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G C A T , Genome Sequencing, & Synthetic Biology

G C A T , Genome Sequencing, & Synthetic Biology. Malcolm Campbell. University of Washington March 5, 2008. www.bio.davidson.edu/GCAT. Ben Kittinger ‘05. How Can Microarrays be Introduced?. Wet-lab microarray simulation kit - fast, cheap, works every time. How Can Students Practice?.

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G C A T , Genome Sequencing, & Synthetic Biology

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  1. GCAT, Genome Sequencing, & Synthetic Biology Malcolm Campbell University of Washington March 5, 2008

  2. www.bio.davidson.edu/GCAT

  3. Ben Kittinger ‘05 How Can Microarrays be Introduced? Wet-lab microarray simulation kit - fast, cheap, works every time.

  4. How Can Students Practice? www.bio.davidson.edu/projects/GCAT/Spot_synthesizer/Spot_synthesizer.html

  5. Open Source and Free Software www.bio.davidson.edu/MAGIC

  6. What Else Can Chips Do? Jackie Ryan ‘05

  7. Comparative Genome Hybridizations

  8. Genome Sequencing

  9. Sarah Elgin at Washington University Genome Education Partnership Students finish and annotate genome sequences Support staff online Free workshops in St. Louis Growing number of schools participating

  10. Tuajuanda Jordan at HHMI Phage Genome InitiativeScience Education Alliance Students isolate phage Students purify phage DNA; Sequenced at JGI Students annotate and compare geneomes National experiment to examine phage variation Free workshop and reagents

  11. Cheryl Kerfeld at Joint Genome Institute Undergraduate Genomics Research Initiative > 1000 prokaryote genomes sequenced Students annotate genome Data posted online Workshop for training of faculty Wide range of species

  12. Synthetic Biology

  13. What is Synthetic Biology?

  14. BioBrick Registry of Standard Parts http://parts.mit.edu/registry/index.php/Main_Page

  15. What is iGEM? Peking University Imperial College

  16. Davidson College Malcolm Campbell (bio.) Laurie Heyer (math) Lance Harden Sabriya Rosemond (HU) Samantha Simpson Erin Zwack SYNTHETIC BIOLOGY iGEM 2006 Missouri Western State U. Todd Eckdahl (bio.) Jeff Poet (math) Marian Broderick Adam Brown Trevor Butner Lane Heard (HS student) Eric Jessen Kelley Malloy Brad Ogden

  17. Enter: Flapjack & The Hotcakes Erin Zwack (Jr. Bio); Lance Harden (Soph. Math); Sabriya Rosemond (Jr. Bio)

  18. Enter: Flapjack & The Hotcakes Erin Zwack (Jr. Bio); Lance Harden (Soph. Math); Sabriya Rosemond (Jr. Bio)

  19. Wooly Mammoths of Missouri Western

  20. Burnt Pancake Problem 1 2 3 4

  21. Burnt Pancake Problem

  22. Burnt Pancake Problem

  23. Look familiar?

  24. Flipping DNA with Hin/hixC

  25. Flipping DNA with Hin/hixC

  26. Flipping DNA with Hin/hixC

  27. How to Make Flippable DNA Pancakes Tet RBS hixC pBad hixC hixC pancake 1 pancake 2 T T Hin LVA RBS pLac All on 1 Plasmid: Two pancakes (Amp vector) + Hin

  28. Hin Flips DNA of Different Sizes

  29. Hin Flips Individual Segments -2 1

  30. No Equilibrium 11 hrs Post-transformation

  31. Hin Flips Paired Segments mRFP off 1 -2 double-pancake flip mRFP on 2 -1 u.v. white light

  32. Modeling to Understand Flipping ( 1, 2) (-2, -1) (-2,-1) (-2,1) ( 1, -2) (-1, 2) (-2, 1) ( 2, -1) (1,2) (-1,2) (1,-2) (-1,-2) (-1, -2) ( 2, 1) (2,-1) (2,1)

  33. Modeling to Understand Flipping ( 1, 2) (-2, -1) (-2,-1) (-2,1) ( 1, -2) (-1, 2) (-2, 1) ( 2, -1) (1,2) (-1,2) (1,-2) (-1,-2) (-1, -2) ( 2, 1) (2,-1) (2,1) 1 flip: 0% solved

  34. Modeling to Understand Flipping ( 1, 2) (-2, -1) (-2,-1) (-2,1) ( 1, -2) (-1, 2) (-2, 1) ( 2, -1) (1,2) (-1,2) (1,-2) (-1,-2) (-1, -2) ( 2, 1) (2,-1) (2,1) 2 flips: 2/9 (22.2%) solved

  35. gene regulator Consequences of DNA Flipping Devices -1,2 -2,-1 in 2 flips! PRACTICAL Proof-of-concept for bacterial computers Data storage n units gives 2n(n!) combinations BASIC BIOLOGY RESEARCH Improved transgenes in vivo Evolutionary insights

  36. Success at iGEM 2006

  37. Living Hardware to Solve the Hamiltonian Path Problem, 2007 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

  38. The Hamiltonian Path Problem 1 4 3 2 5

  39. The Hamiltonian Path Problem 1 4 3 2 5

  40. Advantages of Bacterial Computation Software Hardware Computation Computation Computation

  41. Advantages of Bacterial Computation Software Hardware Computation $ Computation ¢ Computation

  42. Advantages of Bacterial Computation • Non-Polynomial (NP) • No Efficient Algorithms # of Processors Cell Division

  43. 1 4 3 2 5 Using Hin/hixC to Solve the HPP Using Hin/hixC to Solve the HPP 1 3 4 5 4 3 3 2 1 4 2 4 3 5 4 1

  44. 1 4 3 2 5 Using Hin/hixC to Solve the HPP Using Hin/hixC to Solve the HPP 1 3 4 5 4 3 3 2 1 4 2 4 3 5 4 1 hixC Sites

  45. 1 4 3 2 5 Using Hin/hixC to Solve the HPP Using Hin/hixC to Solve the HPP

  46. Using Hin/hixC to Solve the HPP 1 Using Hin/hixC to Solve the HPP 4 3 2 5

  47. Using Hin/hixC to Solve the HPP 1 Using Hin/hixC to Solve the HPP 4 3 2 5

  48. Using Hin/hixC to Solve the HPP 1 4 3 2 5 Solved Hamiltonian Path

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

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