1
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Nickerson JL, Sheridan LV, Doucette AA. Impact of Surfactants on Cumulative Trypsin Activity in Bottom-Up Proteome Analysis. J Proteome Res 2024; 23:3542-3551. [PMID: 38973097 DOI: 10.1021/acs.jproteome.4c00162] [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: 07/09/2024]
Abstract
Trypsin digestion plays a pivotal role in successful bottom-up peptide characterization and quantitation. While denaturants are often incorporated to enhance protein solubility, surfactants are recognized to inhibit enzyme activity. However, several reports have suggested that incorporating surfactants or other solvent additives may enhance digestion and MS detection. Here, we assess the impacts of ionic surfactants on cumulative trypsin activity and subsequently evaluate the total digestion efficiency of a proteome mixture by quantitative MS. Although low surfactant concentrations, such as 0.01% SDS or 0.2% SDC, significantly enhanced the initial trypsin activity (by 14 or 42%, respectively), time course assays revealed accelerated enzyme deactivation, evident by 10- or 40-fold reductions in trypsin activity half-life at these respective surfactant concentrations. Despite enhanced initial tryptic activity, quantitative MS analysis of a common liver proteome extract, digested with various surfactants (0.01 or 0.1% SDS, 0.5% SDC), consistently revealed decreased peptide counts and signal intensity, indicative of a lower digestion efficiency compared to a nonsurfactant control. Furthermore, including detergents for digestion did not improve the detection of membrane proteins, nor hydrophobic peptides. These results stress the importance of assessing cumulative enzyme activity when optimizing the digestion of a proteome mixture, particularly in the presence of denaturants.
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Affiliation(s)
- Jessica L Nickerson
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Allumiqs Corporation, Halifax, Nova Scotia B3H 0A8, Canada
| | - Liam V Sheridan
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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2
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Yan J, Ding Y, Peng Z, Qin L, Gu J, Wan C. Systematic Proteomics Study on the Embryonic Development of Danio rerio. J Proteome Res 2023; 22:2814-2826. [PMID: 37500539 DOI: 10.1021/acs.jproteome.3c00056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The early development of zebrafish (Danio rerio) is a complex and dynamic physiological process involving cell division, differentiation, and movement. Currently, the genome and transcriptome techniques have been widely used to study the embryonic development of zebrafish. However, the research of proteomics based on proteins that directly execute functions is relatively vacant. In this work, we apply label-free quantitative proteomics to explore protein profiling during zebrafish's embryogenesis, and a total of 5961 proteins were identified at 10 stages of zebrafish's early development. The identified proteins were divided into 11 modules according to weighted gene coexpression network analysis (WGCNA), and the characteristics between modules were significantly different. For example, mitochondria-related functions enriched the early development of zebrafish. Primordial germ cell-related proteins were identified at the 4-cell stage, while the eye development event is dominated at 5 days post fertilization (dpf). By combining with published transcriptomics data, we discovered some proteins that may be involved in activating zygotic genes. Meanwhile, 137 novel proteins were identified. This study comprehensively analyzed the dynamic processes in the embryonic development of zebrafish from the perspective of proteomics. It provided solid data support for further understanding of the molecular mechanism of its development.
