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Olsvik PA, Meier S, Zhang X, Goksøyr A, Karlsen OA, Yadetie F. Environmentally realistic concentrations of chlorinated, brominated, and fluorinated persistent organic pollutants induce the unfolded protein response as a shared stress pathway in the liver of Atlantic cod (Gadus morhua). J Appl Toxicol 2023; 43:1859-1871. [PMID: 37528559 DOI: 10.1002/jat.4519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 08/03/2023]
Abstract
In the North Sea and North Atlantic coastal areas, fish experience relatively high background levels of persistent organic pollutants. This study aimed to compare the mode of action of environmentally relevant concentrations of mixtures of halogenated compounds in Atlantic cod. Juvenile male cod with mean weight of 840 g were exposed by gavage to dietary mixtures of chlorinated (PCBs, DDT analogs, chlordane, lindane, and toxaphene), brominated (PBDEs), and fluorinated (PFOS) compounds for 4 weeks. One group received a combined mixture of all three compound groups. The results showed that the accumulated levels of chemicals in cod liver after 4 weeks of exposure reflected concentrations found in wild fish in this region. Pathway analysis revealed that the treatment effects by each of the three groups of chemicals (chlorinated, brominated, and fluorinated) converged on activation of the unfolded protein response (UPR). Upstream regulator analysis predicted that almost all the key transcription factors (XBP1, ERN1, ATF4, EIF2AK3, and NFE2L2) regulating the UPR were significantly activated. No additive effect was observed in cod co-treated with all three compound groups. In conclusion, the genome-wide transcriptomic study suggests that the UPR pathway is a sensitive common target of halogenated organic environmental pollutants in fish.
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Affiliation(s)
- Pål A Olsvik
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Institute of Marine Research, Bergen, Norway
| | | | - Xiaokang Zhang
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Anders Goksøyr
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Odd Andre Karlsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Fekadu Yadetie
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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2
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Baines C, Meitern R, Kreitsberg R, Fort J, Scharsack JP, Nogueira P, Giraudeau M, Sepp T. Correlations between oxidative DNA damage and formation of hepatic tumours in two flatfish species from contaminated environments. Biol Lett 2023; 19:20220583. [PMID: 37254521 PMCID: PMC10230182 DOI: 10.1098/rsbl.2022.0583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/09/2023] [Indexed: 06/01/2023] Open
Abstract
Many species in aquatic environments face increased exposure to oncogenic pollution due to anthropogenic environmental change which can lead to higher cancer prevalence. The mechanistic relationship connecting environmental pollution and cancer is multi-factorial and poorly understood, and the specific mechanisms are so far still uncharacterized. One potential mediator between pollutant exposure and cancer is oxidative damage to DNA. We conducted a study in the field with two flatfish species, European flounder (Platichthys flesus L.) and common dab (Limanda limanda L.) with overlapping distribution and similar ecological niche, to investigate if the link between oncogenic pollutants and cancer described in ecotoxicological literature could be mediated by oxidative DNA damage. This was not the case for flounders as neither polycyclic aromatic hydrocarbon (PAH) bile metabolites nor metallic trace element concentrations were related to oxidative DNA damage measurements. However, dabs with higher PAH concentrations did exhibit increased oxidative damage. High oxidative DNA damage also did not predict neoplasm occurrence, rather, healthy individuals tended to have higher oxidative damage measurements compared to fishes with pre-neoplastic tumours. Our analyses showed that flounders had lower concentrations of PAH bile metabolites, suggesting that compared to dab this species is less exposed or better at eliminating these contaminants.
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Affiliation(s)
- Ciara Baines
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia
- Estonian Marine Institute, University of Tartu, Mäealuse 14, 12618 Tallinn, Harju County, Estonia
| | - Richard Meitern
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Randel Kreitsberg
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Jérôme Fort
- Littoral, Environnement et Sociétés (LIENSs), UMR7266 CNRS - La Rochelle Université, 2 rue Olympe de Gouges, 17000 La Rochelle, France
| | - Jörn Peter Scharsack
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572 Bremerhaven, Germany
| | - Pedro Nogueira
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572 Bremerhaven, Germany
| | - Mathieu Giraudeau
- Littoral, Environnement et Sociétés (LIENSs), UMR7266 CNRS - La Rochelle Université, 2 rue Olympe de Gouges, 17000 La Rochelle, France
| | - Tuul Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia
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3
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Schneeweiss A, Juvigny-Khenafou NPD, Osakpolor S, Scharmüller A, Scheu S, Schreiner VC, Ashauer R, Escher BI, Leese F, Schäfer RB. Three perspectives on the prediction of chemical effects in ecosystems. GLOBAL CHANGE BIOLOGY 2023; 29:21-40. [PMID: 36131639 DOI: 10.1111/gcb.16438] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
The increasing production, use and emission of synthetic chemicals into the environment represents a major driver of global change. The large number of synthetic chemicals, limited knowledge on exposure patterns and effects in organisms and their interaction with other global change drivers hamper the prediction of effects in ecosystems. However, recent advances in biomolecular and computational methods are promising to improve our capacity for prediction. We delineate three idealised perspectives for the prediction of chemical effects: the suborganismal, organismal and ecological perspective, which are currently largely separated. Each of the outlined perspectives includes essential and complementary theories and tools for prediction but captures only part of the phenomenon of chemical effects. Links between the perspectives may foster predictive modelling of chemical effects in ecosystems and extrapolation between species. A major challenge for the linkage is the lack of data sets simultaneously covering different levels of biological organisation (here referred to as biological levels) as well as varying temporal and spatial scales. Synthesising the three perspectives, some central aspects and associated types of data seem particularly necessary to improve prediction. First, suborganism- and organism-level responses to chemicals need to be recorded and tested for relationships with chemical groups and organism traits. Second, metrics that are measurable at many biological levels, such as energy, need to be scrutinised for their potential to integrate across levels. Third, experimental data on the simultaneous response over multiple biological levels and spatiotemporal scales are required. These could be collected in nested and interconnected micro- and mesocosm experiments. Lastly, prioritisation of processes involved in the prediction framework needs to find a balance between simplification and capturing the essential complexity of a system. For example, in some cases, eco-evolutionary dynamics and interactions may need stronger consideration. Prediction needs to move from a static to a real-world eco-evolutionary view.
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Affiliation(s)
- Anke Schneeweiss
- Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | | | - Stephen Osakpolor
- Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Andreas Scharmüller
- Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
- Institut Terre et Environnement de Strasbourg (ITES), UMR 7063, CNRS-Université de Strasbourg-ENGEES, Strasbourg, France
| | - Sebastian Scheu
- Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Verena C Schreiner
- Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Roman Ashauer
- Syngenta Crop Protection AG, Basel, Switzerland
- Department of Environment and Geography, University of York, York, UK
| | - Beate I Escher
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Environmental Toxicology, Center for Applied Geoscience, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Ralf B Schäfer
- Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
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4
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Laurent J, Lavergne E, Couteau J, Le Floch S, Ouddane B, Cachot J, Davail B, Clérandeau C, Devin S, Fisson C, Devaux A, Amara R, Diop M, Pichereau V, Laroche J. Impacts of chemical stress, season, and climate change on the flounder population of the highly anthropised Seine estuary (France). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:59751-59769. [PMID: 35391645 DOI: 10.1007/s11356-022-20000-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
The main objective of this study was to improve our knowledge on the responses of fish populations to multistress (diffuse pollution and warming waters) in estuaries. Adult flounders were caught in two estuaries in the Eastern English Channel: the heavily polluted Seine estuary vs the moderately contaminated Canche estuary. Fish samplings were conducted in January just before the reproduction period, and in July when gonads were at rest. The overall rise in coastal winter water temperatures detected over the Channel impairs the flounder's phenology of reproduction in the two estuaries, inducing a delay of maturation process and probably also spawning. The higher liver histopathology index in Seine vs Canche could be the consequence of the fish exposition to a complex cocktail of contaminants in a strongly industrialized estuary. Higher levels of neurotoxicity, gill lipid peroxidation, and liver EROD activity were observed in Seine vs Canche. Furthermore, a possible impairment in mitochondrial metabolism was suggested in the Seine flounder population. We confirmed in this study the potential role of two membrane lipids (sphingomyelin and phosphatidylserine) in the resistance towards oxidative stress in Seine and Canche. Finally, we suggest that the Seine flounder population (and possibly the connected Eastern English Channel flounder populations over the French Coast) could be seriously impacted in the future by multistress: higher winter temperatures and chemical contamination.
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Affiliation(s)
- Jennifer Laurent
- LEMAR UMR 6539, CNRS/UBO/IRD/Ifremer, Institut Universitaire Européen de La Mer, Université de Bretagne Occidentale, rue Dumont d'Urville, 29280, Plouzané, France
| | - Edouard Lavergne
- LEMAR UMR 6539, CNRS/UBO/IRD/Ifremer, Institut Universitaire Européen de La Mer, Université de Bretagne Occidentale, rue Dumont d'Urville, 29280, Plouzané, France
| | - Jérôme Couteau
- TOXEM, 12 rue des 4 saisons, 76290, Montivilliers, France
| | | | - Baghdad Ouddane
- LASIRE UMR 8516 CNRS, Equipe Physico-Chimie de L'Environnement, Université de Lille, Bâtiment C8, Bureau 105, 59655, Villeneuve d'Ascq Cedex, France
| | - Jérôme Cachot
- Université de Bordeaux, EPOC UMR 5805 CNRS, Bâtiment B2, Allée Geoffroy Saint-Hilaire, CS 50023, 33615, Pessac Cedex, France
| | - Blandine Davail
- Université de Bordeaux, EPOC UMR 5805 CNRS, Bâtiment B2, Allée Geoffroy Saint-Hilaire, CS 50023, 33615, Pessac Cedex, France
| | - Christelle Clérandeau
- Université de Bordeaux, EPOC UMR 5805 CNRS, Bâtiment B2, Allée Geoffroy Saint-Hilaire, CS 50023, 33615, Pessac Cedex, France
| | - Simon Devin
- Université de Lorraine, LIEC UMR 7360 CNRS, Campus Bridoux, Bâtiment IBISE, rue Claude Bernard, 57070, Metz, France
| | - Cédric Fisson
- GIP Seine-Aval, Hangar C - Espace des Marégraphes, CS 41174, 76176, Rouen Cedex 1, France
| | - Alain Devaux
- ENTPE, LEHNA UMR 5023, USC INRAE 1369, 3 rue Maurice Audin, 69120, Vaulx en Velin, France
| | - Rachid Amara
- Université Littoral Côte d'Opale, Université Lille, CNRS, UMR 8187, LOG, Laboratoire d'Océanologie Et de Géosciences, 32 Avenue du Maréchal Foch, 62930, Wimereux, France
| | - Mamadou Diop
- Université Littoral Côte d'Opale, Université Lille, CNRS, UMR 8187, LOG, Laboratoire d'Océanologie Et de Géosciences, 32 Avenue du Maréchal Foch, 62930, Wimereux, France
| | - Vianney Pichereau
- LEMAR UMR 6539, CNRS/UBO/IRD/Ifremer, Institut Universitaire Européen de La Mer, Université de Bretagne Occidentale, rue Dumont d'Urville, 29280, Plouzané, France
| | - Jean Laroche
- LEMAR UMR 6539, CNRS/UBO/IRD/Ifremer, Institut Universitaire Européen de La Mer, Université de Bretagne Occidentale, rue Dumont d'Urville, 29280, Plouzané, France.
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5
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Zhu Y, Zhang Y, Li Y, Guo C, Fan Z, Li Y, Yang M, Zhou X, Sun Z, Wang J. Integrative proteomics and metabolomics approach to elucidate metabolic dysfunction induced by silica nanoparticles in hepatocytes. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128820. [PMID: 35427968 DOI: 10.1016/j.jhazmat.2022.128820] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Silica nanoparticles (SiNPs) are derived from manufactured materials and the natural environment, and they cause detrimental effects on human health via various exposure routes. The liver is proven to be a key target organ for SiNP toxicity; however, the mechanisms causing toxicity remain largely uncertain. Here, we investigated the effects of SiNPs on the metabolic spectrum in hepatocytes via integrative analyses of proteomics and metabolomics. First, a proteomic analysis was used to screen for critical proteins (including RPL3, HSP90AA1, SOD, PGK1, GOT1, and PNP), indicating that abnormal protein synthesis, protein misfolding, oxidative stress, and metabolic dysfunction may contribute to SiNP-induced hepatotoxicity. Next, metabolomic data demonstrated that SiNPs caused metabolic dysfunction by altering vital metabolites (including glucose, alanine, GSH, CTP, and ATP). Finally, a systematic bioinformatic analysis of protein-metabolite interactions showed that SiNPs disturbed glucose metabolism (glycolysis and pentose phosphate pathways, amino acid metabolism (alanine, aspartate, and glutamate), and ribonucleotide metabolism (purine and pyrimidine). These metabolic dysfunctions could exacerbate oxidative stress and lead to liver injury. Moreover, SOD, TKT, PGM1, GOT1, PNP, and NME2 may be key proteins for SiNP-induced hepatotoxicity. This study revealed the metabolic mechanisms underlying SiNP-induced hepatotoxicity and illustrated that integrative omics analyses can be a powerful approach for toxicity evaluations and risk assessments of nanoparticles.
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Affiliation(s)
- Ye Zhu
- aDepartment of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; bBeijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Yukang Zhang
- aDepartment of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; bBeijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Yanbo Li
- aDepartment of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; bBeijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Caixia Guo
- aDepartment of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; bBeijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Zhuying Fan
- aDepartment of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; bBeijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Yang Li
- aDepartment of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; bBeijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Man Yang
- aDepartment of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; bBeijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China.
| | - Xianqing Zhou
- aDepartment of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; bBeijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Zhiwei Sun
- aDepartment of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; bBeijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Ji Wang
- aDepartment of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; bBeijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China.
