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Pan Genome

Simon T Hui, Zeyneb Kurt, Iina Tuominen, Frode Norheim, Richard C Davis, Calvin Pan, Darwin L Dirks, Clara E Magyar, Samuel W French, Karthickeyan Chella Krishnan, Simon Sabir, Francisco Campos-Pérez, Nahum Méndez-Sánchez, Luis Macías-Kauffer, Paola León-Mimila, Samuel Canizales-Quinteros, Xia Yang, Simon W Beaven, Adriana Huertas-Vazquez, Aldons J Lusis
We report the genetic analysis of a "humanized" hyperlipidemic mouse model for progressive nonalcoholic steatohepatitis (NASH) and fibrosis. Mice carrying transgenes for human APOE*3-Leiden and CETP and fed a "Western" diet were studied on the genetic backgrounds of over 100 inbred mouse strains. The mice developed hepatic inflammation and fibrosis that was highly dependent on genetic background, with vast differences in the degree of fibrosis. Histological analysis showed features characteristic of human NASH, including macrovesicular steatosis, hepatocellular ballooning, inflammatory foci and pericellular collagen deposition...
June 16, 2018: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
Ramona Lüthi, Céline L Boujon, Ronja Kauer, Michel C Koch, Ilias G Bouzalas, Torsten Seuberlich
A novel bovine astrovirus genotype species (BoAstV-CH13/NeuroS1) was recently identified in brain tissues of cattle as a plausible cause of encephalitis. The purpose of the present study was to develop and validate real time RT-PCR assays for the detection of BoAstV-CH13/NeuroS1 in brain tissues of cattle. Three different primer-probe combinations were designed based on BoAstV-CH13/NeuroS1 full-genome sequences of 11 different strains identified in cattle, and established in three distinct one-step real time RT-PCR protocols...
June 15, 2018: Scientific Reports
Shiyong Zhang, Xiaohui Chen, Minghua Wang, Wenyi Zhang, Jianlin Pan, Qin Qin, Liqiang Zhong, Junjie Shao, Mengling Sun, Hucheng Jiang, Wenji Bian
The Sox gene family has been systematically characterized in some fish species but not in catfish Ictalurus punctatus. In this study, 25 Sox genes were identified in the channel catfish genome and classified into seven families based on their conserved domains as follows: eight genes in SoxB group (six in SoxB1 subgroup and two in SoxB2 subgroup); five genes in SoxC group; three genes in SoxD and SoxF groups; four genes in SoxE group; and one gene in SoxH and SoxK groups. The mammalian Sox groups SoxA, G, I, and J were not present in catfish...
March 6, 2018: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Luming Yang, Hanqiang Liu, Jianyu Zhao, Yupeng Pan, Siyuan Cheng, Calvin D Lietzow, Changlong Wen, Xiaolan Zhang, Yiqun Weng
Plants employ tight genetic control to integrate intrinsic growth signals and environmental cues to enable organ growth to a defined size. Many genes contributing to cell proliferation and/or cell expansion and consequently organ size control have been identified, but the regulatory pathways are poorly understood. Here we have characterized a cucumber littleleaf (ll) mutant which exhibits smaller organ sizes but more lateral branches than the wildtype. The small organ size in ll was due to a reduction of both cell number and cell size...
June 14, 2018: Plant Journal: for Cell and Molecular Biology
Meng Zhang, Yu Pan, Ranran Jiang, Pingfu Hou, Haixia Shan, Fang Chen, Tao Jiang, Jin Bai, Junnian Zheng
DKC1, an X‑linked gene encoding dyskerin at Xq28, is a crucial component of the telomerase complex and is indispensable for normal telomere function and the post‑-transcriptional modification of precursor rRNA. It has been revealed to exert diverse biological functions and prognostic values in numerous types of cancers. Our present study was aimed at examining DKC1 expression in normal renal tissues and clear cell renal cell carcinoma (ccRCC) samples and the prognostic value of DKC1 in ccRCC. We examined DKC1 protein expression levels in tissue microarrays including 307 cases of ccRCC tissues and in 75 pairs of ccRCC and paracancerous tissues with immunohistochemistry...
June 11, 2018: Oncology Reports
Cheng Zhang, Pan Ni, Hafiz Ishfaq Ahmad, M Gemingguli, A Baizilaitibei, D Gulibaheti, Yaping Fang, Haiyang Wang, Akhtar Rasool Asif, Changyi Xiao, Jianhai Chen, Yunlong Ma, Xiangdong Liu, Xiaoyong Du, Shuhong Zhao
Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native populations, is still lacking. In our study, we generated whole genome sequences from 4 Chinese native horses and combined them with 48 publicly available full genome sequences, from which 15 341 213 high-quality unique single-nucleotide polymorphism variants were identified...
