iGEM @ Imperial

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iGEM _at_ Imperial
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Starting off Week 1

• Week 1
• Engineering/Biology Introduction Lectures
• Journal Club
• Wiki
• Brainstorming
• 3 ideas

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(No Transcript)
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Only three ideas made the cut.
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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

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Bio-Memory
10101000000000111110000101010111111000000001111111
11000001010100010100001000010100101001010000001001
010101001010101001101010101001010

• 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
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The Oscillator

• Culture Wide oscillations of AHL
• Frequency must be tuned easily
• Oscillations must be stable

Changing Concentration of AHL
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• Week 2
• Investigation of all 3 ideas
• Modelling
• Evaluating risks
• Start work in the Wet lab
• Decision on the Oscillator as main projectcan
  use other ideas as further developments

• Week 3
• Further research
• Modelling
• Assembly of parts
• Protocols for testing parts
• Setting up OWW

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Predator Prey Dynamics
Simply Make a Bio-chemical system that can do
this.
Lotka-Voltarra Model output
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Design

• Positive Feedback of A
• AB Induces production of more B
• Both A and B are used to make AB

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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

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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
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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
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Design
The Predator Cell
Detects Prey Population Size
Reduces Prey Population Size
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Design
The Predator Cell
A
LuxR
A
A
LuxR
aiiA
Lux R
aiiA
Plux
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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
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Modelling

• Toms Monster

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Modelling
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Testing parts T9002
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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
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Communication The Wiki

• Wiki-Newspaper
• Documentation for future references
• Communication
• Within the team
• With other teams
• Monitoring progress (Gantt Chart)
• Present ourselves our project

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Outline

• Further modelling testing of parts
• Parts assembly
• Phase 2
• Coupling the oscillator to a biological to
  electrical interface
• Synchronizing oscillations 2 petri dishes

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Thank you