1. Back to the Basics Purdue iGEM 2013

2. The Biomakers

3. Back to the Basics What Do We Mean? Complex Projects Lack of Fundamental Control

4. The Taguchi Method Cheaper, Faster Characterization

5. Explanation of Problem Increase Robustness of Genetic Circuits Assess with Factorial Experiment

6. The Taguchi Method Sources: (2013). IGCSE and GCSE Industry. Retrieved from http://greenfieldgeography.wikispaces.com/IGCSE+and+GCSE+Industry Venil, C. K., & Lakshmanapermalsamy, P. (2009). Taguchi Experiment Design.... Journal of Science & Technology Used in Industry – Maintain quality Our Project – Apply Taguchi to synthetic biology

7. Comparison of Methods Partial-Factorial Method Fewer Combinations Taguchi Method All Possible Combinations Often Not Feasible Full Factorial

8. Experimental Design Parameters Orthogonal Arrays Response Variable: GFP Venil, C. K., & Lakshmanapermalsamy, P. (2009). Taguchi experimental design for medium optimization…. Journal of Science & Technology

9. Intended Data Analysis Determining GFP Expressed Per Cell – Growth curve – Coulter counter JMP Statistical Analysis Actual DataHypothetical Data

10. Challenges Transformations – Competent cells – Altered growing conditions 3A Assembly – Not feasible

11. Future Work Complete Assembly Measure GFP per Cell for All Combinations Compare Results of Taguchi vs. Full Factorial

12. Bicistronic Design Increasing Reliability of Expression

13. Explanation of Problem Variation in Protein Expression Increase Reliability of Genetic Constructs

14. BCD Background Bicistronic Design Sources:Mutalik, V., Endy, D., Guimaraes, J., Cambray, G., Lam, C., Juul, M., Tran, A., & Paull, M. (2013). Precise and reliable gene expression via standard transcription and translation initiation elements. Nature, 10(4)

15. Monocistronic Design

16. Bicistronic Design

17. Supporting Data Protein Expression Variability Decreased Increase Protein Expression Reliability

18. Monocistronic DesignBicistronic Design Sources:Mutalik, V., Endy, D., Guimaraes, J., Cambray, G., Lam, C., Juul, M., Tran, A., & Paull, M. (2013). Precise and reliable gene expression via standard transcription and translation initiation elements. Nature, 10(4)

19. Design BCD Parts Designed Golden Gate Assembly

20. Design

21. Methods Synthesized Constructs Placed Ptrc* into pSB1C3 Growth Rate Assay Re-Assembled Constructs into pSB1C3 Proof of Function

22. Data Promoter Submitted to the Registry Growth Rate Assay Fluorescence Intensity

23. Conclusion Promoter Submitted to Registry Implementation Increase Reliability

24. Future Work Compare Biobrick BCDs to Original BCDs Submit BCDs to iGEM HQ

25. Standardized Datasheets Revolutionizing Characterization

26. Explanation of Problem Lack of Characterization

28. Explanation of Problem Lack of Characterization Vague Requirements Difficult to Judge

29. Background Research Standardized Protocol Researched Past Protocols Found Emails, Sent Survey Survey Results Changed Direction

30. First Draft Prior Art – Drew Endy

32. First Draft Prior Art – Drew Endy – Boston iGEM

34. First Draft Prior Art – Drew Endy – Boston iGEM First Draft – Design

36. Feedback Prior Art – Drew Endy – Boston iGEM First Draft – Design – Implementation

38. Feedback Prior Art – Drew Endy – Boston iGEM First Draft – Design – Implementation Second Survey and Video Conferences Ideas Generated

39. Final Design and Feedback BostonU iGEM Visit Final Draft

41. Final Design and Feedback BostonU iGEM Visit Final Draft Third Survey and Feedback

42. Conclusion and Future Work Implementation Continue Collaboration Bba_K1225000

43. Human Practices

44. Intro and Overview Outreach to Producers Outreach to High School Girl Scouts Workshop Biomaker Bench

45. High School Outreach Teaching modeling to AP Biology Teachers – Educating next generation of Synthetic Biologists

46. Girl Scout Outreach Generate interest in STEM Workshop Curriculum – Lecture – Experiment – Scientific method

47. Biomaker Bench Creating a Community Lab in Noblesville, IN – Business plan – Nonprofit organization

48. Conclusion

49. Accomplishments Statistical analysis method to fit synthetic biology Updated Drew Endy's Bicistronic Design Constructs Designed a Datasheet Standard for the Registry Submitted a New Promoter and 4 BCD Constructs Collaborated with over 75 iGEM Teams Performed Outreach to Local Farmers and Producers Taught High School Teachers About Modeling Worked with the Girls Scouts of America Community Lab Space in Noblesville, Indiana

50. Attributions and Acknowledgements Advisers:Purdue University: Dr. Jenna Rickus Dr. Fernandez Dr. Kari Clase Dr. Dilkes Soo Ha Dr. Akridge Janie Brennan Jen Kahn Bindley Bioscience Center:Research Support: Rajitarun Madangopal Boston University iGEM Dr. Larisa Avramova Drew Endy and the Endy Lab Dr. Lake Paul Dr. Tony Pedley

52. Sponsors

53. Questions?