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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. Building on the thoroughly studies and mapping of the cod genome at UiO and the long research traditions on cod at the Department of Biology at UiB, the dCod project will expand our knowledge with methods based on genomics; ...
Projects: Systems toxicology of Atlantic cod
Web page: http://dcod.no
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 ...
Programme: dCod 1.0: decoding systems toxicology of cod
Public web page: http://www.uib.no/en/dcod
Organisms: Gadus morhua
Includes physiological informations regarding the fish samples: Weight, length, gender, date sampled, comments regarding physical apperance, in addition to calculations of condition factor (K), hepatosomatic index (HSI) and gonadosomatic index (GSI).
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Chemical analyses in Kollevåg includes sediment contaminant concentrations, concentrations of various contaminants in cod liver and concentrations of PAH metabolites in cod bile.
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Study: Caging study - Kollevåg
Organisms: Gadus morhua
SOPs: No SOPs
Data files: Kollevåg biometrics, Liver chemistry_Kollevåg, PAH metabolites in bile Kollevåg, Sediment chemistry
Snapshots: No snapshots
Biosense Vtg assay measuring concentrations of vitellogenin in cod blood plasma
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Study: Caging study - Kollevåg
Organisms: Gadus morhua
SOPs: No SOPs
Data files: Kollevåg biometrics, Vitellogenin_plasma_Kollevåg
Snapshots: No snapshots
Enzyme activity of the oxidative stress enzymes glutathione S-transferase (Gst) and catalase (Cat) measured in cod liver
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: Enzyme activities catalase and glutathione S-tr..., In vivo-1 biometrics
Snapshots: No snapshots
Concentration of the egg yolk precursor protein vitellogenin in cod plasma
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: In vivo-1 biometrics, Vitellogenin concentrations in cod plasma - IV1
Snapshots: No snapshots
Gene expression of cyp1a and acox1 measured by qPCR in liver of Atlantic cod exposed to PAHs and PFASs
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: In vivo-1 biometrics, Liver gene expression cyp1a and acox1
Snapshots: No snapshots
Semi-quantitative determination of Cyp1a protein amount in cod liver, using the ELISA method.
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: Cyp1a protein amount, In vivo-1 biometrics
Snapshots: No snapshots
Transcriptomics results from liver of cod exposed to chlorpyrifos-methyl
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: Effects of agricultural pesticides in aquafeeds..., File name information for RNA seq data, In vivo Nord 1 biometrics, In_Vivo_Nord_1_Olsvik - reads
Snapshots: No snapshots
Global metabolomics screening of 36 liver samples from Atlantic cod exposed to chlorpyrifos-methyl for 30 days.
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: In vivo Nord 1 biometrics, Metabolomics_results
Snapshots: No snapshots
Cyp1a activity (=EROD) measured in liver samples of cod exposed to chlorpyrifos-methyl
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: In vivo Nord 1 biometrics, Liver EROD activity
Snapshots: No snapshots
Concentrations of chlorpyrifos-methyl and its metabolite TCP in cod liver and bile quantified using gas chromatography
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: CPM and TCP concentrations in liver and bile, In vivo Nord 1 biometrics
Snapshots: No snapshots
Measurement of plasma parameters: activities of cholinesterase, alanine aminotransferase, aspartate aminotransferase + cortisol and total protein levels in cod exposed to chlorpyrifos-methyl
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: In vivo Nord 1 biometrics, Plasma parameters
Snapshots: No snapshots
RNA-seq data for In vivo 7 samples. Only 32 RNA samples from liver of male fish sequenced. Illumina poly(A)-RNA sequencing at UiB GCF, as in Yadetie et al., 2018.
Submitter: Fekadu Yadetie
Assay type: RNA-seq
Technology type: Next generation sequencing
Investigation: 1 hidden item
Study: 1 hidden item
Submitter: Fekadu Yadetie
Assay type: RNA-seq
Technology type: Next generation sequencing
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: PCLS_BaP-EE2_RNAseq - analysis, PCLS_BaP-EE2_RNAseq - reads, RNA-seq metadata for BaP and EE2 treated PCLS s...
Snapshots: No snapshots
Measurement of DNA fragmentation using the Comet Assay, in white blood cells of Atlantic cod exposed to PAHs and PFASs
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: Comet assay, In vivo-1 biometrics
Snapshots: No snapshots
Measurements of PAH metabolites in bile (1-OH-napthalene, 2-OH-naphthalene, 1-OH-phenanthrene, 1-OH-pyrene) and PFAS compounds in liver (PFOS, PFOA, PFNA, PFTrDa) in Atlantic cod exposed to mixtures of PAHs and PFASs.
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: In vivo-1 biometrics, PAH and PFAS chemistry
Snapshots: No snapshots
Some results from proteomics analyses of cod liver exposed to PAH and PFAS
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Organisms: Gadus morhua
SOPs: No SOPs
Data files: Protein quantification data
Snapshots: No snapshots
Results from lipidomics analyses performed in cod liver microsomes of cod exposed to PAH and PFAS mixtures.
