Developing Standardized Cell-Free Platforms for Rapid Prototyping of Synthetic Biology Circuits and Pathways
The goal of this project is to further advance standardized cell-free systems from engineered E. coli and other organisms for use in prototyping synthetic circuit and pathway designs. Such standardized systems will both explore the boundaries of cell-free prototyping and characterization, and enable more detailed understanding of key mechanisms, accelerating the usage and broader utility of cell-free systems in industry and academia. The long term vision for this project is to establish cell-free systems as a platform for implementation of synthetic biological circuits, pathways, and systems, where modular and complex biomolecular systems can be engineered in a systematic fashion. This project seeks to overcome some of the current limitations of cell-free systems through a combination of experimental characterization and computational modeling.
The main objectives of this project are:
- Development of well-understood, standardized TX-TL reaction systems that are suitable for prototyping circuits and pathways for a variety of cells
- Characterization and modeling of complex synthetic biology components, circuits, and pathways using TX-TL that enable forward engineering
- Development of new biochemical indicator components for use in TX-TL systems to achieve better understanding and more predictive models
- BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts (William Poole, Ayush Pandey, Zoltan Tuza, Andrey Shur, Richard M Murray, 2020 IWBDA)
- Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits (Ayush Pandey and Richard M. Murray, 2020 Winter q-bio)