Proteome modifications of blue mussel (Mytilus edulis L.) gills as an effect of water pollution

Critical review of the OSPAR risk-based approach for offshore-produced water discharges

The management of produced water (PW) discharges from offshore oil and gas installations in the North Atlantic is under the auspices of OSPAR (Oslo/Paris convention for Protection of the Marine Environment of the North-East Atlantic). In 2010, OSPAR introduced the risk-based approach (RBA) for PW management. The RBA includes a hazard assessment estimating PW ecotoxicity using two approaches: whole-effluent toxicity (WET) and substance-based (SB). Set against the framework of the WET and SB approach, we conducted a literature review on the magnitude and cause of PW ecotoxicity, respectively, and on the challenges of estimating these. A large variability in the reported magnitude of PW WET was found, with EC50 or LC50 values ranging from <1% to >100%, and a median of 11% (n = 301). Across the literature, metals, hydrocarbons, and production chemicals were identified as causing ecotoxicity. However, this review reveals how knowledge gaps on PW composition and high sample and species dependency of PW ecotoxicity make clear identification and generalization difficult. It also highlights how limitations regarding the availability and reliability of ecotoxicity data result in large uncertainties in the subsequent risk estimates, which is not adequately reflected in the RBA output (e.g., environmental impact factors). Thus, it is recommended to increase the focus on improving ecotoxicity data quality before further use in the RBA, and that WET should play a more pronounced role in the testing strategy. To increase the reliability of the SB approach, more attention should be paid to the actual composition of PW. Bioassay-directed chemical analysis, combining outcomes of WET and SB in toxicity identification evaluations, may hold the key to identifying drivers of ecotoxicity in PW. Finally, an uncertainty appraisal must be an integrated part of all reporting of risk estimates in the RBA, to avoid mitigation actions based on uncertainties rather than reliable ecotoxicity estimations. Integr Environ Assess Manag 2023;19:1172-1187. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Amelioration of rotenone-induced alterations in energy/redox system, stress response and cytoskeleton proteins by octanoic acid in zebrafish: A proteomic study

Rotenone is used to generate Parkinson's disease (PD)-like symptoms in experimental animals. Octanoic acid (C8), is the principal fatty acid of medium-chain triglycerides in ketogenic diets. Beneficial effects of ketogenic diets were shown in PD. We applied proteomic methods to reveal the effects of octanoic acid in rotenone toxicity in zebrafish to gain information on the use of ketogenic diets in PD. Zebrafish were exposed to 5 μg/ml rotenone and octanoic acid (20 and 60 mg/ml) for 30 days. LC-MS/MS analysis was performed. Raw files were analyzed by Proteome Discoverer 2.4 software, peptide lists were searched against Danio rerio proteins. STRING database was used for protein annotations or interactions. 2317 unique proteins were quantified, 302 proteins were differentially expressed. Proteins involved in cell organization, biogenesis, transport, response to stimulus were most frequently expressed. Our study is first to report that the alterations in the expressions of proteins related to energy and redox system, stress response, and cytoskeleton proteins caused by rotenone exposure were normalized by octanoic acid treatment in zebrafish.

OMICs Approaches in Diarrhetic Shellfish Toxins Research

Diarrhetic shellfish toxins (DSTs) are among the most prevalent marine toxins in Europe's and in other temperate coastal regions. These toxins are produced by several dinoflagellate species; however, the contamination of the marine trophic chain is often attributed to species of the genus Dinophysis. This group of toxins, constituted by okadaic acid (OA) and analogous molecules (dinophysistoxins, DTXs), are highly harmful to humans, causing severe poisoning symptoms caused by the ingestion of contaminated seafood. Knowledge on the mode of action and toxicology of OA and the chemical characterization and accumulation of DSTs in seafood species (bivalves, gastropods and crustaceans) has significantly contributed to understand the impacts of these toxins in humans. Considerable information is however missing, particularly at the molecular and metabolic levels involving toxin uptake, distribution, compartmentalization and biotransformation and the interaction of DSTs with aquatic organisms. Recent contributions to the knowledge of DSTs arise from transcriptomics and proteomics research. Indeed, OMICs constitute a research field dedicated to the systematic analysis on the organisms' metabolisms. The methodologies used in OMICs are also highly effective to identify critical metabolic pathways affecting the physiology of the organisms. In this review, we analyze the main contributions provided so far by OMICs to DSTs research and discuss the prospects of OMICs with regard to the DSTs toxicology and the significance of these toxins to public health, food safety and aquaculture.

Assessment of fipronil toxicity to the freshwater midge Chironomus riparius: Molecular, biochemical, and organismal responses

