Dawie Van Niekerk
SEEK ID: https://fairdomhub.org/people/411
Location:
South Africa
Disciplines: Modeller
Expertise: Not specified
Tools: Not specified
orcid.org/0000-0003-2633-0537 
Project roles
Project administrator
Dawie's tagsRelated items
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
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Programme: SysMO
Public web page: http://www.sysmo-db.org/
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
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
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
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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
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Drug detoxification dynamics explain the postantibiotic effect
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Protein abundance of AKT and ERK pathway components governs cell-type- specific regulation of proliferation
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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
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
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
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Model of glycolytic oscillations in individual yeast cells in microfluidic flow chamber
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Contributor: Dawie Van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Contributor: Dawie Van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Contributor: Dawie Van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
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.
Contributor: Dawie Van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Download
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
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
Contributor: Dawie Van Niekerk
SOP for the cultivation conditions of Plasmodium falciparum, including the protocol for synchronisation.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of G3PDH activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of ALD activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of glucose transport activity in intact trophozoites.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of GAPDH activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of ENO activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Abstract (Expand)
Author: Gustavsson Anna-Karin,Adiels Caroline B.,Mehlig Bernhard,Goksör Mattias
Date Published: 1st Aug 2015
Journal: Sci Rep
Abstract (Expand)
Authors: Dawie Van Niekerk, Jacky Snoep, du Preez F. B.,Kooi B.,Rohwer J. M.
Date Published: No date defined
Journal: FEBS J
Abstract (Expand)
Authors: Dawie Van Niekerk, Jacky Snoep, du Preez F. B.
Date Published: No date defined
Journal: FEBS J
Abstract:
Authors: Dawie Van Niekerk, Jacky Snoep, Gustavsson Anna-Karin,Adiels Caroline B.,du Preez Franco B.,Goksör Mattias
Date Published: 1st Aug 2012
Journal: Not specified
Abstract:
Authors: Dawie Van Niekerk, Jacky Snoep, Gustavsson Anna-Karin,Adiels Caroline B.,Goksör Mattias
Date Published: 3rd Jan 2014
Journal: Not specified
Abstract:
Authors: Dawie Van Niekerk, Jacky Snoep, Gustavsson Anna-Karin,Adiels Caroline B.,Kooi Bob,Goksör Mattias
Date Published: 1st Jun 2014
Journal: FEBS J
Abstract (Expand)
Authors: Marcel Schilling, Martin Böhm, Jens Timmer, Ursula Klingmüller, Bachmann J.,Raue A.,Kreutz C.,Kaschek D.,Busch H.,Gretz N.,Lehmann W. D.
Date Published: 2011
Journal: Molecular Systems Biology
