Addressable Conjugation in Bacterial Networks High School Matt Fleming Kaitlin A. Davis Undergrads Bryan HernandezFreshman Jennifer LuFreshman Samantha.

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Presentation transcript:

Addressable Conjugation in Bacterial Networks High School Matt Fleming Kaitlin A. Davis Undergrads Bryan HernandezFreshman Jennifer LuFreshman Samantha LiangFreshman Will BosworthSophomore Daniel KluesingJunior Postdocs John E. Dueber J. Christopher Anderson Faculty Advisors Adam P. Arkin Jay D. Keasling The University of California, Berkeley

Every Cell is assigned a Unique RNA Address UGAUCUAAGUGGAGGACGAA GUUCAAGACAAUCACUCACG UCAAUAUAAAACUACAAACU GAUGAUAGAGGUUUCUUUUA Cell 1 Cell 2 Cell 3 Cell 4

Implementation Need: To transfer DNA messages from one bacterial cell to another Means: Bacterial Conjugation Need: To specifically control who can read the DNA message Means: Riboregulation

Our specific goals: Construct high-performance riboregulators Harness bacterial conjugation Transmit a coded message Construct a bacterial learning network

The Riboregulator: DNA Promoter RBS RFP Double T RNA Polymerase

Locked Riboregulator: RNA Ribosome Locked RBS RFP

Unlocked Riboregulator Ribosome Unlocked Revealed RFP Lock RBS + Key

The Locks

Mismatches are not necessary for Unlocking Secondary structure is critical for activity

Shorter loops unlock better Transcriptional terminators but not open reading frames improve activity

Bacterial Conjugation

R System x OriTr Transfer of Message Plasmids F System

Cell Sends a Coded Message to Recipient Cell

Conjugation Does Not Impede Riboregulator Function Conjugation and Riboregulators Riboregulators Don't Effect Conjugation Efficiency

NAND Logic Gates

Building Computational Networks Graded Response Inhibitory Signals Stimulatory Signals Parallel Signals

Concentration in Culture gives Graded Responses enrichment

Trainable Bacterial Networks

Acknowledgements Arkin and Keasling Labs Funding from Microsoft LBL EHS Jonathon Goler, Melissa Li

Nodes are Built from Multiple Cell Types

Addressable Networks

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