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Affiliation(s)
- Jiahao Yan
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Yuhe Ding
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Zhao Peng
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Lu Qin
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Jingyu Gu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
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3
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Khajavi M, Zhou Y, Schiffer AJ, Bazinet L, Birsner AE, Zon L, D'Amato RJ. Identification of Basp1 as a novel angiogenesis-regulating gene by multi-model system studies. FASEB J 2021; 35:e21404. [PMID: 33899275 DOI: 10.1096/fj.202001936rrr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 01/23/2023]
Abstract
We have previously used the genetic diversity available in common inbred mouse strains to identify quantitative trait loci (QTLs) responsible for the differences in angiogenic response using the corneal micropocket neovascularization (CoNV) assay. Employing a mouse genome-wide association study (GWAS) approach, the region on chromosome 15 containing Basp1 was identified as being significantly associated with angiogenesis in inbred strains. Here, we developed a unique strategy to determine and verify the role of BASP1 in angiogenic pathways. Basp1 expression in cornea had a strong correlation with a haplotype shared by mouse strains with varied angiogenic phenotypes. In addition, inhibition of BASP1 demonstrated a dosage-dependent effect in both primary mouse brain endothelial and human microvascular endothelial cell (HMVEC) migration. To investigate its role in vivo, we knocked out basp1 in transgenic kdrl:zsGreen zebrafish embryos using a widely adopted CRISPR-Cas9 system. These embryos had severely disrupted vessel formation compared to control siblings. We further show that basp1 promotes angiogenesis by upregulating β-catenin gene and the Dll4/Notch1 signaling pathway. These results, to the best of our knowledge, provide the first in vivo evidence to indicate the role of Basp1 as an angiogenesis-regulating gene and opens the potential therapeutic avenues for a wide variety of systemic angiogenesis-dependent diseases.
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Affiliation(s)
- Mehrdad Khajavi
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Zhou
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Alex J Schiffer
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren Bazinet
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amy E Birsner
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Leonard Zon
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
| | - Robert J D'Amato
- Department of Surgery, Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
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4
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Spaan K, Haigis AC, Weiss J, Legradi J. Effects of 25 thyroid hormone disruptors on zebrafish embryos: A literature review of potential biomarkers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:1238-1249. [PMID: 30625654 DOI: 10.1016/j.scitotenv.2018.11.071] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 05/28/2023]
Abstract
It is estimated that many organic compounds found in our environment can interfere with the thyroid system and act as thyroid hormone (TH) disruptor. Despite that, there is a clear lack of assays to identify TH disruptors. Recently zebrafish embryos were suggested as screening tool to identify compounds which impact thyroid synthesis. Effects on hormone level, gene transcript expression, eye development and swim bladder inflation are suggested as potential biomarker for TH disruptors. In order to assess the applicability of these biomarkers we performed a literature review. The effects of 25 known TH disrupting compounds were compared between studies. The studies were limited to exposures with embryos prior 7 days of development. The different study designs and the lack of standardized methods complicated the comparison of the results. The most common responses were morphological alterations and gene transcript expression changes, but no specific biomarker for TH disruption could be identified. In studies addressing TH disruption behavioral effects were more commonly monitored than in studies not mentioning the TH pathway. TH disruption in developing zebrafish embryos might be caused by different modes of action e.g. disruption of follicle development, binding of TH, activation of TH receptors causing different effects. Timing of developmental processes in combination with exposure duration might also play a role. On the other side compound characteristics (uptake, stability, metabolization) could also cause differences between substances. Further studies are necessary to gain better understanding into the mechanisms of TH disruption in early zebrafish development.
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Affiliation(s)
- Kyra Spaan
- Department of Environmental Science and Analytical Chemistry (ACES), Stockholm University, 11418 Stockholm, Sweden; Environment & Health, VU University Amsterdam, 1081 HV, Amsterdam, the Netherlands
| | - Ann-Cathrin Haigis
- Institute for Environmental Research, Department of Ecosystem Analysis, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Jana Weiss
- Department of Environmental Science and Analytical Chemistry (ACES), Stockholm University, 11418 Stockholm, Sweden; Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Jessica Legradi
- Environment & Health, VU University Amsterdam, 1081 HV, Amsterdam, the Netherlands; Institute for Environmental Research, Department of Ecosystem Analysis, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
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5
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Wang X, Liang S. Gel Absorption-Based Sample Preparation Method for Shotgun Analysis of Membrane Proteome. Methods Mol Biol 2019; 1855:483-490. [PMID: 30426442 DOI: 10.1007/978-1-4939-8793-1_41] [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: 06/09/2023]
Abstract
Membrane proteins solubilized in a starting buffer containing high concentration of SDS are directly entrapped and immobilized into gel matrix when the membrane protein solution is absorbed by the vacuum-dried polyacrylamide gel. After the detergent and other salts are removed by washing, the proteins are subjected to in-gel digestion, and the tryptic peptides are extracted and analyzed by CapLC-MS/MS. The newly developed method not only avoids protein loss and the adverse protein modifications during gel-embedment but also improves the subsequent in-gel digestion and the recovery of tryptic peptides, particularly hydrophobic peptides. Thus, this method facilitates the identification of membrane proteins, especially integral membrane proteins.
