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https://www.readbyqxmd.com/read/29224130/molecular-epidemiology-and-characterization-of-bovine-leukemia-virus-in-domestic-yaks-bos-grunniens-on-the-qinghai-tibet-plateau-china
#1
Meng Wang, Yun Wang, Abdul Rasheed Baloch, Yangyang Pan, Fang Xu, Lili Tian, Qiaoying Zeng
Bovine leukemia virus (BLV) is a member of the genus Deltaretrovirus of the family Retroviridae and cause a chronic lymphosarcoma, which is extensive in cattle. In yaks (Bos grunniens), the distribution, strains and genetic characteristics of BLV have rarely been studied. The aim of our study was to investigate BLV infections in domestic yaks and determine the genetic variability of BLV circulating in a region of the Qinghai Tibet Plateau, China. Blood samples were collected from 798 yaks, which were from different farms from Gansu, Qinghai and Sichuan provinces surrounding the Qinghai-Tibet Plateau...
December 9, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29223358/genome-wide-mining-of-perfect-microsatellites-and-tetranucleotide-orthologous-microsatellites-estimates-in-six-primate-species
#2
Yongtao Xu, Wujiao Li, Zongxiu Hu, Tao Zeng, Yongmei Shen, Sanxu Liu, Xiuyue Zhang, Jing Li, Bisong Yue
Advancement in genome sequencing and in silico mining tools have provided new opportunities for comparative primate genomics of microsatellites. The SSRs (simple sequence repeats) numbers were not correlated with the genome size (Pearson, r=0.310, p=0.550), and were positively correlated with the total length of SSRs (Pearson, r=0.992, p=0.00). A total of 224,289 tetranucleotide orthologous microsatellites families and 367 single-copy orthologous SSRs loci were found in six primate species by homologous alignment...
December 6, 2017: Gene
https://www.readbyqxmd.com/read/29222100/diversity-of-lactococcus-lactis-in-undefined-mixed-dairy-starter-cultures-revealed-by-comparative-genome-analyses-and-targeted-amplicon-sequencing-of-epsd
#3
Cyril A Frantzen, Hans Petter Kleppen, Helge Holo
Undefined mesophilic mixed (DL) starter cultures are used in the production of continental cheeses and contain unknown strain mixtures of Lactococcus lactis and leuconostocs. The choice of starter culture affects the taste, aroma and quality of the final product. To gain insight into the diversity of Lactococcus lactis strains in starter cultures, we whole-genome sequenced 95 isolates from three different starter cultures. Pan-genomic analyses, which included 30 publically available complete genomes, grouped the strains into 21 subsp...
December 8, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29221202/ezh2-alteration-driven-by-microrna-524-5p-and-microrna-324-5p-promotes-cell-proliferation-and-temozolomide-resistance-in-glioma
#4
Tongle Zhi, Tianfu Yu, Minhong Pan, Er Nie, Weining Wu, Xiefeng Wang, Ning Liu, Yongping You, Yingyi Wang, Junxia Zhang
Recent data have been shown that EZH2 is a critical oncogene via the repression of tumor suppressor genes in human cancers. In our study, we performed a genome-wide miRNA screen with a bioinformatics analysis to identify EZH2 specific miRNAs. Of these miRNAs, miR-524-5p and miR-324-5p were decreased in glioma tissues, and confered poor prognosis for glioma patients. Upregulation of miR-524-5p and miR-324-5p reduced glioma cell proliferation and increased temozolomide (TMZ) chemosensitivity by targeting EZH2...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29220374/a-blaoxa-181-harbouring-multi-resistant-st147-klebsiella-pneumoniae-isolate-from-pakistan-that-represent-an-intermediate-stage-towards-pan-drug-resistance
#5
Fouzia Nahid, Rabaab Zahra, Linus Sandegren
Carbapenem resistant Klebsiella pneumoniae (CR-KP) infections are an ever-increasing global issue, especially in the Indian subcontinent. Here we report genetic insight into a blaOXA-181 harbouring Klebsiella pneumoniae, belonging to the pandemic lineage ST147, that represents an intermediate stage towards pan-drug resistance. The CR-KP isolate DA48896 was isolated from a patient from Pakistan and was susceptible only to tigecycline and colistin. It harboured blaOXA-181 and was assigned to sequence type ST147...
