Projects
The first band of students to enter The Graduate Program in Biophysical Sciences is just beginning (Fall ’07), so we can’t present their work quite yet. Nevertheless, The University of Chicago is renowned for interdisciplinary intellectual work in all areas, including the sciences. Below are a list of on-going or recently completed thesis research projects that demonstrate the types of collaborations students participate in.
Cory Gerdts
Cory Gerdts completed his PhD in September, 2007 at University of Chicago in the lab of Rustem F. Ismagilov. His work focused on creating functional reaction networks and protein crystallization using plug-based microfluidics. The plug-based system for protein crystallization isolates trials into ~20 nL-sized droplets (plugs), and is used for both sparse matrix and gradient (optimization) screening.
While a part of the group, Cory led the University of Chicago's participation in the collaboration with Accelerated Technolgies Center for Gene to 3D Structure (ATCG3D), an NIH-funded specialized center under PSI-2 that is trying to develop a novel system for quickly determining the structures of proteins that traditionally have been difficult to study.
Microfluidics technique could find medical-diagnostic applications
University of Chicago team successfully uses chemistry to predict the dynamics of clotting in human blood. Read article
Young-Sam Lee
Regulation of Pho80/Pho85 cyclin-CDK complex by nutrients and their metabolites. View website
Time-resolved X-ray Crystallography of the Photosynthetic Reaction Center
The photosynthetic reaction center is an elaborate machine that uses light to catalyse electron and proton transfer across a biological membrane. Most of the chemistry that occurs within the reaction center is one-electron transfer between different chromophores and redox components that are embedded within the protein itself. The exception to this is the secondary electron acceptor QB, which is a mobile quinone occupying an active site within the enzyme. View project
Abhishek Jha: A model for the Unfolded State
This application allows one to generate an unfolded state ensemble using a self-avoiding statistical coil model that is based on backbone conformational preferences from a coil library, a subset of protein data bank. View website
Jason Lloyd Wyman
Our group applied the selective-withdrawal coating technique to the microencapsulation of insulin-producing pancreatic islets within thin poly(ethylene glycol) coats. These polymer coatings allow the enclosed islets to respond to changes in glucose concentration by producing insulin in a manner quantitatively indistinguishable from that of unencapsulated islets. Furthermore, the hydrogel capsules exclude large molecules the size of the smallest agents of the immune system. Our results suggest that this microencapsulation technique may be useful for the transplantation of islets for the treatment of Type I diabetes.
A Real-time Study of Genetic Networks Using a Non-coding RNA Reporter System
The ability to measure transcriptional and translational dynamics in real-time and at the level of a single cell is essential to understanding the function of genetic networks. The relatively slow folding and activation time of green fluorescent protein (GFP) precludes its use as a direct measure of promoter activity on timescales less than 30 minutes, and other attempts to study gene dynamics have used ensemble-averaging techniques that mask the underlying temporal fluctuations. Alternatively, RNA transcripts are excellent probes of promoter activity on fast timescales. I present a new approach to the study of genetic networks using fluorescence correlation spectroscopy (FCS) to track RNA molecules tagged with pre-expressed GFP, in real-time and within a single living E. coli.