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6
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Scholz S, Nichols JW, Escher BI, Ankley GT, Altenburger R, Blackwell B, Brack W, Burkhard L, Collette TW, Doering JA, Ekman D, Fay K, Fischer F, Hackermüller J, Hoffman JC, Lai C, Leuthold D, Martinovic-Weigelt D, Reemtsma T, Pollesch N, Schroeder A, Schüürmann G, von Bergen M. The Eco-Exposome Concept: Supporting an Integrated Assessment of Mixtures of Environmental Chemicals. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:30-45. [PMID: 34714945 PMCID: PMC9104394 DOI: 10.1002/etc.5242] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 05/04/2023]
Abstract
Organisms are exposed to ever-changing complex mixtures of chemicals over the course of their lifetime. The need to more comprehensively describe this exposure and relate it to adverse health effects has led to formulation of the exposome concept in human toxicology. Whether this concept has utility in the context of environmental hazard and risk assessment has not been discussed in detail. In this Critical Perspective, we propose-by analogy to the human exposome-to define the eco-exposome as the totality of the internal exposure (anthropogenic and natural chemicals, their biotransformation products or adducts, and endogenous signaling molecules that may be sensitive to an anthropogenic chemical exposure) over the lifetime of an ecologically relevant organism. We describe how targeted and nontargeted chemical analyses and bioassays can be employed to characterize this exposure and discuss how the adverse outcome pathway concept could be used to link this exposure to adverse effects. Available methods, their limitations, and/or requirement for improvements for practical application of the eco-exposome concept are discussed. Even though analysis of the eco-exposome can be resource-intensive and challenging, new approaches and technologies make this assessment increasingly feasible. Furthermore, an improved understanding of mechanistic relationships between external chemical exposure(s), internal chemical exposure(s), and biological effects could result in the development of proxies, that is, relatively simple chemical and biological measurements that could be used to complement internal exposure assessment or infer the internal exposure when it is difficult to measure. Environ Toxicol Chem 2022;41:30-45. © 2021 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Stefan Scholz
- Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Address correspondence to
| | - John W. Nichols
- Office of Research and Development, Great Lakes Ecology and Toxicology Division, US Environmental Protection Agency, Duluth, Minnesota
| | - Beate I. Escher
- Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Environmental Toxicology, Center for Applied Geoscience, Eberhard Karls University Tubingen, Tubingen, Germany
| | - Gerald T. Ankley
- Office of Research and Development, Great Lakes Ecology and Toxicology Division, US Environmental Protection Agency, Duluth, Minnesota
| | - Rolf Altenburger
- Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Institute for Environmental Research, Biologie V, RWTH Aachen University, Aachen, Germany
| | - Brett Blackwell
- Office of Research and Development, Great Lakes Ecology and Toxicology Division, US Environmental Protection Agency, Duluth, Minnesota
| | - Werner Brack
- Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Department of Evolutionary Ecology and Environmental Toxicology, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Lawrence Burkhard
- Office of Research and Development, Great Lakes Ecology and Toxicology Division, US Environmental Protection Agency, Duluth, Minnesota
| | - Timothy W. Collette
- Office of Research and Development, Ecosystem Processes Division, US Environmental Protection Agency, Athens, Georgia
| | - Jon A. Doering
- National Research Council, US Environmental Protection Agency, Duluth, Minnesota
| | - Drew Ekman
- Office of Research and Development, Ecosystem Processes Division, US Environmental Protection Agency, Athens, Georgia
| | - Kellie Fay
- Office of Pollution Prevention and Toxics, Risk Assessment Division, US Environmental Protection Agency, Washington, DC
| | - Fabian Fischer
- Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | | | - Joel C. Hoffman
- Office of Research and Development, Great Lakes Ecology and Toxicology Division, US Environmental Protection Agency, Duluth, Minnesota
| | - Chih Lai
- College of Arts and Sciences, University of Saint Thomas, St. Paul, Minnesota, USA
| | - David Leuthold
- Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | | | | | - Nathan Pollesch
- Office of Research and Development, Great Lakes Ecology and Toxicology Division, US Environmental Protection Agency, Duluth, Minnesota
| | | | - Gerrit Schüürmann
- Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Institute of Organic Chemistry, Technische Universitat Bergakademie Freiberg, Freiberg, Germany
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Ferreira M, Ventorim R, Almeida E, Silveira S, Silveira W. Protein Abundance Prediction Through Machine Learning Methods. J Mol Biol 2021; 433:167267. [PMID: 34563548 DOI: 10.1016/j.jmb.2021.167267] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/09/2021] [Accepted: 09/17/2021] [Indexed: 10/20/2022]
Abstract
Proteins are responsible for most physiological processes, and their abundance provides crucial information for systems biology research. However, absolute protein quantification, as determined by mass spectrometry, still has limitations in capturing the protein pool. Protein abundance is impacted by translation kinetics, which rely on features of codons. In this study, we evaluated the effect of codon usage bias of genes on protein abundance. Notably, we observed differences regarding codon usage patterns between genes coding for highly abundant proteins and genes coding for less abundant proteins. Analysis of synonymous codon usage and evolutionary selection showed a clear split between the two groups. Our machine learning models predicted protein abundances from codon usage metrics with remarkable accuracy, achieving strong correlation with experimental data. Upon integration of the predicted protein abundance in enzyme-constrained genome-scale metabolic models, the simulated phenotypes closely matched experimental data, which demonstrates that our predictive models are valuable tools for systems metabolic engineering approaches.
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Affiliation(s)
- Mauricio Ferreira
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil. https://twitter.com/@mauriciomyces
| | - Rafaela Ventorim
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
| | - Eduardo Almeida
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil. https://twitter.com/@elm_almeida
| | - Sabrina Silveira
- Department of Computer Science, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil. https://twitter.com/@sabrina_as
| | - Wendel Silveira
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
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8
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Ebner JN. Trends in the Application of "Omics" to Ecotoxicology and Stress Ecology. Genes (Basel) 2021; 12:1481. [PMID: 34680873 PMCID: PMC8535992 DOI: 10.3390/genes12101481] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/12/2021] [Accepted: 09/16/2021] [Indexed: 02/08/2023] Open
Abstract
Our ability to predict and assess how environmental changes such as pollution and climate change affect components of the Earth's biome is of paramount importance. This need positioned the fields of ecotoxicology and stress ecology at the center of environmental monitoring efforts. Advances in these interdisciplinary fields depend not only on conceptual leaps but also on technological advances and data integration. High-throughput "omics" technologies enabled the measurement of molecular changes at virtually all levels of an organism's biological organization and thus continue to influence how the impacts of stressors are understood. This bibliometric review describes literature trends (2000-2020) that indicate that more different stressors than species are studied each year but that only a few stressors have been studied in more than two phyla. At the same time, the molecular responses of a diverse set of non-model species have been investigated, but cross-species comparisons are still rare. While transcriptomics studies dominated until 2016, a shift towards proteomics and multiomics studies is apparent. There is now a wealth of data at functional omics levels from many phylogenetically diverse species. This review, therefore, addresses the question of how to integrate omics information across species.
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Affiliation(s)
- Joshua Niklas Ebner
- Spring Ecology Research Group, Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
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9
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Segner H, Bailey C, Tafalla C, Bo J. Immunotoxicity of Xenobiotics in Fish: A Role for the Aryl Hydrocarbon Receptor (AhR)? Int J Mol Sci 2021; 22:ijms22179460. [PMID: 34502366 PMCID: PMC8430475 DOI: 10.3390/ijms22179460] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 02/07/2023] Open
Abstract
The impact of anthropogenic contaminants on the immune system of fishes is an issue of growing concern. An important xenobiotic receptor that mediates effects of chemicals, such as halogenated aromatic hydrocarbons (HAHs) and polyaromatic hydrocarbons (PAHs), is the aryl hydrocarbon receptor (AhR). Fish toxicological research has focused on the role of this receptor in xenobiotic biotransformation as well as in causing developmental, cardiac, and reproductive toxicity. However, biomedical research has unraveled an important physiological role of the AhR in the immune system, what suggests that this receptor could be involved in immunotoxic effects of environmental contaminants. The aims of the present review are to critically discuss the available knowledge on (i) the expression and possible function of the AhR in the immune systems of teleost fishes; and (ii) the impact of AhR-activating xenobiotics on the immune systems of fish at the levels of immune gene expression, immune cell proliferation and immune cell function, immune pathology, and resistance to infectious disease. The existing information indicates that the AhR is expressed in the fish immune system, but currently, we have little understanding of its physiological role. Exposure to AhR-activating contaminants results in the modulation of numerous immune structural and functional parameters of fish. Despite the diversity of fish species studied and the experimental conditions investigated, the published findings rather uniformly point to immunosuppressive actions of xenobiotic AhR ligands in fish. These effects are often associated with increased disease susceptibility. The fact that fish populations from HAH- and PAH-contaminated environments suffer immune disturbances and elevated disease susceptibility highlights that the immunotoxic effects of AhR-activating xenobiotics bear environmental relevance.
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Affiliation(s)
- Helmut Segner
- Centre for Fish and Wildlife Health, Department of Pathobiology and Infectious Diseases, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | | | | | - Jun Bo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Xiamen 361005, China
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10
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Wang X, Li F, Liu J, Ji C, Wu H. Transcriptomic, proteomic and metabolomic profiling unravel the mechanisms of hepatotoxicity pathway induced by triphenyl phosphate (TPP). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 205:111126. [PMID: 32823070 DOI: 10.1016/j.ecoenv.2020.111126] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/22/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Triphenyl phosphate (TPP) has been found in various environmental media and in biota suggesting widespread human exposure. However, there is still insufficient information on the hepatotoxicity mechanisms of health risk exposed to TPP. In this study, TPP could induce human normal liver cell (L02) apoptosis, injury cell ultrastructure and elevate the levels of reactive oxygen species (ROS). The integrated multi-omic (transcriptomic, proteomic, and metabolomic) analysis was used to further investigate the mechanisms. Transcriptomic analysis revealed that TPP exposure markedly affected cell apoptosis, oncogene activation, REDOX homeostasis, DNA damage and repair. Additionally, proteomic analysis found that the related proteins associated with apoptosis, oxidative stress, metabolism and membrane structure were affected. And metabolomic analysis verified that the related metabolic pathways, such as glycolysis, citrate cycle, oxidative phosphorylation, lipid and protein metabolism, were also significantly disrupted. Based on the multi-omic results, a hypothesized network was constructed to discover the key molecular events in response to TPP and illustrate the mechanism of TPP-induced hepatotoxicity in L02 cells. Therefore, molecular responses could be elucidated at multiple biological levels, and multi-omic analysis could provide scientific tools for exploring potential mechanisms of toxicity and chemical risk assessment.
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Affiliation(s)
- Xiaoqing Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Fei Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China.
| | - Jialin Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China
| | - Chenglong Ji
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China
| | - Huifeng Wu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China.
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11
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An Integrated Biomarker Approach Using Flounder to Improve Chemical Risk Assessments in the Heavily Polluted Seine Estuary. J Xenobiot 2020; 10:14-35. [PMID: 33397836 PMCID: PMC7792928 DOI: 10.3390/jox10020004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/16/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023] Open
Abstract
The objective of this study was to develop an integrative approach in ecotoxicology (from biomarkers to population genetics) to assess the ecological status of fish populations. Flounders (Platichthys flesus) collected after the spawning season in the heavily polluted Seine estuary were compared with the moderately polluted Bay of Douarnenez. The muscle energetic reserves were highly depleted in Seine vs. Douarnenez fish. The Seine fish displaying a reduced capacity to manage the oxidative stress and a higher energetic metabolism. An increase in the content of muscle membrane phospholipids (sphingomyelin, phosphatidylserine, free sterols) was detected in the Seine vs. Douarnenez fish. The data integration allowed to hypothesize relationships between membrane phospholipids, xenobiotic metabolism, bioenergetics, and antioxidant defence. The genetic diversity considering neutral markers was maintained in the heavily polluted Seine population compared with the Douarnenez population. Finally, we suggest that the high physiological cost of tolerance to toxicants in the Seine flounder population could compromise its capacity to respond in the future to an additional stressor like warming waters in shallow depth. Thus, this population could be submitted to an ecological risk.
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12
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Ewald JD, Soufan O, Crump D, Hecker M, Xia J, Basu N. EcoToxModules: Custom Gene Sets to Organize and Analyze Toxicogenomics Data from Ecological Species. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:4376-4387. [PMID: 32106671 DOI: 10.1021/acs.est.9b06607] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Traditional results from toxicogenomics studies are complex lists of significantly impacted genes or gene sets, which are challenging to synthesize down to actionable results with a clear interpretation. Here, we defined two sets of 21 custom gene sets, called the functional and statistical EcoToxModules, in fathead minnow (Pimephales promelas) to (1) re-cast predefined molecular pathways into a toxicological framework and (2) provide a data-driven, unsupervised grouping of genes impacted by exposure to environmental contaminants. The functional EcoToxModules were identified by re-organizing KEGG pathways into biological processes that are more relevant to ecotoxicology based on the input from expert scientists and regulators. The statistical EcoToxModules were identified using co-expression analysis of publicly available microarray data (n = 303 profiles) measured in livers of fathead minnows after exposure to 38 different conditions. Potential applications of the EcoToxModules were demonstrated with two case studies that represent exposure to a pure chemical and to environmental wastewater samples. In comparisons to differential expression and gene set analysis, we found that EcoToxModule responses were consistent with these traditional results. Additionally, they were easier to visualize and quantitatively compare across different conditions, which facilitated drawing conclusions about the relative toxicity of the exposures within each case study.
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Affiliation(s)
- Jessica D Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue H9X 3V9, Canada
| | - Othman Soufan
- Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue H9X 3V9, Canada
| | - Doug Crump
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa K1A 0H3, Canada
| | - Markus Hecker
- School of the Environment & Sustainability and Toxicology Centre, University of Saskatchewan, Saskatoon S7N 5B3, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue H9X 3V9, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue H9X 3V9, Canada
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13
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Xu L, Lu Z, Ji C, Cong M, Li F, Shan X, Wu H. Toxicological effects of As (V) in juvenile rockfish Sebastes schlegelii by a combined metabolomic and proteomic approach. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113333. [PMID: 31610518 DOI: 10.1016/j.envpol.2019.113333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/02/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Arsenic (As) is a metalloid element that is ubiquitous in the marine environment and its contamination has received worldwide attention due to its potential toxicity. Arsenic can induce multiple adverse effects, such as lipid metabolism disorder, immune system dysfunction, oxidative stress and carcinogenesis, in animals. Inorganic arsenic includes two chemical forms, arsenite (As (III)) and arsenate (As (V)), in natural environment. As (V) is the dominant form in natural waters. In the present study, metabolomic and proteomic alterations were investigated in juvenile rockfish Sebastes schlegelii exposed to environmentally relevant concentrations of As (V) for 14 d. The analysis of iTRAQ-based proteomics combined with untargeted NMR-based metabolomics indicated apparent toxicological effects induced by As (V) in juvenile rockfish. In details, the metabolites, including lactate, alanine, ATP, inosine and phosphocholine were significantly altered in As-treated groups. Proteomic responses suggested that As (V) could not only affected energy and primary metabolisms and signal transduction, but also influenced cytoskeleton structure in juvenile rockfish. This work suggested that the combined proteomic and metabolomic approach could shed light on the toxicological effects of pollutants in rockfish S. schlegelii.
