- Home
- Programmes Index
- SARCHI: Mechanistic modelling of health and epidemiology

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 regimen all affect viral replication and onward transmission, which may be a single parameter in a model. Or in higher-level scenarios of epidemiological intervention, condom distribution, behavioural messaging, and vaccines may all be affecting a single transmissibility parameter.

**Funding details:**

South African Research Chair in: "Mechanistic modelling of health and epidemiology" hosted by Stellenbosch University, funded by the DST and administered by NRF.

## Related items

- People (7)
- Projects (4)
- Institutions (4)
- Investigations (6)
- Studies (14)
- Assays (45)
- Data files (29+1)
- Models (47+1)
- SOPs (17)
- Publications (9)

**Projects:** Computational pathway design for biotechnological applications, ScyCode

**Institutions:** University Duisburg-Essen

**Projects:** SulfoSys, SulfoSys - Biotec, HOTSOLUTE, Computational pathway design for biotechnological applications, ScyCode

**Institutions:** University Duisburg-Essen, Universitity Duisburg-Essen

**Roles:** Project Coordinator, Vice Coordinator

**Expertise:** Thermoacidohiles, Archaeal physiology, Biotechnology, Hyperthermophiles, Regulation of carbohydrate metabolism, Carbohydrate Metabolism of Archaea, Reconstruction of metabolic pathways

**Tools:** Microbiology, Physiology, Systems Biology, Molecular Biology, Biochemistry

Head of the group of Molecular Enzyme Technology and Biochemistry (Faculty of Chemistry) at the University of Duisburg-Essen. My research interest is on archaeal physiology with a special focuss on the central carbohydrate metabolism of (hyper)thermophilic Archaea and its regulation. The aim is to gain a systems level understanding by the combination of modern highthrouput analyses with classical biochemistry and molecular biology.

Archaea possess many novel enzymes and pathways and our aim is

...

**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

**Roles:** Postdoc

**Expertise:** Data Management, Stoichiometric modelling, Kinetic modelling, metabolic networks, Systems Biology, Metabolic Engineering

**Tools:** COBRA toolbox, Matlab, Python, Copasi

Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.

The goal of the project is to establish a new biotechnological platform for the production of hydroxy-amino acids, since the current production of these important building blocks is very expensive. Enzyme engineering, systems biotechnology and metabolic engineering will be used in a synthetic biology approach.

**Programme**: SARCHI: Mechanistic modelling of health and epidemiology

**Public web page**: Not specified

**Organisms:** Caulobacter

**Programme**: SARCHI: Mechanistic modelling of health and epidemiology

**Public web page**: Not specified

**Organisms:** Saccharomyces cerevisiae

**Programme**: SARCHI: Mechanistic modelling of health and epidemiology

**Public web page**: Not specified

**Organisms:** Homo sapiens

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

**Snapshots: **No snapshots

**Studies:** Substrate preferences for AKR1C3, and implications of varying AKR1C3:17B...

**Assays:** No Assays

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

One pot cascade - pathway analysis for the purified Caulinobacter crescentus Weimberg pathway enzymes. Effect of co-factor recycling, removal of XLA, and optimisation on Xylose to aKG is studied.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig3a/simulate

https://jjj.bio.vu.nl/models/experiments/shen2020_fig3b/simulate

https://jjj.bio.vu.nl/models/experiments/shen2020_fig3c/simulate

https://jjj.bio.vu.nl/models/experiments/shen2020_fig3d/simulate

**Person responsible**: Jacky Snoep

**Snapshots: **No snapshots

**Investigation:** Caulobacter crescentus Weimberg pathway

**Assays:** One pot cascade 10, One pot cascade 12, One pot cascade 13, One pot cascade 16

Cell free extract - pathway analysis for Caulinobacter crescentus Weimberg pathway enzymes. Effect of co-factor recycling, and Mn2+ on Xylose to aKG conversion is studied.

**Person responsible**: Jacky Snoep

**Snapshots: **No snapshots

Progress curves for the purified Caulinobacter crescentus Weimberg pathway enzymes. Each reaction is followed up to completion and then the next enzyme in the pathway is added, i.e. XDH-XLA-XAD-KDXD and finally KGSADH

**Person responsible**: Jacky Snoep

**Snapshots: **No snapshots

Initial rate kinetics for the purified Caulinobacter crescentus Weimberg pathway enzymes, including substrate dependence, and product inhibition.

