iGEM @ ImperialiGEM @ Imperial

Starting off: Week 1Starting off: Week 1

Week 1Week 1

Engineering/Biology Engineering/Biology Introduction LecturesIntroduction LecturesJournal ClubJournal ClubWikiWikiBrainstormingBrainstorming

3 ideas3 ideas

Bio Hard Drive

Cell Networking

Bacterial balloon

Biological to Electrical Interface

Bio-Clock

Bio Calculator

Remote Controlled

Bacteria

Crazy Ideas

Only three ideas Only three ideas made the cut.made the cut.

Bio-Clock Bio-Clock (Re-defining Time)(Re-defining Time)

• Pulse of AHL moves along a gutter of medium

• Cells fluoresce when activated

•Refractory period

•The time period is controlled by

•the radius

•gutter width

•cell density

Bio-MemoryBio-Memory

•Data stored in bacteria written using a green laser

•Data read using a UV laser + fluorimeter

•Cells either 1 (RFP) or 0 (no RFP)

•Data stored in switch

Very High Compression due to small size of bacteria

The OscillatorThe Oscillator

Changing Concentration of AHL

Culture Wide Culture Wide oscillations of AHLoscillations of AHL

Frequency must Frequency must be tuned easilybe tuned easily

Oscillations must Oscillations must be stablebe stable

Week 2Week 2

Investigation of all 3 ideasInvestigation of all 3 ideas ModellingModelling Evaluating risksEvaluating risks

Start work in the Wet labStart work in the Wet lab

Decision on the Oscillator Decision on the Oscillator as main project;as main project;can use other ideas as can use other ideas as further developments further developments

Week 3Week 3

Further researchFurther research

ModellingModelling

Assembly of partsAssembly of parts

Protocols for testing partsProtocols for testing parts

Setting up OWWSetting up OWW

Lotka-Voltarra Model output

Predator Prey DynamicsPredator Prey Dynamics

Simply Make a Bio-

chemical system

that can do this.

DesignDesign

A

B

A B

• Positive Feedback of A

• AB Induces production of more B

• Both A and B are used to make AB

Two Cell SystemTwo Cell SystemTwo independent populations of CellsTwo independent populations of Cells

These cells These cells do notdo not kill each other kill each other

AB

Altering the initial ratios of these cells will Altering the initial ratios of these cells will alter the frequency of oscillationsalter the frequency of oscillations

Design Cell1 (Prey)Design Cell1 (Prey)

Prey cell must produce molecule A exponentiallyPrey cell must produce molecule A exponentially

Pc

Plux

Lux R

Lux I

Pc is always on

Lux R is produced which detects molecule A

Then initiates transcription at Plux

Which Produces More AA

A

A

A

DesignDesign

The Predator CellThe Predator Cell

The role of a predator is to reduce the prey numbers as a function of the predator population numbers.

PredatorDetect Prey Population Size

Reduce Prey Population Size

DesignDesign

Plux Lux R aiiA

The Predator CellThe Predator Cell

Detects Prey Population Size

Reduces Prey Population Size

DesignDesign

Plux Lux R aiiA

The Predator CellThe Predator Cell A

A

LuxR

LuxR A

aiiA

Design (Entire System)Design (Entire System)

Extra cellular pool of A (HSL) (this should oscillate)

Diffusion

Plux

Lux R aiiA

The Predator CellThe Predator CellA

A

LuxR

LuxR

A

aiiA

A

Pc

Plux

Lux R

Lux I

A

The Prey Cell

ModellingModelling

Tom’s Tom’s MonsterMonster

ModellingModelling

Testing parts: T9002Testing parts: T9002

A shocking discovery: at first sight...A shocking discovery: at first sight...

After finishing our oscillator design...After finishing our oscillator design...

MIT Project 2004:MIT Project 2004:Cell-Cell synchronized Oscillator DesignCell-Cell synchronized Oscillator Design

Similar approach using concepts of quorum sensingSimilar approach using concepts of quorum sensing

BUT: This system does not use predator-prey BUT: This system does not use predator-prey dynamics and is implemented in a single cell (ours is dynamics and is implemented in a single cell (ours is multicellular multicellular

MIT Oscillator Design

http://web.mit.edu/~cbatten/www/work/ssbc04/system-spec-ssbc04.pdf

Communication: The WikiCommunication: The Wiki

Wiki-NewspaperWiki-NewspaperDocumentation for Documentation for future referencesfuture referencesCommunicationCommunication Within the teamWithin the team With other teamsWith other teams

Monitoring Monitoring progress (Gantt progress (Gantt Chart)Chart)Present ourselves Present ourselves & our project& our project

OutlineOutline

Further modelling & testing of partsFurther modelling & testing of parts

Parts assemblyParts assembly

Phase 2Phase 2 Coupling the oscillator to a biological to Coupling the oscillator to a biological to

electrical interface electrical interface Synchronizing oscillations 2 petri dishes Synchronizing oscillations 2 petri dishes

Thank youThank you