BactMAP:An R package for integrating, analyzing and visualizing bacterial microscopy data

High-throughput analyses of single-cell microscopy data are a critical tool within the field of bacterial cell biology. Several programs have been developed to specifically segment bacterial cells from phase-contrast images. Together with spot and object detection algorithms, these programs offer powerful approaches to quantify observations from microscopy data, ranging from cell-to-cell genealogy to localization and movement of proteins. Most segmentation programs contain specific post-processing and plotting options, but these options vary between programs and possibilities to optimize or alter the outputs are often limited. Therefore, we developed BactMAP (Bacterial toolbox for Microscopy Analysis & Plotting), a command-line based R package that allows researchers to transform cell segmentation and spot detection data generated by different programs into various plots. Furthermore, BactMAP makes it possible to perform custom analyses and change the layout of the output. Because BactMAP works independently of segmentation and detection programs, inputs from different sources can be compared within the same analysis pipeline. BactMAP complies with standard practice in R which enables the use of advanced statistical analysis tools, and its graphic output is compatible with ggplot2, enabling adjustable plot graphics in every operating system. User feedback will be used to create a fully automated Graphical User Interface version of BactMAP in the future. Using BactMAP, we visualize key cell cycle parameters in Bacillus subtilis and Staphylococcus aureus, and demonstrate that the DNA replication forks in Streptococcus pneumoniae dissociate and associate before splitting of the cell, after the Z-ring is formed at the new quarter positions. BactMAP is available from https://veeninglab.com/bactmap

Noise propagation in synthetic gene circuits for metabolic control

International audienceDynamic control of enzyme expression can be an effective strategy to engineer robust metabolic pathways. It allows a synthetic pathway to self-regulate in response to changes in bioreactor conditions or the metabolic state of the host. The implementation of this regulatory strategy requires gene circuits that couple metabolic signals with the genetic machinery, which is known to be noisy and one of the main sources of cell-to-cell variability. One of the unexplored design aspects of these circuits is the propagation of biochemical noise between enzyme expression and pathway activity. In this article, we quantify the impact of a synthetic feedback circuit on the noise in a metabolic product in order to propose design criteria to reduce cell-to-cell variability. We consider a stochastic model of a catalytic reaction under negative feedback from the product to enzyme expression. On the basis of stochastic simulations and analysis, we show that, depending on the repression strength and promoter strength, transcriptional repression of enzyme expression can amplify or attenuate the noise in the number of product molecules. We obtain analytic estimates for the metabolic noise as a function of the model parameters and show that noise amplification/attenuation is a structural property of the model. We derive an analytic condition on the parameters that lead to attenuation of metabolic noise, suggesting that a higher promoter sensitivity enlarges the parameter design space. In the theoretical case of a switch-like promoter, our analysis reveals that the ability of the circuit to attenuate noise is subject to a trade-off between the repression strength and promoter strength

Évolution de la résistance des entérobactéries aux antibiotiques sur l’île de la Réunion : émergence des bêta-lactamases à spectre élargi

