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

**Abstract:**

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. Using a small subset of experimental data, the original model was adapted by adjusting its parameter values in three optimization steps. Only small adaptations to the original model were required for realistic simulation of experimental data for limit-cycle oscillations. The greatest changes were required for parameter values for the phosphofructokinase reaction. The importance of ATP for the oscillatory mechanism and NAD(H) for inter-and intra-cellular communications and synchronization was evident in the optimization steps and simulation experiments. In an accompanying paper [du Preez F et al. (2012) FEBS J doi:10.1111/j.1742-4658.2012.08658.x], we validate the model for a wide variety of experiments on oscillatory yeast cells. The results are important for re-use of detailed kinetic models in modular modeling approaches and for approaches such as that used in the Silicon Cell initiative. Database The mathematical models described here have been submitted to the JWS Online Cellular Systems Modelling Database and can be accessed at http://jjj.biochem.sun.ac.za/database/dupreez/index.html.

**SEEK ID:** https://fairdomhub.org/publications/176

**PubMed ID:**
22712534

**Projects:** SysMO DB

**Journal:**
The FEBS journal

**Citation:**

**Date Published:**
21st Jun 2012

**Authors:**
Franco Du Preez, David D van Niekerk, Bob Kooi, Johann M Rohwer, Jacky Snoep

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**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

**Institutions:** Manchester Centre for Integrative Systems Biology, University of Manchester

**Expertise:** Glycolysis, Limit cycle oscillations

**Tools:** Mathematica, Java

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 â€˜shelf lifeâ€™ and

...

**Programme**: SysMO

**Public web page**: http://www.sysmo-db.org/

**Organisms:** Not specified

**Contributor**: Katy Wolstencroft

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Investigation:** Yeast Glycolytic Oscillations

**Study:** Detailed kinetics of yeast glycolytic oscillation

**Organisms**: Saccharomyces cerevisiae

**Models:** Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci...

**SOPs:** No SOPs

**Data files:** Das (1991) NADH and ATP concentrations determin..., Das (1991) Time varying concentrations for meta..., Richard (1996) Concentrations of oscillating gl... and 7 hidden items

**Contributor**: Katy Wolstencroft

**Biological problem addressed**: Model Analysis Type

**Snapshots: **No snapshots

**Investigation:** Yeast Glycolytic Oscillations

**Study:** Sustained glycolytic oscillations in individual...

**Organisms**: No organisms

**Models:** Sustained glycolytic oscillations in individual..., Sustained glycolytic oscillations in individual..., Sustained glycolytic oscillations in individual..., Sustained glycolytic oscillations in individual...

**SOPs:** No SOPs

**Data files:** No Data files

**Creators: **Franco Du Preez, Jacky Snoep

**Contributor**: Franco Du Preez

**Investigations:** Yeast Glycolytic Oscillations

**Creator: **Franco Du Preez

**Contributor**: Franco Du Preez

**Investigations:** Yeast Glycolytic Oscillations

**Studies:** Sustained glycolytic oscillations in individual...

**Assays:** 1 hidden item

Using optical tweezers to position yeast cells in a microfluidic chamber, we were able to observe sustained oscillations in individual isolated cells. Using a detailed kinetic model for the cellular reactions, we simulated the heterogeneity in the response of the individual cells, assuming small differences in a single internal parameter. By operating at two different flow rates per experiment, we observe four of categories of cell behaviour. The present model (gustavsson4) predicts the steady-state

...

**Creators: **Franco Du Preez, Jacky Snoep, Dawie Van Niekerk

**Contributor**: Franco Du Preez

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

**Model format**: Not specified

**Environment**: JWS Online

**Organism**: Saccharomyces cerevisiae

**Investigations:** Yeast Glycolytic Oscillations

**Studies:** Sustained glycolytic oscillations in individual...

**Modelling analyses:** Modelling sustained glycolytic oscillations in ...

Using optical tweezers to position yeast cells in a microfluidic chamber, we were able to observe sustained oscillations in individual isolated cells. Using a detailed kinetic model for the cellular reactions, we simulated the heterogeneity in the response of the individual cells, assuming small differences in a single internal parameter. By operating at two different flow rates per experiment, we observe four of categories of cell behaviour. The present model (gustavsson1) predicts the limit

...

**Creators: **Franco Du Preez, Jacky Snoep, David D van Niekerk

**Contributor**: Franco Du Preez

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

**Model format**: Not specified

**Environment**: JWS Online

**Organism**: Saccharomyces cerevisiae

**Investigations:** Yeast Glycolytic Oscillations

**Studies:** Sustained glycolytic oscillations in individual...

**Modelling analyses:** Modelling sustained glycolytic oscillations in ...

Using optical tweezers to position yeast cells in a microfluidic chamber, we were able to observe sustained oscillations in individual isolated cells. Using a detailed kinetic model for the cellular reactions, we simulated the heterogeneity in the response of the individual cells, assuming small differences in a single internal parameter. By operating at two different flow rates per experiment, we observe four of categories of cell behaviour. The present model (gustavsson2) predicts the damped

...

