BioControl:Week5

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Best of 2006-2007

Best of 2007-2008

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Next meeting

  • Friday, 1/19 at 9am in 110 Steele

Topics

  • Bacterial Chemotaxis
    • Perfect adaptation
    • Amplification

Reading

  1. Barkai N and Leibler S. Robustness in simple biochemical networks. Nature. 1997 Jun 26;387(6636):913-7. DOI:10.1038/43199 | PubMed ID:9202124 | HubMed [Barkai]
  2. Keymer JE, Endres RG, Skoge M, Meir Y, and Wingreen NS. Chemosensing in Escherichia coli: two regimes of two-state receptors. Proc Natl Acad Sci U S A. 2006 Feb 7;103(6):1786-91. DOI:10.1073/pnas.0507438103 | PubMed ID:16446460 | HubMed [Keymer]
All Medline abstracts: PubMed | HubMed

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

  1. Korobkova E, Emonet T, Vilar JM, Shimizu TS, and Cluzel P. From molecular noise to behavioural variability in a single bacterium. Nature. 2004 Apr 1;428(6982):574-8. DOI:10.1038/nature02404 | PubMed ID:15058306 | HubMed [Korobdova]
  2. Alon U, Surette MG, Barkai N, and Leibler S. Robustness in bacterial chemotaxis. Nature. 1999 Jan 14;397(6715):168-71. DOI:10.1038/16483 | PubMed ID:9923680 | HubMed [Alon]
  3. Spiro PA, Parkinson JS, and Othmer HG. A model of excitation and adaptation in bacterial chemotaxis. Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7263-8. PubMed ID:9207079 | HubMed [Spiro]
  4. Sourjik V and Berg HC. Binding of the Escherichia coli response regulator CheY to its target measured in vivo by fluorescence resonance energy transfer. Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12669-74. DOI:10.1073/pnas.192463199 | PubMed ID:12232047 | HubMed [Sourjik1]
  5. Sourjik V and Berg HC. Receptor sensitivity in bacterial chemotaxis. Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):123-7. DOI:10.1073/pnas.011589998 | PubMed ID:11742065 | HubMed [Sourjik2]
  6. Cluzel P, Surette M, and Leibler S. An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. Science. 2000 Mar 3;287(5458):1652-5. PubMed ID:10698740 | HubMed [Cluzel]
  7. Vaknin A and Berg HC. Single-cell FRET imaging of phosphatase activity in the Escherichia coli chemotaxis system. Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17072-7. DOI:10.1073/pnas.0407812101 | PubMed ID:15569922 | HubMed [Vaknin]
  8. Yi TM, Huang Y, Simon MI, and Doyle J. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4649-53. PubMed ID:10781070 | HubMed [Yi]
All Medline abstracts: PubMed | HubMed