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Nynca J, Dietrich MA, Ciereszko A. DIGE Analysis of Fish Tissues. Methods Mol Biol 2023; 2596:303-322. [PMID: 36378447 DOI: 10.1007/978-1-0716-2831-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Two-dimensional difference gel electrophoresis (2D-DIGE) appears to be especially useful in quantitative approaches, allowing the co-separation of proteins of control samples and proteins of treated/disease samples on the same gel, eliminating gel-to-gel variability. The principle of 2D-DIGE is to label proteins prior to isoelectric focusing and use three spectrally resolvable fluorescent dyes, allowing the independent labeling of control and experimental samples. This procedure makes it possible to reduce the number of gels in an experiment, allowing the accurate and reproducible quantification of multiple samples. 2D-DIGE has been found to be an excellent methodical tool in several areas of fish research, including environmental pollution and toxicology, the mechanisms of development and disorders, reproduction, nutrition, evolution, and ecology.
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Affiliation(s)
- Joanna Nynca
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Mariola A Dietrich
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland.
| | - Andrzej Ciereszko
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
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2
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Driessen M, van der Plas-Duivesteijn S, Kienhuis AS, van den Brandhof EJ, Roodbergen M, van de Water B, Spaink HP, Palmblad M, van der Ven LTM, Pennings JLA. Identification of proteome markers for drug-induced liver injury in zebrafish embryos. Toxicology 2022; 477:153262. [PMID: 35868597 DOI: 10.1016/j.tox.2022.153262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 10/17/2022]
Abstract
The zebrafish embryo (ZFE) is a promising alternative non-rodent model in toxicology, and initial studies suggested its applicability in detecting hepatic responses related to drug-induced liver injury (DILI). Here, we hypothesize that detailed analysis of underlying mechanisms of hepatotoxicity in ZFE contributes to the improved identification of hepatotoxic properties of compounds and to the reduction of rodents used for hepatotoxicity assessment. ZFEs were exposed to nine reference hepatotoxicants, targeted at induction of steatosis, cholestasis, and necrosis, and effects compared with negative controls. Protein profiles of the individual compounds were generated using LC-MS/MS. We identified differentially expressed proteins and pathways, but as these showed considerable overlap, phenotype-specific responses could not be distinguished. This led us to identify a set of common hepatotoxicity marker proteins. At the pathway level, these were mainly associated with cellular adaptive stress-responses, whereas single proteins could be linked to common hepatotoxicity-associated processes. Applying several stringency criteria to our proteomics data as well as information from other data sources resulted in a set of potential robust protein markers, notably Igf2bp1, Cox5ba, Ahnak, Itih3b.2, Psma6b, Srsf3a, Ces2b, Ces2a, Tdo2b, and Anxa1c, for the detection of adverse responses.
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Affiliation(s)
- Marja Driessen
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O.Box 1, 3720 BA Bilthoven, the Netherlands; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | | | - Anne S Kienhuis
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O.Box 1, 3720 BA Bilthoven, the Netherlands
| | - Evert-Jan van den Brandhof
- Centre for Environmental Quality, National Institute for Public Health and the Environment (RIVM), P.O.Box 1, 3720 BA Bilthoven, the Netherlands
| | - Marianne Roodbergen
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O.Box 1, 3720 BA Bilthoven, the Netherlands; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Herman P Spaink
- Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Leo T M van der Ven
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O.Box 1, 3720 BA Bilthoven, the Netherlands
| | - Jeroen L A Pennings
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O.Box 1, 3720 BA Bilthoven, the Netherlands.
