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Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation
Programme: SysMO
SEEK ID: https://fairdomhub.org/projects/11
Public web page: http://sulfosys.com/
Organisms: Sulfolobus solfataricus
FAIRDOM PALs: Pawel Sierocinski
Project created: 15th Jan 2009
Related items
- People (26)
- Institutions (13)
- Investigations (3+1)
- Studies (7+1)
- Assays (28+1)
- Data files (22+7)
- Models (15)
- SOPs (7+1)
- Publications (5)
- Presentations (1)
Projects: SulfoSys
Institutions: University of Bergen
Projects: SulfoSys
Institutions: University of Groningen
Projects: SulfoSys
Institutions: University of Bergen
Projects: SulfoSys
Institutions: University of Braunschweig
Expertise: Metabolomics
Projects: SulfoSys
Institutions: University Duisburg-Essen
Roles: Student
Tools: Biochemistry, Molecular Biology, Enzyme assays
Projects: SulfoSys
Institutions: eGene Biotechnologie GmbH
Roles: Postdoc
Expertise: Bioinformatics, Comparative Genomics, Phylogenetics, Genome based Taxonomy, Culture Collection, Extremophiles
Tools: Bioinformatics, Genomics, Phylogenetics
Projects: SulfoSys, FAIRDOM user meeting, Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Make Me My Model, Service to University of Lisbon (Portugal) with respect to their CFTR maturation model (Active NOW), Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), Service to Universidade Católica Portugues with respect to their Molecular Insight into Autism Spectrum Disorder (ASD) model (Active NOW), Service to Slovenia with respect to their Protease signaling network in neurodegeneration model (Active NOW), Service to University of Duisburg- Essen (Germany): with respect to their The Yin-Yang of Metabolism; Endometatoxicity (YYME) model (Active NOW), Service to Sheffield University (UK): with respect to Mitochondrial perfect adaptation model (Active NOW), Service to Sanquin (Amsterdam): with respect to Modelling of acute and chronic inflammation (Prospective), Service to Munich (Germany): with respect toCharged peptide to charged membrane binding model (Prospective), Training Hunfeld, EraCoBiotech 2 nd call proposal preparation, ROS detailed model for MSB manucript, Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, COVID-19 Disease Map, Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation
Institutions: University of Amsterdam, VU University Amsterdam, Infrastructure Systems Biology Europe, University of Luxembourg, Luxembourg Centre for Systems Biomedicine (LCSB)
Roles: Project Coordinator
I have modelling expertise in precise kinetic models of metabolism and signal transduction; metabolic control analysis, hierarchical regulation analysis, non-equilibrium dynamics, statistical mechanics, enzyme kinetics, flux balance analysis. Energy and carbohydrate metabolism in Archaea, Bacteria and human; ammonium assimilation in Bacteria; differential network-based drug design; cancer metabolic rewiring; cell cycle; genome wide metabolic map and inborn errors of metabolism; epigenetics.
Projects: SulfoSys, SulfoSys - Biotec
Institutions: University Duisburg-Essen
Projects: SulfoSys
Institutions: University of Vienna
Projects: SulfoSys, SulfoSys - Biotec
Institutions: University of Sheffield
Institutions: University of Stavanger
Expertise: biophysical chemistry, Kinetics
Tools: Perl, Matlab, quantitative western blot analyses, enzyme kinetics, madonna, fortran
Physical chemist with expertise in experimental kinetics, molecular biology, and mathematical modeling.
Projects: SulfoSys
Institutions: University of Vienna
Geneticist and Microbiologist with research focus on Archaea. Professor of Genetics in Ecology (Faculty of Life Sciences/University of Vienna, Austria) and associate professor of the Center of Geobiology (University of Bergen/Norway).
