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

Title	Optimal Experiment Design and Leveraging Competition for Shared Resources in Cell-free Extracts
Authors	Wolfgang Halter, Frank Allgower and 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
DOI
Tag	hamg18-cdc
ID	2018b
Funding	NSF MPP2
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