Maksim Zakhartsev

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 ...

ZucAt - Sucrose (from german Zucker) translocation in Arabidopsis thaliana. Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the ...

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 ...

Glycon proposal preparation

The aim of the project is bioprospecting, isolation and characterization of novel secondary metabolites, produced by extremophilic microorganisms. The project is dedicated to a poorly investigated problem of antagonistic interactions between extremophilic microorganisms in their communities, namely, to the investigation of the ability of extremophiles to produce secondary metabolites with biocidic, cytotoxic and cytostatic activities. Working out this problem will fulfill an important applied ...

MOSES (Micro Organism Systems biology: Energy and Saccharomyces cerevisiae) develops a new Systems Biology approach, which is called 'domino systems biology'. It uses this to unravel the role of cellular free energy ('ATP') in the control and regulation of cell function. MOSES operates though continuous iterations between partner groups through a new systems-biology driven data-management workflow. MOSES also tries to serve as a substrate for three or more other SYSMO programs.

Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped ...

Investigation of dynamics of the central metabolism (glycolysis, PPP, anaplerotic reactions, purines) of yeast Saccharomyces cerevisiae in anaerobic conditions

Steady state metabolic fluxes and metabolite concentrations of yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1

we describe a multi-compartmental model consisting of a mesophyll cell with plastid and mitochondrion, a phloem cell, as well as a root cell with mitochondrion. In this model, the phloem was considered as a non-growing transport compartment, the mesophyll compartment was considered as both autotrophic (growing on CO2 under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue completely dependent on sucrose supply from the mesophyll ...

The steady state anaerobic culture (D = 0.1 h-1) was pertrubed by sudden increase of the extracellular glucose up to 1 g/L and both extra- and intracellular transient metabolite concentrations were measured

Steady state fluxes in yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1

Steady state concentrations of metabolites in yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1

Cellular size and granularity (measured by FACS) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

experimentally measured extracellular fluxes in yeast Saccharomyces cerevisiae in anaerobic glucose limited chemostat (D=0.1 h-1) on minimal medium

Steady state concentrations of extracellular metabolites in yeast Saccharomyces cerevisiae in anaerobic chemostat at D = 0.1 h-1 on minimal medium

Biomass weight during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

Dynamics of extracellular metabolites (glc, pyr, suc, lac, gly, ac, etoh, fum, mal, cit, including loss of akg, g3p, 2pg, 3pg, r5p, f6p, g6p, 6pg) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

Dynamics of intracellular metabolites (pyr, suc, fum, mal, akg, pep, g3p, 2pg, 3pg, cit, r5p, f6p, g6p, 6pg, ATP, ADP, AMP, UTP, GTP, inosine, NAD+, IMP, UDP, NADP+, CTP, AdenyloSuccinate, NADPH, trehalose) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, ...

Dynamics of macromolecules (total RNA) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

The dynamic model describes response of yeast metabolic network on metabolic perturbation (i.e. glucose-pulse). One compartmental ODE-based model of yeast anaerobic metabolism includes: glycolysis, pentose phosphate reactions, purine de novo synthesis pathway, purine salvage reactions, redox reactions and biomass growth. The model describes metabolic perturbation of steady state growing cells in chemostat.

The multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized in order to explain growth stoichiometry of the plant both in light and in dark conditions. Balances and turnover of energy (ATP/ADP) and redox (NAD(P)H/NAD(P)) metabolites as well as proton in different compartments were estimated. The model showed that in light conditions, the plastid ATP balance depended on the relationship between fluxes through photorespiration and photosynthesis including both ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.1 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP formed by non-cyclic photophosphorylation is not sufficient to fulfill ATP/NADPH ratio for ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in the model under light growth conditions. In this solution, (i) the photorespiration was set to 0; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set of 0.1 of flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is under-produced in plastid and therefore is additionally imported to cytoplasm. Flux through FQR represents cyclic electron flow through ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.5 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is over-produced in plastid and a surplus is exported to cytoplasm. Flux through FQR ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; (ii) and ATP transport between plastid and cytoplasm has been set to 0. The last constraint allows finding the ratio between fluxes through FQR (ferredoxin-plastoquinone reductase) and FRN (ferredoxin-NADP oxidoreductase) under which the ATP balance in plastid becomes self-sufficient ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; (ii) and cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set to 0. Under this constraints, ATP formed by non-cyclic photophosphorylation is not sufficient to fulfill ATP/NADPH ratio for carbon fixation, therefore plastid imports ATP from cytoplasm.

The solution of Flux Balance Analysis (FBA) represent metabolic flux distribution in the model under dark growth conditions (i.e. constraints)

Flux Balance Analysis (FBA) constraints for light conditions

Flux Balance Analysis (FBA) constraints for dark conditions

The database in ASCII format includes information on compounds and metabolites (trivial name, elemental composition, charge, external database referece, etc) used in the model

The database in ASCII format includes information on gene (gene models in ATG format, gene definition, catalyzed reactions in the model, external database refeneces, locus information, etc) used in the model

The database in ASCII format includes information on transformers [reactions, transport steps, polymerizations] (model's identifier, trivial name, EC number, stoichiometric equation, external database referece, activators, belonging to a pathway, etc) used in the model

The stoichiometric matrix of the multi-compartment metabolic model of growing Arabidopsis thaliana

The ASCII file includes complete information on used transformers / compounds / genes and their inter-connection in the model. The Transformer information includes: Identifier name, Trivial name, Stoichiometric equation, Compartment, EC number, Pathway, Associated genes). The Compound information includes: Identifier name, Trivial name, Kegg ID, Compartment. The Gene information includes: ATG code of the genes whose products participate in transformations accounted in the model, Association with ...

Monitoring of partial pressure of CO2 in off-gas. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

Dynamics of intracellular metabolites (pyr, suc, fum, mal, akg, pep, g3p, 2pg, 3pg, cit, r5p, f6p, g6p, 6pg, ATP, ADP, AMP, UTP, GTP, inosine, NAD+, IMP, UDP, NADP+, CTP, AdenyloSuccinate, NADPH, trehalose) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, ...

Dynamics of extracellular metabolites (glc, pyr, suc, lac, gly, ac, etoh, fum, mal, cit, including loss of akg, g3p, 2pg, 3pg, r5p, f6p, g6p, 6pg) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

Cellular size and granularity (measured by FACS) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

Dynamics of macromolecules (total RNA) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

Biomass weight during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

Steady state concentrations of intracellular metabolites in yeast Saccharomyces cerevisiae anaerobic chemostat at D = 0.1 h-1 on minimal medium. All metabolite concentrations are in mmol/L(CV).

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 ...

The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that ...

The model includes glycolysis, pentosephosphate pathway, purine salvage reactions, purine de novo synthesis, redox balance and biomass growth. The network balances adenylate pool as opened moiety.

SOP for growing yeast in anaerobic conditions

Biomass sampling - SOP for sampling of biomass

Metabolic perturbations - SOP for metabolic perturbations (i.e. glucose pulse)

Yeast strains used in the project

General protocol for measuring the kinetic parameters of the purified glycolytic enzymes from Saccharomyces cerevisiae - SOP for measuring the kinetic parameters of the purified glycolytic isoenzymes

Sample preparation - SOP for sampling, preparation of cell-free extracts, and determination of total extracted protein

Sample preparation - SOP for sampling, preparation of cell extracts, and general assay set-up

Talk given by Maksim Zakhartsev (Hohenheim University, Stuttgart, Germany, member of MOSES, ZucAt and ExtremoPharm projects)