BioControl:Week5

Next meeting

• Friday, 1/19 at 9am in 110 Steele

Topics

• Bacterial Chemotaxis
  • Perfect adaptation
  • Amplification

Reading

1. Barkai N and Leibler S. . pmid:9202124. PubMed HubMed [Barkai]
2. Keymer JE, Endres RG, Skoge M, Meir Y, and Wingreen NS. . pmid:16446460. PubMed HubMed [Keymer]

Discussion

• The cells are selecting for noisy function[3], but too much noise (particularly with extreme amplification) would seem to be a problem. If you could specify everything in this system, where would you want noise?
• Drunken random walks seem to be a common solution to this kind of problem - why?
  • It looks to me (Jkm) like a good way to deal with noisy inputs. Is there more to it? Are there better (engineering?) ways of solving the same problem?
• Going from experiments to models (particularly in biology) - are assumptions (CheB only demethylates active receptors) good, since they give us testable hypotheses? Or bad, since they're just artificial constraints in order to get the 'right' answer?

Further Reading

3. Korobkova E, Emonet T, Vilar JM, Shimizu TS, and Cluzel P. . pmid:15058306. PubMed HubMed [Korobdova]
4. Alon U, Surette MG, Barkai N, and Leibler S. . pmid:9923680. PubMed HubMed [Alon]
5. Spiro PA, Parkinson JS, and Othmer HG. . pmid:9207079. PubMed HubMed [Spiro]
6. Sourjik V and Berg HC. . pmid:12232047. PubMed HubMed [Sourjik1]
7. Sourjik V and Berg HC. . pmid:11742065. PubMed HubMed [Sourjik2]
8. Cluzel P, Surette M, and Leibler S. . pmid:10698740. PubMed HubMed [Cluzel]
9. Vaknin A and Berg HC. . pmid:15569922. PubMed HubMed [Vaknin]
10. Yi TM, Huang Y, Simon MI, and Doyle J. . pmid:10781070. PubMed HubMed [Yi]