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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.
SEEK ID: https://fairdomhub.org/assays/43
Experimental Assay
Projects: MOSES
Investigation: Kinetic analysis of metabolic system using transient perturbations
Study: Metabolic perturbation of the steady state culture by glucose pulse
Assay type: Metabolomics
Technology type: Technology Type
Organisms: Saccharomyces cerevisiae
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Created: 27th Apr 2010 at 15:09
Last updated: 8th Nov 2017 at 15:21
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Projects: MOSES, ExtremoPharm, ZucAt, GenoSysFat, DigiSal, EraCoBiotech 2 nd call proposal preparation, FAIRDOM & LiSyM & de.NBI Data Structuring Training
Institutions: University of Stuttgart, University of Hohenheim, Norwegian University of Life Sciences, Norwegian University of Science and Technology

Roles: Postdoc
Expertise: yeast, fungi, Metabolomics, Proteomics, Stoichiometric modelling, carbon metabolism, Systems Biology, dynamics and control of biological networks, coupling metabolome and environome, rapid sampling experiments, Biochemistry
Tools: parameter estimation, ODE, HPLC, GC and LC/MS analysis of metabolites, Mass spectrometry (LC-MS/MS), continuous cultivation, Enzyme assay, Material balance based modeling, stimulus response experiments, Chromatography, Fermentation, Matlab, Metabolomics, Biochemistry and protein analysis
I've become a SysMO DB PAL for MOSES project in 2007 being a post-doc in lab of Prof. Matthias Reuss at University of Stuttgart. In the MOSES project, our major efforts were in the experimental data acquisition for dynamic model of primary carbon and anaerobic energy metabolism in yeast. The model implements prediction of perturbations of two types: glucose pulse and temperature jump. We implement “stimulus-response” methodology for the unraveling the dynamic structure of the network and to
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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.
Programme: SysMO
Public web page: http://www.moses.sys-bio.net/
Organisms: Saccharomyces cerevisiae
Investigation of dynamics of the central metabolism (glycolysis, PPP, anaplerotic reactions, purines) of yeast Saccharomyces cerevisiae in anaerobic conditions
Snapshots: No snapshots
Studies: Metabolic perturbation of the steady state culture by glucose pulse
Assays: Biomass weight during glucose pulse, Cellular size and granularity during glucose pulse, Dynamics of extracellular metabolites during glucose pulse, Dynamics of intracellular metabolites during glucose pulse, Dynamics of macromolecules during glucose pulse, MOSES: dynamic model of glucose pulse
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
Person responsible: Maksim Zakhartsev
Snapshots: No snapshots
Investigation: Kinetic analysis of metabolic system using tran...
Assays: Biomass weight during glucose pulse, Cellular size and granularity during glucose pulse, Dynamics of extracellular metabolites during glucose pulse, Dynamics of intracellular metabolites during glucose pulse, Dynamics of macromolecules during glucose pulse, MOSES: dynamic model of glucose pulse
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.
SOP for growing yeast in anaerobic conditions
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
Investigations: Kinetic analysis of metabolic system using tran..., Steady state metabolic fluxes and metabolite co...
Studies: Metabolic perturbation of the steady state cult..., Steady state concentrations of metabolites in y..., Steady state fluxes in yeast Saccharomyces cere...
Assays: Biomass weight during glucose pulse, Cellular size and granularity during glucose pulse, Dynamics of extracellular metabolites during gl..., Dynamics of intracellular metabolites during gl..., Dynamics of macromolecules during glucose pulse, Steady state concentrations of extracellular me..., Steady state concentrations of intracellular me..., Steady state extracellular fluxes in anaerobic ...
Biomass sampling - SOP for sampling of biomass
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
Investigations: Kinetic analysis of metabolic system using tran..., Steady state metabolic fluxes and metabolite co...
Studies: Metabolic perturbation of the steady state cult..., Steady state concentrations of metabolites in y..., Steady state fluxes in yeast Saccharomyces cere...
Assays: Biomass weight during glucose pulse, Cellular size and granularity during glucose pulse, Dynamics of extracellular metabolites during gl..., Dynamics of intracellular metabolites during gl..., Dynamics of macromolecules during glucose pulse, Steady state concentrations of extracellular me..., Steady state concentrations of intracellular me..., Steady state extracellular fluxes in anaerobic ...
Metabolic perturbations - SOP for metabolic perturbations (i.e. glucose pulse)
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
Investigations: Kinetic analysis of metabolic system using tran...
Studies: Metabolic perturbation of the steady state cult...
Assays: Cellular size and granularity during glucose pulse, Dynamics of extracellular metabolites during gl..., Dynamics of intracellular metabolites during gl..., Dynamics of macromolecules during glucose pulse
Yeast strains used in the project
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
Investigations: Kinetic analysis of metabolic system using tran..., Steady state metabolic fluxes and metabolite co...
Studies: Metabolic perturbation of the steady state cult..., Steady state concentrations of metabolites in y..., Steady state fluxes in yeast Saccharomyces cere...
Assays: Biomass weight during glucose pulse, Cellular size and granularity during glucose pulse, Dynamics of extracellular metabolites during gl..., Dynamics of intracellular metabolites during gl..., Dynamics of macromolecules during glucose pulse, Steady state concentrations of extracellular me..., Steady state concentrations of intracellular me..., Steady state extracellular fluxes in anaerobic ...
Sample preparation - SOP for sampling, preparation of cell extracts, and general assay set-up
Creator: Femke Mensonides
Contributor: Maksim Zakhartsev
Investigations: Kinetic analysis of metabolic system using tran..., Steady state metabolic fluxes and metabolite co...
Studies: Metabolic perturbation of the steady state cult..., Steady state concentrations of metabolites in y...
Assays: Cellular size and granularity during glucose pulse, Dynamics of intracellular metabolites during gl..., Dynamics of macromolecules during glucose pulse, Steady state concentrations of intracellular me...