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

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Super Parts Prey Construct
Actual Part
T9002: Test Sensing Prey Construct
Sub Parts F2620 intermediate_part intermediate_part


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 relationship between the heterodimer formed from LuxR and AHL in activating genes is linear
    • LuxR is at steady state since it is under the control of the constitutive promoter tetR
    • LuxR is in excess of AHL (ie not saturated by AHL)

Model description

  • Mathematical Description of GFP levels (prey sensitivity):
 \frac{d[GFP]}{dt} = \frac{a \times [AHL]}{a_{0} + [AHL]} - d_{GFP} \times [GFP]
For a full derivation, see Modelling Prey Sensing Test Construct


Graphical Representation of Model in Cell Designer
Graphical Representation of Model in Cell Designer
Output from model in Cell Designer based on modelling equation above
Output from model in Cell Designer based on modelling equation above

Model variables and parameters

Variables
Name Description Initial Value Confidence Reference
AHL Acyl Homoserince Lactone representing the prey molecule Concentration Range varying between 0nM and 10uM known links
GFP Green Fluorescent Protein to act as PoPs 0 to be measured links
Parameters
Name Description Value Confidence Reference
a population-dependent  ? to be extracted using experimental data links
a0 constant  ? to be extracted using experimental data links
dGFP degradation constant due to GFP degradation (Half-life 45min.)  ? to be extracted using experimental data links

Dynamical and sensitivity analysis

N/A

Characterization

  • Describe how you plan to use the modelling to characterize the part
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