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iGEM @ Imperial
Starting off: Week 1
Week 1
Engineering/Biology
Introduction Lectures
Journal Club
Wiki
Brainstorming
3 ideas
Bio
Hard Drive
Remote
Controlled
Bacteria
Bio
Calculator
Bio-Clock
Cell
Networking
Crazy
Ideas
Bacterial
balloon
Biological to
Electrical
Interface
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
•The time period
is controlled by
•the radius
•gutter width
•cell density
Bio-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 Oscillator
Culture Wide
oscillations of AHL
Frequency must
be tuned easily
Oscillations must
be stable
Changing Concentration of AHL
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
Inte
Predator Prey Dynamics
Stabl
Lotka-Voltarra Model output
•Preda
•The on
species
•The gr
solely d
•The P
growth
carryin
•The P
Design
A
A
• Positive Feedback of A
• AB Induces production of more B
• Both A and B are used to make AB
B
B
Two Cell System
Two independent populations of Cells
These cells do not kill each other
A
B
Altering the initial ratios of these cells will
alter the frequency of oscillations
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
A
A
Plux
Lux I
A
A
Which Produces More A
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
Design
The Predator Cell
Detects Prey Population
Size
Plux
Lux R
Reduces Prey
Population Size
aiiA
Design
The Predator Cell
LuxR A
A
LuxR
Plux
A
Lux R
aiiA
aiiA
Design (Entire System)
P
c
A
Lux R
Diffusion
A
The Prey Cell
Plu
x
Extra cellular pool of A
(HSL)
(this should oscillate)
Lux I
A
The Predator Cell
Lux
R
A
A
Lux
R
Plu
x
Lux R
aii
A
aiiA
Modelling
Tom’s
Monster
Modelling
Testing parts: T9002
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
Wiki-Newspaper
Documentation for
future references
Communication


Within the team
With other teams
Monitoring
progress (Gantt
Chart)
Present ourselves
& our project
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