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Submitter: Xiaokang Zhang
Biological problem addressed: Metabolic Network
Investigation: 1 hidden item
Study: 1 hidden item
Organisms: Gadus morhua
Models: Draft metabolic reconstruction model of Atlanti..., Draft metabolic reconstruction model of Atlanti..., Draft metabolic reconstruction model of Atlanti...
SOPs: No SOPs
Data files: Draft metabolic reconstruction model of Atlanti..., Draft metabolic reconstruction model of Atlanti..., Draft metabolic reconstruction model of Atlanti..., Visualization of gap filling of subsystem "Meta...
Snapshots: Snapshot 1, Snapshot 2
This is an auto-generated model with COBRA Matlab toolbox. This model was deposited in BioModels [1] and assigned the identifier MODEL2010090003.
[1] Malik-Sheriff et al. BioModels — 15 years of sharing computational models in life science. Nucleic Acids Research. 2020 Jan, 48(D1):D407–415
Creators: Xiaokang Zhang, Eileen Marie Hanna, Marta Eide, Shirin Fallahi, Fekadu Yadetie, Anders Goksøyr, Inge Jonassen, Tomasz Furmanek; Daniel Craig Zielinski
Submitter: Xiaokang Zhang
Model type: Metabolic network
Model format: SBML
Environment: Matlab
This is an auto-generated model with COBRA Matlab toolbox. This model was deposited in BioModels [1] and assigned the identifier MODEL2010090002.
[1] Malik-Sheriff et al. BioModels — 15 years of sharing computational models in life science. Nucleic Acids Research. 2020 Jan, 48(D1):D407–415
Creators: Xiaokang Zhang, Eileen Marie Hanna, Marta Eide, Shirin Fallahi, Fekadu Yadetie, Anders Goksøyr, Inge Jonassen, Tomasz Furmanek; Daniel Craig Zielinski
Submitter: Xiaokang Zhang
Model type: Metabolic network
Model format: SBML
Environment: Matlab
This is an auto-generated model with COBRA Matlab toolbox. This model was deposited in BioModels [1] and assigned the identifier MODEL2010090001.
[1] Malik-Sheriff et al. BioModels — 15 years of sharing computational models in life science. Nucleic Acids Research. 2020 Jan, 48(D1):D407–415
Creators: Xiaokang Zhang, Eileen Marie Hanna, Marta Eide, Shirin Fallahi, Fekadu Yadetie, Anders Goksøyr, Inge Jonassen, Tomasz Furmanek; Daniel Craig Zielinski
Submitter: Xiaokang Zhang
Model type: Metabolic network
Model format: SBML
Environment: Matlab
Abstract (Expand)
Authors: F. Yadetie, X. Zhang, E. M. Hanna, L. Aranguren-Abadia, M. Eide, N. Blaser, M. Brun, I. Jonassen, A. Goksoyr, O. A. Karlsen
Date Published: 22nd Jun 2018
Publication Type: Not specified
PubMed ID: 29929084
Citation: Aquat Toxicol. 2018 Aug;201:174-186. doi: 10.1016/j.aquatox.2018.06.003. Epub 2018 Jun 7.
Abstract (Expand)
Author: Fekadu Yadetie, Eystein Oveland, Anne Døskeland, Frode Berven Anders Goksøyr, Odd André Karlsen
Date Published: 1st Apr 2017
Publication Type: Not specified
DOI: 10.1016/j.aquatox.2017.01.014
Citation: Aquatic Toxicology 185 : 19
Abstract (Expand)
Authors: F. Yadetie, S. Bjorneklett, H. K. Garberg, E. Oveland, F. Berven, A. Goksoyr, O. A. Karlsen
Date Published: 9th Aug 2016
Publication Type: Not specified
PubMed ID: 27496535
Citation: BMC Genomics. 2016 Aug 5;17:554. doi: 10.1186/s12864-016-2864-2.
Abstract (Expand)
Authors: F. Yadetie, O. A. Karlsen, M. Eide, C. Hogstrand, A. Goksoyr
Date Published: 19th Jun 2014
Publication Type: Not specified
PubMed ID: 24939016
Citation: BMC Genomics. 2014 Jun 17;15:481. doi: 10.1186/1471-2164-15-481.
Abstract (Expand)
Authors: F. Yadetie, O. A. Karlsen, A. Lanzen, K. Berg, P. Olsvik, C. Hogstrand, A. Goksoyr
Date Published: 30th Oct 2012
Publication Type: Not specified
PubMed ID: 23103053
Citation: Aquat Toxicol. 2013 Jan 15;126:314-25. doi: 10.1016/j.aquatox.2012.09.013. Epub 2012 Oct 8.