Carving :

1
Carving
An Introduction

• Nili Sommovilla
• Lim Lab
• June 11th, 2007

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In the beginning, there was

• One Group
• One School
• One Project
• One Month!

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a few rounds of earnest replication
4
this years count
57 cells!
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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

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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

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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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making cells do cool things

• Silly slogan, or informative statement ?
• What use can we make of it?

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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 examining genes, proteins and
  pathways
• Applying this towards new or useful functions
• Using a standardized methodology

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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?
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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

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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!

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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

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Arsenic sensor system diagram
8.5
7.0
pH
6.0
4.5
A1 binding site
Promoter
(NH2)2CO H2O CO2 2NH3
R1 binding site
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System Level Map
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Device Level Map
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Part Level Map
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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

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iGEM wiki and www.igem2007.com provide central
location for accessing all iGEM materials
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www.igem2006.com

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

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The Registry (free) marketplace for parts
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Our wiki is in your hands

• Record Progress
• Use as a community resource
• Inform other teams of your work
• Be creative!

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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

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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

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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

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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

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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!

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the end

• or is it the beginning??