dCod 1.0

dCod 1.0

Decoding the systems toxicology of Atlantic cod

Project overview

Project lead: Anders Goksøyr
Institution: University of Bergen
Partners: Institute for Marine Research, NIFES, IRIS, NTNU, UiO og NMBU, Universitetet i Gøteborg, Woods Hole Oceanographic
Funding: NOK 38 mill.
Duration: 2016–31/3/2021

Publications

 

  • Strople, Leah C.; Vieweg, Ireen; Yadetie, Fekadu; Odei, Derrick Kwame; Thorsen, Anders & Karlsen, Odd André [Show all 14 contributors for this article] (2023). Spawning time in adult polar cod (Boreogadus saida) altered by crude oil exposure, independent of food availability. Journal of Toxicology and Environmental Health, Part A. ISSN 1528-7394. p. 1–24. doi: 10.1080/15287394.2023.2228535. Full text in Research Archive
  • Olsvik, Pål Asgeir; Meier, Sonnich; Zhang, Xiaokang; Goksøyr, Anders; Karlsen, Odd André & Yadetie, Fekadu (2023). Environmentally realistic concentrations of chlorinated, brominated, and fluorinated persistent organic pollutants induce the unfolded protein response as a shared stress pathway in the liver of Atlantic cod (Gadus morhua). Journal of Applied Toxicology. ISSN 0260-437X. 43(12), p. 1859–1871. doi: 10.1002/jat.4519. Full text in Research Archive
  • Eide, Marta; Goksøyr, Anders; Yadetie, Fekadu; Gilabert, Alejandra; Bartosova, Zdenka & Frøysa, Håvard Guldbrandsen [Show all 15 contributors for this article] (2023). Integrative omics-analysis of lipid metabolism regulation by peroxisome proliferator-activated receptor a and b agonists in male Atlantic cod. Frontiers in Physiology. ISSN 1664-042X. 14. doi: 10.3389/fphys.2023.1129089. Full text in Research Archive
  • Söderström, Sofie Karin; Lille-Langøy, Roger; Yadetie, Fekadu; Rauch, Mateusz; Milinski, Ana & Dejaegere, Annick [Show all 9 contributors for this article] (2022). Agonistic and potentiating effects of perfluoroalkyl substances (PFAS) on the Atlantic cod (Gadus morhua) peroxisome proliferator-activated receptors (Ppars). Environment International. ISSN 0160-4120. 163. doi: 10.1016/j.envint.2022.107203. Full text in Research Archive
  • Aranguren Abadía, Libe; Yadetie, Fekadu; Donald, Carey; Sørhus, Elin; Myklatun, Lars Eirik & Zhang, Xiaokang [Show all 16 contributors for this article] (2022). Photo-enhanced toxicity of crude oil on early developmental stages of Atlantic cod (Gadus morhua). Science of the Total Environment. ISSN 0048-9697. 807(Part 1). doi: 10.1016/j.scitotenv.2021.150697. Full text in Research Archive
  • Dale, Karina; Yadetie, Fekadu; Horvli, Torill; Zhang, Xiaokang; Frøysa, Håvard G & Karlsen, Odd André [Show all 7 contributors for this article] (2022). Single PFAS and PFAS mixtures affect nuclear receptor- and oxidative stress-related pathways in precision-cut liver slices of Atlantic cod (Gadus morhua). Science of the Total Environment. ISSN 0048-9697. 814. doi: 10.1016/j.scitotenv.2021.152732. Full text in Research Archive
  • Zhang, Xiaokang; Jonassen, Inge & Goksøyr, Anders (2021). Machine Learning Approaches for Biomarker Discovery Using Gene Expression Data. In Nakaya, Helder I. (Eds.), Bioinformatics. Exon Publications. ISSN 978-0-6450017-1-6. doi: 10.36255/exonpublications.bioinformatics.2021.ch4.
  • Goksøyr, Siri Øfsthus; Sørensen, Helene; Grøsvik, Bjørn Einar; Pampanin, Daniela Maria; Goksøyr, Anders & Karlsen, Odd André (2021). Toxicity assessment of urban marine sediments from Western Norway using a battery of stress-activated receptors and cell-based bioassays from fish. Environmental Toxicology and Pharmacology. ISSN 1382-6689. 87:103704, p. 1–10. doi: 10.1016/j.etap.2021.103704. Full text in Research Archive
  • Yadetie, Fekadu; Brun, Nadja Rebecca; Vieweg, Ireen; Nahrgang, Jasmine; Karlsen, Odd André & Goksøyr, Anders (2021). Transcriptome responses in polar cod (Boreogadus saida) liver slice culture exposed to benzo[a]pyrene and ethynylestradiol: insights into anti-estrogenic effects. Toxicology in Vitro. ISSN 0887-2333. 75. doi: 10.1016/j.tiv.2021.105193. Full text in Research Archive