**Person responsible**: Jacky Snoep

**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

**Person responsible**: Jacky Snoep

**Snapshots: **No snapshots

**Investigation:** Prostate cancer

**Assays:** No Assays

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

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, without Mn2+ added, but with NAD recycling, metabolites measured enzymatically.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig4d/simulate

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Cell free extract

**Organisms**: No organisms

**Models:** CFE analysis (shen2), CFE no Mn, with NADrec

**SOPs:** No SOPs

**Data files:** CFE no-Mn but with NADrec data

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, with 0.15 mM Mn2+ added, but no NAD recycling, metabolites measured enzymatically.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig4c/simulate

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Cell free extract

**Organisms**: No organisms

**Models:** CFE Mn noNADrec, CFE analysis (shen2)

**SOPs:** No SOPs

**Data files:** CFE Mn no-NADrec data

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, with 0.15 mM Mn2+ added, and with NAD recycling, metabolites measured enzymatically.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig4b/simulate

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Cell free extract

**Organisms**: No organisms

**Models:** CFE Mn NADrec, CFE analysis (shen2)

**SOPs:** No SOPs

**Data files:** CFE Mn NADrec data

Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, using old enzymes with optimal protein distribution, with NAD recycling, measured in NMR.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig3d/simulate

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** One pot cascade

**Organisms**: No organisms

**Models:** Cascade analysis (shen2), One pot cascade 16

**SOPs:** No SOPs

**Data files:** One-Pot-Cascade 16 data

Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, with NAD recycling, measured in NMR.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig3b/simulate

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** One pot cascade

**Organisms**: No organisms

**Models:** Cascade analysis (shen2), One-Pot-Cascade 13

**SOPs:** No SOPs

**Data files:** One-Pot-Cascade 13 data

Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, omitting XLA, measured in NMR.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig3c/simulate

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** One pot cascade

**Organisms**: No organisms

**Models:** Cascade analysis (shen2), One pot cascade 12

**SOPs:** No SOPs

**Data files:** One-Pot-Cascade 12 data

Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, measured in NMR.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig3a/simulate

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** One pot cascade

**Organisms**: No organisms

**Models:** Cascade analysis (shen2), One-Pot-Cascade 10

**SOPs:** No SOPs

**Data files:** One-Pot-Cascade 10 data

Conversion of XYL to KG by sequential addition of Weimberg pathway enzymes of Caulobacter crescentus, measured in NMR.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig2c/simulate

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Progress curves

**Organisms**: No organisms

**Models:** Progress curve analysis (shen1), Progress curve analysis combined

**SOPs:** No SOPs

**Data files:** Progress curve analysis data

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Cell free extract

**Organisms**: No organisms

**Models:** CFE steady state analysis (shen3)

**SOPs:** No SOPs

**Data files:** No Data files

Conversion of KGSA to KG by Caulobacter crescentus KGSADH, measured in NMR.

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Progress curves

**Organisms**: No organisms

**Models:** Progress curve analysis (shen1), Progress curve analysis KGSADH

**SOPs:** No SOPs

**Data files:** Progress curve analysis data

Conversion of KDX to KGSA by Caulobacter crescentus KDXD, measured in NMR.

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Progress curves

**Organisms**: No organisms

**Models:** Progress curve analysis (shen1), Progress curve analysis KDXD

**SOPs:** No SOPs

**Data files:** Progress curve analysis data

Conversion of XA to KDX by Caulobacter crescentus XAD, measured in NMR.

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Progress curves

**Organisms**: No organisms

**Models:** Progress curve analysis (shen1), Progress curve analysis XAD

**SOPs:** No SOPs

**Data files:** Progress curve analysis data

Conversion of XLAC to XA by Caulobacter crescentus XLA, measured in NMR.

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Progress curves

**Organisms**: No organisms

**Models:** Progress curve analysis (shen1), Progress curve analysis XLA

**SOPs:** No SOPs

**Data files:** Progress curve analysis data

Conversion of Xyl to XLAC by Caulobacter crescentus XDH, measured in NMR.

**Contributor**: Jacky Snoep

**Biological problem addressed**: Model Analysis Type

**Snapshots: **Snapshot 1, Snapshot 2

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Progress curves

**Organisms**: No organisms

**Models:** Progress curve analysis (shen1), Progress curve analysis XDH

**SOPs:** No SOPs

**Data files:** Progress curve analysis data

Kinetic characterisation and mathematical modelling of KGSADH.

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Initial rate kinetics

**Organisms**: No organisms

**Models:** KGSADH model

**SOPs:** No SOPs

**Data files:** KGSADH-initial rate kinetics data

Kinetic characterisation and mathematical modelling of KDXD.

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Initial rate kinetics

**Organisms**: No organisms

**Models:** KDXD model

**SOPs:** No SOPs

**Data files:** KDXD-initial rate kinetics data

Kinetic characterisation and mathematical modelling of XAD.

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Initial rate kinetics

**Organisms**: No organisms

**Models:** XAD model

**SOPs:** No SOPs

**Data files:** XAD-initial rate kinetics data

Kinetic characterisation and mathematical modelling of XLA.

