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CHE.496: Biological Systems Design Seminar

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Practical applications

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)

George McArthur's Response

  • Molecular Switches for Cellular Sensors
    • This article presents more synthetic biology background, but especially focuses on the interface between input and processing that could be used in cellular systems. The classic example described here is Caltech's caffeine sensing bacteria. Essentially, these bacteria have been equipped with sensors such that they can determine whether or not they have reached a certain caffeine concentration threshold. Although this project is merely a concept toy, it presents a valuable approach to building cellular sensors and processors in order to perform difficult tasks.
  • Advances in Synthetic Biology : Prototypes to Applications
  • In this article more sophisticated synthetic biology projects are discussed. There is a general push for more "hard" research, moving away from toy projects to real-world applications, especially in the areas of health, environment and energy.

GMcArthurIV 15:01, 5 February 2008 (CST)

Dan Tarjan's Response

  • Molecular Switches for Cellular Sensors
    • This article recaps some achievements with regards to genetic circuits and applications thereof. It mentions the ability of gene circuits to have behaviors approximating digital logic and being able to be insensitive to fluxuations in input. It goes over the repressilator circuit. The article then discusses multi-cellular systems. The sender-receiver method is mentioned as coming from V. fischeri's quorum sensing mechanism. It then goes over some results already mentioned in previous articles. The applications section also doesn't really introduce any new projects. It is pointed out the development is ongoing, for example in designing new ligand-based sensor systems, and so on. The small number of applications mentioned shows how difficult it still is to achieve good, applied, results.
  • Advances in Synthetic Biology : Prototypes to Applications
    • This article describes one lab's efforts at creating different types of switches. They have ligand activated ones, temperature sensitive ones, etc. They talk about the possibilities of what can be done with aptamers that can be adapted to detect different things/conditions. Also the process by which these nucleic acid-based sensors actually cause a regulatory event is described. Biosensors/sensors on a chip using aptamers are mentioned as a near-term application of these techniques.
  • Daniel R Tarjan 16:51, 5 February 2008 (CST):

Eyad's Repsonse

Molecular Switches -- This i thought was the better of the two articles it gave a brief synopsis of synthetic bio today but then talked about the breakthroughs they have had with cells due to the discovery of RNA and DNA not only being genetic storage units but also being repressors and sensors. It's quite amazing how well the switches worked on the caffeine and then to create logic gates like And gates meaning complex circuits are just around the corner.

Advances in Synthetic Biology -- This article was more dense and about more complex signal processing in cells using things like cascades with or without feed back to deal with noise and to make worthwhile circuits to process signals.

Eyad Lababidi 15:37, 5 February 2008 (CST)