BioControl:Reading

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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. Nature: Systems Biology User's Guide References 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 | 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 | 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. DOI:10.1016/s0022-2836(02)00994-4 | 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 | 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 | 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 |