A post-doctoral position is available in the research unit on Physical microfluidics and Bio-engineering, which is a joint research unit between Institut Pasteur and Ecole Polytechnique (Paris). The aim of this project is to explore transfer of information within a 3D aggregate of bacteria using microfluidics.
Scientific summary: Our measurements [1] of bacterial populations in microfluidic droplets have shown that the communities can display widely varying spatial structures, ranging from completely dissociated cells to loosely connected aggregates (see figure) to dense colonies. This variety of structures is likely to be a signature of the biological variability between individual cells, for instance from differential expression of specific adhesins such as Ag43 [2], compounded by the effects of confinement or mechanical forces.
In this project we will first determine the link between the observed 3D structure in the droplets and the expression of Ag43 or other adhesion mechanisms. We will then explore the influence of the geometric organisation of the population on the transfer of genetic material between the cells, by bringing a donor cell into contact with the 3D population using our in-house microfluidic tools [3]. We will look in particular at the spatio-temporal dynamics of the conjugation and how they depend on the 3D structure. This will then allow us to ask further questions, e.g. on the emergence of mutations for different colony structures or on the role of competition between different bacterial strains within a colony.
The research lab: The project will take place at the Phyical Microfluidics and Bioengi- neering research unit, which is jointly affiliated with Institut Pasteur (Paris) and Ecole Polytechnique (Palaiseau). The team is currently made up of about 10 physicists, engineers, and biologists. Our research is focused on understanding the link between the single-cell characteristics and the collective properties that emerge through cellular interactions at the scale of a small population. This is being studied on mammalian 3D cultures (e.g. organization in spheroids and organoids) as well as on micro-organisms (e.g. bacterial response to antibiotics). The lab web page can be found here.
The project will benefit from a collaboration with the group of Jean-Marc Ghigo at Institut Pasteur, who have a long-standing experience with biofilms and collective behavior of bacterial communities.
The candidate: The candidate should have a strong track record in quantitative microbiology, although exceptional candidates in related fields will be considered if they wish to address single-cell issues in bacteria. He/she should be able to run complex experiments that involve both physical and biological aspects, as well as the analysis of microscopy images and large sets of data. Knowledge of microfluidics techniques is not a requirement but mathematical literacy is a plus.
To apply or for further information: Applicants should state clearly their main contributions in the field of quantitative biology in their cover letter. Please send a CV with publication list and the names of three referees to Charles Baroud: charles.baroud@pasteur.fr.
References
[1] Gabriel Amselem, Cyprien Guermonprez, Benoˆıt Drogue, S ́ebastien Michelin, and Charles N. Baroud. Universal microfluidic platform for bioassays in anchored droplets Lab on a Chip. Lab on a Chip, 16:4200–4211, 2016.
[2] Ashwini Chauhan, Chizuko Sakamoto, Jean-marc Ghigo, and Christophe Beloin. Did I Pick the Right Colony ? Pitfalls in the Study of Regulation of the Phase Variable Antigen 43 Adhesin. PLoS One 5;8(9):e73568. doi: 10.1371. 2013.
[3] Raphael Tomasi, Sebastien Sart, Tiphaine Champetier, and Charles N Baroud. Studying 3D cell cultures in a microfluidic droplet array under multiple time-resolved conditions. BIoRxiv, pages 1–10, 2019.