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Henke AN, Chilukuri S, Langan LM, Brooks BW. Reporting and reproducibility: Proteomics of fish models in environmental toxicology and ecotoxicology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168455. [PMID: 37979845 DOI: 10.1016/j.scitotenv.2023.168455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Environmental toxicology and ecotoxicology research efforts are employing proteomics with fish models as New Approach Methodologies, along with in silico, in vitro and other omics techniques to elucidate hazards of toxicants and toxins. We performed a critical review of toxicology studies with fish models using proteomics and reported fundamental parameters across experimental design, sample preparation, mass spectrometry, and bioinformatics of fish, which represent alternative vertebrate models in environmental toxicology, and routinely studied animals in ecotoxicology. We observed inconsistencies in reporting and methodologies among experimental designs, sample preparations, data acquisitions and bioinformatics, which can affect reproducibility of experimental results. We identified a distinct need to develop reporting guidelines for proteomics use in environmental toxicology and ecotoxicology, increased QA/QC throughout studies, and method optimization with an emphasis on reducing inconsistencies among studies. Several recommendations are offered as logical steps to advance development and application of this emerging research area to understand chemical hazards to public health and the environment.
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Affiliation(s)
- Abigail N Henke
- Department of Biology, Baylor University Waco, TX, USA; Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University Waco, TX, USA
| | | | - Laura M Langan
- Department of Environmental Science, Baylor University Waco, TX, USA; Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University Waco, TX, USA.
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University Waco, TX, USA; Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University Waco, TX, USA.
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2
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Correia D, Domingues I, Faria M, Oliveira M. Effects of fluoxetine on fish: What do we know and where should we focus our efforts in the future? THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159486. [PMID: 36257440 DOI: 10.1016/j.scitotenv.2022.159486] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Fluoxetine is one of the most studied and detected selective serotonin reuptake inhibitors in the aquatic environment, found at concentrations ranging from ng/L to μg/L. Its presence in this environment can induce effects on aquatic organisms that may compromise their fitness. Several experimental studies have demonstrated that fluoxetine can induce neurotoxicity, genetic and biochemical changes, and cause behavioral dysfunction in a wide range of fish species. However, contradictory results can be found. There is thus the need for a comprehensive review of the current state of knowledge on the effects of fluoxetine on fish at different levels of biological organization, highlighting inclusive patterns and discussing the potential causes for the contradictory results, that can be found in the available literature. This review also aims to explore and identify the main gaps in knowledge and areas for future research. We conclude that environmentally relevant concentrations of fluoxetine (e.g., from 0.00345 μg/L) produced adverse effects and often this concentration range is not addressed in conventional environmental risk assessment strategies. Its environmental persistence and ionizable properties reinforce the need for standardized testing with representative aquatic models, targeting endpoints sensitive to the specific mode of action of fluoxetine, in order to assess and rank its actual environmental risk to aquatic ecosystems.
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Affiliation(s)
- Daniela Correia
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Inês Domingues
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | | | - Miguel Oliveira
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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3
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Leprêtre M, Geffard O, Espeyte A, Faugere J, Ayciriex S, Salvador A, Delorme N, Chaumot A, Degli-Esposti D. Multiple reaction monitoring mass spectrometry for the discovery of environmentally modulated proteins in an aquatic invertebrate sentinel species, Gammarus fossarum. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 315:120393. [PMID: 36223854 DOI: 10.1016/j.envpol.2022.120393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Multiple reaction monitoring (MRM) mass spectrometry is emerging as a relevant tool for measuring customized molecular markers in freshwater sentinel species. While this technique is typically used for the validation of protein molecular markers preselected from shotgun experiments, recent gains of MRM multiplexing capacity offer new possibilities to conduct large-scale screening of animal proteomes. By combining the strength of active biomonitoring strategies and MRM technologies, this study aims to propose a new strategy for the discovery of candidate proteins that respond to environmental variability. For this purpose, 249 peptides derived from 147 proteins were monitored by MRM in 273 male gammarids caged in 56 environmental sites, representative of the diversity of French water bodies. A methodology is here proposed to identify a set of customized housekeeping peptides (HKPs) used to correct analytical batch effects and allow proper comparison of peptide levels in gammarids. A comparative analysis performed on HKPs-normalized data resulted in the identification of peptides highly modulated in the environment and derived from proteins likely involved in the environmental stress response. Overall, this study proposes a breakthrough approach to screen and identify potential proteins responding to relevant environmental conditions in sentinel species.
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Affiliation(s)
- Maxime Leprêtre
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, F-69625, Villeurbanne, France
| | - Olivier Geffard
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, F-69625, Villeurbanne, France
| | - Anabelle Espeyte
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, F-69625, Villeurbanne, France
| | - Julien Faugere
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Sophie Ayciriex
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Arnaud Salvador
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Nicolas Delorme
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, F-69625, Villeurbanne, France
| | - Arnaud Chaumot
- INRAE, UR RiverLy, Laboratoire d'écotoxicologie, F-69625, Villeurbanne, France
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Freire MM, Gomez C, Moreira JC, Linde Arias AR. Multibiomarker approach in fish to assess a heavily polluted Brazilian estuary, Guanabara Bay. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 195:187. [PMID: 36504393 DOI: 10.1007/s10661-022-10752-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Brazil's Guanabara Bay (GB), located in Rio De Janeiro, is a deeply contaminated, eutrophic waterbody that challenges the understanding of the effects of pollutants on the biota. This paper presents a strategy to evaluate the impact of contamination utilizing a multibiomarker approach in two fish species: corvine (Micropogonias furnieri) and burrfish (Chilomycterus spinosus). The strategy is comprised of a general biomarker of fish' physical condition, the condition factor (CF), and specific biomarkers of pollutant exposure such as acetylcholinesterase (AChE), metallothionein (MT) activity and biliary polycyclic aromatic hydrocarbons (PAH) metabolites. Our results indicate that fish from GB are greatly affected by environmental pollution. CF values were lower in fishes from GB than in the reference site indicating that these fishes were under higher environmental stress. Lower AChE activity level in both species showed vulnerability to the presence of pesticide residues. Higher levels of MT in both species in GB reflect the consequences of heavy metal exposure in the bay, in spite of their bioavailability being restricted specially by the high organic matter content of GB. The levels of PAHs were higher in GB for both fish species, indicating exposure to these substances. However, the fish species showed different behavior regarding the origin of the PAHs. The multibiomarker approach used in this study evidently depicted effects on the health of fish in a waterbody with a complex polluted situation and further categorized the effects of anthropogenic activities in this aquatic system.
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Affiliation(s)
- Marina Moreira Freire
- CESTEH - Centro de Estudos da Saúde do Trabalhador e Ecologia Humana, Escola Nacional de Saúde Pública - Fundação Oswaldo Cruz, Av. Leopoldo Bulhões, 1480, Rio de Janeiro, RJ, 21041-210, Brazil
- Centro Universitário Serra dos Órgãos - UNIFESO, Endereço Av. Alberto Tôrres 111 - Alto, Teresópolis, RJ, 25964-004, Brazil
| | - Cristina Gomez
- Escola de Matematica Aplicada, Fundação Getulio Vargas, Praia de Botafogo, 190, Rio de Janeiro, RJ, 22250-90, Brazil
- Instituto de Estudos em Saude Coletiva, Universidade Federal de Rio de Janeiro, Cidade Universitaria da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-592, Brazil
| | - Josino Costa Moreira
- Instituto de Estudos em Saude Coletiva, Universidade Federal de Rio de Janeiro, Cidade Universitaria da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-592, Brazil
| | - Ana Rosa Linde Arias
- Escola de Matematica Aplicada, Fundação Getulio Vargas, Praia de Botafogo, 190, Rio de Janeiro, RJ, 22250-90, Brazil.
- Instituto de Estudos em Saude Coletiva, Universidade Federal de Rio de Janeiro, Cidade Universitaria da Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-592, Brazil.
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Gajahin Gamage NT, Miyashita R, Takahashi K, Asakawa S, Senevirathna JDM. Proteomic Applications in Aquatic Environment Studies. Proteomes 2022; 10:proteomes10030032. [PMID: 36136310 PMCID: PMC9505238 DOI: 10.3390/proteomes10030032] [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: 06/29/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.
