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Pathogenic infection and microbial composition of yellow catfish(Pelteobagrus fulvidraco)challenged by Aeromonas veronii and Proteus mirabilis

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Aquaculture and Fisheries 2023年第2期8卷 166-173页

作者： Wanying Zhai Qian Wang Xinpeng Zhu Xiaoying Jia liangbiao chen Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of EducationShanghai Ocean UniversityShanghai201306China International Research Center for Marine Biosciences Ministry of Science and TechnologyShanghai Ocean UniversityShanghai201306China Jiangsu Zhongyang Group Co. Ltd.Nantong226600China

The catfishes are a group of economically important freshwater fish in China,which in recent years have suffered heavy losses as a result of bacterial outbreaks.In this study,we examined the diversity of the microbiome of infected skin mucus of yellow catfish(Pelteobagrus fulvidraco)and channel catfish(Ictalurus punctatus)and analyzed the bacterial pathogens.We found several common pathogenic bacteria,such as Aeromonas spp.,Vibrio spp.,Moraxella spp.and Proteus spp.present in both fish species,but with significantly different bacterial community structures.We isolated and cultured Aeromonas veronii and Proteus mirabilis and validated their infectivity in zebrafish(Danio rerio)and yellow catfish.Intraperitoneal injection of either bacteria into zebrafish,but not immersion,caused 100%mortality and ovary fragmentation.Yellow catfish was more sensitive than zebrafish with 100%mortality in the immersion challenges with A.veronii or P.mirabilis,and with a higher abundance of A.veronii in the P.mirabilis-challenged group compared to control.To our knowledge,this is the first study on the pathogenicity of P.mirabilis in yellow catfish,and the results will help to develop effective strategies for the disease prevention and control in catfish farming.

关键词： Aeromonas veronii Proteus mirabilis Yellow catfish Channel catfish Aquaculture

A Prototypic Jun Like Gene in Amphioxus Branchiostoma japonicum Expressed in Female Gonad

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Journal of Genetics and Genomics 2012年第11期39卷 607-611页

作者： Qianghua Xu Jun Tan liangbiao chen Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources Ministry of EducationCollege of Marine SciencesShanghai Ocean University999 Huchenghuan RoadLingang New HarborShanghai 201306China Scientific Observing and Experimental Station of Oceanic Fishery Resources Ministry of AgricultureShanghai Ocean UniversityShanghai 201306China Key Laboratory of Molecular and Developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

Transcription factors are a group of regulatory proteins that bJind to specific DNA sequence in the promoter region of the target genes to regulate gene expression at transcriptional level （Baeuerle, 1991; Jackson, 1992）. Transcription factor activator protein-1 （AP-1） is one of the transcription factors initially identified from mammals. The mammalian AP-1 complex contains multiple members of Jun, Fos, ATF which form homo- or heterodimers to perform the regulatory function （Halazonetis et al., 1988; Angel and Karin, 1991; Karin et al., 1997; Jochum et al.. 2001： Veselv et al.. 2009： Shaulian. 2010）.

关键词： Female Gonad Oceanic Fisheries Resources

The CCAAT/Enhancer Binding Protein Beta(cebpb)is essential for the development of enveloping layer(EVL)in zebrafish

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Aquaculture and Fisheries 2023年第3期8卷 252-260页

作者： Xin Zhang Zhichao Wu Mengdi Bu Ruiqin Hu Xiaowen Zhang Wenhao Li liangbiao chen Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources(Ministry of Education)and International Research Center for Marine Biosciences(Ministry of Science and Technology) Shanghai Ocean UniversityShanghai201306China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao266237China

Epiboly,the coordinated spreading of the enveloping layer(EVL),the yolk syncytial layer(YSL)and the deep cells(DCs)toward the vegetal pole,is required for gastrulation.Interference with the EVL leads to early developmental failure.However,the genetic factors underlying EVL differentiation are so far unknown.By in-depth analyzing of single-cell sequencing data from 4 h post fertilization zebrafish embryos,we identified 105 genes(FDR<0.05)which showed highly specific EVL expression,among which the transcription factor cebpb and genes(krt18,cldne,cldnb,krt4,krt5)involved in cell-cell junction formation were exclusively expressed in EVL.To explore the role of cebpb in EVL differentiation,we knocked down its expression by morpholino-labeled antisense RNA.The morphant embryos showed disrupted EVL and developmental termination prior to epiboly.In accordance,expression of the EVL specific cell-adhesion molecule genes were significantly reduced.Thus,cebpb is the earliest EVL marker and essential for EVL differentiation in zebrafish.The elucidation of the specific EVL gene set provides us new insights into the molecular mechanisms underlying EVL differentiation.

