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

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

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

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 the challenge

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

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

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 examining genes, proteins and pathways Applying this towards new or useful functions Using a standardized methodology making life (not really)

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! selling cells Can any computer can say that much?

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

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!

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

Lac regulatorActivator gene Activator molecule A1 Lactose |A| |R|Promoter Urease gene A1 binding site Urease enzyme (NH 2 ) 2 CO + H 2 O = CO 2 + 2NH 3 Ars regulator 1Repressor gene R1 Arsenic (5ppb) Ars regulator 2LacZ gene Repressor molecule R1 Arsenic (20ppb) LacZ enzyme R1 binding site Arsenic sensor system diagram pH: Ammonia Lactic Acid

System Level Map

Device Level Map

Part Level Map

gimme structure! iGEM Resources 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

iGEM wiki and provide central location for accessing all iGEM materialswww.igem2007.com

Contains presentations (video and slides) from all teams competing last year

The Registry: (free) marketplace for parts

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

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

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

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 An ‘unpolished’ iGEM timeline

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

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!

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