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Emergence of a novel multi-resistance-mediating integrative and conjugative element ICEPmu3 in Pasteurella multocida

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Journal of integrative Agriculture 2024年第11期23卷 3938-3942页

作者： Jiao He Zhishuang Yang Mingshu Wang Renyong Jia Shun Chen Mafeng Liu Xinxin Zhao Qiao Yang Ying Wu Shaqiu Zhang Juan Huang Xumin Ou Di Sun Bin Tian Yu He Zhen Wu Anchun Cheng Dekang Zhu Research center of Avian Diseases College of Veterinary MedicineSichuan Agricultural University International Joint Research center for Animal Disease Prevention and Control of Sichuan Province Engineering Research center of Southwest Animal Disease Prevention and Control Technology Ministry of Education Key Laboratory of Agricultural bioinformatics Ministry of Education

Pasteurella multocida (PM) has been infecting a variety of hosts for a long time,causing sustained economic losses worldwide;however,there have been limited studies on its extensive adaptability (Aktories et al.2012).Analysis of strains data collected in our laboratory revealed that PM typically acquires foreign genes through transformation and conjugation,rather than transformation and *** and conjugative elements (ICEs)are a crucial mechanism that leads to abrupt changes in niche preferences and enhances environmental adaptability for bacteria,with their number far exceeding the number of plasmids and phages (Wozniak and Waldor 2010;Johnson and Grossman 2015;Botelho and Schulenburg 2021).Previous research has shown that the European bovine-sourced strain Pm36950 contains the experimentally transferable resistant ICEPmu1,which could integrate into the host chromosome or forming a circular intermediate (Michael et al.2012).Additionally,a few studies have suggested that PM strains isolated from European bovine and Asian swine might contain ICEs,but these claims lack experimental verification (Klima et al.2014;Moustafa et al.2015;Kadlec et al.2017;Peng et al.2017;Beker et al.2018;Schink et al.2022).Currently,there is no data available on ICE-carrying PM strains isolated from hosts outside of European cattle or Chinses *** letter presents a report on a novel ICE identified in the hypervirulent and multidrug-resistant PM HN141014 strain isolated from Chinese *** ICE was specifically analyzed for its resistance genes,transferable capacity and host diversity.

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Diversity of nivicolous myxomycetes of the Teberda State Biosphere Reserve (Northwestern Caucasus,Russia)

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Fungal Diversity 2013年第2期59卷 109-130页

作者： Y.K.Novozhilov M.Schnittler D.A.Erastova M.V.Okun O.N.Schepin E.Heinrich Komarov Botanical Institute of the Russian Academy of Sciences Prof.Popov St.2197376 St.PetersburgRussia Institute of Botany and Landscape Ecology Ernst Moritz Arndt University GreifswaldGrimmer Str.8817487 GreifswaldGermany cibiv–center for integrative bioinformatics in vienna Max F.Perutz Laboratories(MFPL)University of ViennaMedical University of ViennaCampus Vienna Biocenter 5(VBC5)1030 ViennaAustria

Nivicolous myxomycete assemblages were surveyed on the northwest of the Greater Caucasian ridge in May-June 2010 and 2011 at a north facing transect between 1,700 and 2,920 m elevation of the summit Malaya Khatipara situated within the Teberda State Biosphere *** characters of 396 collections representing 45 taxa(39 species,3 varieties,and 3 forms)of myxomycetes in 8 genera and 5 families were ***(13)taxa are classified as rare(a species represents<0.5%of all records).Only seven species were found to be widely distributed(present in 50%or more of the 17 studied localities).To confirm the assignment of specimens to morphospecies,we obtained independently from determination 145 partial sequences of the 18S SSU rRNA gene from 35 taxa of Lamproderma,Meriderma,Physarum and Diderma,which turned out to represent 58 *** of the taxa represented by more than one sequence had several genotypes,with an average of 1.7 genotypes per *** for three taxonomically difficult groups of species,partial SSU sequences did well correspond with the respective morphospecies and where similar or identical to sequences of specimens from the European Alps,making this marker a good candidate for barcoding in *** richness and diversity increased from subalpine crooked-stem birch forests(23 species,2 varieties,H′02.8,E00.88,D00.08)to alpine dwarf shrub communities(34 species and 2 varieties,2 forms,H′03.2,E00.89,D00.05)but decreased again for alpine meadows(27 species and 2 varieties,2 forms,H′03.1,E00.91,D00.06).Species richness and alpha-diversity reached maximum values for ground litter,whereas leaves and stems of living shrubs above ground harboured a more depauperate myxomycete assemblage.