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Affiliation(s)
- Lanlan Xu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zhen Lu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Chenglong Ji
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China
| | - Ming Cong
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China
| | - Fei Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China
| | - Xiujuan Shan
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China
| | - Huifeng Wu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China.
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14
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Murphy CA, Nisbet RM, Antczak P, Garcia-Reyero N, Gergs A, Lika K, Mathews T, Muller EB, Nacci D, Peace A, Remien CH, Schultz IR, Stevenson LM, Watanabe KH. Incorporating Suborganismal Processes into Dynamic Energy Budget Models for Ecological Risk Assessment. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2018; 14:615-624. [PMID: 29870141 PMCID: PMC6643959 DOI: 10.1002/ieam.4063] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/27/2018] [Accepted: 05/31/2018] [Indexed: 05/19/2023]
Abstract
A working group at the National Institute for Mathematical and Biological Synthesis (NIMBioS) explored the feasibility of integrating 2 complementary approaches relevant to ecological risk assessment. Adverse outcome pathway (AOP) models provide "bottom-up" mechanisms to predict specific toxicological effects that could affect an individual's ability to grow, reproduce, and/or survive from a molecular initiating event. Dynamic energy budget (DEB) models offer a "top-down" approach that reverse engineers stressor effects on growth, reproduction, and/or survival into modular characterizations related to the acquisition and processing of energy resources. Thus, AOP models quantify linkages between measurable molecular, cellular, or organ-level events, but they do not offer an explicit route to integratively characterize stressor effects at higher levels of organization. While DEB models provide the inherent basis to link effects on individuals to those at the population and ecosystem levels, their use of abstract variables obscures mechanistic connections to suborganismal biology. To take advantage of both approaches, we developed a conceptual model to link DEB and AOP models by interpreting AOP key events as measures of damage-inducing processes affecting DEB variables and rates. We report on the type and structure of data that are generated for AOP models that may also be useful for DEB models. We also report on case studies under development that merge information collected for AOPs with DEB models and highlight some of the challenges. Finally, we discuss how the linkage of these 2 approaches can improve ecological risk assessment, with possibilities for progress in predicting population responses to toxicant exposures within realistic environments. Integr Environ Assess Manag 2018;14:615-624. © 2018 SETAC.
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Affiliation(s)
- Cheryl A Murphy
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA
| | - Roger M Nisbet
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
| | - Philipp Antczak
- Institute for Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, Mississippi
| | - Andre Gergs
- gaiac-Research Institute for Ecosystem Analysis and Assessment, Aachen, Germany
| | - Konstadia Lika
- Department of Biology, University of Crete, Voutes University Campus, Heraklion, Greece
| | - Teresa Mathews
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Erik B Muller
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Diane Nacci
- US Environmental Protection Agency, Office of Research and Development, Narragansett, Rhode Island
| | - Angela Peace
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, Texas, USA
| | | | - Irvin R Schultz
- Marine Sciences Lab, Pacific NW National Laboratory, Sequim, Washington, USA
- Present address: Lynker Technologies, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Louise M Stevenson
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
| | - Karen H Watanabe
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, Arizona, USA
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15
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Lavelle C, Smith LC, Bisesi JH, Yu F, Silva-Sanchez C, Moraga-Amador D, Buerger AN, Garcia-Reyero N, Sabo-Attwood T, Denslow ND. Tissue-Based Mapping of the Fathead Minnow ( Pimephales promelas) Transcriptome and Proteome. Front Endocrinol (Lausanne) 2018; 9:611. [PMID: 30459712 PMCID: PMC6232228 DOI: 10.3389/fendo.2018.00611] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/26/2018] [Indexed: 12/11/2022] Open
Abstract
Omics approaches are broadly used to explore endocrine and toxicity-related pathways and functions. Nevertheless, there is still a significant gap in knowledge in terms of understanding the endocrine system and its numerous connections and intricate feedback loops, especially in non-model organisms. The fathead minnow (Pimephales promelas) is a widely used small fish model for aquatic toxicology and regulatory testing, particularly in North America. A draft genome has been published, but the amount of available genomic or transcriptomic information is still far behind that of other more broadly studied species, such as the zebrafish. Here, we used a proteogenomics approach to survey the tissue-specific proteome and transcriptome profiles in adult male fathead minnow. To do so, we generated a draft transcriptome using short and long sequencing reads from liver, testis, brain, heart, gill, head kidney, trunk kidney, and gastrointestinal tract. We identified 30,378 different putative transcripts overall, with the assembled contigs ranging in size from 264 to over 9,720 nts. Over 17,000 transcripts were >1,000 nts, suggesting a robust transcriptome that can be used to interpret RNA sequencing data in the future. We also performed RNA sequencing and proteomics analysis on four tissues, including the telencephalon, hypothalamus, liver, and gastrointestinal tract of male fish. Transcripts ranged from 0 to 600,000 copies per gene and a large portion were expressed in a tissue-specific manner. Specifically, the telencephalon and hypothalamus shared the most expressed genes, while the gastrointestinal tract and the liver were quite distinct. Using protein profiling techniques, we identified a total of 4,045 proteins in the four tissues investigated, and their tissue-specific expression pattern correlated with the transcripts at the pathway level. Similarly to the findings with the transcriptomic data, the hypothalamus and telencephalon had the highest degree of similarity in the proteins detected. The main purpose of this analysis was to generate tissue-specific omics data in order to support future aquatic ecotoxicogenomic and endocrine-related studies as well as to improve our understanding of the fathead minnow as an ecological model.
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Affiliation(s)
- Candice Lavelle
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Ley Cody Smith
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States
| | - Joseph H. Bisesi
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Fahong Yu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Cecilia Silva-Sanchez
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - David Moraga-Amador
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Amanda N. Buerger
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, MS, United States
| | - Tara Sabo-Attwood
- Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Nancy D. Denslow
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States
- *Correspondence: Nancy D. Denslow
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16
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Rodríguez-Romero AJ, Rico-Sánchez AE, Catalá M, Sedeño-Díaz JE, López-López E. Mitochondrial activity in fern spores of Cyathea costaricensis as an indicator of the impact of land use and water quality in rivers running through cloud forests. CHEMOSPHERE 2017; 189:435-444. [PMID: 28957761 DOI: 10.1016/j.chemosphere.2017.09.094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/12/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
Early-warning biomarkers, such as mitochondrial activity, have become a key tool in ecosystem assessment. This study aims to evaluate the response of mitochondrial activity in spores of the autochthonous fern Cyathea costaricensis as a bioassessment tool concurrently with land use and physicochemical evaluation in 11 sites along Bobos River, Veracruz, Mexico, to assess river water quality. Bobos River is located in the Nautla basin, northeastern Veracruz (Mexico); the upper river runs through a protected natural area (Filobobos River and adjacent areas). The study involved three monitoring periods: February, June and September 2014. In each study site, physicochemical water quality parameters were recorded to calculate the Water Quality Index (WQI); also, study sites were characterized in terms of land use. Water samples were collected to perform bioassays where spores of C. costaricensis were exposed to samples to assess mitochondrial activity; a positive control exposure test was run under controlled conditions to maximize mitochondrial activity. A Principal Component Analysis was performed to correlate land-use attributes with environmental variables and mitochondrial activity. Three river sections were identified: the upper portion was characterized by the dominance of native vegetation, the highest WQI (in September), and the lowest mitochondrial activity (63.87%-77.47%), related to the geological nature of the basin and high hardness levels. Mitochondrial activity peaked in September (98.32% ± 9.01), likely resulting from nutrient enrichment in the rainy season, and was lowest in February (74.54% ± 1.60) (p < 0.05). Mitochondrial activity was found to be a good benchmark for the assessment of water quality, reflecting the effects of physicochemical characteristics. Mitochondrial activity showed changes along the river and between seasons, associated with environmental characteristics such as land use and the geological nature of the basin, as well as with those related to human impacts.
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Affiliation(s)
- Alexis Joseph Rodríguez-Romero
- Laboratorio de Evaluación de la Salud de los Ecosistemas Acuáticos, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, C.P. 11340, Delegación Miguel Hidalgo, Ciudad de México, Mexico
| | - Axel Eduardo Rico-Sánchez
- Laboratorio de Evaluación de la Salud de los Ecosistemas Acuáticos, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, C.P. 11340, Delegación Miguel Hidalgo, Ciudad de México, Mexico
| | - Myriam Catalá
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/ Tulipán s/n, E-28933, Móstoles (Madrid), Spain
| | - Jacinto Elías Sedeño-Díaz
- Coordinación Politécnica para la Sustentabilidad, Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional s/n, Esq. Wilfrido Massieu, Col. San Pedro Zacatenco, C.P. 07738, Delegación Gustavo A. Madero, Ciudad de México, Mexico
| | - Eugenia López-López
- Laboratorio de Evaluación de la Salud de los Ecosistemas Acuáticos, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, C.P. 11340, Delegación Miguel Hidalgo, Ciudad de México, Mexico.
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17
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Li F, Wang L, Ji C, Wu H, Zhao J, Tang J. Toxicological effects of tris(2-chloropropyl) phosphate in human hepatic cells. CHEMOSPHERE 2017; 187:88-96. [PMID: 28841435 DOI: 10.1016/j.chemosphere.2017.08.083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Organophosphate flame retardants (OPFRs) are widely used as flame retardants which are ubiquitous in various environment media. As many of OPFRs are toxic and persistent, concerns have been raised in regards to their environmental impact. In this study, the toxicological effects of tris(2-chloropropyl) phosphate (TCPP) in human L02 cells was investigated by cell proliferation and apoptosis, oxidative stress, metabolomic and proteomic responses as well as gene expressions related to apoptosis. Results showed that TCPP did not significantly affect the L02 cell apoptosis, however, a significant increase of ROS production was observed in L02 cells with TCPP treatment compared with that in control group (p < 0.05). The expression levels of Bcl-2 family-encoding genes (Bax, Hrk and Bax/Bcl-2) were up-regulated significantly in 10-4 M group (p < 0.05). Metabolomic and proteomic responses indicated that TCPP mainly caused disturbance in cell growth/division and gene expression, energy and material metabolism, signal transduction, defense and cytoskeleton, which was further confirmed by the western blot analysis.
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Affiliation(s)
- Fei Li
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Yantai, 264003, PR China
| | - Li Wang
- Departments of Integrated Traditional and Western Medicine, Yantai Yuhuangding Hospital, Yuhuangdingdong Road 20, Yantai, Shandong, 264000, PR China
| | - Chenglong Ji
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Yantai, 264003, PR China
| | - Huifeng Wu
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Yantai, 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China.
| | - Jianmin Zhao
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Yantai, 264003, PR China
| | - Jianhui Tang
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS), Yantai, 264003, PR China
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18
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Spanier KI, Jansen M, Decaestecker E, Hulselmans G, Becker D, Colbourne JK, Orsini L, De Meester L, Aerts S. Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia. Genome Biol Evol 2017; 9:1821-1842. [PMID: 28854641 PMCID: PMC5569996 DOI: 10.1093/gbe/evx127] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2017] [Indexed: 02/06/2023] Open
Abstract
Ecological genomics aims to understand the functional association between environmental gradients and the genes underlying adaptive traits. Many genes that are identified by genome-wide screening in ecologically relevant species lack functional annotations. Although gene functions can be inferred from sequence homology, such approaches have limited power. Here, we introduce ecological regulatory genomics by presenting an ontology-free gene prioritization method. Specifically, our method combines transcriptome profiling with high-throughput cis-regulatory sequence analysis in the water fleas Daphnia pulex and Daphnia magna. It screens coexpressed genes for overrepresented DNA motifs that serve as transcription factor binding sites, thereby providing insight into conserved transcription factors and gene regulatory networks shaping the expression profile. We first validated our method, called Daphnia-cisTarget, on a D. pulex heat shock data set, which revealed a network driven by the heat shock factor. Next, we performed RNA-Seq in D. magna exposed to the cyanobacterium Microcystis aeruginosa. Daphnia-cisTarget identified coregulated gene networks that associate with the moulting cycle and potentially regulate life history changes in growth rate and age at maturity. These networks are predicted to be regulated by evolutionary conserved transcription factors such as the homologues of Drosophila Shavenbaby and Grainyhead, nuclear receptors, and a GATA family member. In conclusion, our approach allows prioritising candidate genes in Daphnia without bias towards prior knowledge about functional gene annotation and represents an important step towards exploring the molecular mechanisms of ecological responses in organisms with poorly annotated genomes.
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Affiliation(s)
- Katina I. Spanier
- Department of Biology, Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Belgium
- Department of Human Genetics, Laboratory of Computational Biology, KU Leuven, Belgium
- VIB Center for Brain and Disease Research, KU Leuven, Belgium
| | - Mieke Jansen
- Department of Biology, Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Belgium
| | - Ellen Decaestecker
- Department of Biology, Laboratory of Aquatic Biology, Science and Technology, KU Leuven Campus Kulak, Kortrjik, Belgium
| | - Gert Hulselmans
- Department of Human Genetics, Laboratory of Computational Biology, KU Leuven, Belgium
- VIB Center for Brain and Disease Research, KU Leuven, Belgium
| | - Dörthe Becker
- Environmental Genomics Group, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, United Kingdom
| | - John K. Colbourne
- Environmental Genomics Group, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, United Kingdom
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, United Kingdom
| | - Luc De Meester
- Department of Biology, Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Belgium
| | - Stein Aerts
- Department of Human Genetics, Laboratory of Computational Biology, KU Leuven, Belgium
- VIB Center for Brain and Disease Research, KU Leuven, Belgium
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19
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Wu H, Xu L, Ji C, Yu D. Proteomic and metabolomic responses in D-shape larval mussels Mytilus galloprovincialis exposed to cadmium and arsenic. FISH & SHELLFISH IMMUNOLOGY 2016; 58:514-520. [PMID: 27702675 DOI: 10.1016/j.fsi.2016.09.064] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/28/2016] [Accepted: 09/30/2016] [Indexed: 06/06/2023]
Abstract
Cadmium (Cd) and arsenic (As) are the main metal/metalloid contaminants in the coastal environments of the Bohai Sea, China. In this work, a combined proteomic and metabolomic approach was applied to investigate the biological effects of Cd and As (V) in the early life stage (D-shape larvae) of mussel Mytilus galloprovincialis. Results indicated that Cd was a potential immune toxicant to D-shape larval mussel because of the numerous proteomic responses related to immune system. Additionally, Cd induced oxidative stress, cellular injury and disturbance in nucleic acid metabolism in D-shape larval mussels. However, only two identified proteins were significantly altered in As (V)-treated group, suggesting that D-shape larval mussel was less sensitive to As (V) than to Cd at protein level. These two proteins in response to As (V) suggested that As (V) influenced anti-oxidative system and cell proliferation in D-shape larval mussels. Metabolic responses indicated that Cd and As (V) induced disturbances in osmotic regulation and energy metabolism in D-shape larval mussels via different metabolic pathways. In addition, Cd reduced lipid metabolism as well. This work demonstrated that a combination of proteomics and metabolomics could provide an insightful view in the biological effects of pollutants in mussel M. galloprovincialis at an early life stage.