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Santana PA, Álvarez CA, Sáenz-Martínez DE, Salinas-Parra N, Guzmán F, Paradela A, Mercado L. New insight to the rol of α-enolase (Eno-1) as immunological marker in rainbow trout fry. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 123:104163. [PMID: 34118278 DOI: 10.1016/j.dci.2021.104163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
α-Enolase is an enzyme of the glycolytic pathway that has also been involved in vertebrate inflammatory processes through its interaction with plasminogen. However, its participation in the immune response of lower vertebrates during early life development is unknown. Opportunistic pathogens in salmon farming are the principal cause of mortality in the fry stage. For that reason, molecular indicators of their immunological status are required to ensure the success of the large-scale cultivation. Thus, the objective of this work was to analyze if ENO-1 is involved in the immune response of rainbow trout fry. For this purpose, the coding sequence of trout ENO-1 was characterized, identifying the plasminogen-binding domain that has been described for homologs of this enzyme in higher vertebrates. A peptide-epitope of α-enolase was used for producing mice antiserum. The specificity of polyclonal antibodies was confirmed by dot blot, ELISA and Western blot. Then, the antiserum was used to evaluate α-enolase expression in fry between 152 and 264 degree-days post-hatching after 2, 8, and 12 h of challenge with lipopolysaccharide from Pseudomona auroginosa. The expression of α-enolase at both transcriptional (RT-qPCR) and protein (ELISA) levels was significantly increased after 8 h post-challenge with lipopolysaccharide. These results were confirmed by proteomic analysis by 2D-difference gel electrophoresis (DIGE). This work provides the first evidence of the involvement of α-enolase in the early immune response of salmonids. Future research will be required to understand the possible interaction of α-enolase with plasminogen in cells and tissues of the salmonid immune system.
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Affiliation(s)
- Paula A Santana
- Facultad de Ingeniería, Instituto de Ciencias Químicas Aplicadas, Universidad Autónoma de Chile, el Llano Subercaseaux 2801, San Miguel, Santiago, Chile.
| | - Claudio A Álvarez
- Lab oratorio de Fisiología y Genética Marina, Centro de Estudios Avanzados en Zonas Áridas, Coquimbo, Chile; Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
| | - Daniel E Sáenz-Martínez
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Avenida Universidad #330, 2373223,Valparaíso, Chile; Programa de Doctorado en Biotecnología Pontificia Universidad Católica de Valparaíso/Universidad Técnica Federico Santa María, Valparaíso, Chile.
| | - Nicolás Salinas-Parra
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Avenida Universidad #330, 2373223,Valparaíso, Chile; Programa de Doctorado en Biotecnología Pontificia Universidad Católica de Valparaíso/Universidad Técnica Federico Santa María, Valparaíso, Chile.
| | - Fanny Guzmán
- Núcleo Biotecnológico de Curauma (NBC), Pontificia Universidad Católica de Valparaíso, Avenida Universidad #330, 2373223,Valparaíso, Chile.
| | - Alberto Paradela
- Centro Nacional de Biotecnología, CSIC, C/ Darwin n°3 Cantoblanco, 28049, Madrid, España, Spain.
| | - Luis Mercado
- Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Avenida Universidad #330, 2373223,Valparaíso, Chile; Núcleo Biotecnológico de Curauma (NBC), Pontificia Universidad Católica de Valparaíso, Avenida Universidad #330, 2373223,Valparaíso, Chile.
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4
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Abstract
Two-dimensional difference gel electrophoresis (2D-DIGE) appears to be especially useful in quantitative approaches, allowing the co-separation of proteins of control samples from proteins of treatment/disease samples on the same gel, eliminating gel-to-gel variability. The principle of 2D-DIGE is to label proteins prior to isoelectric focusing and use three spectrally resolvable fluorescent dyes, allowing the independent labeling of control and experimental samples. This procedure makes it possible to reduce the number of gels in an experiment, allowing the accurate and reproducible quantification of multiple samples. 2D-DIGE has been found to be an excellent methodical tool in several areas of fish research, including environmental pollution and toxicology, the mechanisms of development and disorders, reproduction, nutrition, evolution, and ecology.
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Affiliation(s)
- Joanna Nynca
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
| | - Mariola A Dietrich
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland.
| | - Andrzej Ciereszko
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
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Sarasamma S, Varikkodan MM, Liang ST, Lin YC, Wang WP, Hsiao CD. Zebrafish: A Premier Vertebrate Model for Biomedical Research in Indian Scenario. Zebrafish 2017; 14:589-605. [PMID: 29023224 DOI: 10.1089/zeb.2017.1447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The zebrafish (Danio rerio) is a versatile model organism that has been used in biomedical research for several decades to study a wide range of biological phenomena. There are many technical advantages of using zebrafish over other vertebrate models. They are readily available, hardy, easy, and inexpensive to maintain in the laboratory, have a short life cycle, and have excellent fecundity. Due to its optical clarity and reproducible capabilities, it has become one of the predominant models of human genetic diseases. Zebrafish research has made rapid strides in the United States and Europe, but in India the field is at an early stage and many researchers still remain unaware of the full research potential of this tiny fish. The zebrafish model system was introduced into India in the early 2000s. Up to now, more than 200 scientific referred articles have been published by Indian researchers. This review gives an overview of the current state of knowledge for zebrafish research in India, with the aim of promoting wider utilization of zebrafish for high level biological studies.