关键词： Alpine ecosystems Distribution Genotypes Molecular signatures Myxogastria Amoebozoa Plasmodial slime moulds Species inventory Species richness Species delimitation

Comprehensive identification and potential application of genetic alteration-driven enhancer RNAs for eRNA-targeted therapy in breast cancer

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Genes & Diseases 2024年第5期11卷 59-62页

作者： Hongying Zhao Caiyu Zhang Lin Bo Lixia Wang Wangyang Liu Yaopeng Shu Kailai Liu Ying Liu Meiting Fei Li Wang College of bioinformatics Science and Technology Harbin Medical UniversityHarbinHeilongjiang 150081China Ninth People’s Hospital Shanghai Jiao Tong University School of MedicineShanghai 200125China Shanghai Institute of Precision Medicine Shanghai 200125China

Enhancer RNAs(eRNAs)are a class of non-coding RNA,which play a critical role in tumor progression.1 Previous studies have indicated abundant CpG methylation,somatic mutation,and copy number variation in eRNA regions in cancers.2,3 We constructed a landscape of genetic alteration-driven eRNAs and provided an integrative pipeline to identify drug candidates that affect eRNA ***,we explored the prognostic value of genetic alteration-driven eRNAs.

关键词： alteration breast targeted

The OsWRKY72-OsAAT30/OsGSTU26 module mediates reactive oxygen species scavenging to drive heterosis for salt tolerance in hybrid rice

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Journal of integrative Plant Biology 2024年第4期66卷 709-730页

作者： Citao Liu Bigang Mao Yanxia Zhang Lei tian Biao Ma Zhuo Chen Zhongwei Wei Aifu Li Ye Shao Gongye Cheng Lingling Li Wenyu Li Di Zhang Xiaoping Ding Jiangxiang Peng Yulin Peng Jiwai He Nenghui Ye Dingyang Yuan Chengcai Chu Meijuan Duan Hunan Provincial Key Laboratory of Stress Biology College of AgricultureHunan Agricultural UniversityChangsha 410128China State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterChangsha 410125China College of Agriculture South China Agricultural UniversityGuangzhou 510642China State Key Laboratory of Wheat and Maize Crop Science Center for Crop Genome EngineeringCollege of AgronomyHenan Agricultural UniversityZhengzhou 450002China College of Horticulture Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Computational Medicine and bioinformatics University of MichiganAnn ArborMI 48109 USA Biobin Data Science Co. Ltd.Changsha 410221China

Hybrid rice(Oryza sativa)generally outperforms its inbred parents in yield and stress tolerance,a phenomenon termed heterosis,but the underlying mechanism is not completely ***,we combined transcriptome,proteome,physiological,and heterosis analyses to examine the salt response of super hybrid rice Chaoyou1000(CY1000).In addition to surpassing the mean values for its two parents(mid-parent heterosis),CY1000 exhibited a higher reactive oxygen species scavenging ability than both its parents(over-parent heterosis or heterobeltiosis).Nonadditive expression and allele-specific gene expression assays showed that the glutathione S-transferase gene OsGSTU26 and the amino acid transporter gene OsAAT30 may have major roles in heterosis for salt tolerance,acting in an overdominant fashion in ***,we identified OsWRKY72 as a common transcription factor that binds and regulates OsGSTU26 and *** salt-sensitive phenotypes were associated with the OsWRKY72^(paternal)genotype or the OsAAT30^(maternal)genotype in core rice germplasm ***72^(paternal)specifically repressed the expression of OsGSTU26 under salt stress,leading to salinity sensitivity,while OsWRKY72^(maternal)specifically repressed OsAAT30,resulting in salinity *** results suggest that the OsWRKY72-OsAAT30/OsGSTU26 module may play an important role in heterosis for salt tolerance in an overdominant fashion in CY1000 hybrid rice,providing valuable clues to elucidate the mechanism of heterosis for salinity tolerance in hybrid rice.

关键词： allele-specific gene expression(ASE) heterosis hybrid rice nonadditive effect(NAE) salt tolerance transcriptome and proteome

HCCDB v2.0:Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC

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Genomics, Proteomics & bioinformatics 2024年第1期22卷 131-142页