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Affiliation(s)
- Xianchun Wang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China.
| | - Songping Liang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China
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6
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Kwon OK, Kim S, Lee S. Global proteomic analysis of lysine acetylation in zebrafish (Danio rerio) embryos. Electrophoresis 2016; 37:3137-3145. [DOI: 10.1002/elps.201600210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/25/2016] [Accepted: 09/05/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Oh Kwang Kwon
- BK21 Plus KNU Multi-Omics based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu Republic of Korea
| | - Sunjoo Kim
- BK21 Plus KNU Multi-Omics based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu Republic of Korea
| | - Sangkyu Lee
- BK21 Plus KNU Multi-Omics based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences; Kyungpook National University; Daegu Republic of Korea
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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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Rahlouni F, Szarka S, Shulaev V, Prokai L. A Survey of the Impact of Deyolking on Biological Processes Covered by Shotgun Proteomic Analyses of Zebrafish Embryos. Zebrafish 2015; 12:398-407. [PMID: 26439676 DOI: 10.1089/zeb.2015.1121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Deyolking, the removal of the most abundant protein from the zebrafish (Danio rerio) embryo, is a common technique for in-depth exploration of proteome-level changes in vivo due to various environmental stressors or pharmacological impacts during embryonic stage of development. However, the effect of this procedure on the remaining proteome has not been fully studied. Here, we report a label-free shotgun proteomics survey on proteome coverage and biological processes that are enriched and depleted as a result of deyolking. Enriched proteins are involved in cellular energetics and development pathways, specifically implicating enrichment related to mitochondrial function. Although few proteins were removed completely by deyolking, depleted molecular pathways were associated with calcium signaling and signaling events implicating immune system response.
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Affiliation(s)
- Fatima Rahlouni
- 1 Department of Pharmacology and Neuroscience, University of North Texas Health Science Center , Fort Worth, Texas
| | - Szabolcs Szarka
- 1 Department of Pharmacology and Neuroscience, University of North Texas Health Science Center , Fort Worth, Texas
| | - Vladimir Shulaev
- 2 Department of Biological Sciences, University of North Texas , Denton, Texas
| | - Laszlo Prokai
- 1 Department of Pharmacology and Neuroscience, University of North Texas Health Science Center , Fort Worth, Texas
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9
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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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10
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Alli Shaik A, Wee S, Li RHX, Li Z, Carney TJ, Mathavan S, Gunaratne J. Functional Mapping of the Zebrafish Early Embryo Proteome and Transcriptome. J Proteome Res 2014; 13:5536-50. [DOI: 10.1021/pr5005136] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Asfa Alli Shaik
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Sheena Wee
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Rachel Hai Xia Li
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Zhen Li
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, 138672, Singapore
| | - Tom J. Carney
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
- Lee
Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang
Avenue, 639798, Singapore
| | - Sinnakaruppan Mathavan
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, 138672, Singapore
| | - Jayantha Gunaratne
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
- Lee
Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang
Avenue, 639798, Singapore
- Department
of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, 117597, Singapore
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11
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van der Plas-Duivesteijn SJ, Mohammed Y, Dalebout H, Meijer A, Botermans A, Hoogendijk JL, Henneman AA, Deelder AM, Spaink HP, Palmblad M. Identifying proteins in zebrafish embryos using spectral libraries generated from dissected adult organs and tissues. J Proteome Res 2014; 13:1537-44. [PMID: 24460240 DOI: 10.1021/pr4010585] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spectral libraries provide a sensitive and accurate method for identifying peptides from tandem mass spectra, complementary to searching genome-derived databases or sequencing de novo. Their application requires comprehensive libraries including peptides from low-abundant proteins. Here we describe a method for constructing such libraries using biological differentiation to "fractionate" the proteome by harvesting adult organs and tissues and build comprehensive libraries for identifying proteins in zebrafish (Danio rerio) embryos and larvae (an important and widely used model system). Hierarchical clustering using direct comparison of spectra was used to prioritize organ selection. The resulting and publicly available library covers 14,164 proteins, significantly improved the number of peptide-spectrum matches in zebrafish developmental stages, and can be used on data from different instruments and laboratories. The library contains information on tissue and organ expression of these proteins and is also applicable for adult experiments. The approach itself is not limited to zebrafish but would work for any model system.
