CHE.496/2008/Schedule/Systems biology and synthetic biology

Systems biology and synthetic biology

• Discussion leader: George W.

• Systems biology as a foundation for genome-scale synthetic biology link
  • This article discusses the connection between systems biology and synthetic biology, specifically how modern advances in systems biology aid the development of the nascent field of synthetic biology
  • One current approach taken by systems biologists is to 'reconstruct' a system
    • This is done by first incorporating every relevant reaction into a stoichiometric matrix
    • From this, a set of parameters can be identified
    • By applying 'flux balance analysis' to this model, a concrete model that accurately predicts temporal evolution of the system can be achieved
    • Requires many parameters to be defined as well as a 'demand reaction' to drive the system, which is unknown in most cases outside of exponential growth
  • Much of the software developed for systems biology will be useful in the pursuit of computational analysis in synthetic biology
  • In order to deal with unknown parameters, synthetic biologists can use directed evolution to make a system conform to known parameters; in short, make the system imitate the model
  • New experimental techniques are always improving parameter estimation and system reconstruction, and these will clearly benefit both systems and synthetic biologists
  • Maybe we can use some of these techniques in our own work?
    • Developing our own 'reconstruction' seems unlikely to be feasible, although if we're working with a known system, we may be able to use others' results
    • The OptStrain strategy may be feasible if we do metabolic engineering, but I doubt we'll be doing a qualitatively new pathway, so this is likely unnecessary

• Modular approaches to expanding the functions of living matter link
• George Washington 15:48, 2 April 2008 (EDT)