An all-optical biological function generator and oscilloscope framework for characterizing gene circuit dynamics

dc.contributor.advisorTabor, Jeffrey J.en_US
dc.contributor.committeeMemberIgoshin, Oleg A.en_US
dc.contributor.committeeMemberBennett, Matthew R.en_US
dc.creatorOlson, Evan Jamesen_US
dc.date.accessioned2014-10-03T14:55:22Zen_US
dc.date.available2014-10-03T14:55:22Zen_US
dc.date.created2014-05en_US
dc.date.issued2014-04-21en_US
dc.date.submittedMay 2014en_US
dc.date.updated2014-10-03T14:55:23Zen_US
dc.description.abstractGene 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.en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationOlson, Evan James. "An all-optical biological function generator and oscilloscope framework for characterizing gene circuit dynamics." (2014) Master’s Thesis, Rice University. <a href="https://hdl.handle.net/1911/77383">https://hdl.handle.net/1911/77383</a>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/77383en_US
dc.language.isoengen_US
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.subjectOptogeneticsen_US
dc.subjectSynthetic biologyen_US
dc.subjectBioengineeringen_US
dc.titleAn all-optical biological function generator and oscilloscope framework for characterizing gene circuit dynamicsen_US
dc.typeThesisen_US
dc.type.dcmiSoftwareen_US
dc.type.materialTexten_US
thesis.degree.departmentApplied Physicsen_US
thesis.degree.disciplineNatural Sciencesen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelMastersen_US
thesis.degree.nameMaster of Scienceen_US
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