Projects: SulfoSys, PSYSMO, SulfoSys - Biotec
Institutions: University of Braunschweig
Projects: PSYSMO, SulfoSys, SulfoSys - Biotec
Institutions: University of Braunschweig
Projects: MOSES, PSYSMO, SysMO-LAB, SulfoSys
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester
Projects: SulfoSys, SulfoSys - Biotec, HOTSOLUTE, Computational pathway design for biotechnological applications, ScyCode
Institutions: University Duisburg-Essen, Universitity Duisburg-Essen

Roles: Project Coordinator, Vice Coordinator
Expertise: Carbohydrate Metabolism of Archaea, Reconstruction of metabolic pathways, Regulation of carbohydrate metabolism, Archaeal physiology, Hyperthermophiles, Thermoacidohiles, Biotechnology
Tools: Biochemistry, Molecular Biology, Microbiology, Physiology, Systems Biology
Head of the group of Molecular Enzyme Technology and Biochemistry (Faculty of Chemistry) at the University of Duisburg-Essen. My research interest is on archaeal physiology with a special focuss on the central carbohydrate metabolism of (hyper)thermophilic Archaea and its regulation. The aim is to gain a systems level understanding by the combination of modern highthrouput analyses with classical biochemistry and molecular biology.
Archaea possess many novel enzymes and pathways and our aim is
...
Projects: SulfoSys
Institutions: Wageningen University & Research
Expertise: Microbiology, Genetics
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, University of Manchester - Department of Computer Science, Stellenbosch University
The gluconeogenic conversion of 3-phosphoglycerate via 1,3-bisphosphoglycerate to glyceraldehyde-3-phosphate was compared at 30 C and at 70 C. At 30 C it was possible to produce 1,3-bisphosphoglycerate from 3-phosphoglycerate with phosphoglycerate kinase, but at 70 C, 1,3- bisphosphoglycerate was dephosphorylated rapidly to 3-phosphoglycerate, effectively turning the phosphoglycerate kinase into a futile cycle. At both temperatures it was possible to convert 3-phosphoglycerate to glyceraldehyde
...
Snapshots: No snapshots
An investigation in the central carbon metabolism of S. solfataricus with a focus on the unique temperature adaptations and regulation; using a combined modelling and experimental approach.
Snapshots: No snapshots
Studies: Carbon Loss at High Temperature, Model Gluconeogenesis
Assays: Experimental Validation Gluconeogenesis in S. solfataricus, FBPAase, FBPAase Modelling, GAPDH, GAPDH Modelling, Model Validation Gluconeogenesis in S. solfataricus, Modelling Metabolite Degradation at High Temperature, PGK, PGK Modelling, Reconstituted Gluconeogenesis System, TPI, TPI Modelling, Temperature Degradation of Gluconeogenic Intermediates
The Sulfolobus systems biology (‘‘SulfoSYS’’)-project represented the first (hyper-)thermophilic Systems Biology project, funded within the European trans-national research initiative ‘‘Systems Biology of Microorganisms’’. Within the SulfoSYS-project, focus lies on studying the effect of temperature variation on the central carbohydrate metabolism (CCM) of S. solfataricus that is characterized by the branched Entner–Doudoroff (ED)-like pathway for sugar (glucose, galactose) degradation and the
...
Snapshots: No snapshots
Studies: Pilot experiment - S. solfataricus grown at 70 and 80 C.
Assays: Comparison of proteome of S. solfataricus at 70 and 80C, Comparison of transcriptome of S. solfataricus at 70 and 80C, Enzyme activity tests for S. solfataricus, Fermentation of S. solfataricus at 70 and 80C in a batch fermenter, Intracellular metabolomics of S. solfataricus at 70 and 80C
PGK-GAPDH reactions were studied in vitro at 30 and 70 using yeast or Sso enzymes
SED-ML:
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig4b/simulate
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig4c/simulate
Person responsible: Theresa Kouril
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Assays: PGK - GAPDH models, PGK-GAPDH 30, PGK-GAPDH 70
PGK reaction at 30 C. Yeast PGK was incubated at 30 C, in the presence or absence of the ATP recycling system, and the conversion of 3 PG to BPG was followed.
SED-ML simulations
Fig. 1A: https://jjj.bio.vu.nl/models/experiments/kouril2017_fig1a/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Assays: PGK 30C data, PGK 30C model
PGK reaction at 70C. Sulfolobus solfataricus PGK was incubated at 70C in presence and absence of an ATP recycling system.
