Integrative environmental genomics of Cod (Gadus morhua): the proteomics approach

Retene, pyrene and phenanthrene cause distinct molecular-level changes in the cardiac tissue of rainbow trout (Oncorhynchus mykiss) larvae, part 2 - Proteomics and metabolomics

Polycyclic aromatic hydrocarbons (PAHs) are global contaminants of concern. Despite several decades of research, their mechanisms of toxicity are not very well understood. Early life stages of fish are particularly sensitive with the developing cardiac tissue being a main target of PAHs toxicity. The mechanisms of cardiotoxicity of the three widespread model polycyclic aromatic hydrocarbons (PAHs) retene, pyrene and phenanthrene were explored in rainbow trout (Oncorhynchus mykiss) early life stages. Newly hatched larvae were exposed to sublethal doses of each individual PAH causing no detectable morphometric alterations. Changes in the cardiac proteome and metabolome were assessed after 7 or 14 days of exposure to each PAH. Phase I and II enzymes regulated by the aryl hydrocarbon receptor were significantly induced by all PAHs, with retene being the most potent compound. Retene significantly altered the level of several proteins involved in key cardiac functions such as muscle contraction, cellular tight junctions or calcium homeostasis. Those findings were quite consistent with previous reports regarding the effects of retene on the cardiac transcriptome. Significant changes in proteins linked to iron and heme metabolism were observed following exposure to pyrene. While phenanthrene also altered the levels of several proteins in the cardiac tissue, no clear mechanisms or pathways could be highlighted. Due to high variability between samples, very few significant changes were detected in the cardiac metabolome overall. Slight but significant changes were still observed for pyrene and phenanthrene, suggesting possible effects on several energetic or signaling pathways. This study shows that early exposure to different PAHs can alter the expression of key proteins involved in the cardiac function, which could potentially affect negatively the fitness of the larvae and later of the juvenile fish.

Environmental effects of offshore produced water discharges: A review focused on the Norwegian continental shelf

Produced water (PW), a large byproduct of offshore oil and gas extraction, is reinjected to formations or discharged to the sea after treatment. The discharges contain dispersed crude oil, polycyclic aromatic hydrocarbons (PAHs), alkylphenols (APs), metals, and many other constituents of environmental relevance. Risk-based regulation, greener offshore chemicals and improved cleaning systems have reduced environmental risks of PW discharges, but PW is still the largest operational source of oil pollution to the sea from the offshore petroleum industry. Monitoring surveys find detectable exposures in caged mussel and fish several km downstream from PW outfalls, but biomarkers indicate only mild acute effects in these sentinels. On the other hand, increased concentrations of DNA adducts are found repeatedly in benthic fish populations, especially in haddock. It is uncertain whether increased adducts could be a long-term effect of sediment contamination due to ongoing PW discharges, or earlier discharges of oil-containing drilling waste. Another concern is uncertainty regarding the possible effect of PW discharges in the sub-Arctic Southern Barents Sea. So far, research suggests that sub-arctic species are largely comparable to temperate species in their sensitivity to PW exposure. Larval deformities and cardiac toxicity in fish early life stages are among the biomarkers and adverse outcome pathways that currently receive much attention in PW effect research. Herein, we summarize the accumulated ecotoxicological knowledge of offshore PW discharges and highlight some key remaining knowledge needs.

The crystal structure of haemoglobin from Atlantic cod

The isolation of the dominant isoform of haemoglobin from Atlantic cod caught in southwest Norway is reported and its X-ray crystal structure is presented.

The crystal structure of haemoglobin from Atlantic cod has been solved to 2.54 Å resolution. The structure consists of two tetramers in the crystallographic asymmetric unit. The structure of haemoglobin obtained from one individual cod suggests polymorphism in the tetrameric assembly.

RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision-cut liver slices exposed to benzo[a]pyrene and 17α-ethynylestradiol

