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Varied State Expressions

Explore creative alternatives to traditional gene expression detection methods in bacteria, such as creating responses to specific states or compounds to trigger unique behaviors. Discover potential applications in toxin cleanup, disease recognition, and resource-efficient detection solutions. Experiment with different outputs and responses for diverse functionalities.

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Varied State Expressions

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  1. Varied State Expressions Allen Lin Caltech iGEM 2008 Brainstorming

  2. Why? • Currently standard to detect the expression of a gene: attach GPF in DNA so that it becomes transcribed and translated as part of a protein. • Can we be more creative? • What other types of expressions might bacteria be able to produce?

  3. Why II? • Can we make the bacteria do something interesting when it’s in a particular state? • For example, make the bacteria have different phenotypes when • It’s in different stages of mitosis ([cyclin]) • Particular operons are active ([free repressor]) • Certain enzyme pathways are activated

  4. Actually… • These two goals are the same

  5. For example….going off topic • What about have the bacteria make something when its in a particular state • Say, when a bacteria detects lactose, produces another compound • And have the bacteria sensitive to the second compound • … And migrate to the location to the first compound

  6. Compound Detector and Remover • Bacteria start out in one location • Through random walk, spread across • When a bacterium detects a particular compound A, turns red and produces a compound B not normally produced by bacteria • Other bacteria in the region have heightened sensitivity to compound B in chemotaxis; when they detect it, turn green. And they migrate to the location of the initial bacteria. When they reach compound A, turn red + green, produce compound B, and digest compound A • Exponential effect, until compound A is completely digested. Then the bacteria are no longer red, and disperse through random walk.

  7. No CheZ -> Stationary Cells Guiding Bacteria with Small Molecules and RNATopp, S. and Gallivan, J.P.J. Am. Chem. Soc., 129, 21, 6807 - 6811, 2007,  10.1021/ja0692480

  8. Use a RNA switch!

  9. Theophylline presence -> mobility

  10. Proof of concept

  11. Problems • Bacteria are completely non-motile when compound theophylline not present • Is there a system in which chemotaxis is turned on by the presence of a compound, and not mobility is turned off by the lack of a compound? • Need a high concentration of output compound for it to diffuse and attract other bacteria

  12. Having gone off-topic… • Instead of producing GFP when lac operon is transcribed, produce another compound that the bacteria secretes different phenotype • When bacteria sense this second compound, redirect normal chemotaxis scheme • Inputs -> different types of outputs

  13. Uses • So this might be: • An efficient toxin clean up system • An infectious disease recognizer and fighter system • Anything in which don’t need a lot of resources to detect, but need a lot of resources to eliminate

  14. Input -> Library of responses • Then that would be okay • And highly useful • Here, we have • Produce signaling compound • Produce change in mobility • What else can we do? • Produce different phenotype (ex. shiny) • Interrupt mitosis cycle • And more

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