2018: Evolutionary Bioinformatics Online
Xing Li, Mengning Zheng, Jinding Pu, Yumin Zhou, Hui Pan, Wei Hong, Xin Fu, Yan Peng, Wenqu Zhou, Bing Li, Pixin Ran
To investigate the effect of stimulation of Human Bronchial Epithelial Cells (HBEC) by arterial traffic ambient PM2.5 (TAPM2.5) and wood smoke PM2.5 (WSPM2.5) on the expression of lncRNAs in order to find new therapeutic targets for treatment of chronic obstructive pulmonary disease (COPD). HBECs were exposed to TAPM2.5 and WSPM2.5 at a series of concentrations. The microarray analysis was used to detect the lncRNA and mRNA expression profiles. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and gene ontology (GO) enrichment were conducted to analyze the differentially expressed lncRNAs and mRNAs...
June 13, 2018: Bioscience Reports
Marketa Kaucka, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, Karl Annusver, Maria Kasper, Orsolya Symmons, Leslie Pan, Francois Spitz, Jozef Kaiser, Maria Hovorakova, Tomas Zikmund, Kazunori Sunadome, Michael P Matise, Hui Wang, Ulrika Marklund, Hind Abdo, Patrik Ernfors, Pascal Maire, Maud Wurmser, Andrei S Chagin, Kaj Fried, Igor Adameyko
Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium...
June 13, 2018: ELife
Chengjie Zhang, Yanbing Zhu, Song Wang, Zheng Zachory Wei, Michael Qize Jiang, Yongbo Zhang, Yuhualei Pan, Shaoxin Tao, Jimei Li, Ling Wei
A cascade of pathological processes is triggered in the lesion area after ischemic stroke. Unfortunately, our understanding of these complicated molecular events is incomplete. In this investigation, we sought to better understand the detailed molecular and inflammatory events occurring after ischemic stroke. RNA-seq technology was used to identify whole gene expression profiles at days (D1, D3, D7, D14, D21) after focal cerebral ischemia in mice. Enrichment analyses based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms for the differentially expressed genes (DEGs) were then analyzed...
April 2018: Aging and Disease
Norhan Mahfouz, Serena Caucci, Eric Achatz, Torsten Semmler, Sebastian Guenther, Thomas U Berendonk, Michael Schroeder
Wastewater treatment plants play an important role in the emergence of antibiotic resistance. They provide a hot spot for exchange of resistance within and between species. Here, we analyse and quantify the genomic diversity of the indicator Escherichia coli in a German wastewater treatment plant and we relate it to isolates' antibiotic resistance. Our results show a surprisingly large pan-genome, which mirrors how rich an environment a treatment plant is. We link the genomic analysis to a phenotypic resistance screen and pinpoint genomic hot spots, which correlate with a resistance phenotype...
June 12, 2018: Scientific Reports
Xiongming Du, Shouye Liu, Junling Sun, Gengyun Zhang, Yinhua Jia, Zhaoe Pan, Haitao Xiang, Shoupu He, Qiuju Xia, Songhua Xiao, Weijun Shi, Zhiwu Quan, Jianguang Liu, Jun Ma, Baoyin Pang, Liru Wang, Gaofei Sun, Wenfang Gong, Johnie N Jenkins, Xiangyang Lou, Jun Zhu, Haiming Xu
BACKGROUND: Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic architecture in genomic level. GWAS has been an effective way to explore genetic basis of quantitative traits in human and many crops. This study aims to dissect genetic mechanism seven cottonseed traits by a GWAS for genetic improvement...
June 13, 2018: BMC Genomics
J-H Zhou, Y-N Wang, X-R Li, Y-S Liu, Q Pan, X Lan
The prevalence of hepatitis E virus (HEV) in domestic swine threats the public health, due to the risk of zoonotic transmission. In this study, we investigated the prevalence and genetic features of HEV in swine, in Gansu, which is geographically an important province in China. 377 fecal samples were collected from pig farms in Gansu province of China and tested for HEV RNA by RT-PCR. The prevalence rate is about 23% in pig farms of Gansu province. By RT-nPCR, 5' and 3' RACE methods, a whole genome with 7,284 nt in length, termed as swCH189, was obtained and investigated by nucleotide, codon and amino acid usage analyses...
2018: Acta Virologica
Xinshen Li, Xiaomei Huang, Gongyou Chen, Lifang Zou, Lingen Wei, Juling Hua
Ralstonia solanacearum is a soil-borne phytopathogen associated with bacterial wilt disease of sesame. R. solanacearum is the predominant agent causing damping-off from tropical to temperate regions. Because bacterial wilt has decreased the sesame industry yield, we sequenced the SEPPX05 genome using PacBio and Illumina HiSeq 2500 systems and revealed that R. solanacearum strain SEPPX05 carries a bipartite genome consisting of a 3,930,849 bp chromosome and a 2,066,085 bp megaplasmid with 66.84% G+C content that harbors 5,427 coding sequences...
June 2018: Genes & Genomics
Jinhua Li, Xiaoxing Su, Yinlei Wang, Wei Yang, Yu Pan, Chenggang Su, Xingguo Zhang
BTB (broad-complex, tramtrack, and bric-a-brac) family proteins are characterized by the presence of a protein-protein interaction BTB domain. BTB proteins have diverse functions, including transcriptional regulation, protein degradation, chromatin remodeling, and cytoskeletal regulation. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species. In this study, 38 BTB genes were identified based on tomato whole-genome sequence. Phylogenetic analysis of BTB proteins in tomato revealed that SlBTB proteins could be divided into at least 4 subfamilies...
