PhD: Motility study of bacteria of the Pseudomonas genus using original optical tweezers configurations (M/F)

Job Description

Thesis Subject

-Over the last years, optical tweezers (OT) became an essential non-invasive observation, characterization and manipulation tool in microbiology, chemistry and solid-state physics. In particular, optical tweezers permit to get deeper insight into biological species such as cells, viruses, or bacteria. The high bacteria speed of up to hundred micrometers per second presents a challenge for the observation of a single bacterium as it remains only a few seconds within the microscope's field of view. In this context, we are working on the development of original optical tweezers approaches based on nanostructured optical fibers (OFT) which will allow long-term studies of a single bacterium or the investigation of the interaction between a single pathogenic bacterium and a human cell. Moreover, OFT allow to study the bacteria flagella action by fluorescence microscopy. This PhD thesis will focus on three main topics: flagella fate during bacteria division, bacteria flagellar propulsion of Pseudomonas bacteria, and toxin injection by the human pathogen P. aeruginosa. In this context, 3D fiber optic or beam-focusing tweezers will be used to characterize the flagellar movement of trapped bacteria, while a novel 2D tweezers will be used to study the movement of free-swimming bacteria in a tube-shaped volume. Furthermore, the combination of two 3D tweezers will allow control the distance and duration of contact between a single bacterium and a single human cell. Dedicated microfluidic chips will enable the sequential trapping of only one bacterium or cell, and fluorescence imaging will allow the detection of the flagellum or the death of the human cell. Finally, we will deal with an important aspects of pathogenicity: the mechanism of action of antibodies directed against the flagellum and the ability of a single bacterium to kill a human cell.The experimental work will be completed by theoretical and numerical consideration in order to analyse the acquired data and to understand the underlying physics. Through these approaches, the PhD will contribute to deepen the biophysical understanding of the relationship between flagellar status (size, number, position) and bacterial biology (swimming capabilities, division and infection).

Required skills:
- Good background of either optics or biology with the ambition to acquire good knowledge of the complementary domain.
- Capacity to run optics experiments and of experimental development
- Basic knowledge in numerical simulations / data treatment (python)
- Ability to work on an interdisciplinary project

Your Work Environment

The PhD is part of an interdisciplinary collaboration between Jochen Fick, physicist at Institut Néel (IN) and Eric Faudry, biologist at Institut de Biologie Structurale (IBS). The optical experiments will be run at IN, except for pathogen bacteria which requires a temporal transfer of the optical tweezers into a class P2 laboratory at IBS. The bacteria cultures and modifications will be done at IBS. The student will register at the physcal doctoral school and will be supervised by J. Fick and E. Faudry.

The Institut NÉEL is a CNRS unit (UPR 2940) under agreement with the University Grenoble Alpes. The laboratory is related to the CNRS Physique. It is located in Grenoble, in the heart of a unique scientific, industrial and cultural environment. It is one of the largest French national research institutes for fundamental research in condensed matter physics enriched by interdisciplinary activities at the interfaces with chemistry, engineering and biology. It consists of 450 employees, including 175 researchers.
CNRS is a public, scientific and technological organisation.
The core mandate is to identify, carry out ou have carried out, either alone or with partners, all research that advances science or contributes to the country's economic, social, and cultural progress. Internationally recognised for the excellence of its scientific research, the CNRS is a reference in the world of research and development, as well as for the general public.

Constraints and risks

The work with human pathogen bacteria requires to work in a biological safety cabinet in a class P2 laboratory accessible at IBS, and to follow a specific biological safety training.

Compensation and benefits

Compensation

2300 € gross monthly

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

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