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南极中山站伯氏肩孔南极鱼体液和肠道微生物的分离鉴定及功能分析

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大连海洋大学学报 2024年第3期39卷 429-436页

作者：邵琪翟万营蔡爽孙凤宇陈良标上海海洋大学科技部海洋生物科学国际联合研究中心上海201306 上海海洋大学水产种质资源发掘与利用教育部重点实验室上海201306 上海海洋大学水产生物育种研究中心上海201306 上海海洋大学大洋渔业资源可持续开发教育部重点实验室上海201306

为研究南极鱼体微生物的功能,对采自南极中山站附近海域的伯氏肩孔南极鱼(Trematomus bernacchii)体液和肠道内容物中的微生物进行筛选培养,挑选代表性菌株进行生理生化特性测定和次级代谢产物功能验证,并在活体上进行功能初探,观察在... 详细信息

为研究南极鱼体微生物的功能,对采自南极中山站附近海域的伯氏肩孔南极鱼(Trematomus bernacchii)体液和肠道内容物中的微生物进行筛选培养,挑选代表性菌株进行生理生化特性测定和次级代谢产物功能验证,并在活体上进行功能初探,观察在低温环境下其对宿主的影响。结果表明:分离获得的菌株主要分布在变形菌门(Proteobacteria)和厚壁菌门(Firmicutes),通过16S rDNA基因序列比对发现,菌株Ignatzschineria ***11可能是一株潜在新种;伊格纳茨氏菌属(Ignatzschineria)和芽孢杆菌属(Bacillus)菌的菌液粗提物对枯草芽孢杆菌(Bacillus subtilis ATCC 6633)、嗜水气单胞菌(Aeromonas hydrophila ATCC 35654)及金黄色葡萄球菌(Staphylococcus aureus)有明显的抑制作用;用菌株Ignatzschineria ***11和Bacillus ***117饲喂的斑马鱼在低温下存活的时间较对照组更长;肠道微生物多样性分析显示,投喂Bacillus ***117的斑马鱼肠道微生物中气单胞菌属(Aeromonas)细菌占比最高(超过60%),而投喂Ignatzschineria ***11的斑马鱼肠道微生物中弧菌属(Vibrio)为优势属。研究表明,在低温(18℃)条件下使用不同类型培养基从伯氏肩孔南极鱼体液和肠道内容物中分离出的多为变形菌门和厚壁菌门,这些菌株具有新型抗生素潜力,同时还有增强宿主耐寒的潜质,该发现为进一步探究极地细菌功能提供了新的思路。

关键词：南极伯氏肩孔南极鱼细菌分离抑菌作用低温

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

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 Qingdao National Laboratory for Marine Science and Technology Qingdao 266237 China

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/***.

关键词： transcriptome comparison EST protein family reference gene set

Asb14a 基因在斑马鱼肌间骨发育中的作用

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大连海洋大学学报 2024年第2期39卷 259-265页

作者：牛明慧王化敏胡瑞芹胡鹏吴智超陈良标上海海洋大学水产与生命学院上海201306 水产种质资源发掘与利用教育部重点实验室上海201306

为进一步研究肌间骨(intermuscular bone)发育的分子机制,利用CRISPR/Cas9打靶技术、茜素红染色及实时荧光定量PCR方法,研究了斑马鱼(Danio rerio)Asb14a基因敲除后肌间骨的发育情况。结果表明:本研究中成功构建了插入2 bp和缺失50 bp的... 详细信息

为进一步研究肌间骨(intermuscular bone)发育的分子机制,利用CRISPR/Cas9打靶技术、茜素红染色及实时荧光定量PCR方法,研究了斑马鱼(Danio rerio)Asb14a基因敲除后肌间骨的发育情况。结果表明:本研究中成功构建了插入2 bp和缺失50 bp的Asb14a基因敲除纯合斑马鱼品系;茜素红染色显示,成年Asb14a^(-/-)突变体与野生斑马鱼相比,肌间骨数量显著减少了35%(P<0.0001),说明敲除Asb14a基因会减少斑马鱼肌间骨的数量;实时荧光定量PCR结果显示,骨骼发育相关基因(bmp6、sp7、sox6、alpl、collala、sox6和smad1)在Asb14a^(-/-)突变体中的表达水平发生了显著性变化,从分子角度验证了Asb14a基因与肌间骨发育间的关联性。研究表明,Asb14a基因参与了斑马鱼肌间骨发育,敲除该基因会影响斑马鱼肌间骨的生成,这一发现为进一步研究肌间骨发育的分子机制提供了重要线索。

关键词：斑马鱼肌间骨 CRISPR/Cas9 Asb14a基因纯合突变体

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

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 *** 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 *** found several common pathogenic bacteria,such as Aeromonas spp.,Vibrio spp.,Moraxella *** Proteus *** in both fish species,but with significantly different bacterial community *** isolated and cultured Aeromonas veronii and Proteus mirabilis and validated their infectivity in zebrafish(Danio rerio)and yellow *** injection of either bacteria into zebrafish,but not immersion,caused 100%mortality and ovary *** catfish was more sensitive than zebrafish with 100%mortality in the immersion challenges with *** or ***,and with a higher abundance of *** in the ***-challenged group compared to *** our knowledge,this is the first study on the pathogenicity of *** 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

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 *** expression of AFPs has been shown to confer cold tolerance to commercially important plants and *** have previously isolated multiple AFPIII genes in the Antarctic eelpout(Lycodichthys dearborni)that encode larger AFPIII isoforms with up to 12 of the conventional *** we have introduced the fish AFPIII genes that encode for the monomer(ld1),dimer(ld2),trimer(ld3)and tetramer(ld4)AFPIII isoforms in tobacco ***-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 *** indicates considerable improved membrane integrity under low temperature stress and improvement of the plant cold *** 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 *** 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