2017: PloS One
https://www.readbyqxmd.com/read/29219246/identification-and-genomic-characterization-of-the-emerging-senecavirus-a-in-southeast-china-2017
#6
X Zhang, J Xiao, L Ba, F Wang, D Gao, J Zhang, C Pan, P Qi
Senecavirus A (SVA) is an emerging non-enveloped virus with a single-stranded, positive-sense RNA genome that belongs to the Senecavirus genus in the Picornaviridae family. Senecavirus A-associated swine idiopathic vesicular disease and epidemic transient neonatal losses have caused substantial economic losses for the swine industry. Here, we describe a case of re-emerging vesicular disease among sows and finishing pigs on a swine farm in Fujian Province of southeast China. Other causative pathogens, including FMDV, SVDV and VSV, were excluded, and a novel SVA strain, CH-FJZZ-2017, was isolated...
December 8, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29218871/extracting-a-biologically-relevant-latent-space-from-cancer-transcriptomes-with-variational-autoencoders
#7
Gregory P Way, Casey S Greene
The Cancer Genome Atlas (TCGA) has profiled over 10,000 tumors across 33 different cancer-types for many genomic features, including gene expression levels. Gene expression measurements capture substantial information about the state of each tumor. Certain classes of deep neural network models are capable of learning a meaningful latent space. Such a latent space could be used to explore and generate hypothetical gene expression profiles under various types of molecular and genetic perturbation. For example, one might wish to use such a model to predict a tumor's response to specific therapies or to characterize complex gene expression activations existing in differential proportions in different tumors...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218572/complete-genome-sequence-of-a-new-strain-of-lagenaria-siceraria-endornavirus-from-china
#8
Xiaoqin Peng, Hui Pan, Arif Muhammad, Hongliu An, Shouguo Fang, Weimin Li, Songbai Zhang
An RNA virus tentatively named Lagenaria siceraria endornavirus-Hubei (LsEV-HuB) was isolated from Lagenaria siceraria var. hispida in Hubei, China. The LsEV-HuB genome consists of 15,098 bp and contains a single open reading frame (ORF) encoding a large protein with several conserved domains, including one helicase domain, one glycosyltransferase domain, two capsular polysaccharide synthesis protein (CPS) domains, and one RNA-dependent RNA polymerase (RdRp) domain. LsEV-HuB has nucleotide and amino acid sequence identities of 72...
December 7, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29218053/marker-development-for-phylogenomics-the-case-of-orobanchaceae-a-plant-family-with-contrasting-nutritional-modes
#9
Xi Li, Baohai Hao, Da Pan, Gerald M Schneeweiss
Phylogenomic approaches, employing next-generation sequencing (NGS) techniques, have revolutionized systematic and evolutionary biology. Target enrichment is an efficient and cost-effective method in phylogenomics and is becoming increasingly popular. Depending on availability and quality of reference data as well as on biological features of the study system, (semi-)automated identification of suitable markers will require specific bioinformatic pipelines. Here, we established a highly flexible bioinformatic pipeline, BaitsFinder, to identify putative orthologous single copy genes (SCGs) and to construct bait sequences in a single workflow...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29216329/characterization-of-fusobacterium-varium-fv113-g1-isolated-from-a-patient-with-ulcerative-colitis-based-on-complete-genome-sequence-and-transcriptome-analysis
#10
Tsuyoshi Sekizuka, Yumiko Ogasawara, Toshifumi Ohkusa, Makoto Kuroda
Fusobacterium spp. present in the oral and gut flora is carcinogenic and is associated with the risk of pancreatic and colorectal cancers. Fusobacterium spp. is also implicated in a broad spectrum of human pathologies, including Crohn's disease and ulcerative colitis (UC). Here we report the complete genome sequence of Fusobacterium varium Fv113-g1 (genome size, 3.96 Mb) isolated from a patient with UC. Comparative genome analyses totally suggested that Fv113-g1 is basically assigned as F. varium, in particular, it could be reclassified as notable F...
