BioControl:Reading

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Best of 2006-2007

Best of 2007-2008

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Recommendations

Papers that at least one of us has read and enjoyed, with a short summary and explanation of relevance.

  • Important mathematical background that underlies transcriptional regulation, the most prevalent feedback system in biology. I find it interesting that biology separates (to some degree) the amount of protein expressed from a protein's function, and this separation allows for control over the number of proteins in the cell. -Kelsic [1]
  • Modular functional modeling of feedback mechanisms in the heat shock response. An example of how protein numbers can be controlled via feedback vs. parameter tuning. [2]
  • Experiment and modelling that demonstrate how negative transcriptional regulation can change the time-response of a genetic circuit.[3]
  • Engineeging implementation of negative transcriptional feedback for control over the variance of protein distributions. An example of how transcriptional feedback can be used for precise gene control.[4]
  • Theoretical paper discussing the minimum number of molecules required to perform stable switching. It's article #74 on his publications page -Milo
  • A quorum sensing system regulates a gene that causes cell death. The result is a population control circuit. They're able to generate step-response-like plots of cell growth vs. time and show that with control the cells grow to a lower steady state value. [5] --Mary 17:52, 14 November 2006 (EST)
  • This paper uses the population control circuit from the paper above, but runs the reactions in a microfluidic bioreactor. Since they're feeding in fresh media and they can take measurements for ~8 days straight. Under the microfluidic conditions they observe oscillatory behavior from genetic circuits that maintained a constant steady state under the bulk growing conditions. [6] --Mary 18:11, 14 November 2006 (EST)

Possibilities

papers that no one has read, but that might be interesting.

References

  1. Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, and Phillips R. Transcriptional regulation by the numbers: models. Curr Opin Genet Dev. 2005 Apr;15(2):116-24. DOI:10.1016/j.gde.2005.02.007 | PubMed ID:15797194 | HubMed [Phillips1]
  2. El-Samad H, Kurata H, Doyle JC, Gross CA, and Khammash M. Surviving heat shock: control strategies for robustness and performance. Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2736-41. DOI:10.1073/pnas.0403510102 | PubMed ID:15668395 | HubMed [Doyle]
  3. Rosenfeld N, Elowitz MB, and Alon U. Negative autoregulation speeds the response times of transcription networks. J Mol Biol. 2002 Nov 8;323(5):785-93. PubMed ID:12417193 | HubMed [Elowitz]
  4. El-Samad H, Kurata H, Doyle JC, Gross CA, and Khammash M. Surviving heat shock: control strategies for robustness and performance. Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2736-41. DOI:10.1073/pnas.0403510102 | PubMed ID:15668395 | HubMed [Becskei]
  5. You L, Cox RS 3rd, Weiss R, and Arnold FH. Programmed population control by cell-cell communication and regulated killing. Nature. 2004 Apr 22;428(6985):868-71. DOI:10.1038/nature02491 | PubMed ID:15064770 | HubMed [You_Nature2004]
  6. Balagaddé FK, You L, Hansen CL, Arnold FH, and Quake SR. Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science. 2005 Jul 1;309(5731):137-40. DOI:10.1126/science.1109173 | PubMed ID:15994559 | HubMed [Balagadde_Science2005]
All Medline abstracts: PubMed | HubMed