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Henke AN, Chilukuri S, Langan LM, Brooks BW. Reporting and reproducibility: Proteomics of fish models in environmental toxicology and ecotoxicology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168455. [PMID: 37979845 DOI: 10.1016/j.scitotenv.2023.168455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Environmental toxicology and ecotoxicology research efforts are employing proteomics with fish models as New Approach Methodologies, along with in silico, in vitro and other omics techniques to elucidate hazards of toxicants and toxins. We performed a critical review of toxicology studies with fish models using proteomics and reported fundamental parameters across experimental design, sample preparation, mass spectrometry, and bioinformatics of fish, which represent alternative vertebrate models in environmental toxicology, and routinely studied animals in ecotoxicology. We observed inconsistencies in reporting and methodologies among experimental designs, sample preparations, data acquisitions and bioinformatics, which can affect reproducibility of experimental results. We identified a distinct need to develop reporting guidelines for proteomics use in environmental toxicology and ecotoxicology, increased QA/QC throughout studies, and method optimization with an emphasis on reducing inconsistencies among studies. Several recommendations are offered as logical steps to advance development and application of this emerging research area to understand chemical hazards to public health and the environment.
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Affiliation(s)
- Abigail N Henke
- Department of Biology, Baylor University Waco, TX, USA; Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University Waco, TX, USA
| | | | - Laura M Langan
- Department of Environmental Science, Baylor University Waco, TX, USA; Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University Waco, TX, USA.
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University Waco, TX, USA; Center for Reservoir and Aquatic Systems Research (CRASR), Baylor University Waco, TX, USA.
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2
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Madeira C, Costa PM. Proteomics in systems toxicology. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:55-91. [PMID: 34340774 DOI: 10.1016/bs.apcsb.2021.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins are the ultimate product of gene expression. As they hinge between gene transcription and phenotype, they offer a more realistic perspective of toxicopathic effects, responses and even susceptibility to insult than targeting genes and mRNAs while dodging some inter-individual variability that hinders measuring downstream endpoints like metabolites or enzyme activity. Toxicologists have long focused on proteins as biomarkers but the advent of proteomics shifted risk assessment from narrow single-endpoint analyses to whole-proteome screening, enabling deriving protein-centric adverse outcome pathways (AOPs), which are pivotal for the derivation of Systems Biology informally named Systems Toxicology. Especially if coupled pathology, the identification of molecular initiating events (MIEs) and AOPs allow predictive modeling of toxicological pathways, which now stands as the frontier for the next generation of toxicologists. Advances in mass spectrometry, bioinformatics, protein databases and top-down proteomics create new opportunities for mechanistic and effects-oriented research in all fields, from ecotoxicology to pharmacotoxicology.
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Affiliation(s)
- Carolina Madeira
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Caparica, Portugal
| | - Pedro M Costa
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Caparica, Portugal.
