Igem @ imperial
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iGEM @ Imperial. Week 1 Engineering/Biology Introduction Lectures Journal Club Wiki Brainstorming 3 ideas. Starting off: Week 1. Only three ideas made the cut. Bio-Clock (Re-defining Time). Pulse of AHL moves along a gutter of medium Cells fluoresce when activated Refractory period

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iGEM @ Imperial

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Igem @ imperial

iGEM @ Imperial


Starting off week 1

Week 1

Engineering/Biology Introduction Lectures

Journal Club

Wiki

Brainstorming

3 ideas

Starting off: Week 1


Only three ideas made the cut

Only three ideas made the cut.


Bio clock re defining time

Bio-Clock (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 memory

Bio-Memory

1010100000000011111000010101011111100000000111111111000001010100010100001000010100101001010000001001010101001010101001101010101001010

  • 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 oscillator

The Oscillator

  • Culture Wide oscillations of AHL

  • Frequency must be tuned easily

  • Oscillations must be stable

Changing Concentration of AHL


Igem imperial

Week 2

Investigation of all 3 ideas

Modelling

Evaluating risks

Start work in the Wet lab

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

Week 3

Further research

Modelling

Assembly of parts

Protocols for testing parts

Setting up OWW


Predator prey dynamics

Predator Prey Dynamics

Simply Make a Bio-chemical system that can do this.

Lotka-Voltarra Model output


Design

A

A

B

B

Design

  • Positive Feedback of A

  • AB Induces production of more B

  • Both A and B are used to make AB


Two cell system

A

B

Two Cell System

  • Two independent populations of Cells

  • These cells do not kill each other

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


Design cell1 prey

A

A

A

A

Design Cell1 (Prey)

  • Prey cell must produce molecule A exponentially

Lux R is produced which detects molecule A

Pc

Lux R

Then initiates transcription at Plux

Pc is always on

Lux I

Plux

Which Produces More A


Design1

Design

The Predator Cell

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

Predator

Detect Prey Population Size

Reduce Prey Population Size


Design2

Lux R

aiiA

Plux

Design

The Predator Cell

Detects Prey Population Size

Reduces Prey Population Size


Design3

Design

The Predator Cell

A

LuxR

A

A

LuxR

aiiA

Lux R

aiiA

Plux


Design entire system

Pc

Lux R

Lux I

Plux

A

A

A

Design (Entire System)

Diffusion

Extra cellular pool of A (HSL)

(this should oscillate)

The Prey Cell

The Predator Cell

LuxR

A

A

LuxR

aiiA

Lux R

aiiA

Plux


Modelling

Modelling

  • Tom’s Monster


Modelling1

Modelling


Testing parts t9002

Testing parts: T9002


A shocking discovery at first sight

A shocking discovery: at first sight...

  • After finishing our oscillator design...

  • MIT Project 2004:

    • Cell-Cell synchronized Oscillator Design

    • Similar approach using concepts of quorum sensing

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

MIT Oscillator Design

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


Communication the wiki

Communication: The Wiki

  • Wiki-Newspaper

  • Documentation for future references

  • Communication

    • Within the team

    • With other teams

  • Monitoring progress (Gantt Chart)

  • Present ourselves & our project


Outline

Outline

  • Further modelling & testing of parts

  • Parts assembly

  • Phase 2

    • Coupling the oscillator to a biological to electrical interface

    • Synchronizing oscillations 2 petri dishes


Thank you

Thank you


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