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Affiliation(s)
- Huifeng Wu
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China.
| | - Lanlan Xu
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chenglong Ji
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China
| | - Deliang Yu
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
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20
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Hablützel PI, Brown M, Friberg IM, Jackson JA. Changing expression of vertebrate immunity genes in an anthropogenic environment: a controlled experiment. BMC Evol Biol 2016; 16:175. [PMID: 27586387 PMCID: PMC5009682 DOI: 10.1186/s12862-016-0751-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 08/23/2016] [Indexed: 12/01/2022] Open
Abstract
Background The effect of anthropogenic environments on the function of the vertebrate immune system is a problem of general importance. For example, it relates to the increasing rates of immunologically-based disease in modern human populations and to the desirability of identifying optimal immune function in domesticated animals. Despite this importance, our present understanding is compromised by a deficit of experimental studies that make adequately matched comparisons between wild and captive vertebrates. Results We transferred post-larval fishes (three-spined sticklebacks), collected in the wild, to an anthropogenic (captive) environment. We then monitored, over 11 months, how the systemic expression of immunity genes changed in comparison to cohort-matched wild individuals in the originator population (total n = 299). We found that a range of innate (lyz, defbl2, il1r-like, tbk1) and adaptive (cd8a, igmh) immunity genes were up-regulated in captivity, accompanied by an increase in expression of the antioxidant enzyme, gpx4a. For some genes previously known to show seasonality in the wild, this appeared to be reduced in captive fishes. Captive fishes tended to express immunity genes, including igzh, foxp3b, lyz, defbl2, and il1r-like, more variably. Furthermore, although gene co-expression patterns (analyzed through gene-by-gene correlations and mutual information theory based networks) shared common structure in wild and captive fishes, there was also significant divergence. For one gene in particular, defbl2, high expression was associated with adverse health outcomes in captive fishes. Conclusion Taken together, these results demonstrate widespread regulatory changes in the immune system in captive populations, and that the expression of immunity genes is more constrained in the wild. An increase in constitutive systemic immune activity, such as we observed here, may alter the risk of immunopathology and contribute to variance in health in vertebrate populations exposed to anthropogenic environments. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0751-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Martha Brown
- IBERS, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Ida M Friberg
- School of Life and Environmental Sciences, University of Salford, Salford, M5 4WT, UK
| | - Joseph A Jackson
- School of Life and Environmental Sciences, University of Salford, Salford, M5 4WT, UK.
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21
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Martin LB, Burgan SC, Adelman JS, Gervasi SS. Host Competence: An Organismal Trait to Integrate Immunology and Epidemiology. Integr Comp Biol 2016; 56:1225-1237. [DOI: 10.1093/icb/icw064] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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22
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Brown M, Hablützel P, Friberg IM, Thomason AG, Stewart A, Pachebat JA, Jackson JA. Seasonal immunoregulation in a naturally-occurring vertebrate. BMC Genomics 2016; 17:369. [PMID: 27189372 PMCID: PMC4870750 DOI: 10.1186/s12864-016-2701-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 05/06/2016] [Indexed: 11/10/2022] Open
Abstract
Background Fishes show seasonal patterns of immunity, but such phenomena are imperfectly understood in vertebrates generally, even in humans and mice. As these seasonal patterns may link to infectious disease risk and individual condition, the nature of their control has real practical implications. Here we characterize seasonal dynamics in the expression of conserved vertebrate immunity genes in a naturally-occurring piscine model, the three-spined stickleback. Results We made genome-wide measurements (RNAseq) of whole-fish mRNA pools (n = 36) at the end of summer and winter in contrasting habitats (riverine and lacustrine) and focussed on common trends to filter habitat-specific from overarching temporal responses. We corroborated this analysis with targeted year-round whole-fish gene expression (Q-PCR) studies in a different year (n = 478). We also considered seasonal tissue-specific expression (6 tissues) (n = 15) at a third contrasting (euryhaline) locality by Q-PCR, further validating the generality of the patterns seen in whole fish analyses. Extremes of season were the dominant predictor of immune expression (compared to sex, ontogeny or habitat). Signatures of adaptive immunity were elevated in late summer. In contrast, late winter was accompanied by signatures of innate immunity (including IL-1 signalling and non-classical complement activity) and modulated toll-like receptor signalling. Negative regulators of T-cell activity were prominent amongst winter-biased genes, suggesting that adaptive immunity is actively down-regulated during winter rather than passively tracking ambient temperature. Network analyses identified a small set of immune genes that might lie close to a regulatory axis. These genes acted as hubs linking summer-biased adaptive pathways, winter-biased innate pathways and other organismal processes, including growth, metabolic dynamics and responses to stress and temperature. Seasonal change was most pronounced in the gill, which contains a considerable concentration of T-cell activity in the stickleback. Conclusions Our results suggest major and predictable seasonal re-adjustments of immunity. Further consideration should be given to the effects of such responses in seasonally-occurring disease. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2701-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martha Brown
- IBERS, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | | | - Ida M Friberg
- School of Environment and Life sciences, University of Salford, Salford, M5 4WT, UK
| | - Anna G Thomason
- School of Environment and Life sciences, University of Salford, Salford, M5 4WT, UK
| | - Alexander Stewart
- Cardiff School of Biosciences, University of Cardiff, Cardiff, CF10 3AX, UK
| | | | - Joseph A Jackson
- School of Environment and Life sciences, University of Salford, Salford, M5 4WT, UK.
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23
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Liu X, Lai Y, Sun H, Wang Y, Zou N. The interactive effects of mercury and selenium on metabolic profiles, gene expression and antioxidant enzymes in halophyte Suaeda salsa. ENVIRONMENTAL TOXICOLOGY 2016; 31:440-451. [PMID: 25346288 DOI: 10.1002/tox.22057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/25/2014] [Accepted: 10/01/2014] [Indexed: 06/04/2023]
Abstract
Suaeda salsa is the pioneer halophyte in the Yellow River Delta and was consumed as a popular vegetable. Mercury has become a highly risky contaminant in the sediment of intertidal zones of the Yellow River Delta. In this work, we investigated the interactive effects of mercury and selenium in S. salsa on the basis of metabolic profiling, antioxidant enzyme activities and gene expression quantification. Our results showed that mercury exposure (20 μg L(-1)) inhibited plant growth of S. salsa and induced significant metabolic responses and altered expression levels of INPS, CMO, and MDH in S. salsa samples, together with the increased activities of antioxidant enzymes including SOD and POD. Overall, these results indicated osmotic and oxidative stresses, disturbed protein degradation and energy metabolism change in S. salsa after mercury exposures. Additionally, the addition of selenium could induce both antagonistic and synergistic effects including alleviating protein degradation and aggravating osmotic stress caused by mercury.
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Affiliation(s)
- Xiaoli Liu
- School of Life Sciences, Ludong University, Yantai 264025, People's Republic of China
| | - Yongkai Lai
- School of Life Sciences, Ludong University, Yantai 264025, People's Republic of China
| | - Hushan Sun
- School of Life Sciences, Ludong University, Yantai 264025, People's Republic of China
| | - Yiyan Wang
- School of Life Sciences, Ludong University, Yantai 264025, People's Republic of China
| | - Ning Zou
- School of Life Sciences, Ludong University, Yantai 264025, People's Republic of China
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24
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Ji C, Xu H, Wang Q, Zhao J, Wu H. Comparative investigations on the biological effects of As (III) and As (V) in clam Ruditapes philippinarum using multiple biomarkers. FISH & SHELLFISH IMMUNOLOGY 2015; 47:79-84. [PMID: 26327115 DOI: 10.1016/j.fsi.2015.08.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/26/2015] [Accepted: 08/26/2015] [Indexed: 06/04/2023]
Abstract
Inorganic arsenic is a known pollutant with two chemical forms, arsenite (As (III)) and arsenate (As (V)), in marine environment. Clam Ruditapes philippinarum is an important fishery species along the Bohai coast. In this study, the biological effects induced by the two arsenic chemical forms (arsenite and arsenate) were compared using multiple biochemical indices in the digestive glands of clam R. philippinarum. The production of reactive oxygen species, antioxidant enzyme activities and metabolic responses exhibited that both As (III) and As (V) induced immune, oxidative and osmotic stresses in clam digestive glands. The differential metabolic biomarkers, histidine and taurine, indicated the differential responsive mechanisms in osmotic regulation in clam digestive glands. In addition, both arsenic treatments enhanced the anaerobiosis metabolism in clam digestive glands. Overall, this work illustrated that arsenite and arsenate induced similar biological effects in clams, which might be accounted for the biological transformation of arsenate to arsenite in clams.
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Affiliation(s)
- Chenglong Ji
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China
| | - Hai'e Xu
- Clinical Nutrition, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Qing Wang
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China
| | - Jianmin Zhao
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China
| | - Huifeng Wu
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China.
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25
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Antczak P, White TA, Giri A, Michelangeli F, Viant MR, Cronin MTD, Vulpe C, Falciani F. Systems Biology Approach Reveals a Calcium-Dependent Mechanism for Basal Toxicity in Daphnia magna. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11132-11140. [PMID: 26244374 DOI: 10.1021/acs.est.5b02707] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The expanding diversity and ever increasing amounts of man-made chemicals discharged to the environment pose largely unknown hazards to ecosystem and human health. The concept of adverse outcome pathways (AOPs) emerged as a comprehensive framework for risk assessment. However, the limited mechanistic information available for most chemicals and a lack of biological pathway annotation in many species represent significant challenges to effective implementation of this approach. Here, a systems level, multistep modeling strategy demonstrates how to integrate information on chemical structure with mechanistic insight from genomic studies, and phenotypic effects to define a putative adverse outcome pathway. Results indicated that transcriptional changes indicative of intracellular calcium mobilization were significantly overrepresented in Daphnia magna (DM) exposed to sublethal doses of presumed narcotic chemicals with log Kow ≥ 1.8. Treatment of DM with a calcium ATPase pump inhibitor substantially recapitulated the common transcriptional changes. We hypothesize that calcium mobilization is a potential key molecular initiating event in DM basal (narcosis) toxicity. Heart beat rate analysis and metabolome analysis indicated sublethal effects consistent with perturbations of calcium preceding overt acute toxicity. Together, the results indicate that altered calcium homeostasis may be a key early event in basal toxicity or narcosis induced by lipophilic compounds.
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Affiliation(s)
- Philipp Antczak
- Centre for Computational Biology and Modelling, Institute for Integrative Biology, University of Liverpool , L69 7ZB Liverpool, United Kingdom
| | - Thomas A White
- School of Biosciences, University of Birmingham , B15 2TT Birmingham, United Kingdom
| | | | | | - Mark R Viant
- School of Biosciences, University of Birmingham , B15 2TT Birmingham, United Kingdom
| | - Mark T D Cronin
- School of Pharmacy and Chemistry, Liverpool John Moores University , Liverpool L3 3AF, United Kingdom
| | - Chris Vulpe
- Nutritional Sciences and Toxicology & Berkeley Institute of the Environment, University of California, Berkeley , Berkeley, California 94720, United States
| | - Francesco Falciani
- Centre for Computational Biology and Modelling, Institute for Integrative Biology, University of Liverpool , L69 7ZB Liverpool, United Kingdom
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26
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Jackson JA. Immunology in wild nonmodel rodents: an ecological context for studies of health and disease. Parasite Immunol 2015; 37:220-32. [PMID: 25689683 PMCID: PMC7167918 DOI: 10.1111/pim.12180] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 02/04/2015] [Indexed: 12/16/2022]
Abstract
Transcriptomic methods are set to revolutionize the study of the immune system in naturally occurring nonmodel organisms. With this in mind, the present article focuses on ways in which the use of 'nonmodel' rodents (not the familiar laboratory species) can advance studies into the classical, but ever relevant, epidemiologic triad of immune defence, infectious disease and environment. For example, naturally occurring rodents are an interesting system in which to study the environmental stimuli that drive the development and homeostasis of the immune system and, by extension, to identify where these stimuli are altered in anthropogenic environments leading to the formation of immunopathological phenotypes. Measurement of immune expression may help define individual heterogeneity in infectious disease susceptibility and transmission and facilitate our understanding of infection dynamics and risk in the natural environment; furthermore, it may provide a means of surveillance that can filter individuals carrying previously unknown acute infections of potential ecological or zoonotic importance. Finally, the study of immunology in wild animals may reveal interactions within the immune system and between immunity and other organismal traits that are not observable under restricted laboratory conditions. Potentiating much of this is the possibility of combining gene expression profiles with analytical tools derived from ecology and systems biology to reverse engineer interaction networks between immune responses, other organismal traits and the environment (including symbiont exposures), revealing regulatory architecture. Such holistic studies promise to link ecology, epidemiology and immunology in natural systems in a unified approach that can illuminate important problems relevant to human health and animal welfare and production.
