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Huang D, Zhang L, Mi H, Teng T, Liang H, Ren M. Transcriptome-Based Analysis of the Mechanism of Action of Metabolic Disorders Induced by Waterborne Copper Stress in Coilia nasus. BIOLOGY 2024; 13:476. [PMID: 39056671 PMCID: PMC11274096 DOI: 10.3390/biology13070476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/19/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
To reveal the effects of waterborne copper stress on gene expression changes, molecular pathways, and physiological functions in Coilia nasus, juvenile fish were equally divided into two experimental groups, and the copper levels were 1.61 ± 0.03 mg/L (copper-exposed group) and 0 mg/L (control group), respectively. After 4 h, gill tissue samples were collected for transcript sequencing analysis, and two libraries were constructed from the copper treatment group (Cu) and the control group (C) and sequenced using Illumina sequencing technology. The results showed that approximately 40.2-46.0 M clean reads were obtained from each library, and the percentage of uniquely mapped transcripts ranged from 80.57 to 84.93%. A total of 3915 differentially expressed genes (DEGs) were identified under waterborne copper stress, among which 1300 genes were up-regulated, and 2615 genes were down-regulated. Twelve DEGs were randomly selected for quantitative RT-PCR (qRT-PCR) analysis, and the results confirmed that the transcriptome analysis was reliable. Furthermore, the DEGs were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and the results showed that most of the DEGs were involved in metabolic pathways, including steroid biosynthesis, glutathione metabolism, and peroxisome proliferator-activated receptor (PPAR) signaling pathways. Furthermore, due to the waterborne copper levels, gsk-3β was significantly up-regulated, while other metabolism-related genes (tor, pi3k, lpl, aqp7, fabp3) were significantly down-regulated. In addition, the copper-exposed group significantly reduced the expression of some immunity genes (ifn-γ, stat1, cxcl10, and tgf-β), and enhanced the expression of il-1β and tnf-α. In summary, these results indicated that copper causes metabolic disorders and insufficient energy supply in the body, and induces oxidative stress, which results in reduced immune functions.
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Affiliation(s)
- Dongyu Huang
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Lu Zhang
- Tongwei Agricultural Development Co., Ltd., Key Laboratory of Nutrition and Healthy Culture of Aquatic, Livestock and Poultry, Ministry of Agriculture and Rural Affairs, Healthy Aquaculture Key Laboratory of Sichuan Province, Chengdu 610093, China
| | - Haifeng Mi
- Tongwei Agricultural Development Co., Ltd., Key Laboratory of Nutrition and Healthy Culture of Aquatic, Livestock and Poultry, Ministry of Agriculture and Rural Affairs, Healthy Aquaculture Key Laboratory of Sichuan Province, Chengdu 610093, China
| | - Tao Teng
- Tongwei Agricultural Development Co., Ltd., Key Laboratory of Nutrition and Healthy Culture of Aquatic, Livestock and Poultry, Ministry of Agriculture and Rural Affairs, Healthy Aquaculture Key Laboratory of Sichuan Province, Chengdu 610093, China
| | - Hualiang Liang
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Mingchun Ren
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
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Transcriptomic Analysis in Marine Medaka Gill Reveals That the Hypo-Osmotic Stress Could Alter the Immune Response via the IL17 Signaling Pathway. Int J Mol Sci 2022; 23:ijms232012417. [PMID: 36293271 PMCID: PMC9604416 DOI: 10.3390/ijms232012417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/03/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022] Open
Abstract
Fish gills are the major osmoregulatory tissue that contact the external water environment and have developed an effective osmoregulatory mechanism to maintain cellular function. Marine medaka (Oryzias melastigma) has the ability to live in both seawater and fresh water environments. The present study performed a seawater (SW) to 50% seawater (SFW) transfer, and the gill samples were used for comparative transcriptomic analysis to study the alteration of hypo-osmotic stress on immune responsive genes in this model organism. The result identified 518 differentiated expressed genes (DEGs) after the SW to SFW transfer. Various pathways such as p53 signaling, forkhead box O signaling, and the cell cycle were enriched. Moreover, the immune system was highlighted as one of the top altered biological processes in the enrichment analysis. Various cytokines, chemokines, and inflammatory genes that participate in the IL-17 signaling pathway were suppressed after the SW to SFW transfer. On the other hand, some immunoglobulin-related genes were up-regulated. The results were further validated by real-time qPCR. Taken together, our study provides additional gill transcriptome information in marine medaka; it also supports the notion that osmotic stress could influence the immune responses in fish gills.
