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The aim of this study was to examine the transcriptional levels of selected genes in liver and head kidney of Atlantic cod Gadus morhua sampled in Store Lungegårdsvann, a seawater recipient situated in the middle of the city of Bergen, Norway, for effects of contaminants released from municipal sewage effluents and former dump sites. Five males and...
Citations
... Exposure to chlorinated compounds was predicted to have a stronger impact on lipid accumulation than the other two contaminants. Accumulated levels of PCB7 were up to 7,900 ng/g in liver of cod collected from Western Norway (Olsvik et al., 2009) (Green & Knutzen, 2003). Later surveillance has documented levels of 143 ng/μg P PBDE in liver of cod collected in the North Atlantic (Nøstbakken et al., 2018). ...
In the North Sea and North Atlantic coastal areas, fish experience relatively high background levels of persistent organic pollutants. This study aimed to compare the mode of action of environmentally relevant concentrations of mixtures of halogenated compounds in Atlantic cod. Juvenile male cod with mean weight of 840 g were exposed by gavage to dietary mixtures of chlorinated (PCBs, DDT analogs, chlordane, lindane, and toxaphene), brominated (PBDEs), and fluorinated (PFOS) compounds for 4 weeks. One group received a combined mixture of all three compound groups. The results showed that the accumulated levels of chemicals in cod liver after 4 weeks of exposure reflected concentrations found in wild fish in this region. Pathway analysis revealed that the treatment effects by each of the three groups of chemicals (chlorinated, brominated, and fluorinated) converged on activation of the unfolded protein response (UPR). Upstream regulator analysis predicted that almost all the key transcription factors (XBP1, ERN1, ATF4, EIF2AK3, and NFE2L2) regulating the UPR were significantly activated. No additive effect was observed in cod co-treated with all three compound groups. In conclusion, the genome-wide transcriptomic study suggests that the UPR pathway is a sensitive common target of halogenated organic environmental pollutants in fish.
... Unfortunately, cod is increasingly susceptible to marine pollution from petroleum activities [2,3]. Atlantic cod is commonly used as an indicator species in marine environmental monitoring programs, and a useful model organism to investigate the effect of toxicants [4][5][6]. Finding the best set of biomarkers for Atlantic cod exposed to toxicants is of high research and commercial value. Biomarkers can for example be defined based on the expression level of a set of genes or proteins. ...
Univariate and multivariate feature selection methods can be used for biomarker discovery in analysis of toxicant exposure. Among the univariate methods, differential expression analysis (DEA) is often applied for its simplicity and interpretability. A characteristic of methods for DEA is that they treat genes individually, disregarding the correlation that exists between them. On the other hand, some multivariate feature selection methods are proposed for biomarker discovery. Provided with various biomarker discovery methods, how to choose the most suitable method for a specific dataset becomes a problem. In this paper, we present a framework for comparison of potential biomarker discovery methods: three methods that stem from different theories are compared by how stable they are and how well they can improve the classification accuracy. The three methods we have considered are: Significance Analysis of Microarrays (SAM) which identifies the differentially expressed genes; minimum Redundancy Maximum Relevance (mRMR) based on information theory; and Characteristic Direction (GeoDE) inspired by a graphical perspective. Tested on the gene expression data from two experiments exposing the cod fish to two different toxicants (MeHg and PCB 153), different methods stand out in different cases, so a decision upon the most suitable method should be made based on the dataset under study and the research interest.
... Unfortunately, cod is increasingly susceptible to marine pollution from petroleum activities [2,3]. Atlantic cod is commonly used as an indicator species in marine environmental monitoring programs, and a useful model organism to investigate the effect of toxicants [4,5,6]. Finding the best set of biomarkers for Atlantic cod exposed to toxicants is of high research and commercial value. ...
Univariate and multivariate feature selection methods can be used for biomarker discovery in analysis of toxicant exposure. Among the univariate methods, differential expression analysis (DEA) is often applied for its simplicity and interpretability. A characteristic of methods for DEA is that they treat genes individually, disregarding the correlation that exists between them. On the other hand, some multivariate feature selection methods are proposed for biomarker discovery. Provided with various biomarker discovery methods, how to choose the most suitable method for a specific dataset becomes a problem. In this paper, we present a framework for comparison of potential biomarker discovery methods: three methods that stem from different theories are compared by how stable they are and how well they can improve the classification accuracy. The three methods we have considered are: Significance Analysis of Microarrays (SAM) which identifies the differentially expressed genes; minimum Redundancy Maximum Relevance (mRMR) based on information theory; and Characteristic Direction (GeoDE) inspired by a graphical perspective. Tested on the gene expression data from two experiments exposing the cod fish to two different toxicants (MeHg and PCB 153), different methods stand out in different cases, so a decision upon the most suitable method should be made based on the dataset under study and the research interest.