Fipronil is a phenylpyrazole insecticide that entered the market to replace organochlorides and organophosphates. Fipronil impairs the regular inhibition of nerve impulses that ultimately result in paralysis and death of insects. Because of its use as a pest control, and due to runoff events, fipronil has been detected in freshwater systems near agricultural areas, and therefore might represent a threat to non-target aquatic organisms. In this study, the toxicity of fipronil to the freshwater midge Chironomus riparius was investigated at biochemical, molecular, and whole organism (e.g. growth, emergence, and behavior) levels. At the individual level, chronic (28 days) exposure to fipronil resulted in reduced larval growth and emergence with a lowest observed effect concentration (LOEC) of 0.081 μg L^-1. Adult weight, which is directly linked to the flying performance and fecundity of midges, was also affected (LOEC = 0.040 μg L^-1). Additionally, behavioral changes such as irregular burrowing behavior of C. riparius larvae (EC₅₀ = 0.084 μg L^-1) and impairment of adult flying performance were observed. At a biochemical level, acute (48 h) exposure to fipronil increased cellular oxygen consumption (as indicated by the increase of electron transport system (ETS) activity) and decreased antioxidant and detoxification defenses (as suggested by the decrease in catalase (CAT) and glutathione S-transferase (GST) activities). Exposure to fipronil also caused alterations in the fatty acid profile of C. riparius, since high levels of stearidonic acid (SDA) were observed. A comparison between exposed and non-exposed larvae also revealed alterations in the expression of globins, cytoskeleton and motor proteins, and proteins involved in protein biosynthesis. These alterations may aid in the interpretation of potential mechanisms of action that lead to the effects observed at the organism level. Present results show that environmentally relevant concentrations of fipronil are toxic to chironomid populations which call for monitoring of phenylpyrazole insecticides and of their ecological effects in freshwaters. Present results also emphasize the importance of complementing ecotoxicological data with molecular approaches such as proteomics, for a better interpretation of the mode of action of insecticides in aquatic invertebrates.

Accumulation of Polychlorinated Biphenyls in Mussels: A Proteomic Study

Polychlorinated biphenyls (PCBs) are environmental pollutants of industrial origin that can contaminate food, mainly food of animal origin. Although production of PCBs has been banned in many countries since the 1980s, they are still present in the environment and are considered dangerous pollutants for human health. In fact, they can bioaccumulate in living organisms such as marine organisms because of their chemical and physical properties. New analytical approaches are useful to monitor the presence of such contaminants in seafood products and in the environment. In this work, we evaluate changes in protein expression of Mytilus galloprovincialis (Lam.) experimentally exposed to a PCB mixture and identify chemically specific protein expression signatures by using a proteomic approach. In particular, we identify 21 proteins whose levels of expression are sensibly modified after 3 weeks of exposure. The present work shows that a proteomic approach can be a useful tool to study alterations of protein expression in mussels exposed to PCBs and represents a first step toward the development of screening protocols to be used for biomonitoring surveys of fishery products.

Proteomic changes in Corbicula fluminea exposed to wastewater from a psychiatric hospital

The increase use of pharmaceutical compounds in veterinary practice and human population results in the ubiquitous presence of these compounds in aquatic ecosystems. Because pharmaceuticals are highly bioactive, there is concern about their toxicological effects in aquatic organisms. Therefore, the aim of this study was to assess the effects of an effluent from a psychiatric hospital (containing a complex mixture of 25 pharmaceutical compounds from eleven therapeutic classes) on the freshwater clam Corbicula fluminea using a proteomic approach. The exposure of C. fluminea to this complex effluent containing anxiolytics, analgesics, lipid regulators, beta blockers, antidepressants, antiepileptics, antihistamines, antihypertensives, antiplatelets and antiarrhythmics induced protein changes after 1 day of exposure in clam gills and digestive gland more evident in the digestive gland. These changes included increase in the abundance of proteins associated with structural (actin and tubulin), cellular functions (calreticulin, proliferating cell nuclear antigen (PCNA), T complex protein 1 (TCP1)) and metabolism (aldehyde dehydrogenase (ALDH), alcohol dehydrogenase, 6 phosphogluconate dehydrogenase). Results from this study indicate that calreticulin, PCNA, ALDH and alcohol dehydrogenase in the digestive gland and T complex protein 1 (TCP1)) and 6 phosphogluconate dehydrogenase in the gills represent useful biomarkers for the ecotoxicological characterization of psychiatric hospital effluents in this species.

Investigation on the proteome response of transplanted blue mussel (Mytilus sp.) during a long term exposure experiment at differently impacted field stations in the German Bight (North Sea)

In a pilot field study the proteome response of Mytilus sp. was analyzed in relation to the concentration of different trace metal contaminants. Over a period of eight month test organisms have been exposed at a near-shore station in the anthropogenic impacted estuary of the river Elbe and at an off-shore station in the vicinity of the Island of Helgoland in the German Bight (North Sea). The stations differ in their hydrological as well as chemical characteristics. The physiological biomarkers, such as condition index which have been continuously monitored during the experiment clearly indicate the effects of the different environmental conditions. Multiple protein abundance changes were detected utilizing the techniques of two dimensional gel electrophoresis (2dGE) and consequently proteins arising as potential candidates for ecotoxicological monitoring have been identified by MALDI-ToF and ToF/ToF mass spectrometry. Different cytoskeletal proteins, enzymes of energy metabolism, stress proteins and one protein relevant for metal detoxification have been pointed out.

[Analysis of proteomic profile changes of zebrafish embryos during exposure to doxorubicin, built-in the phospholipid transport nanosystem]

The proteome profile of Danio rerio embryos grown in the medium containing doxorubicin, included in the phospholipid transport nanosystem (doxolip) has been investigated using combination of 1D-electrophoresis with subsequent MALDI-TOF-PMF mass spectrometry. Cultivation of growing of D. rerio embryos in the medium with doxolip caused a substantial increase in expression of the cytoskeletal proteins, a decrease in the number of nuclear proteins involved in DNA and RNA synthesis and disappearance of vitellogenin 2 in comparison with control (the cultivation medium containing the phospholipid transport nanosystem). Analysis of the proteomic profiles of doxolip-treated embryos suggests lower toxicity of doxorubicin incorporated in the phospholipid nanosystem.

