CHE.496/2008/Responses/a13

CHE.496: Biological Systems Design Seminar

Home People Schedule Assignments Responses Projects Links Help

Systems biology and synthetic biology

Systems biology as a foundation for genome-scale synthetic biology
- The article by Barrett et al. describes the transition from systems biology to synthetic biology. It describes some of the advances in mathematical understanding of biology, in silico analysis, and how synthetic biology can use these tools. It goes on to discuss software applications to synthetic biology, and how they can be used. It finishes by discussing system biology’s importance in successfully using natural evolution. Natural evolution, combined with synthetic biology’s ability to produce constructs based on mathematical understanding, can be a very powerful tool.
Modular approaches to expanding the functions of living matter
- The review by Chin provides even further analysis of Ellowitz’s repressilator and Weiss’s ‘bullseye’ cell configuration discussed earlier in the course. The article then goes on to discuss Smolke’s system to create the caffeine sensing bacteria discussed earlier in the course. However, a new aspect of synthetic biology is described by Chin’s and Rackham’s manipulation of the ribosome itself. This is novel, because many of the mechanisms studied in this class dealt with the post-transcriptional RNA, rather than the actual machinery. The modified ribosomes allow for new functions.
KPHershey 12:05, 1 April 2008 (EDT)

Systems biology as a foundation for genome-scale synthetic biology
- The purpose of this article is to make connections between the fields of systems biology and synthetic biology, especially with respect to genome engineering. Figure 1 in the article sums up the relationships between systems biology and synthetic biology. An important point that is made in the paper is the use of computer modeling of cellular systems – especially metabolic pathways. This is a very useful tool but requires knowledge of the kinetics and fluxes in a metabolic system, which can be hard to characterize. But this can be done via analysis of molecular components in the various cellular systems. This paper is beneficial in the metabolic engineering aspect by discussing the different aspects of modeling and how that modeling can be brought along by systems biology.
Modular approaches to expanding the functions of living matter