Dawie Van Niekerk

About Dawie Van Niekerk:

No description specified

SEEK ID: https://fairdomhub.org/people/411

Location: South Africa

Expertise: Not specified

Tools: Not specified

ORCID: https://orcid.org/0000-0003-2633-0537

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Project positions

Other Projects: SysMO DB (University of Stellenbosch) ; Whole body modelling of glucose metabolism in malaria patients (University of Stellenbosch) ; Molecular Systems Biology (Stellenbosch University) ; Yeast glycolytic oscillations (Stellenbosch University)

Related items

SysMO DB

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

Yeast glycolytic oscillations

No description specified

Programme: SARCHI: Mechanistic modelling of health and epidemiology

Public web page: Not specified

Organisms: Saccharomyces cerevisiae

Molecular Systems Biology

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

Whole body modelling of glucose metabolism in malaria patients

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

Stellenbosch University

Country: South Africa

City: Not specified

Web page: Not specified

University of Stellenbosch

Country: South Africa

City: Not specified

Web page: Not specified

From steady-state to synchronized yeast glycolytic oscillations

Yeast glycolytic oscillations

No description specified

Snapshots: No snapshots

Studies: From steady-state to synchronized yeast glycolytic oscillations I: model..., From steady-state to synchronized yeast glycolytic oscillations II: mode...

Assays: No Assays

Created: 17th Jul 2018 at 09:13

Glycolytic oscillations in individual isolated yeast cells

Yeast glycolytic oscillations

No description specified

Snapshots: No snapshots

Studies: Allosteric regulation of phosphofructokinase controls the emergence of g..., Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells, Sustained glycolytic oscillations in individual isolated yeast cells

Assays: gustavsson1-4 models, gustavsson5 model

Created: 16th Jul 2018 at 16:08

Phase shift responses in isolated yeast glycolytic oscillators

Yeast glycolytic oscillations

No description specified

Snapshots: No snapshots

Studies: Entrainment of heterogeneous glycolytic oscillations in single cells

Assays: No Assays

Created: 16th Jul 2018 at 15:38

Phosphoglycerate kinase acts as a futile cycle at high temperature

SulfoSys, SulfoSys - Biotec

(Show All)

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

Studies: BPG stability, PGK-30C, PGK-70C, PGK-GAPDH 30C & 70C

Assays: BPG degradation, BPG stability analysis, PGK - GAPDH models, PGK 30C data, PGK 30C model, PGK 70 data, PGK 70C model, PGK-GAPDH 30, PGK-GAPDH 70

Created: 27th Sep 2017 at 14:36

Srimani et al (2017) Molecular Systems Biology

Molecular Systems Biology

Drug detoxification dynamics explain the postantibiotic effect

Snapshots: No snapshots

Studies: Figure 2C Panel ii: After the removal of the extracellular antibiotic, e...

Assays: Kinetic model of antibiotic-mediated inhibition of ribosomes

Created: 26th Sep 2017 at 11:29, Last updated: 27th Sep 2017 at 12:30

Adlung et al (2017) Molecular Systems Biology

Molecular Systems Biology

Protein abundance of AKT and ERK pathway components governs cell-type- specific regulation of proliferation

Snapshots: No snapshots

Studies: Figure 2: Model calibration with time-resolved quantitative immunoblot d...

Assays: Mathematical models of the Epo-induced AKT, ERK and S6 activation., Source data for Figure 2: Experimental time-resolved quantitative immuno...

Created: 11th Jan 2017 at 11:26, Last updated: 11th Jan 2017 at 12:43

Glucose metabolism in Plasmodium falciparum trophozoites

Whole body modelling of glucose metabolism in malaria patients

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

DOI: 10.15490/seek.1.investigation.56

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

Created: 8th Aug 2014 at 15:16, Last updated: 30th Aug 2016 at 15:14

Kolodkin et al (2010) Molecular Systems Biology 6:446

Molecular Systems Biology

Design principles of nuclear receptor signaling: how complex networking improves signal transduction

Snapshots: No snapshots

Studies: Figure 2B: Transcriptional response to a sudden increase in extracellul...

