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https://www.readbyqxmd.com/read/28531233/in-silico-development-and-characterization-of-tri-nucleotide-simple-sequence-repeat-markers-in-hazelnut-corylus-avellana-l
#1
Gehendra Bhattarai, Shawn A Mehlenbacher
Plant genomes are now sequenced rapidly and inexpensively. In silico approaches allow efficient development of simple sequence repeat markers, also known as microsatellite markers, from these sequences. A search of the genome sequence of 'Jefferson' hazelnut (Corylus avellana L.) identified 8,708 tri-nucleotide simple sequence repeats with at least five repeat units, and stepwise removal of the less promising sequences led to the development of 150 polymorphic markers. Fragments in the 'Jefferson' sequence containing tri-nucleotide repeats were used as references and aligned with genomic sequences from seven other cultivars...
2017: PloS One
https://www.readbyqxmd.com/read/28531104/stumbling-across-the-same-phage-comparative-genomics-of-widespread-temperate-phages-infecting-the-fish-pathogen-vibrio-anguillarum
#2
Panos G Kalatzis, Nanna Iben Rørbo, Daniel Castillo, Jesper Juel Mauritzen, Jóhanna Jørgensen, Constantina Kokkari, Faxing Zhang, Pantelis Katharios, Mathias Middelboe
Nineteen Vibrio anguillarum-specific temperate bacteriophages isolated across Europe and Chile from aquaculture and environmental sites were genome sequenced and analyzed for host range, morphology and life cycle characteristics. The phages were classified as Siphoviridae with genome sizes between 46,006 and 54,201 bp. All 19 phages showed high genetic similarity, and 13 phages were genetically identical. Apart from sporadically distributed single nucleotide polymorphisms (SNPs), genetic diversifications were located in three variable regions (VR1, VR2 and VR3) in six of the phage genomes...
May 20, 2017: Viruses
https://www.readbyqxmd.com/read/28530677/whole-genome-resequencing-of-292-pigeonpea-accessions-identifies-genomic-regions-associated-with-domestication-and-agronomic-traits
#3
Rajeev K Varshney, Rachit K Saxena, Hari D Upadhyaya, Aamir W Khan, Yue Yu, Changhoon Kim, Abhishek Rathore, Dongseon Kim, Jihun Kim, Shaun An, Vinay Kumar, Ghanta Anuradha, Kalinati Narasimhan Yamini, Wei Zhang, Sonnappa Muniswamy, Jong-So Kim, R Varma Penmetsa, Eric von Wettberg, Swapan K Datta
Pigeonpea (Cajanus cajan), a tropical grain legume with low input requirements, is expected to continue to have an important role in supplying food and nutritional security in developing countries in Asia, Africa and the tropical Americas. From whole-genome resequencing of 292 Cajanus accessions encompassing breeding lines, landraces and wild species, we characterize genome-wide variation. On the basis of a scan for selective sweeps, we find several genomic regions that were likely targets of domestication and breeding...
May 22, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28529729/characterization-of-the-novel-in1059-harbouring-vim-gene-cassette
#4
Dongguo Wang, Jinhong Yang, Meiyu Fang, Wei He, Ying Zhang, Caixia Liu, Dongsheng Zhou
BACKGROUND: VIM-type enzyme encodes the most widely acquired metallo-β-lactamases in Gram- negative bacteria. To obtain current epidemiological data for integrons from enterobacteriae in hospital, the study characterizes the genetic structure in In1059 by comparison with In846 integrons harbouring VIM gene and other class 1 integrons including In37, In62, In843 and In1021 with the aim of identifying the putative mechanisms involved integron mobilization and infer evolution of relevant integrons...
2017: Antimicrobial Resistance and Infection Control
https://www.readbyqxmd.com/read/28527015/a-genome-wide-association-study-identifies-the-genomic-region-associated-with-shell-color-in-yesso-scallop-patinopecten-yessoensis
#5
Liang Zhao, Yangping Li, Yajuan Li, Jiachen Yu, Huan Liao, Shuyue Wang, Jia Lv, Jun Liang, Xiaoting Huang, Zhenmin Bao
The shell color polymorphism widely exists in economic shellfish, which not only results in a better visual perception but also shows great value as an economic trait for breeding. Small numbers of reddish-orange shell Yesso scallops, Patinopecten yessoensis, were found in cultured populations compared to the brown majority. In this study, a genome-wide association study was conducted to understand the genetic basis of shell color. Sixty-six 2b-RAD libraries with equal numbers of reddish-orange and brown shell individuals were constructed and sequenced using the Illumina HiSeq 2000 platform...
