Transcript Four Projects by MWSU and Davidson

Synthetic Biology
A New Opportunity for Multidisciplinary
Undergraduate Research
Jeff Poet, Laurie Heyer, Todd Eckdahl,
Malcolm Campbell
2010 GCAT Synthetic Biology Workshop
Davidson College
Davidson - Missouri Western
iGEM Collaboration
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Focus on undergraduate education
Pooling human resources
Built on previous collaborations
BioMath connections
Common goals
Our Prioritized Goals
1.
2.
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Everyone learns
Have fun
Contribute to synthetic biology
Missouri Western/Davidson Team
2006 iGEM Jamboree
The Classic Pancake Problem
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1975 by Harry Dweighter (“harried waiter”)
Scenario
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Pancake chef at iHOP
Spatula in one hand
Plate with a stack of delicious pancakes of different
sizes in other hand
No place to set down the plate
Problem
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The chef wishes to serve the pancakes arranged from
smallest to largest
How many flips are needed?
A Simple Pancake Problem
Find the fewest number of flips needed to obtain the
arrangement 1,2,3,4.
?
Pancake Problem Solution
The Burnt Pancake Problem
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Modification of the Classic Pancake Problem
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Each pancake has one burnt side
Problem
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Sort pancakes from smallest to largest, all burnt-side
down
How many flips are needed?
Burnt Pancake Problem
?
Burnt Pancake Problem
The bottom pancake is upside down so more flips are
needed for the burnt pancake problem.
Burnt Pancake Solution
There could be a more efficient way…
Burnt Pancake Solution
Solving the Pancake Problem with a Bacterial Computer
Missouri Western State University
Marian Broderick, Adam Brown, Trevor Butner,
Lane Heard, Eric Jessen, Kelly Malloy, Brad Ogden
Faculty: Todd Eckdahl
and Jeff Poet
Advantages of Bacterial Computation
Software
Hardware
Computation
Computation
Computation
http://www.turbosquid.com
Computational Complexity
• Non-Polynomial (NP)
# of Processors
• No Efficient Algorithms
Cell Division
Hin-Hix
Recombination
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Salmonella uses
recombination to achieve
antigenic variation
Target DNA contains
promoter that drives either
of 2 flagellar protein genes
Image from: Nanassy OZ and Hughe K,
1998 Genetics 149: 1649-1663.
A Two Pancake Construct
pBAD
HixC
RFP
RBS
HixC
HixC
Tet
Pancake
RBS
Pancake
Hin provided by separate plasmid
Starting configuration is Tet sensitive
Flipping results in 8 different configurations,
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1 is Tet resistant
at least 4 have RFP expression
iGEM 2006 Outcomes
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Over 50 parts contributed to Registry
Five awards at iGEM Jamboree, including
Best Oral Presentation
“Computing with Living Hardware” in IET
Synthetic Biology
“Engineering Bacteria to Solve the Burnt
Pancake Problem” in Journal of Biological
Engineering
 awarded 2008 Outstanding paper
News stories, NPR Science Friday
Our iGEM 2007 Team
Hamiltonian Path
Problem:
Given a set of nodes
and directed arcs
between some pairs of
nodes, is there some
path starting at one
vertex and ending at
another that visits each
node exactly once?
Inside MIT Stata Center, November 2007
The Adleman Graph:
A Hamiltonian Path Problem
Encoding an HPP in DNA
How to Split a Gene
RBS
Detectable
Phenotype
Reporter
Promoter
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RBS
Promoter
Repo-
rter
hixC
Detectable
Phenotype
What Genes Can Be Split?
GFP displaying hixC insertion point
Gene Splitter Software
http://gcat.davidson.edu/iGEM07/genesplitter.html
Input
1. Gene Sequence
(cut and paste)
2. Where do you want
your hixC site?
Output
1.
Generates 4 Primers
(optimized for Tm).
2. Biobrick ends are added to
primers.
3. Frameshift is eliminated.
3. Pick an extra base to avoid a
frameshift.
Gene-Splitter Software
Note: Oligos are
optimized for melting
temperatures.
Living Hardware to Solve the
Hamiltonian Path Problem
Students: Oyinade
Adefuye, Will
DeLoache, Jim
Dickson, Andrew
Martens, Amber
Shoecraft, and Mike
Waters, Jordan
Baumgardner, Tom
Crowley, Lane Heard,
Nick Morton, Michelle
Ritter, Jessica Treece,
Matt Unzicker,
Amanda Valencia
Faculty: Malcolm Campbell, Todd Eckdahl, Karmella
Haynes, Laurie Heyer, Jeff Poet
iGEM 2007 Outcomes
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Over 65 parts contributed to
Registry
Gold medal award at iGEM
Jamboree
JBE Manuscript published
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Highly Accessed
Rated by Faculty 1000 Biology
NSF UBM grant funded
2008 iGEM Team
Using E. coli to
compute values of a
cryptographic hash
function
Student Team Members - Alicia Allen, James Barron, Robert Cool,
Kelly Davis, Will DeLoache, Erin Feeney, Andrew Gordon, John Igo, Aaron
Lewis, Kristi Muscalino, Madeline Parra, Pallavi Penumetcha, Karlesha
Roland, Max Win, Xiao Zhu
Faculty Team Leaders - A. Malcolm Campbell, Todd Eckdahl, Laurie
Heyer, Jeff Poet
Cryptographic
Hash Functions
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Input of any length
Output of fixed length
International standard: MD5
International call for new hash function
HGTf34$2
Encoding XOR logic in DNA
High
Osmolarity
(Input A)
3OC6
(Input B)
High Osmolarity
(Input A)
3OC6
(Input B)
Fluorescence
(Output)
0
0
0
1
0
1
0
1
1
1
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Biological Hash Function
1
XOR
0
1
Requires
Unidirectional
Communication
XOR
0
1
XOR
1
0
XOR
1
hash
1
iGEM 2008 Outcomes
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105 new parts contributed to Registry
Online tools developed
XOR logic gates built
Biological hash function designed
E. nigma device constructed
New designs being built for testing
2009 iGEM Team
SATisfiability Problem
Define the SATisfiability Problem
Define the SATisfiability Problem
Define the SATisfiability Problem
Applications
Converting Math to Biology
Central Dogma
Frameshift Mutation
Frameshift Suppression
Suppressor tRNA
Coding 2-SAT Clause
Coding 2-SAT Clause
Coding 2-SAT Clause
Coding 2-SAT Clause
Outcomes of v1.0
Outcomes of v1.0
Redesign System v2.0
Increase Signal with Optimize LuxI
Increase Signal with Optimize LuxI
Optimize tRNA Production
Optimize tRNA Production
Outcomes of v 2.0
Outcomes of v 2.0
Redesign System v2.1
Lessons Learned
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Synthetic Biology provides BioMath
connections
Undergraduates can conduct
synthetic biology research
Multidisciplinary and multiinstitutional collaboration works
Synthetic Biology is fun
Is SB hard or expensive?
• Sophomores, high school students trained
• Less than $5,000 in lab expenses per summer
• NSF Undergraduate Biology and Math Program
• Protocols student-proof and online
• Existing lab equipment and methods
• Math modeling improves design
How can you learn more?
• Attend iGEM 2010 at MIT
• Read synthetic biology papers
www.bio.davidson.edu/Courses/Synthetic/read.html
• Browse iGEM wiki pages
• Form an iGEM team on your campus
Is GCAT participating in iGEM?
•Encouraging PUIs to join the fun
•HHMI synthetic biology workshop
•Sharing protocols
•Freezer sharing
•Making List-serve available
Acknowledgements
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Student collaborators at Missouri
Western and Davidson
Randy Rettberg and iGEM community
Missouri Western SRI, WI, SEF, ASA
Davidson DRI, HHMI
NSF UBM DMS-0733952 and 0733955
Synthetic Biology
A New Opportunity for Multidisciplinary
Undergraduate Research
Todd Eckdahl, Laurie Heyer, Malcolm
Campbell and Jeff Poet
2010 GCAT Synthetic Biology Workshop
Davidson College