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3
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Li J, Levitan B, Gomez-Jimenez S, Kültz D. Development of a Gill Assay Library for Ecological Proteomics of Threespine Sticklebacks ( Gasterosteus aculeatus). Mol Cell Proteomics 2018; 17:2146-2163. [PMID: 30093419 PMCID: PMC6210217 DOI: 10.1074/mcp.ra118.000973] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/07/2018] [Indexed: 12/31/2022] Open
Abstract
A data-independent acquisition (DIA) assay library for quantitative analyses of proteome dynamics has been developed for gills of threespine sticklebacks (Gasterosteus aculeatus). A raw spectral library was generated by data-dependent acquisition (DDA) and annotation of tryptic peptides to MSMS spectra and protein database identifiers. The assay library was constructed from the raw spectral library by removal of low-quality, ambiguous, and low-signal peptides. Only unique proteins represented by at least two peptides are included in the assay library, which consists of 1506 proteins, 5074 peptides, 5104 precursors, and 25,322 transitions. This assay library was used with DIA data to identify biochemical differences in gill proteomes of four populations representing different eco- and morpho-types of threespine sticklebacks. The assay library revealed unique and reproducible proteome signatures. Warm-adapted, low-plated, brackish-water fish from Laguna de la Bocana del Rosario (Mexico) show elevated HSP47, extracellular matrix, and innate immunity proteins whereas several immunoglobulins, interferon-induced proteins, ubiquitins, proteolytic enzymes, and nucleic acid remodeling proteins are reduced. Fully-plated, brackish-water fish from Westchester Lagoon (Alaska) display elevated ion regulation, GTPase signaling, and contractile cytoskeleton proteins, altered abundances of many ribosomal, calcium signaling and immunity proteins, and depleted transcriptional regulators and metabolic enzymes. Low-plated freshwater fish from Lake Solano (California) have elevated inflammasomes and proteolytic proteins whereas several iron containing and ion regulatory proteins are reduced. Gills of fully-plated, marine fish from Bodega Harbor (California) have elevated oxidative metabolism enzymes and reduced transglutaminase 2, collagens, and clathrin heavy chains. These distinct proteome signatures represent targets for testing ecological and evolutionary influences on molecular mechanisms of gill function in threespine sticklebacks. Furthermore, the gill assay library represents a model for other tissues and paves the way for accurate and reproducible network analyses of environmental context-dependent proteome dynamics in complex organisms.
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Affiliation(s)
- Johnathon Li
- From the ‡Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Ave., Davis, CA 95616
| | - Bryn Levitan
- From the ‡Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Ave., Davis, CA 95616
| | - Silvia Gomez-Jimenez
- §Centro de Investigación en Alimentación y Desarrollo, Carretera a la Victoria Km. 0.6, Apartado, Hermosillo, Sonora, México C.P. 83000
| | - Dietmar Kültz
- From the ‡Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Ave., Davis, CA 95616;
- ¶Coastal Marine Sciences Institute, University of California, Davis
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4
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Liang X, Feswick A, Simmons D, Martyniuk CJ. Reprint of: Environmental toxicology and omics: A question of sex. J Proteomics 2018:S1874-3919(18)30113-1. [PMID: 29650353 DOI: 10.1016/j.jprot.2018.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular initiating events and downstream transcriptional/proteomic responses provide valuable information for adverse outcome pathways, which can be used predict the effects of chemicals on physiological systems. There has been a paucity of research that addresses sex-specific expression profiling in toxicology and due to cost, time, and logistic considerations, sex as a variable has not been widely considered. In response to this deficiency, federal agencies in the United States, Canada, and Europe have highlighted the importance of including sex as a variable in scientific investigations. Using case studies from both aquatic and mammalian toxicology, we report that there can be less than ~20-25% consensus in how the transcriptome and proteome of each sex responds to chemicals. Chemicals that have been shown to elicit sex-specific responses in the transcriptome or proteome include pharmaceuticals, anti-fouling agents, anticorrosive agents, and fungicides, among others. Sex-specific responses in the transcriptome and proteome are not isolated to whole animals, as investigations demonstrate that primary cell cultures isolated from each sex responds differently to toxicants. This signifies that sex is important, even in cell lines. Sex has significant implications for predictive toxicology, and both male and female data are required to improve robustness of adverse outcome pathways. BIOLOGICAL SIGNIFICANCE Clinical toxicology recognizes that sex is an important variable, as pharmacokinetics (ADME; absorption, distribution, metabolism, and excretion) can differ between females and males. However, few studies in toxicology have explored the implication of sex in relation to the transcriptome and proteome of whole organisms. High-throughput molecular approaches are becoming more frequently applied in toxicity screens (e.g. pre-clinical experiments, fish embryos, cell lines, synthetic tissues) and such data are expected to build upon reporter-based cell assays (e.g. receptor activation, enzyme inhibition) used in toxicant screening programs (i.e. Tox21, ToxCast, REACH). Thus, computational models can more accurately predict the diversity of adverse effects that can occur from chemical exposure within the biological system. Our studies and those synthesized from the literature suggest that the transcriptome and proteome of females and males respond quite differentially to chemicals. This has significant implications for predicting adverse effects in one sex when using molecular data generated in the other sex. While molecular initiating events are not expected to differ dramatically between females and males (i.e. an estrogen binds estrogen receptors in both sexes), it is important to acknowledge that the downstream transcriptomic and proteomic responses can differ based upon the presence/absence of co-regulators and inherent sex-specific variability in regulation of transcriptional and translational machinery. Transcriptomic and proteomic studies also reveal that cell processes affected by chemicals can differ due to sex, and this can undoubtedly lead to sex-specific physiological responses.