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Affiliation(s)
- Nadeeka Thushari Gajahin Gamage
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
| | - Rina Miyashita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazutaka Takahashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Jayan Duminda Mahesh Senevirathna
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
- Correspondence:
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Mercury-Induced Oxidative Stress Response in Benthic Foraminifera: An In Vivo Experiment on Amphistegina lessonii. BIOLOGY 2022; 11:biology11070960. [PMID: 36101341 PMCID: PMC9312061 DOI: 10.3390/biology11070960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/22/2022] [Accepted: 06/01/2022] [Indexed: 11/17/2022]
Abstract
The evaluation of the effects of pollution (e.g., Hg pollution) is a difficult task and relies mostly on biomonitoring based on bioindicators. The application of biomarkers may represent a complementary or alternative approach in environmental biomonitoring. Mercury is known to pose a significant health hazard due to its ability to cross cellular membranes, bioaccumulate, and biomagnify. In the present research, the effects of short-term (i.e., 24 h) Hg exposure in the symbiont-bearing benthic foraminiferal species Amphistegina lessonii are evaluated using several biomarkers (i.e., proteins and enzymes). Mercury leads to significant changes in the biochemistry of cells. Its effects are mainly associated with oxidative stress (i.e., production of reactive oxygen species: ROS), depletion of glutathione (GSH), and alteration of protein synthesis. Specifically, our findings reveal that exposure to Hg leads to the consumption of GSH by GPx and GST for the scavenging of ROS and the activation of antioxidant-related enzymes, including SOD and GSH-enzymes (GST, GSR, GPx, and Se-GPx), that are directly related to a defense mechanism against ROS. The Hg exposure also activates the MAPK (e.g., p-p38) and HSP (e.g., HSP 70) pathways. The observed biochemical alterations associated with Hg exposure may represent effective and reliable proxies (i.e., biomarkers) for the evaluation of stress in A. lessonii and lead to a possible application for the detection of early warning signs of environmental stress in biomonitoring.
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7
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Armengaud J. Protecting our environment, a motivating outdoor game for proteomics! Proteomics 2022; 22:e2200055. [PMID: 35452157 DOI: 10.1002/pmic.202200055] [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: 02/19/2022] [Revised: 02/19/2022] [Accepted: 02/25/2022] [Indexed: 11/06/2022]
Abstract
The global Earth ecosystem faces many intertwined threats, primarily anthropogenic pollution, drastic reduction of wild spaces, faster spread of pathogens, and global climate warming. Ecotoxicology, the integration of toxicology and ecology, aims to describe the effects of toxicants on organisms, whether at the level of the population, the community, the ecosystem, or the biosphere. Sentinel species are employed to assess threats to life, giving advance warning of danger. In this issue of Proteomics, Wilde and collaborators (Proteomics 2022, 22, https://doi.org/10.1002/pmic.202100289) present a comprehensive coverage of the proteome of the crustacean Daphnia magna, a species used to evaluate aquatic pollution. This study illustrates how current shotgun proteomics technology allows straightforward quantitation of any protein for whole animals or dissected organs, making global molecular phenotyping a reality for animals. Tandem mass spectrometry operated in data-independent acquisition can be used to compare the response of sentinels to various environmental conditions. The current low number of well-annotated animal or plant genomes, the high diversity of genetic backgrounds of each species, and the paucity of knowledge about protein functions for most of the relevant sentinels pose huge challenges for data interpretation. As a result, ecology and ecotoxicology today constitute an exceptional field for proteomics.
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Affiliation(s)
- Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, SPI, Département Médicaments et Technologies pour la Santé (DMTS), Bagnols-sur-Cèze, France
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8
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Chronic Effects of Fluoxetine on Danio rerio: A Biochemical and Behavioral Perspective. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12042256] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fluoxetine is an antidepressant widely used to treat depressive and anxiety states. Due to its mode of action in the central nervous system (selective serotonin reuptake inhibitor (SSRI)), it becomes toxic to non-target organisms, leading to changes that are harmful to their survival. In this work, the effects of fluoxetine on juvenile zebrafish (Danio rerio) were evaluated, assessing biochemical (phase II biotransformation—glutathione S-transferase (GST), neurotransmission—acetylcholinesterase (ChE), energy metabolism—lactate dehydrogenase (LDH), and oxidative stress—glutathione peroxidase (GPx)) and behavior endpoints (swimming behavior, social behavior, and thigmotaxis) after 21 days exposure to 0 (control), 0.1, 1 and 10 µg/L. Biochemically, although chronic exposure did not induce significant effects on neurotransmission and energy metabolism, GPx activity was decreased after exposure to 10 µg/L of fluoxetine. At a behavioral level, exploratory and social behavior was not affected. However, changes in the swimming pattern of exposed fish were observed in light and dark periods (decreased locomotor activity). Overall, the data show that juvenile fish chronically exposed to fluoxetine may exhibit behavioral changes, affecting their ability to respond to environmental stressors and the interaction with other fish.
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9
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Nissa MU, Pinto N, Mukherjee A, Reddy PJ, Ghosh B, Sun Z, Ghantasala S, Chetanya C, Shenoy SV, Moritz RL, Goswami M, Srivastava S. Organ-Based Proteome and Post-Translational Modification Profiling of a Widely Cultivated Tropical Water Fish, Labeo rohita. J Proteome Res 2021; 21:420-437. [PMID: 34962809 DOI: 10.1021/acs.jproteome.1c00759] [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] [Indexed: 11/28/2022]
Abstract
Proteomics has enormous applications in human and animal research. However, proteomic studies in fisheries science are quite scanty particularly for economically important species. Few proteomic studies have been carried out in model fish species, but comprehensive proteomics of aquaculture species are still scarce. This study aimed to perform a comprehensive organ-based protein profiling of important tissue samples for one of the most important aquaculture species,Labeo rohita.Deep proteomic profiling of 17 histologically normal tissues, blood plasma, and embryo provided mass-spectrometric evidence for 8498 proteins at 1% false discovery rate that make up about 26% of the total annotated protein-coding sequences in Rohu. Tissue-wise expression analysis was performed, and the presence of several biologically important proteins was also verified using a targeted proteomic approach. We identified the global post-translational modifications (PTMs) in terms of acetylation (N-terminus and lysine), methylation (N-terminus, lysine, and arginine), and phosphorylation (serine, threonine, and tyrosine) to present a comprehensive proteome resource. An interactive web-based portal has been developed for an overall landscape of protein expression across the studied tissues of Labeo rohita (www.fishprot.org). This draft proteome map of Labeo rohita would advance basic and applied research in aquaculture to meet the most critical challenge of providing food and nutritional security to an increasing world population.
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Affiliation(s)
- Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Nevil Pinto
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Versova, Mumbai, Maharashtra 400061, India
| | - Arijit Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - Biplab Ghosh
- Regional Centre for Biotechnology, Faridabad 121001, India
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Saicharan Ghantasala
- Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Chetanya Chetanya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjyot Vinayak Shenoy
- Department of Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Mukunda Goswami
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Versova, Mumbai, Maharashtra 400061, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Iheanacho SC, Adeolu AI, Nwose R, Ekpenyong J, Offu P, Amadi-Eke A, Iheanacho AC, Ogunji J. Genotoxicity, oxidative stress and lysozyme induction in Clarias gariepinus chronically exposed to water-soluble fraction of burnt tire ash. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1983-1996. [PMID: 34529204 DOI: 10.1007/s10646-021-02474-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
The safety of aquatic ecosystems has been compromised by numerous anthropogenic activities, especially leachates from non-point source toxicants, leaching into aquatic systems. This study evaluated the toxicity of the water-soluble fractions (WSFs) of burnt tire ash (BTA) on Clarias gariepinus via a battery of integrated biomarkers. Juvenile C. gariepinus were exposed to sublethal (0.56, 1.12, and 2.24 g/L) concentrations of BTA, derived from 11.2 g/L median lethal concentration (96 LC50), at duration intervals of 1, 14, and 28 days, followed by a recovery trial that lasted for 14 days. Serum biochemical parameters, antioxidant enzyme activities of the gill and liver, lysozymes activity and erythron profile were assessed. The findings of the present study revealed that BTA-WSF induced prominent alterations on biochemical parameters, lysozymes activity and antioxidant enzymes activities in the exposed fish. Furthermore, toxicant exposure promoted oxidative stress, cellular damage and genotoxicity (erythrocytic nuclear and cellular abnormalities) in the exposed fish. In general, a post-exposure trial showed partial recovery from the exposure effects of the toxicant, following the evident modifications of serum enzymes and erythron pathopathology in the experimental model. Biomonitoring of BTA, using sentinel aquatic species such as C. gariepinus, provides insights into the ecotoxicological potency of this toxicant.
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Affiliation(s)
- Stanley C Iheanacho
- Department of Fisheries and Aquaculture, Alex Ekwueme Federal University Ndufu Alike, Ebonyi, Nigeria.