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12
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Peng XX. Proteomics and its applications to aquaculture in China: infection, immunity, and interaction of aquaculture hosts with pathogens. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 39:63-71. [PMID: 22484215 DOI: 10.1016/j.dci.2012.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 03/19/2012] [Accepted: 03/29/2012] [Indexed: 05/31/2023]
Abstract
China is the largest fishery producer worldwide in term of its aquaculture output, and plays leading and decisive roles in international aquaculture development. To improve aquaculture output further and promote aquaculture business development, infectious diseases and immunity of fishes and other aquaculture species must be studied. In this regard, aquaculture proteomics has been widely carried out in China to get a better understanding of aquaculture host immunity and microbial pathogenesis as well as host-pathogen interactions, and to identify novel disease targets and vaccine candidates for therapeutic interventions. These proteomics studies include development of novel methods, assays, and advanced concepts in order to characterize proteomics mechanisms of host innate immune defense and microbial pathogenesis. This review article summarizes some recently published technical approaches and their applications to aquaculture proteomics with an emphasis on the responses of aquaculture animals to bacteria, viruses, and other aqua-environmental stresses, and development of broadly cross-protective vaccine candidates. The reviewed articles are those that have been published in international peer reviewed journals.
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Affiliation(s)
- Xuan-Xian Peng
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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13
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Huang SM, Xu F, Lam SH, Gong Z, Ong CN. Metabolomics of developing zebrafish embryos using gas chromatography- and liquid chromatography-mass spectrometry. MOLECULAR BIOSYSTEMS 2013; 9:1372-80. [DOI: 10.1039/c3mb25450j] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Wang X, Liang S. Gel-absorption-based sample preparation method for shotgun analysis of membrane proteome. Methods Mol Biol 2012; 869:385-392. [PMID: 22585502 DOI: 10.1007/978-1-61779-821-4_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Membrane proteins solubilized in a starting buffer containing high concentration of sodium dodecyl sulfate (SDS) are directly entrapped and immobilized into gel matrix when the membrane protein solution is absorbed by the vacuum-dried polyacrylamide gel. After the detergent and other salts are removed by washing, the proteins are subjected to in-gel digestion and the tryptic peptides are extracted and analyzed by CapLC-MS/MS. The newly developed method not only avoids protein loss and the adverse protein modifications during gel-embedment but also improves the subsequent in-gel digestion and the recovery of tryptic peptides, particularly the hydrophobic peptides. Thus, this method facilitates the identification of membrane proteins especially the integral membrane proteins.
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Affiliation(s)
- Xianchun Wang
- Hunan Normal University, Changsha, Hunan, People's Republic of China.