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Affiliation(s)
- Xuefang Liang
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; Department of Physiological Sciences and Center for Environmental and Human Toxicology, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - April Feswick
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Denina Simmons
- Department of Chemistry, McMaster University, Hamilton, Ontario, Canada
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA.
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5
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Liang X, Feswick A, Simmons D, Martyniuk CJ. Environmental toxicology and omics: A question of sex. J Proteomics 2018; 172:152-164. [DOI: 10.1016/j.jprot.2017.09.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/19/2017] [Accepted: 09/25/2017] [Indexed: 12/26/2022]
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Comparison of Integrated Responses to Nonlethal and Lethal Hypothermal Stress in Milkfish (Chanos chanos): A Proteomics Study. PLoS One 2016; 11:e0163538. [PMID: 27657931 PMCID: PMC5033585 DOI: 10.1371/journal.pone.0163538] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/10/2016] [Indexed: 11/19/2022] Open
Abstract
Milkfish is an important aquaculture species in Taiwan, and its high mortality during cold snaps in winter usually causes huge economic losses. To understand the effect of hypothermal stress and the corresponding compensatory stress response in milkfish, this study aimed to compare liver and gill protein levels between milkfish exposed to nonlethal (18°C), lethal (16°C), and control (28°C) temperatures. Using a proteomics approach based on two-dimensional electrophoresis and nano-LC-MS/MS analysis, this study identified thirty unique protein spots from milkfish livers and gills for which protein abundance was significantly different between nonlethal, lethal, and control temperature groups. Proteins identified in the liver were classified into three different categories according to their cellular function: (1) anti-oxidative stress, (2) apoptotic pathway, and (3) cytoskeleton. Similarly, proteins identified in the gill were sorted in five different functional categories: (1) cytoskeleton, (2) immune response, (3) protein quality control, (4) energy production, and (5) intracellular homeostasis. Based on functional information derived from the identified proteins, we assumed that different levels of hypothermal stress had a different effect and induced a different cellular response. Upon nonlethal hypothermal stress, the identified proteins were involved in anti-oxidative stress and anti-inflammation pathways, suggesting that milkfish had high levels of oxidative stress in the liver and exhibited inflammation response in the gill. Upon lethal hypothermal stress, however, identified proteins were associated with apoptosis in the liver and regulation of intracellular homeostasis in the gill. The present study provided evidence to illustrate different multi-physiological responses to nonlethal and lethal hypothermal stress in milkfish livers and gills.