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Integrated Omics Approaches Revealed the Osmotic Stress-Responsive Genes and Microbiota in Gill of Marine Medaka. mSystems 2022; 7:e0004722. [PMID: 35285678 PMCID: PMC9040874 DOI: 10.1128/msystems.00047-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This is the first study using the transcriptome and 16S rRNA gene sequencing to report the hypotonic responsive genes in gill cells and the compositions of gill microbiota in marine medaka. The overlapped glycosaminoglycan- and chitin-related pathways suggest host-bacterium interaction in fish gill during osmotic stress.
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Ulhaq ZS, Tse WKF. A Brief Analysis of Proteomic Profile Changes during Zebrafish Regeneration. Biomolecules 2021; 12:biom12010035. [PMID: 35053182 PMCID: PMC8773715 DOI: 10.3390/biom12010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Unlike mammals, zebrafish are capable to regenerate many of their organs, however, the response of tissue damage varies across tissues. Understanding the molecular mechanism behind the robust regenerative capacity in a model organism may help to identify and develop novel treatment strategies for mammals (including humans). Hence, we systematically analyzed the current literature on the proteome profile collected from different regenerated zebrafish tissues. Our analyses underlining that several proteins and protein families responsible as a component of cytoskeleton and structure, protein synthesis and degradation, cell cycle control, and energy metabolism were frequently identified. Moreover, target proteins responsible for the initiation of the regeneration process, such as inflammation and immune response were less frequently detected. This highlights the limitation of previous proteomic analysis and suggested a more sensitive modern proteomics analysis is needed to unfold the mechanism. This brief report provides a list of target proteins with predicted functions that could be useful for further biological studies.
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Affiliation(s)
- Zulvikar Syambani Ulhaq
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Maulana Malik Ibrahim State Islamic University of Malang, Batu 65144, Indonesia;
- National Research and Innovation Agency, Central Jakarta 10340, Indonesia
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
- Correspondence:
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Sokolova I. Bioenergetics in environmental adaptation and stress tolerance of aquatic ectotherms: linking physiology and ecology in a multi-stressor landscape. J Exp Biol 2021; 224:224/Suppl_1/jeb236802. [PMID: 33627464 DOI: 10.1242/jeb.236802] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Energy metabolism (encompassing energy assimilation, conversion and utilization) plays a central role in all life processes and serves as a link between the organismal physiology, behavior and ecology. Metabolic rates define the physiological and life-history performance of an organism, have direct implications for Darwinian fitness, and affect ecologically relevant traits such as the trophic relationships, productivity and ecosystem engineering functions. Natural environmental variability and anthropogenic changes expose aquatic ectotherms to multiple stressors that can strongly affect their energy metabolism and thereby modify the energy fluxes within an organism and in the ecosystem. This Review focuses on the role of bioenergetic disturbances and metabolic adjustments in responses to multiple stressors (especially the general cellular stress response), provides examples of the effects of multiple stressors on energy intake, assimilation, conversion and expenditure, and discusses the conceptual and quantitative approaches to identify and mechanistically explain the energy trade-offs in multiple stressor scenarios, and link the cellular and organismal bioenergetics with fitness, productivity and/or ecological functions of aquatic ectotherms.
