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https://www.readbyqxmd.com/read/29054407/ubiquitination-of-non-lysine-residues-in-the-retroviral-integrase
#1
Zhanxin Wang, Xinhui Hou, Yingchun Wang, Aotian Xu, Weisheng Cao, Ming Liao, Rui Zhang, Jun Tang
Retroviral integrase catalyzes the integration of retroviral genome into host chromosomal DNA, which is a prerequisite of effective viral replication and infection. The human immunodeficiency virus type 1 (HIV-1) integrase has previously been reported to be regulated by the ubiquitination, but the molecular characterization of integrase ubiquitination is still unclear. In this study, we analyzed the ubiquitination of avian leukosis virus (ALV) integrase in detail. The ubiquitination assay showed that, like HIV-1, ALV integrase could also be modified by ubiquitination when expressed in 293 T and DF-1 cells...
October 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29053852/genome-wide-scan-and-analysis-of-positive-selective-signatures-in-dwarf-brown-egg-layers-and-silky-fowl-chickens
#2
Mengmeng Zhang, Liu Yang, Zhencheng Su, Muzhen Zhu, Wenting Li, Keliang Wu, Xuemei Deng
Chinese domestic chickens have been routinely subjected to artificial selection for the production of meats and eggs. Selection results in distinctive signatures in the genome that can reveal the genes underlying phenotypes of interest to breeders. In this study, we used the Chicken60K SNP chip to analyze DNA from Dwarf Brown-egg Layers (DB, n = 203) and Silky Fowls (SF, n = 181) and then examined the relative extended haplotype homozygosity (REHH) and fixation index (FST) to detect selection signatures. Since population structure analysis showed that SF was stratified into 2 subpopulations (SF1 and SF2), we removed the 20 SF1 chickens, and the remaining individuals (DB and SF2) were scanned for genome-wide selection signatures...
October 5, 2017: Poultry Science
https://www.readbyqxmd.com/read/29052939/qtl-mapping-and-analysis-of-heritable-variation-in-affiliative-social-behavior-and-related-traits
#3
Allison T Knoll, Kevin Jiang, Pat Levitt
Humans exhibit broad heterogeneity in affiliative social behavior. Twin and family studies demonstrate that individual differences in core dimensions of social behavior are heritable, yet there are knowledge gaps in understanding the underlying genetic and neurobiological mechanisms. Animal genetic reference panels (GRPs) provide a tractable strategy for examining the behavioral and genetic architecture of complex traits. Here, using males from 50 mouse strains from the BXD GRP, four domains of affiliative social behavior-social approach, social recognition, direct social interaction (partner sniffing), and vocal communication-were examined in two widely used behavioral tasks-the 3-chamber and direct social interaction tasks...
October 20, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/29051750/epidemiology-of-extended-spectrum-%C3%AE-lactamase-producing-e-coli-and-vancomycin-resistant-enterococci-in-the-northern-dutch-german-cross-border-region
#4
Xuewei Zhou, Silvia García-Cobos, Gijs J H M Ruijs, Greetje A Kampinga, Jan P Arends, Dirk M Borst, Lieke V Möller, Nicole D Holman, Theo A Schuurs, Lesla E Bruijnesteijn van Coppenraet, Jan F Weel, Jan H van Zeijl, Robin Köck, John W A Rossen, Alexander W Friedrich
Objectives: To reveal the prevalence and epidemiology of extended-spectrum β-lactamase (ESBL)- and/or plasmid AmpC (pAmpC)- and carbapenemase (CP) producing Enterobacteriaceae and vancomycin-resistant enterococci (VRE) across the Northern Dutch-German border region. Methods: A point-prevalence study on ESBL/pAmpC/CP producing Enterobacteriaceae and VRE was carried out in hospitalized patients in the Northern Netherlands (n = 445, 2012-2013) and Germany (n = 242, 2012). Healthy individuals from the Dutch community (n = 400, 2010-2012) were also screened...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29050278/identification-of-core-genes-and-outcome-in-gastric-cancer-using-bioinformatics-analysis
#5
Chenhua Sun, Qi Yuan, Dongdong Wu, Xiaohu Meng, Baolin Wang
Gastric cancer (GC) is a common malignant neoplasm of gastrointestinal tract. We chose gene expression profile of GSE54129 from GEO database aiming to find key genes during the occurrence and development of GC. 132 samples, including 111 cancer and 21 normal gastric mucosa epitheliums, were included in this analysis. Differentially expressed genes (DEGs) between GC patients and health people were picked out using GEO2R tool, then we performed gene ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis using The Database for Annotation, Visualization and Integrated Discovery (DAVID)...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049454/association-of-mitochondrial-dna-copy-number-with-cardiovascular-disease
#6
Foram N Ashar, Yiyi Zhang, Ryan J Longchamps, John Lane, Anna Moes, Megan L Grove, Josyf C Mychaleckyj, Kent D Taylor, Josef Coresh, Jerome I Rotter, Eric Boerwinkle, Nathan Pankratz, Eliseo Guallar, Dan E Arking
Importance: Mitochondrial dysfunction is a core component of the aging process and may play a key role in atherosclerotic cardiovascular disease. Mitochondrial DNA copy number (mtDNA-CN), which represents the number of mitochondria per cell and number of mitochondrial genomes per mitochondrion, is an indirect biomarker of mitochondrial function. Objective: To determine whether mtDNA-CN, measured in an easily accessible tissue (buffy coat/circulating leukocytes), can improve risk classification for cardiovascular disease (CVD) and help guide initiation of statin therapy for primary prevention of CVD...
