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Carving :

Carving :. Nili Sommovilla Lim Lab June 11th, 2007. An Introduction. In the beginning, there was…. One Group One School One Project One Month!. (?). IAP 2003. iGEM2006. IAP 2004. SBC 2004. iGEM2005. a few rounds of earnest replication…. CSHL Davidson-Missouri Duke Dundee

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Carving :

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  1. Carving: Nili Sommovilla Lim Lab June 11th, 2007 An Introduction

  2. In the beginning, there was… One Group One School One Project One Month!

  3. (?) IAP 2003 iGEM2006 IAP 2004 SBC 2004 iGEM2005 a few rounds of earnest replication…

  4. CSHL Davidson-Missouri Duke Dundee Edinburgh ETHZ Freiburg Glasgow Harvard Imperial Lethbridge Ljubljana McGill Melbourne St. Petersburg Southern Utah Taipei Tianjin Tokyo Tech Toronto Tsinghua Turkey *UCSF* USTC Valencia Virginia Virginia Tech Waterloo Wisconsin Alberta Bangalore Bay Area RSI Berkeley LBL Berkeley UC Bologna Boston University Brown Calgary Caltech Cambridge Cape Peninsula Chiba Colombia-Israel Mexico Michigan Minnesota Mississippi State Missouri Miners MIT Naples Paris Peking Penn State Prairie View Princeton Purdue Rice this year’s count… 57 cells!

  5. what makes an iGEM an iGEM? • Emphasis on Growth, Development, Accumulation • A Challenge of Innovation and Creativity • A Unifying Objective, with Flexibility in Practice (sort of) • Collaboration as the Key

  6. the challenge • Identify a novel system, device or function using basic, biological parts. • Develop new parts • Use old parts • To explore and work towards new outcomes, utilizing the current breadth of resources in synthetic biology • Goals of iGEM should be consistent with the goals of synthetic biology

  7. Or, in other words… “Make cells do cool things!” “I just got back from a lab grown culture, and, boy, are they homogeneous!”

  8. “making cells do cool things” • Silly slogan, or informative statement ? • What use can we make of it?

  9. making life (not really) • Synthetic Biology (and iGEM) focuses on the manipulation and construction of biological systems; not a simple biological inquiry • The idea of iGEM is to focus on creating or making something new • Not only a molecular exploration, but a molecular excavation… • Identifying and examininggenes, proteins and pathways • Applying this towards new or useful functions • Using a standardized methodology

  10. selling cells • Cells are machines that have been tested and refined for millions of years through evolution • Cells are efficient • Cells are specialized • What different ‘specialists’ can you think of? • Cells can replicate themselves! Can any computer can say that much?

  11. the eye of the beholder… • ‘Cool’ and ‘Thing’: two remarkably vague words! • What is a cool thing? • Anything, really • Coolness comes from what is important to you • Who decides what is cool? • YOU ( and the iGEM judges…) • What this means: • We are limited only by our imaginations • We are implicitly guided by our own interests and self-made priorities

  12. How? • For most teams, the first step is identifying an objective, or general project idea • Us: techniques/general experiments first • Build a ‘System’ from ‘Devices,’ ‘Devices’ from ‘Parts’ • Teams work out how, theoretically, they might construct the system • Get physical components from different sources: • New parts • Old Parts (iGEM registry) • Constructs from previous lab work (not yet iGEM related) • Use modeling to analyze the system and its functionality • Lab work!

  13. an example: edinburgh team • Project goal: to develop a bacterial biosensor to detect arsenic in drinking water • Used mathematical modeling to refine and analyze biological output • Developed their circuit with: • 4 parts from the registry • 5 new parts made by the team

  14. Activator molecule A1 Activator gene Lac regulator Lactose Urease gene |A| |R| Repressor molecule R1 Ammonia Arsenic (5ppb) LacZ gene Repressor gene R1 Ars regulator 1 Urease enzyme LacZ enzyme Lactic Acid Arsenic (20ppb) Ars regulator 2 Arsenic sensor system diagram 8.5 pH: 7.0 6.0 4.5 A1 binding site Promoter (NH2)2CO + H2O = CO2 + 2NH3 R1 binding site

  15. System Level Map

  16. Device Level Map

  17. Part Level Map

  18. gimme structure! iGEM Resources www.igem2007.com iGEM wiki site iGEM 2006 website and past projects iGEM Registry of Parts iGEM parts package UCSF Resources People Topics of study in the Lab Our Ideas & collaborative power

  19. iGEM wiki and www.igem2007.com provide central location for accessing all iGEM materials

  20. www.igem2006.com • Contains presentations (video and slides) from all teams competing last year

  21. The Registry: (free) marketplace for parts

  22. Our wiki is in your hands… • Record Progress • Use as a community resource • Inform other teams of your work • Be creative!

  23. Who we are • 3 Faculty Members • Wendell Lim • Hana El-Samad • Tanja Kortemme • Chris Voigt • 8 Instructors: • Post Docs: Andrew, Noah, Sergio • Graduate Students: Angela, David, Reid, and Ryan • Me (Nili) • 7 Students • Lincoln High: Alex, Eric C., Jimmy, Lauren, Robert • Palo Alto High: Eric M. • UC Berkeley: Michael

  24. In the rough: lim lab research • LOGIC OF SIGNALING PATHWAYS • How do certain proteins function? • How do many proteins interact in signaling pathways? • How have signaling systems been constructed, recombined and modified through evolution to produce sophisticated and complex behaviors? • How can we engineer and rewire cellular behaviors? • YEAST & MAMALIAN CELLS

  25. An ‘unpolished’ iGEM timeline • June: Acclimation, Conceptual Focus, Skill Acquisition • First week: Computation Labs, Seminars • Next three weeks: Lab Work with Buddies • Regular brainstorming, synthesis, problem solving sessions and project Formulation • July-August: continued refinement of project • November: Jamboree at MIT

  26. this week. • Daily Seminars and Computational Labs • Seminars: Introducing Synthetic Biology, its biological foci, and the methods we use to study them in the lab • Computational Biology: Analyzing biological systems using mathematical modeling • Learn modeling through looking at classic papers in synthetic biology • Begin thinking about biology from an experimental approach • Adjust to and familiarize yourself to the lab, lab members • Logistical matters • IDs, Safety Training… • Learn more about iGEM! • Become familiar with online resources

  27. our goals • Comprehend and approach biology as a form of engineering • Work together as a team • Collaborate with the iGEM/synthetic biology community • Develop your minds and bodies as biologists • Have fun! • Win!

  28. ::the end:: or is it the beginning??

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