- Department of Zoology and Environmental Biology, University of Nigeria Nsukka, Enugu, Nigeria.
| | - Adewale I Adeolu
- Department of Agriculture, Alex Ekwueme Federal University Ndufu Alike, Ebonyi, Nigeria
| | - Roseline Nwose
- Department of Agriculture, Alex Ekwueme Federal University Ndufu Alike, Ebonyi, Nigeria
| | - Joshua Ekpenyong
- Department of Fisheries and Aquaculture, Alex Ekwueme Federal University Ndufu Alike, Ebonyi, Nigeria
| | - Peter Offu
- Department of Political Science, Alex Ekwueme Federal University Ndufu Alike, Ebonyi, Nigeria
| | - Akunna Amadi-Eke
- Department of Fisheries and Aquaculture Technology, Federal University of Technology Owerri, Imo, Nigeria
| | - Angus C Iheanacho
- Department of Pure and Industrial Chemistry, University of Nigeria Nsukka, Enugu, Nigeria
| | - Johnny Ogunji
- Department of Fisheries and Aquaculture, Alex Ekwueme Federal University Ndufu Alike, Ebonyi, Nigeria
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11
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Guo H, Wang L, Deng Y, Ye J. Novel perspectives of environmental proteomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147588. [PMID: 34023612 DOI: 10.1016/j.scitotenv.2021.147588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/08/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
The connection among genome expression, proteome alteration, metabolism regulation and phenotype change under environmental stresses is very vague. It is a tough task for the traditional research approaches to reveal the related scientific mechanisms of the above connection at molecular and systematic levels. Proteomics approach is an insightful tool for revealing the biological functions, metabolic networks and functional protein interaction networks of cells and organisms under stresses at the systematic level. The purpose of this review is to provide an insightful guideline on how to set up a proteomic investigation for revealing biomolecule mechanisms, protein biomarkers and metabolism networks related to stress response, pollutant recognition, transport and biodegradation, and providing an insightful high-throughput approach for screening functional enzymes and effective microbes based on bioinformatics and functional verification method. Furthermore, the toxicity evaluation of pollutants and byproducts by proteomics approaches provides a scientific insight for early diagnosis of ecological risk and determination of the effectiveness of pollutant treatment techniques.
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Affiliation(s)
- Huiying Guo
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China; Institute of Orthopedic Diseases, Department of Bone and Joint Surgery, The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Lili Wang
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ying Deng
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinshao Ye
- Key Laboratory of Environmental Exposure and Health of Guangdong Province, School of Environment, Jinan University, Guangzhou 510632, China.
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12
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Pollution Biomarkers in the Framework of Marine Biodiversity Conservation: State of Art and Perspectives. WATER 2021. [DOI: 10.3390/w13131847] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Marine biodiversity is threatened by several anthropogenic pressures. Pollution deriving from the discharge of chemical contaminants in the sea represents one of the main threats to the marine environment, influencing the health of organisms, their ability to recover their homeostatic status, and in turn endangering biodiversity. Molecular and cellular responses to chemical pollutants, known as biomarkers, are effect-based methodologies useful for detecting exposure and for assessing the effects of pollutants on biota in environmental monitoring. The present review analyzes and discusses the recent literature on the use of biomarkers in the framework of biodiversity conservation. The study shows that pollution biomarkers can be useful tools for monitoring and assessment of pollution threat to marine biodiversity, both in the environmental quality monitoring of protected areas and the assessment of the health status of species at risk. Moreover, key areas of the research that need further development are suggested, such as the development of omics-based biomarkers specifically addressed to conservation purposes and their validation in the field, the extension of the biomarker study to a wider number of endangered species, and the development of organic guidelines for the application of the biomarker approach in support to conservation policies and management.
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13
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Rosner A, Armengaud J, Ballarin L, Barnay-Verdier S, Cima F, Coelho AV, Domart-Coulon I, Drobne D, Genevière AM, Jemec Kokalj A, Kotlarska E, Lyons DM, Mass T, Paz G, Pazdro K, Perić L, Ramšak A, Rakers S, Rinkevich B, Spagnuolo A, Sugni M, Cambier S. Stem cells of aquatic invertebrates as an advanced tool for assessing ecotoxicological impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144565. [PMID: 33736145 DOI: 10.1016/j.scitotenv.2020.144565] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
Environmental stressors are assessed through methods that quantify their impacts on a wide range of metrics including species density, growth rates, reproduction, behaviour and physiology, as on host-pathogen interactions and immunocompetence. Environmental stress may induce additional sublethal effects, like mutations and epigenetic signatures affecting offspring via germline mediated transgenerational inheritance, shaping phenotypic plasticity, increasing disease susceptibility, tissue pathologies, changes in social behaviour and biological invasions. The growing diversity of pollutants released into aquatic environments requires the development of a reliable, standardised and 3R (replacement, reduction and refinement of animals in research) compliant in vitro toolbox. The tools have to be in line with REACH regulation 1907/2006/EC, aiming to improve strategies for potential ecotoxicological risks assessment and monitoring of chemicals threatening human health and aquatic environments. Aquatic invertebrates' adult stem cells (ASCs) are numerous and can be pluripotent, as illustrated by high regeneration ability documented in many of these taxa. This is of further importance as in many aquatic invertebrate taxa, ASCs are able to differentiate into germ cells. Here we propose that ASCs from key aquatic invertebrates may be harnessed for applicable and standardised new tests in ecotoxicology. As part of this approach, a battery of modern techniques and endpoints are proposed to be tested for their ability to correctly identify environmental stresses posed by emerging contaminants in aquatic environments. Consequently, we briefly describe the current status of the available toxicity testing and biota-based monitoring strategies in aquatic environmental ecotoxicology and highlight some of the associated open issues such as replicability, consistency and reliability in the outcomes, for understanding and assessing the impacts of various chemicals on organisms and on the entire aquatic environment. Following this, we describe the benefits of aquatic invertebrate ASC-based tools for better addressing ecotoxicological questions, along with the current obstacles and possible overhaul approaches.
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Affiliation(s)
- Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 8030, Tel Shikmona, Haifa 3108001, Israel.
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze, France.
| | - Loriano Ballarin
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35121 Padova, Italy.
| | - Stéphanie Barnay-Verdier
- Sorbonne Université; CNRS, INSERM, Université Côte d'Azur, Institute for Research on Cancer and Aging Nice, F-06107 Nice, France.
| | - Francesca Cima
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35121 Padova, Italy.
| | - Ana Varela Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
| | - Isabelle Domart-Coulon
- Muséum National d'Histoire Naturelle, CNRS, Microorganism Communication and Adaptation Molecules MCAM, Paris F-75005, France.
| | - Damjana Drobne
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Večna pot 111,D, 1000 Ljubljana, Slovenia.
| | - Anne-Marie Genevière
- Sorbonne Université, CNRS, Integrative Biology of Marine Organisms, BIOM, F-6650 Banyuls-sur-mer, France.
| | - Anita Jemec Kokalj
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Večna pot 111,D, 1000 Ljubljana, Slovenia.
| | - Ewa Kotlarska
- Institute of Oceanology of the Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland.
| | - Daniel Mark Lyons
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, HR-52210 Rovinj, Croatia.
| | - Tali Mass
- Marine Biology Department, Leon H. Charney School of Marine Sciences, 199 Aba Khoushy Ave, University of Haifa, 3498838, Israel.
| | - Guy Paz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 8030, Tel Shikmona, Haifa 3108001, Israel.
| | - Ksenia Pazdro
- Institute of Oceanology of the Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Lorena Perić
- Rudjer Boskovic Institute, Laboratory for Aquaculture and Pathology of Aquaculture Organisms, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
| | - Andreja Ramšak
- National Institute of Biology, Marine Biology Station, Fornače 41, 6330 Piran, Slovenia.
| | | | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 8030, Tel Shikmona, Haifa 3108001, Israel.
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milano, Italy.
| | - Sébastien Cambier
- Luxembourg Institute of Science and Technology, 5, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
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Can Proteomics Be Considered as a Valuable Tool to Assess the Toxicity of Nanoparticles in Marine Bivalves? JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8121033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Exposure to nanoparticles (NPs) has been identified as a major concern for marine ecosystems. Because of their peculiar physico-chemical features, NPs are accumulated in marine organisms, which suffer a variety of adverse effects. In particular, bivalve mollusks represent a unique target for NPs, mainly because they are suspension-feeders with highly developed processes for cellular internalization of nano- and micrometric particles. Several studies have demonstrated that the uptake and the accumulation of NPs can induce sub-lethal effects towards marine bivalves. However, to understand the real risk of NP exposures the application of the so-called “omics” techniques (e.g., proteomics, genomics, metabolomics, lipidomics) has been suggested. In particular, proteomics has been used to study the effects of NPs and their mechanism(s) of action in marine bivalves, but to date its application is still limited. The present review aims at summarizing the state of the art concerning the application of proteomics as a tool to investigate the effects of nanoparticles on the proteome of marine bivalves, and to critically discuss the advantages and limitations of proteomics in this field of research. Relying on results obtained by studies that applied proteomics on bivalve tissues, proteomics application needs to be considered cautiously as a promising and valuable tool to shed light on toxicity and mechanism(s) of action of NPs. Although on one hand, the analysis of the current literature demonstrated undeniable strengths, potentiality and reliability of proteomics, on the other hand a number of limitations suggest that some gaps of knowledge need to be bridged, and methodological and technical improvements are necessary before proteomics can be readily and routinely applied to nanotoxicology studies.
