Living cells encode a remarkable and diverse set of functions. Cells take in vast amounts of information about the environment, process the information, and make complex decisions about how to respond and direct new phenotypes. The functions that enable these sophisticated behaviors are programmed by circuits of interacting genes and proteins. How are these molecular systems assembled and what specific functions do they encode? How do genetic circuits operate in response to dynamic cellular environments to program new phenotypes? Can we rewire and engineer these systems to program new cellular functions to help solve problems in biotechnology, energy, and health? To address these questions, we use a variety of experimental approaches, with special emphasis on the development of new synthetic and systems biology approaches. Notably, we build synthetic gene circuits in cells from well-understood components and study their functions. We also utilize engineering approaches to recapitulate dynamic cellular environments. We design and build programmable microfluidic devices that enable us to culture cells, program diverse environmental conditions, and monitor single cells. Because the problems we focus on are universal, we work with a range of organisms (bacteria, yeast, and mammalian cells).
Specific classes of problems we are interested in include:
1. Eukaryotic gene regulation. Elucidating the design principles of transcriptional regulatory systems and networks, which are responsible for controlling the thousands of genes in eukaryotic genomes. Programming eukaryotic transcription functions in cells through synthetic biology.
2. Phenotypic plasticity, evolution and engineering. Dissecting the regulatory systems that enable cells to adapt to fluctuating environments and generate new phenotypes. Exploring the environmental parameters that drive new phenotypes in individual cells using multiplexed microfluidic devices. Forward evolution of new and useful cellular functions. Studying drug tolerance mechanisms in bacteria and yeast.
Iterative Plug-and-Play Methodology for Constructing and Modifying Synthetic Gene Networks
Kevin D. Litcofsky, Raffi B. Afeyan, Russell J. Krom, Ahmad S. Khalil* and James J. Collins* (*Co-corresponding)
Nature Methods, 9: 1077-80 (2012)
A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions
Ahmad S. Khalil, Timothy K. Lu, Caleb J. Bashor, Cherie L. Ramirez, Nora C. Pyenson, J. Keith Joung and James J. Collins
Cell, 150: 647-658 (2012)