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 ...

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.

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

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.

Build the chemical defensome gene list for 5 fish: Zebrafish (Danio rerio), Atlantic cod (Gadus morhua), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus) and stickleback (Gasterosteus aculeatus). Source code and relevant files can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/defensomeGenes

To study the defensome genes' expression in early developmental stages of zebrafish and stickleback. Souce code and relevant files can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/developmentalStages

Exposing zebrafish to benzo(a)pyrene (B(a)P) (gene counts from NCBI GEO: GSE64198, previously published by Fang, et al. 2015. Souce code and relevant files can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/exposureResponse

Results from lipidomics analyses performed in cod liver microsomes of cod exposed to PAH and PFAS mixtures.

Some results from proteomics analyses of cod liver exposed to PAH and PFAS

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.

Measurement of DNA fragmentation using the Comet Assay, in white blood cells of Atlantic cod exposed to PAHs and PFASs

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.

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

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

Source code and relevant files can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/developmentalStages/stickleback

There are four datasheets in the Excel file: 1. Gene pattern and the corresponding category (the gene list is then divided into the other three datasheets); 2. These gene names (patterns) can be directly followed by either a letter or a number; 3. These gene names (patterns) should be directly followed by a letter; 4. These gene names (patterns) should be directly followed by a number.

The reactions existing in the auto-generated draft model are shown in blue, and the manually filled gaps are shown in green. Comparing our draft model with the same subsystem from model iHepatocytes2322, the missing reactions are highlighted in pink. The pink dots indicate the parent toxicants.

gadMorTrinity can be found at: https://doi.org/10.6084/m9.figshare.13067354.v1

COBRA Matlab toolbox was used.

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"