关键词： Cebpb Single-cell RNA sequencing Zebrafish Enveloping layer(EVL)

Cold-induced retrotransposition of fish LINEs

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Journal of Genetics and Genomics 2017年第8期44卷 385-394页

作者： Shue chen Mengchao Yu Xu Chu Wenhao Li Xiujuan Yin liangbiao chen Key Laboratory of Aquaculture Resources and Utilization Ministry of EducationCollege of Fisheries and Life SciencesShanghai Ocean UniversityShanghai 201206China Institute of Genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China Qingdao National Laboratory for Marine Science and Technology Qingdao 266237China

Classes of retrotransposons constitute a large portion of metazoan genome. There have been cases re- ported that genomic abundance of retrotransposons is correlated with the severity of low environmental temperatures. However, the molecular mechanisms underlying such correlation are unknown. We show here by cell transfection assays that retrotransposition （RTP） of a long interspersed nuclear element （LINE） from an Antarctic nototbenioid fish Dissostichus mawsoni （droLl） could be activated by low temperature exposure, causing increased dmLl copies in the host cell genome. The cold-induced droll propagation was demonstrated to be mediated by the mitogen-activated protein kinases （MAPK）]p38 signaling pathway, which is activated by accumulation of reactive oxygen species （ROS） in cold-stressed conditions. Surprisingly, droLl transfected cells showed an increase in the number of viable cells after prolonged cold exposures than non-transfected cells. Features of cold inducibility of dmLl were reca- pitulated in LINEs of zebrafish origin both in cultured cell lines and tissues, suggesting existence of a common cold-induced LINE amplification in fishes. The findings reveal an important function of LINEs in temperature adaptation and provid insights into the MAPK/p38 stress responsive pathway that shapes LINE composition in fishes facing cold stresses. Copyright 2017, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press. All rights reserved.

关键词： RetrotransposonROSp38Cold adaptationLINE amplification

A gene family-based method for interspecies comparisons of sequencing-based transcriptomes and its use in environmental adaptation analysis

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Journal of Genetics and Genomics 2010年第3期37卷 205-218页

作者： Zuozhou chen Hua Ye Longhai Zhou Chi-Hing C. cheng liangbiao chen Key Laboratory of Molecular and Developmental Biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China Department of Animal Biology University of illinois at Urbana-Champaign Urbana lL 61801 USA

We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to im- plement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus maw- soni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data （available at： http：//***/ polarbank/） from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the com- parison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diffprogram and operation manual can be downloaded from： http：//***/download/Prodiff.rar.

关键词： transcriptome comparison EST protein family reference gene set

Multi-class cancer classification through gene expression profiles: microRNA versus mRNA

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Journal of Genetics and Genomics 2009年第7期36卷 409-416页

作者： Sihua Peng Xiaomin Zeng Xiaobo Li Xiaoning Peng liangbiao chen Department of Pathology School of Medicine Zhejiang University Hangzhou 310058 China Department of Health Statistics and Epidemiology Central South University Changsha 410008 China School of Medicine Hunan Normal University Changsha 410006 China Key Laboratory of Molecular and Developmental Biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China

Both microRNA （miRNA） and mRNA expression profiles are important methods for cancer type classification. A comparative study of their classification performance will be helpful in choosing the means of classification. Here we evaluated the classification performance of miRNA and mRNA profiles using a new data mining approach based on a novel SVM （Support Vector Machines） based recursive fea- ture elimination （nRFE） algorithm. Computational experiments showed that information encoded in miRNAs is not sufficient to classify cancers; gut-derived samples cluster more accurately when using mRNA expression profiles compared with using miRNA profiles; and poorly differentiated tumors （PDT） could be classified by mRNA expression profiles at the accuracy of 100% versus 93.8% when using miRNA profiles. Furthermore, we showed that mRNA expression profiles have higher capacity in normal tissue classifications than miRNA. We concluded that classification performance using mRNA profiles is superior to that of miRNA profiles in multiple-class cancer classifications.

关键词： cancer classification microRNA mRNA gene expression feature selection SVM

miR-888 in MCF-7 Side Population Sphere Cells Directly Targets E-cadherin

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Journal of Genetics and Genomics 2014年第1期41卷 35-42页

作者： Shengjian Huang Ming Cai Yinghui Zheng Longhai Zhou Qiang Wang liangbiao chen Key Laboratory of Molecular and Developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of Sciences The Department of Urology of PLA 309 Hospital

Side population （SP） cells are a small subset of cells isolated from a cultured cancer cell line that exhibit characteristics similar to those of cancer stem cells （CSCs）, such as high metastatic and tumorigenic potential. The molecular mechanisms that give rise to the malignant properties of SP cells are not clear. We isolated SP cells from the MCF-7 breast cancer cell line and profiled microRNA （miRNA） expression patterns between SP cell-derived spheroids and non-SP cells. SP spheroids were found to possess 42 up-regulated miRNAs and 27 down-regulated ones （above 5-fold changes）. One of the up-regulated miRNAs, miR-888 computationally predicted to participate in the adherens junction （AJ） pathway, was investigated. Over-expression of miR-888 in MCF-7 cells reduced the mRNA levels of all four AJ pathway genes （E-cadherin, ACTG1, PTPRTand CDC42） that were selected for testing, whereas knocking down miR-888 reversed the trends. Western blot and flow cytometric quantitation of the membrane E-cadherin levels showed the same trend of change under these treatments. Luciferase reporter assay showed E-cadherin is a direct target of miR-888. As a potential role in intercellular adhesiveness and maintenance of malignant tissue architecture, the results indicate that miR-888 is a repressor of the AJ pathway in MCF-7 cells and that up-regulation of miR-888 contributes to aggressiveness in MCF-7 SP cells.

