Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software
Matthias Kaiser (University of Basel)
Florian Jug (Max Planck Institute of Molecular Cell Biology and Genetics)
Thomas Julou (University of Basel)
Siddharth Deshpande (University of Basel, TU Delft - BN/Cees Dekker Lab)
Thomas Pfohl (University of Basel)
Olin K. Silander (Massey University, University of Basel)
Gene Myers (Max Planck Institute of Molecular Cell Biology and Genetics)
Erik Van Nimwegen (University of Basel)
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Abstract
Much is still not understood about how gene regulatory interactions control cell fate decisions in single cells, in part due to the difficulty of directly observing gene regulatory processes in vivo. We introduce here a novel integrated setup consisting of a microfluidic chip and accompanying analysis software that enable long-term quantitative tracking of growth and gene expression in single cells. The dual-input Mother Machine (DIMM) chip enables controlled and continuous variation of external conditions, allowing direct observation of gene regulatory responses to changing conditions in single cells. The Mother Machine Analyzer (MoMA) software achieves unprecedented accuracy in segmenting and tracking cells, and streamlines high-throughput curation with a novel leveraged editing procedure. We demonstrate the power of the method by uncovering several novel features of an iconic gene regulatory program: the induction of Escherichia coli's lac operon in response to a switch from glucose to lactose.
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