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- Dawie van Niekerk
SEEK ID: https://fairdomhub.org/people/411
Location:
South Africa
Expertise: Not specified
Tools: Not specified
Related items
- Projects (4)
- Institutions (2)
- Investigations (10)
- Studies (13)
- Assays (32)
- Data files (25)
- Models (36)
- SOPs (17)
- Publications (13)
The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:
* facilitates and maximises the potential for data exchange between SysMO research groups;
* maximises the ‘shelf life’ and
...
Programme: SysMO
Public web page: http://www.sysmo-db.org/
Organisms: Not specified
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Organisms: Saccharomyces cerevisiae
The Molecular Systems Biology project holds information for reproducing simulation figures in the journal. This can include experimental data files, model files and manuscript information.
Programme: Journals
Public web page: http://msb.embopress.org
Organisms: Not specified
Hypoglycaemia and lactic acidosis are key diagnostics for poor chances of survival in malaria patients. In this project we aim to test to what extent the metabolic activity of Plasmodium falciparum contributes to a changed glucose metabolism in malaria patients. The approach is to start with detailed bottom up models for the parasite and then merge these with more coarse grained models at the whole body level.
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Organisms: Plasmodium falciparum, Homo sapiens
The oxidative Weimberg pathway for the five-step pentose degradation to α ketoglutarate from Caulobacter crescentus is a key route for sustainable bioconversion of lignocellulosic biomass to added-value products and biofuels. Here, we developed a novel iterative approach involving initial rate kinetics, progress curves, and enzyme cascades, with high resolution NMR analysis of intermediate dynamics, and multiple cycles of kinetic modelling analyses to construct and validate a quantitative model
...
Snapshots: Snapshot 1, Snapshot 2
Studies: Cell free extract, Initial rate kinetics, One pot cascade, Progress curves
Assays: Cell free extract, with Mn and NAD recycling, Cell free extract, with Mn, no NAD recycling, Cell free extract, without added Mn, with NAD recycling, KDXD, KGSADH, One pot cascade 10, One pot cascade 12, One pot cascade 13, One pot cascade 16, Progress curve KDXD, Progress curve KGSADH, Progress curve XAD, Progress curve XDH, Progress curve XLA, Progress curves combined, Steady state cell free extract, with Mn and NAD recycling, XAD, XDH, XLA
Snapshots: No snapshots
Snapshots: No snapshots
Snapshots: No snapshots
Studies: Entrainment of heterogeneous glycolytic oscillations in single cells
Assays: No Assays
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
Drug detoxification dynamics explain the postantibiotic effect
Snapshots: No snapshots
Protein abundance of AKT and ERK pathway components governs cell-type- specific regulation of proliferation
Snapshots: No snapshots
The investigation entails the construction and validation of a detailed mathematical model for glycolysis of the malaria parasite Plasmodium falciparum in the blood stage trophozoite form.
Snapshots: Snapshot 1
Studies: Model analysis, Model construction, Model validation
Assays: ALD, ATPASE, Culturing and synchronisation of P. falciparum, ENO, G3PDH, GAPDH, GLC incubation, GLCtr, GLYtr, HK, Inhibition of glucose transport, Inhibition of lactate flux, LACtr, LDH, PFK, PGI, PGK, PGM, PK, PYRtr, Steady state, Supply-demand analysis, TPI, Trophozoite Isolation and Lysate Preparation
Design principles of nuclear receptor signaling: how complex networking improves signal transduction
Snapshots: No snapshots
Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range
Snapshots: No snapshots
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: From steady-state to synchronized yeast glycoly...
Assays: No Assays
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: From steady-state to synchronized yeast glycoly...
Assays: No Assays
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: Glycolytic oscillations in individual isolated ...
Assays: gustavsson1-4 models
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: Glycolytic oscillations in individual isolated ...
Assays: No Assays
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: Glycolytic oscillations in individual isolated ...
Assays: gustavsson5 model
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: Phase shift responses in isolated yeast glycoly...
Assays: No Assays
After the removal of the extracellular antibiotic, efflux and inhibition dynamics combine to delay the synthesis of ribosomes in a concentration-dependent manner (panel ii). Colors indicate increasing antibiotic concentration, as shown in panel ii.