Polycyclic aromatic hydrocarbons such as benzo[a]pyrene (BaP) that activate the aryl hydrocarbon receptor (Ahr) pathway, and endocrine disruptors acting through the estrogen receptor pathway are among environmental pollutants of major concern. In this work, we exposed Atlantic cod (Gadus morhua) precision-cut liver slices (PCLS) to BaP (10 nM and 1000 nM), ethynylestradiol (EE2) (10 nM and 1000 nM), and equimolar mixtures of BaP and EE2 (10 nM and 1000 nM) for 48 h, and performed RNA-Seq based transcriptome mapping followed by systematic bioinformatics analyses. Our gene expression analysis showed that several genes were differentially expressed in response to BaP and EE2 treatments in PCLS. Strong up-regulation of genes coding for the cytochrome P450 1a (Cyp1a) enzyme and the Ahr repressor (Ahrrb) was observed in BaP treated PCLS. EE2 treatment of liver slices strongly up-regulated genes coding for precursors of vitellogenin (Vtg) and eggshell zona pellucida (Zp) proteins. As expected, pathway enrichment and network analysis showed that the Ahr and estrogen receptor pathways are among the top affected by BaP and EE2 treatments, respectively. Interestingly, two genes coding for fibroblast growth factor 3 (Fgf3) and fibroblast growth factor 4 (Fgf4) were up-regulated by EE2 in this study. To our knowledge, the fgf3 and fgf4 genes have not previously been described in relation to estrogen signaling in fish liver, and these results suggest the modulation of the FGF signaling pathway by estrogens in fish. The signature expression profiles of top differentially expressed genes in response to the single compound (BaP or EE2) treatment were generally maintained in the expression responses to the equimolar binary mixtures. However, in the mixture-treated groups, BaP appeared to have anti-estrogenic effects as observed by lower number of differentially expressed putative EE2 responsive genes. Our in-depth quantitative analysis of changes in liver transcriptome in response to BaP and EE2, using PCLS tissue culture provides further mechanistic insights into effects of the compounds. Moreover, the analyses demonstrate the usefulness of PCLS in cod for omics experiments.

Proteome response of fish under multiple stress exposure: Effects of pesticide mixtures and temperature increase

Aquatic systems can be subjected to multiple stressors, including pollutant cocktails and elevated temperature. Evaluating the combined effects of these stressors on organisms is a great challenge in environmental sciences. To the best of our knowledge, this is the first study to assess the molecular stress response of an aquatic fish species subjected to individual and combined pesticide mixtures and increased temperatures. For that, goldfish (Carassius auratus) were acclimated to two different temperatures (22 and 32°C) for 15 days. They were then exposed for 96h to a cocktail of herbicides and fungicides (S-metolachlor, isoproturon, linuron, atrazine-desethyl, aclonifen, pendimethalin and tebuconazole) at two environmentally relevant concentrations (total concentrations of 8.4μgL^-1 and 42μgL^-1) at these two temperatures (22 and 32°C). The molecular response in liver was assessed by 2D-proteomics. Identified proteins were integrated using pathway enrichment analysis software to determine the biological functions involved in the individual or combined stress responses and to predict the potential deleterious outcomes. The pesticide mixtures elicited pathways involved in cellular stress response, carbohydrate, protein and lipid metabolisms, methionine cycle, cellular functions, cell structure and death control, with concentration- and temperature-dependent profiles of response. We found that combined temperature increase and pesticide exposure affected the cellular stress response: the effects of oxidative stress were more marked and there was a deregulation of the cell cycle via apoptosis inhibition. Moreover a decrease in the formation of glucose by liver and in ketogenic activity was observed in this multi-stress condition. The decrease in both pathways could reflect a shift from a metabolic compensation strategy to a conservation state. Taken together, our results showed (1) that environmental cocktails of herbicides and fungicides induced important changes in pathways involved in metabolism, cell structure and cell cycle, with possible deleterious outcomes at higher biological scales and (2) that increasing temperature could affect the response of fish to pesticide exposure.

Toxicology of metals and metalloids: Promising issues for future studies in environmental health and toxicology

The function and behavior of chemical elements in ecosystems and in human health probably comprise one of the most studied issues and a theme of great interest and fascination in science. Hot topics are emerging on an annual basis in this field. Bearing this in mind, some promising themes to explore in the field of metals and metalloids in the environment and in toxicology are highlighted and briefly discussed herein.

Top-Down Proteomics and Farm Animal and Aquatic Sciences

Proteomics is a field of growing importance in animal and aquatic sciences. Similar to other proteomic approaches, top-down proteomics is slowly making its way within the vast array of proteomic approaches that researchers have access to. This opinion and mini-review article is dedicated to top-down proteomics and how its use can be of importance to animal and aquatic sciences. Herein, we include an overview of the principles of top-down proteomics and how it differs regarding other more commonly used proteomic methods, especially bottom-up proteomics. In addition, we provide relevant sections on how the approach was or can be used as a research tool and conclude with our opinions of future use in animal and aquatic sciences.

Proteomics and the search for welfare and stress biomarkers in animal production in the one-health context

Stress and welfare are important factors in animal production in the context of growing production optimization and scrutiny by the general public.

Study of the bile proteome of Atlantic cod (Gadus morhua): Multi-biological markers of exposure to polycyclic aromatic hydrocarbons

PAH metabolites present in bile are well-known biological markers of exposure in fish, and their investigation is recommended by the ICES (International Council for the Exploration of the Sea) and the OSPAR convention (Convention for the Protection of the Marine Environment of the North-East Atlantic) for monitoring purposes. Development of analytical strategies for fish bile is encouraged by the need for more sensitive and informative markers (e.g., capable of tracking the PAH composition of contamination sources) and strengthened by recent results in both fish genomics and proteomics. Herein, the study of the Atlantic cod bile proteome is presented. Preliminary testing for discovering new sensitive markers in the form of expressed proteins affected by PAH exposure (i.e., PAH-protein adducts) is reported. Protein markers were identified using LC-MS/MS analysis, as single biological indicators. Through multivariate analyses, the overall proteome was revealed to be a sensitive multi-biological marker of exposure to PAHs.