... However, exposure to prototypical Pxr agonists resulted in upregulated transcription of cyp3a genes in Atlantic killifish (Fundulus heteroclitus), zebrafish liver and rainbow trout (Oncorhynchus mykiss) [46][47][48] . Furthermore, expression patterns of the subfamilies cyp3b, cyp3c, and cyp3d in ray-finned fishes (Actinopterygii) suggest involvement in xenobiotic metabolism, but this role has not yet been demonstrated 11,[49][50][51] . Thus, the widespread absence of pxr orthologs in teleosts, and particularly among Gadiform species, raise interesting questions on how transcriptional regulation of biotransformation enzymes in these species has evolved. ...
Sensitivity to environmental stressors largely depend on the genetic complement of the organism. Recent sequencing and assembly of teleost fish genomes enable us to trace the evolution of defense genes in the largest and most diverse group of vertebrates. Through genomic searches and in-depth analysis of gene loci in 76 teleost genomes, we show here that the xenosensor pregnane X receptor (Pxr, Nr1i2) is absent in more than half of these species. Notably, out of the 27 genome assemblies that belong to the Gadiformes order, the pxr gene was only retained in the Merluccidae family (hakes) and Pelagic cod (Melanonus zugmayeri). As an important receptor for a wide range of drugs and environmental pollutants, vertebrate PXR regulate the transcription of a number of genes involved in the biotransformation of xenobiotics, including cytochrome P450 enzymes (CYP). In the absence of Pxr, we suggest that the aryl hydrocarbon receptor (Ahr) have evolved an extended regulatory role by governing the expression of certain Pxr target genes, such as cyp3a, in Atlantic cod (Gadus morhua). However, as several independent losses of pxr have occurred during teleost evolution, other lineages and species may have adapted alternative compensating mechanisms for controlling crucial cellular defense mechanisms.
... The Atlantic cod (Gadus morhua) is a commercially important species, but increasingly susceptible to marine pollution from sources such as shipping activities, urban effluent discharges, and discharges from offshore petroleum industries. Importantly, Atlantic cod is increasingly becoming a useful model organism to investigate effects of contaminants, and as a sentinel species used in environmental monitoring of marine pollution [28][29][30][31][32][33][34]. It is one of few fish species with a sequenced and annotated genome [35], thus opening the possibility of using omics methods in molecular toxicological studies [25,36,37]. ...
Background
Methylmecury (MeHg) is a widely distributed environmental pollutant with considerable risk to both human health and wildlife. To gain better insight into the underlying mechanisms of MeHg-mediated toxicity, we have used label-free quantitative mass spectrometry to analyze the liver proteome of Atlantic cod (Gadus morhua) exposed in vivo to MeHg (0, 0.5, 2 mg/kg body weight) for 2 weeks. ResultsOut of a toltal of 1143 proteins quantified, 125 proteins were differentially regulated between MeHg-treated samples and controls. Using various bioinformatics tools, we performed gene ontology, pathway and network enrichment analysis, which indicated that proteins and pathways mainly related to energy metabolism, antioxidant defense, cytoskeleton remodeling, and protein synthesis were regulated in the hepatic proteome after MeHg exposure. Comparison with previous gene expression data strengthened these results, and further supported that MeHg predominantly affects many energy metabolism pathways, presumably through its strong induction of oxidative stress. Some enzymes known to have functionally important oxidation-sensitive cysteine residues in other animals are among the differentially regulated proteins, suggesting their modulations by MeHg-induced oxidative stress. Integrated analysis of the proteomics dataset combined with previous gene expression dataset showed a more pronounced effect of MeHg on amino acid, glucose and fatty acid metabolic pathways, and suggested possible interactions of the cellular energy metabolism and antioxidant defense pathways. Conclusions
MeHg disrupts mainly redox homeostasis and energy generating metabolic pathways in cod liver. The energy pathways appear to be modulated through MeHg-induced oxidative stress, possibly mediated by oxidation sensitive enzymes.
... In some species (often invertebrates) metabolism of PAHs by CYP1A and CYP1A-like enzymes can also lead to oxidative stress, which subsequently results in the production of reactive oxygen species (ROS) that can cause altered cell physiology, mutations, or cell death (Livingstone, 2003). However, cells contain multiple antioxidant enzymes that can neutralize these ROSs such as superoxide dismutase (SOD) and gene expression and enzyme activity of SOD have been examined for pollution monitoring in B. saida and other marine fish (Benedetti et al., 2007;Livingstone et al., 1992;Olsvik et al., 2009;Nahrgang et al., 2009Nahrgang et al., , 2010b. If these antioxidant systems are overwhelmed, the oxidative stress by ROSs can lead to DNA damage and particularly single-strand DNA breaks, which are known to result in both the liver and blood cells of B. saida and other marine fish when exposed to PAHs and other pollutants (Curtis et al., 2011;Hartl et al., 2007;Nacci et al., 1996;Nahrgang et al., 2010b;Mitchelmore and Chipman, 1998a,b). ...