May 19, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28526729/phased-genotyping-by-sequencing-enhances-analysis-of-genetic-diversity-and-reveals-divergent-copy-number-variants-in-maize
#6
Heather Manching, Subhajit Sengupta, Keith R Hopper, Shawn W Polson, Yuan Ji, Randall J Wisser
High-throughput sequencing of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires a number of issues encountered with GBS be considered, including the sequencing of non-overlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526032/multiplex-dnase-free-one-step-reverse-transcription-pcr-for-plasmodium-18s-rrna-and-spliced-gametocyte-specific-mrnas
#7
Amelia E Hanron, Zachary P Billman, Annette M Seilie, Tayla M Olsen, Matthew Fishbaugher, Ming Chang, Thomas Rueckle, Nicole Andenmatten, Bryan Greenhouse, Emmanuel Arinaitwe, John Rek, Smita Das, Gonzalo J Domingo, Kelly Shipman, Stefan H Kappe, James G Kublin, Sean C Murphy
BACKGROUND: Plasmodium gametocytes are sexual stages transmitted to female Anopheles mosquitoes. While Plasmodium parasites can be differentiated microscopically on Giemsa-stained blood smears, molecular methods are increasingly used because of their increased sensitivity. Molecular detection of gametocytes requires methods that discriminate between asexual and sexual stage parasites. Commonly tested gametocyte-specific mRNAs are pfs25 and pfs230 detected by reverse transcription polymerase chain reaction (RT-PCR)...
May 19, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28524769/machine-learning-for-epigenetics-and-future-medical-applications
#8
Lawrence B Holder, M Muksitul Haque, Michael K Skinner
Understanding epigenetic processes holds immense promise for medical applications. Advances in Machine Learning (ML) are critical to realize this promise. Previous studies used epigenetic data sets associated with the germline transmission of epigenetic transgenerational inheritance of disease and novel ML approaches to predict genome-wide locations of critical epimutations. A combination of Active Learning (ACL) and Imbalanced Class Learning (ICL) was used to address past problems with ML to develop a more efficient feature selection process and address the imbalance problem in all genomic data sets...
May 19, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28523007/transcriptomic-identification-of-drought-related-genes-and-ssr-markers-in-sudan-grass-based-on-rna-seq
#9
Yongqun Zhu, Xia Wang, Linkai Huang, Chaowen Lin, Xinquan Zhang, Wenzhi Xu, Jianhua Peng, Zhou Li, Haidong Yan, Fuxiang Luo, Xie Wang, Li Yao, Dandan Peng
Sudan grass (Sorghum sudanense) is an annual warm-season gramineous forage grass that is widely used as pasture, hay, and silage. However, drought stress severely impacts its yield, and there is limited information about the mechanisms of drought tolerance in Sudan grass. In this study, we used next-generation sequencing to identify differentially expressed genes (DEGs) in the Sudan grass variety Wulate No.1, and we developed simple sequence repeat (SSR) markers associated with drought stress. From 852,543,826 raw reads, nearly 816,854,366 clean reads were identified and used for analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28522540/orthogonal-estimates-of-variances-for-additive-dominance-and-epistatic-effects-in-populations
#10
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/28521825/association-of-4p14-and-6q27-variation-with-graves-disease-a-case-control-study-and-a-meta-analysis-of-available-evidence
#11
Fa-Mei Li, Lin Liu, Li-Nan Pang, Min Shen, Hong-Wen Lu, Xiao-Hong Zhang, Xun Chu, Zhen-Ju Song
BACKGROUND: The etiology of the Graves' disease (GD) is largely unknown. However, genetic factors are believed to play a major role. A recent genome-wide association study in a Han Chinese sample collection revealed two new Graves' disease (GD) risk loci within chromosome band 4p14 and 6q27. In this study, we aimed to investigate these associations with Weifang Han Chinese population of Shandong province and perform a meta-analysis of associations with GD. METHODS: A case-control study was conducted to investigate association of variation within 4p14 and 6q27 to GD susceptibility in Weifang Han Chinese population of Shandong province...
May 18, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28521758/genome-wide-association-study-for-feed-efficiency-and-growth-traits-in-u-s-beef-cattle
#12
Christopher M Seabury, David L Oldeschulte, Mahdi Saatchi, Jonathan E Beever, Jared E Decker, Yvette A Halley, Eric K Bhattarai, Maral Molaei, Harvey C Freetly, Stephanie L Hansen, Helen Yampara-Iquise, Kristen A Johnson, Monty S Kerley, JaeWoo Kim, Daniel D Loy, Elisa Marques, Holly L Neibergs, Robert D Schnabel, Daniel W Shike, Matthew L Spangler, Robert L Weaber, Dorian J Garrick, Jeremy F Taylor
BACKGROUND: Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28521728/a-method-for-the-allocation-of-sequencing-resources-in-genotyped-livestock-populations
#13
Serap Gonen, Roger Ros-Freixedes, Mara Battagin, Gregor Gorjanc, John M Hickey
BACKGROUND: This paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise the ability to phase and impute sequenced haplotypes into the whole population. METHODS: We present two algorithms. The first selects focal individuals that collectively represent the maximum possible portion of the haplotype diversity in the population. The second allocates a fixed sequencing budget among the families of focal individuals to enable phasing of their haplotypes at the sequence level...
