Carving :

Nili SommovillaLim Lab

June 11th, 2007

An Introduction

In the beginning, there was…

One Group

One School

One Project

One Month!

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IAP 2003

SBC 2004

(?)

IAP 2004

iGEM2005

iGEM2006

a few rounds of earnest replication…

AlbertaBangaloreBay Area RSIBerkeley LBLBerkeley UCBolognaBoston UniversityBrownCalgaryCaltechCambridgeCape PeninsulaChibaColombia-Israel

CSHLDavidson-Missouri DukeDundeeEdinburghETHZFreiburgGlasgowHarvardImperialLethbridgeLjubljanaMcGillMelbourne

MexicoMichiganMinnesotaMississippi StateMissouri MinersMITNaplesParisPekingPenn StatePrairie ViewPrincetonPurdueRice

St. PetersburgSouthern UtahTaipeiTianjinTokyo TechTorontoTsinghuaTurkey

*UCSF*USTCValenciaVirginiaVirginia TechWaterlooWisconsin

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!”

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• 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 biologicaloutput

• Developed their circuit with:• 4 parts from the registry• 5 new parts made by the team

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Lac regulator Activator gene

Activator molecule A1

Lactose

|A| |R|Promoter

Urease gene

A1 binding site

Urease enzyme

(NH2)2CO + H2O = CO2 + 2NH3

Ars regulator 1 Repressor gene R1Arsenic (5ppb)

Ars regulator 2 LacZ gene

Repressor molecule R1

Arsenic (20ppb) LacZ enzyme

R1 binding site

Arsenic sensor system diagram 8.5

7.0

6.0

4.5

pH:

Ammonia

Lactic Acid

System Level Map

Device Level Map

Part Level Map

gimme structure!

iGEM Resourceswww.igem2007.com

iGEM wiki siteiGEM 2006 website and past projects

iGEM Registry of PartsiGEM parts package

UCSF ResourcesPeople

Topics of study in the LabOur Ideas & collaborative power

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

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

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www.igem2006.com

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The Registry: (free) marketplace for parts

Our wiki is in your hands…

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• 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??