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Affiliation(s)
- Inna Sokolova
- Marine Biology Department, Institute of Biological Sciences, University of Rostock, 18059 Rostock, Germany .,Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, 18059 Rostock, Germany
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Nie CH, Wan SM, Liu YL, Liu H, Wang WM, Gao ZX. Development of Teleost Intermuscular Bones Undergoing Intramembranous Ossification Based on Histological-Transcriptomic-Proteomic Data. Int J Mol Sci 2019; 20:E4698. [PMID: 31546739 PMCID: PMC6801895 DOI: 10.3390/ijms20194698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 11/16/2022] Open
Abstract
Intermuscular bones (IBs) specially exist in lower teleost fish and the molecular mechanism for its development remains to be clarified. In this study, different staining methods and comparative proteomics were conducted to investigate the histological structure and proteome of IB development in Megalobrama amblycephala, including four key IB developmental stages (S1-IBs have not emerged in the tail part; S2-several small IBs started to ossify in the tail part; S3-IBs appeared rapidly; S4-all the IBs appeared with mature morphology). Alcian blue and alizarin red S stained results indicated that IBs were gradually formed from S2 to S4, undergoing intramembranous ossification without a cartilaginous phase. A total of 3368 proteins were identified by using the isobaric tags for relative and absolute quantitation (iTRAQ) approach. Functional annotation showed that proteins which were differentially expressed among stages were involved in calcium, MAPK, Wnt, TGF-β, and osteoclast pathways which played a critical role in bone formation and differentiation. Three proteins (collagen9α1, stat1, tnc) associated with chondrocytes did not exhibit significant changes through S2 to S4; however, proteins (entpd5, casq1a, pvalb, anxa2a, anxa5) which associated with osteoblasts and bone formation and differentiation showed significantly a higher expression level from S1 to S2, as well as to S3 and S4. These further demonstrated that development of IBs did not go through a cartilaginous phase. The inhibitors of TGF-β and Wnt pathways were tested on zebrafish (sp7/eGFP) and the results indicated that both inhibitors significantly delayed IB development. This study provides a comprehensive understanding of the IB ossification pattern, which will help further elucidate the molecular mechanisms for IB development in teleosts.
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Affiliation(s)
- Chun-Hong Nie
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan 430070, China.
| | - Shi-Ming Wan
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan 430070, China.
| | - Yu-Long Liu
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA.
| | - Han Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan 430070, China.
| | - Wei-Min Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan 430070, China.
| | - Ze-Xia Gao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan 430070, China.
- National Demonstration Center for Experimental Aquaculture Education, Huazhong Agricultural University, Wuhan 430070, China.
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7
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Hua Y, Wang C, Wang S, Liu Z, Liu X, Zou L, Gu W, Luo Y, Liu J. iTRAQ-Based Quantitative Proteomic Analysis of Pseudostellaria heterophylla from Geo-Authentic Habitat and Cultivated Bases. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164616666181116124050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Pseudostellaria heterophylla is an important tonic traditional Chinese medicine.
However, the molecular changes in the herb from geo-authentic habitat and cultivated bases remain
to be explored.
Objective:
The purpose of this research was to study differences in P. heterophylla from geo-authentic
habitat and cultivated bases.
Methods:
High-throughput technologies of transcriptomic and proteomic were used to identify proteins.
Isobaric Tags for Relative and Absolute Quantification (iTRAQ) MS/MS has been utilized to
evaluate changes in P. heterophylla from geo-authentic habitat and cultivated bases.
Results:
In this study, a total of 3775 proteins were detected, and 140 differentially expressed proteins
were found in P. heterophylla from geo-authentic habitat and cultivated bases. 44 significantly differential
expressed proteins were identified based on functional analysis classified into nine categories.
Five differentially expressed proteins were confirmed at the gene expression level by Quantitative realtime
PCR. Catabolic metabolism, carbohydrate metabolism, and response to stress of oxidoreductases
and transferases in P. heterophylla from geo-authentic habitat were stronger than in those from cultivated
bases, but protein folding and response to stress of heat shock proteins, isomerases, rubisco large
subunit-binding proteins, chaperone proteins, and luminal-binding proteins in herbs from cultivated
bases were more active. ADG1 and TKTA could be the critical proteins to regulate sucrose; MFP2 and
CYS may be the crucial proteins that control the metabolism of fatty acids and amino acids.