Changes in metabolite concentrations was followed via 31P NMR or enzymatic analyses.
SED-ML:
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3b/simulate
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3c/simulate
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3d/simulate
Person responsible: Theresa Kouril
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Assays: PGK 70 data, PGK 70C model
BPG produced with yeast PGK was incubated at 70 C,upon which BPG rapidly dephosphorylates to 3PG.
SED-ML:
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig2b/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Assays: BPG degradation, BPG stability analysis
Carbon loss due to instability of gluconeogenic pathway intermediates (BPG, GAP, DHAP) at high temperature in S. solfataricus
Person responsible: Jacky Snoep
Snapshots: No snapshots
Mathematical model of a subset of reactions comprising the three most temperature sensitive intermediates of the gluconeogenic pathway in S. solfataricus
Person responsible: Jacky Snoep
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Assays: FBPAase, FBPAase Modelling, GAPDH, GAPDH Modelling, Modelling Metabolite Degradation at High Temperature, PGK, PGK Modelling, Reconstituted Gluconeogenesis System, TPI, TPI Modelling, Temperature Degradation of Gluconeogenic Intermediates
The pilot experiment has been set up in order to develop uniform SOPs for the Sulfosys consortium. It comprises proteomics, transcriptomics, metabolomics as well as enzymatic essays. Cells for all the members of the consortium have been obtained from the same batch fermentations according to fermentation SOP of Sulfosys. The pilot resulted in creating a procedures for all the techniques used in consortium.
Person responsible: Pawel Sierocinski
Snapshots: No snapshots
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Assays: Comparison of proteome of S. solfataricus at 70 and 80C, Comparison of transcriptome of S. solfataricus at 70 and 80C, Enzyme activity tests for S. solfataricus, Fermentation of S. solfataricus at 70 and 80C in a batch fermenter, Intracellular metabolomics of S. solfataricus at 70 and 80C
Experimental data for the yeast PGK incubations at 30C, with and without recycling of ATP.
Submitter: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-30C
Organisms: No organisms
SOPs: No SOPs
Data files: PGK yeast with recycling of ATP, PGK yeast without recycling of ATP
Changes in metabolite concentrations were either quantified via 31P NMR or enzymatically
Submitter: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: NMR
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-70C
Organisms: No organisms
SOPs: No SOPs
Data files: Sso PGK (14 ug/ml) in presence of recycling sys..., Sso PGK (28 ug/ml) in presence of recycling sys..., Sso PGK in absence of recycling system, 31P NMR..., Sso PGK in presence of ATP recycling system at ...
BPG degradation at 70C
Submitter: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: BPG stability
Organisms: No organisms
SOPs: No SOPs
Data files: BPG degradation at 70
Submitter: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-GAPDH 30C & 70C
Organisms: No organisms
SOPs: No SOPs
Data files: PGK-GAPDH 30, 3PG, GAP & BPG, PGK-GAPDH 30, PYR
Submitter: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-GAPDH 30C & 70C
Organisms: No organisms
SOPs: No SOPs
Data files: PGK-GAPDH 70
Submitter: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Enzymatic Activity Measurements
Snapshots: No snapshots
Investigation: 1 hidden item
Study: 1 hidden item
Organisms: No organisms
SOPs: No SOPs
Data files: non-enzymatic phosphoenolpyruvate (PEP) degrada...
Kinetic characterisation of glyceraldehyde 3-phosphate dehydrogenase
Submitter: Jacky Snoep
Assay type: Enzymatic Assay
Technology type: Initial Rate Experiment
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Organisms: Sulfolobus solfataricus
SOPs: Cloning and heterologous expression in E. coli, Preparation of cell extracts of recombinant E.coli, Protein purification from E. coli extracts
Data files: GAPDH Kinetic Data
Kinetic characterisation of triose phosphate isomerase
Submitter: Jacky Snoep
Assay type: Enzymatic Assay
Technology type: Initial Rate Experiment
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Organisms: Sulfolobus solfataricus
SOPs: Cloning and heterologous expression in E. coli, Preparation of cell extracts of recombinant E.coli, Protein purification from E. coli extracts
Data files: TPI Kinetic Data
Kinetic characterisation of fructose 1,6-bisphosphate aldolase phosphatase
Submitter: Jacky Snoep
Assay type: Enzymatic Assay
Technology type: Initial Rate Experiment
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Organisms: Sulfolobus solfataricus
SOPs: Cloning and heterologous expression in E. coli, Preparation of cell extracts of recombinant E.coli, Protein purification from E. coli extracts
Data files: FBPAase Kinetic data
Temperature degradation of BPG, GAP and DHAP
Submitter: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Organisms: Sulfolobus solfataricus
SOPs: No SOPs
Data files: Temperature Degradation of Gluconeogenic Interm...