October 11, 2017: JAMA Cardiology
https://www.readbyqxmd.com/read/29049350/an-integrative-in-silico-approach-for-therapeutic-target-identification-in-the-human-pathogen-corynebacterium-diphtheriae
#7
Syed Babar Jamal, Syed Shah Hassan, Sandeep Tiwari, Marcus V Viana, Leandro de Jesus Benevides, Asad Ullah, Adrián G Turjanski, Debmalya Barh, Preetam Ghosh, Daniela Arruda Costa, Artur Silva, Richard Röttger, Jan Baumbach, Vasco A C Azevedo
Corynebacterium diphtheriae (Cd) is a Gram-positive human pathogen responsible for diphtheria infection and once regarded for high mortalities worldwide. The fatality gradually decreased with improved living standards and further alleviated when many immunization programs were introduced. However, numerous drug-resistant strains emerged recently that consequently decreased the efficacy of current therapeutics and vaccines, thereby obliging the scientific community to start investigating new therapeutic targets in pathogenic microorganisms...
2017: PloS One
https://www.readbyqxmd.com/read/29048483/draft-genome-of-the-gayal-bos-frontalis
#8
Ming-Shan Wang, Yan Zeng, Xiao Wang, Wen-Hui Nie, Jin-Huan Wang, Wei-Ting Su, Newton O Otecko, Zi-Jun Xiong, Sheng Wang, Kai-Xing Qu, Shou-Qing Yan, Min-Min Yang, Wen Wang, Yang Dong, Dong-Dong Wu, Ya-Ping Zhang
Background: Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history as well as genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. Findings: We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome...
October 5, 2017: GigaScience
https://www.readbyqxmd.com/read/29046615/integrated-genomic-characterization-of-cancer-genes-in-glioma
#9
Aijun Liang, Bin Zhou, Wei Sun
BACKGROUND: Cancers are caused by the acquisition of somatic mutations. Numerous efforts have been made to characterize the key driver genes and pathways in glioma, however, the etiology of glioma is still not completely known. This study was implemented to characterize driver genes in glioma independently of somatic mutation frequencies. METHODS: Driver genes and pathways were predicted by OncodriveCLUST, OncodriveFM, Icages, Drgap and Dendrix in glioma using 31,958 somatic mutations from TCGA, followed by an integrative characterization of driver genes...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/29046351/an-improved-labeling-strategy-enables-automated-detection-of-single-virus-fusion-and-assessment-of-hiv-1-protease-activity-in-single-virions
#10
Chetan Sood, Ashwanth C Francis, Tanay M Desai, Gregory B Melikyan
Enveloped viruses transfer their genomes into host cells by fusing their membrane to that of the cell. To visualize single-virus fusion in living cells, researchers take advantage of HIV-1's proteolytic maturation, which can generate free fluorescent proteins within the viral particle. Co-labeling viruses with a content marker and a fluorescently tagged Vpr (a viral core protein) enables detection of single-virus fusions, but a major limitation of this approach is that not all viral particles incorporate both markers...
October 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29045818/conformational-plasticity-of-hepatitis-c-virus-core-protein-enables-rna-induced-formation-of-nucleocapsid-like-particles
#11
Erik D Holmstrom, Daniel Nettels, Benjamin Schuler
Many of the unanswered questions associated with hepatitis C virus assembly are related to the core protein (HCVcp), which forms an oligomeric nucleocapsid encompassing the viral genome. The structural properties of HCVcp have been difficult to quantify, at least in part because it is an intrinsically disordered protein (IDP). We have used single-molecule FRET techniques to study the conformational dimensions and dynamics of the HCVcp nucleocapsid domain (HCVncd) at various stages during the RNA-induced formation of nucleocapsid-like particles...
October 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29045613/genome-structure-of-rosa-multiflora-a-wild-ancestor-of-cultivated-roses
#12
Noriko Nakamura, Hideki Hirakawa, Shusei Sato, Shungo Otagaki, Shogo Matsumoto, Satoshi Tabata, Yoshikazu Tanaka
The draft genome sequence of a wild rose (Rosa multiflora Thunb.) was determined using Illumina MiSeq and HiSeq platforms. The total length of the scaffolds was 739,637,845 bp, consisting of 83,189 scaffolds, which was close to the 711 Mbp length estimated by k-mer analysis. N50 length of the scaffolds was 90,830 bp, and extent of the longest was 1,133,259 bp. The average GC content of the scaffolds was 38.9%. After gene prediction, 67,380 candidates exhibiting sequence homology to known genes and domains were extracted, which included complete and partial gene structures...