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Affiliation(s)
- J A Jackson
- IBERS, Aberystwyth University, Aberystwyth, Ceredigion, UK
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27
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Dupuy C, Galland C, Pichereau V, Sanchez W, Riso R, Labonne M, Amara R, Charrier G, Fournier M, Laroche J. Assessment of the European flounder responses to chemical stress in the English Channel, considering biomarkers and life history traits. MARINE POLLUTION BULLETIN 2015; 95:634-645. [PMID: 25499967 DOI: 10.1016/j.marpolbul.2014.11.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 10/31/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
A multi-biomarker approach was developed to evaluate responses of European flounder (Platichthys flesus) in three contrasted estuaries over the English Channel: the Canche (pristine site), Tamar (heavy metals and PAHs contamination) and Seine (heavily pollution with a complex cocktail of contaminants). The condition factor and several biomarkers of the immune system, antioxidant enzymes, energetic metabolism and detoxification processes were investigated in young-of-the-year (0+) and one-year-old (1+) flounder. Results underlined the difference between the pristine site and the Seine estuary which showed a lower condition factor, a modulation of the immune system, a higher Cytochrome C oxidase activity, and an up-regulation of BHMT expression. The moderate biomarker responses in the Tamar fish could be linked to the specific contamination context of this estuary. Flounder life history traits were analyzed by otolith microchemistry, in order to depict how the fish use their habitat and thus respond to chemical stress in estuaries.
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Affiliation(s)
- Célie Dupuy
- Université Européenne de Bretagne, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer, 29280 Plouzané, France; Institut National de la Recherche Scientifique, Institut Armand-Frappier (INRS-IAF), 31 Boulevard des Prairies, Laval, Québec H7V 1B7, Canada.
| | - Claire Galland
- Université Européenne de Bretagne, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer, 29280 Plouzané, France
| | - Vianney Pichereau
- Université Européenne de Bretagne, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer, 29280 Plouzané, France
| | - Wilfried Sanchez
- Institut National de l'Environnement Industriel et des Risques, Pôle "Dangers et impact sur le vivant", Unité d'écotoxicologie in vitro et in vivo, Parc Technologique ALATA, 60550 Verneuil en Halatte, France
| | - Ricardo Riso
- Université Européenne de Bretagne, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer, 29280 Plouzané, France
| | - Maylis Labonne
- Université Européenne de Bretagne, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer, 29280 Plouzané, France; Centre IRD de Bretagne, BP 70, 29280 Plouzané, France
| | - Rachid Amara
- Université Lille Nord de France, ULCO LOG, CNRS UMR 8187, F-62930 Wimereux, France
| | - Grégory Charrier
- Université Européenne de Bretagne, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer, 29280 Plouzané, France
| | - Michel Fournier
- Institut National de la Recherche Scientifique, Institut Armand-Frappier (INRS-IAF), 31 Boulevard des Prairies, Laval, Québec H7V 1B7, Canada
| | - Jean Laroche
- Université Européenne de Bretagne, Université de Bretagne Occidentale, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer, 29280 Plouzané, France
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Lavergne E, Pedron N, Calves I, Claireaux G, Mazurais D, Zambonino-Infante J, Le Bayon N, Cahu C, Laroche J. Does the chronic chemical contamination of a European flounder population decrease its thermal tolerance? MARINE POLLUTION BULLETIN 2015; 95:658-664. [PMID: 25636829 DOI: 10.1016/j.marpolbul.2015.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 12/02/2014] [Accepted: 01/05/2015] [Indexed: 06/04/2023]
Abstract
Juvenile flounders (Platichthys flesus), collected in two estuaries with similar temperature regimes (the heavily polluted Seine and the moderately contaminated Vilaine), were submitted to a common garden experiment. After an acclimation period, both populations were challenged by a thermal stress (9-24°C for 15days, then maintenance at 24°C for 19days). The condition factor of the Vilaine fish increased in both conditions, while it decreased for the heated Seine flounders after 34days. The expression of genes related to the energetic metabolism was measured in the liver. The expression levels for ATP-F0 and COII were significantly reduced for heated vs. standard fish from both estuaries, while a decrease of the 12S expression was detected only in heated vs. standard fish from the Seine estuary. Thus, it is suggested that highly contaminated fish from Seine could display a lower tolerance to thermal stress, compared to moderately contaminated fish from Vilaine.
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Affiliation(s)
- Edouard Lavergne
- Université de Bretagne Occidentale, UMR 6539, CNRS/IRD/UBO/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France.
| | - Nicolas Pedron
- Université de Bretagne Occidentale, UMR 6539, CNRS/IRD/UBO/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France; Ifremer, Laboratoire d'Adaptation, Reproduction et Nutrition des Poissons ARN, Unité de Physiologie Fonctionnelle des Organismes Marins PFOM, Plouzané, France
| | - Isabelle Calves
- Université de Bretagne Occidentale, UMR 6539, CNRS/IRD/UBO/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France
| | - Guy Claireaux
- Université de Bretagne Occidentale, UMR 6539, CNRS/IRD/UBO/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France
| | - David Mazurais
- Université de Bretagne Occidentale, UMR 6539, CNRS/IRD/UBO/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France; Ifremer, Laboratoire d'Adaptation, Reproduction et Nutrition des Poissons ARN, Unité de Physiologie Fonctionnelle des Organismes Marins PFOM, Plouzané, France
| | - José Zambonino-Infante
- Université de Bretagne Occidentale, UMR 6539, CNRS/IRD/UBO/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France; Ifremer, Laboratoire d'Adaptation, Reproduction et Nutrition des Poissons ARN, Unité de Physiologie Fonctionnelle des Organismes Marins PFOM, Plouzané, France
| | - Nicolas Le Bayon
- Université de Bretagne Occidentale, UMR 6539, CNRS/IRD/UBO/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France; Ifremer, Laboratoire d'Adaptation, Reproduction et Nutrition des Poissons ARN, Unité de Physiologie Fonctionnelle des Organismes Marins PFOM, Plouzané, France
| | - Chantal Cahu
- Université de Bretagne Occidentale, UMR 6539, CNRS/IRD/UBO/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France; Ifremer, Laboratoire d'Adaptation, Reproduction et Nutrition des Poissons ARN, Unité de Physiologie Fonctionnelle des Organismes Marins PFOM, Plouzané, France
| | - Jean Laroche
- Université de Bretagne Occidentale, UMR 6539, CNRS/IRD/UBO/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer IUEM, Plouzané, France
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Ji C, Wu H, Zhou M, Zhao J. Multiple biomarkers of biological effects induced by cadmium in clam Ruditapes philippinarum. FISH & SHELLFISH IMMUNOLOGY 2015; 44:430-435. [PMID: 25804494 DOI: 10.1016/j.fsi.2015.03.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/14/2015] [Accepted: 03/15/2015] [Indexed: 06/04/2023]
Abstract
Cadmium (Cd) is a known heavy metal pollutant in the Bohai Sea. Manila clam Ruditapes philippinarum is an important fishery species along the Bohai coast. In this study, the biological effects induced by two concentrations (20 and 200 μg/L) of Cd were characterized using multiple biochemical indices in the digestive glands of clam R. philippinarum. The total hemocyte counts, reactive oxygen species productions and antioxidant enzyme activities exhibited that Cd induced dose-dependent immune and oxidative stresses in clam digestive glands. Metabolic responses indicated that both Cd exposures caused immune stress marked by the elevated branched chain amino acids (valine, leucine and isoleucine), together with the disturbance in energy metabolism. The differential metabolic biomarkers related to osmotic stress, including homarine, betaine, tyrosine and phenylalanine, suggested the differential responsive mechanisms in clam digestive glands induced by Cd exposures. In addition, both Cd treatments enhanced the anaerobiosis metabolism in clam digestive glands via differential metabolic pathways.
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Affiliation(s)
- Chenglong Ji
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China
| | - Huifeng Wu
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China.
| | - Mo Zhou
- Environment College, Northeast Normal University, Changchun 130024, PR China
| | - Jianmin Zhao
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China
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Evans TG. Considerations for the use of transcriptomics in identifying the ‘genes that matter’ for environmental adaptation. J Exp Biol 2015; 218:1925-35. [DOI: 10.1242/jeb.114306] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT
Transcriptomics has emerged as a powerful approach for exploring physiological responses to the environment. However, like any other experimental approach, transcriptomics has its limitations. Transcriptomics has been criticized as an inappropriate method to identify genes with large impacts on adaptive responses to the environment because: (1) genes with large impacts on fitness are rare; (2) a large change in gene expression does not necessarily equate to a large effect on fitness; and (3) protein activity is most relevant to fitness, and mRNA abundance is an unreliable indicator of protein activity. In this review, these criticisms are re-evaluated in the context of recent systems-level experiments that provide new insight into the relationship between gene expression and fitness during environmental stress. In general, these criticisms remain valid today, and indicate that exclusively using transcriptomics to screen for genes that underlie environmental adaptation will overlook constitutively expressed regulatory genes that play major roles in setting tolerance limits. Standard practices in transcriptomic data analysis pipelines may also be limiting insight by prioritizing highly differentially expressed and conserved genes over those genes that undergo moderate fold-changes and cannot be annotated. While these data certainly do not undermine the continued and widespread use of transcriptomics within environmental physiology, they do highlight the types of research questions for which transcriptomics is best suited and the need for more gene functional analyses. Such information is pertinent at a time when transcriptomics has become increasingly tractable and many researchers may be contemplating integrating transcriptomics into their research programs.
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Peng HF, Bao XD, Zhang Y, Huang L, Huang HQ. Identification of differentially expressed proteins of brain tissue in response to methamidophos in flounder (Paralichthys olivaceus). FISH & SHELLFISH IMMUNOLOGY 2015; 44:555-565. [PMID: 25827626 DOI: 10.1016/j.fsi.2015.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/19/2015] [Accepted: 03/19/2015] [Indexed: 06/04/2023]
Abstract
Methamidophos (MAP), an organophosphorus pesticide used around the world, has been associated with a wide spectrum of toxic effects on organisms in the environment. In this study, the flounder Paralichthys olivaceus was subjected to 10 mg/L MAP for 72 h and 144 h, and the morphological and proteomic changes in the brain were observed, analyzed and compared with those in the non-exposed control group. Under the light microscope and transmission electron microscope, MAP had evidently induced changes in or damage to the flounder tissues. Gas chromatography analysis demonstrated that the MAP residues were significantly accumulated in the flounder brain tissues. Proteomic changes in the brain tissue were revealed using two-dimensional gel electrophoresis and 27 protein spots were observed to be significantly changed by MAP exposure. The results indicated that the regulated proteins were involved in immune and stress responses, protein biosynthesis and modification, signal transduction, organismal development, and 50% of them are protease. qRT-PCR was used to further detect the corresponding change of transcription. These data may be beneficial to understand the molecular mechanism of MAP toxicity in flounder, be very useful for MAP-resistance screening in flounder culture. According to our results and analyzing, heat shock protein 90 (HSP90) and granzyme K (GzmK) had taken important part in immune response to MAP-stress and could be biomarkers for MAP-stress in flounder.
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Affiliation(s)
- Hui-Fang Peng
- State Key Laboratory of Stress Cell Biology, School of Life Science, Xiamen University, Xiamen 361102, China
| | - Xiao-Dong Bao
- State Key Laboratory of Stress Cell Biology, School of Life Science, Xiamen University, Xiamen 361102, China
| | - Yong Zhang
- Department of Chemistry, College of Chemistry & Chemical Engineering, and the Key Laboratory of Chemical Biology of Fujian Province, Xiamen University, Xiamen 361102, China
| | - Lin Huang
- Department of Chemistry, Oregon State University, Corvallis, OR 97331-4003, USA
| | - He-Qing Huang
- State Key Laboratory of Stress Cell Biology, School of Life Science, Xiamen University, Xiamen 361102, China; State Key Laboratory of Marine Environmental Science, School of Ocean and Earth Science, Xiamen University, Xiamen 361102, China; Department of Chemistry, College of Chemistry & Chemical Engineering, and the Key Laboratory of Chemical Biology of Fujian Province, Xiamen University, Xiamen 361102, China.
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Wu H, Cao L, Li F, Lian P, Zhao J. Multiple biomarkers of the cytotoxicity induced by BDE-47 in human embryonic kidney cells. CHEMOSPHERE 2015; 126:32-39. [PMID: 25697951 DOI: 10.1016/j.chemosphere.2015.01.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/23/2015] [Accepted: 01/27/2015] [Indexed: 06/04/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs) are widely used as brominated flame-retardants in a variety of industrial products. Among these PBDEs, 2,2',4,4'-tetra-bromodiphenyl ether (BDE-47) is one of the most predominant congeners inducing multiple toxicities, including hepatotoxicity, neurotoxicity, cytotoxicity, genotoxicity, carcinogenecity and immunotoxicity in human body. In this study, the cytotoxicity of BDE-47 in human embryonic kidney cells (HEK293) was investigated by a set of bioassays, including cell proliferation, apoptosis, oxidative stress and metabolic responses as well as gene expressions related to apoptosis. Results showed that BDE-47 induced an inverted U-shaped curve of cell proliferation in HEK293 cells from 10(-6) to 10(-4) M. Cell apoptosis and ROS overproduction were detected at 10(-5) M of BDE-47 (p<0.05). In addition, the expressions of Bcl-2 family-encoding genes (Bad, Hrk and Bcl-2) increased significantly in 10(-4)M group (p<0.05). Metabolic responses indicated that BDE-47 mainly caused disturbance in energy metabolism marked by differentially altered ethanol, glutathione, creatine, aspartate, UDP-glucose and NAD(+). The increased lactate/alanine ratios indicated the higher reductive state induced by BDE-47 in all exposures confirmed by the overproduction of ROS.