May 18, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28521526/the-impact-of-genetics-on-future-drug-discovery-in-schizophrenia
#14
Mitsuyuki Matsumoto, Noah M Walton, Hiroshi Yamada, Yuji Kondo, Gerard J Marek, Katsunori Tajinda
Failures of investigational new drugs (INDs) for schizophrenia have left huge unmet medical needs for patients. Given the recent lackluster results, it is imperative that new drug discovery approaches (and resultant drug candidates) target pathophysiological alterations that are shared in specific, stratified patient populations that are selected based on pre-identified biological signatures. One path to implementing this paradigm is achievable by leveraging recent advances in genetic information and technologies...
May 18, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28521338/klebsiella-pneumoniae-a-major-worldwide-source-and-shuttle-for-antibiotic-resistance
#15
Shiri Navon-Venezia, Kira Kondratyeva, Alessandra Carattoli
Klebsiella pneumoniae is an important multidrug-resistant (MDR) pathogen affecting humans and a major source for hospital infections associated with high morbidity and mortality due to limited treatment options. We summarize the wide resistome of this pathogen, which encompasses plentiful chromosomal and plasmid-encoded antibiotic resistance genes (ARGs). Under antibiotic selective pressure, K. pneumoniae continuously accumulates ARGs, by de novo mutations, and via acquisition of plasmids and transferable genetic elements, leading to extremely drug resistant (XDR) strains harboring a 'super resistome'...
May 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28520890/vcf-filter-interactive-prioritization-of-disease-linked-genetic-variants-from-sequencing-data
#16
Heiko Müller, Raul Jimenez-Heredia, Ana Krolo, Tatjana Hirschmugl, Jasmin Dmytrus, Kaan Boztug, Christoph Bock
Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520499/genome-wide-identification-of-potential-drug-target-in-enterobacteriaceae-family-a-homology-based-method
#17
Morteza Hadizadeh, Seyyede Nasim Tabatabaiepour, Seyyede Zahra Tabatabaiepour, Hossein Hosseini Nave, Mohsen Mohammadi, Seyyed Mohsen Sohrabi
The Enterobacteriaceae is a large family of Gram-negative, facultative anaerobic, non-spore forming rod-shaped bacteria that includes harmless and pathogenic organisms. The emergence and development of drug resistance in Enterobacteriaceae is complicating the treatment of serious infections. The aim of this study is to predict and characterize putative drug targets in Enterobacteriaceae family employing a homology-based computational method. The final putative drug targets were qualitatively characterized via cellular function prediction, subcellular localization prediction, broad-spectrum, and druggability analyses...
May 18, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28517981/a-systematic-review-of-studies-of-dna-methylation-in-the-context-of-a-weight-loss-intervention
#18
Lucia Aronica, A Joan Levine, Kevin Brennan, Jeffrey Mi, Christopher Gardner, Robert W Haile, Megan P Hitchins
AIM: Obesity results from the interaction of genetic and environmental factors, which may involve epigenetic mechanisms such as DNA methylation (DNAm). MATERIALS & METHODS: We have followed the PRISMA protocol to select studies that analyzed DNAm at baseline and end point of a weight loss intervention using either candidate-locus or genome-wide approaches. RESULTS: Six genes displayed weight loss associated DNAm across four out of nine genome-wide studies...
May 2017: Epigenomics
https://www.readbyqxmd.com/read/28516784/in-culture-cross-linking-of-bacterial-cells-reveals-large-scale-dynamic-protein-protein-interactions-at-the-peptide-level
#19
Luitzen de Jong, Edward A de Koning, Winfried Roseboom, Hansuk Buncherd, Martin J Wanner, Irena Dapic, Petra J Jansen, Jan H van Maarseveen, Garry L Corthals, Peter J Lewis, Leendert Willem Hamoen, Chris G de Koster
Identification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). We used the Gram positive model bacterium Bacillus subtilis as an exemplar system. Within 5 min extensive intracellular cross-linking was detected, while intracellular cross-linking in a Gram-negative species, Escherichia coli, was still undetectable after 30 min, in agreement with the low permeability in this organism for lipophilic compounds like BAMG...
May 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28515293/virus-like-vesicles-of-kaposi-s-sarcoma-associated-herpesvirus-activate-lytic-replication-through-triggering-differentiation-signaling
#20
Danyang Gong, Xinghong Dai, Yuchen Xiao, Yushen Du, Travis J Chapa, Jeffrey R Johnson, Xinmin Li, Nevan J Krogan, Hongyu Deng, Ting-Ting Wu, Ren Sun
Virus-like vesicles (VLVs) are membrane enclosed vesicles that resemble native enveloped viruses in organization, but lack viral capsid and genome. During the productive infection of tumor associated gamma-herpesviruses, both virions and VLVs are produced and released into the extracellular space. However, studies of gamma-herpesvirus associated VLVs have been largely restricted by the technical difficulty of separating VLVs from mature virions. Here, we report a strategy of using a Kaposi's sarcoma-associated herpesvirus (KSHV) mutant defective in small capsid protein, unable to produce mature virions, to selectively isolate VLVs...
May 17, 2017: Journal of Virology
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