  • Eide, Marta; Zhang, Xiaokang; Karlsen, Odd André; Goldstone, Jared V.; Stegeman, John & Jonassen, Inge [Show all 7 contributors for this article] (2021). The chemical defensome of five model teleost fish. Scientific Reports. ISSN 2045-2322. 11(1), p. 1–13. doi: 10.1038/s41598-021-89948-0.
  • Strobel, Anneli; Lille-Langøy, Roger; Segner, Helmut; Burkhardt-Holm, Patricia; Goksøyr, Anders & Karlsen, Odd André (2021). Xenobiotic metabolism and its physiological consequences in high-Antarctic Notothenioid fishes. Polar Biology. ISSN 0722-4060. 45, p. 345–358. doi: 10.1007/s00300-021-02992-4. Full text in Research Archive
  • Lille-Langøy, Roger; Jørgensen, Kåre Bredeli; Goksøyr, Anders; Pampanin, Daniela Maria; Sydnes, Magne Olav & Karlsen, Odd André (2021). Substituted Two- To Five-Ring Polycyclic Aromatic Compounds Are Potent Agonists of Atlantic Cod (Gadus morhua) Aryl Hydrocarbon Receptors Ahr1a and Ahr2a. Environmental Science and Technology. ISSN 0013-936X. 55(22), p. 15123–15135. doi: 10.1021/acs.est.1c02946. Full text in Research Archive
  • Goksøyr, Siri Øfsthus; Goldstone, Jed; Lille-Langøy, Roger; Lock, Erik Jan Robert; Olsvik, Pål Asgeir & Goksøyr, Anders [Show all 7 contributors for this article] (2021). Polycyclic aromatic hydrocarbons modulate the activity of Atlantic cod (Gadus morhua) vitamin D receptor paralogs in vitro. Aquatic Toxicology. ISSN 0166-445X. 238, p. 1–11. doi: 10.1016/j.aquatox.2021.105914. Full text in Research Archive
  • Dale, Karina; Yadetie, Fekadu; Müller, Mette Helen Bjørge; Pampanin, Daniela Maria; Gilabert, Alejandra & Zhang, Xiaokang [Show all 13 contributors for this article] (2020). Proteomics and lipidomics analyses reveal modulation of lipid metabolism by perfluoroalkyl substances in liver of Atlantic cod (Gadus morhua). Aquatic Toxicology. ISSN 0166-445X. 227. doi: 10.1016/j.aquatox.2020.105590. Full text in Research Archive
  • Oleynik, Anna; García-Ibáñez, Maribel I.; Blaser, Nello; Omar, Abdirahman & Alendal, Guttorm (2020). Optimal sensors placement for detecting CO2 discharges from unknown locations on the seafloor. International Journal of Greenhouse Gas Control. ISSN 1750-5836. doi: 10.1016/j.ijggc.2019.102951.
  • Aranguren Abadía, Libe; Donald, Carey; Eilertsen, Mariann; Gharbi, Naouel; Tronci, Valentina & Sørhus, Elin [Show all 11 contributors for this article] (2020). Expression and localization of the aryl hydrocarbon receptors and cytochrome P450 1A during early development of Atlantic cod (Gadus morhua). Aquatic Toxicology. ISSN 0166-445X. 226. doi: 10.1016/j.aquatox.2020.105558. Full text in Research Archive
  • Stenseth, Nils Christian; Payne, Mark R.; Bonsdorff, Erik; Dankel, Dorothy Jane; Durant, Joel Marcel & Anderson, Leif G. [Show all 17 contributors for this article] (2020). Attuning to a changing ocean. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 117(34), p. 20363–20371. doi: 10.1073/pnas.1915352117. Full text in Research Archive
  • Fallahi, Shirin; Skaug, Hans J. & Alendal, Guttorm (2020). A comparison of Monte Carlo sampling methods for metabolic network models. PLOS ONE. ISSN 1932-6203. 15:e0235393(7), p. 1–24. doi: 10.1371/journal.pone.0235393.
  • Frøysa, Håvard G; Skaug, Hans J. & Alendal, Guttorm (2020). Experimental design for parameter estimation in steady-state linear models of metabolic networks. Mathematical Biosciences. ISSN 0025-5564. 319. doi: 10.1016/j.mbs.2019.108291.
  • Beyer, Jonny; Goksøyr, Anders; Hjermann, Dag Øystein & Klungsøyr, Jarle (2020). Environmental effects of offshore produced water discharges: A review focused on the Norwegian continental shelf. Marine Environmental Research. ISSN 0141-1136. 162. doi: 10.1016/j.marenvres.2020.105155. Full text in Research Archive
  • Khan, Essa Ahsan; Zhang, Xiaokang; Hanna, Eileen Marie; Yadetie, Fekadu; Jonassen, Inge & Goksøyr, Anders [Show all 7 contributors for this article] (2020). Application of quantitative transcriptomics in evaluating the ex vivo effects of per- and polyfluoroalkyl substances on Atlantic cod (Gadus morhua) ovarian physiology. Science of the Total Environment. ISSN 0048-9697. p. 1–11. doi: 10.1016/j.scitotenv.2020.142904. Full text in Research Archive
