Current Research

We employ the tools of "functional" genomics to understand the regulation of genetic curcuits during applied stresses. In particular, we use DNA microarrays for analyzing gene expression on a global basis. This, coupled with transcriptional promoter probes, quantitative RT-PCR, Northern and Western analyses ultimately enables close to real time detection of gene expression in targeted circuits. We are currently focussing on stress-related and nutritionally- regulated pathways such as those involving s32, sS,and sN.

Our objective for this genomics research 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, 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. Specifically, we are investigating the use of antisense technology and small interfering RNAs to downregulate, in vivo, the level of a 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 when recombinant proteins are overproduced in E. coli. In the putative LuxS-mediated signalling 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). Current efforts include deciphering LuxS regulated genes and the impact of QS on the intracellular biomolecular landscape that influences protein synthesis.

Other exciting targets are found in insect cells and insect larvae. In these eukaryotic systems, we are the first group to examine the utility of dsRNA as a tool for manipulating a protein expression system (Kramer and Bentley, Metabolic Eng, 2003). Current efforts target cell cycle, glycoslyation, and other effectors in Drosophila melanogaster, Spodoptera frugiperda, and Trichoplusia ni (March and Bentley, Biotech. Bioeng. 2006). Drosophila provide us with a genetic system for applied genomics work as described above. Trichoplusia provide nice big juicy insects to make proteins in bulk, and Spodoptera represent a "gold standard" to which we compare our new strategies.
We are developing new analytical tools to monitor gene expression both in vivo and in vitro. While our previous work introduced the utility of GFP for this purpose (Albano 1996, Cha 1997), we are currently developing new platforms for the assembly of biospecies onto smart surfaces and within microchannels. We have an extensive collaboration with the Rubloff, Payne, and Ghodssi groups to develop next generation biofunctionalized devices for probing biological systems. Our work here incorporates the pH-responsive biopolymer, chitosan, as a "transportable scaffold" onto which tethered (using molecular biology) proteins and nucleic acids can be covalently displayed (Lewandowski et al., 2006, Yi et al., 2005). This collaborative effort has introduced the idea of "thermbiolithography" (Fernandes et al., 2004), nanofactories (Fernandes et al., 2007), and "biofabrication" (Wu and Payne, 2004) which exploit biospecies as the building blocks and effectors for constructing devices, sensors, and, eventually, microfactories.