1. Synthetic Biology: A New Engineering Discipline? Summer@Brown 2011

2. Announcements MONDAY: Holiday! TUESDAY: Boston Science Museum – Meet at 8:30 am at Thayer and Charlesfield WEDNESDAY: – Wear closed gym clothes/toe shoes to class! THURSDAY: Class time will be from 1 – 4 pm. FRIDAY: Class time will be from 9 – 12 pm.

3. Overview What is synthetic biology? Where are the applications? Lab 1: Strawberries & DNA How to create a synthetic organism? Lab 2: Restriction enzyme mapping Undergraduate Design Competitions

4. What is synthetic biology? A Living Factory!

5. Design Hierarchies

6. What is Synthetic Biology? The design and construction of new biological parts, devices and systems AND The re-design of existing, natural biological systems for a useful purpose Schubert, C. Nature, 2006(441), 277-279

8. Review: Molecular Biology

9. DNA Biopolymer, a long chain of small units (A,C,T,G) Double-stranded Complementary strands

10. Central Dogma of Biology DNA RNA Protein Replication Transcription Translation

11. Gene Transcription A gene is a region of DNA, corresponding to a unit of inheritance. DNA Protein Many genes produce proteins. RNA Ribosome Binding Site Gene Y Promoter Ribosome Binding Site Gene Y Y Y Transcription Translation

12. Gene Transcription Some genes have the ability to regulate other genes. When placed in the same organism, these genes interact with one another to form a gene network. Gene YGene XGene Z Note that, as pictured, this network has a feedback loop

13. Activation Gene Transcription When one gene or factor induces creation of more of another gene, denoted with an arrow (  ) connecting the two Gene YGene X Gene X is transcribed Repression When one gene or factor prohibits creation of another gene, denoted with a perpendicular symbol (--|) connecting the two Gene YGene X Gene X is not transcribed

14. Genome Network Project, Nature Genetics, 2009

15. Engineering with Synthetic Biology

16. Rational Design Develop initial scheme for a gene network Test smaller circuits in the network Create mathematical model to understand theoretical behavior

17. Rational Design If indicated, modify theory based upon experimental results Construct and test larger network As with other engineering disciplines, this process requires standardization, modularity, and modeling Tweak as needed/desired

18. Standardization US Standard Screw Thread “In this country, no organized attempt has as yet been made to establish any system, each manufacturer having adopted whatever his judgment may have dictated as best, or as most convenient for himself” – William Sellers, Franklin Institute, April 21, 1864

19. Standard Parts Registry http://partsregistry.org/Main_Page

24. Modularity Enabled by standardization Swap interchangeable parts or units in a particular category to achieve new function Groups of parts define a unique functional unit New unit, new function

25. Modularity Analogy: Upgrading the processor on your computer - All other parts of the computer remain the same, but the computer functions differently. Example: Modular promoters Gene Y Higher output of Y Lower output of Y Promoter 1 Promoter 2

26. Mathematical Modeling D Y Z β δ ρ ϒ degradation Β= rate of mRNA transcription γY= rate of mRNA degradation δ= rate of protein translation ρZ= rate of protein degradation

27. Modeling Transcription Same thing for translation…..

28. Where are the applications? Pharmaceuticals and new vaccines (shorten flu vaccine process by 99%) Biofuels Terraforming Research, NASA

29. According to the World Health Organization, each year nearly 500 million people become infected with malaria, and nearly three million — mostly children — die from it. Example 1: Anti-malaria Drug

30. Artemisinin Drug produced from plant (14 month cycle): $2.40/dose Drug produced from microbe (14 days): $0.25/dose Savings: $2.15/dose X 500 million doses = $1 Billion

32. What’s next? Will technology follow through on promise? Contract with Sanofi-Aventis to begin distribution of arteminisin therapeutic in 2012

33. Living Factories

34. Example 2: Biofuels Farnesene – BioFene

35. Biofuels $600 million deal – Exxon and J. Craig Venter Institute – Synthetic algae to output biofuel Pitfall: – Require massive amount of plant material – Land space?

36. Craig Venter One of the first to sequence human genome – 3 billion base pairs of DNA Created the first synthetic cell (2010) Founder of the J. Craig Venter Institute

37. Example 3: Terraforming

38. Where synthetic biology can help in space…? Green aviation and biofuels Develop new technologies to provide: – Food – Medicine – Life support

39. The Past: We took familiar biological organisms into space, and engineered environments to suit them. The Future: We will engineer biological systems to make them suited to extraterrestrial environments, and employ these systems in new kinds of missions.

40. Job Opportunities

41. Lab 1: Strawberries & DNA

42. All you wanted to know about….Strawberries Fruit of the Fragaria – genus of flowering plants from rose family An “octoploid” = 8 complete sets of chromosome in a single cell Contains fiestin – an antioxidant linked to prevention of Alzheimer’s Genome sequenced (2011): 240 million bp of DNA

43. How to create a synthetic organism?

44. Tools of the trade: Plasmids Antibiotic Selection Marker -used to select bacteria containing gene of interest Promoter -enables controlled expression of gene Gene -encodes protein of interest Multiple Cloning Sites -allows other genes to be introduced into the plasmid Units of DNA for controlled transfer of genes between organisms

45. Bacteria expressing green fluorescent protein from jelly fish

46. DNA Scissors: Restriction Enzymes GENE EcoRI XbaI SpeI PstI Vector

47. GENE A EcoRI XbaI SpeI PstI GENE B EcoRI XbaI SpeI PstI Mixed SpeI/XbalI Site XbaISpeI GENE A SpeI PstI GENE B EcoRI XbaISpeI/Xbal

48. GENE A SpeI PstI GENE B EcoRI XbaISpeI/X bal

49. Visualizing DNA: Agarose Gel 969 bp 3.0 kbp 1.0 254 bp 2.0 1.5

50. Lab 2: Restriction enzyme mapping on DNA plasmid

51. http://ung.igem.org/Main_Page International Genetically Engineered Machine competition (for undergraduates) Given a kit of biological parts Goal: design and build new biological systems and operate them in living cells

52. Examples of Ideas BactoBlood, UC Berkeley, 2007 – Develop cost-effective RBC substitute to safely transport O 2 in the bloodstream without inducing sepsis E. Chromi, Cambridge, 2009 – Engineer bacteria to produce different pigments in response to different concentrations of inducer

53. Participation Statisitics

54. Where is iGEM?

55. http://biomod.net International Bio-molecular Design Competition Focus areas: biomolecular robotics, biomolecular logic and computing and structural bionanotechnology

56. DNA Origami Link DNA structures bend with radius of 6 nm Nano-car? Nanoantennae? Nanoscale circuits for drug delivery vehicles?