  • Hanna, Eileen Marie; Zhang, Xiaokang; Eide, Marta; Fallahi, Shirin; Furmanek, Tomasz & Yadetie, Fekadu [Show all 9 contributors for this article] (2020). ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species. Frontiers in Molecular Biosciences. ISSN 2296-889X. 7. doi: 10.3389/fmolb.2020.591406. Full text in Research Archive
  • Fallahi, Shirin; Mlnaříková, Marie; Alvord, Charlotte; Alendal, Guttorm; Frøysa, Håvard G & Lundh, Thorbjörn [Show all 7 contributors for this article] (2020). New Conceptual Toxicokinetic Model to Assess Synergistic Mixture Effects between the Aromatic Hydrocarbon β-Naphthoflavone and the Azole Nocodazole on the CYP1A Biomarker in a Fish Cell Line. Environmental Science and Technology. ISSN 0013-936X. 54, p. 13748–13758. doi: 10.1021/acs.est.0c04839.
  • Aranguren-Abadía, Libe; Lille-Langøy, Roger; Madsen, Alexander Klevedal; Karchner, Sibel I.; Franks, Diana G & Yadetie, Fekadu [Show all 9 contributors for this article] (2020). Molecular and Functional Properties of the Atlantic Cod (Gadus morhua) Aryl Hydrocarbon Receptors Ahr1a and Ahr2a. Environmental Science and Technology. ISSN 0013-936X. 54(2), p. 1033–1044. doi: 10.1021/acs.est.9b05312.
  • Khan, Essa Ahsan; Zhang, Xiaokang; Hanna, Eileen Marie; Bartosova, Zdenka; Yadetie, Fekadu & Jonassen, Inge [Show all 8 contributors for this article] (2020). Quantitative transcriptomics, and lipidomics in evaluating ovarian developmental effects in Atlantic cod (Gadus morhua) caged at a capped marine waste disposal site. Environmental Research. ISSN 0013-9351. 189:109906, p. 1–11. doi: 10.1016/j.envres.2020.109906. Full text in Research Archive
  • Zhang, Xiaokang & Jonassen, Inge (2020). RASflow: an RNA-Seq analysis workflow with Snakemake. BMC Bioinformatics. ISSN 1471-2105. 21. doi: 10.1186/s12859-020-3433-x.
  • Zhang, Xiaokang & Jonassen, Inge (2019). An Ensemble Feature Selection Framework Integrating Stability. In Yoo, Illhoi; Bi, Jinbo & Hu, Xiaohua (Ed.), 2019 IEEE International Conference on Bioinformatics and Biomedicine. IEEE Press. ISSN 9781728118673. p. 2792–2798. doi: 10.1109/BIBM47256.2019.8983310.
  • Zhang, Xiaokang & Jonassen, Inge (2019). A Comparative Analysis of Feature Selection Methods for Biomarker Discovery in Study of Toxicant-Treated Atlantic Cod (Gadus Morhua) Liver, Nordic Artificial Intelligence Research and Development: Third Symposium of the Norwegian AI Society, NAIS 2019. Springer. ISSN 978-3-030-35664-4. p. 114–123. doi: 10.1007/978-3-030-35664-4_11. Full text in Research Archive
  • Olsvik, Pål Asgeir; Larsen, Anett Kristin; Berntssen, Marc; Goksøyr, Anders; Karlsen, Odd Andre & Yadetie, Fekadu [Show all 8 contributors for this article] (2019). Effects of agricultural pesticides in aquafeeds on wild fish feeding on leftover pellets near fish farms. Frontiers in Genetics. ISSN 1664-8021. 10:794, p. 1–18. doi: 10.3389/fgene.2019.00794. Full text in Research Archive
  • Khan, Essa Ahsan; Bertotto, Luisa B.; Dale, Karina; Lille-Langøy, Roger; Yadetie, Fekadu & Karlsen, Odd Andre [Show all 9 contributors for this article] (2019). Modulation of neuro-dopamine homeostasis in juvenile female Atlantic cod (Gadus morhua) exposed to polycyclic aromatic hydrocarbons and perfluoroalkyl substances. Environmental Science and Technology. ISSN 0013-936X. 53, p. 7036–7044. doi: 10.1021/acs.est.9b00637. Full text in Research Archive
  • Dale, Karina; Müller, Mette Bjørge; Tairova, Zhanna; Khan, Essa Ahsan; Hatlen, Kristin & Grung, Merete [Show all 15 contributors for this article] (2019). Contaminant accumulation and biological responses in Atlantic cod (Gadus morhua) caged at a capped waste disposal site in Kollevåg, Western Norway. Marine Environmental Research. ISSN 0141-1136. 145, p. 39–51. doi: 10.1016/j.marenvres.2019.02.003. Full text in Research Archive
  • Yadetie, Fekadu; Zhang, Xiaokang; Hanna, Eileen Marie; Aranguren-Abadía, Libe; Eide, Marta & Blaser, Nello [Show all 10 contributors for this article] (2018). RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision-cut liver slices exposed to benzo[a]pyrene and 17α-ethynylestradiol. Aquatic Toxicology. ISSN 0166-445X. 201, p. 174–186. doi: 10.1016/j.aquatox.2018.06.003.