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Affiliation(s)
- Sreeja Sarasamma
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan .,2 Department of Bioscience Technology, Chung Yuan Christian University , Chung-Li, Taiwan .,3 Department of Chemical Biology, Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram, Kerala, India
| | - Muhammed Muhsin Varikkodan
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan .,2 Department of Bioscience Technology, Chung Yuan Christian University , Chung-Li, Taiwan .,4 Department of Biotechnology and Genetic Engineering, Bharathidasan University , Tiruchirapalli, India
| | - Sung-Tzu Liang
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan
| | - Yen-Chang Lin
- 5 Graduate Institute of Biotechnology, Chinese Culture University , Taipei, Taiwan
| | - Wen-Pin Wang
- 6 Institute of Medical Sciences, Tzu-Chi University , Hualien, Taiwan .,7 Department of Molecular Biology and Human Genetics, Tzu-Chi University , Hualien, Taiwan
| | - Chung-Der Hsiao
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan .,8 Center for Biomedical Technology, Chung Yuan Christian University , Chung-Li, Taiwan .,9 Center for Nanotechnology, Chung Yuan Christian University , Chung-Li, Taiwan
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6
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Kersten S, Arjona FJ. Ion transport in the zebrafish kidney from a human disease angle: possibilities, considerations, and future perspectives. Am J Physiol Renal Physiol 2017; 312:F172-F189. [DOI: 10.1152/ajprenal.00425.2016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 12/31/2022] Open
Abstract
Unique experimental advantages, such as its embryonic/larval transparency, high-throughput nature, and ease of genetic modification, underpin the rapid emergence of the zebrafish ( Danio rerio) as a preeminent model in biomedical research. Particularly in the field of nephrology, the zebrafish provides a promising model for studying the physiological implications of human solute transport processes along consecutive nephron segments. However, although the zebrafish might be considered a valuable model for numerous renal ion transport diseases and functional studies of many channels and transporters, not all human renal electrolyte transport mechanisms and human diseases can be modeled in the zebrafish. With this review, we explore the ontogeny of zebrafish renal ion transport, its nephron structure and function, and thereby demonstrate the clinical translational value of this model. By critical assessment of genomic and amino acid conservation of human proteins involved in renal ion handling (channels, transporters, and claudins), kidney and nephron segment conservation, and renal electrolyte transport physiology in the zebrafish, we provide researchers and nephrologists with an indication of the possibilities and considerations of the zebrafish as a model for human renal ion transport. Combined with advanced techniques envisioned for the future, implementation of the zebrafish might expand beyond unraveling pathophysiological mechanisms that underlie distinct genetic or environmentally, i.e., pharmacological and lifestyle, induced renal transport deficits. Specifically, the ease of drug administration and the exploitation of improved genetic approaches might argue for the adoption of the zebrafish as a model for preclinical personalized medicine for distinct renal diseases and renal electrolyte transport proteins.
