Yeast glycolytic oscillations

Overview
No description specified

Programme: SARCHI: Mechanistic modelling of health and epidemiology

SEEK ID: https://fairdomhub.org/projects/113

Public web page: Not specified

Organisms: Saccharomyces cerevisiae

FAIRDOM PALs: No PALs for this Project

Project created: 16th Jul 2018

Related items

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 ...

Projects: Whole body modelling of glucose metabolism in malaria patients, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications

Web page: http://sacemaquarterly.com/mathematical-modelling/sarchi-project-mechanistic-modelling-health-epidemiology.html

Stellenbosch University

Country:  South Africa

City: Not specified

Web page: Not specified

From steady-state to synchronized yeast glycolytic oscillations II: model validation
Yeast glycolytic oscillations
No description specified

Person responsible: Dawie van Niekerk

Snapshots: No snapshots

From steady-state to synchronized yeast glycolytic oscillations I: model construction
Yeast glycolytic oscillations
No description specified

Person responsible: Dawie van Niekerk

Snapshots: No snapshots

Sustained glycolytic oscillations in individual isolated yeast cells
Yeast glycolytic oscillations
No description specified

Person responsible: Dawie van Niekerk

Snapshots: No snapshots

Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells
Yeast glycolytic oscillations
No description specified

Person responsible: Dawie van Niekerk

Snapshots: No snapshots

Allosteric regulation of phosphofructokinase controls the emergence of glycolytic oscillations in isolated yeast cells
Yeast glycolytic oscillations
No description specified

Person responsible: Dawie van Niekerk

Snapshots: No snapshots

Entrainment of heterogeneous glycolytic oscillations in single cells
Yeast glycolytic oscillations
No description specified

Person responsible: Dawie van Niekerk

Snapshots: No snapshots

gustavsson1-4 models
Yeast glycolytic oscillations
No description specified

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

gustavsson5 model
Yeast glycolytic oscillations

Model of glycolytic oscillations in individual yeast cells in microfluidic flow chamber

Submitter: Dawie van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

gustavsson1-4 models
Yeast glycolytic oscillations
No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

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gustavsson5 model
Yeast glycolytic oscillations
No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

Download
Entrainment of heterogeneous glycolytic oscillations in single cells
Yeast glycolytic oscillations

Abstract (Expand)

Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression … have recently been studied intensively using single-cell experiments. In metabolism heterogeneity may be particularly important because it may affect synchronisation of metabolic oscillations, an important example of cell-cell communication. This synchronisation is notoriously difficult to describe theoretically as the example of glycolytic oscillations shows: neither is the mechanism of glycolytic synchronisation understood nor the role of cell-cell heterogeneity. To pin down the mechanism and to assess its robustness and universality we have experimentally investigated the entrainment of glycolytic oscillations in individual yeast cells by periodic external perturbations. We find that oscillatory cells synchronise through phase shifts and that the mechanism is insensitive to cell heterogeneity (robustness) and similar for different types of external perturbations (universality).

Authors: Anna-Karin Gustavsson, Caroline B. Adiels, Bernhard Mehlig, Mattias Goksör

Date Published: 1st Aug 2015

Publication Type: Not specified

Allosteric regulation of phosphofructokinase controls the emergence of glycolytic oscillations in isolated yeast cells
Yeast glycolytic oscillations

Abstract

Not specified

Authors: Anna-Karin Gustavsson, David D. van Niekerk, Caroline B. Adiels, Bob Kooi, Mattias Goksör, Jacky L. Snoep

Date Published: 1st Jun 2014

Publication Type: Not specified

Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells
Yeast glycolytic oscillations

Abstract

Not specified

Authors: Anna-Karin Gustavsson, David D. van Niekerk, Caroline B. Adiels, Mattias Goksör, Jacky L. Snoep

Date Published: 3rd Jan 2014

Publication Type: Not specified

Sustained glycolytic oscillations in individual isolated yeast cells
Yeast glycolytic oscillations

Abstract

Not specified

Authors: Anna-Karin Gustavsson, David D. van Niekerk, Caroline B. Adiels, Franco B. du Preez, Mattias Goksör, Jacky L. Snoep

Date Published: 1st Aug 2012

Publication Type: Not specified

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

Abstract (Expand)

UNLABELLED: In an accompanying paper [du Preez et al., (2012) FEBS J279, 2810-2822], 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: F. B. du Preez, D. D. van Niekerk, J. L. Snoep

Date Published: No date defined

Publication Type: Not specified

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

Abstract (Expand)

UNLABELLED: 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 J279, 2823-2836], 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: F. B. du Preez, D. D. van Niekerk, B. Kooi, J. M. Rohwer, J. L. Snoep

Date Published: No date defined

Publication Type: Not specified

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