Optimal Experiment Design and Leveraging Competition for Shared Resources in Cell-free Extracts

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Title Optimal Experiment Design and Leveraging Competition for Shared Resources in Cell-free Extracts
Authors Wolfgang Halter, Frank Allgower, Richard M. Murray and Andras Gyorgy
Source To appear, 2018 Conference on Decision and Control (CDC)
Abstract The fact that genes compete for shared cellular resources poses a fundamental challenge when identifying pa- rameters of synthetic gene circuits. A recently developed model of gene expression tackles this problem by explicitly accounting for resource competition. In addition to accurately describing experimental data, this model only depends on a handful of easily identifiable parameters with clear physical interpretation. Based on this model, we outline a procedure how to select the optimal set of experiments to characterize biomolecular parts in synthetic biology. Additionally, we reveal the role competition for shared resources plays, provide guidelines how to minimize its detrimental effects, and how to leverage this phenomenon to extract the most information about unknown parameters. To illustrate the results, we consider the case of part characterization in cell-free extracts, treat plasmid DNA concentrations as decision variables, and demonstrate the significant performance difference between na ̈ıve and optimal experiment design.
Type Conference paper
URL https://www.cds.caltech.edu/~murray/preprints/hamg18-cdc.pdf
Tag hamg18-cdc
ID 2018b
Funding NSF MPP2
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