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7
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Qiao Q, Le Manach S, Sotton B, Huet H, Duvernois-Berthet E, Paris A, Duval C, Ponger L, Marie A, Blond A, Mathéron L, Vinh J, Bolbach G, Djediat C, Bernard C, Edery M, Marie B. Deep sexual dimorphism in adult medaka fish liver highlighted by multi-omic approach. Sci Rep 2016; 6:32459. [PMID: 27561897 PMCID: PMC5000296 DOI: 10.1038/srep32459] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/09/2016] [Indexed: 02/05/2023] Open
Abstract
Sexual dimorphism describes the features that discriminate between the two sexes at various biological levels. Especially, during the reproductive phase, the liver is one of the most sexually dimorphic organs, because of different metabolic demands between the two sexes. The liver is a key organ that plays fundamental roles in various physiological processes, including digestion, energetic metabolism, xenobiotic detoxification, biosynthesis of serum proteins, and also in endocrine or immune response. The sex-dimorphism of the liver is particularly obvious in oviparous animals, as the female liver is the main organ for the synthesis of oocyte constituents. In this work, we are interested in identifying molecular sexual dimorphism in the liver of adult medaka fish and their sex-variation in response to hepatotoxic exposures. By developing an integrative approach combining histology and different high-throughput omic investigations (metabolomics, proteomics and transcriptomics), we were able to globally depict the strong sexual dimorphism that concerns various cellular and molecular processes of hepatocytes comprising protein synthesis, amino acid, lipid and polysaccharide metabolism, along with steroidogenesis and detoxification. The results of this work imply noticeable repercussions on the biology of oviparous organisms environmentally exposed to chemical or toxin issues.
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Affiliation(s)
- Qin Qiao
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Séverine Le Manach
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Benoit Sotton
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Hélène Huet
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France.,Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, BioPôle Alfort, Maisons-Alfort, France
| | - Evelyne Duvernois-Berthet
- UMR 7221 CNRS/MNHN, Évolution des Régulations Endocriniennes, Sorbonne Universités, Muséum Nationale d'Histoire Naturelle, Paris, France
| | - Alain Paris
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Charlotte Duval
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Loïc Ponger
- UMR 7196 MNHN/CNRS, INSERM U1154, Sorbonne Universités, Museum National d'Histoire Naturelle, Paris, France
| | - Arul Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Alain Blond
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Lucrèce Mathéron
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Institut de Biologie Intégrative IFR 83, Sorbonne Universités, Université Pierre et Marie Curie, Paris, France
| | - Joelle Vinh
- USR 3149 ESPCI/CNRS SMPB, Laboratory of Biological Mass Spectrometry and Proteomics, ESPCI Paris, PSL Research University, Paris, France
| | - Gérard Bolbach
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Institut de Biologie Intégrative IFR 83, Sorbonne Universités, Université Pierre et Marie Curie, Paris, France
| | - Chakib Djediat
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Cécile Bernard
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Marc Edery
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Benjamin Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
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8
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Le Manach S, Khenfech N, Huet H, Qiao Q, Duval C, Marie A, Bolbach G, Clodic G, Djediat C, Bernard C, Edery M, Marie B. Gender-Specific Toxicological Effects of Chronic Exposure to Pure Microcystin-LR or Complex Microcystis aeruginosa Extracts on Adult Medaka Fish. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:8324-8334. [PMID: 27409512 DOI: 10.1021/acs.est.6b01903] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cyanobacterial blooms often occur in freshwater lakes and constitute a potential health risk to human populations, as well as to other organisms. However, their overall and specific implications for the health of aquatic organisms that are chronically and environmentally exposed to cyanobacteria producing hepatotoxins, such as microcystins (MCs), together with other bioactive compounds have still not been clearly established and remain difficult to assess. The medaka fish was chosen as the experimental aquatic model for studying the cellular and molecular toxicological effects on the liver after chronic exposures (28 days) to environmentally relevant concentrations of pure MC-LR, complex extracts of MC producing or nonproducing cyanobacterial biomasses, and of a Microcystis aeruginosa natural bloom. Our results showed a higher susceptibility of females to the different treatments compared to males at both the cellular and the molecular levels. Although hepatocyte lysis increased with MC-containing treatments, lysis always appeared more severe in the liver of females compare to males, and the glycogen cellular reserves also appeared to decrease more in the liver of females compared to those in the males. Proteomic investigations reveal divergent responses between males and females exposed to all treatments, especially for proteins involved in metabolic and homeostasis processes. Our observations also highlighted the dysregulation of proteins involved in oogenesis in female livers. These results suggest that fish populations exposed to cyanobacteria blooms may potentially face several ecotoxicological issues.