Experimental data for the conversion of 3PG to F6P and the gluconeogenic pathway intermediates
Submitter: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Carbon Loss at High Temperature
Organisms: Sulfolobus solfataricus
SOPs: No SOPs
Data files: Experimental Data for Reconstituted Gluconeogen..., Simulation for Reconstituted Gluconeogenic System
Kinetic characterisation of phosphoglycerate kinase
Submitter: Jacky Snoep
Assay type: Enzymatic Assay
Technology type: Initial Rate Experiment
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Organisms: Sulfolobus solfataricus
SOPs: Cloning and heterologous expression in E. coli, Preparation of cell extracts of recombinant E.coli, Protein purification from E. coli extracts
Data files: PGK Kinetic Data
The pilot experiment was conducted in order to create SOPs and to gain insight in transcriptome of cells grown at 70 and 80C
Submitter: Pawel Sierocinski
Assay type: Transcriptional Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Study: Pilot experiment - S. solfataricus grown at 70 ...
Organisms: Sulfolobus solfataricus (batch)
SOPs: Sulfosys - SOP microarray
Data files: No Data files
Samples obtained form the central fermentation facility of Sulfosys have been compared using iTRAQ (isobaric tag for relative and absolute quantification). A pilot experiment resulted in creation of SOP and initial data on cells grown at 70 and 80C
Submitter: Pawel Sierocinski
Assay type: Protein Expression Profiling
Technology type: Isotope Ratio Mass Spectrometry
Snapshots: No snapshots
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Study: Pilot experiment - S. solfataricus grown at 70 ...
Organisms: Sulfolobus solfataricus (batch)
SOPs: Sulfosys - SOP proteomics
Data files: 1 hidden item
In order to get uniform data from all geographically separated partners in a consortium, central fermentation facility has been set-up. Based on empirical data, standard procedures for growing S. solfataricus cells have been developed.
Submitter: Pawel Sierocinski
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Study: Pilot experiment - S. solfataricus grown at 70 ...
Organisms: Sulfolobus solfataricus (batch)
SOPs: Sulfosys - SOP fermentation
Data files: 6 hidden items
Based on initial cell material, series of SOPs connected with assays of enzymes involved in Central Carbon Metabolism of S. solfataricus have been developed.
Submitter: Pawel Sierocinski
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Study: Pilot experiment - S. solfataricus grown at 70 ...
Organisms: Sulfolobus solfataricus (chemostat)
SOPs: 1 hidden item
Data files: 2 hidden items
Pilot experiment concerning metabolome of S. solfataricus was conducted in order to acquire SOPs regarding the technique and gain insight on differences in metabolite concentrations at 70 and 80C
Submitter: Pawel Sierocinski
Assay type: Metabolomics
Technology type: Gas Chromatography Mass Spectrometry
Snapshots: No snapshots
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Study: Pilot experiment - S. solfataricus grown at 70 ...
Organisms: Sulfolobus solfataricus (batch)
SOPs: Sulfosys - SOP metabolomics
Data files: No Data files
A model for the PGK reaction of yeast in presence or absence of the ATP recycling reactions
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-30C
Organisms: No organisms
Models: PGK yeast Fig1a, PGK yeast with/without recycling
SOPs: No SOPs
Data files: No Data files
BPG stability analysis
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: BPG stability
Organisms: No organisms
Models: BPG stability notebook
SOPs: No SOPs
Data files: No Data files
PGK 70C model
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-70C
Organisms: No organisms
Models: PGK 70C, PGK 70C SBML
SOPs: No SOPs
Data files: No Data files
Creators: Theresa Kouril, Jacky Snoep
Submitters: Jacky Snoep, Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Assays: PGK 70 data
Experimental data for 3PG conversion to fructose-6-phosphase in reconstituted systems of gluconeogenesis of S. solfataricus
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Simulation results of TPI experimental data for GAP and DHAP saturation.