Conclusion:
These results will provide the basic information for exploring the differences in secondary
metabolites in P. heterophylla from geo-authentic habitat and cultivated bases and the protein mechanism
of its quality formation.
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Affiliation(s)
- Yujiao Hua
- School of Pharmacy, Nanjing University of Chinese Medicine, No. 138, Xianlin Road, Nanjing 210023, China
| | - Chengcheng Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, No. 138, Xianlin Road, Nanjing 210023, China
| | - Shengnan Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, No. 138, Xianlin Road, Nanjing 210023, China
| | - Zixiu Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, No. 138, Xianlin Road, Nanjing 210023, China
| | - Xunhong Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, No. 138, Xianlin Road, Nanjing 210023, China
| | - Lisi Zou
- School of Pharmacy, Nanjing University of Chinese Medicine, No. 138, Xianlin Road, Nanjing 210023, China
| | - Wei Gu
- School of Pharmacy, Nanjing University of Chinese Medicine, No. 138, Xianlin Road, Nanjing 210023, China
| | - Yiyuan Luo
- School of Pharmacy, Nanjing University of Chinese Medicine, No. 138, Xianlin Road, Nanjing 210023, China
| | - Juanxiu Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, No. 138, Xianlin Road, Nanjing 210023, China
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Analyses of the molecular mechanisms associated with salinity adaption of Trachidermus fasciatus through combined iTRAQ-based proteomics and RNA sequencing-based transcriptomics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 136:40-53. [DOI: 10.1016/j.pbiomolbio.2018.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/30/2018] [Accepted: 02/06/2018] [Indexed: 01/16/2023]
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9
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iTRAQ-based quantitative proteomic analysis of embryonic developmental stages in Amur sturgeon, Acipenser schrenckii. Sci Rep 2018; 8:6255. [PMID: 29674748 PMCID: PMC5908867 DOI: 10.1038/s41598-018-24562-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 04/05/2018] [Indexed: 11/20/2022] Open
Abstract
The Amur sturgeon, Acipenser schrenckii, is an important aquaculture species in China with annual production of about 150 thousand tons in 2015. In this study, we investigated the regulatory proteins and pathways affecting embryonic development of Amur sturgeon, by analyzing of the differential proteomes among four embryonic developmental stages using isobaric tags for relative and absolute quantitation (iTRAQ), combined with the analysis of effects of microelements and antioxidants on embryonic development. Seventy-four, 77, and 76 proteins were differentially expressed according to iTRAQ analysis between the fertilized egg and blastula, blastula and neurula, and neurula and heart-beat stages, respectively. GO and KEGG enrichment analyses indicated that Gluconeogenesis, Ribosome and Proteasome were the most enriched pathways, which may promote energy formation, immune system protection and protein synthesis process in A. schrenckii. The measurement of microelements indicated that Mn, Cu and Fe were obtained from their parents or water environment in A. schrenckii, while Zn plays vital roles throughout embryonic development. The dramatically high level of malondialdehyde (MDA) across the embryonic development may be the main reason leading to a low hatching rate in A. schrenckii. This study provides the basis for further proteome analysis of embryonic development in A. schrenckii.
