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coMPUT-E.COLI
The Team:
Anas Ambri
Gabriel Belmonte
Jeremy Glass-Pilon
Lance Lafontaine
Laura Leclerc
Melissa Valente Paterno
CoMPUT-E.COLI
'Views of a Foetus in the Womb''' (c. 1510 – 1512) Leonardo da Vinci <http://www.visi.com/~reuteler/leonardo.html>
“Early Blastula” K. Wynne <http://science.tjc.edu/Course/BIOLOGY/1413/>
CoMPUT-E.COLI
Definition
• 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.
Examples Examples Definition
CoMPUT-E.COLI
Definition
• Take a grid in n-dimensions, with some
initial state, and a rule on how to
change states.
• Press GO.
Examples Examples Definition
CoMPUT-E.COLI
Definition Examples
CoMPUT-E.COLI
Definition Examples
CoMPUT-E.COLI
Definition Examples
CoMPUT-E.COLI
Definition Examples
CoMPUT-E.COLI
Definition Examples
CoMPUT-E.COLI
Definition Examples
CoMPUT-E.COLI
Definition Examples
CoMPUT-E.COLI
Definition Examples
CoMPUT-E.COLI
Definition Examples
In Vivo Cellular Automata
CoMPUT-E.COLI
2 3
1 2 3 1
In Vivo Cellular Automata
CoMPUT-E.COLI
Next state
0 0 0 0
0 0 1 0
0 1 0 0
0 1 1 1
1 0 0 1
1 0 1 1
1 1 0 1
1 1 1 0
Next state
0 0 0 0
0 0 1 0
0 1 0 0
0 1 1 1
1 0 0 1
1 0 1 1
1 1 0 1
1 1 1 0
Next state
0 0 0 0
0 0 1 0
0 1 0 0
0 1 1 1
1 0 0 1
1 0 1 1
1 1 0 1
1 1 1 0
CoMPUT-E.COLI
4 Requirements:
I. Cell Synchronization II. Cell-Cell Communication III. Memory IV. Information Processing
In Vivo Cellular Automata
Memory Interface
CoMPUT-E.COLI
Gas Clock Logic
PTet SAM Synthetase
Ethylene Synthesis Cassette (ESC)
ACC Synthase ACC Oxidase
ESC Tet Repressor PTet PompC
Memory Interface
CoMPUT-E.COLI
Logic Gas Clock
Computer Simulation
Memory Interface Logic Gas Clock
CoMPUT-E.COLI
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)
Memory Logic Gas Clock Interface
CoMPUT-E.COLI
Cell-Cell Communication:
Acyl-homoserine Lactone (AHL): • Small, hormone-like • Easily diffusible
AHL Synthase
R
AHL Receptor
I
LuxI ; RhlI ; CepI LuxR ; RhlR ; CepR
Memory Logic Gas Clock Interface
CoMPUT-E.COLI
Organism AHL Structure Chemical
Name Synthase Receptor
Vibrio fischeri 3-Oxo-C6-
HSL (OHHL)
Pseudomonas aeruginosa
C4-HSL (BHL)
Burkholderia cenocepacia
C8-HSL (OHL)
Lux I Lux R
Rhl I Rhl R
Cep R Cep I
CoMPUT-E.COLI
ESC Tet Repressor PTet PompC
Memory Logic
SPC PompC
AHL Synthesis PTet
Gas Clock Interface
PompC LuxR
Signal Processing Cassette
CepR RhlR
AHL Synthesis
PompC
crR12 LuxI PompC
crR12 RhlI PompC
crR12 CepI
CoMPUT-E.COLI
ESC Tet Repressor PTet PompC
Memory Logic
SPC PompC
AHL Synthesis PTet
Gas Clock Interface
PompC LuxR
Signal Processing Cassette
CepR RhlR
AHL Synthesis
PompC
crR12 LuxI PompC
crR12 RhlI PompC
crR12 CepI
CoMPUT-E.COLI
Gas Clock Interface Logic Memory
Memory:
CI CI434 GFP RFP
PCI PCI434
PCI PCI434
taR12 CI CI434 GFP
CoMPUT-E.COLI
Gas Clock Interface Logic Memory
PCI PCI434
taR12 CI CI434
AHL- I crR12
PTetR
GFP
CoMPUT-E.COLI
Gas Clock Interface Logic Memory
PCI PCI434
taR12 CI CI434
AHL- I crR12
PTetR
GFP
CoMPUT-E.COLI
Gas Clock Interface Logic Memory
PCI PCI434
taR12 CI CI434
AHL- I crR12
PTetR
GFP
CoMPUT-E.COLI
Gas Clock Interface Logic Memory
PCI PCI434
taR12 CI CI434
AHL- I crR12
PTetR
GFP
CoMPUT-E.COLI
Memory Interface Gas Clock
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
1 1 0 1
1 1 1 0
Qt+1= NOT( (Qt AND Qr) XOR Ql )
Logic
Memory Interface Gas Clock Logic
CoMPUT-E.COLI
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
Memory Interface Gas Clock
AHLLeft
AHLSelf
AHLRight
Plac
Plac
Plac
XOR Gate
AND Gate
Ribozyme 1
Anti-silencer 1
Silencer 2
Silencer 1
Anti-silencer 2
Ribozyme 2
Logic
Memory Interface
CoMPUT-E.COLI
Ribozyme A
Gas Clock
Ribozyme B
Target mRNA
Logic
CoMPUT-E.COLI
Ribozyme A
Ribozyme B
XOR Gate
Memory Interface Gas Clock Logic
CoMPUT-E.COLI
Gas Clock
CI434 CI
PCI PCI434
taR12 GFP
Bistable Memory
PTetR crR12 CepI
LuxR
OHHL
PompC CepR
OHL
RhlR
BHL
TetR PompC
Gas Synthesis PTetR
Interface Logic
Rz1 Rz2
S1
S2
AS1
AS2
Rz2 Rz3
S3
S4
AS3
AS4
Rz4
PenI XOR
Parts
CoMPUT-E.COLI
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
Part Characterization
CoMPUT-E.COLI
Cross-Faculty Club Human Practices
CoMPUT-E.COLI
Collaboration
iGEM Concordia 2013: How To Design Fusion Proteins Produced for University of Copenhagen’s Bricks of Knowledge
Collaboration
CoMPUT-E.COLI
Cross-Faculty Club Human Practices
Collaboration
CoMPUT-E.COLI
Cross-Faculty Club Human Practices
To come…
Collaboration
CoMPUT-E.COLI
Cross-Faculty Club Human Practices
CoMPUT-E.COLI
