Introduction Comparator E.coliRuler in silico work lab work Further applications Conclusions

2. Introduction • Comparator • E.coliRuler • in silico work • lab work • Further applications • Conclusions

3. Introduction The idea • Electronic comparator • small, useful device • Biological comparator • few genes • highly modular • E.coliRuler: Promoter calibrator

4. Comparator G A E B L What is the Comparator? Its electronic counterpart: A > B A = B A < B

5. Comparator What is the Comparator? We prove it with a simple simulation In biological language: A > B A B A < B Compares two inputs and amplifies the bigger one. Outputs can be fluorescence proteins or another kind of proteins.

6. Comparator The effective model: repression activation

7. Comparator Simulations with typical part parameters: A > B A = B A < B (decay rate) (basal state) (transcription rate)

8. E.coliRuler E.coliRuler • Calibrating promoters with a biological comparator. • Can be used to: • Compare relative strenghts of different promoters

9. E.coliRuler pOmpR vs. pOmpRm • pOmpR: • Promoter of the gene for OmpC in E.coli • 3 binding sites • pOmpRm: • only 1 binding site • Regulated by osmolarity • EnvZ-OmpR regulatory system • pOmpR is stronger than pOmpRm

10. E.coliRuler EXPERIMENTAL PROCESS Two types of experiments: 1) Promoters A and B pOmpR 2) Promoter A pOmpR Promoter B pOmpRm

11. E.coliRuler   Parts      kan amp 

12. E.coliRuler Future Work • complete the constructs –next week • FACS experiments • different osmolarity at steady state • dinamical measurements at a given osmolarity • Estimate the specific parameters of our system

13. E.coliRuler Further applications • Controller • Filters • Discrete level detector: happy bacteria

14. Proportional controller Controller upper threshold A controller is a device which maintains a protein value given two thresholds mathematical modelling lower threshold Let’s go simulating…

15. Proportional controller upper threshold desired protein lower threshold

16. Conclusions Conclusions • Biological comparator: simple, robust, useful • implemented in silico • in vivo built and sequenced • we have tested two applications, but your imagination is the limit • E.coliRuler: promoter calibrator • developed in silico • 75% implemented in vivo • Controller: • elaborated in silico… soon in vivo

17. Our team:

18. The E.nd