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Assays: TPI Modelling
Simulation results of temperature degradation of gluconeogenic intermediates
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Simulation results of experimental data of the reconstituted gluconeogenic system
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Simulation results of PGK experimental data for ADP, ATP, 3PG and BPG saturation.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Assays: PGK Modelling
Simulation results of FBPAase of experimental data for DHAP and GAP saturation
Creator: Jacky Snoep
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Assays: FBPAase Modelling
Simulation results of GAPDH experimental data for BPG, NADPH, NADP, GAP, and Pi
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Assays: GAPDH Modelling
Creators: Theresa Kouril, Jacky Snoep
Submitter: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Assays: PGK 70 data
Creator: Theresa Kouril
Submitter: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Assays: PGK 70 data
incubations with yeast enzymes at 30C
Creators: Theresa Kouril, Jacky Snoep
Submitter: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-GAPDH 30C & 70C
Assays: PGK-GAPDH 30
Creators: Theresa Kouril, Jacky Snoep
Submitter: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-GAPDH 30C & 70C
Assays: PGK-GAPDH 30
Creators: Theresa Kouril, Jacky Snoep
Submitter: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-GAPDH 30C & 70C
Assays: PGK-GAPDH 70
metabolite quantification via enzymatic analysis
Creators: Theresa Kouril, Jacky Snoep
Submitter: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Assays: PGK 70 data
Creators: Theresa Kouril, Jacky Snoep
Submitter: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: BPG stability
Assays: BPG degradation
PGK yeast without recycling of ATP
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-30C
Assays: PGK 30C data
PGK yeast with recycling of ATP
Creator: Jacky Snoep
Submitter: Jacky Snoep
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-30C
Assays: PGK 30C data
Kinetic characterisation of FBPAase. Expermental data for enzyme reaction rates with increasing concentrations of DHAP and GAP.
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Assays: FBPAase, FBPAase Modelling
Kinetic characterisation of TPI. Experimental data for enzyme reaction rates with increasing concentrations of DHAP and GAP, and inhibition with 3PG and PEP.
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Assays: TPI, TPI Modelling
Kinetic characterisation of GAPDH. Expermental data for enzyme reaction rates with increasing concentrations of BPG, NADPH, NADP, GAP and Pi.
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Assays: GAPDH, GAPDH Modelling
BPG stability notebook
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: BPG stability
Modelling analyses: BPG stability analysis
PGK model for S. solfataricus
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Organism: Sulfolobus solfataricus
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Modelling analyses: PGK 70C model
PGK-GAPDH model Sulfolobus kouril8
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Sulfolobus solfataricus
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-GAPDH 30C & 70C
Modelling analyses: PGK - GAPDH models
PGK-GAPDH model yeast kouril7
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Saccharomyces cerevisiae
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-GAPDH 30C & 70C
Modelling analyses: PGK - GAPDH models
PGK-GAPDH models yeast and Sulfolobus Fig. 4 in manuscript
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-GAPDH 30C & 70C
Modelling analyses: PGK - GAPDH models
PGK 70C SBML
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Sulfolobus solfataricus
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Modelling analyses: PGK 70C model
PGK yeast Fig1a
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Organism: Saccharomyces cerevisiae
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-30C
Modelling analyses: PGK 30C model
PGK yeast with/without recycling
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Saccharomyces cerevisiae
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-30C
Modelling analyses: PGK 30C model
Model of reconstituted gluconeogenesis system in S. solfataricus based on the individual kinetic models for PGK, GAPDH, TPI, FBPAase.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Sulfolobus solfataricus
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Carbon Loss at High Temperature, Model Gluconeogenesis
Modelling analyses: Model Validation Gluconeogenesis in S. solfatar..., Reconstituted Gluconeogenesis System
Exponential decay model of gluconeogenic intermediates
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Modelling analyses: Modelling Metabolite Degradation at High Temper..., Reconstituted Gluconeogenesis System
Mathematical model for TPI kinetics, GAP and DHAP saturation, and inhibition with 3PG and PEP.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Modelling analyses: Reconstituted Gluconeogenesis System, TPI Modelling
Mathematical model for GAPDH kinetics, BPG, NADPH, NADP, GAP and Pi saturation.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Modelling analyses: GAPDH Modelling, Reconstituted Gluconeogenesis System
Mathematical model for FBPAase kinetics, saturation with DHAP and GAP
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Modelling analyses: FBPAase Modelling, Reconstituted Gluconeogenesis System
Mathematical model for PGK kinetics, ADP, ATP, 3PG and BPG saturation.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Modelling analyses: PGK Modelling, Reconstituted Gluconeogenesis System
The model describes the Entner-Doudoroff pathway in Sulfolobus solfataricus under temperature variation. The package contains source code written in FORTRAN as well as binaries for Mac OSX, Linux, and Windows. If compiling from source code, a FORTRAN compiler is required.
