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MakeHub:Fully Automated Generation of UCSC Genome Browser Assembly Hubs

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Genomics, Proteomics & Bioinformatics 2019年第5期17卷 546-549页

作者： Katharina Jasmin Hoff University of Greifswald Institute for Mathematics and Computer Science17489 GreifswaldGermany University of Greifswald Center for Functional Genomics of Microbes17489 GreifswaldGermany

Novel genomes are today often annotated by small consortia or individuals whose background is not from bioinformatics.This audience requires tools that are easy to use.Such need has been addressed by several genome annotation tools and pipelines.Visualizing resulting annotation is a crucial step of quality control.The UCSC Genome Browser is a powerful and popular genome visualization tool.Assembly Hubs,which can be hosted on any publicly available web server,allow browsing genomes via UCSC Genome Browser servers.The steps for creating custom Assembly Hubs are well documented and the required tools are publicly available.However,the number of steps for creating a novel Assembly Hub is large.In some cases,the format of input files needs to be adapted,which is a difficult task for scientists without programming background.Here,we describe Make Hub,a novel command line tool that generates Assembly Hubs for the UCSC Genome Browser in a fully automated fashion.The pipeline also allows extending previously created Hubs by additional tracks.Make Hub is freely available for downloading at https://***/Gaius-Augustus/Make Hub.

关键词： Genome annotation Annotation visualization RNA-seq Genome browser

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Isolation and Characterization of Monkeypox Virus from the First Case of Monkeypox—Chongqing Municipality,China,2022

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China CDC weekly 2022年第46期4卷 1019-1024页

作者： Baoying Huang Hua Zhao Jingdong Song Li Zhao Yao Deng Wen Wang Roujian Lu Wenling Wang Jiao Ren Fei Ye Houwen Tian Guizhen Wu Hua Ling Wenjie Tan Key Laboratory of Biosafety National Health and Family Planning CommissionNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing MunicipalityChina Chongqing center for Disease Control and Prevention Chongqing Municipal Key Laboratory for High Pathogenic MicrobesChongqing MunicipalityChina

Introduction:The first imported case of monkeypox(MPX)from the mainland of China was reported in September 2022.Herein,the study reports the isolation and characterization of MPX virus(MPXV)in this case.Methods:Clinical specimens including skin blister fluid,oropharyngeal and nasopharyngeal swabs,and blood were collected and inoculated onto Vero cells.The isolated virus was identified as MPXV using quantitative polymerase chain reaction(qPCR),cytopathic effects(CPEs),immunofluorescence assay(IFA)and transmission electron microscopy(TEM).Plaque assays were employed to quantify infectious plaque-forming units(PFUs).The plaque reduction neutralization test(PRNT)was developed to determine the neutralizing antibody(nAb)against MPXV.Results:MPXV replication was confirmed with qPCR.Typical CPEs were observed 48 h postincubation.The isolated virus was named MPXV-B.1-China-C-Tan-CQ01.IFA showed that MPXV reacted with serum of MPX case.Orthopoxvirus morphology was observed using TEM.The virus titer increased to>106 PFU/mL after three passages.The serum PRNT 50%neutralization titer(NT50)was 35 for the MPX patient 6 days after symptom onset.Discussion:The study successfully isolated the first MPXV strain in the mainland of China,MPXV-B.1-China-C-Tan-CQ01.Infectious titration and PRNT methods have been developed.The study provides key resources and technical platforms for further research as well as anti-viral drug and vaccine development against MPX.

关键词： mainland Chongqing fir

Nitric Oxide and Brassinosteroids Mediated Fungal Endophyte-Induced Volatile Oil Production Through Protein Phosphorylation Pathways in Atractylodes lancea Plantlets

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Journal of Integrative Plant Biology 2013年第11期55卷 1136-1146页

作者： Cheng-Gang Ren Chuan-Chao Dai Jiangsu Key Laboratory for microbes and Functional Genomics Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources College of Life Sciences in Nanjing Normal University

Fungal endophytes have been isolated from almost every plant, infecting their hosts without causing visible disease symptoms, and yet have still proved to be involved in plant secondary metabolites accumulation. To decipher the possible physiological mechanisms of the endophytic fungus-host interaction, the role of protein phosphorylation and the relationship between endophytic fungus-induced kinase activity and nitric oxide （NO） and brassinolide （BL） in endophyte-enhanced volatile oil accumulation in Atractylodes lancea plantlets were investigated using pharmacological and biochemical approaches. Inoculation with the endophytic fungus Gilmaniella sp. ALl2 enhanced the activities of total protein phosphorylation, Ca2^-dependent protein kinase, and volatile oil accumulation in A. lancea plantlets. The upregulation of protein kinase activity could be blocked by the BL inhibitor brassinazole. Furthermore, pretreatments with the NO-specific scavenger cPTIO significantly reduced the increased activities of protein kinases in A. lancea plantlets inoculated with endophytic fungus. Pretreatments with different protein kinase inhibitors also reduced fungus-induced NO production and volatile oil accumulation, but had barely no effect on the BL level. These data suggest that protein phosphorylation is required for endophyte- induced volatile oil production in A. lancea plantlets, and that crosstalk between protein phosphorylation and the NO pathway may occur and act as a downstream signaling event of the BL pathway.

