Development of a Brownian Dynamics Simulation Software dedicated to Live Cell Fluorescence Imaging
Thèse soutenue le 27 novembre 2017
Supervisor: Olivier Thoumine team leader: cell adhesion molecules in Synapse Assembly – IINS.
Fluorescence has revolutionized cellular imaging: by deeply increasing contrast, it permits to image cellular structures, and to follow molecular dynamics, which were not achievable by other optical imaging methods. Nowadays, a great number of optical microscopy techniques use the properties of fluorescent dyes and proteins. They have allowed scientists to observe finer and finer structures, to study the dynamics of an ensemble of molecules (FRAP, PAF) or of individual particles (SPT, FCS) but also to investigate the interactions between molecules in live conditions (FCCS, FRET). However, these experimental paradigms are complex and numerous biases can introduce inaccuracy in the obtained results.
To the aim of precisely interpreting live cell fluorescence imaging experiments, we have developed a simulation software which takes into account the characteristic parameters of these experiments. This software, which provides a graphical interface to adjust in real time the simulation parameters, utilizes Monte Carlo Methods to simulate the Brownian motion of single molecules and the photophysics of associated fluorophores. These molecules diffuse in a user-defined geometry and can transit between fast and slow diffusion (trapping state), depending on the cellular compartment. Fluorophores can be fluorescent, blinked or photobleached. Transition rates between these states are used to simulate the fluorescence experiments. We show that the simulations generated by the algorithm are in accordance with the theoretical results typically used to analyze fluorescence experiment outputs. Then, we use the software to study an artificial cell-cell junction made up with two COS cells overlapping with each other. This junction, called adhesive contact, is mediated by two adhesion proteins called neurexin and neuroligin which establish a heterologous complex. Fluorescence imaging experiments (SPT, FRAP, FCS) have been performed, and are interpreted using simulations generated by our software. In this study, we show that the dynamic properties of neurexin are modified in the cell-cell contact area in accordance with the model.
Keywords : Simulation Software, Monte Carlo Methods, Brownian Dynamics, Diffusion-Trapping, Fluorescence Imaging, Cell-Cell junction, Single Particle Tracking (SPT), Fluorescence Recovery After Photobleaching (FRAP), Fluorescence Correlation Spectroscopy (FCS)
Matthieu Lagardère, Ingrid Chamma and Olivier Thoumine. FluoSim: a simulator of single molecule dynamics for live cell fluorescence imaging and super-resolution microscopy. In Preparation
Mikael Garcia, Cécile Leduc, Matthieu Lagardère, Amélie Argento, Jean-Baptiste Sibarita, and Olivier Thoumine. Two-tiered coupling between flowing actin and immobilized N-cadherin/catenin complexes in neuronal growth cones. PNAS 2015.
Macha Nikolski DR, CNRS, Président
Marianne Renner Prof., UPMC, Reviewer
François Nédélec EMBL, Reviewer
Jean-Baptiste Sibarita CNRS, Examiner
Arnauld Sergé Aix Marseille Université, Examiner
Olivier Thoumine DR, CNRS, Supervisor