2-DE Mapping of the Blue Mussel Gill Proteome: The Usual Suspects Revisited

The Blue Mussel (Mytilus edulis, L. 1758) is an ecologically important and commercially relevant bivalve. Because of its ability to bioconcentrate xenobiotics, it is also a widespread sentinel species for environmental pollution, which has been used in ecotoxicological studies for biomarker assessment. Consequently, numerous proteomics studies have been carried out in various research contexts using mussels of the genus Mytilus, which intended to improve our understanding of complex physiological processes related to reproduction, adaptation to physical stressors or shell formation and for biomarker discovery. Differential-display 2-DE proteomics relies on an extensive knowledge of the proteome with as many proteoforms identified as possible. To this end, extensive characterization of proteins was performed in order to increase our knowledge of the Mytilus gill proteome. On average, 700 spots were detected on 2-DE gels by colloidal blue staining, of which 122 different, non-redundant proteins comprising 203 proteoforms could be identified by tandem mass spectrometry. These proteins could be attributed to four major categories: (i) “metabolism”, including antioxidant defence and degradation of xenobiotics; (ii) “genetic information processing”, comprising transcription and translation as well as folding, sorting, repair and degradation; (iii) “cellular processes”, such as cell motility, transport and catabolism; (iv) “environmental information processing”, including signal transduction and signalling molecules and interaction. The role of cytoskeleton proteins, energetic metabolism, chaperones/stress proteins, protein trafficking and the proteasome are discussed in the light of the exigencies of the intertidal environment, leading to an enhanced stress response, as well as the structural and physiological particularities of the bivalve gill tissue.

Next-generation proteomics: toward customized biomarkers for environmental biomonitoring

Because of their ecological representativeness, invertebrates are commonly employed as test organisms in ecotoxicological assessment; however, to date, biomarkers employed for these species were the result of a direct transposition from vertebrates, despite deep evolutionary divergence. To gain efficiency in the diagnostics of ecosystem health, specific biomarkers must be developed. In this sense, next-generation proteomics enables the specific identification of proteins involved in key physiological functions or defense mechanisms, which are responsive to ecotoxicological challenges. However, the analytical investment required restricts use in biomarker discovery. Routine biomarker validation and assays rely on more conventional mass spectrometers. Here, we describe how proteomics remains a challenge for ecotoxicological test organisms because of the lack of appropriate protein sequences databases, thus restricting the analysis on conserved and ubiquitous proteins. These limits and some strategies used to overcome them are discussed. These new tools, such as proteogenomics and targeted proteomics, should result in new biomarkers specific to relevant environmental organisms and applicable to routine ecotoxicological assessment.

Proteomic responses to metal-induced oxidative stress in hydrothermal vent-living mussels, Bathymodiolus sp., on the Southwest Indian Ridge

Bathymodiolin mussels are amongst the dominant fauna occupying hydrothermal vent ecosystems throughout the World's oceans. This subfamily inhabits a highly ephemeral and variable environment, where exceptionally high concentrations of reduced sulphur species and heavy metals necessitate adaptation of specialised detoxification mechanisms. Whilst cellular responses to common anthropogenic pollutants are well-studied in shallow-water species, they remain limited in deep-sea vent fauna. Bathymodiolus sp. were sampled from two newly-discovered vent sites on the Southwest Indian Ridge (Tiamat and Knuckers Gaff) by the remotely operated vehicle (ROV) Kiel 6000 during the RRS James Cook cruise, JC 067 in November 2011. Here, we use redox proteomics to investigate the effects of tissue metal accumulation on protein expression and thiol oxidation in gill. Following 2D PAGE, we demonstrate a significant difference in intensity in 30 protein spots in this organ between the two vent sites out of 205 matched spots. We also see significant variations in thiol oxidation in 15 spots, out of 143 matched. At Tiamat, 23 protein spots are up-regulated compared to Knuckers Gaff and we identify 5 of these with important roles in metabolism, cell structure, stress response, and redox homeostasis. We suggest that increased metal exposure triggers changes in the proteome, regulating tissue uptake. This is evident both between vent sites and across a chemical gradient within the Knuckers Gaff vent site. Our findings highlight the importance of proteomic plasticity in successful adaptation to the spatially and temporally fluctuating chemical environments that are characteristic of hydrothermal vent habitats.

Proteomic Analysis of the Reproductive Organs of the Hermaphroditic Gastropod Lymnaea stagnalis Exposed to Different Endocrine Disrupting Chemicals

