Garde2020-Minimal model describing metabolic oscillations in Bacillus subtilis biofilms

Model Identifier
BIOMD0000000932
Short description
Biofilms offer an excellent example of ecological interaction among bacteria. Temporal and spatial oscillations in biofilms are an emerging topic. In this paper, we describe the metabolic oscillations in Bacillus subtilis biofilms by applying the smallest theoretical chemical reaction system showing Hopf bifurcation proposed by Wilhelm and Heinrich in 1995. The system involves three differential equations and a single bilinear term. We specifically select parameters that are suitable for the biological scenario of biofilm oscillations. We perform computer simulations and a detailed analysis of the system including bifurcation analysis and quasi-steady-state approximation. We also discuss the feedback structure of the system and the correspondence of the simulations to biological observations. Our theoretical work suggests potential scenarios about the oscillatory behaviour of biofilms and also serves as an application of a previously described chemical oscillator to a biological system.
Format
SBML
(L2V4)
Related Publication
-
Differential equation-based minimal model describing metabolic oscillations in Bacillus subtilis biofilms.
- Garde R, Ibrahim B, Kovács ÁT, Schuster S
- Royal Society open science , 2/ 2020 , Volume 7 , Issue 2 , pages: 190810 , PubMed ID: 32257302
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
- Biofilms offer an excellent example of ecological interaction among bacteria. Temporal and spatial oscillations in biofilms are an emerging topic. In this paper, we describe the metabolic oscillations in Bacillus subtilis biofilms by applying the smallest theoretical chemical reaction system showing Hopf bifurcation proposed by Wilhelm and Heinrich in 1995. The system involves three differential equations and a single bilinear term. We specifically select parameters that are suitable for the biological scenario of biofilm oscillations. We perform computer simulations and a detailed analysis of the system including bifurcation analysis and quasi-steady-state approximation. We also discuss the feedback structure of the system and the correspondence of the simulations to biological observations. Our theoretical work suggests potential scenarios about the oscillatory behaviour of biofilms and also serves as an application of a previously described chemical oscillator to a biological system.
Contributors
Submitter of the first revision: Ahmad Zyoud
Submitter of this revision: Ahmad Zyoud
Modellers: Ahmad Zyoud
Submitter of this revision: Ahmad Zyoud
Modellers: Ahmad Zyoud
Metadata information
is (2 statements)
hasTaxon (1 statement)
isDerivedFrom (7 statements)
hasProperty (5 statements)
isDescribedBy (2 statements)
hasTaxon (1 statement)
isDerivedFrom (7 statements)
Mathematical Modelling Ontology
Ordinary differential equation model
NCIt Metabolic
Environment Ontology biofilm
TEDDY TEDDY_0000072
Gene Ontology glutamate metabolic process
NCIt Metabolic
Environment Ontology biofilm
TEDDY TEDDY_0000072
Gene Ontology glutamate metabolic process
hasProperty (5 statements)
Mathematical Modelling Ontology
Ordinary differential equation model
Gene Ontology glutamate metabolic process
TEDDY TEDDY_0000072
Environment Ontology biofilm
NCIt Metabolic
Gene Ontology glutamate metabolic process
TEDDY TEDDY_0000072
Environment Ontology biofilm
NCIt Metabolic
isDescribedBy (2 statements)
Curation status
Curated
Modelling approach(es)
Tags
Connected external resources
Name | Description | Size | Actions |
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Model files |
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Garde2020.xml | SBML L2V4 Garde2020-Minimal model describing metabolic oscillations in Bacillus subtilis biofilms_Curated | 34.67 KB | Preview | Download |
Additional files |
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Garde2020-Fig2.sedml | sed-ml L1V2 Garde2020-Minimal model describing metabolic oscillations in Bacillus subtilis biofilms_Curated-Fig2 | 6.42 KB | Preview | Download |
Garde2020-Fig4.sedml | sed-ml L1V2 Garde2020-Minimal model describing metabolic oscillations in Bacillus subtilis biofilms_Curated-Fig4 | 6.41 KB | Preview | Download |
Garde2020.cps | COPASI version 4.27 (Build 217) Garde2020-Minimal model describing metabolic oscillations in Bacillus subtilis biofilms_Curated | 65.03 KB | Preview | Download |
- Model originally submitted by : Ahmad Zyoud
- Submitted: Apr 14, 2020 4:07:50 PM
- Last Modified: Apr 14, 2020 4:07:50 PM
Revisions
Legends
: Variable used inside SBML models
: Variable used inside SBML models
Species
Species | Initial Concentration/Amount |
---|---|
A ammonia |
1.0 mmol |
Gp CHEBI:32484 ; C25233 |
1.0 mmol |
Gi CHEBI:32484 ; C25234 |
1.0 mmol |
B biomass production |
1.0E11 mmol |
Reactions
Reactions | Rate | Parameters |
---|---|---|
A => | compartment*k3*A | k3 = 4.0 |
=> Gp; A | compartment*(k1*GE*Gp-k2*A*Gp) | GE = 30.0; k2 = 5.3; k1 = 0.3426 |
Gp => Gi | compartment*k4*Gp | k4 = 2.0 |
Gi => A | compartment*k5*Gi | k5 = 2.3 |
=> B; A, Gp | compartment*b*A*Gp*B | b = 0.1 |
Curator's comment:
(added: 14 Apr 2020, 16:06:41, updated: 14 Apr 2020, 16:06:41)
(added: 14 Apr 2020, 16:06:41, updated: 14 Apr 2020, 16:06:41)
Figure 2 and 4 were reproduced by using Copasi 4.27 (Build 217)