AbstractAbstractAbstractAbstract

2006: The Burnt Pancake Problem2006: The Burnt Pancake Problem2006: The Burnt Pancake Problem2006: The Burnt Pancake Problem

AcknowledgementsAcknowledgements AcknowledgementsAcknowledgements

Faculty and undergraduates at Missouri Western State University and Davidson College have successfully collaborated in synthetic biology research since 2006. Each campus has a faculty team of a mathematician and a biologist to co-mentor multidisciplinary cohorts of undergraduates conducting intensive summer research projects. Each year, the combined team has participated in the international Genetically Engineered Machines (iGEM) competition. Our focus, unique among the iGEM teams, has been to design and engineer bacteria to carry out mathematical computation of interesting combinatorial problems. In particular, we designed and built E. coli that compute solutions to the Burnt Pancake Problem, the Hamiltonian Path Problem, and a cryptographic hash function. We are currently addressing SAT problems using suppressor tRNAs. We have disseminated our research process and outcomes through presentations at multiple conferences and workshops. We have published two research articles about bacterial computers in BioMed Central’s Journal of Biological Engineering.

Undergraduate Synthetic Biology Research Collaboration between Missouri Western State University and Davidson College: 2006 to present

Jeffrey L. Poet, Missouri Western State University, Todd T. Eckdahl, Missouri Western State UniversityLaurie J. Heyer, Davidson College, A. Malcolm Campbell, Davidson College

7th Annual National Academies Keck Futures Initiative (NAKFI)Synthetic Biology: Building on Nature’s Inspiration

I gratefully acknowledge the collaboration of my colleagues, Todd Eckdahl of Missouri Western State University and A. Malcolm Campbell and Laurie Heyer of Davidson College and of our 50+ undergraduate student researchers. Our collaborative projects have been funded by National Science Foundation Grants #DMS-0733952 & 0733955, HHMI, and other resources from the two campuses.

2007: The Hamiltonian Path Problem2007: The Hamiltonian Path Problem2007: The Hamiltonian Path Problem2007: The Hamiltonian Path Problem

Publications Publications (* indicates undergraduate co-author)(* indicates undergraduate co-author)Publications Publications (* indicates undergraduate co-author)(* indicates undergraduate co-author)

In our first year of collaboration, the combined team took on Bill Gates’ Burnt Pancake Problem – reconstituting the hin/Hix recombination system from Salmonella and using this system to engineer E.coli bacteria to randomly flip selected portions of its DNA to find a solution where the DNA segments (the pancakes) are in the correct order and orientation. The work received several awards at iGEM, was the subject of a research article in the Journal of Biological Engineering in May 2008, and is the subject of an upcoming 2010 article in Math Horizons.

2009: SAT Problems2009: SAT Problems2009: SAT Problems2009: SAT Problems

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2008: Cryptographic Hash Functions2008: Cryptographic Hash Functions2008: Cryptographic Hash Functions2008: Cryptographic Hash Functions

Our team research goal was to engineering E. coli to solve a Satisfiability (SAT) logic problem. Logical clauses are composed of two (2-SAT) or three (3-SAT) true-false variables connected by OR operators and a series of logical clauses linked by AND operators forms a SAT problem. Our design uses frameshift suppressor tRNAs as inputs that can be processed by frameshift suppressor leaders (FSLs) enabling the translation of antibiotic resistance or fluorescence reporter constructs only when an appropriate combination of inputs is present.

X

RBSRBS HinHin TT TT RBSRBS TetTet TT TT

HixC HixC REpLac pBADrev

Pancake

In our second year, we extended the use of the hin/Hix system to apply to the Hamiltonian Path Problem, a special case of the more famous Traveling Salesperson Problem. GFP and RFP genes were split in novel ways as to allow for the insertion of a 22 bp hix site and biobrick scars but yet remain function upon recombination. This work was then used to show further proof-of-concept for bacterial computing, was presented at the iGEM Jamboree, and was published in the June 2009 Journal of Biological Engineering becoming the only article in the journal’s 2-year history with over 20,000 downloads.

K. Haynes, M. Broderick*, A. Brown*, T. Butner*, L. Harden*, L. Heard*, E. Jessen*, K. Malloy*, B. Ogden*, S. Rosemond*, S. Simpson*, E. Zwack, A. M. Campbell, T. Eckdahl, L. Heyer, J. Poet. Computing with living hardware. IET Synthetic Biology. June 2007. 1:1-2, pp. 44-47

K. Haynes, M. Broderick*, A. Brown*, T. Butner*, L. Harden*, L. Heard*, E. Jessen*, K. Malloy*, B. Ogden*, S. Rosemond*, S. Simpson*, E. Zwack, A. M. Campbell, T. Eckdahl, L. Heyer, J. Poet. Engineering bacteria to solve the Burnt Pancake Problem. Journal of Biological Engineering. May 2008. 2:8

J. Baumgardner*, K. Acker*, O. Adefuye*, S. T. Crowley*, W. DeLoache*, J. Dickson*, L. Heard*, A. Martens*, N. Morton*, M. Ritter*, A. Shoecraft*, J. Treece*, M. Unzicker*, A. Valencia*, M. Waters*, A. M. Campbell, L. Heyer, J. Poet, T. Eckdahl. Solving the Hamiltonian Path Problem with a bacterial computer. Journal of Biological Engineering. June 2009. 3:11.

Our team designed, modeled, and constructed bacterial computers that use novel biological XOR gates to compute a cryptographic hash function. We contributed 105 new parts to the Registry, improved upon the existing LacI repressor, and produced web-based tools to enhance the research experience of future synthetic biology researchers.

XOR

XOR

XOR

XOR

hash

1 0

0

1

1

1

1

0

1

aTcLasRconst + 3OC12

MntLasR CI LuxI CIpTet Mnt LuxI

TetR3OC6 3OC6

aug RRRRR g RRRRR  RRRRR g RRRRR gg RRRRR g RRRRR  RRRRR g RRRRR gUGAgUGAg cag