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15
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Saxena S, Singh SK, Lakshmi MGM, Meghah V, Sundaram CS, Swamy CVB, Idris MM. Proteome profile of zebrafish kidney. J Proteomics 2011; 74:2937-47. [DOI: 10.1016/j.jprot.2011.07.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 07/19/2011] [Accepted: 07/23/2011] [Indexed: 11/25/2022]
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16
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Buske C, Gerlai R. Shoaling develops with age in Zebrafish (Danio rerio). Prog Neuropsychopharmacol Biol Psychiatry 2011; 35:1409-15. [PMID: 20837077 PMCID: PMC3021101 DOI: 10.1016/j.pnpbp.2010.09.003] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 09/03/2010] [Accepted: 09/04/2010] [Indexed: 02/04/2023]
Abstract
The biological mechanisms of human social behavior are complex. Animal models may facilitate the understanding of these mechanisms and may help one to develop treatment strategies for abnormal human social behavior, a core symptom in numerous clinical conditions. The zebrafish is perhaps the most social vertebrate among commonly used laboratory species. Given its practical features and the numerous genetic tools developed for it, it should be a promising tool. Zebrafish shoal, i.e. from a tight multimember groups, but the ontogenesis of this behavior has not been described. Analyzing the development of shoaling is a step towards discovering the mechanisms of this behavior. Here we study age-dependent changes of shoaling in zebrafish from day 7 post fertilization to over 5months of age by measuring the distance between all pairs of fish in freely swimming groups of ten subjects. Our longitudinal (repeated measure within subject) and cross sectional (non-repeated measure between subject) analyses both demonstrated a significant increase of shoaling with age (decreased distance between shoal members). Given the sophisticated genetic and developmental biology methods already available for zebrafish, we argue that our behavioral results open a new avenue towards the understanding of the development of vertebrate social behavior and of its mechanisms and abnormalities.
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Affiliation(s)
- Christine Buske
- Department of Cell and Systems Biology, Neuroscience, University of Toronto, Canada.
| | - Robert Gerlai
- Department of Cell & Systems Biology, Neuroscience, University of Toronto, Psychology Department, University of Toronto, Mississauga
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17
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Sanchez BC, Ralston-Hooper K, Sepúlveda MS. Review of recent proteomic applications in aquatic toxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2011; 30:274-282. [PMID: 21072841 DOI: 10.1002/etc.402] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Over the last decade, the environmental sciences have witnessed an incredible movement towards the utilization of high-throughput molecular tools that are capable of detecting simultaneous changes of hundreds, and even thousands, of molecules and molecular components after exposure of organisms to different environmental stressors. These techniques have received a great deal of attention because they not only offer the potential to unravel novel mechanisms of physiological and toxic action but are also amenable to the discovery of biomarkers of exposure and effects. In this article, we review the state of knowledge of one of these tools in ecotoxicological research: proteomics. We summarize the state of proteomics research in fish, and follow with studies conducted with aquatic invertebrates. A brief discussion on proteomic methods is also presented. We conclude with some ideas for future proteomic studies with fish and aquatic invertebrates.
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Singh SK, Meena Lakshmi MG, Saxena S, Swamy CVB, Idris MM. Proteome profile of zebrafish caudal fin based on one-dimensional gel electrophoresis LCMS/MS and two-dimensional gel electrophoresis MALDI MS/MS analysis. J Sep Sci 2010; 34:225-32. [DOI: 10.1002/jssc.201000626] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/18/2010] [Accepted: 10/18/2010] [Indexed: 11/10/2022]
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Proteomic Signatures of the Zebrafish (Danio rerio) Embryo: Sensitivity and Specificity in Toxicity Assessment of Chemicals. INTERNATIONAL JOURNAL OF PROTEOMICS 2010; 2010:630134. [PMID: 22084678 PMCID: PMC3200224 DOI: 10.1155/2010/630134] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 05/26/2010] [Accepted: 07/19/2010] [Indexed: 12/25/2022]
Abstract
Studies using embryos of the zebrafish Danio rerio (DarT) instead of adult fish for characterising the (eco-) toxic potential of chemicals have been proposed as animal replacing methods. Effect analysis at the molecular level might enhance sensitivity, specificity, and predictive value of the embryonal studies. The present paper aimed to test the potential of toxicoproteomics with zebrafish eleutheroembryos for sensitive and specific toxicity assessment. 2-DE-based toxicoproteomics was performed applying low-dose (EC10) exposure for 48 h with three-model substances Rotenone, 4,6-dinitro-o-cresol (DNOC) and Diclofenac. By multivariate “pattern-only” PCA and univariate statistical analyses, alterations in the embryonal proteome were detectable in nonetheless visibly intact organisms and treatment with the three substances was distinguishable at the molecular level. Toxicoproteomics enabled the enhancement of sensitivity and specificity of the embryonal toxicity assay and bear the potency to identify protein markers serving as general stress markers and early diagnosis of toxic stress.
