Presentation Outline

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Western Presentation

  • Define our goals
    • Solve a mathematical problem using bacteria
    • Integrate math and biology students holistically
    • Work in tandem with two campuses to test parallel processing of PUIs for iGEM
    • Design a device that would be more than just a widget
    • Have a lot of fun learning
  • Introduction
    • Synthetic biology
      • tests our understanding of biological units and
      • allows us to design new devices using DNA.
    • Define burnt pancake problem
    • Schematic design of 1, 2, 3, and 4 pancake stacks
    • Mathematics behind solution and possible number of flips per n pancakes
    • Describe Biological equivalent problem

Bubble Topics - split as time demands

  • Methods
    • Hin (+/- LVA)and Hix and RE and Fis (list of basic parts)
    • How to assemble small DNA segments too big for oligos (Lance’s web site)
    • How to generate backwards biobrick parts with PCR (switch-a-roo)
    • Modeling the behavior of pancake flipping – deducing kinetics and size biases
    • Using modeling to choose which families of pancake stacks to build
    • Distinguishing 1,2 from -2,1 → add in promoterless RFP

Davidson Presentation

  • Data
    • Promoterless RBS+TF = tet resistant
    • Backwarks Tet + backwards RBS = tet resistant
    • Therefore, pSB1A2 and 3 have readthrough transcription in both directions
    • Design and build pSB1A4 (describe construction and demonstrate function)
    • Combine Hix with 1 pancake stacks (promoter-flavored and coding-flavored)
    • Uncontrolled flipping
    • Western blot of Hin….
    • Building 2 pancakes….
  • Consequences of Devices:
    • Data storage
    • Improved transgenic organisms (two states)
    • Proof-of-concept for bacterial computers
    • Next steps
  • Conclusions
    • Can solve problem but need control over kinetics
    • Math and Biology meshed really well – even uncovered a new proof
    • Multiple campuses can increase capacity through communication and cooperation. Size of school is not a limiting factor.
    • First in vivo controlled flipping of DNA??
    • We had a blast and learned heaps.
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