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Physics Colloquium - Monday, March 1st, 2010, 3:00 P.M.

E300 Math/Science Center; Refreshments at 2:30 P.M. in Room E200

Savas Tay
Department of Bioengineering
Stanford University

Decoding signaling networks using microfluidics: NF-&kappaB dynamics reveal digital responses to inflammatory signals

The mammalian immune response is a striking example of the coordinated operation of many cell types. Intercellular communication is mediated by signaling molecules that form concentration gradients, which requires cells to respond to a wide range of signal intensities. We used high-throughput microfluidic cell culture, quantitative gene expression analysis and mathematical modeling to investigate how mammalian cells respond to different concentrations of the signaling molecule TNF-&alpha, and modulate gene expression via the transcription factor NF-&kappaB. We measured NF-&kappaB activity in thousands of live cells under TNF-&alpha doses covering four orders of magnitude. In contrast to population studies (i.e. Western Blot's), NF-&kappaB activation is found to be a switch-like process at the single cell level with fewer cells responding at lower doses. The activated cells up-regulate early genes independent of the TNF-&alpha concentration, while only high dose stimulation results in the expression of late-term genes. Cells also encode a subtle set of analog parameters such as the NF-&kappaB peak intensity, response time and number of oscillations to modulate the outcome. Using our comprehensive data, we developed a mathematical model that reproduces both the digital and analog dynamics as well as the gene expression profiles at all measured conditions, constituting a broadly applicable model of NF-&kappaB signaling. In addition to their biological significance, our results highlight the value of high-throughput quantitative measurements at the single-cell level in understanding how biological systems operate.