关键词： Atractylodes lancea endophytic fungus protein phosphorylation signal molecule volatile oi1.

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Three Cases Infected with Avian Influenza A(H5N6)Virus-Chongqing Municipality,China,January-September,2021

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China CDC weekly 2022年第1期4卷 11-16页

作者： Kun Su Zhen Yu Yu Lan Ju Wang Shuang Chen Li Qi Yaokai Chen Yun Tang Yu Xiong Zhangping Tan Mingyue Wang Sheng Ye Dayan Wang Hua Ling William JLiu Xiaoni Zhong Qin Li Wenge Tang Chongqing Municipal center for Disease Control and Prevention ChongqingChina College of Public Health and Management Chongqing Medical UniversityChongqingChina Chongqing Public Health Medical center ChongqingChina Chongqing Municipal Key Laboratory for High Pathogenic microbes ChongqingChina NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina

Summary What is already known about this topic?The World Health Organization(WHO)has reported a total of 48 cases by October 15,2021.The continuous genomic reassortments of H5N6 and other subtype avian influenza viruses(AIVs)pose a long-term threat to public health and the poultry industry.What is added by this report?Three new cases of H5N6 that occurred from January to September 2021 in Chongqing Municipality,China were reported in this study.Epidemiological information of the three cases showed raising poultry and visiting live poultry market contributed to these infections,and there was no evidence of human-to-human transmission of H5N6 currently but a potential spatial cluster.An increase of H5N6 cases was recorded in the area.What are the implications for public health practice?In case of unexplained pneumonia or severe respiratory infection,the patients’epidemiological history of contact with poultry or live poultry markets(LPMs)may be an important interrogation to help diagnose.Extensive and long-term surveillance of avian influenza viruses in LPMs is essential.

关键词： Chongqing poultry H5N6

Generation of a Triple-Shuttling Vector and the Application in Plant Plus-Strand RNA Virus Infectious cDNA Clone Construction

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Generation of a Triple-Shuttling Vector and the Application ...

The First Imported Case of Monkeypox in the Mainland of China—Chongqing Municipality,China,September 16,2022

中国植物病理学会2023年学术年会

作者： FENG Chenwei GUO Xiao GU Tianxiao HUA Yanhong ZHUANG Xinjian ZHANG Kun Jiangsu Key Laboratory for microbes and Functional Genomics Jiangsu Engineering and Technology Research Center for MicrobiologyCollege of Life SciencesNanjing Normal University

Infectious cloning of plant viruses is a powerful tool for studying the reverse genetic manipulation of viral genes in virus-host plant interactions, contributing to a deeper understanding of the life history and pathogenesis of viruses.Yet, most of the infectious clones of RNA virus constructed inE.coli are unstable and toxic.Therefore, we modified the binary vector pCass4-Rz and constructed the ternary shuttle vector pCA4 Y.The pCA4 Y vector has a higher copy number in the E.coli than the conventional pCB301 vector, can obtain a high concentration of plasmid, and is economical and practical, so it is suitable for the construction of plant virus infectious clones in basic laboratories.The constructed vector can be directly extracted from yeast and transformed into Agrobacterium tumefaciens to avoid toxicity in E.coli.Taking advantage of the pCA4 Y vector, we established a detailed large and multiple DNA HRbased cloning method in yeast using endogenous recombinase.We successfully constructed the Agrobacterium-based infectious cDNA clone of ReMV.This study provides a new choice for the construction of infectious viral clones.

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China CDC weekly 2022年第38期4卷 853-854页

作者： Hua Zhao Wenling Wang Li Zhao Sheng Ye Jingdong Song Roujian Lu Hua Zong Changcheng Wu Wei Huang Baoying Huang Yao Deng Ruhan A Wujuan Xie Li Qi Wenbo Xu Hua Ling Wenjie Tan Chongqing Municipal center for Disease Control and Prevention Chongqing MunicipalityChina Chongqing Municipal Key Laboratory for High Pathogenic microbes Chongqing MunicipalityChina National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and PreventionBeijing MunicipalityChina Nan’an center for Disease Control and Prevention Nan’an DistrictChongqing MunicipalityChina.&Joint first authors

Monkeypox is a zoonotic viral disease caused by the monkeypox virus(MPXV),and historically,all outbreaks have been linked to Africa;however,monkeypox has been posing an alarming challenge to the world in 2022(1)as approximately 60,000 cases have been reported in more than 100 nations and regions worldwide(2).Currently,many cases of monkeypox were identified in many nonendemic countries outside of Central and West Africa,and human-to-human transmission has occurred frequently,especially among men who have sex with men(MSM)presenting new clinical symptoms similar to syphilis and other sexually transmitted infections(3).