SED-ML simulation
https://jjj.bio.vu.nl/models/experiments/srimani2017_fig2cii/simulate
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Growth-factor deprived mCFU-E cells (5x106 cells per condition) and BaF3-EpoR cells (1x107 cells per condition) were stimulated with different Epo doses and absolute concentrations were determined for pEpoR (B), pAKT (C), ppERK (D). The scale for pS6 (E) was estimated in arbitrary units. GTP-Ras (F) and ppERK were determined upon stimulation with indicated, color-coded Epo doses. pEpoR was analyzed by immunoprecipitation followed by immunoblotting, GTP-Ras was analyzed after pulldown using a
...
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Transcriptional response to a sudden increase in extracellular ligand (hormone), for the six network designs of (A). The transcriptional response is taken to equal the ratio ReNrL/Retotal, i.e., the fraction of REs attaching ligand-bound NR. The ligand concentration was increased from 0 to 0.005 nM and maintained constant at the latter level. The observation that design 6 is higher than all other designs at long times is robust for parameter changes up to a factor of 3.
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: Kolodkin et al (2010) Molecular Systems Biology...
For all experiments, primary CFU-E cells were starved and stimulated with 5 U/ml Epo. At the indicated time points, samples were subjected to quantitative immunoblotting. Experimental data (black circles) with estimated standard errors and trajectories of the best fit (solid lines) are represented. Mass spectrometry data represent replicates of four independent experiments.
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
This study includes the experimental data for model validation and the model predictions of that data set.
Person responsible: Dawie van Niekerk
Snapshots: No snapshots
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Assays: GLC incubation, Steady state
This study includes all the experimental data, SOPs and modelling files for the individual reactions used for the model construction.
Person responsible: Jacky Snoep
Snapshots: No snapshots
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Glycolytic oscillations in individual isolated ...
Study: Sustained glycolytic oscillations in individual...
Organisms: No organisms
Models: gustavsson1-4 models
SOPs: No SOPs
Data files: No Data files
Model of glycolytic oscillations in individual yeast cells in microfluidic flow chamber
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Glycolytic oscillations in individual isolated ...
Study: Allosteric regulation of phosphofructokinase co...
Organisms: No organisms
Models: gustavsson5 model
SOPs: No SOPs
Data files: No Data files
Submitter: Dawie van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Adlung et al (2017) Molecular Systems Biology
Study: Figure 2: Model calibration with time-resolved ...
Organisms: No organisms
SOPs: No SOPs
Data files: Source data for Figure 2B, Source data for Figure 2C, Source data for Figure 2D, Source data for Figure 2E, Source data for Figure 2F BaF3, Source data for Figure 2F mCFU-E, Source data for Figure 2G BaF3, Source data for Figure 2G mCFU-E
Submitter: Dawie van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Organisms: No organisms
SOPs: No SOPs
Data files: No Data files
Assay for the isolation of intact Plasmodium falciparum trophozoites from infected red blood cells and the preparation of a cell free extract that can be used for kinetic analyses.
Submitter: Dawie van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Organisms: No organisms
SOPs: No SOPs
Data files: No Data files
Submitter: Dawie van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Bachmann et al (2011) Molecular Systems Biology...
Study: Figure 3A: Model calibration with experimental ...
Organisms: No organisms
SOPs: No SOPs
Data files: Source data for Figure 3A: Experimental quantit...
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Srimani et al (2017) Molecular Systems Biology
Study: Figure 2C Panel ii: After the removal of the ex...
Organisms: No organisms
Models: Kinetic model of antibiotic-mediated inhibition...
SOPs: No SOPs
Data files: No Data files
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Adlung et al (2017) Molecular Systems Biology
Study: Figure 2: Model calibration with time-resolved ...
