The completion of the efforts to sequence the human genome, as well as the genomes of other organisms, will bring about a new era in biomedical and biochemical engineering research. Advances in genomic technology open a new repertoire of tools for bioengineering applications. In the near future, genetic manipulations will offer novel strategies for diagnosing and treating diseases, maximizing agricultural output, and using living cells to generate chemical compounds. As chemical engineers, we bring an important set of skills to implementing this exciting technology.
In order to utilize the power of genomic techniques fully, we must better understand how quantitative changes in the expression or activity of individual genes can affect global cellular processes. Living cells are extremely complex systems, comprised of 1000-100,000 different gene products. Each gene product can interact with several others, often forming regulatory mechanisms with elaborate features such as pathway redundancies or feedback loops. In our efforts to design cells for a particular function, we generate mathematical models of the relevant cellular processes in an attempt to identify candidate genes which strongly and specifically regulate that function. Then we test our models by genetically altering the expression or activity of the prime candidate genes. This combination of modeling and experiments can enhance our efficiency in developing an understanding of cellular processes as dynamic systems.
One limitation of modeling biological systems is the relative lack of quantitative data on intracellular reactions responsible for transmitting biochemical signals. We are developing new techniques to fuse pro-teins to surfaces and to detect their binding to, or modification by, other proteins. These "protein chip" experiments will permit us to analyze the kinetics of hundreds or thousands of different enzyme-ligand reactions in parallel, and obtain data for accurate models of cell behavior. This will improve our understanding of how chemical signaling reactions in cells regulate cell behavior, allowing us to experimentally alter those signaling pathways to achieve the desired cell function.
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