coMPUT-E.COLI The Team: m: Anas Ambri Gabriel Belmonte Jeremy - PowerPoint PPT Presentation

coMPUT-E.COLI The Team: m: Anas Ambri Gabriel Belmonte Jeremy Glass-Pilon Lance Lafontaine Laura Leclerc Melissa Valente Paterno

CoMPUT-E.COLI “Early Blastula” K. Wynne 'Views of a Foetus in the Womb''' (c. 1510 – <http://science.tjc.edu/Course/BIOLOGY/1413/> 1512) Leonardo da Vinci <http://www.visi.com/~reuteler/leonardo.html>

CoMPUT-E.COLI Definition Examples Definition Examples • System of arranged discrete units in one of a finite number of states. • Its state changes at a regular interval according to the states of neighboring units according to a fixed set of rules.

CoMPUT-E.COLI Definition Examples Definition Examples • Take a grid in n-dimensions, with some initial state, and a rule on how to change states. • Press GO.

CoMPUT-E.COLI Examples Definition

CoMPUT-E.COLI Examples Definition

CoMPUT-E.COLI Examples Definition

CoMPUT-E.COLI Examples Definition

CoMPUT-E.COLI Examples Definition

CoMPUT-E.COLI Examples Definition

CoMPUT-E.COLI Examples Definition

CoMPUT-E.COLI Examples Definition

CoMPUT-E.COLI Examples Definition

CoMPUT-E.COLI In Vivo Cellular Automata 2 3 1 1 2 3

CoMPUT-E.COLI In Vivo Cellular Automata Next Next Next state state state 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 0 0 1 0 0 0 1 0 0 0 1 0 0 0 1 1 1 0 1 1 1 0 1 1 1 1 0 0 1 1 0 0 1 1 0 0 1 1 0 1 1 1 0 1 1 1 0 1 1 1 1 0 1 1 1 0 1 1 1 0 1 1 1 1 0 1 1 1 0 1 1 1 0

CoMPUT-E.COLI In Vivo Cellular Automata 4 Requirements: I. Cell Synchronization II. Cell-Cell Communication III. Memory IV. Information Processing

CoMPUT-E.COLI Gas Cloc k Interface Memory Logic ESC Tet Repressor P Tet P ompC SAM Synthetase ACC Synthase ACC Oxidase P Tet Ethylene Synthesis Cassette (ESC)

CoMPUT-E.COLI Gas Cloc k Interface Memory Logic Computer Simulation

CoMPUT-E.COLI Gas Cloc k Interface Memory Logic ETR1: Ethylene Receptor 1 : • Arabidopsis thaliana • Ethylene receptor with TWO-COMPONENT HISTIDINE KINASE EnvZ: Osmolarity Sensor Protein • Eschericia coli • Osmotic pressure sensor with TWO-COMPONENT HISTIDINE KINASE E. coli compatible Ethylene inducible Histidine Kinase (EEHK)

CoMPUT-E.COLI Interface Gas Clock Memory Logic Cell-Cell Communication: Acyl-homoserine Lactone (AHL): • Small, hormone-like • Easily diffusible AHL Synthase AHL Receptor I R LuxI ; RhlI ; CepI LuxR ; RhlR ; CepR

CoMPUT-E.COLI Interface Gas Clock Memory Logic Chemical Organism AHL Structure Synthase Receptor Name 3-Oxo-C6- Vibrio fischeri HSL Lux I Lux R (OHHL) C4-HSL Pseudomonas Rhl R Rhl I (BHL) aeruginosa C8-HSL Burkholderia Cep I Cep R (OHL) cenocepacia

CoMPUT-E.COLI Interface Gas Clock Memory Logic SPC P ompC ESC Tet Repressor P Tet AHL Synthesis P ompC P Tet crR12 LuxI crR12 RhlI crR12 CepI P ompC P ompC P ompC CepR RhlR LuxR P ompC Signal Processing AHL Synthesis Cassette

CoMPUT-E.COLI Interface Gas Clock Memory Logic SPC P ompC ESC Tet Repressor P Tet AHL Synthesis P ompC P Tet crR12 LuxI crR12 RhlI crR12 CepI P ompC P ompC P ompC CepR RhlR LuxR P ompC Signal Processing AHL Synthesis Cassette

CoMPUT-E.COLI Memory Gas Clock Interface Logic Memory: GFP CI RFP CI434 P CI P CI434 CI434 CI GFP taR12 P CI P CI434

CoMPUT-E.COLI Memory Gas Clock Interface Logic CI434 CI GFP taR12 P CI P CI434 crR12 AHL- I P TetR

CoMPUT-E.COLI Memory Gas Clock Interface Logic CI434 CI GFP taR12 P CI P CI434 crR12 AHL- I P TetR

CoMPUT-E.COLI Memory Gas Clock Interface Logic CI434 CI GFP taR12 P CI P CI434 crR12 AHL- I P TetR

CoMPUT-E.COLI Memory Gas Clock Interface Logic CI434 CI GFP taR12 P CI P CI434 crR12 AHL- I P TetR

CoMPUT-E.COLI Logic Gas Clock Interface Memory Ql Qt Qr Qt+1 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 1 0 0 1 1 0 1 1 Q t+1 = NOT( (Q t AND Q r ) XOR Q l ) 1 1 0 1 1 1 1 0

CoMPUT-E.COLI Logic Gas Clock Interface Memory Information Processing: Ribozymes: Small RNA molecules that can be designed to cleave specific RNA sequences. • Expedient, robust processing. • Simpler logic gates: AND, XOR, etc. • Modular design for any target.

CoMPUT-E.COLI Logic Gas Clock Interface Memory XOR Gate Ribozyme 1 Ribozyme 2 Plac AHL Left Anti-silencer 1 Silencer 1 Plac AHL Self AND Gate Anti-silencer 2 Silencer 2 Plac AHL Right

CoMPUT-E.COLI Logic Gas Clock Interface Memory Ribozyme A Ribozyme B Target mRNA

CoMPUT-E.COLI Logic Gas Clock Interface Memory XOR Gate Ribozyme A Ribozyme B

CoMPUT-E.COLI Bistable Memory Gas Clock Gas Synthesis TetR taR12 PompC CI434 CI GFP PTetR PCI PCI434 PTetR crR12 CepI PenI XOR LuxR RhlR CepR PompC Rz1 Rz2 Rz3 Rz4 Rz2 OHL AS1 S1 AS3 S3 BHL OHHL AS2 S2 AS4 S4 Interface Logic

CoMPUT-E.COLI Parts Generated : • PompC-GFP (marker for EEHK assay) K1165001 • pTet-SAM Synthetase K1165016 In Progress: • Ribozymes K1165002-5 • EEHK K1165006-8 • Ethylene Synthesis Cassette K1165012 • crR12-LuxI K1165018 • crR12-RhlI K1165019 Future Works: • CepI K1665009 • CepR K1665010 • Signal Processing Cassette K1665011 • Optimized Bistable Memory K1665013 • PompC-TetR K1665014 • crR12-CepI K1665017 • pLac-PenI K1665019

CoMPUT-E.COLI Part Characterization

CoMPUT-E.COLI Collaboration Human Practices Cross-Faculty Club iGEM Concordia 2013: How To Design Fusion Proteins Produced for University of Copenhagen’s Bricks of Knowledge

CoMPUT-E.COLI Human Practices Collaboration Cross-Faculty Club

CoMPUT-E.COLI Human Practices Collaboration Cross-Faculty Club To come…

CoMPUT-E.COLI Cross-Faculty Club Collaboration Human Practices

CoMPUT-E.COLI