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Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks

  • Hidde de JongEmail author
  • Johannes Geiselmann
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7699)

Abstract

The understanding of the regulatory networks controlling the adaptation of bacteria to changes in their environment is critically dependent on the ability to monitor the dynamics of gene expression. Here, we review the use of fluorescent reporter genes for dynamically quantifying promoter activity and other quantities characterizing gene expression. We discuss critical physical and biological parameters in the design, development, and use of fluorescent reporter strains. Moreover, we review measurement models that have been proposed to interpret primary fluorescence data and inference methods for estimating gene expression profiles from these data. As an illustration of the use of fluorescent reporter strains for analyzing bacterial regulatory networks, we consider two applications in the model bacterium Escherichia coli in some detail: the joint control of gene expression by global physiological effects and specific regulatory interactions, and the importance of protein stability for the inference and analysis of transcriptional regulatory networks. We conclude by discussing some current trends in the use of fluorescent reporter genes.

Keywords

Fluorescent reporter genes Bacterial regulatory networks Growth Gene expression Bioinformatics Systems biology 

Notes

Acknowledgements

This work was supported by the Investissements d’avenir Bio-informatique programme under project Reset (ANR-11-BINF-0005).

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.INRIA, Grenoble - Rhône-Alpes Research CentreSaint-Ismier CedexFrance
  2. 2.Laboratoire Interdisciplinaire de Physique (LIPhy, CNRS UMR 5588)Université Grenoble AlpesSaint Martin d’HèresFrance

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