Organisms: No organisms
Models: BaF3 model, mCFU-E model
SOPs: No SOPs
Data files: No Data files
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model analysis
Organisms: Plasmodium falciparum
Models: GLCtr kinetic model incorporating inhibition
SOPs: No SOPs
Data files: GLCtr inhibition kinetic data
Inhibition of lactate flux due to glucose transport inhibitor
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model analysis
Organisms: Plasmodium falciparum
Models: Kinetic model for steady state (penkler1), Kinetic model incorporating glucose transport i..., Validation of lactate flux inhibition by glucos...
SOPs: No SOPs
Data files: Lactate flux inhibition data
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model analysis
Organisms: Plasmodium falciparum
Models: Kinetic model for steady state (penkler1), Supply demand analysis on penkler1 model
SOPs: No SOPs
Data files: No Data files
SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Bachmann et al (2011) Molecular Systems Biology...
Study: Figure 3A: Model calibration with experimental ...
Organisms: No organisms
Models: JAK2/STAT5 model
SOPs: No SOPs
Data files: No Data files
SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Kolodkin et al (2010) Molecular Systems Biology...
Study: Figure 2B: Transcriptional response to a sudde...
Organisms: No organisms
Models: NR model 1, NR model 2, NR model 3, NR model 4, NR model 5, NR model 6
SOPs: No SOPs
Data files: No Data files
Kinetic characterisation en mathematical modelling of HK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Organisms: No organisms
Models: HK Kinetic model
SOPs: HK Kinetic characterisation
Data files: HK Kinetic data
Kinetic characterisation en mathematical modelling of PGI.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Organisms: No organisms
Models: PGI Kinetic model
SOPs: PGI Kinetic characterisation
Data files: PGI Kinetic data
Kinetic characterisation en mathematical modelling of PFK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Organisms: No organisms
Models: PFK Kinetic model
SOPs: PFK Kinetic characterisation
Data files: PFK Kinetic data
Kinetic characterisation en mathematical modelling of ALD.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Organisms: No organisms
Models: ALD Kinetic model
SOPs: ALD Kinetic characterisation
Data files: ALD Kinetic data
Kinetic characterisation en mathematical modelling of TPI.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Organisms: No organisms
Models: TPI Kinetic model
SOPs: TPI Kinetic characterisation
Data files: TPI Kinetic data
Kinetic characterisation en mathematical modelling of G3PDH.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Organisms: No organisms
Models: G3PDH Kinetic model
SOPs: G3PDH Kinetic characterisation
Data files: G3PDH Kinetic data
Kinetic characterisation en mathematical modelling of GAPDH.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Organisms: No organisms
Models: GAPDH Kinetic model
SOPs: GAPDH Kinetic characterisation
Data files: GAPDH Kinetic data
See 'Figure 3 legend' and 'Materials and methods - Time course experiments, cell lysis and quantitative immunoblotting' for details.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model analysis
Assays: Inhibition of lactate flux
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model analysis
Assays: Inhibition of glucose transport
Experimental data set for the kinetic characterisation of G3PDH
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: G3PDH
Experimental data set for the kinetic characterisation of ALD
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: ALD
Experimental data set for the kinetic characterisation of ENO
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: ENO
Experimental data set for the kinetic characterisation of GAPDH
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: GAPDH
Experimental data set for the kinetic characterisation of LDH
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: LDH
Experimental data set for the kinetic characterisation of PGI
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PGI
Experimental data set for the kinetic characterisation of HK
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: HK
Experimental data set for the kinetic characterisation of PFK
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PFK
Experimental data set for the kinetic characterisation of PGK
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PGK
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Glycolytic oscillations in individual isolated ...
Studies: Sustained glycolytic oscillations in individual...
Modelling analyses: gustavsson1-4 models
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Saccharomyces cerevisiae
Investigations: Glycolytic oscillations in individual isolated ...
Studies: Allosteric regulation of phosphofructokinase co...
Modelling analyses: gustavsson5 model
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Srimani et al (2017) Molecular Systems Biology
Studies: Figure 2C Panel ii: After the removal of the ex...
Modelling analyses: Kinetic model of antibiotic-mediated inhibition...
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Adlung et al (2017) Molecular Systems Biology
Studies: Figure 2: Model calibration with time-resolved ...
Modelling analyses: Mathematical models of the Epo-induced AKT, ERK...