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Affiliation(s)
- Simone Kersten
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; and
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, Charlestown, Massachusetts
| | - Francisco J. Arjona
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; and
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7
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Kwon OK, Kim SJ, Lee YM, Lee YH, Bae YS, Kim JY, Peng X, Cheng Z, Zhao Y, Lee S. Global analysis of phosphoproteome dynamics in embryonic development of zebrafish (Danio rerio). Proteomics 2015; 16:136-49. [DOI: 10.1002/pmic.201500017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 09/04/2015] [Accepted: 10/01/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Oh Kwang Kwon
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
| | - Sun Ju Kim
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
| | - You-Mie Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
| | - Young-Hoon Lee
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program); Kyungpook National University; Daegu Korea
| | - Young-Seuk Bae
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program); Kyungpook National University; Daegu Korea
| | - Jin Young Kim
- Mass Spectrometry Research Center; Korea Basic Science Institute; Ochang Chungbuk Republic of Korea
| | - Xiaojun Peng
- Jingjie PTM Biolabs (Hangzhou) Co. Ltd; Hangzhou P. R. China
| | - Zhongyi Cheng
- Advanced Institute of Translational Medicine; Tongji University; Shanghai P. R. China
| | - Yingming Zhao
- Ben May Department for Cancer Research; University of Chicago; Chicago IL USA
| | - Sangkyu Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu South Korea
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8
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Petushkova NA, Kuznetsova GP, Larina OV, Kisrieva YS, Samenkova NF, Trifonova OP, Miroshnichenko YV, Zolotarev KV, Karuzina II, Ipatova OM, Lisitsa AV. One-dimensional proteomic profiling of Danio rerio embryo vitellogenin to estimate quantum dot toxicity. Proteome Sci 2015; 13:17. [PMID: 25964724 PMCID: PMC4426544 DOI: 10.1186/s12953-015-0072-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 04/21/2015] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Vitellogenin (Vtg) is the major egg yolk protein (YP) in most oviparous species and may be useful as an indicator in ecotoxicological testing at the biochemical level. In this study, we obtained detailed information about the Vtgs of Danio rerio embryos by cutting SDS-PAGE gel lanes into thin slices, and analyzing them slice-by-slice with (MALDI-TOF) mass spectrometry. RESULTS We conducted three proteomic analyses, comparing embryonic Danio rerio Vtg cleavage products after exposure for 48 h to CdSecore/ZnSshell quantum dots (QDs), after exposure to a mixture of the components used for quantum dot synthesis (MCS-QDs), and in untreated embryos. The Vtg mass spectrometric profiles of the QDs-treated embryos differed from those of the unexposed or MCS-QDs-treated embryos. CONCLUSION This study demonstrates the possible utility of Vtg profiling in D. rerio embryos as a sensitive diagnostic tool to estimate nanoparticle toxicity.
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Affiliation(s)
- Natalia A Petushkova
- />Orekhovich Institute of Biomedical Chemistry, 119121, Pogodinskaya St. 10, Moscow, Russia
- />Postgen Tech LLC, 119121, Pogodinskaya St. 10, Moscow, Russia
| | - Galina P Kuznetsova
- />Orekhovich Institute of Biomedical Chemistry, 119121, Pogodinskaya St. 10, Moscow, Russia
| | - Olesya V Larina
- />Orekhovich Institute of Biomedical Chemistry, 119121, Pogodinskaya St. 10, Moscow, Russia
| | - Yulia S Kisrieva
- />Orekhovich Institute of Biomedical Chemistry, 119121, Pogodinskaya St. 10, Moscow, Russia
| | - Natalia F Samenkova
- />Orekhovich Institute of Biomedical Chemistry, 119121, Pogodinskaya St. 10, Moscow, Russia
| | - Oxana P Trifonova
- />Orekhovich Institute of Biomedical Chemistry, 119121, Pogodinskaya St. 10, Moscow, Russia
| | | | - Konstantin V Zolotarev
- />Orekhovich Institute of Biomedical Chemistry, 119121, Pogodinskaya St. 10, Moscow, Russia
| | - Irina I Karuzina
- />Orekhovich Institute of Biomedical Chemistry, 119121, Pogodinskaya St. 10, Moscow, Russia
| | - Olga M Ipatova
- />Orekhovich Institute of Biomedical Chemistry, 119121, Pogodinskaya St. 10, Moscow, Russia
| | - Andrey V Lisitsa
- />Orekhovich Institute of Biomedical Chemistry, 119121, Pogodinskaya St. 10, Moscow, Russia
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9
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Groh KJ, Suter MJF. Stressor-induced proteome alterations in zebrafish: a meta-analysis of response patterns. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 159:1-12. [PMID: 25498419 DOI: 10.1016/j.aquatox.2014.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 11/05/2014] [Accepted: 11/18/2014] [Indexed: 06/04/2023]
Abstract
