Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture (DigiSal)

Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. Project DigiSal will lay the foundations for a Digital Salmon: an ensemble of mathematical descriptions of salmon physiology, combining ...

A joint NTNU and SINTEF project to establish a knowledge platform on DHA synthesis and lipid accumulation in the native DHA-producing thraustochytrids, and to develop these into high productivity omega-3 fatty acid producing cell factories.

Salmon farmed on modern feeds contains less of the healthy, long-chain fatty acids (EPA and DHA) than before. Up until the turn of the millennium, farmed salmon were fed fish oil as a replacement for their omega-3 rich natural prey. However, fish oil is now a scarce resource, and more than half of the fat in modern feeds comes from plant oils that are inexpensive, but devoid of long-chain omega-3 fatty acids. How can we increase the omega-3 content of salmon on sustainable feeds?

One option is ...

This is a sandbox where DigiSal members can learn to use the SEEK.

Tutorial document: http://tinyurl.com/seek-ds17

The SEEK is a web interface to a database of research "assets" organised in a hierarchical "ISA structure" (investigation-study-assay) [1]. These are further organised into projects and programmes.

• Programme = Overarching research theme (The Digital Salmon)
• Project = Research grant (DigiSal, GenoSysFat)
• Investigation = a particular biological process, phenomenon or thing ...

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.

NB! The files here are the old version for the files in Lipidomics (Experimental Assay)

Lipidomic analysis by LC-MS of tissue samples from the GSF1 feed-switch experiment. Samples were analyzed at NTNU by Zdenka Bartosova and Per Bruheim.

There are two separate data files of lipid analysis in muscle and liver samples. Excel sheets contains both raw and normalised data of compounds abundance. Normalization to all compounds was used as a normalization method.

We have also performed a "normalization ...

Lipidomic analysis by UPC2-MS of tissue samples from the GSF1 feed-switch experiment. Samples were analyzed at NTNU by Zdenka Bartosova and Per Bruheim.

There are three separate data files of lipid analysis in muscle, liver and gut tissue samples. Excel sheets contains both raw and normalised data of compounds abundance. Normalization to all compounds was used as a normalization method.

Columns: Compound 0.93_858.7669n Anova (p) 0,044998264 q Value 0,009417222 Max Fold Change 1,644961431 Maximum ...

Salmon feed switch experiment: Lipid class quantitation for liver tissue samples (POS mode).

Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.

Salmon feed switch experiment: Lipid class quantitation for muscle tissue samples (POS mode).

Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.

Salmon feed switch experiment: Lipidomic data (POS mode) of gut tissue samples.

Salmon feed switch experiment: Lipidomic data (POS mode) of muscle tissue samples.

Salmon feed switch experiment: Lipid identification for muscle tissue samples (POS mode).

Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.

The 'O-' ...

Salmon feed switch experiment: Lipid identification for liver tissue samples (POS mode).

Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.

The 'O-' ...

Salmon feed switch experiment: Lipid identification for gut tissue samples (POS mode).

Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.

The 'O-' prefix ...

Salmon feed switch experiment: Lipid class quantitation for gut tissue samples (POS mode).

Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.

Salmon feed switch experiment: Lipidomics data (POS mode) of liver samples.

Muscle samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.

Negative mode lipidomics of muscle samples from saltwater sampling.

Muscle samples (salt water sampling) - Identification of compounds based on the LipidBlast database.

Liver samples (salt water sampling) - Identification of compounds based on the LipidBlast database.

Liver samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.

Liver samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.

Muscle samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.

Salmon feed experiment: Lipidomic data (NEG mode) of muscle samples from fresh water sampling.

Salmon feed experiment: Lipidomic data (NEG mode) of liver samples from fresh water sampling.

Negative mode lipidomics of liver samples from saltwater sampling.

Positive mode metabolomics of muscle samples from saltwater sampling.

Extraction procedure and lipid analysis.

DigiSal Metabolomics and Lipidomics Update

Conclusion:

• Organic acid test ok
• Next

1. Analyze all samples for OA (or selection? – include days and feed variation)
2. Then aminoacids?
3. Evaluate results – choose some samples for CapIC?