1. iGEM @ Imperial

2. Starting off: Week 1 Week 1 Engineering/Biology Introduction Lectures Journal Club WikiBrainstorming 3 ideas

4. Only three ideas made the cut.

5. 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

6. 1010100000000011111000010101011111100000000111111111000001010100010100001000010100101001010000001001010101001010101001101010101001010 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

7. The Oscillator Changing Concentration of AHL Culture Wide oscillations of AHL Frequency must be tuned easily Oscillations must be stable

8. Week 2 Investigation of all 3 ideas Modelling Modelling Evaluating risks 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

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

10. Design A B A B Positive Feedback of A AB Induces production of more B Both A and B are used to make AB

11. 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

12. Design Cell1 (Prey) Prey 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 A A AAA

13. 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

14. Design Plux Lux RaiiA The Predator Cell Detects Prey Population Size Reduces Prey Population Size

15. Design Plux Lux RaiiA The Predator Cell A A LuxR A aiiA

16. Design (Entire System) Extra cellular pool of A (HSL) (this should oscillate) Diffusion Plu x Lux RaiiA The Predator Cell A A Lux R A aii A A PcPc Plu x Lux R Lux I A The Prey Cell

17. Modelling Tom’s Monster

18. Modelling

19. Testing parts: T9002

20. 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

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

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

23. Thank you