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10
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Gu J, Dai S, Liu H, Cao Q, Yin S, Lai KP, Tse WKF, Wong CKC, Shi H. Identification of immune-related genes in gill cells of Japanese eels (Anguilla japonica) in adaptation to water salinity changes. FISH & SHELLFISH IMMUNOLOGY 2018; 73:288-296. [PMID: 29269288 DOI: 10.1016/j.fsi.2017.12.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/06/2017] [Accepted: 12/17/2017] [Indexed: 06/07/2023]
Abstract
The changes in ambient salinity influence ion and water homeostasis, hormones secretion, and immune response in fish gills. The physiological functions of hormones and ion transporters in the regulation of gill-osmoregulation have been widely studied, however the modulation of immune response under salinity changes is not determined. Using transcriptome sequencing, we obtained a comprehensive profile of osmo-responsive genes in gill cells of Japanese eel (Anguilla japonica). Herein, we applied bioinformatics analysis to identify the immune-related genes that were significantly higher expressed in gill pavement cells (PVCs) and mitochondrial-rich cells (MRCs) in freshwater (FW) than seawater (SW) adapted fish. We validated the data using the real-time qPCR, which showed a high correlation between the RNA-seq and real-time qPCR data. In addition, the immunohistochemistry results confirmed the changes of the expression of selected immune-related genes, including C-reactive protein (CRP) in PVCs, toll-like receptor 2 (TLR2) in MRCs and interleukin-1 receptor type 2 (IL-1R2) in both PVCs and MRCs. Collectively our results demonstrated that those immune-related genes respond to salinity changes, and might trigger related special signaling pathways and network. This study provides new insights into the impacts of ambient salinity changes on adaptive immune response in fish gill cells.
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Affiliation(s)
- Jie Gu
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Shuya Dai
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Haitao Liu
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Quanquan Cao
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Shaowu Yin
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Keng Po Lai
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | | | | | - Haifeng Shi
- Institute of Life Science, Jiangsu University, Zhenjiang, Jiangsu, 212000, China.
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11
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Zhang G, Zhang J, Wen X, Zhao C, Zhang H, Li X, Yin S. Comparative iTRAQ-Based Quantitative Proteomic Analysis ofPelteobagrus vachelliLiver under Acute Hypoxia: Implications in Metabolic Responses. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700140] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/04/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Guosong Zhang
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
- Department of Life Science; Heze University; Heze Shandong P. R. China
| | - Jiajia Zhang
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province; Lianyungang Jiangsu P. R. China
| | - Xin Wen
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
| | - Cheng Zhao
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
| | - Hongye Zhang
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
| | - Xinru Li
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
| | - Shaowu Yin
- College of Life Sciences; Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province; Nanjing Normal University; Nanjing Jiangsu P. R. China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province; Lianyungang Jiangsu P. R. China
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12
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Schmitz M, Ziv T, Admon A, Baekelandt S, Mandiki SN, L'Hoir M, Kestemont P. Salinity stress, enhancing basal and induced immune responses in striped catfish Pangasianodon hypophthalmus (Sauvage). J Proteomics 2017; 167:12-24. [DOI: 10.1016/j.jprot.2017.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 12/12/2022]
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13
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Liu PF, Du Y, Meng L, Li X, Liu Y. Proteomic analysis in kidneys of Atlantic salmon infected with Aeromonas salmonicida by iTRAQ. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 72:140-153. [PMID: 28235584 DOI: 10.1016/j.dci.2017.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/18/2017] [Accepted: 02/18/2017] [Indexed: 06/06/2023]
Abstract
Aeromonas salmonicida is a major etiologic agent which induces furunculosis and is globally harmful in salmonid and turbot cultures, especially in Atlantic salmon (Salmo salar) farming. In order to improve knowledge of its poorly understood pathogenesis, we utilized high-throughput proteomics to display differentially expressed proteins in the kidney of Atlantic salmon challenged with high and low infection dose of A. salmonicida at 7 and 14 days. In quantitative proteomic assays, isobaric tags for relative and absolute quantitation (iTRAQ) combined with 2D LC-MS/MS is emerging as a powerful methodology in the search for disease-specific targets and biomarkers. In this study, 4009 distinct proteins (unused ≥ 1.3, which is a confidence ≥ 95%) were identified in three two-dimensional LC/MS/MS analyses. Then we chose 140 proteins (fold change ratio ≥ 1.5 and P < 0.01) combined with protein-protein interaction analysis to ultimately obtain 39 proteins in network which could be considered as potential biomarkers for Atlantic salmon immune responses. Nine significant differentially expressed proteins were consistent with those at the proteomic level used to validate genes at the transcriptomic level by qPCR. Collectively, these data was first reported using an iTRAQ approach to provide additional elements for consideration in the pathophysiology of A. salmonicida and pave the way to resolve the influence of this disease in Atlantic salmon.