Assays: Model nuclear receptor (NR) signaling

Created: 17th May 2016 at 14:09

Bachmann et al (2011) Molecular Systems Biology 7:516

Molecular Systems Biology

Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range

Snapshots: No snapshots

Studies: Figure 3A: Model calibration with experimental data of JAK2-STAT5 signal...

Assays: Model for JAK2/STAT5 signaling, Source data for Figure 3A: Experimental quantitative immunoblotting data.

Created: 3rd Mar 2016 at 10:42, Last updated: 3rd Mar 2016 at 11:06

1 hidden item

From steady-state to synchronized yeast glycolytic oscillations II: model validation

Yeast glycolytic oscillations

No description specified

Person responsible: Dawie Van Niekerk

Snapshots: No snapshots

Investigation: From steady-state to synchronized yeast glycoly...

Assays: No Assays

Created: 17th Jul 2018 at 09:15

From steady-state to synchronized yeast glycolytic oscillations I: model construction

Yeast glycolytic oscillations

No description specified

Person responsible: Dawie Van Niekerk

Snapshots: No snapshots

Investigation: From steady-state to synchronized yeast glycoly...

Assays: No Assays

Created: 17th Jul 2018 at 09:14

Sustained glycolytic oscillations in individual isolated yeast cells

Yeast glycolytic oscillations

No description specified

Person responsible: Dawie Van Niekerk

Snapshots: No snapshots

Investigation: Glycolytic oscillations in individual isolated ...

Assays: gustavsson1-4 models

Created: 16th Jul 2018 at 16:32

Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells

Yeast glycolytic oscillations

No description specified

Person responsible: Dawie Van Niekerk

Snapshots: No snapshots

Investigation: Glycolytic oscillations in individual isolated ...

Assays: No Assays

Created: 16th Jul 2018 at 16:27

Allosteric regulation of phosphofructokinase controls the emergence of glycolytic oscillations in isolated yeast cells

Yeast glycolytic oscillations

No description specified

Person responsible: Dawie Van Niekerk

Snapshots: No snapshots

Investigation: Glycolytic oscillations in individual isolated ...

Assays: gustavsson5 model

Created: 16th Jul 2018 at 16:09

Entrainment of heterogeneous glycolytic oscillations in single cells

Yeast glycolytic oscillations

No description specified

Person responsible: Dawie Van Niekerk

Snapshots: No snapshots

Investigation: Phase shift responses in isolated yeast glycoly...

Assays: No Assays

Created: 16th Jul 2018 at 16:01

Figure 2C Panel ii: After the removal of the extracellular antibiotic, efflux and inhibition dynamics combine to delay the synthesis of ribosomes in a concentration-dependent manner.

Molecular Systems Biology

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

Investigation: Srimani et al (2017) Molecular Systems Biology

Assays: Kinetic model of antibiotic-mediated inhibition of ribosomes

Created: 26th Sep 2017 at 11:33, Last updated: 27th Sep 2017 at 12:30

Figure 2: Model calibration with time-resolved quantitative immunoblot data of mCFU-E cells and BaF3-EpoR cells.

Molecular Systems Biology

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

Investigation: Adlung et al (2017) Molecular Systems Biology

Assays: Mathematical models of the Epo-induced AKT, ERK and S6 activation., Source data for Figure 2: Experimental time-resolved quantitative immuno...

Created: 11th Jan 2017 at 11:33, Last updated: 12th Jan 2017 at 09:02

Figure 2B: Transcriptional response to a sudden increase in extracellular ligand (hormone).

Molecular Systems Biology

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...

Assays: Model nuclear receptor (NR) signaling

Created: 17th May 2016 at 14:13

Figure 3A: Model calibration with experimental data of JAK2-STAT5 signaling obtained by different experimental techniques.

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

Investigation: Bachmann et al (2011) Molecular Systems Biology...

Assays: Model for JAK2/STAT5 signaling, Source data for Figure 3A: Experimental quantitative immunoblotting data.

Created: 3rd Mar 2016 at 10:52, Last updated: 3rd Mar 2016 at 11:06

Model analysis

Whole body modelling of glucose metabolism in malaria patients