in analysis of other organisms, including human pathogens. This is in part due to the lack of statistical methodologies for non-diploid genomes in addition to the added complexity of multiclonal infections. As such, we have developed an IBD methodology, called isoRelate, for analysis of haploid recombining microorganisms in the presence of multiclonal infections...
May 23, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29790980/contrasting-patterns-of-genomic-diversity-reveal-accelerated-genetic-drift-but-reduced-directional-selection-on-x-chromosome-in-wild-and-domestic-sheep-species
#9
Ze-Hui Chen, Min Zhang, Feng-Hua Lv, Xue Ren, Wen-Rong Li, Ming-Jun Liu, Kiwoong Nam, Michael W Bruford, Meng-Hua Li
Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world's sheep populations and 110 whole genomes of wild and domestic sheep...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29790964/evidence-of-evolutionary-history-and-selective-sweeps-in-the-genome-of-meishan-pig-reveals-its-genetic-and-phenotypic-characterization
#10
Pengju Zhao, Ying Yu, Wen Feng, Heng Du, Jian Yu, Huimin Kang, Xianrui Zheng, Zhiquan Wang, George E Liu, Catherine W Ernst, Xueqin Ran, Jiafu Wang, Jian-Feng Liu
Background: Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with the unique features are still poorly understood. The goal of this study is to investigate the genomic signatures and evolutionary evidence related to phenotypic traits of Meishan by large-scale sequencing. Results: We found the unique domestication of Meishan pigs happened at the Taihu Basin area between the Majiabang and the Liangzhu culture, during which 300 protein-coding genes have undergone positive selection...
May 22, 2018: GigaScience
https://www.readbyqxmd.com/read/29790070/genotyping-single-sperm-cells-by-universal-marsala-enables-the-acquisition-of-linkage-information-for-combined-pre-implantation-genetic-diagnosis-and-genome-screening
#11
Haitao Wu, Xiaoting Shen, Lei Huang, Yanhong Zeng, Yumei Gao, Lin Shao, Baomin Lu, Yiping Zhong, Benyu Miao, Yanwen Xu, Yali Wang, Yubin Li, Luoxing Xiong, Sijia Lu, X Sunney Xie, Canquan Zhou
PURPOSE: This paper aims to investigate the feasibility of performing pre-implantation genetic diagnosis (PGD) and pre-implantation genetic screening (PGS) simultaneously by a universal strategy without the requirement of genotyping relevant affected family members or lengthy preliminary work on linkage analysis. METHODS: By utilizing a universal Mutated Allele Revealed by Sequencing with Aneuploidy and Linkage Analyses (MARSALA) strategy based on low depth whole genome sequencing (~3x), not involving specific primers' design nor the enrichment of SNP markers for haplotype construction...
May 22, 2018: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/29789881/characterization-of-recombinant-e-coli-expressing-arsr-from-rhodopseudomonas-palustris-cga009-that-displays-highly-selective-arsenic-adsorption
#12
Changdong Ke, Chungui Zhao, Christopher Rensing, Suping Yang, Yi Zhang
Innovative methods to lower arsenic (As) exposure are sought. The As regulatory protein (ArsR) is reported of having high affinity and specificity to arsenite [As(III)]. Rhodopseudomonas palustris CGA009 is a good model organism for studying As detoxification due to at least three ars operons and four diverse arsRRP1-4 on the genome. In this study, four Escherichia coli harboring arsRRP1-4 derived from CGA009 were engineered and tested regarding their As resistance. The results showed that E. coli (arsRRP2 ) displayed robust As(III) resistance, and its growth inhibition rate was only 2...
May 22, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29789590/heterozygous-diploid-and-interspecies-scrambleing
#13
Michael J Shen, Yi Wu, Kun Yang, Yunxiang Li, Hui Xu, Haoran Zhang, Bing-Zhi Li, Xia Li, Wen-Hai Xiao, Xiao Zhou, Leslie A Mitchell, Joel S Bader, Yingjin Yuan, Jef D Boeke
SCRaMbLE (Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution) is a genome restructuring technique that can be used in synthetic genomes such as that of Sc2.0, the synthetic yeast genome, which contains hundreds to thousands of strategically positioned loxPsym sites. SCRaMbLE has been used to induce rearrangements in yeast strains harboring one or more synthetic chromosomes, as well as plasmid DNA in vitro and in vivo. Here we describe a collection of heterozygous diploid strains produced by mating haploid semisynthetic Sc2...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789543/rapid-pathway-prototyping-and-engineering-using-in-vitro-and-in-vivo-synthetic-genome-scramble-in-methods
#14
Wei Liu, Zhouqing Luo, Yun Wang, Nhan T Pham, Laura Tuck, Irene Pérez-Pi, Longying Liu, Yue Shen, Chris French, Manfred Auer, Jon Marles-Wright, Junbiao Dai, Yizhi Cai
Exogenous pathway optimization and chassis engineering are two crucial methods for heterologous pathway expression. The two methods are normally carried out step-wise and in a trial-and-error manner. Here we report a recombinase-based combinatorial method (termed "SCRaMbLE-in") to tackle both challenges simultaneously. SCRaMbLE-in includes an in vitro recombinase toolkit to rapidly prototype and diversify gene expression at the pathway level and an in vivo genome reshuffling system to integrate assembled pathways into the synthetic yeast genome while combinatorially causing massive genome rearrangements in the host chassis...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789541/identifying-and-characterizing-scrambled-synthetic-yeast-using-rescues
#15