View all works in Cristin

  • Hoven, Sigrid Setsaas; Haslene-Hox, Hanne; Chahal, Aman S; Goksøyr, Anders; Routti, Heli Anna Irmeli & Strand, Berit Løkensgard (2022). Establishing robust 2D cultures of killer whale primary cells: an optimization study .
  • Strople, Leah Catherine; Vieweg, Ireen; Yadetie, Fekadu; Odei, Derrick Kwame; Goksøyr, Anders & Karlsen, Odd André [Show all 11 contributors for this article] (2022). Reproductive development in polar cod (Boreogadus saida) exposed to crude oil and food variability.
  • Goksøyr, Anders (2021). Hunnsnegl med penis og hannfisk med egg. In Aslaksen, Knut Olav (Eds.), Årbok for Universitetsmuseet 2021. Universitetet i Bergen. ISSN 9788278870532. p. 74–84.
  • Stenseth, Nils Christian; Baalsrud, Helle Tessand; Jakobsen, Kjetill Sigurd; Brautaset, Trygve; Goksøyr, Anders & Jensen, Nina [Show all 9 contributors for this article] (2021). Havgenomet – bevaring og bærekraftig bruk av marine genetiske ressurser i Norge. In Rist, Therese & Elvevoll, Edel O. (Ed.), Blått kompass - Stø kurs mot bærekraft i norske havnæringer. Senter for hav og Arktis. ISSN 978-82-93806-08-0.
  • Goksøyr, Anders; Goksøyr, Siri Øfsthus; Yadetie, Fekadu & Karlsen, Odd André (2021). Development of a battery of Atlantic cod receptor-based reporter bioassays for assessing environmental toxicity of sediments and chemicals.
  • Goksøyr, Anders (2021). U-864: Heving eller tildekking.
  • Dankel, Dorothy Jane (2020). SDG110 Aquatic Biodiversity.
  • Dankel, Dorothy Jane (2020). SDG110 Food & Pollution in Ocean .
  • Dankel, Dorothy Jane (2020). Welcome to the Post-Normal Science in Practice Symposium: Putting PNS in Practice during COVID-19 times.
  • Eide, Marta; Goksøyr, Anders; Yadetie, Fekadu; Gilabert, Alejandra; Bartosova, Zdenka & Frøysa, Håvard G [Show all 15 contributors for this article] (2020). A multi-omics approach to study Ppar-mediated regulation of lipid metabolism in Atlantic cod (Gadus morhua).
  • Yadetie, Fekadu; Brun, Nadja; Vieweg, Ireen; Nahrgang, Jasmine; Karlsen, Odd Andre & Goksøyr, Anders (2020). Adapting a liver slice culture method for ex vivo toxicological studies in arctic and sub-arctic fish species during sampling cruises.
  • Yadetie, Fekadu; Brun, Nadja R; Vieweg, Ireen; Nahrgang, Jasmine; Karlsen, Odd Andre & Goksøyr, Anders (2020). ANTIESTROGENIC EFFECTS OF BENZO[a]PYRENE REVEALED BY TRANSCRIPTOME ANALYSIS IN POLAR COD LIVER SLICE CULTURE.
  • Yadetie, Fekadu; Zhang, Xiaokang; Hanna, Eileen Marie; Reboa, Anna; Aranguren-Abadía, Libe & Eide, Marta [Show all 11 contributors for this article] (2019). Toxicogenomic responses in Atlantic cod (Gadus morhua) after treatment with selected environmental contaminants in vivo and ex vivo.
  • Zhang, Xiaokang & Jonassen, Inge (2019). RASflow: An Easy-to-use RNA-Seq Analysis Workflow.
  • Zhang, Xiaokang & Jonassen, Inge (2019). A Comparative Analysis of Feature Selection Methods for Biomarker Discovery in Study of Toxicant-treated Atlantic Cod (Gadus morhua) Liver.
  • Zhang, Xiaokang & Jonassen, Inge (2019). An Ensemble Feature Selection Framework Integrating Stability.
  • Dankel, Dorothy Jane; Jørgensen, Christian & Årthun, Marius (2019). Havet konsert med Bergen Filharmonisk Orkestra.
  • Vieweg, Ireen; Strople, Leah; Odei, Derrick Kwame; Bender, Morgan Lizabeth; Hansen, Øyvind J & Velmurugu, Puvanendran [Show all 11 contributors for this article] (2019). Sensitivity of adult polar cod (Boreogadus saida) to the water-soluble fraction of crude oil under low and high food regimes.
  • Goksøyr, Siri Øfsthus; Johansen, Christine T.; Viken, Kristianne Hjort; Yadetie, Fekadu; Steinkopf, Oline Marie & Lille-Langøy, Roger [Show all 8 contributors for this article] (2019). In vitro assessment of estrogenic and androgenic effects of bisphenols on Atlantic cod (Gadus morhua).
  • Johansen, Christine T.; Goksøyr, Siri Øfsthus; Yadetie, Fekadu; Goksøyr, Anders & Karlsen, Odd Andre (2019). Evaluation of estrogenic effects of bisphenols using luciferase reporter assay and Atlantic cod (Gadus morhua) liver slice culture.
  • Olsvik, Pål Asgeir; Larsen, Anett Kristin; Berntssen, Marc; Goksøyr, Anders; Karlsen, Odd Andre & Yadetie, Fekadu [Show all 8 contributors for this article] (2019). Effects of agricultural pesticides in aquafeeds on wild fish feeding on leftover pellets near fish farms. Conference talk.
  • Goksøyr, Anders (2019). Spiser oss sterile. [Internet]. https://www.tv-helse.no/miljogifter-spiser-oss-sterile/.
  • Hanna, Eileen Marie; Zhang, Xiaokang; Fallahi, Shirin; Eide, Marta; Yadetie, Fekadu & Blaser, Nello [Show all 9 contributors for this article] (2019). A draft metabolic reconstruction of Atlantic cod (Gadus morhua) liver .
  • Hanna, Eileen Marie; Zhang, Xiaokang; Eide, Marta; Yadetie, Fekadu; Blaser, Nello & Alendal, Guttorm [Show all 8 contributors for this article] (2019). A draft metabolic reconstruction of Atlantic cod (Gadus morhua) liver: how to and what for?
