An experimental approach to identify dynamical models of transcriptional regulation in living cells

Gianfranco Fiore, Filippo Menolascina, Mario Di Bernardo, Diego di Bernardo

Research output: Contribution to journalArticle (Academic Journal)peer-review

10 Citations (Scopus)

Abstract

We describe an innovative experimental approach, and a proof of principle investigation, for the application of System Identification techniques to derive quantitative dynamical models of transcriptional regulation in living cells. Specifically, we constructed an experimental platform for System Identification based on a microfluidic device, a time-lapse microscope, and a set of automated syringes all controlled by a computer. The platform allows delivering a time-varying concentration of any molecule of interest to the cells trapped in the microfluidics device (input) and real-time monitoring of a fluorescent reporter protein (output) at a high sampling rate. We tested this platform on the GAL1 promoter in the yeast Saccharomyces cerevisiae driving expression of a green fluorescent protein (Gfp) fused to the GAL1 gene. We demonstrated that the System Identification platform enables accurate measurements of the input (sugars concentrations in the medium) and output (Gfp fluorescence intensity) signals, thus making it possible to apply System Identification techniques to obtain a quantitative dynamical model of the promoter. We explored and compared linear and nonlinear model structures in order to select the most appropriate to derive a quantitative model of the promoter dynamics. Our platform can be used to quickly obtain quantitative models of eukaryotic promoters, currently a complex and time-consuming process.
Original languageEnglish
JournalChaos
Volume23
Issue number2
DOIs
Publication statusPublished - 2013

Structured keywords

  • Bristol BioDesign Institute

Keywords

  • Microfluidics
  • System Identification
  • Control Theory
  • Nonlinear Dynamics
  • Systems biology
  • SYNTHETIC BIOLOGY
  • Fluorescence Microscopy

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