Section: New Results

Analysis of fluorescent reporter gene data

The use of fluorescent and luminescent reporter genes allows real-time monitoring of gene expression, both at the level of individual cells and cell populations (Section 3.2). Over the years, many useful resources have appeared, such as libraries of reporter strains for model organisms and computer tools for designing reporter plasmids. Moreover, the widespread adoption of thermostated microplate readers in experimental laboratories has made it possible to automate and multiplex reporter gene assays on the population level. This has resulted in large time-series data sets, typically comprising ${10}^5-{10}^6$ measurements of absorbance, fluorescence, and luminescence for ${10}^3$ wells on the microplate. In order to fully exploit these data sets, we need sound mathematical methods to infer biologically relevant quantities from the primary data and computer tools to apply the methods in an efficient and user-friendly manner.

In the past few years we developed novel methods for the analysis of reporter gene data obtained in microplate experiments, based on the use of regularized linear inversion. This allows a range of estimation problems to be solved, notably the inference of growth rate, promoter activity, and protein concentration profiles. The linear inversion methods, published in Bioinformatics in 2015 [13], have been implemented in the Python package WellFARE and integrated in the web application WellInverter . Funded by a grant from the Institut Français de Bioinformatique (IFB), we improved WellInverter by developing a parallel computational architecture with a load balancer to distribute the analysis queries over several back-end servers, a new graphical user interface, and a plug-in system for defining high-level routines for parsing data files produced by microplate readers from different manufacturers. This has resulted in a scalable and user-friendly web service providing a guaranteed quality of service, in terms of availability and response time. The web service has been redeployed on the new IFB cloud and on an Inria server, accompanied by extensive user documentation, online help, and a tutorial. An article on WellInverter , illustrating the use of the tool by analyzing data of the expression of a fluorescent reporter gene controlled by a phage promoter in growing Escherichia coli populations, was published in BMC Bioinformatics this year [22]. We notably show that the expression pattern in different growth media, supporting different growth rates, corresponds to the pattern expected for a constitutive gene.