  • Fallahi, Shirin; Kleppe, Rune; Goksøyr, Anders & Alendal, Guttorm (2019). Mathematical modeling of allosteric regulation in fatty acid synthesis.
  • Fallahi, Shirin; Skaug, Hans J. & Alendal, Guttorm (2019). Bayesian flux balance analysis of metabolic pathways.
  • Goksøyr, Anders; Alendal, Guttorm; Aranguren-Abadía, Libe; Arukwe, Augustine; Blaser, Nello & Brun, Morten [Show all 29 contributors for this article] (2019). dCOD 1.0: DECODING THE SYSTEMS TOXICOLOGY OF ATLANTIC COD (GADUS MORHUA) – HIGHLIGHTS SO FAR.
  • Eide, Marta; Zhang, Xiaokang; Karlsen, Odd Andre; Hanna, Eileen Marie; Goldstone, Jared V. & Stegeman, John J. [Show all 8 contributors for this article] (2019). Chemical warfare in the aquatic environment - The chemical defensome networks of model fish species.
  • Goksøyr, Anders; Alendal, Guttorm; Aranguren-Abadía, Libe; Arukwe, Augustine; Blaser, Nello & Brun, Morten [Show all 29 contributors for this article] (2019). dCOD 1.0: DECODING THE SYSTEMS TOXICOLOGY OF ATLANTIC COD (GADUS MORHUA) – HIGHLIGHTS SO FAR.
  • Goksøyr, Siri Øfsthus; Johansen, Christine T.; Viken, Kristianne Hjort; Yadetie, Fekadu; Steinkopf, Oline Marie & Lille-Langøy, Roger [Show all 9 contributors for this article] (2019). Assessment of endocrine disrupting effects of bisphenols in Atlantic cod (Gadus morhua) using luciferase reporter assays and precision-cut liver slices.
  • Tairova, Zhanna; Müller, Mette Helen Bjørge; Meier, Sonnich; Lie, Kai Kristoffer; Myklatun, Lars & Sørhus, Elin [Show all 12 contributors for this article] (2019). Biological effects in Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) exposed to crude oil with and without UV radiation.
  • Eide, Marta; Zhang, Xiaokang; Karlsen, Odd Andre; Hanna, Eileen Marie; Goldstone, Jared V. & Stegeman, John J. [Show all 8 contributors for this article] (2019). Chemical warfare in the marine environment.
  • Eide, Marta; Zhang, Xiaokang; Karlsen, Odd Andre; Hanna, Eileen Marie; Blaser, Nello & Jonassen, Inge [Show all 7 contributors for this article] (2019). The chemical defensome of Atlantic cod (Gadus morhua).
  • Goksøyr, Anders (2019). On cod, contaminants, and the cod genome.
  • Espeland, Chris Inge Reiersen; Pampanin, Daniela Maria; Sydnes, Magne Olav & Petrik, Leslie (2019). Review: Marine Sewage Outfalls in Cape Town, South Africa.
  • Johansen, Christine T.; Goksøyr, Siri Øfsthus; Yadetie, Fekadu; Goksøyr, Anders & Karlsen, Odd Andre (2019). In vitro assessment of estrogenic effects of bisphenols on Atlantic cod (Gadus morhua).
  • Goksøyr, Siri Øfsthus; Ueland, Elisabeth; Lille-Langøy, Roger; Goldstone, Jed; Goksøyr, Anders & Karlsen, Odd Andre (2019). Polycyclic aromatic hydrocarbons potentiate vitamin D receptor (Vdr) activation by calcitriol in Atlantic cod (Gadus morhua).
  • Goksøyr, Anders (2019). Comparative reproductive toxicology of environmental contaminants.
  • Zhang, Xiaokang; Eide, Marta; Karlsen, Odd Andre; Hanna, Eileen Marie; Brun, Morten & Blaser, Nello [Show all 8 contributors for this article] (2019). THE CHEMICAL DEFENSOME OF ATLANTIC COD (GADUS MORHUA): HOW DOES IT DIFFER FROM DEFENSOME NETWORKS IN OTHER TELEOST SPECIES?
  • Dale, Karina; Söderström, Sofie; Zamanzad Ghavidel, Fatemeh & Goksøyr, Anders (2019). Managing data through the FAIR principles: Collaborations for achieving open science.
  • Dale, Karina; Yadetie, Fekadu; Müller, Mette Helen Bjørge; Tairova, Zhanna; Haarr, Ane & Khan, Essa Ahsan [Show all 11 contributors for this article] (2019). Contaminant accumulation and biological responses in Atlantic cod (Gadus morhua) exposed to polycyclic aromatic hydrocarbons and perfluoroalkyl substances.
  • Dale, Karina; Eide, Marta & Haanæs, Øystein Rygg (2019). Forskarar bura torsken inne for å studere effektane av miljøgifter. [Internet]. Forskning.no.
  • Dale, Karina (2019). Contaminant accumulation and biological responses in atlantic cod (Gadus morhua) caged at a capped waste disposal site in Kollevåg, Western Norway.
  • Dale, Karina; Müller, Mette Helen Bjørge; Tairova, Zhanna; Pampanin, Daniela Maria; Haarr, Ane & Lille-Langøy, Roger [Show all 10 contributors for this article] (2019). Biological responses of Atlantic cod (Gadus morhua) exposed to polycyclic aromatic hydrocarbons (PAHs) and perfluoroalkyl substances (PFASs) .
  • Dale, Karina; Müller, Mette Helen Bjørge; Tairova, Zhanna; Pampanin, Daniela Maria; Haarr, Ane & Yadetie, Fekadu [Show all 13 contributors for this article] (2019). Biological responses of Atlantic cod (Gadus morhua) exposed to polycyclic aromatic hydrocarbons and perfluoroalkyl substances.
  • Brun, Morten; Dale, Karina & Zhang, Xiaokang (2019). Multiexposure Proteomics.
  • Gundersen, Kristian; Oleynik, Anna; Blaser, Nello & Alendal, Guttorm (2019). Bayesian convolutional neural networks as a tool to detect discharges of pollutants to marine waters through time series classification.
