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Systems toxicology of Atlantic cod

Overview

Coastal zones and oceans constitute an essential fundament for Norway’s history as well as current economy, providing ecosystem services for fisheries, aquaculture, transport, tourism, and recreation. The petroleum activities in Norwegian waters have been crucial for Norway’s financial growth and in financing the Norwegian welfare state. As the pressure on the oceans continuously increases, both the petroleum industry and the seafood industries have acknowledged that awareness and actions are required to maintain a healthy marine environment to secure Norway´s future marine bioeconomy. Marine industries must also comply with governmental and international regulations regarding sustainable practices of marine activities, and novel technologies are needed in order to efficiently cope with such future demands.

The goal of the dCod-project is to combine the competencies in environmental toxicology, biology, bioinformatics and mathematics across the traditional department boundaries, to create a deeper understanding of cods' adaptations and reactions to stressors in the environment. The projects aims to generate large amounts of experimental data to be the basis of mathematical models that can describe these responses based on different scenarios. Furthermore, the overall goal is to create a tool for environmental monitoring and risk assessment that can be used in assessing the impacts of for example the oil industry, sewage discharge into harbours and industrial discharge into Norwegian fjords.

The project is associated with the Centre for Digital Life Norway.

Programme: dCod 1.0: decoding systems toxicology of cod

SEEK ID: https://fairdomhub.org/projects/60

Public web page: http://www.uib.no/en/dcod

Organisms: Gadus morhua

FAIRDOM PALs: No PALs for this Project

Project created: 5th Feb 2017

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Libe Aranguren Abadía

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

Nello Blaser project_administratorprogramme_administrator

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

Morten Brun

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

Karina Dale project_administratorprogramme_administrator

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

Dorothy Dankel

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

https://orcid.org/0000-0002-8839-3333
Marta Eide

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

Shirin Fallahi

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

Anders Goksøyr project_administratorprogramme_administrator

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

https://orcid.org/0000-0003-4054-9842
Siri Øfsthus Goksøyr

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

https://orcid.org/0000-0003-0073-3282
Eileen Marie Hanna

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

Ketil Hylland

Projects: Systems toxicology of Atlantic cod

Institutions: University of Olso

https://orcid.org/0000-0001-5453-2932
Inge Jonassen

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

https://orcid.org/0000-0003-4110-0748
Odd André Karlsen

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

Essa Ahsan Khan

Projects: Systems toxicology of Atlantic cod

Institutions: Norwegian University of Science and Technology

Pål A. Olsvik

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

https://orcid.org/0000-0002-5641-9420
Sofie Söderström project_administrator

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

Zhanna Tairova project_administratorprogramme_administrator

Projects: Systems toxicology of Atlantic cod

Institutions: University of Olso

Kidane Tekle

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

https://orcid.org/0000-0002-4296-5068
Jon Olav Vik project_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

Projects: GenoSysFat, DigiSal, FAIRDOM user meeting, SEEK tutorial for DigiSal, Systems toxicology of Atlantic cod

Institutions: Norwegian University of Life Sciences

https://orcid.org/0000-0002-7778-4515
Fekadu Yadetie project_administratorprogramme_administrator

Projects: Systems toxicology of Atlantic cod

Institutions: University of Bergen

https://orcid.org/0000-0002-2484-9047
Norwegian University of Life Sciences

Country:  Norway

City: N-1432 Ås

Web page: http://www.nmbu.no/en

University of Olso

Country:  Norway

City: Oslo

Web page: https://www.uio.no/

Norwegian University of Science and Technology

Country:  Norway

City: Trondheim

Web page: http://www.ntnu.edu/

University of Bergen

Country:  Norway

City: Not specified

Web page: Not specified

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Caging study - Kollevåg
Systems toxicology of Atlantic cod

This study involves all data gathered from the Kollevåg study - studying environmental pollution at a capped waste disposal site in Kollevåg, Askøy.

Cod were caged in Kollevåg (Stations 1, 2 and 3 - from inner to outer parts) and at a reference location (Ref station) for a period of six weeks, from 2nd September 2016, to 17-18th October 2016.

