- Home
- Projects Index
- MOSES
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
SEEK ID: https://fairdomhub.org/projects/8
Public web page: http://www.moses.sys-bio.net/
Organisms: Saccharomyces cerevisiae
FAIRDOM PALs: Femke Mensonides, Walter Glaser, Maksim Zakhartsev
Project created: 15th Jan 2009
Related items
- People (20)
- Institutions (6)
- Investigations (3)
- Studies (8)
- Assays (13)
- Strains (1)
- Data files (9+1)
- Models (8+1)
- SOPs (11)
- Publications (8)
- Presentations (1)
- Samples (4)
Projects: MOSES
Institutions: VU University Amsterdam
Projects: MOSES
Institutions: Medical University Vienna
Expertise: Bioinformatics
Tools: PHP, SQL, R, Microarray analysis, Perl, Transcriptomics, Computational and theoretical biology, Data Management
General Bioinformatics
Projects: MOSES
Institutions: University of Heidelberg
Projects: MOSES
Institutions: Medical University Vienna
Projects: MOSES
Institutions: Medical University Vienna
Projects: MOSES
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: MOSES
Institutions: VU University Amsterdam
Projects: MOSES
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: PSYSMO, MOSES, COSMIC, BaCell-SysMO
Institutions: University of Stuttgart
Expertise: Regulatory Networks, Mathematical modeling, Systems Biology, dynamics and control of biological networks, Reactor models, rapid sampling experiments
Tools: fed-batch cultivation, In silico Metabolic Network Analysis, Dynamic modelling, including:- Dynamic modelling- Parameter estimation- Optimal experimental design- Dynamic optimization, Computational Systems Biology, continuous cultivation, evaluation of process dynamics, stimulus response experiments, Fermentation
Professor for Biochemcial Engineering, University Stuttgart
Institutions: University of Stavanger
Expertise: biophysical chemistry, kinetics
Tools: fortran, madonna, enzyme kinetics, quantitative western blot analyses, Matlab, Perl
Physical chemist with expertise in experimental kinetics, molecular biology, and mathematical modeling.
Projects: MOSES, PSYSMO, SysMO-LAB, SulfoSys
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: PSYSMO, MOSES, SysMO DB, SysMO-LAB, SulfoSys, SulfoSys - Biotec, Whole body modelling of glucose metabolism in malaria patients, FAIRDOM, Molecular Systems Biology, COMBINE Multicellular Modelling, HOTSOLUTE, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, University of Stellenbosch, School of Computer Science, University of Manchester, Stellenbosch University
Projects: MOSES
Institutions: Medical University Vienna
Projects: MOSES, SysMO-LAB, BaCell-SysMO
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: MOSES
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: MOSES, ExtremoPharm
Institutions: University of Heidelberg
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, stimulus response experiments, Material balance based modeling, 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
...
This investigation examines the effect of benzoic acid, a food preservative, on the ATP levels of yeast cells.
Snapshots: No snapshots
Studies: ATP levels after benzoic acid pretreatments, ATP levels under 10 mM benzoic acid stress, ATP levels under 30 mM and 50 mM benzoic acid stress, Cell survival under different benzoic acid concentrations, Test different ATP extraction protocols and conditions
Assays: ATP measurement under 10mM benzoic acid stress, ATP measurement under 30mM benzoic acid stress, ATP measurement under 50mM benzoic acid stress, Compare ATP extraction methods
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
Cell survival was determined under different benzoic acid concentrations
Person responsible: Martin Valachovic
Snapshots: No snapshots
Investigation: Effect of Benzoic Acid on ATP Levels
Assays: No Assays
Effect of benzoate treatment (high concentrations) on ATP levels and Pdr12 expression after pretreatment of cells with low concentrations of benzoic acid.
Person responsible: Martin Valachovic
Snapshots: No snapshots
Investigation: Effect of Benzoic Acid on ATP Levels
Assays: No Assays
ATP levels of cells stressed with higher concentrations of benzoic acid (30 mM and 50 mM).