  • Karlsen, Odd Andre; Madsen, Alexander Klevedal; Sørensen, Lisbet; Hansen, Bjørn Henrik & Goksøyr, Anders (2019). Assessment of produced water toxicity using in vitro tools developed from Atlantic cod (Gadus morhua).
  • Olsvik, Pål Asgeir; Larsen, Anett Kristin; Berntssen, Marc; Goksøyr, Anders; Karlsen, Odd Andre & Sanden, Monica [Show all 7 contributors for this article] (2019). Agricultural pesticides in aquafeeds might harm wild fish feeding on leftover pellets near fish farms.
  • Yadetie, Fekadu; Zhang, Xiaokang; Hanna, Eileen Marie; Reboa, Anna; Aranguren-Abadía, Libe & Eide, Marta [Show all 11 contributors for this article] (2019). EFFECTS OF SELECTED ENVIRONMENTAL ESTROGENS ON EXPRESSION OF FIBROBLAST GROWTH FACTOR SIGNALING PATHWAY GENES IN THE LIVER OF ATLANTIC COD (GADUS MORHUA) IN VIVO AND EX VIVO.
  • Sôderstrôm, Sofie; Goksøyr, Anders & Karlsen, Odd Andre (2018). Effects of perfluorinated compounds on Atlantic cod (Gadus morhua) PPARαa and PPARαb nuclear receptors.
  • Aranguren Abadía, Libe; Lille-Langøy, Roger; Karchner, Sibel I.; Franks, Diana; Hahn, Mark E. & Yadetie, Fekadu [Show all 8 contributors for this article] (2018). Characterization of the aryl hydrocarbon receptors Ahr1a and Ahr2a in Atlantic cod (Gadus morhua).
  • Sôderstrôm, Sofie; Goksøyr, Anders & Karlsen, Odd Andre (2018). Agonistic and antagonistic effects of perfluorinated compounds on Atlantic cod (Gadus morhua) PPARαa and PPARαb nuclear receptors.
  • Karlsen, Odd Andre; Sôderstrôm, Sofie; Goksøyr, Siri Øfsthus; Aranguren, Libe; Lille-Langøy, Roger & Eide, Marta [Show all 10 contributors for this article] (2018). The nuclear receptor complement of Atlantic cod (Gadus morhua) as potential targets for endocrine disrupting compounds.
  • Hylland, Ketil (2018). dCod - effekter av miljøgifter på torsk. [Radio]. NRK - Nyhetslunsj.
  • Goksøyr, Siri Øfsthus; Söderström, Sofie; Ueland, Elisabeth; Grøsvik, Bjørn Einar; Pampanin, Daniela Maria & Goksøyr, Anders [Show all 7 contributors for this article] (2018). Establishing a cell-free method for xenobiotic detection using ligand activated receptors from the Atlantic cod (Gadus morhua).
  • Eide, Marta; Zhang, Xiaokang; Karlsen, Odd Andre; Hanna, Eileen Marie; Blaser, Nello & Puntervoll, Pål [Show all 8 contributors for this article] (2018). Modelling the chemical defensome network - a dynamic visualisation of the involved genes and pathways in two fish species and humans .
  • Tairova, Zhanna; Müller, Mette Helen Bjørge; Lyche, Jan Ludvig; Mayer, Ian; Berg, Vidar & Blaser, Nello [Show all 14 contributors for this article] (2018). Adverse health effects related to chemical exposure in Atlantic cod (Gadus morhua) from Norwegian fjords.
  • Zhang, Xiaokang & Jonassen, Inge (2018). EFSIS: Ensemble Feature Selection Integrating Stability.
  • Eide, Marta; Zhang, Xiaokang; Karlsen, Odd Andre; Hanna, Eileen Marie; Blaser, Nello & Puntervoll, Pål [Show all 8 contributors for this article] (2018). Modelling The Chemical Defensome Networks - A Comparative Dynamic Visualisation Of The Involved Genes And Interactions In Two Fish Species And Humans.
  • Dale, Karina; Karlsen, Odd Andre; Yadetie, Fekadu; Eide, Marta; Goksøyr, Siri Øfsthus & Aranguren Abadía, Libe [Show all 14 contributors for this article] (2018). Ecotoxicological responses in Atlantic cod (Gadus morhua) after caging at a capped waste disposal site in Kollevåg, Western Norway .
  • Fallahi, Shirin; Skaug, Hans J. & Alendal, Guttorm (2018). Bayesian flux balance analysis; concepts and computation.
  • Aranguren Abadía, Libe; Lille-Langøy, Roger; Karchner, Sibel I.; Franks, Diana; Hahn, Mark E. & Madsen, Alexander K [Show all 9 contributors for this article] (2018). Characterization of the aryl hydrocarbon receptors Ahr1a and Ahr2a in Atlantic cod (Gadus morhua).
  • Yadetie, Fekadu; Zhang, Xiaokang; Hanna, Eileen Marie; Aranguren Abadía, Libe; Eide, Marta & Blaser, Nello [Show all 9 contributors for this article] (2018). RNA-seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision cut liver slices exposed to benzo[a]pyrene and 17α-ethynylestradiol.
  • Goksøyr, Siri Øfsthus; Grøsvik, Bjørn Einar; Pampanin, Daniela Maria; Goksøyr, Anders & Karlsen, Odd Andre (2018). Establishing a cellfree method for xenobiotic detection using ligand activated receptors from the Atlantic cod, Gadus morhua.
  • Dale, Karina (2018). Adverse outcome pathways as framework for studying effects of environmental contaminants in Atlantic cod (Gadus morhua).
  • Strople, Leah; Goksøyr, Anders & Vieweg, Ireen (2020). Spawning during an oil spill - How exposure to the water-accommodated fraction of crude oil may disrupt polar cod (Boreogadus saida) reproduction. Universitetet i Bergen.
  • Frøysa, Håvard G; Alendal, Guttorm; Skaug, Hans J. & Nilsen, Frank (2020). Estimation and identifiability of kinetic parameters in dynamical models of biochemical reaction networks. Universitetet i Bergen. ISSN 9788230855782.