... While other studies have examined relative gene expression (ΔCT) for cytochrome p4501a1, glutathione-S-transferase, and Cu/Zn superoxide dismutase in B. saida and other cod species (Nahrgang et al., 2009(Nahrgang et al., , 2010bOlsvik et al., 2009), their results could not be directly comparable to this study as they converted ΔCT to either relative gene expression by a standard dilution curve (geNorm software) or mean fold change in mRNA expression with a reference site using the 2 À ΔΔCT method. However, Nahrgang et al. (2010b) suggest that that cyp1a1 is a promising marker with gst as a suitable complement for examining exposure to watersoluble fractions of crude oil as they observed a concentrationdependent up-regulation of both genes. ...
As part of the Chukchi Sea Offshore Monitoring in Drilling Area-Chemical and Benthos (COMIDA CAB) project, we determined the distribution and concentrations of aliphatic n-alkanes and polycyclic aromatic hydrocarbons (PAHs) in surface sediments (0–1 cm) among 52 sites across the Chukchi Sea and in muscle tissues of the benthic Northern whelk, Neptunea heros, collected opportunistically. In addition, downcore profiles of contaminants were determined at three targeted sites to establish historic patterns. Baseline responses of PAH exposure and its potential toxicological effects were examined in the common Arctic cod, Boreogadus saida, through measures of cytochrome P4501A/ ethoxyresorufin O-deethylase (CYP1A/EROD), glutathione-S-transferase (GST), and Cu/Zn superoxide dismutase (SOD) activity in liver tissue. The total concentration of PAHs in surface sediments throughout the study area, including parent and alkyl-homologs, were very low (<1600 ng g−1 dry wt) except for a single station, where values were 2–20-fold greater than at other baseline sites (2956 ng g−1 dry wt). Alkyl-substituted PAHs were the dominant form in all surface (54–93%) and subsurface sediments (50–81% of the total), with a general decrease in total PAH concentrations observed downcore. In biota, larger Neptunea showed lower total concentrations of PAHs in foot muscles (4.5–10.7 ng g−1 wet wt) compared to smaller animals; yet aliphatic n-alkane (C19–C33) concentrations (0.655–5.20 μg g−1 wet wt) increased in larger organisms with distributions dominated by long-chain (C23–C33) hydrocarbons. In B. saida, CYP1A1, GST, and SOD enzyme levels were comparable to baseline levels previously reported in other pristine systems. Of the three assays, only SOD had a significant correlation between gene expression and enzyme activity.
... The real-time PCR was performed by using the SYBR Green Master Mix containing FastStart DNA polymerase (LightCycler 480 SYBR Green Master Mix Kit; Roche Applied Sciences) and gene-specific primers (500 nM). The PCR was achieved with a 5 min activation and denaturation step at 958C, followed by forty-five cycles of a denaturing step at 958C, a 10 s annealing step at 608C and a 10 s synthesis step at 728C according to Olsvik et al. (35) . The mean normalised expression of the target genes was determined using a normalisation factor calculated in geNorm software (Ghent University) using the reference genes (36) . ...
Se is an essential trace element, and is incorporated into selenoproteins which to play important roles in human health. Mammalian selenoprotein-coding genes are often present as paralogues in teleost fish, and it is unclear whether the expression patterns or functions of these fish paralogues reflect their mammalian orthologues. Using the model species zebrafish (Danio rerio; ZF), we aimed to assess how dietary Se affects key parameters in Se metabolism and utilisation including glutathione peroxidase (GPX) activity, the mRNA expression of key Se-dependent proteins (gpx1a, gpx1b, sepp1a and sepp1b), oxidative status, reproductive success and F1 generation locomotor activity. From 27 d until 254 d post-fertilisation, ZF were fed diets with graded levels of Se ranging from deficient ( < 0·10 mg/kg) to toxic (30 mg/kg). The mRNA expression of gpx1a and gpx1b and GPX activity responded in a similar manner to changes in Se status. GPX activity and mRNA levels were lowest when dietary Se levels (0·3 mg/kg) resulted in the maximum growth of ZF, and a proposed bimodal mechanism in response to Se status below and above this dietary Se level was identified. The expression of the sepp1 paralogues differed, with only sepp1a responding to Se status. High dietary Se supplementation (30 mg/kg) decreased reproductive success, while the offspring of ZF fed above 0·3 mg Se/kg diet had lower locomotor activity than the other groups. Overall, the novel finding of low selenoprotein expression and activity coinciding with maximum body growth suggests that even small Se-induced variations in redox status may influence cellular growth rates.
