2007 Synthetic Biology Team Challenge

1. 2007 Synthetic Biology Team Challenge March 19-23, 26 Instructors: Howard Salis, Jeff Tabor

2. Course Information • Monday – Friday: 9AM-5PM • Final Presentations: Monday 3/26 1:30-3PM GH 114 • Course wiki: http://openwetware.org/wiki/Jeff_Tabor/UCSF_Synthetic_Biology_Team_Challenge

3. Schedule • Monday • Intro to Synthetic Biology • Lab: Registry of Standard Biological Parts • Tuesday • Survey of useful parts • Journal Club • Lab: Engineer novel genetic logic • Wednesday • Modeling gene networks in MATLAB (H. Salis) • Homework: Brainstorm synthetic system • Thursday • Develop plan for system • Optimize system with model • Friday • Specify system with appropriate parts from literature • Document parts and systems in the registry • Simulations of final systems • Monday (1:30-3:00) • ~15 min Final presentations. • 5 Faculty judges decide winner • Winning group’s design is synthesized.

4. Outline - Monday • Brief History of Molecular Biology • Dawn of Synthetic Biology • Concepts driving early designs • Building genomes from scratch • Landmark efforts in system design • System talks • Liz Clarke • Dan Widmaier • Matt Eames • Abstracting/formalizing the design process • Lunch • Afternoon Lab. MIT’s registry of Standard Biological Parts.

6. Chronology of Molecular Biology • 1953. Structure of DNA. Watson and Crick • 1961. Concept of mRNA, Regulator/operator pairs, Operons. Jacob and Monod. -(Gene networks of any desired property can be assembled from combinations of simple regulatory elements) • 1961+. Discovery of codons and the genetic code • 1973. Recombinant DNA technology (Cohen and Boyer, UCSF) • 1977. DNA Sequencing Technology. • 1983. Invention of PCR. "Beginning with a single molecule of the genetic material DNA, the PCR can generate 100 billion similar molecules in an afternoon.“ –K. Mullis • 1987. First Automated Sequencer (Applied Biosystems Prism 373) • 1997. Sequence of E.coli genome published (Blattner, UW) • 2001. Sequence of human genome published (HGP/Celera) • 2002. CSI:Miami debuts on CBS

7. Synthetic Biology Nature403, January 2000

8. Cells are composed of complex networks Adapted From: Lee et al., Science, 2004

9. Complex networks are composed of simpler modules

10. Modules can be reconfigured into synthetic networks Elowitz and Leibler. Nature, 2000

11. Simulating a synthetic gene network Continuous Model Discreet Model Elowitz and Leibler. Nature, 2000

12. Genetic Toggle Switch Gardner et al. Nature, 2000

13. -DNA synthesis capacity has doubled each 1.5 years over the past 10 years -System design and fabrication can routinely be decoupled (Endy, Nature 2005) Carlson, Pace & Proliferation of Biological Technologies, Biosec. & Bioterror.1(3):1 (2003) c/o Drew Endy

14. Building genomes from scratch • 2002. Assembly of functional poliovirus genome (~7.5kb; Cello et al., Science 2002). • Oligos designed computationally, ordered commercially • [C332652 H492388 N98245 O131196 P7501 S2340] • 2003. Assembly of a bacteriophage genome (~5kb; Smith et al., PNAS 2003). • 2 weeks assembly time • 2005. Assembly of the 1918 flu virus (~13kb). (Tumpey et al., Science 2005). • Craig Venter’s Mycoplasma genitalium genome = 580kb

15. Rewriting genomes (Chan et al., Molecular Systems Biology, 2005)

16. wt refactored

17. Genetic pulse generator Sender E.coli Receiver E.coli http://www.pnas.org/content/vol0/issue2004/images/data/0307571101/DC1/07571Movie1.mov Basu et al., PNAS 2005

18. Genetic pattern formation circuit Basu et al., Nature 2005

19. 2004 UT-Austin/UCSF Bugwarz Team Not pictured: Andy Ellington, Chris Voigt

20. Agar plate High-resolution spatial control of gene expression Projector Agar plate

21. Engineering light-dependent gene expression in E. coli

22. Bacterial photography Mask Bacterial lawn Wild-type EnvZ

23. Mercury vapor lamp 632nm bandpass filter Concave grating spectrometer 35 mm slide Actuator Double Guass focusing lens Projected image 37 degree incubator “Light Cannon”

24. Improved black and white photography Endyrichia coli Escherichia ellington

25. ‘Biofilm’ capable of continuous expression response Levskaya et al., Nature, 2005

26. Continuous response allows capture of high information images

27. Projector Bacterial edge detector Agar plate

28. Genetic logic for edge detection Only occurs at edge of light/dark

29. Gates mismatched: LOW output from gate 1 interpreted as HIGH input at gate 2 Light repression is incomplete

30. Matching gates through RBS redesign

31. Contributed Talks • 10:00-10:30: L. Clarke ‘A Bacterial Thermometer’ • 10:30-11:00: D. Widmaier ‘Secreting Spider Silk in Salmonella’ • 11:00-11:30: M. Eames ‘Remote Controlled Bacteria’

32. Genetic “Parts” for programming living cells Voigt, Curr. Opin Biotechnol., 2006

33. Genetic “devices” integrate signal inputs Voigt, Curr. Opin Biotechnol., 2006

34. Device outputs control “actuators” which determine cellular behaviors Voigt, Curr. Opin Biotechnol., 2006

35. Making Biology a reliable engineering discipline • Standardization • Composability • Characterization • ‘off the shelf’ functionality • Centralization • Well documented repositories • Abstraction • Distribution of expertise/labor

36. Device characterization

37. http://parts.mit.edu/registry/index.php/Part:BBa_F2620

38. Abstraction hierarchy for the engineering of biology Endy, Nature 2005

40. Lunch • GH 114 sai