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Initial rate kinetics

**Organisms**: No organisms

**Models:** XLA model

**SOPs:** No SOPs

**Data files:** XLA-initial rate kinetics data

Kinetic characterisation and mathematical modelling of XDH.

**Investigation:** Caulobacter crescentus Weimberg pathway

**Study:** Initial rate kinetics

**Organisms**: No organisms

**Models:** XDH model

**SOPs:** No SOPs

**Data files:** XDH-initial rate kinetics data

**Contributor**: 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

Data files for the conversion of XYL to KG, via the sequential addition of the Caulobacter crescentus Weimberg pathway enzymes, XDH, XLA, XAD, KDXD, KGSADH.

**Creators: **Jacky Snoep, Lu Shen

**Contributor**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Progress curves

**Assays:** Progress curve KDXD, Progress curve KGSADH, Progress curve XAD, Progress curve XDH, Progress curve XLA, Progress curves combined

Initial rate kinetics for the α-ketoglutarate semialdehyde dehydrogenase of Caulobacter crescentus, α-ketoglutarate semialdehyde and NAD saturation, and α-ketoglutarate, NADH and 2-keto-3-deoxy-D-xylonate inhibition.

**Creators: **Jacky Snoep, Lu Shen

**Contributor**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Initial rate kinetics

**Assays:** KGSADH

Initial rate kinetics for the 2-keto-3-deoxy-D-xylonate dehydrates of Caulobacter crescentus, 2-keto-3-deoxy-D-xylonate saturation and inhibitor titrations.

**Creators: **Jacky Snoep, Lu Shen

**Contributor**: Jacky Snoep

Initial rate kinetics for the xylonate dehydratase of Caulobacter crescentus, xylonate saturation.

**Creators: **Jacky Snoep, Lu Shen

**Contributor**: Jacky Snoep

Initial rate kinetics for the xylonolactonase reaction of Caulobacter crescentus, xylonolactone saturation for the enzyme catalysed reaction, and for the non-enzymatic reaction.

**Creators: **Jacky Snoep, Lu Shen

**Contributor**: Jacky Snoep

Initial rate kinetics for xylose dehydrogenase of Caulobacter crescentus, saturation with xylose and NAD, and inhibition by NADH and xylonolactone.

Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, with NAD recycling, but without additional Mn2+ added.

**Creators: **Jacky Snoep, Lu Shen

**Contributor**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Cell free extract

Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, without NAD recycling, but with additional Mn2+ (0.15 mM) added.

**Creators: **Jacky Snoep, Lu Shen

**Contributor**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Cell free extract

Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, with NAD recycling, and additional Mn2+ (0.15 mM) added.

**Creators: **Jacky Snoep, Lu Shen

**Contributor**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Cell free extract

Data files for the conversion of XYL to KG, via the Caulobacter crescentus Weimberg pathway, using old enzymes: XDH, XLA, XAD, KDXD, KGSADH, with NAD recycling, and optimal protein distribution.

**Creators: **Jacky Snoep, Lu Shen

**Contributor**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 16

Data files for the conversion of XYL to KG, via the Caulobacter crescentus Weimberg pathway enzymes: XDH, XLA, XAD, KDXD, KGSADH, with NAD recycling.

**Creators: **Jacky Snoep, Lu Shen

**Contributor**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 13

Data files for the conversion of XYL to KG, via the Caulobacter crescentus Weimberg pathway enzymes, omitting XLA: XDH, XAD, KDXD, KGSADH.

**Creators: **Jacky Snoep, Lu Shen

**Contributor**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 12

Data files for the conversion of XYL to KG, via the Caulobacter crescentus Weimberg pathway enzymes, XDH, XLA, XAD, KDXD, KGSADH.

**Creators: **Jacky Snoep, Lu Shen

**Contributor**: Jacky Snoep

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Assays:** One pot cascade 10

**Creators: **Dawie Van Niekerk, Jacky Snoep

**Contributor**: Dawie Van Niekerk

**Investigations:** Glucose metabolism in Plasmodium falciparum tro...

**Studies:** Model analysis

**Assays:** Inhibition of glucose transport

**Creators: **Dawie Van Niekerk, Jacky Snoep

**Contributor**: Dawie Van Niekerk

**Investigations:** Glucose metabolism in Plasmodium falciparum tro...

**Studies:** Model analysis

**Assays:** Inhibition of lactate flux

Experimental data set for the kinetic characterisation of G3PDH

**Creators: **Dawie Van Niekerk, Jacky Snoep

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: Dawie Van Niekerk

**Investigations:** Glucose metabolism in Plasmodium falciparum tro...

**Studies:** Model construction

**Assays:** LDH

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Progress curves

**Modelling analyses:** Progress curve KGSADH

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Progress curves

**Modelling analyses:** Progress curve KDXD

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Progress curves

**Modelling analyses:** Progress curve XAD

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Progress curves

**Modelling analyses:** Progress curve XLA

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Progress curves

**Modelling analyses:** Progress curve XDH

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Progress curves

**Modelling analyses:** Progress curves combined

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with added Mn, but no NAD rec, will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Cell free extract

