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November 14, 2005

Synthetic Clock PhD plan

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Results of the meeting with Markus and Isabelle last Friday (11.Nov). Email to get the E.Coli strain used by Atkinson 2003 is under way..

Motivating or guiding Question

  • How accurately can synthetic systems be described by mathematical models?
  • How well can specific parameters of the in vivo system be changed?

Main Goals:

  • Review the theoretical model (kinetics and structure) to make it more realistic.
  • Identify relevant parameters to move system into the region of sustained oscillations.
  • Achieve this parameter shift by mutagenesis of transcription factors by error prone PCR.
  • Compare responses of theoretical and in vivo system.

Postulated Results:

  • Model predictions can be improved by using more realistic kinetic description of the regulation events.
  • Mutagenesis by PCR allows are more precise manipulation of model parameters than the method used previously.

Schedule of the Experimental Work:

  • Check if the strains are still rythmic, i.e. if the previous work can be reproduced (~ 1mth.)
  • Intoduce a luciferase reporter gene to measure clock function via luminescence assays (~ 1mth.)
  • Test, if cells can be grown on agar plates rather than in liquid cultures
  • mutagenise the sequence of relevant transcription factor to change chosen model parameters by erroneous PCR (~ 2mth)
  • Identify mutated colonies by changed clock behaviour caused by changes in the affinites of the transcription factor (~ 4mths)
    These are 8mths, make it 12mths.

about the advisor(s):

Ulrich Janus

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