Many studies have reported perturbations of mollusc reproduction following exposure to low concentrations (ng/L range) of endocrine disrupting chemicals (EDCs). However, the mechanisms of action of these molecules on molluscs are still poorly understood. Investigation of the modifications of protein expression in organisms exposed to chemicals using proteomic methods can provide a broader and more comprehensive understanding of adverse impacts of pollution on organisms than conventional biochemical biomarkers (e.g., heat-shock proteins, metallothioneins, GST, EROD). In this study we have investigated the impacts of four chemicals, which exhibit different endocrine disrupting properties in vertebrates, on the proteome of the hermaphroditic freshwater pulmonate gastropod Lymnaea stagnalis after 21 days of exposure. Testosterone, tributyltin, chlordecone and cyproterone acetate were chosen as tested compounds as they can induce adverse effects on the reproduction of this snail. The 2D-DIGE method was used to identify proteins whose expression was affected by these compounds. In addition to modifying the expression of proteins involved in the structure and function of the cytoskeleton, chemicals had impacts on the expression of proteins involved in the reproduction of L. stagnalis. Exposure to 19.2 µg/L of chlordecone increased the abundance of ovipostatin, a peptide transmitted during mating through seminal fluid, which reduces oviposition in this species. The expression of yolk ferritin, the vitellogenin equivalent in L. stagnalis, was reduced after exposure to 94.2 ng Sn/L of tributyltin. The identification of yolk ferritin and the modification of its expression in snails exposed to chemicals were refined using western blot analysis. Our results showed that the tested compounds influenced the abundance of yolk ferritin in the reproductive organs. Alteration in proteins involved in reproductive pathways (e.g., ovipostatin and yolk ferritin) could constitute relevant evidence of interaction of EDCs with reproductive pathways that are under the control of the endocrine system of L. stagnalis.

Impact of benzo(a)pyrene, Cu and their mixture on the proteomic response of Mytilus galloprovincialis

In natural waters, chemical interactions between mixtures of contaminants can result in potential synergistic and/or antagonic effects in aquatic animals. Benzo(a)pyrene (BaP) and copper (Cu) are two widespread environmental contaminants with known toxicity towards mussels Mytilus spp. The effects of the individual and the interaction of BaP and Cu exposures were assessed in mussels Mytilus galloprovincialis using proteomic analysis. Mussels were exposed to BaP [10 μg L(-1) (0.396 μM)], and Cu [10 μg L(-1) (0.16 μM)], as well as to their binary mixture (mixture) for a period of 7 days. Proteomic analysis showed different protein expression profiles associated to each selected contaminant condition. A non-additive combined effect was observed in mixture in terms of new and suppressed proteins. Proteins more drastically altered (new, suppressed and 2-fold differentially expressed) were excised and analyzed by mass spectrometry, and eighteen putatively identified. Protein identification demonstrated the different accumulation, metabolism and chemical interactions of BaP, Cu and their mixture, resulting in different modes of action. Proteins associated with adhesion and motility (catchin, twitchin and twitchin-like protein), cytoskeleton and cell structure (α-tubulin and actin), stress response (heat shock cognate 71, heat shock protein 70, putative C1q domain containing protein), transcription regulation (zinc-finger BED domain-containing and nuclear receptor subfamily 1G) and energy metabolism (ATP synthase F0 subunit 6 protein and mannose-6-phosphate isomerase) were assigned to all three conditions. Cu exposure alone altered proteins associated with oxidative stress (glutathione-S-transferase) and digestion, growth and remodelling processes (chitin synthase), while the mixture affected only one protein (major vault protein) possibly related to multi drug resistance. Overall, new candidate biomarkers, namely zinc-finger BED domain-containing protein, chitin synthase and major vault protein, were also identified for BaP, Cu and mixture, respectively.

A proteomic evaluation of the effects of the pharmaceuticals diclofenac and gemfibrozil on marine mussels (Mytilus spp.): evidence for chronic sublethal effects on stress-response proteins

Human pharmaceuticals (e.g. the lipid regulator gemfibrozil and the non-steroidal anti-inflammatory drug diclofenac) are an emerging environmental threat in the aquatic environment. This study aimed to evaluate sublethal effects of these two commonly found pharmaceuticals on the protein profiles of marine mussels (Mytilus spp.). Mytilus spp. was exposed to environmentally relevant and elevated concentrations (1 and 1000 µg/l respectively) of both drugs for 14 days. In addition, mussels were maintained for seven days post treatment to examine the potential of blue mussels to recover from such an exposure. Differential protein expression signatures (PES) in the digestive gland of mussels were obtained using two-dimensional gel electrophoresis after 7, 14, and 21 days of exposure. Twelve spots were significantly increased or decreased by gemfibrozil and/or diclofenac, seven of which were successfully identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. These proteins were involved in energy metabolism, oxidative stress response, protein folding, and immune responses. Changes in the PES over time suggested that mussels were still experiencing oxidative stress for up to seven days post exposure. In addition, a suite of biomarkers comprising glutathione transferase, lipid peroxidation, and DNA damage were studied. An oxidative stress response was confirmed by biomarker responses. To our knowledge, this is the first investigation using proteomics to assess the potential effects of human pharmaceuticals on a non-target species in an environmentally-relevant model. The successful application of this proteomic approach supports its potential use in pollution biomonitoring and highlights its ability to aid in the discovery of new biomarkers.

Proteomic analysis of Sydney Rock oysters (Saccostrea glomerata) exposed to metal contamination in the field

This study used proteomics to assess the impacts of metal contamination in the field on Sydney Rock oysters. Oysters were transplanted into Lake Macquarie, NSW, for two weeks in both 2009 and 2010. Two-dimensional electrophoresis identified changes in protein expression profiles of oyster haemolymph between control and metal contaminated sites. There were unique protein expression profiles for each field trial. Principal components analysis attributed these differences in oyster proteomes to the different combinations and concentrations of metals and other environmental variables present during the three field trials. Identification of differentially expressed proteins showed that proteins associated with cytoskeletal activity and stress responses were the most commonly affected biological functions in the Sydney Rock oyster. Overall, the data show that proteomics combined with multivariate analysis has the potential to link the effects of contaminants with biological consequences.

