User:Ty M. Thomson

Thesis Topic

The main objectives of my work is to develop the tools to perform time-dependent stimulation and analysis of signaling pathways, and show that this is more powerful than traditional time-independent or step response analysis. I am using a computational model of the prototype system, the yeast pheromone response pathway, to generate hypotheses about the pathway. In order to test these hypotheses, time-dependent stimuli will be delivered to cells via a microfluidic device, and in vivo fluorescent reporters will be used to observe the system state. In addition to showing the strengths of this new approach to studying biological systems, I would like to use it to further our understanding of the pheromone response pathway.

Research Goals

My research can be broken down into 4 main goals that follow (for the most part) chronologically).

1. Build a model of the pheromone response pathway
   • Develop a model of the pheromone response pathway that can be used in conjunction with time-dependent stimulation and analysis of the pathway to propose and test hypotheses. Once completed, this model can be used as a predictive tool for pathway response.
     • This model is largely already built (with instanced in Matlab and Moleculizer). It needs to be further refined using data from the literature, and data that I will generate myself.
2. Build a microfluidic device for time-dependent stimulation of cells
   • Design, build and characterize a device to allow for rapid variation of extracellular conditions for cells fixed in a microfluidic channel.
     • This chip has been designed using the technology out of the Quake Lab at Stanford (formerly Caltech). See Protocols#Microfluidics for more info on chip design. The most recent design of the Stimulator is currently being made by the Microfluidic Foundry (Caltech). Previous instances have shown great promise for my purposes. Preliminary tests have shown that I can vary the extracellular environment (with NO cells in the channel) on a sub 100ms timescale. I've also successfully adhered cells to the bottom of the channel, and had them resist detachment under fluid flow, though this needs further characterization.
3. Investigate the pathway with time-dependent stimulation
   • Examine the frequency filtering characteristics of the pheromone response pathway in order to study the limits of propagation of time-varying signals through the pathway. Use the model to form and test hypotheses generated by studying the response of the pathway to time-dependent stimulation.
4. Identify and apply techniques for non-linear system identification
   • Identify and apply tools developed for other fields to the analysis of signaling pathways, particularly with respect to time-dependent stimulation.