On-line versions of the model are also available at:
http://bioinfo.ux.uis.no/sulfosys
http://jjj.biochem.sun.ac.za/sysmo/projects/Sulfo-Sys/index.html
Creator: Peter Ruoff
Submitter: Peter Ruoff
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
Preparation of cell free extracts of the recombinant E. coli strains expressing the gluconeogenic S. solfataricus enzymes.
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Cloning and heterologous expression of gluconeogenic enzymes from S. solfataricus in E. coli
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
Purification of gluconeogenic enzymes from S. solfataricus in recombinant E.coli extracts
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model Gluconeogenesis
SOPs related with medium composition, fermentation and stocking of S. solfataricus.
Creator: Pawel Sierocinski
Submitter: Pawel Sierocinski
Investigations: Analysis of Central Carbon Metabolism of Sulfol... and 1 hidden item
Studies: Pilot experiment - S. solfataricus grown at 70 ... and 1 hidden item
Assays: Fermentation of S. solfataricus at 70 and 80C i... and 1 hidden item
Standard procedure regarding intracellular metabolome analysis using GC-MS.
Creator: Pawel Sierocinski
Submitter: Pawel Sierocinski
Protocol for RNA isolation, cDNA synthesis and labeling and hybridization and cleanup of Sulfolobus solfataricus microarray
Creator: Pawel Sierocinski
Submitter: Pawel Sierocinski
Standard operating procedures regarding iTraq based proteomics.
Creator: Pawel Sierocinski
Submitter: Pawel Sierocinski
Abstract (Expand)
Authors: T. Kouril, J. J. Eicher, B. Siebers, J. L. Snoep
Date Published: 7th Oct 2017
Publication Type: Not specified
PubMed ID: 28982396
Citation: Microbiology. 2017 Nov;163(11):1604-1612. doi: 10.1099/mic.0.000542. Epub 2017 Oct 6.
Abstract (Expand)
Authors: A. S. Figueiredo, T. Kouril, D. Esser, P. Haferkamp, P. Wieloch, D. Schomburg, P. Ruoff, B. Siebers, J. Schaber
Date Published: 12th Jul 2017
Publication Type: Not specified
PubMed ID: 28692669
Citation: PLoS One. 2017 Jul 10;12(7):e0180331. doi: 10.1371/journal.pone.0180331. eCollection 2017.
Abstract (Expand)
Authors: , Dominik Esser, Julia Kort, , ,
Date Published: 20th Jul 2013
Publication Type: Not specified
PubMed ID: 23865479
Citation:
Abstract (Expand)
Editor:
Date Published: 4th Dec 2009
Publication Type: Not specified
PubMed ID: 19954172
Citation:
All contributors
Abstract (Expand)
Authors: , Dominik Esser, , , , , , Julia Reimann, , , Daniela Teichmann, Marleen van Wolferen, , , , , , , , , ,
Date Published: 31st Aug 2009
Publication Type: Not specified
PubMed ID: 19802714
Citation: