Wolf2000 - Cellular interaction on glycolytic oscillations in yeast
This model is described in the article:
Abstract:
On the basis of a detailed model of yeast glycolysis, the effect of intercellular dynamics is analysed theoretically. The model includes the main steps of anaerobic glycolysis, and the production of ethanol and glycerol. Transmembrane diffusion of acetaldehyde is included, since it has been hypothesized that this substance mediates the interaction. Depending on the kinetic parameter, the single-cell model shows both stationary and oscillatory behaviour. This agrees with experimental data with respect to metabolite concentrations and phase shifts. The inclusion of intercellular coupling leads to a variety of dynamical modes, such as synchronous oscillations, and different kinds of asynchronous behavior. These oscillations can co-exist, leading to bi- and tri-rhythmicity. The corresponding parameter regions have been identified by a bifurcation analysis. The oscillatory dynamics of synchronized cell populations are investigated by calculating the phase responses to acetaldehyde pulses. Simulations are performed with respect to the synchronization of two subpopulations that are oscillating out of phase before mixing. The effect of the various process on synchronization is characterized quantitatively. While continuous exchange of acetaldehyde might synchronize the oscillations for appropriate sets of parameter values, the calculated synchronization time is longer than that observed experimentally. It is concluded either that addition to the transmembrane exchange of acetaldehyde, other processes may contribute to intercellular coupling, or that intracellular regulator feedback plays a role in the acceleration of the synchronization. for appropriate sets of parameter values, the calculated synchronization time is longer than that observed experimentally. It is concluded either that addition to the transmembrane exchange of acetaldehyde, other processes may contribute to intercellular coupling, or that intracellular regulator feedback plays a role in the acceleration of the synchronization.
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Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation.
- Wolf J, Heinrich R
- The Biochemical journal , 1/ 2000 , Volume 345 Pt 2 , pages: 321-334 , PubMed ID: 10702114
- Humboldt-Universität zu Berlin, Institut für Biologie, Theoretische Biophysik, Invalidenstrasse 42, D-10115 Berlin, Germany.
- On the basis of a detailed model of yeast glycolysis, the effect of intercellular dynamics is analysed theoretically. The model includes the main steps of anaerobic glycolysis, and the production of ethanol and glycerol. Transmembrane diffusion of acetaldehyde is included, since it has been hypothesized that this substance mediates the interaction. Depending on the kinetic parameter, the single-cell model shows both stationary and oscillatory behaviour. This agrees with experimental data with respect to metabolite concentrations and phase shifts. The inclusion of intercellular coupling leads to a variety of dynamical modes, such as synchronous oscillations, and different kinds of asynchronous behavior. These oscillations can co-exist, leading to bi- and tri-rhythmicity. The corresponding parameter regions have been identified by a bifurcation analysis. The oscillatory dynamics of synchronized cell populations are investigated by calculating the phase responses to acetaldehyde pulses. Simulations are performed with respect to the synchronization of two subpopulations that are oscillating out of phase before mixing. The effect of the various process on synchronization is characterized quantitatively. While continuous exchange of acetaldehyde might synchronize the oscillations for appropriate sets of parameter values, the calculated synchronization time is longer than that observed experimentally. It is concluded either that addition to the transmembrane exchange of acetaldehyde, other processes may contribute to intercellular coupling, or that intracellular regulator feedback plays a role in the acceleration of the synchronization. for appropriate sets of parameter values, the calculated synchronization time is longer than that observed experimentally. It is concluded either that addition to the transmembrane exchange of acetaldehyde, other processes may contribute to intercellular coupling, or that intracellular regulator feedback plays a role in the acceleration of the synchronization.
