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This research introduces the concept of a Biological Comparator, inspired by electronic comparators, and the E.coliRuler, a promoter calibrator. The Biological Comparator functions by amplifying the bigger of two inputs, potentially outputting fluorescence proteins. The E.coliRuler, exemplified by the pOmpR vs. pOmpRm promoters, can compare relative strengths of promoters. Experimental processes include testing promoter pairs and assessing different osmolarity effects. Future work involves completing constructs, FACS experiments, and dynamic measurements to estimate system parameters. Further applications include controllers, filters, and discrete level detectors. Conclusions highlight the simplicity and usefulness of the Biological Comparator and E.coliRuler, emphasizing their in silico and in vivo implementations and urging imaginative exploration. The team, known as The E.nd, is dedicated to advancing genetic applications.
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Introduction • Comparator • E.coliRuler • in silico work • lab work • Further applications • Conclusions
Introduction The idea • Electronic comparator • small, useful device • Biological comparator • few genes • highly modular • E.coliRuler: Promoter calibrator
Comparator G A E B L What is the Comparator? Its electronic counterpart: A > B A = B A < B
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.
Comparator The effective model: repression activation
Comparator Simulations with typical part parameters: A > B A = B A < B (decay rate) (basal state) (transcription rate)
E.coliRuler E.coliRuler • Calibrating promoters with a biological comparator. • Can be used to: • Compare relative strenghts of different promoters
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
E.coliRuler EXPERIMENTAL PROCESS Two types of experiments: 1) Promoters A and B pOmpR 2) Promoter A pOmpR Promoter B pOmpRm
E.coliRuler Parts kan amp
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
E.coliRuler Further applications • Controller • Filters • Discrete level detector: happy bacteria
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…
Proportional controller upper threshold desired protein lower threshold
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
