Transcript UCSF_iGEMintro

Carving
:
An Introduction
Nili Sommovilla
Lim Lab
June 11th, 2007
In the beginning, there
was…
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
One Group
One School
One Project
One Month!
a few rounds of earnest
replication…
IAP 2003
(?)
iGEM2006
IAP 2004
SBC 2004
iGEM2005
this year’s count…57 cells!
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
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
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
Or, in other words…
“Make cells do cool things!”
QuickTime™ and a
TIF F (Uncompressed) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
“I just got back from a
lab grown culture, and,
boy, are they
homogeneous!”
“making cells do cool
things”
• Silly slogan, or informative statement ?
• What use can we make of it?
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
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?
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
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Arsenic sensor system diagram
8.5
Lactose
Lac regulator
Activator gene
pH:
7.0
6.0
Activator molecule A1
4.5
A1 binding site
Urease gene
Promoter
|A|
Urease enzyme
|R|
(NH2)2CO + H2O = CO2 + 2NH3
Repressor molecule R1
R1 binding site
Ammonia
Arsenic (5ppb)
Ars regulator 1
Repressor gene R1
LacZ enzyme
Arsenic (20ppb)
Ars regulator 2
LacZ gene
Lactic Acid
System Level Map
Device Level Map
Part Level Map
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
iGEM wiki and www.igem2007.com provide central
location for accessing all iGEM materials
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
www.igem2006.com
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
• Contains presentations (video and slides) from all
teams competing last year
The Registry: (free) marketplace for parts
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Our wiki is in your hands…
• Record
Progress
• Use as a
community
resource
• Inform other
teams of
your work
• Be creative!
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
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
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
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??