Protein expression from zooplankton communities in a metal contaminated NW mediterranean coastal ecosystem

Bidimensional and monodimensional polyacrylamide gel electrophoresis were used to study protein expression from zooplankton collected in thirteen stations of Toulon Bay (NW Mediterranean). In this ecosystem, Little Bay showed higher trace metal concentrations (13.5-23.8 nM for Cu, 0.73-1.24 nM for Pb, 27.8-58.7 nM for Zn) than Large Bay (Cu 2.2-15.6 nM; Pb 0.19-0.78 nM; Zn 9.0-38.8 nM). Trace metals positively correlated (p < 0.05) with expression of four zooplankton proteins (MW in kDa/pI: 25.0/5.6; 48.8/4.1; 38.2/4.4; 38.3/5.8) and with biomass of Oithona nana, predominant copepod in Little Bay. Sequencing by LC-MS/MS putatively provided zooplankton identity of these proteins: they were cytoskeleton actin, except one protein that was the chaperone calreticulin. We suggest that actin and calreticulin could be regarded as zooplankton markers of metal stress and be involved in a possible tolerance of O. nana to contamination, contributing to its development in a marine perturbed ecosystem.

Effects of triclosan in the freshwater mussel Dreissena polymorpha: a proteomic investigation

Triclosan (TCS, 5-chloro-2-(2,4-dichlorophenoxy)phenol) is commonly used in several personal care products, textiles, and children's toys. Because the removal of TCS by wastewater treatment plants is incomplete, its environmental fate is to be discharged into freshwater ecosystems, where its ecotoxicological impact is still largely unexplored. Previously, we began a structured multi-tiered approach in order to evaluate TCS toxicity in the freshwater mussel Dreissena polymorpha. The results of our previous studies, based on in vitro and in vivo experiments, highlighted a pronounced cytogenotoxic effect exerted by TCS, and showed that an increase in oxidative stress was likely to be one of its main toxic mechanisms. In this work, in order to investigate TCS toxicity mechanisms in aquatic non-target species in greater depth, we decided to use a proteomic approach, analysing changes in protein expression profiles in gills of D. polymorpha exposed for seven days to TCS. Moreover, thiobarbituric acid reactive substances (TBARS) were measured to investigate further the role played by TCS in inducing oxidative stress. Finally, TCS bioaccumulation in mussel tissues was also assessed, to ensure an effective accumulation of the toxicant. Our results not only confirmed the role played by TCS in inducing oxidative stress, but furthered knowledge about the mechanism exerted by TCS in inducing toxicity in an aquatic non-target organisms. TCS induced significant alterations in protein expression profiles in gills of D. polymorpha. The wide range of proteins affected suggested that this chemical has marked effects on various biological processes, especially those involved in calcium binding or stress response. We also confirmed that the proteomic analysis, using 2-DE and de novo sequencing, is a reliable and powerful approach to investigate cellular responses to pollutants in a non-model organism with few genomic sequences available in databases.

PROTEOMICS in aquaculture: applications and trends

Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.

Review of recent proteomic applications in aquatic toxicology

Over the last decade, the environmental sciences have witnessed an incredible movement towards the utilization of high-throughput molecular tools that are capable of detecting simultaneous changes of hundreds, and even thousands, of molecules and molecular components after exposure of organisms to different environmental stressors. These techniques have received a great deal of attention because they not only offer the potential to unravel novel mechanisms of physiological and toxic action but are also amenable to the discovery of biomarkers of exposure and effects. In this article, we review the state of knowledge of one of these tools in ecotoxicological research: proteomics. We summarize the state of proteomics research in fish, and follow with studies conducted with aquatic invertebrates. A brief discussion on proteomic methods is also presented. We conclude with some ideas for future proteomic studies with fish and aquatic invertebrates.

Liquid chromatography and mass spectrometry in food allergen detection

Food allergy is an important issue in the field of food safety because of the hazards for affected persons and the hygiene requirements and legal regulations imposed on the food industry. Consumer protection and law enforcement require suitable analytical techniques for the detection of allergens in foods. Immunological methods are currently preferred; however, confirmatory alternatives are needed. The determination of allergenic proteins by liquid chromatography and mass spectrometry has greatly advanced in recent years, and gel-free allergenomics is becoming a routinely used approach for the identification and quantitation of food allergens. The present review provides a brief overview of the principles of proteomic procedures, various chromatographic set ups, and mass spectrometry instrumentation used in allergenomics. A compendium of published liquid chromatography methods, proteomic analyses, typical marker peptides, and quantitative assays for 14 main allergy-causing foods is also included.

Environmental proteomics: changes in the proteome of marine organisms in response to environmental stress, pollutants, infection, symbiosis, and development

Environmental proteomics, the study of changes in the abundance of proteins and their post-translational modifications, has become a powerful tool for generating hypotheses regarding how the environment affects the biology of marine organisms. Proteomics discovers hitherto unknown cellular effects of environmental stressors such as changes in thermal, osmotic, and anaerobic conditions. Proteomic analyses have advanced the characterization of the biological effects of pollutants and identified comprehensive and pollutant-specific sets of biomarkers, especially those highlighting post-translational modifications. Proteomic analyses of infected organisms have highlighted the broader changes occurring during immune responses and how the same pathways are attenuated during the maintenance of symbiotic relationships. Finally, proteomic changes occurring during the early life stages of marine organisms emphasize the importance of signaling events during development in a rapidly changing environment. Changes in proteins functioning in energy metabolism, cytoskeleton, protein stabilization and turnover, oxidative stress, and signaling are common responses to environmental change.