关键词： Side population Cancer stem cell MicroRNA Adherens junction Cancer metastasis

Generation and characterisation of rabbit monoclonal antibodies against the native cell surface antigens of embryonic stem cells

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Journal of Genetics and Genomics 2010年第7期37卷 483-492页

作者： Yongliang Lu Zhongyuan Su Ying Li Jingfeng Luo Zhou Tan Huijiao Ji Weimin Zhu Guoliang Yu liangbiao chen Ming Zhang Institute of Cell Biology and Genetics College of Life Sciences Zhejiang University Hangzhou 310058 China Huzhou Teachers College Huzhou 313000 China Epitomics Inc. 863 Mitten Road Suite 103 Burlingame CA 94010-1303 USA Institute of Genetics and Developmental Biology Chinese Academic of Sciences Beijing 100101 China

Embryonic stem （ES） cells are potent resources for cell therapy,and monoclonal antibodies （mAbs） against native cell surface markers of ES cells could be useful tools for therapeutic applications.Here,we report the development of a feasible approach,which could be used in mass production,for experimentally producing rabbit mAbs against native cell surface antigens on the cell surface.Two of the 14 mAbs,which were selected at random,could be bound to the cell surface antigens of mES cells.The immunocytochemistry （ICC） and Western blot results showed that mAb 39 recognises conformational epitopes.The target antigen of mAb 39 was then successfully purified using an improved immunoprecipitation approach in which mAb was bounded to intact mES cells before the cells were lysed.The LC-LTQ mass spectrum analysis showed that the target antigen of mAb 39 was Glut3.This result was further confirmed by Western blot using commercially available antibodies against Glut3.Further experiments showed that mAb 39 exhibited an antiproliferative effect on mES cells.We also found that Glut3 was differentially expressed among the mES cell population as detected by flow cytometry.

关键词： rabbit monoclonal antibody embryonic stem cells native conformation cell surface markers Glut3

Expression of multi-domain type III antifreeze proteins from the Antarctic eelpout (Lycodichths dearborni) in transgenic tobacco plants improves cold resistance

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Aquaculture and Fisheries 2021年第2期6卷 186-191页

作者： Qiao Huang Ruiqin Hu Hui zhu Changlian Peng liangbiao chen Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources(Ministry of Education)and International Research Center for Marine Biosciences College of Fisheries and Life ScienceShanghai Ocean UniversityShanghai200120China Internal Joint Research Center for Marine Biosciences(Ministry of Science and Technology) College of Fisheries and Life ScienceShanghai Ocean UniversityShanghai200120China Guangdong Provincial Key Laboratory of Biotechnology for Plant Development College of Life ScienceSouth China Normal UniversityGuangzhou510631China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyShandongQingdao266000China School of Food Engineering and Biotechnology Hanshan Normal UniversityGuangzhou521041China

Type III antifreeze proteins(AFPIIIs)are a group of small globular proteins found in some polar fishes to protect them against freezing damage.Transgenic expression of AFPs has been shown to confer cold tolerance to commercially important plants and animals.We have previously isolated multiple AFPIII genes in the Antarctic eelpout(Lycodichthys dearborni)that encode larger AFPIII isoforms with up to 12 of the conventional domains.Here we have introduced the fish AFPIII genes that encode for the monomer(ld1),dimer(ld2),trimer(ld3)and tetramer(ld4)AFPIII isoforms in tobacco plants.Pot-grown 4-week-old transgenic tobacco plants were exposed to cold stress at 4◦C for 30 days and the results show that ld1,ld2,ld3 and ld4 transgenic plants present relatively lower electrolyte leakage and lower content of malondialdehyde(MDA),but accumulated higher content of proline when compared to control plants.This indicates considerable improved membrane integrity under low temperature stress and improvement of the plant cold resistance.The plants transformed with the AFPIII tetramer-and trimer-domains demonstrated a higher cold-tolerant levels when compared with plants transformed with the dimer-and monomer AFPIII domains.Our study further supports that fish AFPIIIs,especially the multidomain proteins,protect cells from non-freezing hypothermic stresses,apart from there well-known function as ice inhibitors molecules at freezing temperature.

关键词： Type III antifreeze proteins Multidomain proteins Cold tolerance Electrolyte leakage MDA Proline