October 16, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29038254/characterization-of-copy-number-control-of-two-haloferax-volcanii-replication-origins-using-deletion-mutants-and-haloarchaeal-artificial-chromosomes-hacs
#13
Sandy Maurer, Katharina Ludt, Jörg Soppa
Haloferax volcanii is polyploid and contains about 20 genome copies under optimal conditions. However, the chromosome copy number is highly regulated and ranges from two during phosphate starvation to more than 40 under phosphate surplus. The aim of this study was the characterization of the influence of two replication origins on the genome copy number. The origin repeats and the genes encoding Origin Recognition Complex (ORC) proteins were deleted. The core origin oriC1-orc1 (ori1) deletion mutant had a lower genome copy number and a higher fitness than the wild-type, in stark contrast to the oriC2-orc5 (ori2) deletion mutant...
October 16, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/29038160/a-high-resolution-genome-wide-crispr-cas9-viability-screen-reveals-structural-features-and-contextual-diversity-of-the-human-cell-essential-proteome
#14
Thierry Bertomeu, Jasmin Coulombe-Huntington, Andrew Chatr-Aryamontri, Karine Bourdages, Etienne Coyaud, Brian Raught, Yu Xia, Mike Tyers
To interrogate genes essential for cell growth, proliferation and survival in human cells, we carried out a genome-wide CRISPR/Cas9 screen in a B-cell lymphoma line using a custom extended knockout (EKO) library of 278,754 sgRNAs that targeted 19,084 RefSeq genes, 20,852 alternatively-spliced exons and 3,872 hypothetical genes. A new statistical analysis tool called RANKS identified 2,280 essential genes, 234 of which were unique. Individual essential genes were validated experimentally and linked to ribosome biogenesis and stress responses...
October 16, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/29038125/modulators-of-enterococcus-faecalis-cell-envelope-integrity-and-antimicrobial-resistance-influence-stable-colonization-of-the-mammalian-gastrointestinal-tract
#15
Ismael L Banla, Sushma Kommineni, Michael Hayward, Marinelle Rodrigues, Kelli L Palmer, Nita H Salzman, Christopher J Kristich
The Gram-positive bacterium Enterococcus faecalis is both a colonizer of the gastrointestinal tract (GIT) and an agent of serious nosocomial infections. Although typically required for pathogenesis, GIT colonization by E. faecalis is poorly understood. E. faecalis tolerates high concentrations of GIT antimicrobials like cholate and lysozyme, leading us to hypothesize that resistance to intestinal antimicrobials is essential for long-term GIT colonization. Analyses of E. faecalis mutants exhibiting defects in antimicrobial resistance revealed that IreK, a determinant of envelope integrity and antimicrobial resistance, is required for long-term GIT colonization...
October 16, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/29037158/genomic-divergence-and-cohesion-in-a-species-of-pelagic-freshwater-bacteria
#16
Matthias Hoetzinger, Martin W Hahn
BACKGROUND: In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwaters with low habitat connectivity - i.e. elevated geographic barriers to gene flow - is unclear. To investigate further we studied genomic trends within the globally abundant PnecC cluster (genus Polynucleobacter, Betaproteobacteria) and analyzed homologous recombination within the affiliated species P...
October 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29036542/database-resources-of-the-big-data-center-in-2018
#17
(no author information available yet)
The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations)...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29034857/minimal-standards-for-describing-new-species-belonging-to-the-families-campylobacteraceae-and-helicobacteraceae-campylobacter-arcobacter-helicobacter-and-wolinella-spp
#18
Stephen L W On, William G Miller, Kurt Houf, James G Fox, Peter Vandamme
Ongoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae. This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae, thus including species in Campylobacter, Arcobacter, Helicobacter, and Wolinella...
October 16, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29034848/characterization-of-thermotolerant-phototrophic-bacteria-rhodoplanes-tepidicaeni-sp-nov-and-rhodoplanes-azumiensis-sp-nov-isolated-from-a-geothermal-spring
#19
Akira Hiraishi
Two strains of thermotolerant phototrophic alphaproteobacteria, designated strains TUT3542(T) and TUT3581(T), were isolated from sediment mud and cyanobacterial mats in a geothermal spring in Japan, respectively, and taxonomically characterized. Both the strains were budding motile rods and were able to grow at 45 °C. Phototrophically grown cells of strains TUT3542(T) and TUT3581(T) produced pink and brownish red cultures, respectively, and showed in vivo absorption maxima at 800, 858-859 and 892-895 nm in the near infrared region, indicating the presence of a core reaction centre and peripheral pigment complexes with bacteriochlorophyll a...
October 16, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29034626/-sequence-analysis-and-expression-patterns-of-histone-h2a-variants-in-phytophthora-infestans
#20
Xiaowen Wang, Liyun Guo
In eukaryotic cells, DNA is packaged inside the nucleus together with histones to form nucleosomes. Each histone molecule contains two of each core histone subunits H2A, H2B, H3 and H4. Among core histones, the H2A family is of great interest due to the high diversity of specialized variants. These variants have shown important role in critical cellular processes. Epigenetic mechanism in oomycetes is barely known. Phytophthora infestans is a severe pathogen and a model species in oomycetes. In this study, we studied the sequence and expression pattern of H2A variants of P...
November 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
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