In addition to the lab's regular research activities, Professor Bentley is also a member of the Biochip Collaborative.
Metabolic and Biomolecular Engineering - Quorum Sensing and in vivo Genetic Manipulation
We create molecular tools to understand the regulation of genetic curcuits during applied stresses. We also use transcriptional promoter probes, quantitative RT-PCR, Western analyses to gain near real time information on the dynamics of metabolites, genes, proteins, and protein assemblies in targeted circuits.
One objective is to alter the intracellular environment to improve cellular processes, including the production of recombinant proteins. In order to make use of the vast quantities of data, we need to organize them in reduced dimensional space, develop appropriate mathematical models, and then ultimately control phenotypic behavior. This is a component of Systems Biology. One modeling technique currently under investigation is the stochastic Petri net. We are also actively pursuing transient metabolic controllers to minimize pleiotropy. We incorporate signal transduction modalities and RNA controllers to modulate, in vivo, the level of specific regulatory proteins, and downstream proteins in cascaded control loops.
One exciting target is a newly characterized signal transduction pathway that communicates cell population, enabling individual bacteria to act with multicellularity. This phenomenon, also known as "quorum sensing, (QS)", results in cell-to-cell communication and plays a significant role in regulating cell behavior. In the LuxS-mediated signaling system of E. coli, we are the first group to explore the impact of AI-2 on the transcriptome (Delisa et al., J. Bact, 2001; Wang et al., J. Bact. 2005) and we are the first group to elucidate the impact of quorum regulator, LsrR and kinase, LsrK (Li, et. al., J. Bact. 2007). We are the first group to mathematically model quorum circuitry (Li, et. al., Nature Mol. Sys. Biol., 2006). Our efforts to develop innovative controllers of signal transduction have yielded biological nanofactories that bring biochemical enzyme activities to the outer surfaces of cells so that molecules can be synthesized directly where they can be used…in our case to interrupt bacterial communication (Fernandes et al., Nature Nanotech., 2010). Current efforts include deciphering LuxS regulated genes and the impact of QS on the intracellular biomolecular landscape that influences protein synthesis; we have just created a completely new system for expressing proteins that requires no operator input or sampling (Tsao et al., Met. Eng., 2010).
Biofabrication Engineering of Biological Signaling (bBIOS)
We are engaged in a multidisciplinary effort to create system that serve to bridge the communication gap between biology and electronic microfabricated devices. Since biology “communicates” via small molecule signaling (like in quorum sensing above) and ion flow and because we can program devices with electrons, we have a problem in translation. We employ Nature’s second most abundant biopolymer, chitosan, to serve as a “smart” stimuli-responsive interface. We are generating at biofabrication tool box that enables the assembly of complex biological structures onto programmable devices that allows for the accurate interrogation of the biological system. In our case, quorum sensing and bacterial communication (and even cross-Kingdom signaling) serves as a wonderful test bed for listening in on biology. We are developing all sorts of new methods for localizing DNA, proteins, cells and cell assemblies onto devices that will serve to break down complexities so that discoveries can be attributed to specific molecules, gradients, patterns, etc. We anticipate developing new tools for deciphering the presence of pathogens, for understanding and treating metabolic diseases, cancer, and hemorrhagic shock. For a glimpse of some of these activities, please visit the Biochip Collaborative web site.