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iGEM 2007 ETH Zurich

iGEM 2007 ETH Zurich. 04.06.2007. ETH Zurich team. ETH Zurich iGEM Team. Learning. Memory. Recognition. Learning. Memory. Recognition. System design. System output 1. Sensors. Memory. Decoder. System input 1. System output 2. System output 3. System input 2. System output 4.

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iGEM 2007 ETH Zurich

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  1. iGEM 2007 ETH Zurich 04.06.2007

  2. ETH Zurich team ETH Zurich iGEM Team

  3. Learning Memory Recognition

  4. Learning Memory Recognition

  5. System design System output 1 Sensors Memory Decoder System input 1 System output 2 System output 3 System input 2 System output 4

  6. Memory

  7. Memory

  8. Memory

  9. Memory

  10. Memory How can the switch keep its state with a new input?

  11. Memory

  12. Memory

  13. Gated SR with latch

  14. Mapping with AND gates

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

  16. Biological Implementation of our system

  17. cI cI cI cI cI cI cI cI cI System overview OLuxR OCI Pconst cII tetR Pconst OCII OLuxR Pconst cI lacI Pconst OTetR OCII RFP Pconst luxR Pconst OCI OLacI GFP Pconst YFP OlacI OCII CFP OCI OTetR Pconst cI Pconst cII

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

  19. cI cI cI cI cI cI cI cI cI TetR TetR OLuxR OCI Pconst cII tetR Pconst LacI LacI OCII OLuxR Pconst cI lacI Pconst OTetR OCII RFP Pconst LuxR luxR Pconst OCI OLacI GFP Pconst LacI TetR YFP OlacI OCII CFP OCI OTetR Pconst cI Pconst cII

  20. Learning aTc

  21. cI cI cI cI cI cI cI cI cI TetR TetR OLuxR OCI Pconst cII tetR Pconst LacI LacI aTc OCII OLuxR Pconst cI TetR lacI Pconst OTetR OCII RFP Pconst LuxR LacI luxR Pconst OCI OLacI GFP Pconst aTc LacI TetR CII CII CII CII YFP OlacI OCII CFP OCI OTetR Pconst cI Pconst cII

  22. Memorizing

  23. AHL AHL AHL cI cI cI cI cI cI cI cI cI CII TetR TetR OLuxR OCI Pconst cII tetR Pconst CII aTc LacI LacI TetR OCII OLuxR Pconst cI CII lacI Pconst OTetR OCII RFP Pconst + AHL LuxR LacI luxR Pconst OCI OLacI GFP Pconst aTc TetR LacI CII CII YFP OlacI OCII CFP OCI OTetR Pconst cI Pconst cII

  24. Testing for aTc

  25. AHL AHL cI cI cI cI cI cI cI cI cI CII TetR TetR OLuxR OCI Pconst cII tetR Pconst CII aTc LacI LacI OCII OLuxR Pconst cI TetR CII lacI Pconst OTetR OCII RFP Pconst + AHL LuxR LacI luxR Pconst OCI OLacI GFP Pconst aTc LacI CII TetR CII YFP OlacI OCII CFP OCI OTetR Pconst cI Pconst cII

  26. Testing for IPTG

  27. AHL AHL cI cI cI cI cI cI cI cI cI CII TetR TetR OLuxR OCI Pconst cII tetR Pconst CII LacI LacI OCII OLuxR Pconst cI TetR CII lacI Pconst OTetR OCII RFP Pconst IPTG + AHL LuxR LacI luxR Pconst OCI OLacI GFP Pconst IPTG LacI CII TetR YFP OlacI OCII CFP OCI OTetR Pconst cI Pconst cII

  28. Equations

  29. Parameters

  30. Simulation of Equations

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

  32. Sensitivity Analysis

  33. Lab work IPTG LacI LacI LacI + lacI OCI OLacI GFP Pconst Pconst

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

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

  36. Acknowledgments

  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. Introduction, Motivation 3 Phases • Learning • Memory • Recognition

  40. Lab work BD FACSAria™Cell-Sorting System

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