Precision-cut liver slices of Atlantic cod (Gadus morhua): an in vitro system for studying the effects of environmental contaminants

The Atlantic cod (Gadus morhua) is an economically important species commonly consumed by humans. The widespread distribution of cod in the North Atlantic Ocean makes it vulnerable to effluents from human activities, such as coastal industries and offshore petroleum exploration. It has been demonstrated that many effluents have adverse effects on cod reproduction and health, e.g. by disrupting endocrine signaling pathways. The liver, expressing important components of the biotransformation and the endocrine system, is one of the main target organs. Thus, reliable and reproducible in vitro systems of the liver are important for studying effects of environmental contaminants. The aim of this study was to investigate precision-cut liver slices (PCLS) as an alternative in vitro system for toxicological studies of the Atlantic cod liver. Slices of 8 mm in diameter and 250 μm thickness were prepared and cultivated from immature cod. Several analyses to measure the liver slice viability were performed: enzyme assays, histology, and morphometric analysis, all confirming cell viability for up to 72 h in culture. The liver slices were also exposed to two well-known model environmental contaminants, β-naphthoflavone (BNF) and 17α-ethynylestradiol (EE2), representing established agonists for the aryl hydrocarbon receptor (AHR) and the estrogen receptor (ER), respectively. The results showed increased transcription of the target genes cytochrome P450 1A (CYP1A) and vitellogenin (VTG), both well-established biomarkers for exposure of fish to the selected compounds. In conclusion, PCLS is a promising in vitro system for toxicological studies of cod liver cells. The liver slices are viable in culture for several days and respond to environmental contaminants in a dose- and time-specific manner.

Liver transcriptome analysis of Atlantic cod (Gadus morhua) exposed to PCB 153 indicates effects on cell cycle regulation and lipid metabolism

BACKGROUND

Polychlorinated biphenyls (PCBs) are persistent organic pollutants (POPs) with harmful effects in animals and humans. Although PCB 153 is one of the most abundant among PCBs detected in animal tissues, its mechanism of toxicity is not well understood. Only few studies have been conducted to explore genes and pathways affected by PCB 153 by using high throughput transcriptomics approaches. To obtain better insights into toxicity mechanisms, we treated juvenile Atlantic cod (Gadus morhua) with PCB 153 (0.5, 2 and 8 mg/kg body weight) for 2 weeks and performed gene expression analysis in the liver using oligonucleotide arrays.

RESULTS

Whole-genome gene expression analysis detected about 160 differentially regulated genes. Functional enrichment, interactome, network and gene set enrichment analysis of the differentially regulated genes suggested that pathways associated with cell cycle, lipid metabolism, immune response, apoptosis and stress response were among the top significantly enriched. Particularly, genes coding for proteins in DNA replication/cell cycle pathways and enzymes of lipid biosynthesis were up-regulated suggesting increased cell proliferation and lipogenesis, respectively.

CONCLUSIONS

PCB 153 appears to activate cell proliferation and lipogenic genes in cod liver. Transcriptional up-regulation of marker genes for lipid biosynthesis resembles lipogenic effects previously reported for persistent organic pollutants (POPs) and other environmental chemicals. Our results provide new insights into mechanisms of PCB 153 induced toxicity.

Environmental impacts of produced water and drilling waste discharges from the Norwegian offshore petroleum industry

Operational discharges of produced water and drill cuttings from offshore oil and gas platforms are a continuous source of contaminants to continental shelf ecosystems. This paper reviews recent research on the biological effects of such discharges with focus on the Norwegian Continental Shelf. The greatest concern is linked to effects of produced water. Alkylphenols (AP) and polyaromatic hydrocarbons (PAH) from produced water accumulate in cod and blue mussel caged near outlets, but are rapidly metabolized in cod. APs, naphtenic acids, and PAHs may disturb reproductive functions, and affect several chemical, biochemical and genetic biomarkers. Toxic concentrations seem restricted to <2 km distance. At the peak of discharge of oil-contaminated cuttings fauna disturbance was found at more than 5 km from some platforms, but is now seldom detected beyond 500 m. Water-based cuttings may seriously affect biomarkers in filter feeding bivalves, and cause elevated sediment oxygen consumption and mortality in benthic fauna. Effects levels occur within 0.5-1 km distance. The stress is mainly physical. The risk of widespread, long term impact from the operational discharges on populations and the ecosystem is presently considered low, but this cannot be verified from the published literature.

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.