2017: PloS One
https://www.readbyqxmd.com/read/29209073/integrating-clinical-and-multiple-omics-data-for-prognostic-assessment-across-human-cancers
#11
Bin Zhu, Nan Song, Ronglai Shen, Arshi Arora, Mitchell J Machiela, Lei Song, Maria Teresa Landi, Debashis Ghosh, Nilanjan Chatterjee, Veera Baladandayuthapani, Hongyu Zhao
Multiple omic profiles have been generated for many cancer types; however, comprehensive assessment of their prognostic values across cancers is limited. We conducted a pan-cancer prognostic assessment and presented a multi-omic kernel machine learning method to systematically quantify the prognostic values of high-throughput genomic, epigenomic, and transcriptomic profiles individually, integratively, and in combination with clinical factors for 3,382 samples across 14 cancer types. We found that the prognostic performance varied substantially across cancer types...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29208130/novel-large-scale-chromosomal-transfer-in-bacteroides-fragilis-contributes-to-its-pan-genome-and-rapid-environmental-adaptation
#12
Fasahath Husain, Kevin Tang, Yaligara Veeranagouda, Renata Boente, Sheila Patrick, Garry Blakely, Hannah M Wexler
Bacteroides fragilis, an important component of the human gastrointestinal microbiota, can cause lethal extra-intestinal infection upon escape from the gastrointestinal tract. We demonstrated transfer and recombination of large chromosomal segments from B. fragilis HMW615, a multidrug resistant clinical isolate, to B. fragilis 638R. In one example, the transfer of a segment of ~435 Kb/356 genes replaced ~413 Kb/326 genes of the B. fragilis 638R chromosome. In addition to transfer of antibiotic resistance genes, these transfers (1) replaced complete divergent polysaccharide biosynthesis loci; (2) replaced DNA inversion-controlled intergenic shufflons (that control expression of genes encoding starch utilization system outer membrane proteins) with more complex, divergent shufflons; and (3) introduced additional intergenic shufflons encoding divergent Type 1 restriction/modification systems...
November 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29207648/casc15-gene-polymorphisms-reduce-neuroblastoma-risk-in-chinese-children
#13
Jiao Zhang, Zhen-Jian Zhuo, Jiaxiang Wang, Jing He, Lin Yang, Da Zhang, Pan Qin, Lizhao Yan
In this case-control study, we analyzed the association between three single nucleotide polymorphisms (SNPs) in the CASC15 gene (rs6939340 A>G, rs4712653 T>C, and rs9295536 C>A) and neuroblastoma susceptibility in the Guangdong and Henan populations of China. We genotyped and analyzed 118 cases and 281 control subjects from Henan province and combined them with previously published data from the Guangdong population. In the Henan population, only the rs6939340 G>A variant homozygote AA was associated with decreased neuroblastoma risk [AA vs...
October 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/29206296/comparative-plastome-genomics-and-phylogenomics-of-brachypodium-flowering-time-signatures-introgression-and-recombination-in-recently-diverged-ecotypes
#14
Rubén Sancho, Carlos P Cantalapiedra, Diana López-Alvarez, Sean P Gordon, John P Vogel, Pilar Catalán, Bruno Contreras-Moreira
Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B...
December 5, 2017: New Phytologist
https://www.readbyqxmd.com/read/29206184/high-density-linkage-map-construction-and-mapping-of-salt-tolerant-qtls-at-seedling-stage-in-upland-cotton-using-genotyping-by-sequencing-gbs
#15
Latyr Diouf, Zhaoe Pan, Shou-Pu He, Wen-Fang Gong, Yin Hua Jia, Richard Odongo Magwanga, Kimbembe Romesh Eric Romy, Harun Or Rashid, Joy Nyangasi Kirungu, Xiongming Du
Over 6% of agricultural land is affected by salinity. It is becoming obligatory to use saline soils, so growing salt-tolerant plants is a priority. To gain an understanding of the genetic basis of upland cotton tolerance to salinity at seedling stage, an intra-specific cross was developed from CCRI35, tolerant to salinity, as female with Nan Dan (NH), sensitive to salinity, as the male. A genetic map of 5178 SNP markers was developed from 277 F2:3 populations. The map spanned 4768.098 cM, with an average distance of 0...