Proteomic Signatures of the Zebrafish (Danio rerio) Embryo: Sensitivity and Specificity in Toxicity Assessment of Chemicals

Studies using embryos of the zebrafish Danio rerio (DarT) instead of adult fish for characterising the (eco-) toxic potential of chemicals have been proposed as animal replacing methods. Effect analysis at the molecular level might enhance sensitivity, specificity, and predictive value of the embryonal studies. The present paper aimed to test the potential of toxicoproteomics with zebrafish eleutheroembryos for sensitive and specific toxicity assessment. 2-DE-based toxicoproteomics was performed applying low-dose (EC₁₀) exposure for 48 h with three-model substances Rotenone, 4,6-dinitro-o-cresol (DNOC) and Diclofenac. By multivariate “pattern-only” PCA and univariate statistical analyses, alterations in the embryonal proteome were detectable in nonetheless visibly intact organisms and treatment with the three substances was distinguishable at the molecular level. Toxicoproteomics enabled the enhancement of sensitivity and specificity of the embryonal toxicity assay and bear the potency to identify protein markers serving as general stress markers and early diagnosis of toxic stress.

Proteins in ecotoxicology - how, why and why not?

The growing interest in the application of proteomic technologies to solve toxicology issues and its relevance in ecotoxicology research has resulted in the emergence of "ecotoxicoproteomics". There is a general consensus that ecotoxicoproteomics is a powerful tool to spot early molecular events involved in toxicant responses, which are responsible for the adverse effects observed at higher levels of biological organization, thus contributing to elucidate the mode of action of stressors and to identify specific biomarkers. Ultimately, early-warning indicators can then be developed and deployed in "in situ" bioassays and in environmental risk assessment. The number of field experiments or laboratory trials using ecologically relevant test-species and involving proteomics has been, until recently, insufficient to allow a critical analysis of the real benefits of the application of this approach to ecotoxicology. This article intends to present an overview on the applications of proteomics in the context of ecotoxicology, focusing mainly on the prospective research to be done in invertebrates. Although these represent around 95% of all animal species and in spite of the key structural and functional roles they play in ecosystems, proteomic research in invertebrates is still in an incipient stage. We will review applications of ecotoxicoproteomics by evaluating the technical methods employed, the organisms and the contexts studied, the advances achieved until now and lastly the limitations yet to overcome will be discussed.

Microarray-based identification of gonad transcripts differentially expressed between lines of Pacific oyster selected to be resistant or susceptible to summer mortality

Summer mortality of the Pacific oyster Crassostrea gigas is the result of a complex interaction between oysters, their environment, and pathogens. Heredity appears to be a major factor determining the sensitivity of oysters to summer mortality, allowing resistant (R) and susceptible (S) lines to be produced. We conducted genome-wide expression profiling of R and S gonads during the 3-month period preceding a summer mortality event, using a cDNA microarray that we designed. ANOVA analysis revealed that 34 genes were differentially expressed between R and S lines on four dates preceding the mortality event. Annotation of some of these genes highlights reproduction and its allocation and antioxidant defenses as the main pathways that operate differentially between R and S lines. This transcriptional analysis provides new indications to define markers for quantitative trait loci searches and functional studies and evaluate the potential role of each gene in the resistance to summer mortality.

Peroxisomal proteomics: biomonitoring in mussels after the Prestige's oil spill

Peroxisomal proteomics was applied to assess possible biological effects after the Prestige's oil spill. Mussels were sampled in July 2004 and 2005 in four stations in the NW (closest to the spill) and NE coasts of the Iberian Peninsula. Principal components analysis (PCA) suggested differences in protein expression among stations and sampling years. Several proteins were putatively identified by mass spectrometry and immunolocalization. PC1 separated the NW stations in 2004 from the rest of the stations and sampling years mainly due to up-regulation of peroxisomal beta-oxidation proteins and PMP70. PC3 separated the NE stations, based on up-regulation of the antioxidant enzyme catalase in 2004 compared to 2005. PC4 separated the stations in the NE and the NW. This work shows that environmental proteomics, together with multivariate data analysis, could provide information to interpret the effects of oil spills at cellular level in mussels.

Effect of cadmium in the clam Ruditapes decussatus assessed by proteomic analysis

Cadmium, an environmental stressor due to its toxicity, persistence and accumulation in biota, is widespread in the aquatic environment. Cadmium accumulation kinetics have revealed that Ruditapes decussatus has a high affinity to this metal. Proteomics is an effective tool to evaluate the toxic effects of contaminants. The aim of this study was to investigate the Cd effects in the gill and digestive gland of the sentinel species R. decussatus. Protein expression profiles (PEPs) in the clam tissues exposed to Cd (40 microg l(-1), 21 days) were compared to unexposed ones. Cd induces major changes in tissue-specific protein expression profiles in gill and digestive gland. This tissue dependent response results mainly from differences in Cd accumulation, protein inhibition and/or autophagy. An overall decrease of protein spots was detected in both treated tissues, being higher in gill. Some of the spots more drastically altered after pollutants exposure were excised and nine were identified by micro liquid chromatography tandem mass spectrometry (LC-MS/MS). Proteins identified by homology search in databases included: three proteins (8-fold) up-regulated, one down-regulated, four suppressed and one induced. Cd induces major changes in proteins involved in cytoskeletal structure maintenance (muscle-type actin, adductor muscle actin and beta-tubulin), cell maintenance (Rab GDP) and metabolism (ALDH and MCAD, both identified by de novo sequencing) suggesting potential energetic change. They provide a valuable knowledge of Cd effects at biochemical and molecular levels in the gill and digestive gland of R. decussatus.

