Synthetic Biology at Davidson College Building Bacterial Computers.

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Presentation transcript:

Synthetic Biology at Davidson College Building Bacterial Computers

Advantages of Bacterial Computation $ ¢ Computation Hardware Software Computation

Advantages of Biological Computers go anywhere - arctic, thermal vents, inside organisms no electricity self-replicating no immune rejection

Self-replicating Computers

Two Recent Research Projects

Outstanding Publication of 2008 in the Journal of Biological Engineering 12 undergraduate coauthors

Flipping DNA with Hin/hixC

Hamiltonian Path Problem

Hamiltonian Path Solution

Engineering Biological HPP

Hin-mediated recombination

Engineering Biological HPP

Predicting Outcomes of Bacterial Computing

Does Starting Place Matter?

Equilibrium Does Starting Place Matter?

How Many Plasmids Do We Need?

Split Genes to Encode Problem

gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Proto cols

Split Reporter Genes Green Fluorescent Protein Red Fluorescent Protein

Split Reporter Genes RFP Split by hixC GFP Split by hixC

Bacteria Start Computation Yellow colonies indicate solution found Unflipped Flipped

Bacteria Report Solutions Yellow colonies indicate solution found Unflipped Flipped

Bacteria Report Solutions Yellow colonies indicate solution found Unflipped Flipped

Paper Published 7/09 15 undergraduate coauthors Paper of the year, 2009

Can we solve the SATisfiability problem?

Define the SATisfiability Problem

Converting Math to Biology

Central Dogma

Frameshift Mutation

Frameshift Suppression

Suppressor tRNA

Coding 2-SAT Clause

Outcomes of v 1.0

Redesign System v2.0 positive feedback loop

Outcomes of v control+ control

Outcomes of v control frame shift “leak” +tRNA CGGUC +tRNA CCACU + control

Outcomes of v 2.0 frame shift “leak” +tRNA CGGUC +tRNA CCACU + control

Why build bacterial computers?

Evolution of Computers 1943

iPhone in 2011 Evolution of Computers

E. coli in 2011 ? Living Hardware in 2021 Evolution of Bacterial Computers