Browsing by Author "Olson, Evan James"
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Item An all-optical biological function generator and oscilloscope framework for characterizing gene circuit dynamics(2014-04-21) Olson, Evan James; Tabor, Jeffrey J.; Igoshin, Oleg A.; Bennett, Matthew R.Gene circuits are dynamical systems that regulate cellular behaviors, often using protein signals as inputs and outputs. Here we have developed an optogenetic ‘function generator’ for programming tailor-made gene expression signals in live E. coli. We designed light sequences with experimentally calibrated models of light-switchable two-component systems and used them to drive intracellular protein levels to match user-defined reference time-courses. This approach enabled generation of accelerated and linearized dynamics, sinusoidal oscillations with desired amplitudes and periods, and a complex waveform, all with unprecedented accuracy and precision. We also combined the function generator with a dual fluorescent protein reporter system, analogous to a dual-channel oscilloscope, to reveal that a synthetic repressible promoter linearly transforms repressor signals with an approximate 7-min delay. Our approach will enable a new generation of dynamic analyses of synthetic and natural gene circuits, providing an essential step toward the predictive design and rigorous understanding of biological systems.