Zhouqing Luo, Lihui Wang, Yun Wang, Weimin Zhang, Yakun Guo, Yue Shen, Linghuo Jiang, Qingyu Wu, Chong Zhang, Yizhi Cai, Junbiao Dai
SCRaMbLE is a novel system implemented in the synthetic yeast genome, enabling massive chromosome rearrangements to produce strains with a large genotypic diversity upon induction. Here we describe a reporter of SCRaMbLEd cells using efficient selection, termed ReSCuES, based on a loxP-mediated switch of two auxotrophic markers. We show that all randomly isolated clones contained rearrangements within the synthetic chromosome, demonstrating high efficiency of selection. Using ReSCuES, we illustrate the ability of SCRaMbLE to generate strains with increased tolerance to several stress factors, such as ethanol, heat and acetic acid...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789446/validation-of-ion-torrent-tm-inherited-disease-panel-with-the-pgm-tm-sequencing-platform-for-rapid-and-comprehensive-mutation-detection
#16
Abeer E Mustafa, Tariq Faquih, Batoul Baz, Rana Kattan, Abdulelah Al-Issa, Asma I Tahir, Faiqa Imtiaz, Khushnooda Ramzan, Moeenaldeen Al-Sayed, Mohammed Alowain, Zuhair Al-Hassnan, Hamad Al-Zaidan, Mohamed Abouelhoda, Bashayer R Al-Mubarak, Nada A Al Tassan
Quick and accurate molecular testing is necessary for the better management of many inherited diseases. Recent technological advances in various next generation sequencing (NGS) platforms, such as target panel-based sequencing, has enabled comprehensive, quick, and precise interrogation of many genetic variations. As a result, these technologies have become a valuable tool for gene discovery and for clinical diagnostics. The AmpliSeq Inherited Disease Panel (IDP) consists of 328 genes underlying more than 700 inherited diseases...
May 22, 2018: Genes
https://www.readbyqxmd.com/read/29789417/mapping-the-hla-ligandome-of-colorectal-cancer-reveals-an-imprint-of-malignant-cell-transformation
#17
Markus W Löffler, Daniel J Kowalewski, Linus Backert, Jörg Bernhardt, Patrick Adam, Heiko Schuster, Florian Dengler, Daniel Backes, Hans-Georg Kopp, Stefan Beckert, Silvia Wagner, Ingmar Königsrainer, Oliver Kohlbacher, Lothar Kanz, Alfred Königsrainer, Hans-Georg Rammensee, Stefan Stevanovic, Sebastian P Haen
Immune cell infiltrates have proven highly relevant for colorectal carcinoma (CRC) prognosis, making CRC a promising candidate for immunotherapy. Since tumors interact with the immune system via HLA-presented peptide ligands, exact knowledge of the peptidome constitution is fundamental for understanding this relationship. Here we comprehensively describe the naturally presented HLA-ligandome of CRC and corresponding non-malignant colon (NMC) tissue. Mass spectrometry identified 35,367 and 28,132 HLA-class I ligands on CRC and NMC, attributable to 7,684 and 6,312 distinct source proteins, respectively...
May 22, 2018: Cancer Research
https://www.readbyqxmd.com/read/29789384/mutations-in-eid1-and-lnk2-caused-light-conditional-clock-deceleration-during-tomato-domestication
#18
Niels A Müller, Lei Zhang, Maarten Koornneef, José M Jiménez-Gómez
Circadian period and phase of cultivated tomato ( Solanum lycopersicum ) were changed during domestication, likely adapting the species to its new agricultural environments. Whereas the delayed circadian phase is mainly caused by allelic variation of EID1 , the genetic basis of the long circadian period has remained elusive. Here we show that a partial deletion of the clock gene LNK2 is responsible for the period lengthening in cultivated tomatoes. We use resequencing data to phylogenetically classify hundreds of tomato accessions and investigate the evolution of the eid1 and lnk2 mutations along successive domestication steps...
May 22, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29788925/de-novo-transcriptome-assembly-of-the-eight-major-organs-of-sacha-inchi-plukenetia-volubilis-and-the-identification-of-genes-involved-in-%C3%AE-linolenic-acid-metabolism
#19
Xiao-Di Hu, Bang-Zhen Pan, Qiantang Fu, Longjian Niu, Mao-Sheng Chen, Zeng-Fu Xu
BACKGROUND: Sacha Inchi (Plukenetia volubilis L.), which belongs to the Euphorbiaceae, has been considered a new potential oil crop because of its high content of polyunsaturated fatty acids in its seed oil. The seed oil especially contains high amounts of α-linolenic acid (ALA), which is useful for the prevention of various diseases. However, little is known about the genetic information and genome sequence of Sacha Inchi, which has largely hindered functional genomics and molecular breeding studies...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29788905/genomic-prediction-of-the-polled-and-horned-phenotypes-in-merino-sheep
#20
Naomi Duijvesteijn, Sunduimijid Bolormaa, Hans D Daetwyler, Julius H J van der Werf
BACKGROUND: In horned sheep breeds, breeding for polledness has been of interest for decades. The objective of this study was to improve prediction of the horned and polled phenotypes using horn scores classified as polled, scurs, knobs or horns. Derived phenotypes polled/non-polled (P/NP) and horned/non-horned (H/NH) were used to test four different strategies for prediction in 4001 purebred Merino sheep. These strategies include the use of single 'single nucleotide polymorphism' (SNP) genotypes, multiple-SNP haplotypes, genome-wide and chromosome-wide genomic best linear unbiased prediction and information from imputed sequence variants from the region including the RXFP2 gene...
May 22, 2018: Genetics, Selection, Evolution: GSE
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