Probing delays and memory in gene activation using a gene oscilloscope

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This NSF award by the Biotechnology, Biochemical and Biomass Engineering program supports the development and application of a novel tool, the 'gene oscilloscope', to measure the kinetics of gene activation at the single cell level. The 'gene oscilloscope' consists of a yeast strain containing observable, dynamically controllable input transcription factor and a fluorescent reporter as the observable output. Input/output behavior is extracted from movies of single cells grown in microfluidic devices. It can be used to examine the dynamics of simple components in a gene regulatory network. The intellectual merit of this work is to quantify delays and memory in the activation of a promoter using simple lumped kinetic models that connect model parameters to promoter architecture. This work will yield mechanistic insights by comparing how different features of promoters and activators affect kinetics. In addition, it will inform and update large scale in silico modeling efforts of gene networks aimed at understanding how changes in network components lead to qualitatively different dynamics, aberrant function, and disease states. Broader impacts: Apart from basic insights into transcriptional dynamics, this work should further the concept of a gene oscilloscope and potentially enable synthetic biologists and metabolic engineers to characterize the dynamical properties of transcriptional device 'parts'. Apart from traditional research opportunities this project has and will provide both graduates and undergraduates in the PI's lab, the gene oscilloscope serves as a foundation for a set of research projects within the undergraduate Chemical-Biological Engineering laboratory. The goal is to expose the next generation of bioprocess engineers and biologists to the importance of single cell analysis in biotechnology, which traditionally has treated cultures as monolithic.