International audienceAim of the study : The antibiotic resistance of enterobacteriacae knows a worldwide worrying evolution with an increase of the extended spectrum betalactamases (ESBL) that spread into the community. Few publications describe this problem in the Indian Ocean area. The aim of this study is first to identify in Félix Guyon Hospital (Reunion Island) the emergent antibiotics resistance for enterobacteriaceae between 1997/1998 and 2006/2007 periods, at second, to update the prophylactic and therapeutic measures for handling the risk linked to multiresistant enterobacteriaceae in our hospital and third, to assess the risk in Reunion Island and especially at the community level. Methods : The antibiotic susceptibility of 7814 enterobacteriaceae strains collected among patients, during 1997/1998 and 2006/2007 periods, were analysed as well as the consumption of the third generation cephalosporins, imipenem and fluoroquinolones. Results : Within a span of time of 10 years, an important increase (+ 57 %) of the resistance prevalence of enterobacteriaceae is observed. The resistance by the ESBL production mechanism is predominant especially for Enterobacter cloacae and Escherichia coli. An important use of broad spectrum antibiotics is correlated with this resistance evolution. Conclusion :The emergence of ESBL-producing enterobacteriaceae in our hospital is impairing both therapeutic and health care. It requires a much better control of antibiotics prescriptions and therefore, an important multidisciplinary implication. A proof molecular analysis would allow to evaluate the risk more precisely, especially at the community level.But de l’étude : La résistance des entérobactéries aux antibiotiques connaît une évolution mondiale préoccupante avec un impact croissant des bêtalactamases à spectre élargi (BLSE) qui diffusent notamment dans le secteur communautaire. Peu de publications permettent de connaître la situation actuelle dans la région Océan Indien (R-OI). Le but de cette étude était d’identifier, au centre hospitalier Félix Guyon (CHFG) (Île de La Réunion) entre les périodes 1997/98 et 2006/07, les phénomènes émergents en termes de résistance bactérienne afin d’actualiser les mesures prophylactiques et thérapeutiques pour la gestion du risque lié aux entérobactéries multirésistantes dans l’établissement et d’appréhender l’importance du risque engendré par ce problème à l’échelle régionale et en particulier, dans le secteur communautaire. Méthodes : Analyse de la sensibilité aux antibiotiques de 7814 souches d’entérobactéries isolées chez des patients hospitalisés au sein de prélèvements à visée diagnostique au cours des deux périodes considérées et mesure de la consommation en céphalosporine de 3e génération (C3G), imipénème (IMP) et fluoroquinolones (FQ). Résultats : On observe en dix ans, une augmentation considérable (+ 57 %) de la prévalence des entérobactéries résistantes aux C3G. La résistance par production de BLSE émerge nettement (prévalence multipliée par 3) notamment chez Enterobacter cloacae et Escherichia coli (prévalence multipliée par 30). Une consommation importante en antibiotiques à large spectre est associée à cette évolution. Conclusion : L’émergence des BLSE dans notre établissement expose à un problème croissant de prise en charge thérapeutique. L’absence actuelle de maîtrise du phénomène nécessite une implication particulière pluridisciplinaire. Une analyse approfondie, notamment moléculaire, permettrait d’envisager de façon plus précise le risque encouru, notamment à l’échelle communautaire, par la population réunionnaise

Solving Optimal Control Problems for Monotone Systems Using the Koopman Operator

peer reviewedaudience: researcher, professional, studentKoopman operator theory offers numerous techniques for analysis and control of complex systems. In particular, in this chapter we will argue that for the problem of convergence to an equilibrium, the Koopman operator can be used to take advantage of the geometric properties of controlled systems, thus making the optimal solutions more transparent, and easier to analyse and implement. The motivation for the study of the convergence problem comes from biological applications, where easy-to-implement and easy-to-analyse solutions are of particular value. At the moment, theoretical results have been developed for a class of nonlinear systems called monotone systems. However, the core ideas presented here can be applied heuristically to non-monotone systems. Furthermore, the convergence problem can serve as a building block for solving other control problems such as switching between stable equilibria, or inducing oscillations. These applications are illustrated on biologically inspired numerical examples

Predictive biology: modelling, understanding and harnessing microbial complexity

Predictive biology is the next great chapter in synthetic and systems biology, particularly for microorganisms. Tasks that once seemed infeasible are increasingly being realized such as designing and implementing intricate synthetic gene circuits that perform complex sensing and actuation functions, and assembling multi-species bacterial communities with specific, predefined compositions. These achievements have been made possible by the integration of diverse expertise across biology, physics and engineering, resulting in an emerging, quantitative understanding of biological design. As ever-expanding multi-omic data sets become available, their potential utility in transforming theory into practice remains firmly rooted in the underlying quantitative principles that govern biological systems. In this Review, we discuss key areas of predictive biology that are of growing interest to microbiology, the challenges associated with the innate complexity of microorganisms and the value of quantitative methods in making microbiology more predictable.Defence Threat Reduction Agency (Grant HDTRA1-15-1-0051