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15
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Liang X, Martyniuk CJ, Simmons DBD. Are we forgetting the "proteomics" in multi-omics ecotoxicology? COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100751. [PMID: 33142247 DOI: 10.1016/j.cbd.2020.100751] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 07/19/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
Abstract
Proteomics plays a significant role in discerning the effects of chemical exposures in animal taxa. Multi-omics applications have become more pervasive in toxicology, however questions remain about whether proteomics is being utilized by the community to its full potential - are we placing too much stock in transcriptomics and other omics approaches for developing adverse outcome pathways? Proteins are more relevant than transcripts because they are direct mediators of the resulting phenotype. There is also rarely perfect stoichiometry between transcript and protein abundance and transcript abundance may not accurately predict physiologic response. Proteins direct all levels of phenotype: structural proteins dictate physical form, enzymes catalyze biochemical reactions, and proteins act as signaling proteins, antibodies, transporters, ion pumps, and transcription factors to control gene expression. Molecular initiating events (MIEs) of AOPs predominantly occur at the level of the protein (e.g. ligand-receptor binding) and proteomics can elucidate novel MIEs and mapping KEs in AOPs. This critical review highlights the need for proteomics in multi-omics studies in environmental toxicology and outlines steps required for inclusion and wider acceptance in chemical risk assessment. We also present case studies of multi-omics approaches that utilize proteomics and discuss some of the challenges and opportunities for proteomics in comparative ecotoxicology. Our intention is not to minimize the importance of other omics technologies, as each has strengths and limitations, but rather to encourage researchers to consider proteomics-based methods in multi-omics studies and AOP development.
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Affiliation(s)
- Xuefang Liang
- Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Christopher J Martyniuk
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, UF Genetics Institute, University of Florida, Gainesville, FL, USA
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16
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Radwan MA, El-Gendy KS, Gad AF. Biomarker responses in terrestrial gastropods exposed to pollutants: A comprehensive review. CHEMOSPHERE 2020; 257:127218. [PMID: 32497833 DOI: 10.1016/j.chemosphere.2020.127218] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/23/2020] [Accepted: 05/24/2020] [Indexed: 06/11/2023]
Abstract
The chemical contamination of terrestrial ecosystems is a great concern as these ecosystems are the target of most of the pollutants derived from anthropogenic activities such as pesticides, heavy metals, nanoparticles, and others. Terrestrial gastropods are considered to be excellent sentinel organisms for biological monitoring of environmental pollution, as they have the ability to accumulate chemicals in their tissues and exhibit a great potential to evaluate the ecological effects of pollutants in terrestrial ecosystems. The use of biomarkers as sensitive parameters to estimate the exposure or resulting effects of chemicals have received considerable attention. The successful biomarker must be applicable in the laboratory and field conditions. Many biomarkers have been examined to understand the adverse effects of pollutants. In this review, we shed light on different types of biomarkers, such as oxidative stress, genotoxicity and immunotoxicity as diagnostic tools for monitoring the impacts of pollution. These biomarkers can provide information about early detection and quantification of these impacts during their initial manifestations and can facilitate the implementation of a rapid preventive and/or restorative responses in the affected ecosystems, as well as single or multiple biomarkers can be integrated into routine monitoring programs.
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Affiliation(s)
- M A Radwan
- Department of Pesticide Chemistry and Technology, Faculty of Agriculture, University of Alexandria, El-Shatby, 21545, Alexandria, Egypt.
| | - K S El-Gendy
- Department of Pesticide Chemistry and Technology, Faculty of Agriculture, University of Alexandria, El-Shatby, 21545, Alexandria, Egypt
| | - A F Gad
- Department of Animal Pests, Plant Protection Research Institute, Agricultural Research Center, Alexandria, Egypt
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17
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Cogne Y, Gouveia D, Chaumot A, Degli-Esposti D, Geffard O, Pible O, Almunia C, Armengaud J. Proteogenomics-Guided Evaluation of RNA-Seq Assembly and Protein Database Construction for Emergent Model Organisms. Proteomics 2020; 20:e1900261. [PMID: 32249536 DOI: 10.1002/pmic.201900261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 03/24/2020] [Indexed: 11/10/2022]
Abstract
Proteogenomics is gaining momentum as, today, genomics, transcriptomics, and proteomics can be readily performed on any new species. This approach allows key alterations to molecular pathways to be identified when comparing conditions. For animals and plants, RNA-seq-informed proteomics is the most popular means of interpreting tandem mass spectrometry spectra acquired for species for which the genome has not yet been sequenced. It relies on high-performance de novo RNA-seq assembly and optimized translation strategies. Here, several pre-treatments for Illumina RNA-seq reads before assembly are explored to translate the resulting contigs into useful polypeptide sequences. Experimental transcriptomics and proteomics datasets acquired for individual Gammarus fossarum freshwater crustaceans are used, the most relevant procedure is defined by the ratio of MS/MS spectra assigned to peptide sequences. Removing reads with a mean quality score of less than 17-which represents a single probable nucleotide error on 150-bp reads-prior to assembly, increases the proteomics outcome. The best translation using Transdecoder is achieved with a minimal open reading frame length of 50 amino acids and systematic selection of ORFs longer than 900 nucleotides. Using these parameters, transcriptome assembly and translation informed by proteomics pave the way to further improvements in proteogenomics.
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Affiliation(s)
- Yannick Cogne
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| | - Duarte Gouveia
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| | - Arnaud Chaumot
- INRAE, UR RiverLY Laboratoire d'écotoxicologie, Centre de Lyon-Villeurbanne, Villeurbanne, F-69625, France
| | - Davide Degli-Esposti
- INRAE, UR RiverLY Laboratoire d'écotoxicologie, Centre de Lyon-Villeurbanne, Villeurbanne, F-69625, France
| | - Olivier Geffard
- INRAE, UR RiverLY Laboratoire d'écotoxicologie, Centre de Lyon-Villeurbanne, Villeurbanne, F-69625, France
| | - Olivier Pible
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| | - Christine Almunia
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, SPI, 30200, Bagnols-sur-Cèze, France
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18
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Kwan YH, Zhang D, Mestre NC, Wong WC, Wang X, Lu B, Wang C, Qian PY, Sun J. Comparative Proteomics on Deep-Sea Amphipods after in Situ Copper Exposure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:13981-13991. [PMID: 31638389 DOI: 10.1021/acs.est.9b04503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The interest in deep-sea mining increased along with the environmental concerns of these activities to the deep-sea fauna. The discovery of optimal biomarkers of deep-sea mining activities in deep-sea species is a crucial step toward the supply of important ecological information for environmental impact assessment. In this study, an in situ copper exposure experiment was performed on deep-sea scavenging amphipods. Abyssorchomene distinctus individuals were selected among all the exposed amphipods for molecular characterization. Copper concentration within the gut was assessed, followed by a tandem mass tag-based coupled with two-dimensional liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) applied to identify and quantify the protein expression changes after 48 h of exposure. 2937 proteins were identified and annotated, and 1918 proteins among all identified proteins were assigned by at least two nonambiguous peptides. The screening process was performed based on the differences in protein abundance and the specific correlation between the proteins and copper in previous studies. These differentially produced proteins include Na+/K+ ATPase, cuticle, chitinase, and proteins with unknown function. Their abundances showed correlation with copper and had high sensitivity to indicate the copper level, being here proposed as biomarker candidates for deep-sea mining activities in the future. This is a key step in the development of environmental impact assessment of deep-sea mining activities integrating ecotoxicological data.
