Imperial College/Courses/Spring2008/Synthetic Biology/Computer Modelling Practicals/Practical 3

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Synthetic Biology (Spring2008): Computer Modelling Practicals

Home        CellDesigner Tutorial        Practical 1        Practical 2        Practical 3        Schedule        Back to Synthetic Biology Course       

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...UNDER DEVELOPMENT...

Practical 3


Objectives:

  • To explore computationally some simple genetic circuits:
    • Genetic Cascade To Be Tuned.
    • A genetic oscillator: the Repressilator.
    • A mystery device.

Deliverables

  • A report is expected by ... (Word or PDF format, sent to XXX@XXX)
  • When you find in the text (illustration needed), it means that you will have to provide an image export of your simulation results in your report.


Part I: Genetic Cascade To Be Tuned


In Practical 2, we have explored how gene expression can be controlled (positively or negatively) by other proteins. Here, we start to assemble genetic circuit by connecting genes. The model studied here is a simple genetic cascade, where a Gene_1 produces a protein which repressed the expression of Gene_2. Additionally, you are able to induce the expression of Gene_1 thanks to an inducer.

To start, launch the CellDesigner Application: Double Click on the Icon found on your Desktop. Then follow the instructions below to build the model.


Model CellDesigner Instructions

Gene \xrightarrow{k_{1}} mRNA \xrightarrow{k_{2}} Protein

Define the topology of the reaction network:

  • Open a NEW document: File -> New.

Genetic Cascade

Following the Law of Mass action, the dynamic of the system is described as:

...
  • ....

Questions:

  • Using the default kinetics parameters, build the following 3 transfer functions:
    • first, between the [inducer] concentration, and the Protein_1 steady-state expression level. Take the inducer level to vary between [0, 10000]. Comment on the behaviour observed (Illustrations)
    • second, between the Protein_1 concentration (to be kept constant during the simulations), and the Protein_2 steady-state expression level. Make sure that the range covered by the concentration of Protein_1 helps to explore the full dynamic range of system behaviour.
    • third, between the [inducer] concentration, and the Protein_2 steady-state expression level. Take the inducer level to vary between [0, 10000]. Comment on the behaviour observed (Illustrations)
  • We want to tune this cascade so that when using our maximal [inducer] concentration we are able to completely shut-down the expression of Protein_2. Suggest 2 independent strategies to achieve that result.

Additional Resources:

Part II: Genetic Oscillator: The Repressilator

...

  1. Elowitz MB and Leibler S. . pmid:10659856. PubMed HubMed [Elowitz2000]
Model CellDesigner Instructions

Repressilator Elowitz Plasmids

Repressilator Genetic Circuit

Repressilator Elowitz Experimental Observations

Repressilator Deterministic Simulations



Questions:

  • Focus on the modelling section of the published paper, and build your own 'Repressilator' model in CellDesigner.
  • Run a simple sensitivity analysis on each parameter, and suggest some strategies to control the amplitude of the oscillations.
  • Do the same to suggest ways to control the frequency of the oscillations.
  • Bonus: Could you explain the drift observed on the experimental data ? Provide a simulation supporting your hypothesis.

Additional Resources:


Part III: A mystery device

...

Model CellDesigner Instructions

Gene \xrightarrow{k_{1}} mRNA \xrightarrow{k_{2}} Protein

Define the topology of the reaction network:

  • Open a NEW document: File -> New.

Mystery Device Network

Questions:

  • Suggest a strategy to characterise this model (Establish clear simulation scenarii to illustrate the properties of this genetic circuit. Tip: The cell designer function related to 'Change Amount' might be handy)
  • From your characterisation, how would you call this device ?
  • Imagine an application where this genetic device would be useful.


Additional Resources:

  • ...
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