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Affiliation(s)
- Huifeng Wu
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai, Shandong 264003, PR China
| | - Lulu Cao
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai, Shandong 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fei Li
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai, Shandong 264003, PR China.
| | - Peiwen Lian
- Department of Center Laboratory, Yantai Yuhuangding Hospital, Yuhuangdingdong Road 20, Yantai 264000, PR China
| | - Jianmin Zhao
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, Yantai, Shandong 264003, PR China
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Hala D, Petersen LH, Martinović D, Huggett DB. In Silico analysis of perturbed steroidogenesis and gonad growth in fathead minnows (P. promelas) exposed to 17α-ethynylestradiol. Syst Biol Reprod Med 2015; 61:122-38. [PMID: 25910217 DOI: 10.3109/19396368.2015.1035817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The multi-factorial nature of adverse reproductive effects mediated by endocrine disrupting compounds (or EDCs) makes understanding the mechanistic basis of reproductive dysfunction a highly pertinent area of research. As a consequence, a main motivator for continued research is to integrate 'multi-leveled' complexity (i.e., from genes to phenotype) using mathematical methods capable of encapsulating properties of physiological relevance. In this study, an in silico stoichiometric model of piscine steroidogenesis was augmented with a 'biomass' reaction associating the underlying stoichiometry of steroidogenesis with a reaction representative of gonad growth. The ability of the in silico model to predict perturbed steroidogenesis and subsequent effects on gonad growth was tested by exposing reproductively active male and female fathead minnows (Pimephales promelas) to 88 ng/L of the synthetic estrogen, 17α-ethynylestradiol (EE2). The in silico model was parameterized (or constrained) with experimentally quantified concentrations of selected steroid hormones (using mass spectrometry) and fold changes in gene expression (using RT-qPCR) for selected steroidogenic enzyme genes, in gonads of male and female fish. Once constrained, the optimization framework of flux balance analysis (FBA) was used to calculate an optimal flux through the biomass reaction (analogous to gonad growth) and associated steroidogenic flux distributions required to generate biomass. FBA successfully predicted effects of EE2 exposure on fathead minnow gonad growth (%gonadosomatic index or %GSI) and perturbed production of steroid hormones. Specifically, FBA accurately predicted no effects of exposure on male %GSI and a significant reduction for female %GSI. Furthermore, in silico simulations accurately identified disrupted reaction fluxes catalyzing productions of androgens (in male fish) and progestogens (in female fish), an observation which agreed with in vivo experimentation. The analyses presented is the first-ever to successfully associate underlying flux properties of the steroidogenic network with gonad growth in fish, an approach which can incorporate in silico predictions with toxicological risk assessments.
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Affiliation(s)
- David Hala
- Department of Biology, University of North Texas , Denton, TX , USA
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Altenburger R, Ait-Aissa S, Antczak P, Backhaus T, Barceló D, Seiler TB, Brion F, Busch W, Chipman K, de Alda ML, de Aragão Umbuzeiro G, Escher BI, Falciani F, Faust M, Focks A, Hilscherova K, Hollender J, Hollert H, Jäger F, Jahnke A, Kortenkamp A, Krauss M, Lemkine GF, Munthe J, Neumann S, Schymanski EL, Scrimshaw M, Segner H, Slobodnik J, Smedes F, Kughathas S, Teodorovic I, Tindall AJ, Tollefsen KE, Walz KH, Williams TD, Van den Brink PJ, van Gils J, Vrana B, Zhang X, Brack W. Future water quality monitoring--adapting tools to deal with mixtures of pollutants in water resource management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 512-513:540-551. [PMID: 25644849 DOI: 10.1016/j.scitotenv.2014.12.057] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/18/2014] [Accepted: 12/18/2014] [Indexed: 05/18/2023]
Abstract
Environmental quality monitoring of water resources is challenged with providing the basis for safeguarding the environment against adverse biological effects of anthropogenic chemical contamination from diffuse and point sources. While current regulatory efforts focus on monitoring and assessing a few legacy chemicals, many more anthropogenic chemicals can be detected simultaneously in our aquatic resources. However, exposure to chemical mixtures does not necessarily translate into adverse biological effects nor clearly shows whether mitigation measures are needed. Thus, the question which mixtures are present and which have associated combined effects becomes central for defining adequate monitoring and assessment strategies. Here we describe the vision of the international, EU-funded project SOLUTIONS, where three routes are explored to link the occurrence of chemical mixtures at specific sites to the assessment of adverse biological combination effects. First of all, multi-residue target and non-target screening techniques covering a broader range of anticipated chemicals co-occurring in the environment are being developed. By improving sensitivity and detection limits for known bioactive compounds of concern, new analytical chemistry data for multiple components can be obtained and used to characterise priority mixtures. This information on chemical occurrence will be used to predict mixture toxicity and to derive combined effect estimates suitable for advancing environmental quality standards. Secondly, bioanalytical tools will be explored to provide aggregate bioactivity measures integrating all components that produce common (adverse) outcomes even for mixtures of varying compositions. The ambition is to provide comprehensive arrays of effect-based tools and trait-based field observations that link multiple chemical exposures to various environmental protection goals more directly and to provide improved in situ observations for impact assessment of mixtures. Thirdly, effect-directed analysis (EDA) will be applied to identify major drivers of mixture toxicity. Refinements of EDA include the use of statistical approaches with monitoring information for guidance of experimental EDA studies. These three approaches will be explored using case studies at the Danube and Rhine river basins as well as rivers of the Iberian Peninsula. The synthesis of findings will be organised to provide guidance for future solution-oriented environmental monitoring and explore more systematic ways to assess mixture exposures and combination effects in future water quality monitoring.
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Affiliation(s)
- Rolf Altenburger
- UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany; RWTH Aachen University, Aachen, Germany
| | - Selim Ait-Aissa
- Institut National de l'Environnement Industriel et des Risques INERIS, BP2, 60550 Verneuil-en-Halatte, France
| | - Philipp Antczak
- Centre for Computational Biology and Modelling, University of Liverpool, L69 7ZB, UK
| | - Thomas Backhaus
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottbergs Gata 22b, 40530 Gothenburg, Sweden
| | - Damià Barceló
- Water and Soil Quality Research Group, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | | | - Francois Brion
- Institut National de l'Environnement Industriel et des Risques INERIS, BP2, 60550 Verneuil-en-Halatte, France
| | - Wibke Busch
- UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
| | - Kevin Chipman
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK
| | - Miren López de Alda
- Water and Soil Quality Research Group, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | | | - Beate I Escher
- National Research Centre for Environmental Toxicology (Entox), The University of Queensland, Brisbane, Australia; UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
| | - Francesco Falciani
- Centre for Computational Biology and Modelling, University of Liverpool, L69 7ZB, UK
| | - Michael Faust
- Faust & Backhaus Environmental Consulting, Fahrenheitstr. 1, 28359 Bremen, Germany
| | - Andreas Focks
- Alterra, Wageningen University and Research Centre, P.O. Box 47, 6700 AA Wageningen, The Netherlands
| | - Klara Hilscherova
- Masaryk University, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Juliane Hollender
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | | | - Felix Jäger
- Synchem UG & Co. KG, Am Kies 2, 34587 Felsberg-Altenburg, Germany
| | - Annika Jahnke
- UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
| | - Andreas Kortenkamp
- Brunel University, Institute of Environment, Health and Societies, Uxbridge UB8 3PH, United Kingdom
| | - Martin Krauss
- UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
| | - Gregory F Lemkine
- WatchFrog, Bâtiment Genavenir 3, 1 rue Pierre Fontaine, 91000 Evry, France
| | - John Munthe
- IVL Swedish Environmental Research Institute, P.O. Box 53021, 400 14 Göteborg, Sweden
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Emma L Schymanski
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Mark Scrimshaw
- Brunel University, Institute of Environment, Health and Societies, Uxbridge UB8 3PH, United Kingdom
| | - Helmut Segner
- University of Bern, Centre for Fish and Wildlife Health, PO Box 8466, CH-3001 Bern, Switzerland
| | | | - Foppe Smedes
- Masaryk University, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Subramaniam Kughathas
- Brunel University, Institute of Environment, Health and Societies, Uxbridge UB8 3PH, United Kingdom
| | - Ivana Teodorovic
- University of Novi Sad, Faculty of Sciences¸ Trg Dositeja Obradovića, 321000 Novi Sad, Serbia
| | - Andrew J Tindall
- WatchFrog, Bâtiment Genavenir 3, 1 rue Pierre Fontaine, 91000 Evry, France
| | - Knut Erik Tollefsen
- Norwegian Institute for Water Research NIVA, Gaustadalléen 21, N-0349 Oslo, Norway
| | - Karl-Heinz Walz
- MAXX Mess- und Probenahmetechnik GmbH, Hechinger Straße 41, D-72414 Rangendingen, Germany
| | - Tim D Williams
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK
| | - Paul J Van den Brink
- Alterra, Wageningen University and Research Centre, P.O. Box 47, 6700 AA Wageningen, The Netherlands
| | - Jos van Gils
- Foundation Deltares, Potbus 177, 277 MH Delft, The Netherlands
| | - Branislav Vrana
- Masaryk University, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Collaborative Innovation Center for Regional Environmental Quality, Nanjing University, Nanjing 210023, PR China
| | - Werner Brack
- UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
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Ji C, Cao L, Li F. Toxicological evaluation of two pedigrees of clam Ruditapes philippinarum as bioindicators of heavy metal contaminants using metabolomics. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2015; 39:545-554. [PMID: 25681705 DOI: 10.1016/j.etap.2015.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 01/05/2015] [Accepted: 01/10/2015] [Indexed: 06/04/2023]
Abstract
Heavy metal pollution has been of great concern in the Bohai marine environment. Manila clam Ruditapes philippinarum has been used as a bioindicator in marine toxicology. In this study, NMR-based metabolomics was used to ascertain whether there were significant biological differences between two dominant pedigrees (White and Zebra) of clam and evaluate the suitability of two pedigrees for marine environmental toxicology, together with antioxidant enzymatic analysis. Our results indicated that there were significant biological differences between White and Zebra clams based on the metabolic profiles and antioxidant enzyme activities. In details, the metabolic profiles showed higher levels of amino acids and succinate in Zebra clam digestive glands and higher levels of ATP in White clam digestive glands, respectively. The superoxide dismutase activities in control White and Zebra clam samples were significantly different. Additionally, White clam was more sensitive to Cd based on the significant accumulation of Cd, antioxidant enzymatic alterations and sensitive metabolic changes. Overall, we concluded that White clam could be a preferable bioindicator for marine environmental toxicology.
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Affiliation(s)
- Chenglong Ji
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China
| | - Lulu Cao
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fei Li
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China.
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McElroy AE, Hice LA, Frisk MG, Purcell SL, Phillips NC, Fast MD. Spatial patterns in markers of contaminant exposure, glucose and glycogen metabolism, and immunological response in juvenile winter flounder (Pseudoplueronectes americanus). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2015; 14:53-65. [PMID: 25946204 DOI: 10.1016/j.cbd.2015.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 01/16/2015] [Accepted: 01/26/2015] [Indexed: 12/13/2022]
Abstract
Inshore winter flounder (Pseudoplueronectes americanus) populations in NY, USA have reached record low numbers in recent years, and recruitment into the fishery appears to be limited by survival of post-settlement juvenile fish. In order to identify cellular pathways associated with site-specific variation in condition and mortality, we examined differential mRNA expression in juvenile winter flounder collected from six different bays across a gradient in human population density and sewage inputs. Illumina sequencing of pooled samples of flounder from contrasting degraded sites and less impacted sites was used to guide our choice of targets for qPCR analysis. 253 transcripts of >100bp were differentially expressed, with 60% showing strong homology to mostly teleost sequences within the NCBI database. Based on these data, transcripts representing nine genes of interest associated with contaminant exposure, immune response and glucose and glycogen metabolism were examined by qPCR in individual flounder from each site. Statistically significant site-specific differences were observed in expression of all but one gene, although patterns in expression were complex with only one (vitellogenin), demonstrating a west to east gradient consistent with known loadings of municipal sewage effluent. Principal components analysis (PCA) identified relationships among the genes evaluated. Our data indicate that juvenile winter flounder are responding to estrogenic chemicals in more urbanized coastal bays, and suggests potential mechanistic links between immune response, contaminant exposure and energy metabolism.
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Affiliation(s)
- A E McElroy
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA.
| | - L A Hice
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - M G Frisk
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - S L Purcell
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - N C Phillips
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - M D Fast
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA; Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
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Harris RM, Williams TD, Waring RH, Hodges NJ. Molecular basis of carcinogenicity of tungsten alloy particles. Toxicol Appl Pharmacol 2015; 283:223-33. [PMID: 25620057 DOI: 10.1016/j.taap.2015.01.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/10/2015] [Accepted: 01/13/2015] [Indexed: 11/18/2022]
Abstract
The tungsten alloy of 91% tungsten, 6% nickel and 3% cobalt (WNC 91-6-3) induces rhabdomyosarcoma when implanted into a rat thigh muscle. To investigate whether this effect is species-specific human HSkMc primary muscle cells were exposed to WNC 91-6-3 particles and responses were compared with those from a rat skeletal muscle cell line (L6-C11). Toxicity was assessed by the adenylate kinase assay and microscopy, DNA damage by the Comet assay. Caspase 3 enzyme activity was measured and oligonucleotide microarrays were used for transcriptional profiling. WNC 91-6-3 particles caused toxicity in cells adjacent to the particles and also increased DNA strand breaks. Inhibition of caspase 3 by WNC 91-6-3 occurred in rat but not in human cells. In both rat and human cells, the transcriptional response to WNC 91-6-3 showed repression of transcripts encoding muscle-specific proteins with induction of glycolysis, hypoxia, stress responses and transcripts associated with DNA damage and cell death. In human cells, genes encoding metallothioneins were also induced, together with genes related to angiogenesis, dysregulation of apoptosis and proliferation consistent with pre-neoplastic changes. An alloy containing iron, WNF 97-2-1, which is non-carcinogenic in vivo in rats, did not show these transcriptional changes in vitro in either species while the corresponding cobalt-containing alloy, WNC 97-2-1 elicited similar responses to WNC 91-6-3. Tungsten alloys containing both nickel and cobalt therefore have the potential to be carcinogenic in man and in vitro assays coupled with transcriptomics can be used to identify alloys, which may lead to tumour formation, by dysregulation of biochemical processes.
