Presentation Outline

From 2006.igem.org

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.