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Singh SK, Sundaram CS, Shanbhag S, Idris MM. Proteomic profile of zebrafish brain based on two-dimensional gel electrophoresis matrix-assisted laser desorption/ionization MS/MS analysis. Zebrafish 2010; 7:169-77. [PMID: 20528263 DOI: 10.1089/zeb.2010.0657] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Zebrafish is one of the most widely studied model organisms for understanding the neurodevelopment and neurological disorders of humans because of its similar brain structure, genome, and proteome. Understanding the zebrafish brain proteome is particularly useful as no data of zebrafish brain proteome are available despite its wide use as an alternative neurological animal model. We have determined the proteome profile of the zebrafish brain based on two-dimensional gel electrophoresis covering 161 proteins including 96 protein identities reported to the Swiss-Prot database. The proteins identified in this study were found to be associated with various pathways such as cell death, free radical scavenging, cell signaling, nervous system development, and cell cycle. The identified proteins were also observed to play important roles in various brain-related diseases and genetic disorders, such as Huntington's disease, Parkinson's disease, and schizophrenia. This article provides the zebrafish brain two-dimensional gel electrophoresis proteome map and the details of the 161 brain tissue-specific proteins. Also we have established the roles of the identified proteins in various neurological functions and diseases based on pathway analysis.
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Abramsson A, Westman-Brinkmalm A, Pannee J, Gustavsson M, von Otter M, Blennow K, Brinkmalm G, Kettunen P, Zetterberg H. Proteomics profiling of single organs from individual adult zebrafish. Zebrafish 2010; 7:161-8. [PMID: 20392139 DOI: 10.1089/zeb.2009.0644] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The model organism zebrafish (Danio rerio) is extensively utilized in studies of developmental biology but is also being investigated in the context of a growing list of human age-related diseases. To facilitate such studies, we here present protein expression patterns of adult zebrafish organs, including blood, brain, fin, heart, intestine, liver, and skeletal muscle. Protein extracts were prepared from the different organs of two zebrafish and analyzed using liquid chromatography coupled to high-resolution tandem mass spectrometry. Zebrafish tissue was digested directly after minimal fractionation and cleaned up (the shotgun approach). Proteins were identified using Mascot software. In total, 1394 proteins were identified of which 644 were nonredundant. Of these, 373 demonstrated an organ-specific expression pattern and 57 had not been shown on protein level before. These data emphasize the need for increased research at the protein level to facilitate the selection of candidate proteins for targeted quantification and to refine systematic genetic network analysis in vertebrate development, biology, and disease.
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Affiliation(s)
- Alexandra Abramsson
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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Gel absorption-based sample preparation for the analysis of membrane proteome by mass spectrometry. Anal Biochem 2010; 404:204-10. [DOI: 10.1016/j.ab.2010.05.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 05/14/2010] [Accepted: 05/18/2010] [Indexed: 11/17/2022]
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Stegeman JJ, Goldstone JV, Hahn ME. Perspectives on zebrafish as a model in environmental toxicology. FISH PHYSIOLOGY 2010. [DOI: 10.1016/s1546-5098(10)02910-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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