CHE.496/2008/Responses/a6

Practical applications

• Discussion leader: George Washington (Discussion guide)

Patrick Gildea's Response

• Molecular Switches for Cellular Sensors
  • The purpose of this article was to give a run-through of the research driving synthetic biology, i.e. metabolic pathways, apoptosis, molecular therapeutics, etc. However, the main focus was on designing sensors using nucleic acids to detect and identify other molecules in the cell. I think the outline of the lab’s protocol for designing and identifying the desired sensor was very edifying in understanding the “wet work” aspect because the majority of paper’s I have read don’t really delve deeply into describing procedures. I really thought the caffeine sensor was described very well with the methodologies of inserting different switches that respond to specific inputs. The most beneficial part of the paper is the thought process that goes toward designing and building a switch to be used in a cellular network. First start out with a sensor that detects whatever molecule that you want based on nucleic acids and engineer different domains on the molecule to respond visually (GFP). I think doing some work in building logic gates would be a beneficial project since more complex sensors will be needed for multiple inputs/outputs. I feel like reading this paper gave me a good sense of the kind of work we all will be doing over the summer.

• Advances in Synthetic Biology : Prototypes to Applications
  • The purpose of this article was to discuss how networks can be designed in synthetic systems (i.e. cascades) with the emphasis on multi-cellular networks. Furthermore, the article also discusses how these cellular networks are being applied toward applications for the “real world” (i.e. E. Coli producing artemisinin). The main benefit of the article is describing how the transcriptional cascade works where genes are arranged in series to regulate the expression of a downstream target. An issue in engineering synthetic circuits is altering the kinetics of individual elements until they are impedence-matched. Does this “kinetics of individual elements” have to do with codon bias or is this something else? Furthermore, I don’t quite understand how negative auto-regulation has to do with reducing gene expression noise. If we do decide on doing fundamental research in synthetic biology for our project, working on coordinating cell behaviors will be a good topic for us to delve into. However, I was wondering if we could work on something related to integrating more than one signaling systems instead of working with one signaling system like that described of the band-detect network that forms pictures or images based on a solid media. Two important notes were made in the topic of circuit engineering; to do with optimizing cellular systems where sensitivity analysis and directed evolution to fix problems in circuit design of whatever project idea we pursue.
• Patrick Gildea 11:53, 5 February 2008 (CST):

Kevin Hershey's Response

• Molecular Switches for Cellular Sensors
  • The purpose of the article was to present the project done by CalTech for their iGEM competition. It was written by Christina Smolke regarding the bio-sensing of caffeine. If caffeine was present, the sample glowed blue (a combination of YFP and GFP), if it was decaffinated, it glowed green, and if it was high caffeine (called 'espresso'), it glowed yellow. In doing this, they were able to create a threshold sensor, where high and low levels of caffeine had different outputs. They accomplished this using antiswitches of RNA aptamers which sensed the caffeine and gave them their desired output.

• Advances in Synthetic Biology : Prototypes to Applications
  • The purpose of this review by McDaniel and Weiss is to present a few of the mechanisms in synthetic biology. Weiss and McDaniel discuss bistaibility, oscillations, biosensing, drug synthesis, and spatial pattern formation. They go into further detail by discussing cascade systems, such as the MAPK system, where these cascades are able to create an '...ultrasensitive step-like dosage-response function.' They then discuss 'larger picture' engineering involving applications of synthetic systems and circuit engineering. They discuss Weiss's research of spatial recognition, where AHL is sent to receiver cells and binds to the LUXR. Depending on the concentration (i.e. a medium concentration), GFP production is induced. At low and high concentrations of AHL, no GFP is produces. This gives a "bullseye" shape. This technique is important as it combines both cell-cell signaling and threshold outputs similar to the caffeine output.
• KPHershey 14:09, 5 February 2008 (CST)