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Affiliation(s)
- Yick Hang Kwan
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory , The Hong Kong University of Science and Technology , Hong Kong , China
| | - Dongsheng Zhang
- Second Institute of Oceanography, Ministry of Natural Resources , Hangzhou 310012 , China
- Key Laboratory of Marine Ecosystem and Biochemistry , State Oceanic Administration , Hangzhou 311000 , China
| | - Nélia C Mestre
- CIMA - Centro de Investigação Marinha e Ambiental , Universidade do Algarve , Campus de Gambelas, 8005-139 Faro , Portugal
| | - Wai Chuen Wong
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory , The Hong Kong University of Science and Technology , Hong Kong , China
| | - Xiaogu Wang
- Second Institute of Oceanography, Ministry of Natural Resources , Hangzhou 310012 , China
- Key Laboratory of Marine Ecosystem and Biochemistry , State Oceanic Administration , Hangzhou 311000 , China
| | - Bo Lu
- Second Institute of Oceanography, Ministry of Natural Resources , Hangzhou 310012 , China
- Key Laboratory of Marine Ecosystem and Biochemistry , State Oceanic Administration , Hangzhou 311000 , China
| | - Chunsheng Wang
- Second Institute of Oceanography, Ministry of Natural Resources , Hangzhou 310012 , China
- Key Laboratory of Marine Ecosystem and Biochemistry , State Oceanic Administration , Hangzhou 311000 , China
| | - Pei-Yuan Qian
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory , The Hong Kong University of Science and Technology , Hong Kong , China
| | - Jin Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory , The Hong Kong University of Science and Technology , Hong Kong , China
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19
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Cogne Y, Degli-Esposti D, Pible O, Gouveia D, François A, Bouchez O, Eché C, Ford A, Geffard O, Armengaud J, Chaumot A, Almunia C. De novo transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups. Sci Data 2019; 6:184. [PMID: 31562330 PMCID: PMC6764967 DOI: 10.1038/s41597-019-0192-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 08/13/2019] [Indexed: 11/17/2022] Open
Abstract
Gammarids are amphipods found worldwide distributed in fresh and marine waters. They play an important role in aquatic ecosystems and are well established sentinel species in ecotoxicology. In this study, we sequenced the transcriptomes of a male individual and a female individual for seven different taxonomic groups belonging to the two genera Gammarus and Echinogammarus: Gammarus fossarum A, G. fossarum B, G. fossarum C, Gammarus wautieri, Gammarus pulex, Echinogammarus berilloni, and Echinogammarus marinus. These taxa were chosen to explore the molecular diversity of transcribed genes of genotyped individuals from these groups. Transcriptomes were de novo assembled and annotated. High-quality assembly was confirmed by BUSCO comparison against the Arthropod dataset. The 14 RNA-Seq-derived protein sequence databases proposed here will be a significant resource for proteogenomics studies of these ecotoxicologically relevant non-model organisms. These transcriptomes represent reliable reference sequences for whole-transcriptome and proteome studies on other gammarids, for primer design to clone specific genes or monitor their specific expression, and for analyses of molecular differences between gammarid species. Measurement(s) | transcription profiling assay | Technology Type(s) | RNA sequencing | Factor Type(s) | sex • species | Sample Characteristic - Organism | Gammarus • Echinogammarus | Sample Characteristic - Environment | habitat |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9777905
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Affiliation(s)
- Yannick Cogne
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Davide Degli-Esposti
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Olivier Pible
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Duarte Gouveia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
| | - Adeline François
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, F-31320, Castanet-Tolosan, France
| | - Camille Eché
- GeT-PlaGe, Genotoul, INRA Auzeville, F-31320, Castanet-Tolosan, France
| | - Alex Ford
- School of Biological Sciences, Institute of Marine Sciences Laboratories, P04 9LY, Portsmouth, United Kingdom
| | - Olivier Geffard
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France.
| | - Arnaud Chaumot
- Irstea, UR MALY Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, F-69625, Villeurbanne, France
| | - Christine Almunia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols-sur-Cèze, France
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Kuplik Z, Novak L, Shenkar N. Proteomic profiling of ascidians as a tool for biomonitoring marine environments. PLoS One 2019; 14:e0215005. [PMID: 30964904 PMCID: PMC6456167 DOI: 10.1371/journal.pone.0215005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/25/2019] [Indexed: 02/04/2023] Open
Abstract
Applying a proteomic approach for biomonitoring marine environments offers a useful tool for identifying organisms’ stress responses, with benthic filter-feeders being ideal candidates for this practice. Here, we investigated the proteomic profile of two solitary ascidians (Chordata, Ascidiacea): Microcosmus exasperatus, collected from five sites along the Mediterranean coast of Israel; and Polycarpa mytiligera collected from four sites along the Red Sea coast. 193 and 13 proteins in M. exasperatus and P. mytiligera, respectively, demonstrated a significant differential expression. Significant differences were found between the proteomes from the northern and the southern sites along both the Mediterranean and the Red Sea coasts. Some of the significant proteins had previously been shown to be affected by environmental stressors, and thus have the potential to be further developed as biomarkers. Obtaining a proteomic profile of field-collected ascidians provides a useful tool for the early-detection of a stress response in ascidians worldwide.
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Affiliation(s)
- Zafrir Kuplik
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
| | - Lion Novak
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies Tel Aviv University, Tel Aviv, Israel
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21
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Gouveia D, Almunia C, Cogne Y, Pible O, Degli-Esposti D, Salvador A, Cristobal S, Sheehan D, Chaumot A, Geffard O, Armengaud J. Ecotoxicoproteomics: A decade of progress in our understanding of anthropogenic impact on the environment. J Proteomics 2019; 198:66-77. [DOI: 10.1016/j.jprot.2018.12.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/19/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022]
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22
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Abreu IO, Monteiro C, Rocha ACS, Reis-Henriques MA, Teixeira C, Basto MCP, Ferreira M, Almeida CMR, Oliva-Teles L, Guimarães L. Multibiomarker interactions to diagnose and follow-up chronic exposure of a marine crustacean to Hazardous and Noxious Substances (HNS). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:1137-1145. [PMID: 30098540 DOI: 10.1016/j.envpol.2018.07.106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 07/16/2018] [Accepted: 07/22/2018] [Indexed: 06/08/2023]
Abstract
Integrated compensatory responses of physiological systems towards homeostasis are generally overlooked when it comes to analysing alterations in biochemical parameters indicative of such processes. Here an hypothesis-driven multivariate analysis accounting for interactive multibiomarker responses was used to investigate effects of long-term exposure of Carcinus maenas to Hazardous and Noxious Substances (HNS). Adult male crabs were exposed to low and high post-spill levels of acrylonitrile (ACN) or aniline (ANL) for 21d. Bioaccumulation, feeding behaviour, and biomarkers related to mode-of-action (MoA) (detoxification, neurotransmission and energy production) were evaluated over time. Distinct temporal patterns of response to low and high exposure concentrations were depicted, with a main set of interactive multibiomarker predictors identified for each HNS (five for ACN and three for ANL), useful to follow coupled evolvement of biomarker responses. ACN caused peripheral neurotoxic effects coupled with enhanced biotransformation and significant oxidative damage particularly relevant in gills. ANL elicited alterations in central neurotransmission affecting ventilation coupled with very low levels of oxidative damage in gills. Results indicate chronic toxicity data are determinant to improve HNS hazard assessment if the aim is to obtain reliable risk calculations, and develop effective predictive models avoiding overestimation but sufficiently protective. Accounting for multibiomarker interactions brought otherwise overlooked information about C. maenas responses and MoA of ACN and ANL.
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Affiliation(s)
- Isabel Oliveira Abreu
- CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar, Rua de Jorge Viterbo Ferreira no 228, 4050-313, Porto, Portugal
| | - Catarina Monteiro
- CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar, Rua de Jorge Viterbo Ferreira no 228, 4050-313, Porto, Portugal
| | - A Cristina S Rocha
- CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; MARE-UC, Incubadora de Empresas da Figueira da Foz, Parque Industrial e Empresarial da Figueira da Foz (Laboratório MAREFOZ), Rua das Acácias Lote 40A, 3090-380, Figueira da Foz, Portugal
| | - Maria Armanda Reis-Henriques
- CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Catarina Teixeira
- CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; Instituto de Ciências Biomédicas Abel Salazar, Rua de Jorge Viterbo Ferreira no 228, 4050-313, Porto, Portugal
| | - Maria Clara Pires Basto
- CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Marta Ferreira
- CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; School of Marine Studies, Faculty of Science, Technology and Environment, The University of The South Pacific, Laucala Bay Road, Suva, Fiji
| | - C Marisa R Almeida
- CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Luís Oliva-Teles
- CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal; Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
| | - Laura Guimarães
- CIIMAR-Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
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Vogt ÉL, Model JFA, Vinagre AS. Effects of Organotins on Crustaceans: Update and Perspectives. Front Endocrinol (Lausanne) 2018; 9:65. [PMID: 29535684 PMCID: PMC5835110 DOI: 10.3389/fendo.2018.00065] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/13/2018] [Indexed: 12/17/2022] Open
Abstract
Organotins (OTs) are considered some of the most toxic chemicals introduced into aquatic environments by anthropogenic activities. They are widely used for agricultural and industrial purposes and as antifouling additives on boat hull's paints. Even though the use of OTs was banned in 2008, elevated levels of OTs can still be detected in aquatic environments. OTs' deleterious effects upon wildlife and experimental animals are well documented and include endocrine disruption, immunotoxicity, neurotoxicity, genotoxicity, and metabolic dysfunction. Crustaceans are key members of zooplankton and benthic communities and have vital roles in food chains, so the endocrine-disrupting effects of tributyltin (TBT) on crustaceans can affect other organisms. TBT can disrupt carbohydrate and lipid homeostasis of crustaceans by interacting with retinoid X receptor (RXR) and crustacean hyperglycemic hormone (CHH) signaling. Moreover, it can also interact with other nuclear receptors, disrupting methyl farnesoate and ecdysteroid signaling, thereby altering growth and sexual maturity, respectively. This compound also interferes in cytochrome P450 system disrupting steroid synthesis and reproduction. Crustaceans are also important fisheries worldwide, and its consumption can pose risks to human health. However, some questions remain unanswered. This mini review aims to update information about the effects of OTs on the metabolism, growth, and reproduction of crustaceans; to compare with known effects in mammals; and to point aspects that still needs to be addressed in future studies. Since both macrocrustaceans and microcrustaceans are good models to study the effects of sublethal TBT contamination, novel studies should be developed using multibiomarkers and omics technology.
