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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

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

bmp10 maintains cardiac function by regulating iron homeostasis

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Journal of Genetics and Genomics 2024年第12期51卷 1459-1473页

作者： Ruiqin Hu Genfang Li Peng Hu Hongbo Niu Wenhao Li Shouwen Jiang Guijun Guan Qianghua Xu Mingli Liu liangbiao chen International Research Center for Marine Bioscience (Ministry of Science and Technology) Shanghai Ocean University Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) Shanghai Ocean University Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources College of Marine Science Shanghai Ocean University

Heart disease remains the leading cause of death worldwide. Iron imbalance, whether deficiency or overload, contributes to heart failure. However, the molecular mechanisms governing iron homeostasis in the heart are poorly understood. Here, we demonstrate that mutation of bmp10, a heart-born morphogen crucial for embryonic heart development, results in severe anemia and cardiac hypertrophy in ***, bmp10 deficiency causes cardiac iron deficiency, which later progresses to iron overload due to the dysregulated hepcidin/ferroportin axis in cardiac cells, leading to ferroptosis and heart failure. Early iron supplementation in bmp10-/-mutants rescues erythropoiesis, while iron chelation in juvenile fishes significantly alleviates cardiac hypertrophy. We further demonstrate that the interplay between HIF1adriven hypoxic signaling and the IL6/p-STAT3 inflammatory pathways is critical for regulating cardiac iron metabolism. Our findings reveal BMP10 as a key regulator of iron homeostasis in the vertebrate heart and highlight the potential of targeting the BMP10-hepcidin-iron axis as a therapeutic strategy for iron-related cardiomyopathy.

关键词： Anemia Cardiac hypertrophy Ferroptosis Inflammation Iron bmp10

Effects of Vapor Pressure and Super-Hydrophobic Nanocomposite Coating on Microelectronics Reliability

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Engineering 2015年第3期1卷 384-390页

作者： Xuejun Fan liangbiao chen C.P.Wong Hsing-Wei Chu G.Q.Zhang Department of Mechanical Engineering Lamar University State Key Laboratory of Solid State Lighting School of Materials Science and Engineering Georgia Tech Delft University of Technology Institute of Semiconductors Chinese Academy of Sciences

Modeling vapor pressure is crucial for studying the moisture reliability of microelectronics, as high vapor pressure can cause device failures in environments with high temperature and humidity. To minimize the impact of vapor pressure, a super-hydrophobic(SH) coating can be applied on the exterior surface of devices in order to prevent moisture penetration. The underlying mechanism of SH coating for enhancing device reliability, however, is still not fully understood. In this paper, we present several existing theories for predicting vapor pressure within microelectronic materials. In addition, we discuss the mechanism and effectiveness of SH coating in preventing water vapor from entering a device, based on experimental results. Two theoretical models, a micro-mechanics-based whole-field vapor pressure model and a convection-diffusion model, are described for predicting vapor pressure. Both methods have been successfully used to explain experimental results on uncoated samples. However, when a device was coated with an SH nanocomposite, weight gain was still observed, likely due to vapor penetration through the SH surface. This phenomenon may cast doubt on the effectiveness of SH coatings in microelectronic devices. Based on current theories and the available experimental results, we conclude that it is necessary to develop a new theory to understand how water vapor penetrates through SH coatings and impacts the materials underneath. Such a theory could greatly improve microelectronics reliability.

关键词： vapor pressure moisture semiconductor reliability microelectromechanical systems (MEMS) superhydrophobic nanocomposite coating

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 *** with the EVL leads to early developmental ***,the genetic factors underlying EVL differentiation are so far *** 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 *** explore the role of cebpb in EVL differentiation,we knocked down its expression by morpholino-labeled antisense *** morphant embryos showed disrupted EVL and developmental termination prior to *** accordance,expression of the EVL specific cell-adhesion molecule genes were significantly ***,cebpb is the earliest EVL marker and essential for EVL differentiation in *** 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)

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：哺乳动物基因基因 fos 碱基序列内皮缩血管肽类人科转录因子转录因子AP-1 女(雌)性

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

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