Kinetic characterisation en mathematical modelling of GAPDH.
SEEK ID: https://fairdomhub.org/assays/254
Modelling Analysis
Projects: Whole body modelling of glucose metabolism in malaria patients
Investigation: Glucose metabolism in Plasmodium falciparum trophozoites
Study: Model construction
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: No organisms
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Created: 11th Aug 2014 at 09:33
Last updated: 8th Nov 2017 at 15:21

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The currently used mathematical models for medical treatment at the individual or population level are largely phenomenological and have limited quantitative predictive power. It is usually not possible to predict the effect of an intervention in a specific process or to predict the effect of a pharmaceutical drug since the step or enzyme on which the intervention/drug works is not explicit in the model.
Taking HIV pathogenesis as an example, the immune system response, vaccine exposure, and drug ...
Projects: Whole body modelling of glucose metabolism in malaria patients, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications
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 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.
Submitter: Dawie van Niekerk
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
Snapshots: Snapshot 1
This study includes all the experimental data, SOPs and modelling files for the individual reactions used for the model construction.
Submitter: Dawie van Niekerk
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Assays: ALD, ATPASE, Culturing and synchronisation of P. falciparum, ENO, G3PDH, GAPDH, GLCtr, GLYtr, HK, LACtr, LDH, PFK, PGI, PGK, PGM, PK, PYRtr, TPI, Trophozoite Isolation and Lysate Preparation
Snapshots: No snapshots
Experimental data set for the kinetic characterisation of GAPDH
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
DOI: 10.15490/seek.1.datafile.1153.2
Relationship type: Construction data
Investigations: Glucose metabolism in Plasmodium falciparum tro...
Studies: Model construction
Assays: GAPDH
Mathematica notebook for the parameterisation of the GAPDH 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
Assays: GAPDH
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