IGEM:IMPERIAL/2006/project/Oscillator/project browser/Test Sensing Predator Construct/Modelling

Super Parts	Predator Construct
Actual Part
Sub Parts	<bbpart>R0062</bbpart>	<bbpart>B0034</bbpart>	<bbpart>C0062</bbpart>	<bbpart>I13504</bbpart>

• Specifications
• Design
• Modelling
• Implementation
• Testing/Validation

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.

• 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 degradation rate of luxR and aiiA is mainly due to the growth dilution.

Model description of the oscillator

Full derivation of the above equations.

Model description of the growth of the predator

• mathematical description of the predator growth and death:
  • [math]\displaystyle{ \frac{d[luxR]}{dt} = \frac{c * [AHL] * [luxR]}{(c0 + [AHL] * [luxR])} - gd * [luxR] }[/math]
  • [math]\displaystyle{ \frac{d[aiiA]}{dt} = \frac{c * [AHL] * [luxR]}{(c0 + [AHL] * [luxR])} - gd * [aiiA] }[/math]

• insert a graphical representation if possible (e.g. CellDesigner display)
• link to SBML file or matlab.

Model variables and parameters for the growth of the predator

(list all the variables and parameters of the model in a table, specifying if their values are known, unknown, to be measured.)

Variables
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	links
luxR	molecule acting as the sensing module for the predator	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 for the predator	0	to be measured as we might have to deal with some leakage of the promoter	links

Parameters
Name	Description	Value	Confidence	Reference
c	maximum synthesis rate of the pLux promoter	to be characterized	to be measured	links
c0	dissociation constant according to Hill eq	to be characterized	to be measured	links
gd	growth dilution	to be characterized	to be measured	links

Characterization

• Parameters c & c0 for characterization have to be extracted.
• gd[luxR] and gd[aiiA] can be controlled by the chemostat.