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Affiliation(s)
- Séverine Le Manach
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle , CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Nour Khenfech
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle , CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Hélène Huet
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle , CP 39, 12 Rue Buffon, 75005 Paris, France
- Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est , BioPôle Alfort, 94700 Maison-Alfort, France
| | - Qin Qiao
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle , CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Charlotte Duval
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle , CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Arul Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle , CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Gérard Bolbach
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Sorbonne Universités, Université Pierre et Marie Curie , 75005 Paris, France
| | - Gilles Clodic
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Sorbonne Universités, Université Pierre et Marie Curie , 75005 Paris, France
| | - Chakib Djediat
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle , CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Cécile Bernard
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle , CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Marc Edery
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle , CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Benjamin Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle , CP 39, 12 Rue Buffon, 75005 Paris, France
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9
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Atasaral-Şahin Ş, Romero MR, Cueto R, González-Lavín N, Marcos M, Diz AP. Subtle tissue and sex-dependent proteome variation in mussel (Mytilus galloprovincialis) populations of the Galician coast (NW Spain) raised in a common environment. Proteomics 2015; 15:3993-4006. [PMID: 26449374 DOI: 10.1002/pmic.201500241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/21/2015] [Accepted: 10/02/2015] [Indexed: 12/11/2022]
Abstract
The mussel Mytilus galloprovincialis is one of the most important marine resources for aquaculture in Europe, and Galicia (NW Spain) is the EU's leading region for production. Variation in environmental and ecological factors exists in Northern and Southern estuaries of this region, and natural selection could have modulated genetic variation among populations with adaptation to local conditions as the driving force. Results from a previous genetic study using neutral markers suggested subtle genetic differentiation between mussel populations from both estuarine areas. In this new study, mussel samples from Northern and Southern estuaries were brought into a common environment to test for proteome differences due to genetic and permanent non-genetic effects in populations from both estuarine areas, using both foot and mantle border tissues. Because the sex of the mussels was determined through histological tests, sex-specific effects were also examined. Evidence of subtle differences in the foot proteome, dependent on mussel sex, were detected between populations from both estuaries. These differences were more marked for female samples. No evidence of proteome differences was found for the factors estuaries and sex in mantle border tissue. Candidate proteins with a potential role in local adaptation were identified and point to molecular functions that might be involved in responses to different stressors.
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Affiliation(s)
- Şebnem Atasaral-Şahin
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain.,Department of Fisheries Technology Engineering, Faculty of Marine Sciences, Karadeniz Technical University, Surmene, Trabzon, Turkey
| | - Mónica R Romero
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain.,Toralla Marine Science Station (ECIMAT), University of Vigo, Isla de Toralla, Vigo, Spain
| | - Rosa Cueto
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain
| | - Nerea González-Lavín
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain.,Toralla Marine Science Station (ECIMAT), University of Vigo, Isla de Toralla, Vigo, Spain
| | - Manuel Marcos
- Structural Determination, Proteomics and Genomics Service, CACTI, University of Vigo, Vigo, Spain
| | - Angel P Diz
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, Spain.,Toralla Marine Science Station (ECIMAT), University of Vigo, Isla de Toralla, Vigo, Spain
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10
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Kültz D, Li J, Zhang X, Villarreal F, Pham T, Paguio D. Population-specific plasma proteomes of marine and freshwater three-spined sticklebacks (Gasterosteus aculeatus