View all works in Cristin

Research group

As it swims along the Norwegian coastline, the cod can be a good indicator on the state of our marine environment. Now scientists want to find out how different pollutants and combinations of them affect the cod.

The cod – our new canary bird

The goal is to make a tool for monitoring the environment and to assess risk during release of potentially polluting such as from oil industry, release of sewage in harbors and industrial waste in the fjords.

The costal cod is particularly suitable for monitoring environmental pollutants as it is rather stationary and the pollutants accumulate in the liver. The scientists take out the cod liver and investigate the cod genes and how they used. Which genes are turned on or off, which proteins are encoded by these genes and what is the effect on the cells? When each cell contains about 20 000 genes and each gene can encode many proteins, the scientists will soon get an enormous amount of data to go through.

In the project biologists, toxicologists, physiologists, veterinarians, mathematicians, statisticians and bioinformaticians are working together to supervise and analyze how the cod reacts, to understand how the cod is affected by pollutants and how this knowledge can be used to monitor the environment. They also want to learn how changes in the environment and climate affect the cod stock.

The results will be useful for public agencies like The Norwegian Food Safety Authority, the Environment Agency, the Directorate of Fisheries and for the fish industry.

The experiments using living fish follow the regulations for fish welfare, but most of the experiments are and will be performed on cod liver slices.