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Affiliation(s)
- Robert M Harris
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Tim D Williams
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Rosemary H Waring
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Nikolas J Hodges
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Brack W, Altenburger R, Schüürmann G, Krauss M, López Herráez D, van Gils J, Slobodnik J, Munthe J, Gawlik BM, van Wezel A, Schriks M, Hollender J, Tollefsen KE, Mekenyan O, Dimitrov S, Bunke D, Cousins I, Posthuma L, van den Brink PJ, López de Alda M, Barceló D, Faust M, Kortenkamp A, Scrimshaw M, Ignatova S, Engelen G, Massmann G, Lemkine G, Teodorovic I, Walz KH, Dulio V, Jonker MTO, Jäger F, Chipman K, Falciani F, Liska I, Rooke D, Zhang X, Hollert H, Vrana B, Hilscherova K, Kramer K, Neumann S, Hammerbacher R, Backhaus T, Mack J, Segner H, Escher B, de Aragão Umbuzeiro G. The SOLUTIONS project: challenges and responses for present and future emerging pollutants in land and water resources management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 503-504:22-31. [PMID: 24951181 DOI: 10.1016/j.scitotenv.2014.05.143] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/09/2014] [Accepted: 05/27/2014] [Indexed: 05/07/2023]
Abstract
SOLUTIONS (2013 to 2018) is a European Union Seventh Framework Programme Project (EU-FP7). The project aims to deliver a conceptual framework to support the evidence-based development of environmental policies with regard to water quality. SOLUTIONS will develop the tools for the identification, prioritisation and assessment of those water contaminants that may pose a risk to ecosystems and human health. To this end, a new generation of chemical and effect-based monitoring tools is developed and integrated with a full set of exposure, effect and risk assessment models. SOLUTIONS attempts to address legacy, present and future contamination by integrating monitoring and modelling based approaches with scenarios on future developments in society, economy and technology and thus in contamination. The project follows a solutions-oriented approach by addressing major problems of water and chemicals management and by assessing abatement options. SOLUTIONS takes advantage of the access to the infrastructure necessary to investigate the large basins of the Danube and Rhine as well as relevant Mediterranean basins as case studies, and puts major efforts on stakeholder dialogue and support. Particularly, the EU Water Framework Directive (WFD) Common Implementation Strategy (CIS) working groups, International River Commissions, and water works associations are directly supported with consistent guidance for the early detection, identification, prioritisation, and abatement of chemicals in the water cycle. SOLUTIONS will give a specific emphasis on concepts and tools for the impact and risk assessment of complex mixtures of emerging pollutants, their metabolites and transformation products. Analytical and effect-based screening tools will be applied together with ecological assessment tools for the identification of toxicants and their impacts. The SOLUTIONS approach is expected to provide transparent and evidence-based candidates or River Basin Specific Pollutants in the case study basins and to assist future review of priority pollutants under the WFD as well as potential abatement options.
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Affiliation(s)
- Werner Brack
- Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany.
| | - Rolf Altenburger
- Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany
| | | | - Martin Krauss
- Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany
| | | | | | | | - John Munthe
- IVL Swedish Environmental Research Institute, Gothenburg, Sweden
| | - Bernd Manfred Gawlik
- Institute for Environment and Sustainability - IES - of the European Commission's Joint Research Centre JRC, Ispra, Italy
| | | | - Merijn Schriks
- KWR Watercycle Research Institute, Nieuwegein, The Netherlands
| | - Juliane Hollender
- Swiss Federal Institute of Aquatic Science and Technology Eawag, Dübendorf, Switzerland
| | | | - Ovanes Mekenyan
- Laboratory of Mathematical Chemistry - Asen Zlatarov University, Bourgas, Bulgaria
| | - Saby Dimitrov
- Laboratory of Mathematical Chemistry - Asen Zlatarov University, Bourgas, Bulgaria
| | - Dirk Bunke
- Oeko-Institut e.V. - Institute for Applied Ecology, Freiburg, Germany
| | | | - Leo Posthuma
- National Institute for Public Health and the Environment RIVM, Bilthoven, The Netherlands
| | | | - Miren López de Alda
- Agencia Estatal Consejo Superior de Investigaciones Científicas CSIC, Barcelona, Spain
| | - Damià Barceló
- Agencia Estatal Consejo Superior de Investigaciones Científicas CSIC, Barcelona, Spain
| | - Michael Faust
- Faust & Backhaus Environmental Consulting, Bremen, Germany
| | - Andreas Kortenkamp
- Brunel University, Institute for the Environment, London, United Kingdom
| | - Mark Scrimshaw
- Brunel University, Institute for the Environment, London, United Kingdom
| | - Svetlana Ignatova
- Brunel University, Institute for Bioengineering, London, United Kingdom
| | - Guy Engelen
- Flemish Institute for Technological Research VITO, Mol, Belgium
| | | | | | | | | | - Valeria Dulio
- Institut National de l'Environnement Industriel et des Risques INERIS, Verneuil-en-Halatte, France
| | | | - Felix Jäger
- Synchem UG & Co. KG, Felsberg/Altenburg, Germany
| | - Kevin Chipman
- University of Birmingham, Birmingham, United Kingdom
| | | | - Igor Liska
- International Commission for the Protection of the Danube River ICPDR, Vienna, Austria
| | | | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, PR China
| | | | - Branislav Vrana
- Masaryk University - Research Centre for Toxic Compounds in the Environment (RECETOX), Brno, Czech Republic
| | - Klara Hilscherova
- Masaryk University - Research Centre for Toxic Compounds in the Environment (RECETOX), Brno, Czech Republic
| | | | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | | | | | | | | | - Beate Escher
- The University of Queensland, National Research Centre for Environmental Toxicology (Entox), Brisbane, Australia; Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany
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Ji C, Wang Q, Wu H, Tan Q, Wang WX. A metabolomic investigation of the effects of metal pollution in oysters Crassostrea hongkongensis. MARINE POLLUTION BULLETIN 2015; 90:317-322. [PMID: 25499180 DOI: 10.1016/j.marpolbul.2014.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 11/04/2014] [Accepted: 11/08/2014] [Indexed: 06/04/2023]
Abstract
Metal pollution has been of great concern in the estuaries in Southern China. In this study, metabolic differences between oysters Crassostrea hongkongensis from clean and metal-polluted sites were characterized using NMR-based metabolomics. We collected oyster samples from one clean (Jiuzhen) and two metal polluted sites (Baijiao and Fugong). The metal concentrations in oyster gills indicated that both the Baijiao and Fugong sites were severely polluted by several metals, including Cr, Ni, Cu, Zn, Ag, Cd and Pb. In particular, Cu and Zn were the major contaminants from the Baijiao and Fugong sites. Compared with those oysters from the clean site (JZ), metal pollution in BJ and FG induced disturbances in osmotic regulation and energy metabolism via different metabolic pathways, as indicated by different metabolic biomarkers. This study demonstrates that NMR-based metabolomics is a useful tool for characterizing metabolic responses induced by metal pollution.
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Affiliation(s)
- Chenglong Ji
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China
| | - Qing Wang
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China
| | - Huifeng Wu
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China.
| | - Qiaoguo Tan
- Key Laboratory of the Coastal and Wetland Ecosystems, Ministry of Education, College of Environment and Ecology, Xiamen University, Xiamen 361102, PR China
| | - Wen-Xiong Wang
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Clearwater Bay, Kowloon, Hong Kong
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40
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Liu S, Wang W, Zhou X, Ding Z, Gu R. A 2-DE-based proteomic study on the toxicological effects of cisplatin in L02 cells. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2015; 39:167-175. [PMID: 25528407 DOI: 10.1016/j.etap.2014.11.018] [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: 08/08/2014] [Revised: 11/21/2014] [Accepted: 11/26/2014] [Indexed: 06/04/2023]
Abstract
Cisplatin is a chemotherapeutic agent for the treatment of various cancers. In this study, cisplatin-induced effects were characterized in vitro model of human liver cells (L02) using 2-DE-based proteomics. Results indicated that different cisplatin treatments primarily induced disturbances in protein synthesis and oxidative stress via differential mechanisms. Since the experimental concentrations of cisplatin described a hormesis effect in cell proliferation of L02 cells, it was expected to reveal the hormesis effects using proteomic markers. However, only confilin-1 was commonly up-regulated in three concentrations of cisplatin treatments showing a hormesis effects with a U-shape regulation. These results were highly consistent with many other toxico-proteomic studies, indicating that the toxico-proteomic responses based on dose-dependent protein responses were incongruent with the theoretically linear or hormetic concentration-effect relationship. Our findings suggested that a macroscopic hormesis phenomenon on the cell proliferation could not be reflected by proteomic responses induced by cisplatin treatments.
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Affiliation(s)
- Shu Liu
- The 2nd People's Hospital of Huaian, No. 62, Huaihainan Road, Huaian 223002, PR China
| | - Wei Wang
- The 2nd People's Hospital of Huaian, No. 62, Huaihainan Road, Huaian 223002, PR China.
| | - Xueyi Zhou
- The 2nd People's Hospital of Huaian, No. 62, Huaihainan Road, Huaian 223002, PR China
| | - Zongli Ding
- The 2nd People's Hospital of Huaian, No. 62, Huaihainan Road, Huaian 223002, PR China
| | - Runhuan Gu
- The 2nd People's Hospital of Huaian, No. 62, Huaihainan Road, Huaian 223002, PR China
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41
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Porreca I, D'Angelo F, Gentilcore D, Carchia E, Amoresano A, Affuso A, Ceccarelli M, De Luca P, Esposito L, Guadagno FM, Mallardo M, Nardone A, Maccarone S, Pane F, Scarfò M, Sordino P, De Felice M, Ambrosino C. Cross-species toxicogenomic analyses and phenotypic anchoring in response to groundwater low-level pollution. BMC Genomics 2014; 15:1067. [PMID: 25475078 PMCID: PMC4301944 DOI: 10.1186/1471-2164-15-1067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 11/24/2014] [Indexed: 01/02/2023] Open
Abstract
Background Comparison of toxicogenomic data facilitates the identification of deregulated gene patterns and maximizes health risk prediction in human. Results Here, we performed phenotypic anchoring on the effects of acute exposure to low-grade polluted groundwater using mouse and zebrafish. Also, we evaluated two windows of chronic exposure in mouse, starting in utero and at the end of lactation. Bioinformatic analysis of livers microarray data showed that the number of deregulated biofunctions and pathways is higher after acute exposure, compared to the chronic one. It also revealed specific profiles of altered gene expression in all treatments, pointing to stress response/mitochondrial pathways as major players of environmental toxicity. Of note, dysfunction of steroid hormones was also predicted by bioinformatic analysis and verified in both models by traditional approaches, serum estrogens measurement and vitellogenin mRNA determination in mice and zebrafish, respectively. Conclusions In our report, phenotypic anchoring in two vertebrate model organisms highlights the toxicity of low-grade pollution, with varying susceptibility based on exposure window. The overlay of zebrafish and mice deregulated pathways, more than single genes, is useful in risk identification from chemicals implicated in the observed effects. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1067) contains supplementary material, which is available to authorized users.
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42
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Kanerva M, Vehmas A, Nikinmaa M, Vuori KA. Spatial variation in transcript and protein abundance of Atlantic salmon during feeding migration in the Baltic Sea. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:13969-13977. [PMID: 25356801 DOI: 10.1021/es502956g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The fitness and reproductive output of fishes can be affected by environmental disturbances. In this study, transcriptomics and label-free proteomics were combined to investigate Atlantic salmon (Salmo salar) sampled from three different field locations within the Baltic Sea (Baltic Main Basin (BMB), Gulf of Finland (GoF), and Bothnian Sea (BS)) during marine migration. The expression of several stress related mRNAs and proteins of xenobiotic metabolism, oxidative stress, DNA damage, and cell death were increased in salmon from GoF compared to salmon from BMB or BS. Respiratory electron chain and ATP synthesis related gene ontology-categories were upregulated in GoF salmon, whereas those associated with RNA processing and synthesis, translation, and protein folding decreased. Differences were seen also in metabolism and immune function related gene expression. Comparisons of the transcriptomic and proteomic profiles between salmon from GoF and salmon from BMB or BS suggest environmental stressors, especially exposure to contaminants, as a main explanation for differences. Salmon feeding in GoF are thus “disturbed by hazardous substances”. The results may also be applied in evaluating the conditions of pelagic ecosystems in the different parts of Baltic Sea.
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Affiliation(s)
- Mirella Kanerva
- Laboratory of Animal Physiology, Department of Biology, University of Turku, Turku FI-20014, Finland.
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43
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Dupuy C, Galland C, Devaux A, Bony S, Loizeau V, Danion M, Pichereau V, Fournier M, Laroche J. Responses of the European flounder (Platichthys flesus) to a mixture of PAHs and PCBs in experimental conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:13789-13803. [PMID: 24504773 DOI: 10.1007/s11356-014-2563-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 01/16/2014] [Indexed: 06/03/2023]
Abstract
A multibiomarker approach was developed to evaluate the juvenile European flounder responses to a complex mixture of 9 polycyclic aromatic hydrocarbons (PAHs) and 12 polychlorinated biphenyls (PCBs). Exposure was performed through contaminated food pellets displaying: (1) PAH and PCB levels similar to those detected in the heavily polluted Seine estuary, respectively in sediments and in flatfish and (2) ten times these concentrations. Several biomarkers of the immune system (e.g., lysozyme concentration and gene expression of complement component C3 and TNF-receptor), DNA damage (e.g., Comet assay), energetic metabolism (e.g., activity of cytochrome C oxidase), detoxification process (e.g., cytochrome P450 1A1 expression level: CYP1A1; betaine homocysteine methyl transferase expression level: BHMT) were investigated after 14 and 29 days of contamination, followed by a 14-days recovery period. After 29 days of contamination, the detoxification activity (CYP1A1 expression level) was positively correlated with DNA damages; the increase of the BHMT expression level could also be related to the detoxification process. Furthermore, after the recovery period, some biomarkers were still upregulated (i.e., CYP1A1 and BHMT expression levels). The immune system was significantly modulated by the chemical stress at the two concentration levels, and the lysozyme appeared to be the most sensitive marker of the mixture impact.
