1. iGEM 2007 ETH Zurich 04.06.2007

2. ETH Zurich iGEM Team 2 ETH Zurich team

3. Learning Memory Recognition

4. Learning Memory Recognition

5. System design System input 1 System input 2 System output 1 System output 2 System output 3 System output 4 SensorsDecoderMemory

6. Memory Input 1Memory Input 2State variable 1State variable 2

7. Memory Memory Input 1Memory Input 2State variable 1State variable 2 0000

8. Memory Memory Input 1Memory Input 2State variable 1State variable 2 0000 1010

9. Memory Memory Input 1Memory Input 2State variable 1State variable 2 0000 1010 0101

10. Memory Memory Input 1Memory Input 2State variable 1State variable 2 0000 1010 0101 How can the switch keep its state with a new input?

11. Memory Memory Input 1Memory Input 2 Latch State variable 1State variable 2 00100 10110 01101

12. Memory Memory Input 1Memory Input 2 Latch State variable 1State variable 2 00100 10110 01101 xx0keep state

13. Gated SR with latch

14. Mapping with AND gates

15. System design System input 1 System input 2 System output 1 System output 2 System output 3 System output 4 Sensors Decoder Memory Latch Sensor 1 Sensor 2 Sensor 3 aTc IPTG AHL TetR LuxR LacI CFP RFP YFP GFP cI cII

16. Biological Implementation of our system

17. cI P const lacI cI P const tetR cI P const luxR cI P const cII O CI O LuxR cI O LuxR O CII cI P const O CII O TetR cI P const O LacI O CI cI P const cI O CII O lacI cI P const cII O TetR O CI RFP GFP CFP YFP P const System overview

18. System in the initial state (without any chemicals present)

19. cI P const lacI cI P const tetR cI P const luxR cI P const cII O CI O LuxR cI O LuxR O CII cI P const O CII O TetR cI P const O LacI O CI cI P const cI O CII O lacI cI P const cII O TetR O CI RFP GFP CFP YFP TetR LacI LuxR TetR LacI P const LacITetR

20. Learning aTc

21. cI P const lacI cI P const tetR cI P const luxR cI P const cII O CI O LuxR cI O LuxR O CII cI P const O CII O TetR cI P const O LacI O CI cI P const cI O CII O lacI cI P const cII O TetR O CI RFP GFP CFP YFP TetR LacI LuxR TetR LacI P const LacI aTc CII TetR

22. Memorizing

23. cI P const lacI cI P const tetR cI P const luxR cI P const cII O CI O LuxR cI O LuxR O CII cI P const O CII O TetR cI P const O LacI O CI cI P const cI O CII O lacI cI P const cII O TetR O CI RFP GFP CFP YFP TetR LacI LuxR TetR LacI P const LacI aTc CII TetR AHL + CII

24. Testing for aTc

25. cI P const lacI cI P const tetR cI P const luxR cI P const cII O CI O LuxR cI O LuxR O CII cI P const O CII O TetR cI P const O LacI O CI cI P const cI O CII O lacI cI P const cII O TetR O CI RFP GFP CFP YFP TetR LacI LuxR TetR LacI P const LacI aTc CII TetR AHL + CII TetR CII

26. Testing for IPTG

27. cI P const lacI cI P const tetR cI P const luxR cI P const cII O CI O LuxR cI O LuxR O CII cI P const O CII O TetR cI P const O LacI O CI cI P const cI O CII O lacI cI P const cII O TetR O CI RFP GFP CFP YFP TetR LacI LuxR TetR LacI P const CII TetR AHL + CII TetR IPTG LacI

28. Equations 28

29. Parameters 29

30. Simulation of Equations 30

31. Sensitivity Questions – Parameter accuracy? – “Dangerous” parameters? – Target parameters for biological changes?

32. Sensitivity Analysis

33. Lab work P const lacI P const O LacI O CI GFP + LacI IPTG LacI

34. Summary Learning, Memory, Recognition Successful System Simulations Realistic Parameters – Robust Design Toggle switch design – dual promoter 11 Parts to registry 34

35. Applications Bio-Memory Bio-Chip Multiple Purpose Cell Lines – Patient Specific Medicine – Intelligent Biosensors 35

36. Acknowledgments 36

37. Thank you! Thank you for your attention! Questions?

38. Sensitivity analysis results Robustness System sensitive to: – Protein basal production levels (???) – Parameters elated to the cI, cII function cI, cII repressors dissociation constant cI, cII repressors Hill cooperativity cI, cII degradation rates Candidates for biological changes: – Basal production levels – cI, cII degradation rates

39. Sensors System input 1 System input 2 Sensors Memory input 1 Memory input 2 Sensor 1 Sensor 2

40. Memory Memory input 1 Memory input 2 Memory output 1 Memory output 2 ? State variable 1 State variable 2

41. Decoder State variable 1 State variable 2 System output 1 System output 2 System output 3 System output 4 Current input 1 in2 ANDsv2 in2ANDsv1 in1 ANDsv2 in1 ANDsv1

42. Introduction, Motivation 3 Phases Learning Memory Recognition 42

43. Lab work BD FACSAria™ Cell-Sorting System