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Affiliation(s)
- Éverton L. Vogt
- Laboratório de Metabolismo e Endocrinologia Comparada (LAMEC), Departamento de Fisiologia, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Jorge F. A. Model
- Laboratório de Metabolismo e Endocrinologia Comparada (LAMEC), Departamento de Fisiologia, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Anapaula S. Vinagre
- Laboratório de Metabolismo e Endocrinologia Comparada (LAMEC), Departamento de Fisiologia, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Krosch MN, Bryant LM, Vink S. Differential gene expression of Australian Cricotopus draysoni (Diptera: Chironomidae) populations reveals seasonal association in detoxification gene regulation. Sci Rep 2017; 7:14263. [PMID: 29079848 PMCID: PMC5660232 DOI: 10.1038/s41598-017-14736-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/16/2017] [Indexed: 12/03/2022] Open
Abstract
Understanding the molecular mechanisms of organismal response to human-derived ecosystem change is recognised as a critical tool in monitoring and managing impacts, especially in freshwater systems. Fundamental to this approach is to determine the genes involved in responding to ecosystem change and detect modifications to their expression and activity in natural populations. Potential targets for this approach include well-known detoxification genes that are upregulated in response to stress. Here, we tested whether expression of such genes varied in association with differences in ecosystem health and could be detected in the field. We sampled populations of the freshwater midge, Cricotopus draysoni, from two geographically proximate sites in southeast Queensland, Australia, which differed in their ecosystem health, at multiple time points. We assessed transcriptome-level differential gene expression and predicted greatest differential expression between sites, associated with organismal responses to local physico-chemical factors. In contrast, we observed a clear and dramatic difference in gene expression – including of known detoxification genes – between time points, specifically between periods at the start and end of the austral summer rainfall when in-stream water levels are most different. These data suggest that these waterways experience greatest pollution load when water levels are high following rainfall events.
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Affiliation(s)
- Matt N Krosch
- Queensland University of Technology, Brisbane, QLD, 4001, Australia. .,University of Queensland, St Lucia, QLD, 4072, Australia.
| | | | - Sue Vink
- University of Queensland, St Lucia, QLD, 4072, Australia
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Gouveia D, Chaumot A, Charnot A, Queau H, Armengaud J, Almunia C, Salvador A, Geffard O. Assessing the relevance of a multiplexed methodology for proteomic biomarker measurement in the invertebrate species Gammarus fossarum: A physiological and ecotoxicological study. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 190:199-209. [PMID: 28750222 DOI: 10.1016/j.aquatox.2017.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/07/2017] [Accepted: 07/14/2017] [Indexed: 06/07/2023]
Abstract
Recently, a protein sequence database was built specifically for the sentinel non-model species Gammarus fossarum using a proteogenomics approach. A quantitative multiplexed targeted proteomics assay (using Selected Reaction Monitoring mass spectrometry) was then developed for a fast and simultaneous quantification of dozens of biomarker peptides specific of this freshwater sentinel crustacean species. In order to assess the relevance of this breakthrough methodology in ecotoxicology, the response patterns of a panel of 26 peptides reporting for 20 proteins from the Gammarus fossarum proteome with putative key functional roles (homeostasis, osmoregulation, nutrition, reproduction, molting,…) were recorded through male and female reproductive cycles and after exposure to environmental concentrations of cadmium and lead in laboratory-controlled conditions. Based on these results, we validated the implication of annotated vtg-like peptides in the oogenesis process, and the implication of Na+/K+ ATPase proteins in the molt cycle of organisms. Upon metal (cadmium and lead) contamination, peptides belonging to proteins annotated as involved in antioxidant and detoxification functions, immunity and molting were significantly down-regulated. Overall, this multiplex assay allowed gaining relevant insights upon disruption of different main functions in the sentinel species Gammarus fossarum. This breakthrough methodology in ecotoxicology offers a valid and high throughput alternative to currently used protocols, paving the way for future practical applications of proteogenomics-derived protein biomarkers in chemical risk assessment and environmental monitoring.
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Affiliation(s)
- D Gouveia
- IRSTEA, UR MALY, Laboratoire d'ecotoxicologie, centre de Lyon-Villeurbanne, F-69616 Villeurbanne, France; CEA-Marcoule, DRF/Joliot/DMTS/SPI/Li2D, Laboratory-Innovative Technologies for Detection and Diagnostics, Bagnols-sur-Ceze, F-30207, France
| | - A Chaumot
- IRSTEA, UR MALY, Laboratoire d'ecotoxicologie, centre de Lyon-Villeurbanne, F-69616 Villeurbanne, France
| | - A Charnot
- UMR 5180, Institut des Sciences Analytiques, Université de Lyon 1, F-69100 Villeurbanne, France
| | - H Queau
- IRSTEA, UR MALY, Laboratoire d'ecotoxicologie, centre de Lyon-Villeurbanne, F-69616 Villeurbanne, France
| | - J Armengaud
- CEA-Marcoule, DRF/Joliot/DMTS/SPI/Li2D, Laboratory-Innovative Technologies for Detection and Diagnostics, Bagnols-sur-Ceze, F-30207, France
| | - C Almunia
- CEA-Marcoule, DRF/Joliot/DMTS/SPI/Li2D, Laboratory-Innovative Technologies for Detection and Diagnostics, Bagnols-sur-Ceze, F-30207, France
| | - A Salvador
- UMR 5180, Institut des Sciences Analytiques, Université de Lyon 1, F-69100 Villeurbanne, France
| | - O Geffard
- IRSTEA, UR MALY, Laboratoire d'ecotoxicologie, centre de Lyon-Villeurbanne, F-69616 Villeurbanne, France.
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26
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Ciliberti A, Chaumot A, Recoura-Massaquant R, Chandesris A, François A, Coquery M, Ferréol M, Geffard O. Caged Gammarus as biomonitors identifying thresholds of toxic metal bioavailability that affect gammarid densities at the French national scale. WATER RESEARCH 2017; 118:131-140. [PMID: 28431346 DOI: 10.1016/j.watres.2017.04.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 03/28/2017] [Accepted: 04/09/2017] [Indexed: 06/07/2023]
Abstract
Bioaccumulated concentrations of toxic elements in biomonitor invertebrate species have already been used to successfully link metal bioavailability and impairments of stream macroinvertebrate communities at the scale of the watershed. However, implementing this empirical comparative approach at a greater spatial scale remains a challenge due to the diversity of biogeographical contexts encompassed by regional and national scales. We showed in previous studies that the use of standard organisms caged permits the use of a common biomonitor over a far greater geographical range, while limiting the influence of confounding factors on levels of bioavailable contamination. In this study, levels of Cd, Hg, Ni and Pb contamination assessed by active biomonitoring with caged Gammarus fossarum were compared to abundances of on-site gammarids on 94 sites in France. Based on this national dataset of in situ bioassays, we first re-determined bioavailable background assessment concentrations (BBACs), i.e. concentrations measured in caged G. fossarum indicating a significant bioavailable contamination, which we had previously defined at a regional scale for these four metallic elements. On-site gammarid abundances were retrieved from monitoring programs implemented by French water agencies for the evaluation of ecological status for the European Water Framework Directive. These abundances were corrected for the influence of stream physico-chemical typology in order to permit a reliable comparison of gammarid densities between sites at the national scale. Clear trends of degradation of gammarid densities with increasing levels of bioaccumulated concentrations were identified for three of the four elements (Cd, Ni and Pb). Threshold concentrations in caged organisms above which the numbers of free-ranging gammarids were abnormally low - namely bioavailable ecological assessment concentrations (BEACs) - were determined. The reliability and validity of the BEACs, their comparison with BBACs and their usefulness in terms of prioritisation of contaminants, sites in freshwater management, are discussed.