Person responsible: Karina Dale

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.study.361.1

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Fish Biometrics
Systems toxicology of Atlantic cod

Information about the fish from the Kollevåg study

Contributor: Karina Dale

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Enzyme activity assays
Systems toxicology of Atlantic cod

Enzyme activity of glutathione-s-transferase (Gst) and catalase (Cat) in Kollevåg samples

Contributor: Karina Dale

Assay type: Experimental Assay Type

Technology type: Enzymatic Activity Measurements

Snapshots: No snapshots

Enzyme immunoassay
Systems toxicology of Atlantic cod

Concentrations of steroid hormones E2 and T in female cod plasma from Kollevåg fish

Contributor: Karina Dale

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Chemical analyses
Systems toxicology of Atlantic cod

Chemical analyses in Kollevåg includes sediment contaminant concentrations, concentrations of various contaminants in cod liver and concentrations of PAH metabolites in cod bile.

Contributor: Karina Dale

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Western blot - protein expression
Systems toxicology of Atlantic cod

Western blot results for Kollevåg samples.

Contributor: Karina Dale

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Gene expression
Systems toxicology of Atlantic cod

Analyses of gene expression: qPCR analyses in liver (relative expression) and ovaries (absolute expression).

Contributor: Karina Dale

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

TBARS: Oxidative stress
Systems toxicology of Atlantic cod

TBARS assay measured oxidative stress as levels of malondialdehyde in samples.
Performed in cod liver samples.

Contributor: Karina Dale

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Vitellogenin in blood plasma
Systems toxicology of Atlantic cod

Biosense Vtg assay measuring concentrations of vitellogenin in cod blood plasma

Contributor: Karina Dale

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

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Vitellogenin_plasma_Kollevåg
Systems toxicology of Atlantic cod

Concentrations of vitellogenin in blood plasma in cod caged in Kollevåg and at reference location.

Creators: None

Contributor: Karina Dale

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TBARS_Kollevåg
Systems toxicology of Atlantic cod

Measurement of oxidative stress (TBARS) assay in liver of cod caged in Kollevåg and at reference location.

Creators: None

Contributor: Karina Dale

Download
qPCR ovaries_Kollevåg
Systems toxicology of Atlantic cod

Gene expression data of genes involved in steroidogenic pathways, measured in cod ovaries.

Creators: None

Contributor: Karina Dale

Download
qPCR liver_Kollevåg
Systems toxicology of Atlantic cod

Gene expression data of various genes from cod liver.

Creators: None

Contributor: Karina Dale

Download
Protein expression Cyp3a+Mt Western Blot_Kollevåg
Systems toxicology of Atlantic cod

Relative protein expression of the proteins Cyp3a and Mt in cod from the Kollevåg study

Creators: None

Contributor: Karina Dale

Download
PAH metabolites in bile Kollevåg
Systems toxicology of Atlantic cod

Measurements of PAH metabolites in bile in fish caged in Kollevåg.

Creator: Karina Dale

Contributor: Karina Dale

Download
Liver chemistry_Kollevåg
Systems toxicology of Atlantic cod

Concentrations of various contaminants in liver from cod caged in Kollevåg and at reference location.

Creators: None

Contributor: Karina Dale

Download
Steroid hormones plasma Kollevåg
Systems toxicology of Atlantic cod

Concentrations of E2 and T in cod plasma of female cod caged in Kollevåg measured by enzyme immunoassay.

Creators: None

Contributor: Karina Dale

Download
Sediment chemistry
Systems toxicology of Atlantic cod

Concentrations of metals, PAHs and PCBs in sediment samples from Kollevåg and reference site.

Creators: None

Contributor: Karina Dale

Download
Enzyme activity Gst+Cat_Kollevåg
Systems toxicology of Atlantic cod

Measurement of Gst and Cat enzyme activity in liver of fish caged in Kollevåg.

