Research Engineer position (M/F): Digital holography to uncover the physics of bacterial biofilm formation

Job Description

Missions

The project probes the physics of bacterial motility and biofilm formation from an experimental biophysics perspective.
The successful candidate will take a leading role in the development, integration, validation, and use of a custom optical microscopy platform combining digital inline holography, light-sheet microscopy, fluorescence microscopy, and quantitative image analysis.

Activity

• digital inline holography and computational reconstruction of holograms;
• light-sheet microscopy, TIRF microscopy, and fluorescence microscopy;
• translation of scientific needs into technical specifications and experimental strategies;
• leadership in microscope design, construction, alignment, characterization, performance validation, and troubleshooting;
• definition, development, validation, and maintenance of experimental acquisition and analysis pipelines;
• image analysis, particle tracking, time-series analysis, and quantitative data analysis;
• programming, primarily in Python;
• use of machine-learning or artificial-intelligence tools for image analysis when useful;
• single-cell and single-molecule biophysics measurements;
• wet-lab activities and cell/molecular biology with bacteria, with training provided as needed;
• documentation of protocols, code, optical setups, and experimental procedures;
• technical coordination, training, and guidance of students, postdocs, engineers, and collaborators in an interdisciplinary environment;
• technology watch and presentation, dissemination, and valorization of technical and scientific developments.

Your Profil

Skills

We seek an outstanding and experienced candidate who has a master's degree, engineering degree, or equivalent, and who:

• has advanced expertise in physics, optics, instrumentation, biophysics, computational imaging, or a related discipline;
• has substantial practical experience with optical microscopy, optical alignment, lasers, cameras, or custom instrumentation;
• has experience with digital holography and numerical reconstruction of holograms, or a demonstrated ability to rapidly master comparable optical and computational techniques;
• has experience with light-sheet microscopy, TIRF microscopy, or fluorescence microscopy, or a demonstrated ability to rapidly master comparable microscopy techniques;
• has experience with image analysis, time-series analysis, and quantitative data analysis;
• has strong programming skills, preferably in Python;
• has experience with machine learning or computer vision, or is motivated to develop these skills;
• either has experience in a wet lab, or is eager to learn to work with bacteria;
• has demonstrated ability to lead technical developments or complex experimental projects;
• is careful, organized, and able to maintain clear experimental and technical documentation;
• enjoys troubleshooting and pushing the limits of custom optical microscopy setups;
• is able to train, advise, and communicate effectively with users and collaborators;
• enjoys working in an interdisciplinary environment;
• is creative, enthusiastic, highly motivated, and able to work both independently and as a member of a team.
High-level English communication skills are an asset; no knowledge of French is required.

Your Work Environment

Most of our knowledge of bacteria comes from studies of independent swimming cells. Yet, most bacteria on earth are found in non-motile aggregated communities, called biofilms, which bear little resemblance to their motile counterparts. Biofilms are acutely resistant to antibiotics, extremely difficult to eradicate, and are implicated in important global challenges, from deadly infections and antimicrobial resistance to food safety and water security.

Under the current paradigm, biofilms begin when a motile cell adheres and senses a surface, triggering a change in 'lifestyle'. But this crucial nucleation step remains poorly understood: what mechanochemical signal underlies surface sensing? Moreover, many natural biofilms, including many that cause chronic infections, exist in the absence of a substrate, suggesting that biofilms can nucleate via multiple mechanisms. Can nucleation be understood, not only as a biochemical switch in an individual cell, but also as an emergent behavior of active colloids?

By developing a unique setup which combines digital holographic microscopy and light-sheet microscopy, this project seeks to capture and resolve rare nucleation events and the resulting physiological response, thereby uncovering the physical mechanisms of biofilm initiation in various microenvironments.

This is a new project and new line of research funded by the Fondation Bettencourt Schueller Impulscience award and by the 'Physics and Mechanics of Biological Systems' team, comprised of three permanent CNRS researchers with backgrounds in physics and biophysics. The team is highly interactive and dynamic, and the successful candidate will have the opportunity to collaborate on other ongoing projects within the team, depending on their interests.

The Centre de Biologie Structurale (CBS) is an interdisciplinary and international research institute located in Montpellier, France. It is comprised of research teams combining biophysics, bioengineering, and structural biology. Its expertise spans cutting-edge optical microscopy, optical and magnetic tweezers, atomic force microscopy, NMR, X-ray crystallography, bioinformatics, bioengineering, and biomolecular modelling. It is home to many PhD students, postdocs, engineers, and researchers of diverse backgrounds and nationalities.

Constraints and risks

The position is initially for one year and is renewable, with multi-year funding available.
The position is well suited to an experienced candidate with a master's or engineering-level background in optics, physics, instrumentation, computational imaging, biophysics, or a related field. A PhD is desired, but not required.

Compensation and benefits

Compensation

From €3175 gross per month

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

The research professions