Person responsible: Martin Valachovic
Snapshots: No snapshots
To see changes in ATP levels in cells with induced ABC transporters. Cells with Pdr12 pump by 10 mM benzoic acid are used.
Person responsible: Martin Valachovic
Snapshots: No snapshots
Investigation: Effect of Benzoic Acid on ATP Levels
This study aims to establish the optimum conditions and assay methods for measuring ATP levels
Person responsible: Martin Valachovic
Snapshots: No snapshots
Investigation: Effect of Benzoic Acid on ATP Levels
Assays: Compare ATP extraction methods
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
Steady state fluxes 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
Contributor: Walter Glaser
Assay type: Metabolomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Effect of Benzoic Acid on ATP Levels
Study: ATP levels under 30 mM and 50 mM benzoic acid s...
Organisms: Saccharomyces cerevisiae : YSBN2 diploid (wild-type / wild-type) (batch)
SOPs: ATP determination with ROCHE kit “ATP Biolumin...
Data files: No Data files
Contributor: Walter Glaser
Assay type: Metabolomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Effect of Benzoic Acid on ATP Levels
Study: ATP levels under 30 mM and 50 mM benzoic acid s...
Organisms: Saccharomyces cerevisiae : YSBN2 diploid (wild-type / wild-type) (batch)
SOPs: ATP determination with ROCHE kit “ATP Biolumin...
Data files: No Data files
Contributor: Walter Glaser
Assay type: Metabolomics
Technology type: Imaging
Snapshots: No snapshots
Investigation: Effect of Benzoic Acid on ATP Levels
Study: ATP levels under 10 mM benzoic acid stress
Organisms: Saccharomyces cerevisiae : YSBN2 diploid (wild-type / wild-type) (batch)
SOPs: ATP determination with ROCHE kit “ATP Biolumin...
Data files: No Data files
We will compare two different procedures to extract ATP from yeast cells: Standard kit procedure (hot Tris/EDTA) and Serrano procedure (cold perchloric acid). In addition we have tested different condition as it turned out that some are important.
Contributor: Walter Glaser
Assay type: Metabolomics
Technology type: Imaging
Snapshots: No snapshots
Investigation: Effect of Benzoic Acid on ATP Levels
Study: Test different ATP extraction protocols and con...
Organisms: Saccharomyces cerevisiae : YSBN2 diploid (wild-type / wild-type) (batch)
SOPs: ATP determination with ROCHE kit “ATP Biolumin...
Data files: No Data files
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...
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...
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
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
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 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...
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
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
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.
Contributor: Maksim Zakhartsev
Biological problem addressed: Metabolic Network
Snapshots: No snapshots
Investigation: Kinetic analysis of metabolic system using tran...
Study: Metabolic perturbation of the steady state cult...
Organisms: Saccharomyces cerevisiae : CEN.PK113-7D haploid (wild-type / wild-type) (chemostat)
Models: SBML model of yeast central carbon metabolism
SOPs: No SOPs
Data files: Dynamics of extracellular metabolites during gl..., Dynamics of intracellular metabolites during gl..., Measured steady state concentrations of extrace..., Measured steady state concentrations of intrace..., Measured steady state metabolic fluxes, Off-gas monitoring during glucose pulse
Contributor: Maksim Zakhartsev
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Saccharomyces cerevisiae
Genotypes: del ura3;del his3;del leu2;del trp1;del mal2-8c;del suc2
Phenotypes: no adenylate cyclase activity
Comment: Not specified
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.
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
Investigations: Kinetic analysis of metabolic system using tran...
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,
...
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
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.
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
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.
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
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.
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
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.
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
Investigations: Kinetic analysis of metabolic system using tran...
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).
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...
Assays: MOSES: dynamic model of glucose pulse, Steady state concentrations of intracellular me...
Steady state concentrations of extracellular metabolites in yeast Saccharomyces cerevisiae anaerobic chemostat at D = 0.1 h-1 on minimal medium. All metabolite concentrations are in mmol/L(R) except CO2, which is in parts of the partial pressure.
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...