Creator: Karina Dale

Contributor: Karina Dale

Download
Kollevåg biometrics
Systems toxicology of Atlantic cod

Biometry data of fish from Kollevåg caging study

Creator: Karina Dale

Contributor: Karina Dale

Download
Count files
Systems toxicology of Atlantic cod
No description specified

Creator: Fatemeh Zamanzad Ghavidel

Contributor: Fatemeh Zamanzad Ghavidel

Download
Bam files
Systems toxicology of Atlantic cod
No description specified

Creator: Fatemeh Zamanzad Ghavidel

Contributor: Fatemeh Zamanzad Ghavidel

Download
FASTQ Paired
Systems toxicology of Atlantic cod
No description specified

Creator: Fatemeh Zamanzad Ghavidel

Contributor: Fatemeh Zamanzad Ghavidel

Download
Library preparation
Systems toxicology of Atlantic cod
No description specified

Creator: Fatemeh Zamanzad Ghavidel

Contributor: Fatemeh Zamanzad Ghavidel

Download
Samples for dCod
Systems toxicology of Atlantic cod
No description specified

Creator: Fatemeh Zamanzad Ghavidel

Contributor: Fatemeh Zamanzad Ghavidel

Download
38 hidden items
Quantitative proteomics analysis reveals perturbation of lipid metabolic pathways in the liver of Atlantic cod (Gadus morhua) treated with PCB 153
Systems toxicology of Atlantic cod

Abstract (Expand)

PCB 153 is one of the most abundant PCB congeners detected in biological samples. It is a persistent compound that is still present in the environment despite the ban on production and use of PCBs in … the late 1970s. It has strong tendencies to bioaccumulate and biomagnify in biota, and studies have suggested that it is an endocrine and metabolic disruptor. In order to study mechanisms of toxicity, we exposed Atlantic cod (Gadus morhua) to various doses of PCB 153 (0, 0.5, 2 and 8 mg/kg body weight) for two weeks and examined the effects on expression of liver proteins using label-free quantitative proteomics. Label-free liquid chromatography-mass spectrometry analysis of the liver proteome resulted in the quantification of 1272 proteins, of which 78 proteins were differentially regulated in the PCB 153-treated dose groups compared to the control group. Functional enrichment analysis showed that pathways significantly affected are related to the lipid metabolism, cytoskeletal remodeling, cell cycle and cell adhesion. Importantly, the main effects appear to be on lipid metabolism, with up-regulation of enzymes in the de novo fatty acid synthesis pathway, consistent with previous transcriptomics results. Increased plasma triglyceride levels were also observed in the PCB 153 treated fish, in agreement with the induction of the lipogenic genes and proteins. The results suggest that PCB 153 perturbs lipid metabolism in the Atlantic cod liver. Elevated levels of lipogenic enzymes and plasma triglycerides further suggest increased synthesis of fatty acids and triglycerides.

Author: Fekadu Yadetie, Eystein Oveland, Anne Døskeland, Frode Berven Anders Goksøyr, Odd André Karlsen

Date Published: 1st Apr 2017

Journal: Aquatic Toxicology

Quantitative analyses of the hepatic proteome of methylmercury-exposed Atlantic cod (Gadus morhua) suggest oxidative stress-mediated effects on cellular energy metabolism
Systems toxicology of Atlantic cod

Abstract (Expand)

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. RESULTS: Out 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.

Authors: Fekadu Yadetie, S. Bjorneklett, H. K. Garberg, E. Oveland, F. Berven, A. Goksoyr, O. A. Karlsen

Date Published: 9th Aug 2016

Journal: BMC Genomics

Global transcriptome analysis of Atlantic cod (Gadus morhua) liver after in vivo methylmercury exposure suggests effects on energy metabolism pathways
Systems toxicology of Atlantic cod

Abstract (Expand)

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 2 mg/kg of body weight) for 14 days. 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.

Authors: Fekadu Yadetie, O. A. Karlsen, A. Lanzen, K. Berg, P. Olsvik, C. Hogstrand, A. Goksoyr

Date Published: 30th Oct 2012

Journal: Aquat Toxicol

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

Abstract (Expand)

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.

Authors: F. Yadetie, O. A. Karlsen, M. Eide, C. Hogstrand, A. Goksoyr

Date Published: 19th Jun 2014

Journal: BMC Genomics

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16087
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16088
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16089
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16073
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16074
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16075
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16076
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16077
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16078
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16079
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16080
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16081
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16082
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16083
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16084
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16085
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16086
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16053
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16054
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

16055
Systems toxicology of Atlantic cod

Type: Vitellogenin concentration in plasma field studies

Creators: None

Contributor: Karina Dale

2161 hidden items
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