Mike Ferry

Postdoctoral Fellow
(858) 361-5515

Research Interests

My research is focused on the metabolic network known as the Gal network in brewers yeast, Saccharomyces cerevisiae. The Gal network of yeast is responsible for metabolizing the sugar galactose, which is an alternative cellular energy source when its preferred sugar, glucose, is unavailable. The yeast cell has evolved to tightly regulate the Gal network genes in response to environmental carbon source availability. This regulation ensures that the cell only produces the genes necessary for optimal success in its current environment, preventing wasteful energy expenditures on unnecessary gene products. The Gal network is composed of both positive and negative feedback components, which regulate the production of the structural genes in the network responsible for the biochemical breakdown of galactose. Interestingly, in response to galactose stimulus both the positive and negative feedback components of the network are induced which at first appears counter intuitive. For example, what is the advantage to expressing the components responsible for shutting off the network when stimulus is present? To explore this question I have created a yeast strain with the native negative feedback regulation altered so that I can control its levels independently from the state of the Gal network. I am currently comparing the response of these cells to unaltered cells in both static and dynamic environments.

Traditionally genetic networks have been studied using populations of cells under static conditions or dynamic conditions with relatively poor temporal resolution. However in recent years much interest has developed in studying the gene expression dynamics in response to changing environments. Furthermore studying the response of individual cells to changing environments has become critical to understanding the role of gene expression noise in genetic networks. To accomplish these studies researchers have increasingly turned to microfluidic devices. These devices are small fluidic networks with chambers that can be loaded with cells and visualized using fluorescence microscopy. The environment surrounding these cell chambers can be closely controlled, giving the researcher the ability to follow the dynamics of gene expression at the single cell level. I have recently designed a new microfluidic device known as the m-daw or multiple dial - a - wave device. This device greatly increases the power of each microfluidic experiment by expanding the number of cell chambers eight fold. The device features an optimized brewers yeast trap allowing cells to be efficiently removed upon filling and thus prevents clogging. Furthermore the fluidic system responsible for generating arbitrary external environments has been optimized to produce high fidelity, rapidly changing concentration profiles of inducer with periods as small as one minute to several hours. The wave form of the concentration profile can be arbitrary; square waves, sawtooth waves, sine waves and even random inputs are possible. I am currently using this system to probe the response of the genetically altered yeast mentioned previously to fluctuations in environmental galactose.