Whole body modelling of glucose metabolism in malaria patients
OverviewHypoglycaemia 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
SEEK ID: https://fairdomhub.org/projects/17
Public web page: Not specified
Organisms: Plasmodium falciparum, Homo sapiens
FAIRDOM PALs: No PALs for this Project
Project created: 31st Jul 2014
Related items
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: SysMO DB, Whole body modelling of glucose metabolism in malaria patients, Manchester Institute for Biotechnology, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meeting, FAIRDOM Templates
Institutions: School of Computer Science, University of Manchester, Manchester Centre for Integrative Systems Biology, University of Manchester
https://orcid.org/0000-0003-4958-0184
Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.
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
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
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
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
Inhibition of lactate flux due to glucose transport inhibitor
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Kinetic characterisation en mathematical modelling of HK.
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: Snapshot 1
Kinetic characterisation en mathematical modelling of PGI.
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Kinetic characterisation en mathematical modelling of PFK.
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Kinetic characterisation en mathematical modelling of ALD.
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Kinetic characterisation en mathematical modelling of TPI.
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Kinetic characterisation en mathematical modelling of G3PDH.
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Kinetic characterisation en mathematical modelling of GAPDH.
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Kinetic characterisation en mathematical modelling of PGK.
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Kinetic characterisation en mathematical modelling of PGM.
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Kinetic characterisation en mathematical modelling of ENO.
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Kinetic characterisation en mathematical modelling of PK.
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Kinetic characterisation and mathematical modelling of LDH.
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Contributor: Dawie Van Niekerk
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
DownloadExperimental data set for the kinetic characterisation of G3PDH
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Experimental data set for the kinetic characterisation of ALD
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Experimental data set for the kinetic characterisation of ENO
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Experimental data set for the kinetic characterisation of GAPDH
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Experimental data set for the kinetic characterisation of LDH
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Experimental data set for the kinetic characterisation of PGI
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Experimental data set for the kinetic characterisation of HK
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Experimental data set for the kinetic characterisation of PFK
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Experimental data set for the kinetic characterisation of PGK
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Experimental data set for the kinetic characterisation of TPI
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Experimental data set for the kinetic characterisation of the glucose transport reaction
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Experimental data set for the kinetic characterisation of PK
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Experimental data for the phosphoglycerate mutase (EC 5.4.2.12) activity.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Timecourses of GLC (starting at 5 mM) and LAC, PYR, GLY in the closed system.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
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: Mathematica
Environment: Not specified
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Glycolytic model for Plasmodium falciparum; open system
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Mathematica notebook for the parameterisation of the glucose transport rate equation based on SEEK linked experimental data.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Glycolytic model for Plasmodium falciparum; closed system
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Mathematica notebook for the parameterisation of the G3PDH rate equation based on SEEK linked experimental data.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the parameterisation of the ALD rate equation based on SEEK linked experimental data.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the ATPase reaction.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the parameterisation of the ENO rate equation based on SEEK linked experimental data.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the lactate transport rate equation, based on literature data.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the glycerol transport rate equation.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the parameterisation of the GAPDH rate equation based on SEEK linked experimental data.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the parameterisation of the PGI rate equation based on SEEK linked experimental data.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the parameterisation of the LDH rate equation based on SEEK linked experimental data.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the parameterisation of the TPI rate equation based on SEEK linked experimental data.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the parameterisation of the PFK rate equation based on SEEK linked experimental data.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the pyruvate transport rate equation, based on literature data.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Mathematica notebook for the parameterisation of the PGK rate equation based on SEEK linked experimental data.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
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
SOP for measurement of HK activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of PFK activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of LDH activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of PGK activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of PK activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of PGM activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of PGI activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of PGM activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
SOP for measurement of TPI activity in extracts.
Creators: Dawie Van Niekerk, Jacky Snoep
Contributor: Dawie Van Niekerk
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
Contributor: Dawie Van Niekerk
Abstract (Expand)
Authors: Jacky Snoep, Kathleen Green, J. Eicher, D. C. Palm, G. Penkler, F. du Toit, N. Walters, R. Burger, H. V. Westerhoff, Dawie Van Niekerk
Date Published: 27th Nov 2015
Journal: Biochemical Society Transactions
Abstract (Expand)
Authors: Gerald Penkler, Francois du Toit, Waldo Adams, Marina Rautenbach, Daniel C. Palm, Dawie Van Niekerk, Jacky Snoep
Date Published: 1st Apr 2015
Journal: FEBS J
Abstract (Expand)
Authors: Dawie Van Niekerk, Gerald P. Penkler, Francois du Toit, Jacky Snoep
Date Published: 1st Feb 2016
Journal: FEBS J