Peroxisomal proteomic approach for protein profiling in blue mussels (Mytilus edulis) exposed to crude oil

Peroxisomal proteomic protein profiles of exposure to marine pollution have been recently introduced in biomonitoring experiments. However, laboratory experiments to study the independent effect of common pollutants are needed to define a minimal protein expression signature (PES) of exposure to a specific pollutant. The aim of this study was to obtain PESs in blue mussels (Mytilus edulis) exposed to two different crude oil mixtures for future application in biomonitoring areas affected by oil spills. In the study, peroxisome-enriched fractions from digestive gland of M. edulis (L., 1758) were analysed by two-dimensional fluorescence difference electrophoresis (DIGE) and mass spectrometry (MS) after 3 weeks of exposure to crude oil mixtures: crude oil or crude oil spiked with alkylated phenols (AP) and extra polycyclic aromatic hydrocarbons (PAH) in a laboratory flow-through system. A minimal PES composed by 13 protein spots and unique PESs of exposure to the two different mixtures were identified. A total of 22 spots from the two-dimensional maps that had shown a significant increase or decrease in abundance in each of the exposed groups exposed were analysed. The hierarchical clustering analysis succeeded in discriminating the exposed groups from the control groups based on the unique PES. The PESs obtained were consistent with protein patterns obtained in previous field experiments. The results suggest that the protein profiles obtained by peroxisomal proteomics could be used to assess oil exposure in marine pollution assessments.

Genetic variation underlying protein expression in eggs of the marine mussel Mytilus edulis

Study of the genetic basis of gene expression variation is central to attempts to understand the causes of evolutionary change. Although there are many transcriptomics studies estimating genetic variance and heritability in model organisms such as humans there is a lack of equivalent proteomics studies. In the present study, the heritability underlying egg protein expression was estimated in the marine mussel Mytilus. We believe this to be the first such measurement of genetic variation for gene expression in eggs of any organism. The study of eggs is important in evolutionary theory and life history analysis because maternal effects might have profound effects on the rate of evolution of offspring traits. Evidence is presented that the egg proteome varies significantly between individual females and that heritability of protein expression in mussel eggs is moderate to high suggesting abundant genetic variation on which natural selection might act. The study of the mussel egg proteome is also important because of the unusual system of mitochondrial DNA inheritance in mussels whereby different mitochondrial genomes are transmitted independently through female and male lineages (doubly uniparental inheritance). It is likely that the mechanism underlying this system involves the interaction of specific egg factors with sperm mitochondria following fertilization, and its elucidation might be advanced by study of the proteome in females having different progeny sex ratios. Putative identifications are presented here for egg proteins using MS/MS in Mytilus lines differing in sex ratio. Ontology terms relating to stress response and protein folding occur more frequently for proteins showing large expression differences between the lines. The distribution of ontology terms in mussel eggs was compared with those for previous mussel proteomics studies (using other tissues) and with mammal eggs. Significant differences were observed between mussel eggs and mussel tissues but not between the two types of eggs.

Proteomics-based method for risk assessment of peroxisome proliferating pollutants in the marine environment

Pollution in aquatic environment is of increasing concern for its impact on both human and natural populations. Applying proteomics to monitor marine pollution is a new approach to evaluate the effects of environmental pollutants on the biota. Aquatic organisms living in coastal and estuarine areas are particularly prone to exposures to a variety of pollutants, some of which can act as peroxisome proliferators. However, peroxisomal responses in particular and biomarker responses in general can be influenced by several biotic and abiotic factors. Utilizing proteomics-based techniques that permit the evaluation of hundreds to thousands of proteins in a single experiment can circumvent those drawbacks. Applying this method, the peroxisomal proteome from digestive glands of mussels Mytilus sp. can be analyzed by two-dimensional electrophoresis (2-DE) and the 2-DE maps from control samples and samples obtained in a polluted area can be compared. The up- and down-regulated proteins compose the protein expression signature (PES) associated with exposure to peroxisome proliferating pollutants. This method generates highly reproducible patterns that can be applied to laboratory or field experiments.

Proteomic applications in ecotoxicology

Within the growing body of proteomics studies, issues addressing problems of ecotoxicology are on the rise. Generally speaking, ecotoxicology uses quantitative expression changes of distinct proteins known to be involved in toxicological responses as biomarkers. Unlike these directed approaches, proteomics examines how multiple expression changes are associated with a contamination that is suspected to be detrimental. Consequently, proteins involved in toxicological responses that have not been described previously may be revealed. Following identification of key proteins indicating exposure or effect, proteomics can potentially be employed in environmental risk assessment. To this end, bioinformatics may unveil protein patterns specific to an environmental stress that would constitute a classifier able to distinguish an exposure from a control state. The combined use of sets of marker proteins associated with a given pollution impact may prove to be more reliable, as they are based not only on a few unique markers which are measured independently, but reflect the complexity of a toxicological response. Such a proteomic pattern might also integrate some of the already established biomarkers of environmental toxicity. Proteomics applications in ecotoxicology may also comprise functional examination of known classes of proteins, such as glutathione transferases or metallothioneins, to elucidate their toxicological responses.

