Systems toxicology of Atlantic cod

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; ...

Aim: To investigate whether Atlantic cod that feed close to aquatic breeding facilities are affected by chlorpyrifos-methyl. Feeding experiment with chlorpyrifos-methyl, an organophosphorous pesticide detected in plant based salmon feed. Based on previous experiments using salmon.

Doses: 0, 0.5, 5.0, 25 mg/kg) chlorpyrifos-methyl. Duration: 30 days Set-up: Three tanks per treatment (12 in total)

Samples include: Liver, plasma, bile, brain. Analysis include:

• Have RNAseq and metabolomics from 36 ...

Interspecies differences in sensitivity to chemical exposures pose a great challenge in toxicological risk assessments. How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical ...

Location: UiB Date: 8-20 June 2017 Compounds tested: WY-14,643 (PPAR alpha agonist), GW501516 (PPAR beta agonist) No. of test groups: 5 (Control 1: DMSO/saline/PEG, WY-14.643 High (40 mg/kg), WY-14.643 Low (4.0 mg/kg), GW501516 High (4.0 mg/kg), GW501516 Low (0.4 mg/kg)) No. of fish per group: 22

Aim: *To investigate effects on lipid metabolism in Atlantic cod ( Gadus morhua) mediated by peroxisome proliferator-activated receptors (Ppars) by in vivo exposure to two mammalian PPAR agonists.

BERGEN PUBLICATION Location: UiB Duration: 14 days, injections at day 0 and day 7 Sampling dates: 29-30 March 2017 Compounds tested: Polycyclic aromatic hydrocarbons (PAHs)/ Per- and polyfluoroalkyl substances (PFAS) No. of test groups: 10 No. of fish per group: 21-22 No. of dead fish:

Aim: *To investigate biological responses in Atlantic cod ( Gadus morhua) after in vivo exposure to a mixture of PAHs and PFASs, either singly or combined, at low (1x) or high (20x) doses. *PFAS concentrations were ...

To map genome wide transcriptome responses in Atlantic cod PCLS treated with BaP and EE2. See Yadetie et al., 2018.

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.

Information about the fish from the Kollevåg study

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).

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

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

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

Western blot results for Kollevåg samples.

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

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

Biosense Vtg assay measuring concentrations of vitellogenin in cod blood plasma

Enzyme activity of the oxidative stress enzymes glutathione S-transferase (Gst) and catalase (Cat) measured in cod liver

Concentration of the egg yolk precursor protein vitellogenin in cod plasma

Gene expression of cyp1a and acox1 measured by qPCR in liver of Atlantic cod exposed to PAHs and PFASs

Semi-quantitative determination of Cyp1a protein amount in cod liver, using the ELISA method.

Fish weight (start - end), length, total growth and specific growth rate (SGR)

Transcriptomics results from liver of cod exposed to chlorpyrifos-methyl

Global metabolomics screening of 36 liver samples from Atlantic cod exposed to chlorpyrifos-methyl for 30 days.

Cyp1a activity (=EROD) measured in liver samples of cod exposed to chlorpyrifos-methyl

Concentrations of chlorpyrifos-methyl and its metabolite TCP in cod liver and bile quantified using gas chromatography

Measurement of plasma parameters: activities of cholinesterase, alanine aminotransferase, aspartate aminotransferase + cortisol and total protein levels in cod exposed to chlorpyrifos-methyl

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.

The aim of the exposure was to study the effects of activation of peroxisome proliferator-activated receptors (PPARs) in Atlantic cod (Gadus morhua), by injecting the fish with the compounds WY-14,643 and GW501516. Using luciferase reporter assay in vitro, we have shown that WY-14,643 activate Atlantic cod Ppara1 and Ppara2, while GW501516 activate Ppara1, Ppara2, and Pparb. The experimental set-up was as follows: Immature cod were injected at day 0 and day 4 with either high dose (40 mg/kg ...

Untargeted lipidomics analysis was performed on plasma and liver samples of four male fish from each group (n = 4) at Per Bruheim’s lab at NTNU, Norway, using Liquid Chromatography Hybrid Quadrupole Mass Spectrometry (UPLC-HDMS).

Normalisation: The fraction of each lipid compound among all measured lipids in every sample was calculated and was used in the downstream analysis.

Quantification of CPM and TCP concentrations in cod liver and bile using gas chromatography

Levels of cortisol+total protein and activities of cholinesterase, alanine aminotransferase (ALAT) and aspartate aminotransferase (ASAT) in plasma of cod exposed to chlorpyrifos-methyl

EROD activity in liver of cod exposed to chlorpyrifos-methyl

Overview of metabolomics results from liver of cod exposed to chlorpyrifos-methyl

Biometrics of IVN fish exposed to chlorpyrifos-methyl

Information connecting RNA seq fastq-files to corresponding fish ID/exposure regime

The four treatment groups were Control (0 mg CPM/kg, with DMSO), 0.5 mg CPM/kg, 4.2 mg CPM/kg and 23.2 mg CPM/kg. Each treatment group consisted of 9 fish. These fish were sampled from 3 different tanks per treatment, with n=9 per treatment. A total of 36 samples were sequenced. For each sample, about 50 million 150 bp paired-end reads were generated.

More information can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/developmentalStages/zebrafish

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

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

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

Supplementary Tables 1-4 for manuscript "The chemical defensome of five model teleost fish"

Supplementary Table1 and Table2 for manuscript "The chemical defensome of fish"

Concentrations of PAH metabolites in bile and PFAS parent compounds in liver

Measurement of tail intensities in the Comet Assay - used in in vivo 1

Measurement of cholinesterase, ALAT and ASAT activities + cortisol and total protein levels - in vivo studies

Template for chemical quantification of CPM and TCP in liver and bile.

Template for biometrics for IV-nord experiment

Template for EROD activity measured in exposure studies

Semi-quantitative measurement of Cyp1a protein amount using the ELISA methods. Cyp1a amount is expressed as absorbance values at 450 nm.

Concentration of vitellogenin measured in cod blood plasma - in vivo studies

Enzyme activity of glutathione S-transferase and catalase in in vivo exposure studies

Concentrations of vitellogenin in blood plasma measured in field studies

TBARS assay: Measurement of oxidative stress

Gene expression data of cod liver including the genes cyp1a, cat, hsp70, gsta3b, fabp7, fasn, acly, and scd.

qPCR results using absolute quantification, genes involved in steroidogenic pathways

Concentrations of contaminants in cod liver

Template for relative protein expression of Cyp3a and MT in field studies

Concentrations of estradiol (E2) and testosterone (T) in cod plasma in field studies (groups defined by stations).

Template for in vivo biometrics data

Measurements of Gst and Cat enzyme activity in field studies such as Kollevåg.