Submitter of this revision: administrator
Modellers: administrator, Camille Laibe
Metadata information
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hasTaxon (1 statement)
hasProperty (1 statement)
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| Name | Description | Size | Actions |
|---|---|---|---|
Model files |
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| BIOMD0000000691_url.xml | SBML L2V4 representation of Wolf2000 - Cellular interaction on glycolytic oscillations in yeast | 100.67 KB | Preview | Download |
Additional files |
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| BIOMD0000000691-biopax2.owl | Auto-generated BioPAX (Level 2) | 36.77 KB | Preview | Download |
| BIOMD0000000691-biopax3.owl | Auto-generated BioPAX (Level 3) | 55.60 KB | Preview | Download |
| BIOMD0000000691.m | Auto-generated Octave file | 8.57 KB | Preview | Download |
| BIOMD0000000691.pdf | Auto-generated PDF file | 191.90 KB | Preview | Download |
| BIOMD0000000691.png | Auto-generated Reaction graph (PNG) | 87.14 KB | Preview | Download |
| BIOMD0000000691.sci | Auto-generated Scilab file | 154.00 Bytes | Preview | Download |
| BIOMD0000000691.svg | Auto-generated Reaction graph (SVG) | 35.87 KB | Preview | Download |
| BIOMD0000000691.vcml | Auto-generated VCML file | 897.00 Bytes | Preview | Download |
| BIOMD0000000691.xpp | Auto-generated XPP file | 7.06 KB | Preview | Download |
| BIOMD0000000691_urn.xml | Auto-generated SBML file with URNs | 100.57 KB | Preview | Download |
| MODEL1006230022.cps | Curated and annotated model COPASI file. | 112.08 KB | Preview | Download |
| MODEL1006230022.sedml | SED-ML file for figure 6A and 6B. | 3.52 KB | Preview | Download |
- Model originally submitted by : Camille Laibe
- Submitted: Jun 23, 2010 10:12:00 AM
- Last Modified: Mar 18, 2018 12:58:45 PM
Revisions
-
Version: 3
- Submitted on: Mar 18, 2018 12:58:45 PM
- Submitted by: administrator
- With comment: Notes updated using online editor.
-
Version: 2
- Submitted on: Mar 16, 2011 3:21:53 PM
- Submitted by: Camille Laibe
- With comment: Current version of Wolf2000_AnaerobicGlycolysis
-
Version: 1
- Submitted on: Jun 23, 2010 10:12:00 AM
- Submitted by: Camille Laibe
- With comment: Original import of Wolf2000_GlycolyticOscillation
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: Variable used inside SBML models
| Species | Initial Concentration/Amount |
|---|---|
| S2 Cell 2 Glyceraldehyde 3-phosphate ; Glycerone phosphate |
0.45 mmol |
| A2 Cell 2 ADP ; ADP |
3.8 mmol |
| A2 Cell 1 ADP ; ADP |
0.8 mmol |
| S3 Cell 2 Glyceric acid 1,3-biphosphate ; 3-Phospho-D-glyceroyl phosphate |
0.1 mmol |
| A3 Cell 1 ATP ; ATP |
3.2 mmol |
| N1 Cell 2 NAD+ ; NAD(+) |
0.95 mmol |
| S2 Cell 1 Glyceraldehyde 3-phosphate ; Glycerone phosphate |
0.9 mmol |
| S4 Cell 1 Pyruvate ; Acetaldehyde |
0.2 mmol |
| N2 Cell 2 NADH ; NADH |
0.05 mmol |
| A3 Cell 2 ATP ; ATP |
0.2 mmol |
| Reactions | Rate | Parameters |
|---|---|---|
| S2__Cell_2_ + N2__Cell_2_ => | Cell_2*k6*S2__Cell_2_*N2__Cell_2_ | k6 = 12.0 |
| A2__Cell_2_ = A-A3__Cell_2_ | [] | [] |
| S3__Cell_1_ + A2__Cell_1_ => S4__Cell_1_ + A3__Cell_1_ | Cell_1*k3*S3__Cell_1_*A2__Cell_1_ | k3 = 16.0 |
| S3__Cell_2_ + A2__Cell_2_ => S4__Cell_2_ + A3__Cell_2_ | Cell_2*k3*S3__Cell_2_*A2__Cell_2_ | k3 = 16.0 |
| S1__Cell_1_ + A3__Cell_1_ => S2__Cell_1_ | Cell_1*k1*S1__Cell_1_*A3__Cell_1_*(1+(A3__Cell_1_/K_I)^q)^(-1) | q = 4.0; k1 = 100.0; K_I = 0.52 |
| N1__Cell_2_ = N-N2__Cell_2_ | [] | [] |
| S2__Cell_1_ + N1__Cell_1_ => S3__Cell_1_ + N2__Cell_1_ | Cell_1*k2*S2__Cell_1_*N1__Cell_1_ | k2 = 6.0 |
| S4__Cell_1_ => | Cell_1*J_cell_1 | J_cell_1 = 1.3 |
| S4__Cell_2_ + N2__Cell_2_ => | Cell_2*k4*S4__Cell_2_*N2__Cell_2_ | k4 = 100.0 |
| S1__Cell_2_ + A3__Cell_2_ => S2__Cell_2_ | Cell_2*k1*S1__Cell_2_*A3__Cell_2_*(1+(A3__Cell_2_/K_I)^q)^(-1) | q = 4.0; k1 = 100.0; K_I = 0.52 |
(added: 18 Mar 2018, 14:49:38, updated: 18 Mar 2018, 14:49:38)