December 5, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29204317/bgdmdocker-a-docker-workflow-for-data-mining-and-visualization-of-bacterial-pan-genomes-and-biosynthetic-gene-clusters
#16
Gong Cheng, Quan Lu, Ling Ma, Guocai Zhang, Liang Xu, Zongshan Zhou
Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker...
2017: PeerJ
https://www.readbyqxmd.com/read/29203920/pan-arthropod-analysis-reveals-somatic-pirnas-as-an-ancestral-defence-against-transposable-elements
#17
Samuel H Lewis, Kaycee A Quarles, Yujing Yang, Melanie Tanguy, Lise Frézal, Stephen A Smith, Prashant P Sharma, Richard Cordaux, Clément Gilbert, Isabelle Giraud, David H Collins, Phillip D Zamore, Eric A Miska, Peter Sarkies, Francis M Jiggins
In animals, small RNA molecules termed PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. Here, we report that somatic piRNAs were probably present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and messenger RNAs are common among arthropods...
December 4, 2017: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29203910/tet-proteins-safeguard-bivalent-promoters-from-de-novo-methylation-in-human-embryonic-stem-cells
#18
Nipun Verma, Heng Pan, Louis C Doré, Abhijit Shukla, Qing V Li, Bobbie Pelham-Webb, Virginia Teijeiro, Federico González, Andrei Krivtsov, Chan-Jung Chang, Eirini P Papapetrou, Chuan He, Olivier Elemento, Danwei Huangfu
TET enzymes oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which can lead to DNA demethylation. However, direct connections between TET-mediated DNA demethylation and transcriptional output are difficult to establish owing to challenges in distinguishing global versus locus-specific effects. Here we show that TET1, TET2 and TET3 triple-knockout (TKO) human embryonic stem cells (hESCs) exhibit prominent bivalent promoter hypermethylation without an overall corresponding decrease in gene expression in the undifferentiated state...
December 4, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29202454/fentanyl-related-designer-drugs-w-18-and-w-15-lack-appreciable-opioid-activity-in-vitro-and-in-vivo
#19
Xi-Ping Huang, Tao Che, Thomas J Mangano, Valerie Le Rouzic, Ying-Xian Pan, Michael D Cameron, Michael H Baumann, Gavril W Pasternak, Bryan L Roth
W-18 (4-chloro-N-[1-[2-(4-nitrophenyl)ethyl]-2-piperidinylidene]-benzenesulfonamide) and W-15 (4-chloro-N-[1-(2-phenylethyl)-2-piperidinylidene]-benzenesulfonamide) represent two emerging drugs of abuse chemically related to the potent opioid agonist fentanyl (N-(1-(2-phenylethyl)-4-piperidinyl)-N-phenylpropanamide). Here, we describe the comprehensive pharmacological profiles of W-18 and W-15, as examination of their structural features predicted that they might lack opioid activity. We found W-18 and W-15 to be without detectible activity at μ, δ, κ, and nociception opioid receptors in a variety of assays...
November 16, 2017: JCI Insight
https://www.readbyqxmd.com/read/29201149/complete-genome-sequence-of-the-vibrio-vulnificus-strain-vv2014djh-a-human-pathogenic-bacterium-isolated-from-a-death-case-in-china
#20
Junhang Pan, Yi Sun, Wenwu Yao, Haiyan Mao, Yanjun Zhang, Muyuan Zhu
Background: Vibrio vulnificus, an opportunistic pathogen, is the causative agent of life-threatening septicemia and severe wound infections. However, the pathogenicity and virulence factors of V. vulnificus are not fully understood. Here we report the complete genome sequence of V. vulnificus VV2014DJH, which was isolated from a death case. Results: The genome of the V. vulnificus VV2014DJH contains two circular chromosomes with a mean G+C content of 46.8%, but does not consists of any plasmids...
2017: Gut Pathogens
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