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

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Oct 08, 2022 135 likes •554 views

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

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coMPUT-E.COLI

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

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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/>

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CoMPUT-E.COLI

Definition

System of arranged discrete units in
ne 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

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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

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CoMPUT-E.COLI

Definition Examples

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CoMPUT-E.COLI

Definition Examples

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CoMPUT-E.COLI

Definition Examples

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CoMPUT-E.COLI

Definition Examples

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CoMPUT-E.COLI

Definition Examples

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CoMPUT-E.COLI

Definition Examples

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CoMPUT-E.COLI

Definition Examples

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CoMPUT-E.COLI

Definition Examples

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CoMPUT-E.COLI

Definition Examples

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In Vivo Cellular Automata

CoMPUT-E.COLI

2 3 1 2 3 1

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In Vivo Cellular Automata

CoMPUT-E.COLI

Next state 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Next state 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Next state 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

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CoMPUT-E.COLI

4 Requirements:

I. Cell Synchronization
II. Cell-Cell Communication
III. Memory
IV. Information Processing

In Vivo Cellular Automata

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Memory Interface

CoMPUT-E.COLI

Gas Clock Logic

PTet

SAM Synthetase Ethylene Synthesis Cassette (ESC) ACC Synthase ACC Oxidase ESC Tet Repressor

PTet PompC

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Memory Interface

CoMPUT-E.COLI

Logic Gas Clock

Computer Simulation

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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)

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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

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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

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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

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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

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CoMPUT-E.COLI

Gas Clock

Interface

Logic Memory

Memory:

CI CI434 GFP RFP PCI PCI434 PCI PCI434 taR12 CI CI434 GFP

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CoMPUT-E.COLI

Gas Clock

Interface

Logic Memory

PCI PCI434 taR12 CI CI434 AHL- I crR12 PTetR GFP

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CoMPUT-E.COLI

Gas Clock

Interface

Logic Memory

PCI PCI434 taR12 CI CI434 AHL- I crR12 PTetR GFP

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CoMPUT-E.COLI

Gas Clock

Interface

Logic Memory

PCI PCI434 taR12 CI CI434 AHL- I crR12 PTetR GFP

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CoMPUT-E.COLI

Gas Clock

Interface

Logic Memory

PCI PCI434 taR12 CI CI434 AHL- I crR12 PTetR GFP

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CoMPUT-E.COLI

Memory Interface Gas Clock

Ql Qt Qr Qt+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

Qt+1= NOT( (Qt AND Qr) XOR Ql )

Logic

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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.

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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

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Memory Interface

CoMPUT-E.COLI

Ribozyme A

Gas Clock

Ribozyme B Target mRNA

Logic

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CoMPUT-E.COLI

Ribozyme A Ribozyme B

XOR Gate

Memory Interface Gas Clock Logic

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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

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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

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Part Characterization

CoMPUT-E.COLI

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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

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Collaboration

CoMPUT-E.COLI

Cross-Faculty Club Human Practices

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Collaboration

CoMPUT-E.COLI

Cross-Faculty Club Human Practices

To come…

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Collaboration

CoMPUT-E.COLI

Cross-Faculty Club Human Practices

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