**Modelling analyses:** Cell free extract, with Mn, no NAD recycling

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 12 will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Modelling analyses:** One pot cascade 12

Steady state model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. Protein levels need to be adapted to CFE levels, see SED-ML scripts.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

**Organism**: Caulobacter

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Cell free extract

**Modelling analyses:** Steady state cell free extract, with Mn and NAD...

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with no added Mn, but with NAD rec, will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Cell free extract

**Modelling analyses:** Cell free extract, without added Mn, with NAD r...

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. Protein levels need to be adapted to CFE levels, see SED-ML scripts

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Cell free extract

**Modelling analyses:** Cell free extract, with Mn and NAD recycling, Cell free extract, with Mn, no NAD recycling, Cell free extract, without added Mn, with NAD r...

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with added Mn and NAD rec will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Cell free extract

**Modelling analyses:** Cell free extract, with Mn and NAD recycling

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Modelling analyses:** One pot cascade 10, One pot cascade 12, One pot cascade 13, One pot cascade 16

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, using old enzymes, with optimal protein distribution. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 16 will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Modelling analyses:** One pot cascade 16

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 10 will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Modelling analyses:** One pot cascade 10

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, with NAD recycling. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 13 will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** One pot cascade

**Modelling analyses:** One pot cascade 13

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, with sequential addition of purified enzymes.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Progress curves

**Modelling analyses:** Progress curve KDXD, Progress curve KGSADH, Progress curve XAD, Progress curve XDH, Progress curve XLA, Progress curves combined

Model for the Caulobacter crescentus Î±-ketoglutarate semialdehyde dehydrogenase, describing the initial rate kinetics for substrate dependence and product inhibition. If the Mathematica notebook is downloaded and the data file for the XAD kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for KGSADH will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Initial rate kinetics

**Modelling analyses:** KGSADH

Model for the Caulobacter crescentus 2-keto-3-deoxy-D-xylonate dehydratase, describing the initial rate kinetics for substrate dependence and product inhibition. If the Mathematica notebook is downloaded and the data file for the XAD kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for KDXD will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Initial rate kinetics

**Modelling analyses:** KDXD

Model for the Caulobacter crescentus xylonate dehydratase, describing the initial rate kinetics for substrate dependence. If the Mathematica notebook is downloaded and the data file for the XAD kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for XAD will be reproduced.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Organism**: Not specified

**Investigations:** Caulobacter crescentus Weimberg pathway

**Studies:** Initial rate kinetics

**Modelling analyses:** XAD

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

**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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: Dawie Van Niekerk

**Investigations:** No Investigations

**Studies:** No Studies

**Assays:** No Assays

**Abstract** (Expand)

**Authors: **F. B. du Preez, Dawie Van Niekerk, B. Kooi, J. M. Rohwer, Jacky Snoep

**Date Published**: No date defined

**Journal**: FEBS J

**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.

**Abstract** (Expand)

**Authors: **F. B. du Preez, Dawie Van Niekerk, Jacky Snoep

**Date Published**: No date defined

**Journal**: FEBS J

**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: **Dawie Van Niekerk, Gerald P. Penkler, Francois du Toit, Jacky Snoep

**Date Published**: 1st Feb 2016

**Journal**: FEBS J

**DOI: **10.1111/febs.13615

**Citation**: FEBS J 283(4) : 634

**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

**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

**Journal**: Sci Rep

**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, Dawie Van Niekerk, Jacky Snoep

**Date Published**: 1st Apr 2015

**Journal**: FEBS J

**DOI: **10.1111/febs.13237

**Citation**: FEBS J 282(8) : 1481

**Abstract**

**Authors: **Anna-Karin Gustavsson, Dawie Van Niekerk, Caroline B. Adiels, Bob Kooi, Mattias Goksör, Jacky Snoep

**Date Published**: 1st Jun 2014

**Journal**: FEBS J

**DOI: **10.1111/febs.12820

**Citation**: FEBS J 281(12) : 2784

**Abstract**

**Authors: **Anna-Karin Gustavsson, Dawie Van Niekerk, Caroline B. Adiels, Mattias Goksör, Jacky Snoep

**Date Published**: 3rd Jan 2014

**Journal**: 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, Dawie Van Niekerk, Caroline B. Adiels, Franco B. du Preez, Mattias Goksör, Jacky Snoep

**Date Published**: 1st Aug 2012

**Journal**: Not specified

**DOI: **10.1111/j.1742-4658.2012.08639.x

**Citation**: Sustained glycolytic oscillations in individual isolated yeast cells 279(16) : 2837