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Affiliation(s)
- Alexandre Ciliberti
- Irstea, UR MALY, 5 rue de la Doua, BP 32108, F-69616, Villeurbanne Cedex, France
| | - Arnaud Chaumot
- Irstea, UR MALY, 5 rue de la Doua, BP 32108, F-69616, Villeurbanne Cedex, France
| | | | - André Chandesris
- Irstea, UR MALY, 5 rue de la Doua, BP 32108, F-69616, Villeurbanne Cedex, France
| | - Adeline François
- Irstea, UR MALY, 5 rue de la Doua, BP 32108, F-69616, Villeurbanne Cedex, France
| | - Marina Coquery
- Irstea, UR MALY, 5 rue de la Doua, BP 32108, F-69616, Villeurbanne Cedex, France
| | - Martial Ferréol
- Irstea, UR MALY, 5 rue de la Doua, BP 32108, F-69616, Villeurbanne Cedex, France
| | - Olivier Geffard
- Irstea, UR MALY, 5 rue de la Doua, BP 32108, F-69616, Villeurbanne Cedex, France.
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Multiplexed assay for protein quantitation in the invertebrate Gammarus fossarum by liquid chromatography coupled to tandem mass spectrometry. Anal Bioanal Chem 2017; 409:3969-3991. [DOI: 10.1007/s00216-017-0348-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 03/20/2017] [Accepted: 03/28/2017] [Indexed: 11/26/2022]
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Bedulina D, Meyer MF, Gurkov A, Kondratjeva E, Baduev B, Gusdorf R, Timofeyev MA. Intersexual differences of heat shock response between two amphipods ( Eulimnogammarus verrucosus and Eulimnogammarus cyaneus) in Lake Baikal. PeerJ 2017; 5:e2864. [PMID: 28243524 PMCID: PMC5322754 DOI: 10.7717/peerj.2864] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/05/2016] [Indexed: 12/14/2022] Open
Abstract
Acute temperature fluctuations are common in surface waters, and aquatic organisms may manifest physiological responses to punctuated temperature spikes long before behavioral responses. Ectotherms, especially cryophilic stenotherms such as those endemic to Lake Baikal (Siberia), may demonstrate specialized physiological responses to acute temperature increases because their proteomes have evolved to function most efficiently at lower temperatures (e.g., <10 °C). Therefore, our study questioned the nature and degree of variation in physiological response to acute thermal stress in two congenerous, endemic Baikal amphipod species, Eulimnogammarus verrucosus and Eulimnogammarus cyaneus. We hypothesized that because interspecific and intersexual thermosensitivity varies significantly among ectotherms, there would be divergent intersexual and interspecific strategies to withstand acute thermal stress, manifested in different protein compositions and concentrations. We exposed individuals to the species’ respective LT50 for one hour followed by a three-hour recovery period. We then performed 1D-PAGE, Western blotting, 2D-PAGE, and Mass Spectrometry techniques and assessed relative intersexual and interspecific changes in proteomic composition and heat shock protein 70 level. Our results demonstrate that females tend to be more sensitive to an acute thermal stimulus than males, most likely because females allocate significant energy to reproduction and less to heat shock response, evidenced by females’ significantly lower LT50time. Lower level of Hsp70 was found in females of the thermosensitive E. verrucosus compared to males of this species. No intersexual differences were found in Hsp70 level in thermotolerant E. cyaneus. Higher levels of hemocyanin subunits and arginine kinase were found in E. cyaneus females after heat shock and recovery compared to males, which was not found for E. verrucosus, suggesting interspecific mechanisms for E. cyaneus’s higher thermotolerance. These differing responses between species and sexes of Baikal amphipods may reflect more general strategies for maintaining homeostatic conditions during acute thermal stress. As mean surface water temperatures increase worldwide, the net efficiency and efficacy of these strategies could give rise to long term changes in physiology, behavior, and interactions with other species, potentially precipitating population and community level alterations.
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Affiliation(s)
- Daria Bedulina
- Institute of Biology, Irkutsk State University , Irkutsk , Russia
| | - Michael F Meyer
- School of the Environment, Washington State University , Pullman , WA , USA
| | - Anton Gurkov
- Institute of Biology, Irkutsk State University, Irkutsk, Russia; Baikal Research Centre, Irkutsk, Russia
| | | | - Boris Baduev
- Institute of Biology, Irkutsk State University, Irkutsk, Russia; Baikal Research Centre, Irkutsk, Russia
| | - Roman Gusdorf
- University of Notre Dame , Notre Dame , United States
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Trapp J, McAfee A, Foster LJ. Genomics, transcriptomics and proteomics: enabling insights into social evolution and disease challenges for managed and wild bees. Mol Ecol 2017; 26:718-739. [DOI: 10.1111/mec.13986] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Judith Trapp
- Department of Biochemistry & Molecular Biology; Michael Smith Laboratories; University of British Columbia; 2125 East Mall Vancouver BC V6T 1Z4 Canada
| | - Alison McAfee
- Department of Biochemistry & Molecular Biology; Michael Smith Laboratories; University of British Columbia; 2125 East Mall Vancouver BC V6T 1Z4 Canada
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology; Michael Smith Laboratories; University of British Columbia; 2125 East Mall Vancouver BC V6T 1Z4 Canada
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30
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Trapp J, Gaillard JC, Chaumot A, Geffard O, Pible O, Armengaud J. Ovary and embryo proteogenomic dataset revealing diversity of vitellogenins in the crustacean Gammarus fossarum. Data Brief 2016; 8:1259-62. [PMID: 27547807 PMCID: PMC4983104 DOI: 10.1016/j.dib.2016.07.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 07/18/2016] [Accepted: 07/21/2016] [Indexed: 11/16/2022] Open
Abstract
Ovaries and embryos from sexually mature Gammarus fossarum were sampled at different stages of the reproductive cycle. The soluble proteome was extracted for five biological replicates and samples were subjected to trypsin digestion. The resulting peptides were analyzed by high resolution tandem mass spectrometry with a LTQ-Orbitrap XL instrument. The MS/MS spectra were assigned with a previously described RNAseq-derived G. fossarum database. The proteins highlighted by proteogenomics were monitored and their abundance kinetics over the different stages revealed a large panel of vitellogenins. Criteria were i) accumulation during oogenesis, ii) decrease during embryogenesis, iii) classified as female-specific, and iv) sequence similarity and phylogenetic analysis. The data accompanying the manuscript describing the database searches and comparative analysis (“High-throughput proteome dynamics for discovery of key proteins in sentinel species: unsuspected vitellogenins diversity in the crustacean Gammarus fossarum” by Trapp et al. [1]) have been deposited to the ProteomeXchange via the PRIDE repository with identifiers PRIDE: PXD001002.
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Affiliation(s)
- Judith Trapp
- Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France; CEA-Marcoule, DSV/IBITEC-S/SPI/Li2D, Laboratory "Innovative technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France
| | - Jean-Charles Gaillard
- CEA-Marcoule, DSV/IBITEC-S/SPI/Li2D, Laboratory "Innovative technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France
| | - Arnaud Chaumot
- Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France
| | - Olivier Geffard
- Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France
| | - Olivier Pible
- CEA-Marcoule, DSV/IBITEC-S/SPI/Li2D, Laboratory "Innovative technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- CEA-Marcoule, DSV/IBITEC-S/SPI/Li2D, Laboratory "Innovative technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France
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31
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Sajjad W, Rafiq M, Ali B, Hayat M, Zada S, Sajjad W, Kumar T. Proteogenomics: New Emerging Technology. HAYATI JOURNAL OF BIOSCIENCES 2016. [DOI: 10.1016/j.hjb.2016.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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32
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Kalantari R, Hicks JA, Li L, Gagnon KT, Sridhara V, Lemoff A, Mirzaei H, Corey DR. Stable association of RNAi machinery is conserved between the cytoplasm and nucleus of human cells. RNA (NEW YORK, N.Y.) 2016; 22:1085-98. [PMID: 27198507 PMCID: PMC4911916 DOI: 10.1261/rna.056499.116] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/25/2016] [Indexed: 05/25/2023]
Abstract
Argonaute 2 (AGO2), the catalytic engine of RNAi, is typically associated with inhibition of translation in the cytoplasm. AGO2 has also been implicated in nuclear processes including transcription and splicing. There has been little insight into AGO2's nuclear interactions or how they might differ relative to cytoplasm. Here we investigate the interactions of cytoplasmic and nuclear AGO2 using semi-quantitative mass spectrometry. Mass spectrometry often reveals long lists of candidate proteins, complicating efforts to rigorously discriminate true interacting partners from artifacts. We prioritized candidates using orthogonal analytical strategies that compare replicate mass spectra of proteins associated with Flag-tagged and endogenous AGO2. Interactions with TRNC6A, TRNC6B, TNRC6C, and AGO3 are conserved between nuclei and cytoplasm. TAR binding protein interacted stably with cytoplasmic AGO2 but not nuclear AGO2, consistent with strand loading in the cytoplasm. Our data suggest that interactions between functionally important components of RNAi machinery are conserved between the nucleus and cytoplasm but that accessory proteins differ. Orthogonal analysis of mass spectra is a powerful approach to streamlining identification of protein partners.