January 2018: Genes & Genomics
Xue-Yin Pan, Yang Yang, Hong-Wu Meng, Hai-di Li, Xin Chen, Hui-Min Huang, Fang-Tian Bu, Hai-Xia Yu, Qin Wang, Cheng Huang, Xiao-Ming Meng, Jun Li
The activation of hepatic stellate cells (HSCs) is a central event in the progression of liver fibrosis. Multiple studies proved that DNA methylation might accelerate HSCs activation. However, the specific pathogenesis of liver fibrosis remains not fully addressed. Our laboratory performed Genome methylation screening to find out the methylated gene in mice with liver fibrosis. The pilot experiments showed that the promoter of prostacyclin synthase ( PTGIS ) gene was hypermethylated in CCl4 -induced liver fibrosis mouse model...
2018: Frontiers in Pharmacology
Matthieu Legendre, Elisabeth Fabre, Olivier Poirot, Sandra Jeudy, Audrey Lartigue, Jean-Marie Alempic, Laure Beucher, Nadège Philippe, Lionel Bertaux, Eugène Christo-Foroux, Karine Labadie, Yohann Couté, Chantal Abergel, Jean-Michel Claverie
With DNA genomes reaching 2.5 Mb packed in particles of bacterium-like shape and dimension, the first two Acanthamoeba-infecting pandoraviruses remained up to now the most complex viruses since their discovery in 2013. Our isolation of three new strains from distant locations and environments is now used to perform the first comparative genomics analysis of the emerging worldwide-distributed Pandoraviridae family. Thorough annotation of the genomes combining transcriptomic, proteomic, and bioinformatic analyses reveals many non-coding transcripts and significantly reduces the former set of predicted protein-coding genes...
June 11, 2018: Nature Communications
Jessica S Russell, Leon Caly, Renata Kostecki, Sarah L McGuinness, Glen Carter, Dieter Bulach, Torsten Seemann, Tim P Stinear, Rob Baird, Mike Catton, Julian Druce
Murray Valley Encephalitis virus (MVEV) is a mosquito-borne Flavivirus. Clinical presentation is rare but severe, with a case fatality rate of 15⁻30%. Here we report a case of MVEV from the cerebrospinal fluid (CSF) of a patient in the Northern Territory in Australia. Initial diagnosis was performed using both MVEV-specific real-time, and Pan- Flavivirus conventional, Polymerase Chain Reaction (PCR), with confirmation by Sanger sequencing. Subsequent isolation, the first from CSF, was conducted in Vero cells and the observed cytopathic effect was confirmed by increasing viral titre in the real-time PCR...
June 11, 2018: Viruses
Yiou Pan, Pujin Chai, Chao Zheng, Hongfei Xu, Yongqiang Wu, Xiwu Gao, Jinghui Xi, Qingli Shang
The cytochrome P450 monooxygenases play a key role in detoxification mechanism for spirotetramat resistance in Aphis gossypii Glover. However, only one P450 genes (CYP6DA2), among thirty-five P450 genes identified from Aphis gossypii transcriptome database, has been reported to play important role in spirotetramat resistance in previous resistance level until now. In this study, after the confirmation of the rise of resistance level and important roles of P450s in spirotetramat resistance by the synergism analysis, the gene expression changes were determined for P450 genes in spirotetramat susceptible and resistant strains...
June 2018: Pesticide Biochemistry and Physiology
Xin Fang, Jonathan M Monk, Nathan Mih, Bin Du, Anand V Sastry, Erol Kavvas, Yara Seif, Larry Smarr, Bernhard O Palsson
BACKGROUND: Escherichia coli is considered a leading bacterial trigger of inflammatory bowel disease (IBD). E. coli isolates from IBD patients primarily belong to phylogroup B2. Previous studies have focused on broad comparative genomic analysis of E. coli B2 isolates, and identified virulence factors that allow B2 strains to reside within human intestinal mucosa. Metabolic capabilities of E. coli strains have been shown to be related to their colonization site, but remain unexplored in IBD-associated strains...
June 11, 2018: BMC Systems Biology
Hang Su, He Zhang, Xinghua Wei, Daian Pan, Li Jing, Daqing Zhao, Yu Zhao, Bin Qi
As one of most important traditional Chinese medicine resources, the oviduct of female Rana chensinensis (Chinese brown frog) was widely used in the treatment of asthenia after sickness or delivery, deficiency in vigor, palpitation, and insomnia. Unlike other vertebrates, the oviduct of Rana chensinensis oviduct significantly expands during prehibernation, in contrast to the breeding period. To explain this phenomenon at the molecular level, the protein expression profiles of Rana chensinensis oviduct during the breeding period and prehibernation were observed using isobaric tags for relative and absolute quantitation (iTRAQ) technique...
June 8, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
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