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Carving :

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A Challenge of Innovation and Creativity ... what makes an iGEM an iGEM? ... An unpolished' iGEM timeline. this week. Daily Seminars and Computational Labs ... – PowerPoint PPT presentation

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Title: Carving :


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

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

3
a few rounds of earnest replication…
4
this years 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 examining genes, 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
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
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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