). Proteomics 2015. [DOI: 10.1002/pmic.201500132] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dietmar Kültz
- Department of Animal Science; University of California; Davis CA USA
| | - Johnathon Li
- Department of Animal Science; University of California; Davis CA USA
| | - Xuezhen Zhang
- Department of Animal Science; University of California; Davis CA USA
- College of Fisheries; Huazhong Agricultural University; Wuhan P. R. China
| | | | - Tuan Pham
- Department of Animal Science; University of California; Davis CA USA
| | - Darlene Paguio
- Department of Animal Science; University of California; Davis CA USA
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11
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Transcriptomic dissection of sexual differences in Bemisia tabaci, an invasive agricultural pest worldwide. Sci Rep 2014; 4:4088. [PMID: 24526031 PMCID: PMC3924218 DOI: 10.1038/srep04088] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 01/03/2014] [Indexed: 11/08/2022] Open
Abstract
Sex difference involving chromosomes and gene expression has been extensively documented. In this study, the gender difference in the sweetpotato whitefly Bemisia tabaci was investigated using Illumina-based transcriptomic analysis. Gender-based RNAseq data produced 27 Gb reads, and subsequent de novo assembly generated 93,948 transcripts with a N50 of 1,853 bp. A total of 1,351 differentially expressed genes were identified between male and female B. tabaci, and majority of them were female-biased. Pathway and GO enrichment experiments exhibited a gender-specific expression, including enriched translation in females, and enhanced structural constituent of cuticle in male whiteflies. In addition, a putative transformer2 gene (tra2) was cloned, and the structural feature and expression profile of tra2 were investigated. Sexually dimorphic transcriptome is an uncharted territory for the agricultural insect pests. Molecular understanding of sex determination in B. tabaci, an emerging invasive insect pest worldwide, will provide potential molecular target(s) for genetic pest control alternatives.
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12
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DeFaveri J, Jonsson PR, Merilä J. Heterogeneous Genomic Differentiation in marine threespine sticklebacks: adaptation along an environmental gradient. Evolution 2013; 67:2530-46. [PMID: 24033165 DOI: 10.1111/evo.12097] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/18/2013] [Indexed: 02/03/2023]
Abstract
Evolutionary divergence among populations occupying ecologically distinct environments can occur even in the face of on-going gene flow. However, the genetic underpinnings, as well as the scale and magnitude at which this differentiation occurs in marine habitats are not well understood. We investigated the patterns and degree of genomic heterogeneity in threespine sticklebacks (Gasterosteus aculeatus) by assessing genetic variability in 20 nongenic and 20 genic (associated with genes important for freshwater adaptation) microsatellite loci in samples collected from 38 locations spanning the entire Baltic Sea coast to the North Sea boundary. Population divergence (F(ST) ≈ 0.026) and structuring (five genetic clusters) was significantly more pronounced in the genic as compared to nongenic markers (F(ST) ≈ 0.008; no genetic clusters). Patterns of divergence in the genic markers--45% of which were identified as outliers--correlated with local differences in salinity. Yet, a strong positive correlation between divergence in genic and nongenic markers, and their association with environmental factors suggests that adaptive divergence is reducing gene flow across the genome. Apart from providing a clear demonstration of heterogeneous genomic patterns of differentiation in a marine species, the results are indicative of adaptive population structuring across the relatively young Baltic Sea in spite of ample opportunities for gene flow.
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Affiliation(s)
- Jacquelin DeFaveri
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, PO Box 65, FI 00014, Finland.
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Leskinen PK, Laaksonen T, Ruuskanen S, Primmer CR, Leder EH. The proteomics of feather development in pied flycatchers (Ficedula hypoleuca) with different plumage coloration. Mol Ecol 2012; 21:5762-77. [DOI: 10.1111/mec.12073] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 08/28/2012] [Accepted: 08/31/2012] [Indexed: 02/04/2023]
Affiliation(s)
| | - Toni Laaksonen
- Department of Biology; University of Turku; Turku; 20014; Finland
| | - Suvi Ruuskanen
- Department of Biology; University of Turku; Turku; 20014; Finland
| | - Craig R. Primmer
- Department of Biology; University of Turku; Turku; 20014; Finland
| | - Erica H. Leder
- Department of Biology; University of Turku; Turku; 20014; Finland
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