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Biomass sampling - SOP for sampling of biomass
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Created: 2nd Mar 2010 at 23:14
Last updated: 1st Mar 2012 at 11:57
Last used: 16th Feb 2019 at 03:57

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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
Steady state metabolic fluxes and metabolite concentrations of yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1
Snapshots: No snapshots
Studies: Steady state concentrations of metabolites in yeast Saccharomyces cerevi..., Steady state fluxes in yeast Saccharomyces cerevisiae in anaerobic chemo...
Assays: Steady state concentrations of extracellular metabolites in yeast Saccha..., Steady state concentrations of intracellular metabolites in yeast Saccha..., Steady state extracellular fluxes in anaerobic yeast Saccharomyces cerev...
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
Steady state fluxes in yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1
Person responsible: Maksim Zakhartsev
Snapshots: No snapshots
Steady state concentrations of metabolites in yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1
Person responsible: Maksim Zakhartsev
Snapshots: No snapshots
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
experimentally measured extracellular fluxes in yeast Saccharomyces cerevisiae in anaerobic glucose limited chemostat (D=0.1 h-1) on minimal medium
Contributor: Maksim Zakhartsev
Assay type: Metabolite Profiling
Technology type: HPLC
Snapshots: No snapshots
Investigation: Steady state metabolic fluxes and metabolite co...
Study: Steady state fluxes in yeast Saccharomyces cere...
Organisms: Saccharomyces cerevisiae (chemostat)
SOPs: Anaerobic media composition, Sampling of biomass, Yeast strains
Data files: Measured steady state metabolic fluxes
Steady state concentrations of extracellular metabolites in yeast Saccharomyces cerevisiae in anaerobic chemostat at D = 0.1 h-1 on minimal medium
Contributor: Maksim Zakhartsev
Assay type: Metabolite Profiling
Technology type: HPLC
Snapshots: No snapshots
Investigation: Steady state metabolic fluxes and metabolite co...
Study: Steady state concentrations of metabolites in y...
Organisms: Saccharomyces cerevisiae (chemostat)
SOPs: Anaerobic media composition, Sampling of biomass, Yeast strains
Data files: Measured steady state concentrations of extrace...
Contributor: Maksim Zakhartsev
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Snapshots: No snapshots
Investigation: Steady state metabolic fluxes and metabolite co...
Study: Steady state concentrations of metabolites in y...
Organisms: Saccharomyces cerevisiae (chemostat)
SOPs: Anaerobic media composition, Determination of intracellular metabolites, Sampling of biomass, Yeast strains
Data files: Measured steady state concentrations of intrace...
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.
Contributor: Maksim Zakhartsev
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Kinetic analysis of metabolic system using tran...
Study: Metabolic perturbation of the steady state cult...
Organisms: Saccharomyces cerevisiae (chemostat)
SOPs: Anaerobic media composition, Sampling of biomass, Yeast strains
Data files: Biomass weight during glucose pulse
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.
Contributor: Maksim Zakhartsev
Assay type: Metabolite Profiling
Technology type: HPLC
Snapshots: No snapshots
Investigation: Kinetic analysis of metabolic system using tran...
Study: Metabolic perturbation of the steady state cult...
Organisms: Saccharomyces cerevisiae (chemostat)
SOPs: Anaerobic media composition, Perturbation conditions, Sampling of biomass, Yeast strains
Data files: Dynamics of extracellular metabolites during gl...
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,
...
Contributor: Maksim Zakhartsev
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Snapshots: No snapshots
Investigation: Kinetic analysis of metabolic system using tran...
Study: Metabolic perturbation of the steady state cult...
Organisms: Saccharomyces cerevisiae (chemostat)
SOPs: Anaerobic media composition, Determination of intracellular metabolites, Perturbation conditions, Sampling of biomass, Yeast strains
Data files: Dynamics of intracellular metabolites during gl...
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.
Contributor: Maksim Zakhartsev
Assay type: Metabolomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Kinetic analysis of metabolic system using tran...
Study: Metabolic perturbation of the steady state cult...
Organisms: Saccharomyces cerevisiae
SOPs: Anaerobic media composition, Determination of intracellular metabolites, Perturbation conditions, Sampling of biomass, Yeast strains
Data files: Dynamics of macromolecules during glucose pulse
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.
Contributor: Maksim Zakhartsev
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Kinetic analysis of metabolic system using tran...
Study: Metabolic perturbation of the steady state cult...
Organisms: Saccharomyces cerevisiae (chemostat)
SOPs: Anaerobic media composition, Determination of intracellular metabolites, Perturbation conditions, Sampling of biomass, Yeast strains
Data files: Cellular size and granularity during glucose pulse