IGEM:IMPERIAL/2006/project/Oscillator/project browser/Full System/Modelling
|Super Parts||Not applicable|
|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.
|A detailed theoretical study and simulations have shown that the properties of this system are able to fulfill our specifications:
Model variables and parameters
|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|
|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|
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 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.