关键词： Chongqing clinical outside

A newly characterized Zn2Cys6 transcript factor-Irh1 is required for iron acquisition under the iron-limited environment in Aspergillus fumigatus

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A newly characterized Zn2Cys6 transcript factor-Irh1 is requ...

Heteromerization of short-chain trans-prenyltransferase controls precursor allocation within a plastidial terpenoid network

中国菌物学会2015年学术年会

作者： Nanbiao Long Shizhu Zhang Xiaoling Xu Ling Lu Jiangsu Key Laboratory for microbes and Functional Genomics Jiangsu Engineering and Technology Research Center for Microbiology Jiangsu Key Laboratory for microbes and Functional Genomics Jiangsu Engineering and Technology Research Center for Microbiology

＜正＞Aspergillus fumigatus,a saprophytic fungus with a worldwide distribution,has become one of the major opportunistic fungal pathogen with high mortality so far.During the infection of A.fumigatus,iron plays important roles in its development and virulence.Thus,this organism must cope with host to get iron.However,the knowledge for the mechanism of iron regulation in A.fumigatus is limited.Here we demonstrated a putative

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Journal of Integrative Plant Biology 2023年第5期65卷 1170-1182页

作者： Yihua Ma Qingwen Chen Yaoyao Wang Fengxia Zhang Chengyuan Wang Guodong Wang State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing 100101China UniversityofChineseAcademyof Sciences Beijing100039China center for microbes Development and HealthInstitut Pasteur of ShanghaiChinese Academy of SciencesShanghai 200031China

Terpenes are the largest and most diverse class of plant specialized metabolites.Sesterterpenes(C25),which are derived from the plastid methylerythritol phosphate pathway,were recently characterized in plants.In Arabidopsis thaliana,four genes encoding geranylfarnesyl diphosphate synthase(GFPPS)(AtGFPPS1 to 4)are responsible for the production of GFPP,which is the common precursor for sesterterpene biosynthesis.However,the interplay between sesterterpenes and other known terpenes remain elusive.Here,we first provide genetic evidence to demonstrate that GFPPSs are responsible for sesterterpene production in Arabidopsis.Blockage of the sesterterpene pathway at the GFPPS step increased the production of geranylgeranyl diphosphate(GGPP)-derived terpenes.Interestingly,co-expression of sester TPSs in GFPPSOE(overexpression)plants rescued the phenotypic changes of GFPPS-OE plants by restoring the endogenous GGPP.We further demonstrated that,in addition to precursor(DMAPP/IPP)competition by GFPPS and GGPP synthase(GGPPS)in plastids,GFPPS directly decreased the activity of GGPPS through protein-protein interaction,ultimately leading to GGPP deficiency in planta.Our study provides a new regulatory mechanism of the plastidial terpenoid network in plant cells.

关键词： Arabidopsis geranylfarnesyl diphosphate synthase geranylgeranyl pyrophosphate synthase plastid sesterterpene terpene network

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Epigenetic regulation of covalently closed circular DNA minichromosome in hepatitis B virus infection

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Biophysics Reports 2020年第4期6卷 115-126页

作者： Zhaoning Wang Weiwei Wang Lanfeng Wang School of Life Sciences Shanghai University The Center for Microbes Development and Health CAS Key Laboratory of Molecular Virology & ImmunologyInstitut Pasteur of Shanghai Chinese Academy of Sciences

Hepatitis B is caused by hepatitis B virus(HBV), and persistent HBV infection is a global public health problem, with 257 million people as HBV chronic carriers. Viral covalently closed circular DNA(cccDNA) is a key factor to establish persistent infection in infected hepatocytes. Current antiviral therapies have no direct impact on pre-existing cccDNA reservoir, which can be assembled into minichromosome by hijacking host factors. Understanding the mechanisms of epigenetic regulation in cccDNA minichromosome is crucial to develop new therapy on cccDNA, an attractive target for HBV cure. This review summarizes the current advances in epigenetic regulation of cccDNA minichromosome, which might provide clues to novel druggable targets to cure hepatitis B by either silencing or eliminating cccDNA reservoir.

关键词： HBV cccDNA Minichromosome Epigenetic regulation