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Contact Information:
Office: CIS E315 Email: r-ismagilov@uchicago.edu Voice: 773 702 5816 Fax: 773 834 3544 Mailing Address: 929 East 57th Street, Chicago, IL 60637 Directions
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Research Interests: Our research goal is to control and understand complex chemical and biological systems in space and time using microfluidics. Our research is highly interdisciplinary, involving components of Chemistry, Physics, Biology, and Engineering. We work towards our goal in three directions.
I. Developing new microfluidic technology:
Movies of plug transport and mixing of reagents:
(Flash Player 6 required)
II. Validating
technology by applying it to functional and structural
characterization of proteins.
II.a Droplet-based microfluidic system for evaluation protein crystallization conditions with on-chip x-ray diffraction. A microfluidic method was developed to screen protein crystallization conditions in nL-sized droplets, each droplet representing a different crystallization condition. By systematically changing the flow rates of aqueous reagent streams and flowing these streams into a flow of immiscible fluorinated oil on a microfluidic chip, hundreds of trials contained in droplets could be performed in a single experiment. After the formation of a droplets containing assays, the droplets could be flowed directly into a glass capillary where precise control over evaporation allowed the experimenter to perform microfluidic crystallizations analogous to either large-scale microbatch or vapor diffusion experiments. Crystals formed in glass capillaries could be diffracted directly “on-chip”. We are now collaborating on a structural genomic project with the goal of integrating several promising instrumental, methodological, and software technologies, including our high-throughput microfluidic screening, into a program for low-cost structure determination.
For more information, please see Accelerated Technologies Center for Gene to 3D structure (ATCG3D) -- New approach to protein crystallization: www.atcg3d.org
II. b Millisecond Kinetics on a Microfluidic Chip Using Nanoliters of Reagents
We are also developing a system for kinetic measurements in which a complete ms-resolved reaction profile can be obtained in a few seconds from a single spatially resolved image using < 100 nL of solutions. We use this system as a research tool for studying time-dependent processes -- especially those that involve complex networks and autocatalytic reactions -- in chemistry, biochemistry and biophysics.
In the first set of projects, we develop and implement using microfluidics "minimal functional models" of complex biochemical networks (10-100 reactions). We aim to reproduce the function of the network using a few (2-4) carefully chosen chemical (non-biological) reactions with proper kinetics; these chemical networks serve as the basis of biomimetic chemical systems. We are applying this philosophy to hemostasis and cell differentiation. In the second set of projects, we apply the technology and the knowledge from minimal models to study the biochemical networks themselves, e.g. hemostasis and developmental pathways.
III.a Dynamics of Drosophila Embryonic Patterning Network Perturbed in Space and Time with Microfluidics
The first step in patterning the embryo is determining the middle of the embryo. This is accomplished through precise expression of the protein Hunchback in half of the embryo. Amazingly, the embryo can determine its middle precisely under different environmental conditions such as temperature. This is not surprising since the embryo experienced these conditions during evolution and developed a compensation mechanism to correct for its varying environment. However, the critical compensation event in the network which sets the middle of the embryo remains unknown. The reductionism approach – looking at a single component of a network of reactions – has been important in determining which genes and proteins are present in the network which determines the middle of the embryo. Looking at the network as a whole can provide information on where and when critical events occur. We used the approach of looking at this developmental network in Drosophila embryos as a whole. We used microfluidics to control development of wild-type Drosophila embryos in space and time. Two streams of fluid flow, one at a lower temperature and one at a warmer temperature, were used to cool one half of the embryo and warm the other half of the embryo (Figure 1a). Using this system, we asked three questions: 1) Will the embryo feel the effect of the unnatural environment, 2) Will the middle of the embryo still be correctly determined under these extremely unnatural conditions, and 3) Can we learn something about the mechanism by which the embryo determines its middle? Embryos developed with one half cool and one half warm (Figure 1a) felt the effect of the temperature step – the warm half of the embryo developed more rapidly than the cool half. Surprisingly, these embryos still determined the correct middle. The network responsible for determining the middle still functioned under these conditions not seen during evolution. However, one specific perturbation in space and time (Figure 1a-c) disrupted the developmental network. In these experiments, first the embryo was developed with its anterior warm and its posterior cool from 0-65 minutes (Figure 1a). Then, the temperatures were reversed and the embryo developed with its anterior cool and its posterior warm from 65-100 minutes (Figure 1b). Finally, the temperatures were reversed back and the embryo developed with its anterior warm and its posterior cool from 100 minutes to the conclusion of the experiment (Figure 1c). Embryos from these experiments did not always determine the correct middle. These experiments suggested that the time at which the compensation mechanism performs its critical function is between 65 and 100 minutes in development. Ultimately, to determine both how the chemical network is orchestrated in space and time and the molecular players involved in the compensation mechanism, the reductionism approach will have to be combined with the approach of looking at the entire network. Microfluidic technology could prove to be a powerful tool in combining these two approaches for both this developmental network and other biochemical networks. III. b Predicting the dynamics of blood clotting using a minimal functional model
Using the chemical model we have also generated a testable hypothesis for how clotting can remain localized to regions of damage after clotting has initiated. The chemical model predicts that vessel geometry and flow rates are regulators of clot propagation, and these predictions are currently being tested with human blood plasma.
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© 2003 Rustem Ismagilov Group, The University of Chicago