IGEM:IMPERIAL/2006/project/Oscillator/project browser/Full System/Modelling
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Super Parts | Not applicable | |
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Actual Part | Full System logo | |
Sub Parts | Prey Molecule Generator | Predator Molecule Generator |
Model description of the Molecular Predation Oscillator
This system of ODEs describes the full system in a chemostat.
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A detailed theoretical study and simulations have shown that the properties of this system are able to fulfill our specifications:
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Model variables and parameters
Variables | ||||
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Name | Description | Initial Value | Confidence | Reference |
AHL | homoserine lactone acting as the prey-molecule | 0 | depends how good is the control of the prey positive feedback. Should be measured. | links |
luxR | molecule acting as the sensing module for the predator generator | 0 | to be measured as we might have to deal with some leakage of the promoter | links |
aiiA | molecule acting as the killing module of the prey molecule for the predator generator | to be measured | to be measured as we might have to deal with some leakage of the promoter | links |
Parameters | ||||
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Name | Description | Value | Confidence | Reference |
a | maximum synthesis rate of the pLux promoter | to be characterized | to be measured | links |
a0 | dissociation constant | to be characterized | to be measured | links |
b | catalysis rate of the AHL-lactonase(aiiA) | variable | to be measured/can be varied by chemostat | links |
b0 | Michaelis constant for the AHL-lactonase(aiiA) | to be characterized | to be measured | links |
c | maximum synthesis rate of the pLux promoter | to be characterized | to be measured | links |
c0 | dissociation constant | variable | to be measured/can be varied by chemostat | links |
dg | growth dilution due to chemostat wash-out | to be characterized | to be measured | links |
Full derivation of the above equations.
SBML Model
Media:IGEM_IMPERIAL_FullSystem_Model.sbml
Model assumptions and relevance
- General assumptions on gene expression modelling:
- Quasi-steady state hypothesis on mRNA expression.
- Gene activation can be approximated by Hill equations.
- Assumption on the Chemostat:
- It assumes that the prey molecule generator and the predator molecule generator populations are stable (the cell populations have reached steady-state).
- the degradation of the molecules is mainly due to the wash-out of the chemostat.
- Assumptions linked to the quorum sensing:
- As a first approximation, we assume that luxR and AHL molecules form a heterodimer (even if it has been found that the complex formed is more complicated)
- The concentration of the heterodimer is in equilibrium with the concentration of AHL
- LuxR is constitutively produced and reaches steady state before AHL production begins. [LuxR] in the prey can be considered constant
- The degradation rate of luxR and AHL-lactonase is due to the growth dilution which, in this case, is controlled by the chemostat
- AHL is diffusing freely throughout the system
Characterization
- Characterization of the parameters a, ao shall be done using the Prey Generator Test Contstruct
- Characterization of the parameters c, c0 shall be done using the Predator Generator Sensing Test Construct
- Characterization of the parameters b, b0 shall be done using the Predator Generator Killing Test Construct
- The growth dilution can be controlled by the chemostat washout.