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Not specified
Investigations: Adlung et al (2017) Molecular Systems Biology
Studies: Figure 2: Model calibration with time-resolved ...
Modelling analyses: Mathematical models of the Epo-induced AKT, ERK...
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Kolodkin et al (2010) Molecular Systems Biology...
Studies: Figure 2B: Transcriptional response to a sudde...
Modelling analyses: Model nuclear receptor (NR) signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Kolodkin et al (2010) Molecular Systems Biology...
Studies: Figure 2B: Transcriptional response to a sudde...
Modelling analyses: Model nuclear receptor (NR) signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Kolodkin et al (2010) Molecular Systems Biology...
Studies: Figure 2B: Transcriptional response to a sudde...
Modelling analyses: Model nuclear receptor (NR) signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Kolodkin et al (2010) Molecular Systems Biology...
Studies: Figure 2B: Transcriptional response to a sudde...
Modelling analyses: Model nuclear receptor (NR) signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Kolodkin et al (2010) Molecular Systems Biology...
Studies: Figure 2B: Transcriptional response to a sudde...
Modelling analyses: Model nuclear receptor (NR) signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Kolodkin et al (2010) Molecular Systems Biology...
Studies: Figure 2B: Transcriptional response to a sudde...
Modelling analyses: Model nuclear receptor (NR) signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Bachmann et al (2011) Molecular Systems Biology...
Studies: Figure 3A: Model calibration with experimental ...
Modelling analyses: Model for JAK2/STAT5 signaling
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Plasmodium falciparum
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model analysis
Modelling analyses: Inhibition of lactate flux
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Plasmodium falciparum
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model analysis
Modelling analyses: Inhibition of glucose transport
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Plasmodium falciparum
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model analysis
Modelling analyses: Inhibition of lactate flux
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Not specified
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model analysis
Modelling analyses: Supply-demand analysis
Glycolytic model for Plasmodium falciparum; open system
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model analysis, Model validation
Modelling analyses: Inhibition of lactate flux, Steady state, Supply-demand analysis
Mathematica notebook for the parameterisation of the glucose transport rate equation based on SEEK linked experimental data.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Not specified
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Modelling analyses: GLCtr
Glycolytic model for Plasmodium falciparum; closed system
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model validation
Modelling analyses: GLC incubation
Mathematica notebook for the parameterisation of the G3PDH rate equation based on SEEK linked experimental data.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Not specified
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Modelling analyses: G3PDH
SOP for the determination of external metabolites (Glc, Pyr, Gly, Lac) in intact trophozoite incubations, and for the determination of intracellular metabolite concentrations.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model validation
Assays: GLC incubation, Steady state
SOP for the cultivation conditions of Plasmodium falciparum, including the protocol for synchronisation.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
SOP for measurement of G3PDH activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: G3PDH
SOP for measurement of ALD activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: ALD
SOP for measurement of glucose transport activity in intact trophozoites.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
SOP for measurement of GAPDH activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: GAPDH
SOP for measurement of ENO activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: ENO
SOP for measurement of HK activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: HK
SOP for measurement of PFK activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PFK
SOP for measurement of LDH activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: LDH
SOP for measurement of PGK activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PGK
SOP for measurement of PK activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PK
SOP for measurement of PGM activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
SOP for measurement of PGI activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PGI
SOP for measurement of PGM activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: PGM
SOP for measurement of TPI activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: TPI
SOP for the isolation of intact Plasmodium falciparum trophozoites from infected red blood cells and the preparation of a cell free extract that can be used for kinetic analyses.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Abstract (Expand)
Authors: Lu Shen, Martha Kohlhaas, Junichi Enoki, Roland Meier, Bernhard Schönenberger, Roland Wohlgemuth, Robert Kourist, Felix Niemeyer, David van Niekerk, Christopher Bräsen, Jochen Niemeyer, Jacky Snoep, Bettina Siebers
Date Published: 1st Dec 2020
Publication Type: Not specified
DOI: 10.1038/s41467-020-14830-y
Citation: Nat Commun 11(1) : 82
Abstract (Expand)
Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble
Date Published: 4th Jan 2017
Publication Type: Journal
PubMed ID: 27899646
Citation: Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28.