The use of biomarkers in biomonitoring: a 2-tier approach assessing the level of pollutant-induced stress syndrome in sentinel organisms

The paper outlines a 2-tier approach for wide-scale biomonitoring programmes. To obtain a high level of standardization, we suggest the use of caged organisms (mussels or fish). An "early warning", highly sensitive, low-cost biomarker is employed in tier 1 (i.e. lysosomal membrane stability (LMS) and survival rate, a marker for highly polluted sites). Tier 2 is used only for animals sampled at sites in which LMS changes are evident and there is no mortality, with a complete battery of biomarkers assessing the levels of pollutant-induced stress syndrome. Possible approaches for integrating biomarker data in a synthetic index are discussed, along with our proposal to use a recently developed Expert System. The latter system allows a correct selection of biomarkers at different levels of biological organisation (molecular/cellular/tissue/organism) taking into account trends in pollutant-induced biomarker changes (increasing, decreasing, bell-shape). A selection of biomarkers of stress, genotoxicity and exposure usually employed in biomonitoring programmes is presented, together with a brief overview of new biomolecular approaches.

The potential of proteomics for providing new insights into environmental impacts on human health

The effects of environmental chemicals have traditionally been detected by monitoring biomarkers of exposure or biomarkers of effect. Proteomics, the study of the complete profile of proteins in a given cell, tissue or biological system, is a new approach using a set of high-throughput methodologies with a wide dynamic range that makes possible the discovery of novel biomarkers. This article reviews the application of two-dimensional electrophoresis and mass-spectrometry methods to environmental toxicology. Emphasis is placed on the protein-expression signature approach and on identifying redox-based post-translational protein modifications. The methodological links between studies in sentinel organisms and humans are explored. Significant limitations and challenges are placed on this approach by the shortage of genome sequence data necessary for protein identification and the growing requirement for more stringent study design. Proteomics will continue to be an important toolkit to help address the growing environmental threat posed by nanoparticles and endocrine disrupting agents.

Proteomics-Based Method for the Assessment of Marine Pollution Using Liquid Chromatography Coupled with Two-Dimensional Electrophoresis

Using a proteomic approach, we have developed a new method for the assessment of marine pollution that generates highly reproducible protein expression patterns and it is simple and scalable. The protocol is based on applying liquid chromatography (LC) coupled with two-dimensional electrophoresis (2-DE) to analyze changes in the protein expression pattern after exposure to marine pollution. The digestive gland of the sentinel "blue mussel" (Mytilus edulis) was batch-processed through a simple cell fractionation followed by ion-exchange chromatography and 2-DE. The selection of ligands, elution method, and small volume design was carefully considered to define a protocol that could be mainly robotized. A pilot study with samples collected from different Gothenburg harbor areas indicated that the clean area could be distinguished from the polluted ones based on a protein expression pattern (PES) composed of 13 proteins. Principal component analysis (PCA) and hierarchical clustering confirmed that the PES was sufficient to discriminate polluted and unpolluted areas and to provide a spatial gradient from the polluted source. Several proteins from the PES were identified by electrospray ionization tandem mass spectrometry (ESI-MS/MS), and they are involved in beta-oxidation, amino acid metabolism, detoxification, protein degradation, organelle biogenesis, and protein folding. In the near future, this methodology could show potential advantages to assess marine pollution and could become a stable platform to elucidate ecotoxicological questions.

Data processing and classification analysis of proteomic changes: a case study of oil pollution in the mussel, Mytilus edulis

BACKGROUND

Proteomics may help to detect subtle pollution-related changes, such as responses to mixture pollution at low concentrations, where clear signs of toxicity are absent. The challenges associated with the analysis of large-scale multivariate proteomic datasets have been widely discussed in medical research and biomarker discovery. This concept has been introduced to ecotoxicology only recently, so data processing and classification analysis need to be refined before they can be readily applied in biomarker discovery and monitoring studies.

RESULTS

Data sets obtained from a case study of oil pollution in the Blue mussel were investigated for differential protein expression by retentate chromatography-mass spectrometry and decision tree classification. Different tissues and different settings were used to evaluate classifiers towards their discriminatory power. It was found that, due the intrinsic variability of the data sets, reliable classification of unknown samples could only be achieved on a broad statistical basis (n > 60) with the observed expression changes comprising high statistical significance and sufficient amplitude. The application of stringent criteria to guard against overfitting of the models eventually allowed satisfactory classification for only one of the investigated data sets and settings.

CONCLUSION

Machine learning techniques provide a promising approach to process and extract informative expression signatures from high-dimensional mass-spectrometry data. Even though characterisation of the proteins forming the expression signatures would be ideal, knowledge of the specific proteins is not mandatory for effective class discrimination. This may constitute a new biomarker approach in ecotoxicology, where working with organisms, which do not have sequenced genomes render protein identification by database searching problematic. However, data processing has to be critically evaluated and statistical constraints have to be considered before supervised classification algorithms are employed.