The project is executed by a consortium led by the Department of Biology at the University of Bergen (UiB), with partners at the Department of Mathematics and Department of Informatics at UiB, The Norwegian University of Science and Technology (NTNU), University of Oslo (UiO), Norwegian University of Life Sciences (NMBU), Institute for Marine Research (IMR), National Institute of Nutrition and Seafood Research (NIFES) and International Research Institute of Stavanger (IRIS). There are also international partners in Sweden (Gothenburg), Spain (Barcelona) and USA (Woods Hole, Florida and Stanford).

Using cod to monitor the marine environment

In the project dCod 1.0: Decoding the systems toxicology of Atlantic cod scientists want to find out how the cod respond to environmental stress, either by pollutants or by climate change. This can be done by investigating liver samples and the cod genome. The project is the first to use cod as a model at this scale.

The studies are based on knowledge about the cod genome (its DNA). This genome was fist mapped in 2011 by scientists at the University of Oslo and Bergen together with international collaborators. Later, scientists in Oslo have mapped the genome of more cods. Now, these data can be used to learn how the cod responds to different environmental stresses.

The scientists are looking at genes, proteins and the metabolism of the fish. One important part of the project is to extract information from the large amounts of data and develop mathematical models of the processes that are changed in the cod.

Big Data

For each tissue sample, the scientists will extract data about the transcriptome, proteome and metabolome. The transcriptome is the active parts of the genome (DNA), the genes that are actively transcribed (into messenger RNA) in a cell. The proteome is the total amount of proteins (transcribed from active genes) in a cell and their chemical modification states (usually modified after translation). One gene can give rise to several proteins, e.g. through the process of RNA splicing, and they can become chemically modified as a result of many cellular processes, such as cell signaling. The metabolome of a cell is the total amount of smaller organic molecules, metabolites, in the cell, which are formed as the result of chemical reactions catalyzed by enzymes. With each cell having about 20 000 genes and each one can give rise to proteins in many different activity states, producing more or less of different metabolites, this soon becomes Big Data. Bioinformaticians are needed to extract the interesting parts, that is, the genes, proteins and metabolites that are influenced by environmental stress.

By using topological data analysis, mathematicians can find patterns in the data and how the data is connected. This knowledge can be used to make systems biological models of the cod and how pollutants give rise to cellular responses.

The results can provide answers to how different environmental stressors affect the inner life of the cod, so that scientists can make models of how environmental changes affect the population size and develop tools for risk assessment and for monitoring the environment.

Cod cells from many sources

Pollution is not necessarily lethal or directly damaging to the fish, but if it affects the growth or its reproduction; even low doses of pollution will have consequences on the stock and in that way affect the fisheries.

Scientists get their «raw materials» from four sources:

They catch cod that lives in areas of high pollution and sample tissue such as liver.
They grow slices of liver from cod in the lab, a technique that is also used in DigiSal, a different project in the Centre. Each slice can be exposed to pollutants to investigate the effect on the cells. The advantage is that the experiments can be performed under controlled conditions and that fewer animals are needed.

They keep live cods in cages at different locations in the sea where they are investigating the environment. One such experiment has been performed already, at Kollevåg outside Bergen, to check if environmental pollutants are leaking from an old dump site. The cods live in their cages for four to six weeks before sacrificed and sampled.

They use aquaria containing living fish that is exposed to mixtures of environmental pollutants to see how the fish behaves.

Interdisciplinary

The project, which is led from the University of Bergen, bringings together scientists from a range of different disciplines: Biologists, toxicologists, physiologists, mathematicians, statisticians and bioinformaticians. This is the first time an environmental research project on fish has a consortium of such wide spread disciplinary composition.

All scientists in the project meet physically a couple of times every year. The majority of project employees are located in Bergen, and there the scientists meet every second week, whereas others can join by Skype.

It has always been important to meet and talk together, to discuss scientific problems from the different angles and using their own language. Slowly, a common language and understanding will be developed across the disciplinary boundaries. For most of the project participants it is new for biologists and mathematicians to work together. The interaction is particularly important for PhDs and postdocs that work full time in the project.

Responsible Research and Innovation (RRI)

A pervading philosophy in the project is that the science should be beneficial for the society. One example is the tools that will be developed for monitoring the marine ecosystem to provide the environment agency with better models for risk assessing the level of pollution. In addition, the dCod 1.0 scientists will engage in dialogue with stake holders like the Institute for Marine Research, Environmental Agency, Directorate of Fisheries, stake holders in fisheries and the society in general.

The project follows the 3R-prnciples of animal experiments (reduction, refinement, replacement), that is, to reduce the number of fishes to be used, to ensure minimal suffering and to get best use of the data from the experiments. One important experimental design to reduce the number of fishes used is to use liver slices.

Innovation

The project will develop tools for environmental monitoring in a new way, using new software tools and modeling methods. The results will be important for biological research, for risk assessing environmental stress and to understand how it affects the fish stock. The goal is to commercialize the some of the tools developed in the project.

Watch project video and presentation of the project

Video made for the Digital Life 2020 conference.

At the conference postdoctoral fellow Marta Eide talked about the project. 
Watch recording of her talk.