Abstract (Expand)
Authors: David D. van Niekerk, Gerald P. Penkler, Francois du Toit, Jacky L. Snoep
Date Published: 1st Feb 2016
Publication Type: Not specified
DOI: 10.1111/febs.13615
Citation: FEBS J 283(4) : 634
Abstract (Expand)
Authors: J. L. Snoep, K. Green, J. Eicher, D. C. Palm, G. Penkler, F. du Toit, N. Walters, R. Burger, H. V. Westerhoff, D. D. van Niekerk
Date Published: 27th Nov 2015
Publication Type: Not specified
DOI: 10.1042/BST20150145
Citation: Biochemical Society Transactions 43(6) : 1157
Abstract (Expand)
Authors: Anna-Karin Gustavsson, Caroline B. Adiels, Bernhard Mehlig, Mattias Goksör
Date Published: 1st Aug 2015
Publication Type: Not specified
DOI: 10.1038/srep09404
Citation: Sci Rep 5(1) : 415
Abstract (Expand)
Authors: Gerald Penkler, Francois du Toit, Waldo Adams, Marina Rautenbach, Daniel C. Palm, David D. van Niekerk, Jacky L. Snoep
Date Published: 1st Apr 2015
Publication Type: Not specified
DOI: 10.1111/febs.13237
Citation: FEBS J 282(8) : 1481
Abstract
Authors: Anna-Karin Gustavsson, David D. van Niekerk, Caroline B. Adiels, Bob Kooi, Mattias Goksör, Jacky L. Snoep
Date Published: 1st Jun 2014
Publication Type: Not specified
DOI: 10.1111/febs.12820
Citation: FEBS J 281(12) : 2784
Abstract
Authors: Anna-Karin Gustavsson, David D. van Niekerk, Caroline B. Adiels, Mattias Goksör, Jacky L. Snoep
Date Published: 3rd Jan 2014
Publication Type: Not specified
DOI: 10.1016/j.febslet.2013.11.028
Citation: Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells 588(1) : 3
Abstract
Authors: Anna-Karin Gustavsson, David D. van Niekerk, Caroline B. Adiels, Franco B. du Preez, Mattias Goksör, Jacky L. Snoep
Date Published: 1st Aug 2012
Publication Type: Not specified
DOI: 10.1111/j.1742-4658.2012.08639.x
Citation: Sustained glycolytic oscillations in individual isolated yeast cells 279(16) : 2837
Abstract (Expand)
Authors: J. Bachmann, A. Raue, M. Schilling, M. E. Bohm, C. Kreutz, D. Kaschek, H. Busch, N. Gretz, W. D. Lehmann, J. Timmer, U. Klingmuller
Date Published: 2011
Publication Type: Not specified
DOI: 10.1038/msb.2011.50
Citation: Molecular Systems Biology 7(1) : 516
Abstract (Expand)
Authors: Alexey N Kolodkin, Frank J Bruggeman, Nick Plant, Martijn J Moné, Barbara M Bakker, Moray J Campbell, Johannes P T M van Leeuwen, Carsten Carlberg, Jacky L Snoep, Hans V Westerhoff
Date Published: 21st Dec 2010
Publication Type: Not specified
DOI: 10.1038/msb.2010.102
Citation: Mol Syst Biol 6
Abstract (Expand)
Authors: F. B. du Preez, D. D. van Niekerk, J. L. Snoep
Date Published: No date defined
Publication Type: Not specified
PubMed ID: 22686585
Citation: FEBS J. 2012 Aug;279(16):2823-36. doi: 10.1111/j.1742-4658.2012.08658.x. Epub 2012 Jul 5.
Abstract (Expand)
Authors: F. B. du Preez, D. D. van Niekerk, B. Kooi, J. M. Rohwer, J. L. Snoep
Date Published: No date defined
Publication Type: Not specified
PubMed ID: 22712534
Citation: FEBS J. 2012 Aug;279(16):2810-22. doi: 10.1111/j.1742-4658.2012.08665.x. Epub 2012 Jul 9.