Proteomics approaches are being increasingly applied in ecotoxicology on the premise that the identification of specific protein expression changes in response to a particular chemical would allow elucidation of the underlying molecular pathways leading to an adverse effect. This in turn is expected to promote the development of focused testing strategies for specific groups of toxicants. Although both gel-based and gel-free global characterization techniques provide limited proteome coverage, the conclusions regarding the cellular processes affected are still being drawn based on the few changes detected. To investigate how specific the detected responses are, we analyzed a set of studies that characterized proteome alterations induced by various physiological, chemical and biological stressors in zebrafish, a popular model organism. Our analysis highlights several proteins and protein groups, including heat shock and oxidative stress defense proteins, energy metabolism enzymes and cytoskeletal proteins, to be most frequently identified as responding to diverse stressors. In contrast, other potentially more specifically responding protein groups are detected much less frequently. Thus, zebrafish proteome responses to stress reported by different studies appear to depend mostly on the level of stress rather than on the specific stressor itself. This suggests that the most broadly used current proteomics technologies do not provide sufficient proteome coverage to allow in-depth investigation of specific mechanisms of toxicant action. We suggest that the results of any differential proteomics experiment performed with zebrafish should be interpreted keeping in mind the list of the most frequent responders that we have identified. Similar reservations should apply to any other species where proteome responses are analyzed by global proteomics methods. Careful consideration of the reliability and significance of observed changes is necessary in order not to over-interpret the experimental results and to prevent the proliferation of false positive linkages between the chemical and the cellular functions it perturbs. We further discuss the implications of the identified "top lists" of frequently responding proteins and protein families, and suggest further directions for proteomics research in ecotoxicology. Apart from improving the proteome coverage, further research should focus on defining the significance of the observed stress response patterns for organism phenotypes and on searching for common upstream regulators that can be targeted by specific assays.
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Affiliation(s)
- Ksenia J Groh
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Chemistry and Applied Biosciences, 8093 Zürich, Switzerland.
| | - Marc J-F Suter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Environmental Systems Science, 8092 Zürich, Switzerland
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10
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Mitra A, Basak T, Ahmad S, Datta K, Datta R, Sengupta S, Sarkar S. Comparative Proteome Profiling during Cardiac Hypertrophy and Myocardial Infarction Reveals Altered Glucose Oxidation by Differential Activation of Pyruvate Dehydrogenase E1 Component Subunit β. J Mol Biol 2014; 427:2104-20. [PMID: 25451023 DOI: 10.1016/j.jmb.2014.10.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/09/2014] [Accepted: 10/29/2014] [Indexed: 12/19/2022]
Abstract
Cardiac hypertrophy and myocardial infarction (MI) are two etiologically different disease forms with varied pathological characteristics. However, the precise molecular mechanisms and specific causal proteins associated with these diseases are obscure to date. In this study, a comparative cardiac proteome profiling was performed in Wistar rat models for diseased and control (sham) groups using two-dimensional difference gel electrophoresis followed by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry. Proteins were identified using Protein Pilot™ software (version 4.0) and were subjected to stringent statistical analysis. Alteration of key proteins was validated by Western blot analysis. The differentially expressed protein sets identified in this study were associated with different functional groups, involving various metabolic pathways, stress responses, cytoskeletal organization, apoptotic signaling and other miscellaneous functions. It was further deciphered that altered energy metabolism during hypertrophy in comparison to MI may be predominantly attributed to induced glucose oxidation level, via reduced phosphorylation of pyruvate dehydrogenase E1 component subunit β (PDHE1-B) protein during hypertrophy. This study reports for the first time the global changes in rat cardiac proteome during two etiologically different cardiac diseases and identifies key signaling regulators modulating ontogeny of these two diseases culminating in heart failure. This study also pointed toward differential activation of PDHE1-B that accounts for upregulation of glucose oxidation during hypertrophy. Downstream analysis of altered proteome and the associated modulators would enhance our present knowledge regarding altered pathophysiology of these two etiologically different cardiac disease forms.
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Affiliation(s)
- Arkadeep Mitra
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700 019, India
| | - Trayambak Basak
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110 020, India
| | - Shadab Ahmad
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110 020, India
| | - Kaberi Datta
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700 019, India
| | - Ritwik Datta
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700 019, India
| | - Shantanu Sengupta
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110 020, India
| | - Sagartirtha Sarkar
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700 019, India.