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Affiliation(s)
- Roya Kalantari
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jessica A Hicks
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Liande Li
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Viswanadham Sridhara
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hamid Mirzaei
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - David R Corey
- Department of Pharmacology, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Roland K, Kestemont P, Dieu M, Raes M, Silvestre F. Using a novel “Integrated Biomarker Proteomic” index to assess the effects of freshwater pollutants in European eel peripheral blood mononuclear cells. J Proteomics 2016; 137:83-96. [DOI: 10.1016/j.jprot.2016.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 12/30/2015] [Accepted: 01/05/2016] [Indexed: 01/04/2023]
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Bahamonde PA, Feswick A, Isaacs MA, Munkittrick KR, Martyniuk CJ. Defining the role of omics in assessing ecosystem health: Perspectives from the Canadian environmental monitoring program. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2016; 35:20-35. [PMID: 26771350 DOI: 10.1002/etc.3218] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 05/16/2015] [Accepted: 08/20/2015] [Indexed: 05/22/2023]
Abstract
Scientific reviews and studies continue to describe omics technologies as the next generation of tools for environmental monitoring, while cautioning that there are limitations and obstacles to overcome. However, omics has not yet transitioned into national environmental monitoring programs designed to assess ecosystem health. Using the example of the Canadian Environmental Effects Monitoring (EEM) program, the authors describe the steps that would be required for omics technologies to be included in such an established program. These steps include baseline collection of omics endpoints across different species and sites to generate a range of what is biologically normal within a particular ecosystem. Natural individual variability in the omes is not adequately characterized and is often not measured in the field, but is a key component to an environmental monitoring program, to determine the critical effect size or action threshold for management. Omics endpoints must develop a level of standardization, consistency, and rigor that will allow interpretation of the relevance of changes across broader scales. To date, population-level consequences of routinely measured endpoints such as reduced gonad size or intersex in fish is not entirely clear, and the significance of genome-wide molecular, proteome, or metabolic changes on organism or population health is further removed from the levels of ecological change traditionally managed. The present review is not intended to dismiss the idea that omics will play a future role in large-scale environmental monitoring studies, but rather outlines the necessary actions for its inclusion in regulatory monitoring programs focused on assessing ecosystem health.
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Affiliation(s)
- Paulina A Bahamonde
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - April Feswick
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - Meghan A Isaacs
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - Kelly R Munkittrick
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
| | - Christopher J Martyniuk
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada
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35
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Braconi D, Bernardini G, Santucci A. Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. J Proteomics 2015; 137:19-34. [PMID: 26365628 DOI: 10.1016/j.jprot.2015.09.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/29/2015] [Accepted: 09/02/2015] [Indexed: 12/13/2022]
Abstract
The budding yeast Saccharomyces cerevisiae represents a well-consolidated and widely used eukaryotic model, with a number of features that make it an ideal organism to carry out functional toxicological studies. Several advantages are permitted by the use of yeast cells, as the possibility to identify molecular biomarkers, unknown mechanisms of action and novel potential targets. Thanks to the evolutionary conservation, yeast can provide also useful clues allowing the prioritization of more complex analyses and toxicity predictions in higher eukaryotes. The last two decades were incredibly fruitful for yeast "omics", but referring to the analysis of the effects of pesticides on yeast much still remains to be done. Furthermore, a deeper knowledge of the effects of environmental pollutants on biotechnological processes associated with the use of yeasts is to be hoped.
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Affiliation(s)
- Daniela Braconi
- Dipartimento di Biotecnologie, Chimica e Farmacia, via A. Moro 2, Università degli Studi di Siena, 53100 Siena, Italy
| | - Giulia Bernardini
- Dipartimento di Biotecnologie, Chimica e Farmacia, via A. Moro 2, Università degli Studi di Siena, 53100 Siena, Italy
| | - Annalisa Santucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, via A. Moro 2, Università degli Studi di Siena, 53100 Siena, Italy.
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Trapp J, Almunia C, Gaillard JC, Pible O, Chaumot A, Geffard O, Armengaud J. Proteogenomic insights into the core-proteome of female reproductive tissues from crustacean amphipods. J Proteomics 2015; 135:51-61. [PMID: 26170043 DOI: 10.1016/j.jprot.2015.06.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/11/2015] [Accepted: 06/29/2015] [Indexed: 11/27/2022]
Abstract
As a result of the poor genome sequence coverage of crustacean amphipods, characterization of their evolutionary biology relies mostly on phenotypic traits. Here, we analyzed the proteome of ovaries from five amphipods, all from the Senticaudata suborder, with the objective to obtain insights into the core-proteome of female reproductive systems. These amphipods were from either the Gammarida infraorder: Gammarus fossarum, Gammarus pulex, Gammarus roeseli, or the Talitrida infraorder: Parhyale hawaiensis and Hyalella azteca. Ovaries from animals sampled at the end of their reproductive cycle were dissected. Their whole protein contents were extracted and their proteomes were recorded by high-throughput nanoLC-MS/MS with a high-resolution mass spectrometer. We interpreted tandem mass spectrometry data with the protein sequence resource from G. fossarum and P. hawaiensis, both recently established by RNA sequencing. The large molecular biodiversity within amphipods was assessed by the ratio of MS/MS spectra assigned for each sample, which tends to diverge rapidly along the taxonomic level considered. The core-proteome was defined as the proteins conserved along all samples, thus detectable by the homology-based proteomic assignment procedure. This specific subproteome may be further enriched in the future with the analysis of new species and update of the protein sequence resource.
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Affiliation(s)
- Judith Trapp
- Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France; CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France
| | - Christine Almunia
- CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France
| | - Jean-Charles Gaillard
- CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France
| | - Olivier Pible
- CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France
| | - Arnaud Chaumot
- Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France
| | - Olivier Geffard
- Irstea, Unité de Recherche MALY, Laboratoire d'écotoxicologie, CS70077, F-69626 Villeurbanne, France.
| | - Jean Armengaud
- CEA-Marcoule, DSV/IBICTEC-S/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostic", BP 17171, F-30200 Bagnols-sur-Cèze, France.
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37
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Faulkner S, Dun MD, Hondermarck H. Proteogenomics: emergence and promise. Cell Mol Life Sci 2015; 72:953-7. [PMID: 25609363 PMCID: PMC11113406 DOI: 10.1007/s00018-015-1837-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/08/2015] [Accepted: 01/12/2015] [Indexed: 12/14/2022]
Abstract
Proteogenomics, or the integration of proteomics with genomics and transcriptomics, is emerging as the next step towards a unified understanding of cellular functions. Looking globally and simultaneously at gene structure, RNA expression, protein synthesis and post-translational modifications have become technically feasible and offer a new perspective to molecular processes. Recent publications have highlighted the value of proteogenomics in oncology for defining the molecular signature of human tumors, and translation to other areas of biomedicine and life sciences is anticipated. This mini-review will discuss recent developments, challenges and perspectives in proteogenomics.
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Affiliation(s)
- Sam Faulkner
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy and Hunter Medical Research Institute, Life Science Building, University of Newcastle, Callaghan, NSW 2308 Australia
| | - Matthew D. Dun
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy and Hunter Medical Research Institute, Life Science Building, University of Newcastle, Callaghan, NSW 2308 Australia
| | - Hubert Hondermarck
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy and Hunter Medical Research Institute, Life Science Building, University of Newcastle, Callaghan, NSW 2308 Australia
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38
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Trapp J, Armengaud J, Pible O, Gaillard JC, Abbaci K, Habtoul Y, Chaumot A, Geffard O. Proteomic Investigation of Male Gammarus fossarum, a Freshwater Crustacean, in Response to Endocrine Disruptors. J Proteome Res 2014; 14:292-303. [DOI: 10.1021/pr500984z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Judith Trapp
- Irstea, Unité
de Recherche MALY, Laboratoire d’écotoxicologie, CS70077, F-69626 Villeurbanne, France
- CEA, DSV, IBEB,
Lab Biochim System Perturb, F-30207 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- CEA, DSV, IBEB,
Lab Biochim System Perturb, F-30207 Bagnols-sur-Cèze, France
| | - Olivier Pible
- CEA, DSV, IBEB,
Lab Biochim System Perturb, F-30207 Bagnols-sur-Cèze, France
| | | | - Khedidja Abbaci
- Irstea, Unité
de Recherche MALY, Laboratoire d’écotoxicologie, CS70077, F-69626 Villeurbanne, France
| | - Yassine Habtoul
- Irstea, Unité
de Recherche MALY, Laboratoire d’écotoxicologie, CS70077, F-69626 Villeurbanne, France
| | - Arnaud Chaumot
- Irstea, Unité
de Recherche MALY, Laboratoire d’écotoxicologie, CS70077, F-69626 Villeurbanne, France
| | - Olivier Geffard
- Irstea, Unité
de Recherche MALY, Laboratoire d’écotoxicologie, CS70077, F-69626 Villeurbanne, France
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