**Creators: **Franco Du Preez, Jacky Snoep, David D van Niekerk

**Contributor**: Franco Du Preez

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

**Model format**: Not specified

**Environment**: JWS Online

**Organism**: Saccharomyces cerevisiae

**Investigations:** Yeast Glycolytic Oscillations

**Studies:** Sustained glycolytic oscillations in individual...

**Modelling analyses:** Modelling sustained glycolytic oscillations in ...

Using optical tweezers to position yeast cells in a microfluidic chamber, we were able to observe sustained oscillations in individual isolated cells. Using a detailed kinetic model for the cellular reactions, we simulated the heterogeneity in the response of the individual cells, assuming small differences in a single internal parameter. By operating at two different flow rates per experiment, we observe four of categories of cell behaviour. The present model (gustavsson3) predicts the steady-state

...

**Creators: **Franco Du Preez, Jacky Snoep, David D van Niekerk

**Contributor**: Franco Du Preez

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

**Model format**: Not specified

**Environment**: JWS Online

**Organism**: Saccharomyces cerevisiae

**Investigations:** Yeast Glycolytic Oscillations

**Studies:** Sustained glycolytic oscillations in individual...

**Modelling analyses:** Modelling sustained glycolytic oscillations in ...

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez1) is the basis kinetic model derived from that published by Teusink et al., 2000 (PMID: 10951190).

**Creators: **Franco Du Preez, David D van Niekerk

**Contributor**: Franco Du Preez

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

**Model format**: Not specified

**Environment**: JWS Online

**Organism**: Saccharomyces cerevisiae

**Investigations:** Yeast Glycolytic Oscillations

**Studies:** Detailed kinetics of yeast glycolytic oscillation

**Modelling analyses:** Detailed kinetic model of yeast glycolytic osci...

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez2) is an oscillating version of the basis kinetic model (dupreez1) derived from that published by Teusink et al., 2000 (PMID: 10951190).

**Creators: **Franco Du Preez, Jacky Snoep, David D van Niekerk

**Contributor**: Franco Du Preez

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

**Model format**: Not specified

**Environment**: JWS Online

**Organism**: Saccharomyces cerevisiae

**Investigations:** Yeast Glycolytic Oscillations

**Studies:** Detailed kinetics of yeast glycolytic oscillation

**Modelling analyses:** Detailed kinetic model of yeast glycolytic osci...

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez3) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes data for glycolytic intermediates in oscillating yeast cultures reported by Richard et al., 1996 (PMID: 8813760).

**Creators: **Franco Du Preez, Jacky Snoep, David D van Niekerk

**Contributor**: Franco Du Preez

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

**Model format**: Not specified

**Environment**: JWS Online

**Organism**: Saccharomyces cerevisiae

**Investigations:** Yeast Glycolytic Oscillations

**Studies:** Detailed kinetics of yeast glycolytic oscillation

**Modelling analyses:** Detailed kinetic model of yeast glycolytic osci...

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez4) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes data for glycolytic intermediates in oscillating yeast cultures reported by Richard et al., 1996a (PMID: 8813760) as well as the rapid synchronization following the mixing of two yeast cultures that oscillate 180 degrees out of

...

**Creators: **Franco Du Preez, Jacky Snoep, David D van Niekerk

**Contributor**: Franco Du Preez

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

**Model format**: Not specified

**Environment**: JWS Online

**Organism**: Saccharomyces cerevisiae

**Investigations:** Yeast Glycolytic Oscillations

**Studies:** Detailed kinetics of yeast glycolytic oscillation

**Modelling analyses:** Detailed kinetic model of yeast glycolytic osci...

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez5) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes the amplitude bifurcation of oscillating yeast cultures in a CSTR setup reported by Hynne et al., 2001 (PMID: 11744196).

**Creators: **Franco Du Preez, Jacky Snoep, David D van Niekerk

**Contributor**: Franco Du Preez

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

**Model format**: Not specified

**Environment**: JWS Online

**Organism**: Saccharomyces cerevisiae

**Investigations:** Yeast Glycolytic Oscillations

**Studies:** Detailed kinetics of yeast glycolytic oscillation

**Modelling analyses:** Detailed kinetic model of yeast glycolytic osci...

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez6) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes data for glycolytic intermediates in cell free extracts of oscillating yeast cultures reported by Das and Busse, 1991 (PMCID: 1260073).

**Creators: **Franco Du Preez, Jacky Snoep, David D van Niekerk

**Contributor**: Franco Du Preez

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

**Model format**: Not specified

**Environment**: JWS Online

**Organism**: Saccharomyces cerevisiae

**Investigations:** Yeast Glycolytic Oscillations

**Studies:** Detailed kinetics of yeast glycolytic oscillation

**Modelling analyses:** Detailed kinetic model of yeast glycolytic osci...

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez7) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes the fluorescence signal of NADH in oscillating yeast cultures reported by Nielsen et al., 1998 (PMID: 17029704).

**Creators: **Franco Du Preez, Jacky Snoep, David D van Niekerk

**Contributor**: Franco Du Preez

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

**Model format**: Not specified

**Environment**: JWS Online

**Organism**: Saccharomyces cerevisiae

**Investigations:** Yeast Glycolytic Oscillations

**Studies:** Detailed kinetics of yeast glycolytic oscillation

**Modelling analyses:** Detailed kinetic model of yeast glycolytic osci...