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 project for the Digital Salmon use case in BT8121 - Transdisciplinary biotechnology - a Digital Life Norway course.

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 ...

The aim of this investigation is to understand molecular mechanisms of PUFA biosynthesis and regulation in order to enable the sustainable use of vegetable oils in aquafeeds as current sources of fish oils are unable to meet increasing demands for omega-3 PUFAs. By generating gene knockouts, we would like to study the genes that are crucial for multi-tissue synthesis of PUFA synthesis in vivo.

Atlantic salmon is a main source of essential ω-3 long-chain polyunsaturated fatty acids (LC-PUFA) in many Western diets, especially eicosapentaenoic acid (20:5n-3, EPA) and docosahexaenoic acid (22:6n-3, DHA). However, farmed salmon meat now contains less healthy ω-3 fatty acids (FA) than before, due to the shift from marine to vegetable lipid feed sources. An important future aquaculture challenge is therefore to maintain a healthy and high EPA/DHA content when farmed salmon is fed a vegetable ...

This experiment is designed to pinpoint where in the metabolic network there are differences between salmon of different genetic families and on different diets. Analyses of this material will help inform feeding and breeding strategies.

Salmon will be reared on feeds with contrasting levels of very-long-chain polyunsaturated fatty acids. Then some fish will be crossed over to the other diet while others remain as controls. This perturbation of diet should provoke changes in omega-3 metabolism ...

By generating CRISPR-mediated elovl2 knockout, we are planning to study the crucial role of elovl2 for multi-tissue synthesis of 22:6n-3 in vivo. Endogenously synthesized PUFAs are important for transcriptional regulation of lipogenic genes in Atlantic salmon. This study demonstrates key roles of elovl2 at two penultimate steps of PUFA synthesis in vivo and suggests Srebp-1 as a main regulator of endogenous PUFA synthesis in Atlantic salmon.

16S rRNA amplicon sequencing (Illumina MiSeq, V3-V4 region) to assess community structure.

Targeted proteomics for peptides related to fatty acid metabolism. Aim: Check which of these proteins we are able to detect in this experiment.

From the "data accessibility" section of Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon. (Publication):

Supplementary files have been deposited to datadryad.org under the accession: https://doi.org/10.5061/dryad.j4h65. Raw RNA-Seq data have been deposited into European Nucleotide Archive (ENA) under the project Accession no. PRJEB24480.

Dead links 2022-06-29 (the Shiny ...

Record of weight, length and sex of fish sampled after feed switch between vegetable and marine oil, in September 2015 (freshwater) and January 2016 (seawater). Young fry arrived at Solbergstranda 2015-02-05 17:20.

Fatty acids are extracted from samples and converted to fatty acid methyl esters (FAMEs) followed by separation by gas chromatography. This yields fatty acid profiles for each sample as percent of total FAME or milligram FAME per gram of biomass.

Source:

Hei Magny,

Takk!

Et par ting:

1. vi trenger å få orden på data... Lurer derfor på om du kan du lage ett dokument som inneholder alle resultat fra GCen? Uten ...

Fatty acids are extracted from samples and converted to fatty acid methyl esters (FAMEs) followed by separation by gas chromatography. This yields fatty acid profiles for each sample as percent of total FAME or milligram FAME per gram of biomass.

Source:

Hei Magny,

Takk!

Et par ting:

1. vi trenger å få orden på data... Lurer derfor på om du kan du lage ett dokument som inneholder alle resultat fra GCen? Uten ...

An overview of RNA sequencing data generated in GenoSysFat (and a couple of others).

Source: Email from Simen Rød Sandve to Jon Olav Vik and Fabian Grammes 2017-02-10, titled "RNAseq generert i GSF".

This should be turned into separate RNAseq Assays when we can allocate people for it. Currently the following have records already:

Tissue panel for gene expression in ZF, Med, RT https://fairdomhub.org/assays/324

Tissue panel for gene expression in ZF,Med,RT- RNA sequencing https://fairdomhub.org/assays/395 ...

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 ...

Stranded RNAseq libraries were prepared from 1µg total RNA from liver tissue using TruSeq Stranded mRNA library preparation kit (Illumina, San Diego, USA) using double unique indices (#20022371), according to the manufacturer's instruction (Part 15031057 Rev.E). Libraries were sequenced at the Norwegian Sequencing Centre (NSC). All libraries were pooled, and the same pool was sequenced on 4 flow cell lanes on a HiSeq 3000 machine (Illumina), generating 100bp single-end reads. RNA sequencing files ...

Total lipids are extracted from tissues of white muscle, liver and whole brain from three fish per dietary treatment.

The three different CRISPR target sites within the elovl2 gene (T1-3) were characterised by Sanger sequencing, sequencing on average 8 clones per individual.

RNAseq is utilised to validate the SnpEff annotation predictions for aberrant splicing. For this purpose the percentage exon retention for exons 4, 6 and 7 are calculated using RNAseq data.

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 ...

