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November 14, 2005

Synthetic Clock PhD plan

Writing about web page http://blogs.warwick.ac.uk/ulrichjanus/entry/todo_1/

Writing about an entry you don't have permission to view

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):
Postponed…


Ulrich Janus

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