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Affiliation(s)
- Peng-Fei Liu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - Yishuai Du
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lingjie Meng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xian Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ying Liu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Dalian Ocean University, Dalian, China.
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14
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Gao K, Deng XY, Shang MK, Qin GX, Hou CX, Guo XJ. iTRAQ-based quantitative proteomic analysis of midgut in silkworm infected with Bombyx mori cytoplasmic polyhedrosis virus. J Proteomics 2017; 152:300-311. [DOI: 10.1016/j.jprot.2016.11.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/24/2016] [Accepted: 11/25/2016] [Indexed: 12/17/2022]
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15
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Pavey SA, Laporte M, Normandeau E, Gaudin J, Letourneau L, Boisvert S, Corbeil J, Audet C, Bernatchez L. Draft genome of the American Eel (Anguilla rostrata). Mol Ecol Resour 2016; 17:806-811. [PMID: 27754597 DOI: 10.1111/1755-0998.12608] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 11/28/2022]
Abstract
Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American eel. This genome contained 305 043 contigs (N50 = 7397) and 79 209 scaffolds (N50 = 86 641) for a total size of 1.41 Gb, which is in the middle of the range of previous estimations for this species. In addition, protein-coding regions, including introns and flanking regions, are very well represented in the genome, as 95.2% of the 458 core eukaryotic genes and 98.8% of the 248 ultra-conserved subset were represented in the assembly and a total of 26 564 genes were annotated for future functional genomics studies. We performed a candidate gene analysis to compare three genes among all three freshwater eel species and, congruent with the phylogenetic relationships, Japanese eel (A. japanica) exhibited the most divergence. Overall, the sequenced genome presented in this study is a crucial addition to the presently available genetic tools to help guide future conservation efforts of freshwater eels.
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Affiliation(s)
- Scott A Pavey
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada.,Department of Biological Sciences and Canadian Rivers Institute, University of New Brunswick, Saint-John, NB, E2L 4L5, Canada
| | - Martin Laporte
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada
| | - Jérémy Gaudin
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada
| | - Louis Letourneau
- McGill University and Génome Québec Innovation Centre, Montréal, QC, H3A0G1, Canada
| | - Sébastien Boisvert
- Faculty of Medicine, CHUL Research Center, Université Laval, Québec, QC, G1V4G2, Canada
| | - Jacques Corbeil
- Faculty of Medicine, CHUL Research Center, Université Laval, Québec, QC, G1V4G2, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, Rimouski, Québec, G5L 3A1, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, QC, G1V 0A6, Canada
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Wang H, Li C, Wang Z, Shao Y, Lv Z, Zhang W. p44/42MAPK and p90RSK modulate thermal stressed physiology response in Apostichopus japonicus. Comp Biochem Physiol B Biochem Mol Biol 2016; 196-197:57-66. [DOI: 10.1016/j.cbpb.2016.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 01/31/2023]
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17
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Hua Y, Wang S, Liu Z, Liu X, Zou L, Gu W, Hou Y, Ma Y, Luo Y, Liu J. iTRAQ-based quantitative proteomic analysis of cultivated Pseudostellaria heterophylla and its wild-type. J Proteomics 2016; 139:13-25. [DOI: 10.1016/j.jprot.2016.02.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/20/2016] [Accepted: 02/23/2016] [Indexed: 01/24/2023]
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18
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Lai KP, Li JW, Gu J, Chan TF, Tse WKF, Wong CKC. Transcriptomic analysis reveals specific osmoregulatory adaptive responses in gill mitochondria-rich cells and pavement cells of the Japanese eel. BMC Genomics 2015; 16:1072. [PMID: 26678671 PMCID: PMC4683740 DOI: 10.1186/s12864-015-2271-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Homeostasis of ions and water is important for the maintenance of cellular functions. The regulation of the homeostasis is particularly important in euryhaline fish that migrate between freshwater (FW) and seawater (SW) environments. The fish gill, the major tissue that forms an interface separating the extracellular fluids and external water environment, has an effective transport system to maintain and regulate a constant body osmolality. In