Differential expression analysis (using R package edgeR) on liver gene expression between salmon with all four fads2 genes knockout, only fads2d6b & fads2d6c knockout and wildtype. All salmon was given either a low-PUFA diet or a high-PUFA diet

Spreadsheet of weight, length and sex of fish sampled after feed switch between vegetable and marine oil, in September 2015 (freshwater) and January 2016 (seawater).

Spreadsheet columns are:

• Date (YYYY-MM-DD)
• Day (day zero is the day before first feeding with new feed)
• Inputter (person entering data into Excel)
• Tank (1, 2, 4, 5 with Atlantic salmon, 3 and 6 with rainbow trout)
• Section (tanks were divided in half using perforated walls)
• Treatment (explained in sheet "treatments")

...

CPM is a descriptive measures for the expression level of a gene.

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.

Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species ...

Extraction procedure and lipid analysis.

Winter conditions for 5 weeks (6th october – 10th November):

• Light on 12 hours per day
• Turn off water heating
• Feeding probably needs to be adjusted according to lower metabolism and feed intake in cold water

Spring condition (10th of November – 15th of December):

• Water heating on
• constant light (24hrs/day)

Vaccination (when and by whom?)

Transfer to sea-water (15th of December)

Last sampling for GenoSysFat in sea water (5th January – 25th of January).

Source: email with subject ...

Source: Tom Harvey [E- mail from Jon Olav 19 May 2016]

Use this template when you upload RNA sequencing data. Email : 31 May 2016 More columns need to be added PE/SE etc?

Describes the workflow used for preparation of a 16S rRNA gene amplicon (V3-V4 region) Library for sequencing on a MiSeq platform (Illumina) using V3 sequencing chemistry with 300 base pairs paired-end reads.

Describes how the DNA was isolated from salmon intestinal samples before preparations of 16S rRNA gene amplicons for the Illumina MiSeq system.

We have adapted the definitions of terms in [ISA best practice][1] and [programmes and projects][2]:

Programme = Overarching research theme (The Digital Salmon) Project = Research grant (DigiSal, GenoSysFat) Investigation = a particular biological process, phenomenon or thing (typically corresponds to [plans for] one or more closely related papers) Study = experiment whose design reflects a specific biological research question Assay = standardized measurement or diagnostic experiment using a ...

1. Digital biotechnology
2. The value chain
3. Examples
4. Tools and funding
5. Data sharing

https://www.dnvgl.com/ocean-space/index.html

Björgólfur Hávarðsson is Innovation Manager in the NCE Seafood Innovation Cluster, Norway. He leads AquaCloud, a sea-louse forecast system that streams data from 3000 netcages to provide individually tailored precautionary recommendations to its participants. What do the participants contribute, and what do they get out? What are their motivations, and how was the collaboration organised?

Look to medicine: Computer models enter clinical practice. The genotype x environment --> phenotype map. The Digital Life Norway network and researcher projects. The Digital Salmon: a library of models and data. The merits of mathematical modelling. Commoditizing models and data. Goals for the workshop:

• Participants' input!
• Is there support for a Digital Salmon knowledge base? -- Moral commitment from industry, academia, funders. -- Some form of consortium, reponsible for next workshop. ...

How do you communicate a complex research endeavour in simple words and pictures using only two minutes? In my case that turned out to be scientifically impossible, but we managed to shave it down to three. This poster shows and tells how we went about it.

Three-minute presentation of the Digital Salmon research programme. Explains the societal challenge of sustainable fish feed, how systems biology helps speed up the search for better solutions, and the grand aim to build a library of mathematical models of salmon physiology linked to omics data.

My graduation project presentation given on 22 of June at the Hanze University of Applied Sciences Groningen in The Netherlands.

Improve project deployment by letting your team focus on code quality instead of fixes problems. Spend more time on new features and let your project progress getting tested automatically.

The first Digital Salmon industry workshop raised awareness of the Digital Salmon vision and engaged major industry players in discussions on data sharing and reuse, guidelines and best practices for private-public collaboration. The workshop was a success, and a Digital Salmon working group was formed, comprising industry, academia and funding bodies. Its first task is to develop a white paper to be presented to the industry in summer of 2020.

Our 2018 DigiSal project meeting is held as a satellite meeting of Digital Life 2018 (https://digitallifenorway.org/arrangementer/digitallife-2018).

Most of DS18 will be spent on breakout sessions to work on upcoming publications. Task leaders will prepare:

• Abstracts to DLN18. (Deadline was 15 Feb.) Presenting DigiSal progress here rather than at DS18 frees up time for the paper preparation sessions.

• Identify two papers in preparation, which will be worked on at DS18: Title, first and ...

Abstracts and posters from DigiSal for Digital Life 2018.

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?

Data modelling methods that are capable of maintaining block structure, as for example the block structure of the blocks of lipid classes, are called multi-block methods e.g. Consensus Principal Component Analysis (CPCA) and Multi-block Partial Least Squares Regression (MBPLSR). CPCA and MBPLR are two large families of MB methods. The developed methods can still be transferred to other data analysis methods. CPCA and MBPLSR which are extensions of PCA and PLSR to multi-block data sets can be ...

Detailed programme with organizers' notes.