iGEM 2007 ETH Zurich

ETH Zurich iGEM Team 2 ETH Zurich team

Learning Memory Recognition

Learning Memory Recognition

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

Memory Input 1Memory Input 2State variable 1State variable 2

Memory Memory Input 1Memory Input 2State variable 1State variable

Memory Memory Input 1Memory Input 2State variable 1State variable

Memory Memory Input 1Memory Input 2State variable 1State variable

Memory Memory Input 1Memory Input 2State variable 1State variable How can the switch keep its state with a new input?

Memory Memory Input 1Memory Input 2 Latch State variable 1State variable

Memory Memory Input 1Memory Input 2 Latch State variable 1State variable xx0keep state

Gated SR with latch

Mapping with AND gates

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

Biological Implementation of our system

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

System in the initial state (without any chemicals present)

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

Learning aTc

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

Memorizing

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

Testing for aTc

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

Testing for IPTG

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

Equations 28

Parameters 29

Simulation of Equations 30

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

Sensitivity Analysis

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

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

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

Acknowledgments 36

Thank you! Thank you for your attention! Questions?

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

Sensors System input 1 System input 2 Sensors Memory input 1 Memory input 2 Sensor 1 Sensor 2

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

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

Introduction, Motivation 3 Phases Learning Memory Recognition 42

Lab work BD FACSAria™ Cell-Sorting System