... RNA was extracted and analysed using real-time RT-qPCR according to Olsvik, Lie, Goksoyr, Midtun, Frantzen and Maage (2009), with some modification. The PCR primer sequences used for the quantification of the transcriptional levels of the nine target and three reference genes (eef1a1la, uba52 and actb1) are shown in Table 2. ...
It currently remains unclear if rotifers contain sufficient mineral levels to meet larval fish requirements. In this study, rotifers were enriched with a commercial enrichment (control), or with additional iodine, iodine and copper, or iodine, copper and manganese, and the effects of feeding these rotifers to Atlantic cod (Gadus morhua) larvae from 3 to 18 days post hatch were investigated. Rotifer enrichment with minerals was successful, but Mn enrichment also increased rotifer zinc levels. No differences were observed between treatments in larval growth or survival, or in the mRNA levels in the majority of the redox system genes analysed. Only Zn levels increased in cod larvae in response to mineral enrichment of rotifers. Apart from Zn, little evidence was found to suggest that cod larvae require increased concentrations above the control rotifer levels of the essential elements studied here.
... PCR efficiencies ranged from 1.87 to 2.20. A two-step reverse transcription qPCR (RT-qPCR) method previously described by Olsvik et al. (2009) was used to measure the mRNA levels of MT-A and Ubi in Atlantic salmon. Briefly, the RT reactions were run in duplicates on 96-well reaction plates with the GeneAmp PCR 9700 machine (Applied Biosystems, Foster City, CA, USA) using TaqMan Reverse Transcription Reagent containing Multiscribe Reverse Transcriptase (50 U ml À1 ) (Applied Biosystems, Foster City, CA, USA). ...
... The Atlantic cod is an important species in both North Atlantic fisheries and in a developing aquaculture industry, and its genome has been sequenced recently (Star et al., 2011). Atlantic cod can be susceptible to environmental contaminants in coastal regions and it is commonly used in environmental toxicology studies (Amlund et al., 2007; Balk et al., 2011; Bohne-Kjersem et al., 2009; Goksøyr et al., 1987 Goksøyr et al., , 1994 Lie et al., 2009; Meier et al., 2007; Olsvik et al., 2009 ). Toxicogenomics studies can be used to illuminate the molecular targets and may help to better understand mechanisms of toxicity of environmental pollutants (Hahn, 2011). ...
... DNJC3, GRP78, ENPL and four heat shock proteins (HSP22, HSP90 beta, HSP90 and HSP70) were also represented in the GeneGO process network Response to unfolded proteins (Fig. 5). Some of the HSP genes such as HSP70 are commonly used as biomarkers of exposure to diverse pollutants including mercury compounds (Olsvik et al., 2011Olsvik et al., , 2009 ) and their up-regulation by MeHg here further suggests their usefulness as biomarkers of exposure to MeHg in fish. Another induced gene coding for CBS, which metabolises a crucial step in the synthesis of cysteine, may be evaluated as a biomarker of MeHg exposure. ...
Methylmercury (MeHg) is a widely distributed contaminant polluting many aquatic environments, with health risks to humans exposed mainly through consumption of seafood. The mechanisms of toxicity of MeHg are not completely understood. In order to map the range of molecular targets and gain better insights into the mechanisms of toxicity, we prepared Atlantic cod (Gadus morhua) 135k oligonucleotide arrays and performed global analysis of transcriptional changes in the liver of fish treated with MeHg (0.5 and 2mg/kg of body weight) for 14days. Inferring from the observed transcriptional changes, the main pathways significantly affected by the treatment were energy metabolism, oxidative stress response, immune response and cytoskeleton remodeling. Consistent with known effects of MeHg, many transcripts for genes in oxidative stress pathways such as glutathione metabolism and Nrf2 regulation of oxidative stress response were differentially regulated. Among the differentially regulated genes, there were disproportionate numbers of genes coding for enzymes involved in metabolism of amino acids, fatty acids and glucose. In particular, many genes coding for enzymes of fatty acid beta-oxidation were up-regulated. The coordinated effects observed on many transcripts coding for enzymes of energy pathways may suggest disruption of nutrient metabolism by MeHg. Many transcripts for genes coding for enzymes in the synthetic pathways of sulphur containing amino acids were also up-regulated, suggesting adaptive responses to MeHg toxicity. By this toxicogenomics approach, we were also able to identify many potential biomarker candidate genes for monitoring environmental MeHg pollution. These results based on changes on transcript levels, however, need to be confirmed by other methods such as proteomics.