Assays: MOSES: dynamic model of glucose pulse, Steady state concentrations of extracellular me...
Steady state metabolic fluxes measured in glucose-limited chemostat of Saccharomyces cerevisiae at D = 0.1 h-1 growing on minimal medium. Fluxes are: glucose, ethanol, glycerol, acetate, succinate, pyruvate, lactate, citrate, malate, a-ketoglutarate, fumarate
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 fluxes in yeast Saccharomyces cere...
Assays: MOSES: dynamic model of glucose pulse, Steady state extracellular fluxes in anaerobic ...
Copasi file chronic inflammation Abulikemu et al 2020 (altered units TNF and MMP8); see supplemntal material:
TNF and MMP7 concentration upgrade of the models
All computations for the present paper were completed by using the model prepared and tested in Abulikemu et al 2018. Then, little attention was paid to the unit in which concentrations were expressed, except for the concentration of fibroblasts, which we found important for modelling the effect of confluency. This led to a predicted TNF
...
Creators: Hans Westerhoff, Abulikemu Abudukelimu and Matteo Barberis
Contributor: Hans Westerhoff
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
Copasi file chronic inflammation Abulikemu et al 2020 (altered units TNF and MMP8); see supplemntal material:
TNF and MMP7 concentration upgrade of the models
All computations for the present paper were completed by using the model prepared and tested in Abulikemu et al 2018. Then, little attention was paid to the unit in which concentrations were expressed, except for the concentration of fibroblasts, which we found important for modelling the effect of confluency. This led to a predicted TNF
...
Creators: Hans Westerhoff, Ablikim Abulikemu, Matteo Barberis
Contributor: Hans Westerhoff
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
This is a model about a ROS network that exhibits five design principles, and has been calibrated so as to predict quantitatively various steady state concentrations. 10191125.
Instructions
RUN the model for steady state.
For the Menadione experiment set the initial concentration of 'Menadione' species to experimental dosing i.e. 100 000 nM (0.1 mM) and make the simulation type "reaction" for both the species i.e. 'Menadione' and 'Menadione_internal'. Then run for 24 hr i.e. 1500 minutes approx.
...
Creators: Hans Westerhoff, Raju Prasad Sharma, Alexey Kolodkin
Contributor: Hans Westerhoff
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
Model that can be used to obtain the figures of Abudulikemu et al 2018:
Abudukelimu, A., Barberis, M., Redegeld, F.A., Sahin, N., and Westerhoff, H.V. (2018). Predictable Irreversible Switching Between Acute and Chronic Inflammation. Front Immunol 9, 1596.
Creators: Hans Westerhoff, Ablikim Abudukelimu
Contributor: Hans Westerhoff
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
(Abudulikemu et al 2000 (also 2018) Standard model of acute mode Figure 32.
Creators: Hans Westerhoff, Ablikim Abudukelimu
Contributor: Hans Westerhoff
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
Particularly figure 2 of of Abudulikemu et al 2020 in press
Creator: Hans Westerhoff
Contributor: Hans Westerhoff
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
The principles of Stealthy Engineering (Adamczyk et al.: Biotechnology Journal 2012; 7(7):877-83) are illustrated in this model by emulating a cross engineering intervention between L. lactis and S. cerevisiae.
The case study consists of replacing the native glucose uptake system of L. lactis with that native to the yeast S. cerevisiae. A modified version of Hoefnagel et al.’s model of L. lacrtis’ central metabolism was used as starting point. The total functional replacement of the PTS with the
...
Creators: Malgorzata Adamczyk, Hans Westerhoff, Ettore Murabito
Contributor: Ettore Murabito
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Organism: Lactococcus lactis
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
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.
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
Model type: Metabolic network
Model format: SBML
Environment: Copasi
Organism: Saccharomyces cerevisiae
Investigations: Kinetic analysis of metabolic system using tran...
Studies: Metabolic perturbation of the steady state cult...
