Systems Biology x Network Biology GOAL: develop a quantitative understanding of the biological function of genetic and biochemical networks INPUT

I Systems Microbiology(13 Lectures 7hece∥ as a we∥}- stirred boc/ nem/ca/ reactor Introduction 2 Chemical kinetics, Equilibrium binding, cooperativity L3 Lambda phage L4 Stability analysis L5-6 Genetic switches

Note final ps For question 2(a)the value of k'in the final equation(Eq 3b) needs to be rescaled Tuesday lecture will be for questions on the last problem set Juan)

Alternative views on gradient sensing Postma and van hastert. 'a diffusion-translocation model for gradient sensing by chemotactic cells Biophys.J.81,1314(2001) Levchenko and Iglesias. Models of eukaryotic gradient sensing: applications to chemotaxis of amoeba and neutrophils

Review L15 Turing-Gierer-Meinhardt models Local excitation, global inhibition

Review Turing-Gierer-Meinhardt models Local excitation, global inhibition 22r+hq

creation of membrane associated minD first order first order autocatalytic inhibited by (linear, oligomerization) membrane minE, MM)

Wrapping up E coli chemotaxis (L7& L8) Main points of last 2 lectures L7: Biological background what is the function of the individual molecules L8: modeling of all possible chemotactic reactions why doesn't this model reproduce experimentally observed perfect adaptation

Organizational Remarks: ps#2,1b: Correction: Plot k, and for L= 0...2/K L (NOT: Plot ka and for L 0...2KL) Tomorrow's recitation topic: 'PS #2 support

L14: 14 Lectures past and 1 1 to go Part 'The cell as a well-stirred bioreactor topICs Lambda phage lysis-lysogeny switch Synthetic genetic switch Switches as memory storage Chemotaxis: perfect adaptation or not? Synthetic genetic oscillators