fish gills, the two major epithelial cells, pavement cells (PVCs) and mitochondria-rich cells (MRCs), are known to play key and complementary roles in ion transport at the interface. Discovering the robust mechanisms underlying the two cell types' response to osmotic stress would benefit our understanding of the fundamental mechanism allowing PVCs and MRCs to handle osmotic stress. Owing to the limited genomic data available on estuarine species, existing knowledge in this area is slim. In this study, transcriptome analyses were conducted using PVCs and MRCs isolated from Japanese eels adapted to FW or SW environments to provide a genome-wide molecular study to unravel the fundamental processes at work. RESULTS The study identified more than 12,000 transcripts in the gill cells. Interestingly, remarkable differential expressed genes (DEGs) were identified in PVCs (970 transcripts) instead of MRCs (400 transcripts) in gills of fish adapted to FW or SW. Since PVCs cover more than 90 % of the gill epithelial surface, the greater change in gene expression patterns in PVCs in response to external osmolality is anticipated. In the integrity pathway analysis, 19 common biological functions were identified in PVCs and MRCs. In the enriched signaling pathways analysis, most pathways differed between PVCs and MRCs; 14 enriched pathways were identified in PVCs and 12 in MRCs. The results suggest that the osmoregulatory responses in PVCs and MRCs are cell-type specific, which supports the complementary functions of the cells in osmoregulation. CONCLUSIONS This is the first study to provide transcriptomic analysis of PVCs and MRCs in gills of eels adapted to FW or SW environments. It describes the cell-type specific transcriptomic network in different tonicity. The findings consolidate the known osmoregulatory pathways and provide molecular insight in osmoregulation. The presented data will be useful for researchers to select their targets for further studies.
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Affiliation(s)
- Keng Po Lai
- School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong
| | - Jing-Woei Li
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.,Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Je Gu
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Ting-Fung Chan
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - William Ka Fai Tse
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
| | - Chris Kong Chu Wong
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong. .,Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Pok Fu Lam, Hong Kong.
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Tse WKF, Sun J, Zhang H, Lai KP, Gu J, Sheung Law AY, Yee Yeung BH, Ching Chow S, Qiu JW, Wong CKC. Data for transcriptomic and iTRAQ proteomic analysis of Anguilla japonica gills in response to osmotic stress. Data Brief 2015. [PMID: 26217731 PMCID: PMC4510098 DOI: 10.1016/j.dib.2015.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
This article contains data related to the two research articles titled Transcriptomic and iTRAQ proteomic approaches reveal novel short-term hyperosmotic stress responsive proteins in the gill of the Japanese eel (Anguilla japonica) (Tse et al. [1]) and iTRAQ-based quantitative proteomic analysis reveals acute hypo-osmotic responsive proteins in the gills of the Japanese eel (Anguilla japonica) (Tse et al. [2]). The two research articles show the usefulness of combining transcriptomic and proteomic approaches to provide molecular insights of osmoregulation mechanism in a non-model organism, the Japanese eel. The information presented here combines the raw data from the two studies and provides an overview on the physiological functions of fish gills.
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Affiliation(s)
- William Ka Fai Tse
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Jin Sun
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Huoming Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Keng Po Lai
- School of Biological Science, the University of Hong Kong, Hong Kong SAR, China
| | - Jie Gu
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | | | | | - Sheung Ching Chow
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Chris Kong Chu Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China ; Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Hong Kong SAR, China
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Transcriptomic and proteomic analyses of splenic immune mechanisms of rainbow trout (Oncorhynchus mykiss) infected by Aeromonas salmonicida subsp. salmonicida. J Proteomics 2015; 122:41-54. [DOI: 10.1016/j.jprot.2015.03.031] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/28/2015] [Accepted: 03/30/2015] [Indexed: 01/17/2023]
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