作者： Ziming Jiang Yanhong Wu Yuxin Miao Kaige Deng Fan Yang Shuhuan Xu Yupeng Wang Renke You Lei Zhang Yuhan Fan Wenbo Guo Qiuyu Lian Lei Chen Xuegong Zhang Yongchang Zheng Jin Gu Eight-Year Program of Clinical Medicine Peking Union Medical College HospitalChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100006China MOE Key Laboratory of bioinformatics BNRIST Bioinformatics DivisionInstitute for Precision Medicine&Department of AutomationTsinghua UniversityBeijing 100084China Department of Liver Surgery Peking Union Medical College HospitalChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100730China Fuzhou Institute for Data Technology Fuzhou 350207China University of Michigan-Shanghai Jiao Tong University Joint Institute Shanghai Jiao Tong UniversityShanghai 200240China Department of Automation Shanghai Jiao Tong UniversityShanghai 200240China International Cooperation Laboratory on Signal Transduction Eastern Hepatobiliary Surgery InstituteSecond Military Medical UniversityShanghai 200438China National center for Liver Cancer Shanghai 201805China

Large-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma(HCC).Integrated 15 transcriptomic datasets of HCC clinical samples,the first version of HCC database(HCCDB v1.0)was released in *** the meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets,it provides a systematic view of the altered biological processes and the inter-patient heterogeneities of HCC with high reproducibility and *** four years having passed,the database now needs integration of recently published ***,the latest single-cell and spatial transcriptomics have provided a great opportunity to decipher complex gene expression variations at the cellular level with spatial ***,we present HCCDB v2.0,an updated version that combines bulk,single-cell,and spatial transcriptomic data of HCC clinical *** dramatically expands the bulk sample size by adding 1656 new samples from 11 datasets to the existing 3917 samples,thereby enhancing the reliability of transcriptomic meta-analysis.A total of 182,832 cells and 69,352 spatial spots are added to the single-cell and spatial transcriptomics sections,respectively.A novel single-cell level and 2-dimension(sc-2D)metric is proposed as well to summarize cell type-specific and dysregulated gene expression *** are all graphically visualized in our online portal,allowing users to easily retrieve data through a user-friendly interface and navigate between different *** extensive clinical phenotypes and transcriptomic data in the database,we show two applications for identifying prognosis-associated cells and tumor *** v2.0 is available at http://***/database/hccdb2.

关键词： Hepatocellular carcinoma Database integrative analysis Single-cell RNA sequencing Spatial transcriptomics

Higher Plant Proteins of Cyanobacterial Origin:Are They or Are They Not Preferentially Targeted to Chloroplasts?

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Molecular Plant 2014年第12期7卷 1797-1800页

作者： Roman G.Bayer Tina Kostler, Arpit Jain Simon Stael Ingo Ebersberger Markus Teige Department of Biochemistry and Cell Biology MFPLUniversity of ViennaDr Bohr Gasse 9A-1030 ViennaAustria cibiv—center for integrative bioinformatics vienna MFPLDr.Bohr Gasse 9A-1030 ViennaAustria Department for Applied bioinformatics Institute for Cell Biology and NeuroscienceGoethe UniversityMax-von-Laue Str.13D-60438 FrankfurtGermany VIB Department of Plant Systems Biology Ghent UniversityTechnologiepark 9279052 GentBelgium Department of Ecogenomics and Systems Biology University of ViennaAlthanstr 14A-1090 ViennaAustria Department of Applied Genetics and Cell Biology University of Natural Resources and Life SciencesMuthgasse 18A-1190 ViennaAustria

Dear Editor, What does the evolutionary origin of a plant protein tell about its subcellular localization？ Naively thinking, one would assume that plant proteins that were originally encoded in the endosymbiont genome are targeted to the chloroplast. However, published data seem to support only a loose link between evolutionary origin and subcel- lular localization. About half of the Arabidopsis proteins with a detectable cyanobacterial ortholog are targeted to subcellular compartments other than the chloroplast （Martin et al., 2002）. H

关键词： Plant protein The origin of evolution chloroplast

Large-scale loss-of-function perturbations reveal a comprehensive epigenetic regulatory network in breast cancer

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Cancer Biology & Medicine 2024年第1期21卷 83-103页

作者： Yumei Wang Haiyan Wang Wei Shao Yuhui Chen Yu Gui Chao Hu Xiaohong Yi Lijun Huang Shasha Li Dong Wang School of Basic Medical Sciences State Key Laboratory of Southwestern Chinese Medicine ResourcesChengdu University of Traditional Chinese MedicineChengdu 611137China Department of Pathology School of MedicineQinghai UniversityXining 810001China Omics Biosciences Inc Beijing 100871China Laboratory of integrative Medicine Clinical Research Center for BreastState Key Laboratory of BiotherapyWest China HospitalSichuan University and Collaborative Innovation CenterChengdu 610041China State Key Laboratory of Southwestern Chinese Medicine Resources School of PharmacyChengdu University of Traditional Chinese MedicineChengdu 611137China Department of Endocrinology and Metabolism Guangdong Provincial Key Laboratory of Diabetology&Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity ResearchMedical Center for Comprehensive Weight ControlThe Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510630China