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11
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Ahmad S, Kumar KA, Basak T, Bhardwaj G, Yadav DK, Lalitha A, Chandak GR, Raghunath M, Sengupta S. PPAR signaling pathway is a key modulator of liver proteome in pups born to vitamin B12 deficient rats. J Proteomics 2013; 91:297-308. [DOI: 10.1016/j.jprot.2013.07.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/22/2013] [Accepted: 07/26/2013] [Indexed: 02/02/2023]
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12
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Abstract
Zebrafish offer a unique vertebrate model for research areas such as drug development, disease modeling and other biological exploration. There is significant conservation of genetics and other cellular networks among zebrafish and other vertebrate models, including humans. Here we discuss the recent work and efforts made in different fields of biology to explore the potential of zebrafish. Along with this, we also reviewed the concept of systems biology. A biological system is made up of a large number of components that interact in a huge variety of combinations. To understand completely the behavior of a system, it is important to know its components and interactions, and this can be achieved through a systems biology approach. At the end of the paper we present a concept of integrating zebrafish into the systems biology approach.
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Affiliation(s)
- Mian Yahya Mushtaq
- a Natural Products Laboratory, Institute of Biology, Leiden University , Leiden , The Netherlands
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13
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Chattopadhyay S, Basak T, Nayak MK, Bhardwaj G, Mukherjee A, Bhowmick R, Sengupta S, Chakrabarti O, Chatterjee NS, Chawla-Sarkar M. Identification of cellular calcium binding protein calmodulin as a regulator of rotavirus A infection during comparative proteomic study. PLoS One 2013; 8:e56655. [PMID: 23437200 PMCID: PMC3577757 DOI: 10.1371/journal.pone.0056655] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 01/14/2013] [Indexed: 01/21/2023] Open
Abstract
Rotavirus (RV) being the major diarrhoegenic virus causes around 527000 children death (<5years age) worldwide. In cellular environment, viruses constantly adapt and modulate to survive and replicate while the host cell also responds to combat the situation and this results in the differential regulation of cellular proteins. To identify the virus induced differential expression of proteins, 2D-DIGE (Two-dimensional Difference Gel Electrophoresis) based proteomics was used. For this, HT-29 cells were infected with RV strain SA11 for 0 hours, 3 hours and 9 hours post infection (hpi), differentially expressed spots were excised from the gel and identified using MALDI-TOF/TOF mass spectrometry. 2D-DIGE based proteomics study identified 32 differentially modulated proteins, of which 22 were unique. Some of these were validated in HT-29 cell line and in BALB/c mice model. One of the modulated cellular proteins, calmodulin (CaM) was found to directly interact with RV protein VP6 in the presence of Ca2+. Ca2+-CaM/VP6 interaction positively regulates RV propagation since both CaM inhibitor (W-7) and Ca2+ chelator (BAPTA-AM) resulted in decreased viral titers. This study not only identifies differentially modulated cellular proteins upon infection with rotavirus in 2D-DIGE but also confirmed positive engagement of cellular Ca2+/CaM during viral pathogenesis.
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Affiliation(s)
- Shiladitya Chattopadhyay
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Trayambak Basak
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Mukti Kant Nayak
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Gourav Bhardwaj
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Anupam Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Rahul Bhowmick
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Shantanu Sengupta
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, India
| | - Oishee Chakrabarti
- Structural Genomics Section, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
| | - Nabendu S. Chatterjee
- Division of Biochemistry, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
- * E-mail:
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14
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Yamanaka I, Miki M, Asakawa K, Kawakami K, Oda Y, Hirata H. Glycinergic transmission and postsynaptic activation of CaMKII are required for glycine receptor clusteringin vivo. Genes Cells 2013; 18:211-24. [DOI: 10.1111/gtc.12032] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 11/29/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Iori Yamanaka
- Division of Biological Science; Graduate School of Science; Nagoya University; Nagoya; 464-8602; Japan
| | - Mariko Miki
- Division of Biological Science; Graduate School of Science; Nagoya University; Nagoya; 464-8602; Japan
| | | | | | - Yoichi Oda
- Division of Biological Science; Graduate School of Science; Nagoya University; Nagoya; 464-8602; Japan
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