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

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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

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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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Things to keep in mind...

1. We should have each team work as separate units to facilitate team spirit and ability to practice. However, we will share slides for continuity of presentations.
2. We will probably have to let go of who did what in order to have two smooth presentations. We can have a color-coded schematic slide early on that shows where different parts were built but this does not affect who presents what. In fact, this chart will help people see how well the two schools worked in parallel.
3. We need to have talks ready and two posters.

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Here is my suggestion for an outline of the presentations...

• INTRODUCTION (MO Western)
  • 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
  • What is Synthetic Biology? Synthetic biology tests our understanding of biological units and allows us to design new devices using DNA.
  • Define the math problem: burnt pancake problem
  • Schematic design of 1, 2, 3 and 4 pancake stacks
  • Mathematics behind solution and possible number of flips per n pancakes
  • Computing with E. coli - detecting orientation of DNA pancakes using the antibiotic resistance screen (two-pancake system, animation by Karmella)
  • Biological equivalence problem - will be solved using backwards RFP (described later)
  • The Hin invertase system in E. coli – key parts, their origins, functions, etc.
  • Turning the Hin invertase system into a BioBricks system
    • how we assembled small DNA segments too big for oligos (Lance’s web site)
    • how we generated backwards biobrick parts with PCR (switch-a-roo)
  • List of Basic Parts – Hin (+/- LVA), Hix, RE, etc.; end with this; highlight who did what. Davidson will start with this list in talk #2.
  • Summary

• METHODS & DATA (Davidson)
  • Modeling the behavior of pancake flipping – deducing kinetics and size biases
  • Using modeling to choose which families of unsolved pancake stacks to start with
  • Illustration of assembled pancakes (without RFP)
  • Distinguishing 1,2 from -2,-1 using RFP-RBS, updated panckaes
  • Flipping DNA - animation (Karmella) of pLac-Hin control by LacI/ IPTG, DNA flipping, and pBad control by AraC/ arabinose
  • Insulating the device from read-through transcription – describe evidence for read-through, design of pSB1A4, pSB1A4 works
  • Hin expression – Western blot
  • Uncontrolled flipping with one-pancake constructs – MO Western and Davidson data

• CONCLUSIONS
  • Consequences of devices
    • Data storage
    • Possible application for rearranging transgenes in vivo
    • Proof-of-concept for bacterial computers
    • Next steps
  • 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.