Objective:Epigenetic abnormalities have a critical role in breast cancer by regulating gene expression;however,the intricate interrelationships and key roles of approximately 400 epigenetic regulators in breast cancer remain *** is important to decipher the comprehensive epigenetic regulatory network in breast cancer cells to identify master epigenetic regulators and potential therapeutic ***:We employed high-throughput sequencing-based high-throughput screening(HTS^(2))to effectively detect changes in the expression of 2,986 genes following the knockdown of 400 epigenetic ***,bioinformatics analysis tools were used for the resulting gene expression signatures to investigate the epigenetic regulations in breast ***:Utilizing these gene expression signatures,we classified the epigenetic regulators into five distinct clusters,each characterized by specific *** discovered functional similarities between BAZ2B and SETMAR,as well as CLOCK and ***,we observed that CLOCK functions in a manner opposite to that of HDAC8 in downstream gene ***,we constructed an epigenetic regulatory network based on the gene expression signatures,which revealed 8 distinct modules and identified 10 master epigenetic regulators in breast ***:Our work deciphered the extensive regulation among hundreds of epigenetic *** identification of 10 master epigenetic regulators offers promising therapeutic targets for breast cancer treatment.

关键词： Epigenetic regulators breast cancer regulatory network HTS^(2)

Plant biotic interactions

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Journal of integrative Plant Biology 2016年第4期58卷 282-283页

作者： Hailing Jin Special Issue EditorUC President's Chair Director of Genetics Genomics and Bioinformatics Graduate ProgramCenter for Plant Cell BiologyInstitute for Integrative Genome BiologyUniversity of CaliforniaRiversideUSA

Plants are constantly under attack by pathogens,pests,and parasites,resulting in severe consequences on global food production and human *** pathogens and pests find their ways to invade and communicate with their hos... 详细信息

关键词： communicate constantly sophisticated consequences microbial fight biotic evolved pathogen volatile

Woody plant cell walls:Fundamentals and utilization

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Molecular Plant 2024年第1期17卷 112-140页

作者： Wei Li Ying-Chung Jimmy Lin Ying-Lan Chen Chenguang Zhou Shuang Li Nette De Ridder Dyoni M.Oliveira Lanjun Zhange Baocai Zhang Jack P.Wang Changzheng Xu Xiaokang Fu Keming Luo Ai-Min Wu Taku Demura Meng-Zhu Lu Yihua Zhou Laigeng Li Toshiaki Umezawa Wout Boerjan Vincent L.Chiang State Key Laboratory of Tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040China Department of Life Science National Taiwan UniversityTaipeiTaiwanChina Department of Biotechnology and Bioindustry Sciences College of Bioscience and BiotechnologyNational Cheng Kung UniversityTainanTaiwanChina Department of Plant Biotechnology and bioinformatics Ghent UniversityTechnologiepark 719052 GhentBelgium VIB center for Plant Systems Biology Technologiepark 719052 GhentBelgium State Key Laboratory of Plant Genomics Insttute of Genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Forest Biotechnology Group Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNC 27695USA Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation Integrative Science Center of Germplasm CreationSchool of Life SciencesSouthwest UniversityChongqing 400715China Guangdong Key Laboratory for Innovative Developmentand Utilization of Forest Plant Germplasm College of Forestry and Landscape ArchitecturesSouth China Agricultural UniversityGuangzhou510642China center for Digital Green-innovation Nara Institute of Science and TechnologykomaNara 630-0192Japan State Key Laboratory of Subtropical Siviculture College of Forestry and BiotechnologyZhejang A&F UniversityHangzhou 311300China CAS center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences300 Fenglin RoadShanghai 200032China Laboratoryof MetabolicScienceofForest Plants and Microorganisms Rsearch Institute for Sustainable HumanosphereKyoto UniversityUjiKyoto 611-0011 Japan

Cell walls in plants,particularly forest trees,are the major carbon sink of the terrestrial *** and biosynthetic features of plant cell walls were revealed early on,focusing mostly on herbaceous model *** developments in genomics,transcriptomics,epigenomics,transgenesis,and associated analytical techniques are enabling novel insights into formation of woody cell ***,we review multilevel regulation of cell wall biosynthesis in forest tree *** highlight current approaches to engineering cell walls as potential feedstock for materials and energy and survey reported field tests of such engineered transgenic *** outline opportunities and challenges in future research to better understand cell type biogenesis for more efficient wood cell wall modification and utilization for biomaterials or for enhanced carbon capture and storage.

关键词： regulation of cell wall formation biosynthesis of cell wall components lignin cellulose hemicellulose cell wall utilization