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Affiliation(s)
- Célie Dupuy
- UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des Sciences de l'Environnement Marin LEMAR, Institut Universitaire Européen de la Mer, Université Européenne de Bretagne, Université de Bretagne occidentale, Plouzané, 29280, France,
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44
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Liu X, Sun H, Wang Y, Ma M, Zhang Y. Gender-specific metabolic responses in hepatopancreas of mussel Mytilus galloprovincialis challenged by Vibrio harveyi. FISH & SHELLFISH IMMUNOLOGY 2014; 40:407-413. [PMID: 25123832 DOI: 10.1016/j.fsi.2014.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 07/28/2014] [Accepted: 08/03/2014] [Indexed: 06/03/2023]
Abstract
Mussel Mytilus galloprovincialis is a marine aquaculture shellfish and frequently studied in shellfish immunology. In this work, the gender-specific metabolic responses induced by Vibrio harveyi in hepatopancreas from M. galloprovincialis were characterized using NMR-based metabolomics. In details, V. harveyi challenge increased the levels of amino acids including (valine, leucine, isoleucine, threonine, alanine, arginine and tyrosine) and ATP, and decreased the level of glucose in male mussel hepatopancreas. In V. harveyi-challenged female mussel hepatopancreas, both threonine and AMP were significantly elevated, and choline, phoshphocholine, sn-glycero-3-phosphocholine, taurine, betaine and ATP were depleted. Obviously, only threonine was similarly altered to that in V. harveyi-challenged male mussel hepatopancreas. These findings confirmed the gender-specific metabolic responses in mussels challenged by V. harveyi. Overall, V. harveyi induced an enhanced energy demand through activated glycolysis and immune response indicated by increased BCAAs in male mussel hepatopancreas. In female mussel hepatopancreas, V. harveyi basically caused disturbances in both osmotic regulation and energy metabolism through the metabolic pathways of conversions of phosphocholine and ADP to choline and ATP, and sn-glycero-3-phosphocholine and H2O into choline and sn-glycerol 3-phosphate. The altered mRNA expression levels of related genes (Cu/Zn-SOD, HSP90, lysozyme and defensin) suggested that V. harveyi induced obvious oxidative and immune stresses in both male and female mussel hepatopancreas. This work demonstrated that V. harveyi could induce gender-specific metabolic responses in mussel M. galloprovincialis hepatopancreas using NMR-based metabolomics.
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Affiliation(s)
- Xiaoli Liu
- School of Life Sciences, Ludong University, Yantai 264025, PR China.
| | - Hushan Sun
- School of Life Sciences, Ludong University, Yantai 264025, PR China
| | - Yiyan Wang
- School of Life Sciences, Ludong University, Yantai 264025, PR China
| | - Mengwen Ma
- School of Life Sciences, Ludong University, Yantai 264025, PR China
| | - Yuemei Zhang
- School of Life Sciences, Ludong University, Yantai 264025, PR China
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45
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Taffi M, Paoletti N, Angione C, Pucciarelli S, Marini M, Liò P. Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis. Front Genet 2014; 5:319. [PMID: 25309577 PMCID: PMC4162388 DOI: 10.3389/fgene.2014.00319] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/26/2014] [Indexed: 11/13/2022] Open
Abstract
The pressure to search effective bioremediation methodologies for contaminated ecosystems has led to the large-scale identification of microbial species and metabolic degradation pathways. However, minor attention has been paid to the study of bioremediation in marine food webs and to the definition of integrated strategies for reducing bioaccumulation in species. We propose a novel computational framework for analysing the multiscale effects of bioremediation at the ecosystem level, based on coupling food web bioaccumulation models and metabolic models of degrading bacteria. The combination of techniques from synthetic biology and ecological network analysis allows the specification of arbitrary scenarios of contaminant removal and the evaluation of strategies based on natural or synthetic microbial strains. In this study, we derive a bioaccumulation model of polychlorinated biphenyls (PCBs) in the Adriatic food web, and we extend a metabolic reconstruction of Pseudomonas putida KT2440 (iJN746) with the aerobic pathway of PCBs degradation. We assess the effectiveness of different bioremediation scenarios in reducing PCBs concentration in species and we study indices of species centrality to measure their importance in the contaminant diffusion via feeding links. The analysis of the Adriatic sea case study suggests that our framework could represent a practical tool in the design of effective remediation strategies, providing at the same time insights into the ecological role of microbial communities within food webs.
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Affiliation(s)
- Marianna Taffi
- Department of Biosciences and Biotechnology, University of CamerinoCamerino, Italy
| | - Nicola Paoletti
- Department of Computer Science, University of OxfordOxford, UK
| | | | - Sandra Pucciarelli
- Department of Biosciences and Biotechnology, University of CamerinoCamerino, Italy
| | - Mauro Marini
- National Research Council (CNR), Institute of Marine Sciences (ISMAR)Ancona, Italy
| | - Pietro Liò
- Computer Laboratory, University of CambridgeCambridge, UK
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46
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Williams TD, Davies IM, Wu H, Diab AM, Webster L, Viant MR, Chipman JK, Leaver MJ, George SG, Moffat CF, Robinson CD. Molecular responses of European flounder (Platichthys flesus) chronically exposed to contaminated estuarine sediments. CHEMOSPHERE 2014; 108:152-158. [PMID: 24534155 DOI: 10.1016/j.chemosphere.2014.01.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 01/13/2014] [Accepted: 01/25/2014] [Indexed: 06/03/2023]
Abstract
Molecular responses to acute toxicant exposure can be effective biomarkers, however responses to chronic exposure are less well characterised. The aim of this study was to determine chronic molecular responses to environmental mixtures in a controlled laboratory setting, free from the additional variability encountered with environmental sampling of wild organisms. Flounder fish were exposed in mesocosms for seven months to a contaminated estuarine sediment made by mixing material from the Forth (high organics) and Tyne (high metals and tributyltin) estuaries (FT) or a reference sediment from the Ythan estuary (Y). Chemical analyses demonstrated that FT sediment contained significantly higher concentrations of key environmental pollutants (including polycyclic aromatic hydrocarbons (PAHs), chlorinated biphenyls and heavy metals) than Y sediment, but that chronically exposed flounder showed a lack of differential accumulation of contaminants, including heavy metals. Biliary 1-hydroxypyrene concentration and erythrocyte DNA damage increased in FT-exposed fish. Transcriptomic and (1)H NMR metabolomic analyses of liver tissues detected small but statistically significant alterations between fish exposed to different sediments. These highlighted perturbance of immune response and apoptotic pathways, but there was a lack of response from traditional biomarker genes. Gene-chemical association annotation enrichment analyses suggested that polycyclic aromatic hydrocarbons were a major class of toxicants affecting the molecular responses of the exposed fish. This demonstrated that molecular responses of sentinel organisms can be detected after chronic mixed toxicant exposure and that these can be informative of key components of the mixture.
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Affiliation(s)
- Tim D Williams
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Ian M Davies
- Marine Scotland Science, Marine Laboratory, 375 Victoria Rd., Aberdeen AB11 9DB, UK
| | - Huifeng Wu
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Amer M Diab
- Institute of Aquaculture, The University of Stirling, Stirling FK9 4LA, UK
| | - Lynda Webster
- Marine Scotland Science, Marine Laboratory, 375 Victoria Rd., Aberdeen AB11 9DB, UK
| | - Mark R Viant
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - J Kevin Chipman
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Michael J Leaver
- Institute of Aquaculture, The University of Stirling, Stirling FK9 4LA, UK
| | - Stephen G George
- Institute of Aquaculture, The University of Stirling, Stirling FK9 4LA, UK
| | - Colin F Moffat
- Marine Scotland Science, Marine Laboratory, 375 Victoria Rd., Aberdeen AB11 9DB, UK
| | - Craig D Robinson
- Marine Scotland Science, Marine Laboratory, 375 Victoria Rd., Aberdeen AB11 9DB, UK
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47
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Liu X, Ji C, Zhao J, Wang Q, Li F, Wu H. Metabolic profiling of the tissue-specific responses in mussel Mytilus galloprovincialis towards Vibrio harveyi challenge. FISH & SHELLFISH IMMUNOLOGY 2014; 39:372-377. [PMID: 24911264 DOI: 10.1016/j.fsi.2014.05.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 04/07/2014] [Accepted: 05/27/2014] [Indexed: 06/03/2023]
Abstract
Mussel Mytilus galloprovincialis is a marine aquaculture shellfish distributing widely along the coast in north China. In this work, we studied the differential metabolic responses induced by Vibrio harveyi in digestive gland and gill tissues from M. galloprovincialis using NMR-based metabolomics. The differential metabolic responses in the two tissue types were detected, except the similarly altered taurine and betaine. These metabolic responses suggested that V. harveyi mainly induced osmotic disruption and reduced energy demand via the metabolic pathways of glucose synthesis and ATP/AMP conversion in mussel digestive gland. In mussel gill tissues, V. harveyi basically caused osmotic stress and possible reduced energy demand as shown by the elevated phosphocholine that is involved in one of the metabolic pathways of ATP synthesis from ADP and phosphocholine. The altered mRNA expression levels of related genes (superoxide dismutase with copper and zinc, heat shock protein 90, defensin and lysozyme) suggested that V. harveyi induced clear oxidative and immune stresses in both digestive gland and gill tissues. However, the mRNA expression levels of both lysozyme and defensin in digestive gland were more significantly up-regulated than those in gill from V. harveyi-challenged mussel M. galloprovincialis, meaning that the immune organ, digestive gland, was more sensitive than gill. Overall, our results indicated that V. harveyi could induce tissue-specific metabolic responses in mussel M. galloprovincialis.
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Affiliation(s)
- Xiaoli Liu
- School of Life Sciences, Ludong University, Yantai 264025, PR China.
| | - Chenglong Ji
- Laboratory of Coastal Ecotoxicology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China
| | - Jianmin Zhao
- Laboratory of Coastal Ecotoxicology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China
| | - Qing Wang
- Laboratory of Coastal Ecotoxicology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China
| | - Fei Li
- Laboratory of Coastal Ecotoxicology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China
| | - Huifeng Wu
- Laboratory of Coastal Ecotoxicology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, PR China
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48
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Roede JR, Uppal K, Park Y, Tran V, Jones DP. Transcriptome-metabolome wide association study (TMWAS) of maneb and paraquat neurotoxicity reveals network level interactions in toxicologic mechanism. Toxicol Rep 2014; 1:435-444. [PMID: 27722094 PMCID: PMC5053767 DOI: 10.1016/j.toxrep.2014.07.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A combination of the herbicide paraquat (PQ) and fungicide maneb (MB) has been linked to Parkinson's disease. Previous studies show that this involves an additive toxicity with at least two different mechanisms. However, detailed understanding of mixtures is often difficult to elucidate because of the multiple ways by which toxic agents can interact. In the present study, we used a combination of transcriptomics and metabolomics to investigate mechanisms of toxicity of PQ and MB in a neuroblastoma cell line. Conditions were studied with concentrations of PQ and MB that each individually caused 20% cell death and together caused 50% cell death. Transcriptomic and metabolomic samples were collected at time points prior to significant cell death. Statistical and bioinformatic methods were applied to the resulting 30,869 transcripts and 1358 metabolites. Results showed that MB significantly changed more transcripts and metabolites than PQ, and combined PQ + MB impacted more than MB alone. Transcriptome-metabolome-wide association study (TMWAS) showed that significantly changed transcripts and metabolites mapped to two network substructures, one associating with significant effects of MB and the other included features significantly associated with PQ + MB. The latter contained 4 clusters of genes and associated metabolites, with one containing genes for two cation transporters and a cation transporter regulatory protein also recognized as a pro-apoptotic protein. Other clusters included stress response genes and transporters linked to cytoprotective mechanisms. MB also had a significant network structure linked to cell proliferation. Together, the results show that the toxicologic mechanism of the combined neurotoxicity of PQ and MB involves network level interactions and that TMWAS provides an effective approach to investigate such complex mechanisms.
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Affiliation(s)
- James R Roede
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, United States
| | - Karan Uppal
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, United States; Clinical Biomarkers Laboratory, Emory University, Atlanta, GA 30322, United States; School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Youngja Park
- College of Pharmacy, Korea University, Sejong City, Republic of Korea
| | - ViLinh Tran
- Clinical Biomarkers Laboratory, Emory University, Atlanta, GA 30322, United States
| | - Dean P Jones
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, United States; Clinical Biomarkers Laboratory, Emory University, Atlanta, GA 30322, United States
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49
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Garcia-Reyero N, Tingaud-Sequeira A, Cao M, Zhu Z, Perkins EJ, Hu W. Endocrinology: advances through omics and related technologies. Gen Comp Endocrinol 2014; 203:262-73. [PMID: 24726988 DOI: 10.1016/j.ygcen.2014.03.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/20/2014] [Accepted: 03/22/2014] [Indexed: 12/27/2022]
Abstract
The rapid development of new omics technologies to measure changes at genetic, transcriptomic, proteomic, and metabolomics levels together with the evolution of methods to analyze and integrate the data at a systems level are revolutionizing the study of biological processes. Here we discuss how new approaches using omics technologies have expanded our knowledge especially in nontraditional models. Our increasing knowledge of these interactions and evolutionary pathway conservation facilitates the use of nontraditional species, both invertebrate and vertebrate, as new model species for biological and endocrinology research. The increasing availability of technology to create organisms overexpressing key genes in endocrine function allows manipulation of complex regulatory networks such as growth hormone (GH) in transgenic fish where disregulation of GH production to produce larger fish has also permitted exploration of the role that GH plays in testis development, suggesting that it does so through interactions with insulin-like growth factors. The availability of omics tools to monitor changes at nearly any level in any organism, manipulate gene expression and behavior, and integrate data across biological levels, provides novel opportunities to explore endocrine function across many species and understand the complex roles that key genes play in different aspects of the endocrine function.
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Affiliation(s)
- Natàlia Garcia-Reyero
- Institute for Genomics Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39759, USA.
| | - Angèle Tingaud-Sequeira
- Laboratoire MRMG, Maladies Rares: Génétique et Métabolisme, Université de Bordeaux, 33405 Talence Cedex, France
| | - Mengxi Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Edward J Perkins
- US Army Engineer Research and Development Center, Vicksburg, MS 39180, USA
| | - Wei Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Angione C, Costanza J, Carapezza G, Lió P, Nicosia G. A design automation framework for computational bioenergetics in biological networks. MOLECULAR BIOSYSTEMS 2014; 9:2554-64. [PMID: 23925151 DOI: 10.1039/c3mb25558a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The bioenergetic activity of mitochondria can be thoroughly investigated by using computational methods. In particular, in our work we focus on ATP and NADH, namely the metabolites representing the production of energy in the cell. We develop a computational framework to perform an exhaustive investigation at the level of species, reactions, genes and metabolic pathways. The framework integrates several methods implementing the state-of-the-art algorithms for many-objective optimization, sensitivity, and identifiability analysis applied to biological systems. We use this computational framework to analyze three case studies related to the human mitochondria and the algal metabolism of Chlamydomonas reinhardtii, formally described with algebraic differential equations or flux balance analysis. Integrating the results of our framework applied to interacting organelles would provide a general-purpose method for assessing the production of energy in a biological network.
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Affiliation(s)
- Claudio Angione
- Computer Laboratory, University of Cambridge, William Gates Building, 15 JJ Thomson Avenue, Cambridge, UK.
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