Modelling analyses: MOSES: dynamic model of glucose pulse
Assay methodologies for individual glycolytic isoenzymes from the Mendes Group, University of Manchester, UK
Creator: Hanan Messiha
Contributor: Walter Glaser
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This is the general protocol for the glycolytic enzyme measurements. Detailed Information for each Enzyme can be found in the SOP: Assays for measuring the activities of the individual glycolytic isoenzymes of Saccharomyces cerevisiae
Creator: Hanan Messiha
Contributor: Walter Glaser
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
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 ...
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
Creator: Hanan Messiha
Contributor: Maksim Zakhartsev
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Sample preparation - SOP for sampling, preparation of cell-free extracts, and determination of total extracted protein
Creator: Femke Mensonides
Contributor: Maksim Zakhartsev
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
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...
The kit is used for the quantitative detection of ATP in yeast cells by luciferase driven
bioluminescence. ATP extraction is done by boiling cells in TE buffer.
Creators: Martin Valachovic, Cornelia Klein
Contributor: Walter Glaser
Investigations: Effect of Benzoic Acid on ATP Levels
Studies: ATP levels under 10 mM benzoic acid stress, ATP levels under 30 mM and 50 mM benzoic acid s..., Test different ATP extraction protocols and con...
Assays: ATP measurement under 10mM benzoic acid stress, ATP measurement under 30mM benzoic acid stress, ATP measurement under 50mM benzoic acid stress, Compare ATP extraction methods
This protocol is designed to prepare sufficient amounts of high-quality total
RNA from the yeast saccharomyces cerevisiae grown in liquid culture for
analysis on microarrays.
Creators: Walter Glaser, Christa Gregori
Contributor: Walter Glaser
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Abstract (Expand)
Authors: Maksim Zakhartsev, Matthias Reuss
Date Published: 26th Apr 2018
Journal: Not specified
Citation: Cell size and morphological properties of yeast Saccharomyces cerevisiae in relation to growth temperature 18(6) : 603
Abstract (Expand)
Authors: Maksim Zakhartsev, Xuelian Yang, Matthias Reuss, Hans Otto Pörtner
Date Published: 1st Aug 2015
Journal: Journal of Thermal Biology
DOI: 10.1016/j.jtherbio.2015.05.008
Citation: Journal of Thermal Biology 52 : 117
Abstract (Expand)
Authors: Maksim Zakhartsev, Oliver Vielhauer, Thomas Horn, Xuelian Yang, Matthias Reuss
Date Published: 1st Apr 2015
Journal: Metabolomics
DOI: 10.1007/s11306-014-0700-8
Citation: Metabolomics 11(2) : 286
Abstract (Expand)
Authors: None
Date Published: 1st Sep 2012
Journal: Biochimica et Biophysica Acta (BBA) - Bioenergetics
DOI: 10.1016/j.bbabio.2012.09.014
Citation:
Abstract (Expand)
Authors: Oliver Vielhauer, Maksim Zakhartsev, Thomas Horn, Ralf Takors, Matthias Reuss
Date Published: 1st Dec 2011
Journal: Journal of Chromatography B
DOI: 10.1016/j.jchromb.2011.10.036
Citation:
Abstract (Expand)
Authors: Maksim Zakhartsev, Christian Bock
Date Published: 1st Feb 2010
Journal: Analytical Biochemistry
Citation:
Abstract (Expand)
Authors: Felix Bonowski, Ana Kitanovic, Peter Ruoff, Jinda Holzwarth, Igor Kitanovic, Van Ngoc Bui, Elke Lederer, Stefan Wölfl
Date Published: 23rd Dec 2009
Journal: PLoS ONE
PubMed ID: 20502716
Citation:
Abstract (Expand)
Authors: Hans Westerhoff, Catherine Winder, Hanan Messiha, Evangelos Simeonidis, Malgorzata Adamczyk, Malkhey Verma, Frank J Bruggeman, Warwick Dunn
Date Published: 6th Nov 2009
Journal: FEBS Lett.
PubMed ID: 19913018
Citation:
Talk given by Maksim Zakhartsev (Hohenheim University, Stuttgart, Germany, member of MOSES, ZucAt and ExtremoPharm projects)
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev