Synthetic Biology A New Opportunity for Multidisciplinary Undergraduate Research Jeff Poet, Laurie Heyer, Todd Eckdahl, Malcolm Campbell 2010 GCAT Synthetic Biology Workshop Davidson College.
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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 Focus on undergraduate education Pooling human resources Built on previous collaborations BioMath connections Common goals Our Prioritized Goals 1. 2. 3. Everyone learns Have fun Contribute to synthetic biology Missouri Western/Davidson Team 2006 iGEM Jamboree The Classic Pancake Problem 1975 by Harry Dweighter (“harried waiter”) Scenario 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 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 Modification of the Classic Pancake Problem Each pancake has one burnt side Problem 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 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, 1 is Tet resistant at least 4 have RFP expression iGEM 2006 Outcomes 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 ? 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 Over 65 parts contributed to Registry Gold medal award at iGEM Jamboree JBE Manuscript published 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 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 1 0 Biological Hash Function 1 XOR 0 1 Requires Unidirectional Communication XOR 0 1 XOR 1 0 XOR 1 hash 1 iGEM 2008 Outcomes 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 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 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