Detailed kinetic model of yeast glycolytic oscillation - III
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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).

SEEK ID: https://fairdomhub.org/models/76?version=2

1 item is associated with this Model:

dupreez3.dat (uuencoded file - 11.1 KB)

Organism: Saccharomyces cerevisiae

Model type: Ordinary differential equations (ODE)

Model format: Not specified

Execution or visualisation environment: JWS Online

Model image: No image specified

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Creators and Submitter

Creators

Franco du Preez
Jacky Snoep

Additional credit

David D van Niekerk

Submitter

Franco du Preez

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Views: 4983 Downloads: 228 Runs: 0

Created: 23rd Jul 2012 at 19:24

Last updated: 23rd Jul 2012 at 23:23

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Version 2 (latest) Created 23rd Jul 2012 at 23:23 by Franco du Preez

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People (2)
Programmes (1)
Projects (1)
Investigations (1)
Studies (1)
Assays (1)
Publications (2)

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Franco du Preez

Projects: SysMO DB

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

Expertise: Glycolysis, Limit cycle oscillations

Tools: Java, Mathematica

Jacky Snoep

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, SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers, Project Coordination, WP 3: Drug release kinetics study, Glucose metabolism in cancer cell lines

Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, University of Stellenbosch, University of Manchester - Department of Computer Science, Stellenbosch University

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SysMO

SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".

The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.

Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...

Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep

Web page: http://sysmo.net/

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SysMO DB

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 ...

Programme: SysMO

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

Organisms: Not specified

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Yeast Glycolytic Oscillations

SysMO DB

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Katy Wolstencroft

Investigating oscillations at the level of yeast populations and individual cells

Submitter: Katy Wolstencroft

Studies: Detailed kinetics of yeast glycolytic oscillation, Sustained glycolytic oscillations in individual isolated yeast cells

Assays: Detailed kinetic model of yeast glycolytic oscillation, Metabolite concentrations in yeast glycolytic oscillations, Modelling sustained glycolytic oscillations in individual isolated yeast...

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Created: 20th Feb 2013 at 14:33

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Detailed kinetics of yeast glycolytic oscillation

SysMO DB

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Katy Wolstencroft

No description specified

Submitter: Katy Wolstencroft

Investigation: Yeast Glycolytic Oscillations

Assays: Detailed kinetic model of yeast glycolytic oscillation, Metabolite concentrations in yeast glycolytic oscillations

Snapshots: No snapshots

Created: 20th Feb 2013 at 14:40, Last updated: 28th Feb 2013 at 13:30

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Detailed kinetic model of yeast glycolytic oscillation

SysMO DB

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Katy Wolstencroft

No description specified

Submitter: Katy Wolstencroft

Biological problem addressed: Model Analysis Type

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

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Created: 20th Feb 2013 at 15:13, Last updated: 8th Nov 2017 at 14:21

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

SysMO DB

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Franco du Preez

Jacky Snoep

Abstract (Expand)

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.

Authors: , David D van Niekerk, Bob Kooi, Johann M Rohwer,

Date Published: 21st Jun 2012

Publication Type: Not specified

PubMed ID: 22712534

Citation:

Created: 16th Jul 2012 at 09:35, Last updated: 8th Dec 2022 at 17:26

From steady-state to synchronized yeast glycolytic oscillations II: model validation

SysMO DB

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Franco du Preez

Jacky Snoep

Abstract (Expand)

In an accompanying paper [du Preez et al., (2012) FEBS J doi: 10.1111/j.1742-4658.2012.08665.x], we adapt an existing kinetic model for steady-state yeast glycolysis to simulate limit-cycle oscillations. … Here we validate the model by testing its capacity to simulate a wide range of experiments on dynamics of yeast glycolysis. In addition to its description of the oscillations of glycolytic intermediates in intact cells and the rapid synchronization observed when mixing out-of-phase oscillatory cell populations (see accompanying paper), the model was able to predict the Hopf bifurcation diagram with glucose as the bifurcation parameter (and one of the bifurcation points with cyanide as the bifurcation parameter), the glucose- and acetaldehyde-driven forced oscillations, glucose and acetaldehyde quenching, and cell-free extract oscillations (including complex oscillations and mixed-mode oscillations). Thus, the model was compliant, at least qualitatively, with the majority of available experimental data for glycolytic oscillations in yeast. To our knowledge, this is the first time that a model for yeast glycolysis has been tested against such a wide variety of independent data sets. 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.

Authors: , David D van Niekerk,

Date Published: 13th Jun 2012

Publication Type: Not specified

PubMed ID: 22686585

Citation:

Created: 16th Jul 2012 at 09:32, Last updated: 8th Dec 2022 at 17:26

Detailed kinetic model of yeast glycolytic oscillation - III Version 2

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Version History

Version 2 (latest) Created 23rd Jul 2012 at 23:23 by Franco du Preez

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Detailed kinetic model of yeast glycolytic oscillation - III
Version 2