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Synthetic Biology

Synthetic Biology. A New Opportunity for Multidisciplinary Undergraduate Research. Jeff Poet, Laurie Heyer, Todd Eckdahl, Malcolm Campbell. 2010 G C A T Synthetic Biology Workshop Davidson College. Davidson - Missouri Western iGEM Collaboration. Focus on undergraduate education

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Synthetic Biology

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  1. Synthetic Biology A New Opportunity for Multidisciplinary Undergraduate Research Jeff Poet, Laurie Heyer, Todd Eckdahl, Malcolm Campbell 2010 GCAT Synthetic Biology Workshop Davidson College

  2. Davidson - Missouri Western iGEM Collaboration • Focus on undergraduate education • Pooling human resources • Built on previous collaborations • BioMath connections • Common goals

  3. Our Prioritized Goals • Everyone learns • Have fun • Contribute to synthetic biology

  4. Missouri Western/Davidson Team 2006 iGEM Jamboree

  5. The Classic Pancake Problem 1975 by Harry Dweighter (“harried waiter”) Scenario Pancake chef at iHOP Spatula in one hand Plate with a stack of delicious pancakes of different sizes in other hand No place to set down the plate Problem The chef wishes to serve the pancakes arranged from smallest to largest How many flips are needed?

  6. A Simple Pancake Problem Find the fewest number of flips needed to obtain the arrangement 1,2,3,4. ?

  7. Pancake Problem Solution

  8. The Burnt Pancake Problem • Modification of the Classic Pancake Problem • Each pancake has one burnt side • Problem • Sort pancakes from smallest to largest, all burnt-side down • How many flips are needed?

  9. Burnt Pancake Problem ?

  10. Burnt Pancake Problem The bottom pancake is upside down so more flips are needed for the burnt pancake problem.

  11. Burnt Pancake Solution There could be a more efficient way…

  12. Burnt Pancake Solution

  13. Solving the Pancake Problem with a Bacterial Computer Missouri Western State University Marian Broderick, Adam Brown, Trevor Butner, Lane Heard, Eric Jessen, Kelly Malloy, Brad Ogden Faculty: Todd Eckdahl and Jeff Poet

  14. http://www.turbosquid.com Advantages of Bacterial Computation Software Hardware Computation Computation Computation

  15. Non-Polynomial (NP) Computational Complexity • No Efficient Algorithms # of Processors Cell Division

  16. Hin-Hix Recombination • Salmonella uses recombination to achieve antigenic variation • Target DNA contains promoter that drives either of 2 flagellar protein genes Image from: Nanassy OZ and Hughe K, 1998 Genetics 149: 1649-1663.

  17. RFP A Two Pancake Construct pBAD HixC HixC HixC Tet RBS RBS Pancake Pancake • Hin provided by separate plasmid • Starting configuration is Tet sensitive • Flipping results in 8 different configurations, • 1 is Tet resistant • at least 4 have RFP expression

  18. iGEM 2006 Outcomes • Over 50 parts contributed to Registry • Five awards at iGEM Jamboree, including Best Oral Presentation • “Computing with Living Hardware” in IET Synthetic Biology • “Engineering Bacteria to Solve the Burnt Pancake Problem” in Journal of Biological Engineering • awarded 2008 Outstanding paper • News stories, NPR Science Friday

  19. Our iGEM 2007 Team Hamiltonian Path Problem: Given a set of nodes and directed arcs between some pairs of nodes, is there some path starting at one vertex and ending at another that visits each node exactly once? Inside MIT Stata Center, November 2007

  20. The Adleman Graph:A Hamiltonian Path Problem

  21. Encoding an HPP in DNA

  22. How to Split a Gene Reporter Detectable Phenotype RBS Promoter ? Detectable Phenotype Repo- rter RBS hixC Promoter

  23. What Genes Can Be Split? GFP displaying hixC insertion point

  24. Gene Splitter Software http://gcat.davidson.edu/iGEM07/genesplitter.html Input Output Generates 4 Primers (optimized for Tm). 2. Biobrick ends are added to primers. 3. Frameshift is eliminated. 1. Gene Sequence (cut and paste) 2. Where do you want your hixC site? 3. Pick an extra base to avoid a frameshift.

  25. Gene-Splitter Software Note: Oligos are optimized for melting temperatures.

  26. Living Hardware to Solve the Hamiltonian Path Problem Students: Oyinade Adefuye, Will DeLoache, Jim Dickson, Andrew Martens, Amber Shoecraft, and Mike Waters, Jordan Baumgardner, Tom Crowley, Lane Heard, Nick Morton, Michelle Ritter, Jessica Treece, Matt Unzicker, Amanda Valencia Faculty: Malcolm Campbell, Todd Eckdahl, Karmella Haynes, Laurie Heyer, Jeff Poet

  27. iGEM 2007 Outcomes • Over 65 parts contributed to Registry • Gold medal award at iGEM Jamboree • JBE Manuscript published • Highly Accessed • Rated by Faculty 1000 Biology • NSF UBM grant funded

  28. 2008 iGEM Team

  29. Using E. coli to compute values of a cryptographic hash function Student Team Members - Alicia Allen, James Barron, Robert Cool, Kelly Davis, Will DeLoache, Erin Feeney, Andrew Gordon, John Igo, Aaron Lewis, Kristi Muscalino, Madeline Parra, Pallavi Penumetcha, Karlesha Roland, Max Win, Xiao Zhu Faculty Team Leaders - A. Malcolm Campbell, Todd Eckdahl, Laurie Heyer, Jeff Poet

  30. Cryptographic Hash Functions • Input of any length • Output of fixed length • International standard: MD5 • International call for new hash function HGTf34$2

  31. Encoding XOR logic in DNA High Osmolarity (Input A) 3OC6 (Input B)

  32. Biological Hash Function XOR XOR XOR 0 1 XOR 1 Requires Unidirectional Communication 0 1 1 0 1 1 hash

  33. iGEM 2008 Outcomes • 105 new parts contributed to Registry • Online tools developed • XOR logic gates built • Biological hash function designed • E. nigma device constructed • New designs being built for testing

  34. 2009 iGEM Team

  35. SATisfiability Problem

  36. Define the SATisfiability Problem

  37. Define the SATisfiability Problem

  38. Define the SATisfiability Problem

  39. Applications

  40. Converting Math to Biology

  41. Central Dogma

  42. Frameshift Mutation

  43. Frameshift Suppression

  44. Suppressor tRNA

  45. Coding 2-SAT Clause

  46. Coding 2-SAT Clause

  47. Coding 2-SAT Clause

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