PhD in UPtoPARIS MSCA programme : Physics of virus diffusion : from environmental studies to medical applications

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ESPCI Paris

Lieu de travail

Paris - Ile-de-France - France

Intitulé du sujet

Physics of virus diffusion : from environmental studies to medical applications

Champs scientifiques

Physique

Description

At the Institut Langevin, in collaboration with various Biology laboratories, we study the diffusion properties of nanoparticles in different aquatic environments. We have developed a new, sensitive, interferometric, and non-destructive optical approach to detect label-free single nanoparticles that allows us to count and sort different types of nanoparticles (Boccara et al, Biomed. Opt. Exp. 2016). In short, we measure the light scattered by the nanoparticles and obtain an interferometric signal related to their size ; this measurement is complemented with single particle tracking of their Brownian motion.

So far, different types of viruses have been the focus of our main studies for their vital role in the balance of oceans microbiome as well as their importance in our intestinal tract. During these studies, we noticed that the trajectories of some viruses characterized by the existence of a rigid tail deviated from pure Brownian diffusion. These observations are particularly relevant as diffusion and spatial exploration by the viruses are critical to understand how microbial interactions shape the biogeochemical cycles in the ocean.

The proposed thesis project will consist of an experimental approach to perform a statistical study of the different parameters giving rise to trajectories anisotropy of different natural viruses and mutant derivatives. The PhD candidate will also develop analytical and numerical models of the hydrodynamic behavior of a structure with different geometries consisting of a head, a tail (rigid or flexible) and filaments of various lengths.

The ability of classifying virus in a given environment according to their size and structure is an essential tool in applications ranging from environmental to medical studies. In our previous experiments, we tested a number of samples from the Tara-Oceans expedition, as well as samples taken from the Marne River. One of the main concerns in rivers and water bodies remains the risk of fecal contamination and an abundance of small viruses has been correlated to fecal contamination. Our experiments indicated indeed an increase in viral abundance correlated with an increase in algal populations, often associated to toxin contamination.

More recently, we studied mouse intestinal virome samples. It has been hypothesized that dysregulations of bacterial populations by viruses constitute a favorable ground for inflammatory diseases of the intestine. Several studies have suggested that the presence of small viruses in the intestine and in aquatic environments has its origins in anthropogenic pollution. The quantification of viruses plays thus an important role not only in gastrointestinal diseases, environmental contamination assays, and microbial ecology but also in vaccine development, clinical diagnostics, and phagotherapy. Phagotherapy is of particular importance since it represents an emerging alternative to the impending crisis caused by bacteria resistance to antibiotics.

3i Aspects

This project falls into the category of several key enabling technologies of the EU : photonics, industrial biotechnology, and nanotechnology. The development of such a photonic tool for the detection of label-free nano-objects has strong industrial applications potential, not only in the context of virus detection for environmental studies but also on other nanotechnology fields. The device has already been patented and a start-up for its commercialization has been created.

Due to the interdisciplinary nature of the project, the selected PhD candidate will have to interact with researchers and develop skills in several disciplines : physics and biophysics, environmental and metagenomics biologists, as well as medical doctors. Moreover, the PhD candidate will be with the Tara Oceans international expedition and its global network. The candidate will also be encouraged to participate in international interdisciplinary schools as well as other international conferences where the candidate will present their results.

PhD supervisor(s) Ignacio Izzedin and Claude Boccara (co-supervisor)

Présentation établissement et labo d’accueil

ESPCI Paris
The Hosting Lab

The Institut Langevin (https://www.institut-langevin.espci.fr/) was created in 2009 following the merging of two institutes of the ESPCI Paris : the Laboratoire d’Optique Physique, directed by Claude Boccara, and the Laboratoire Ondes et Acoustique, created and directed by Mathias Fink. This CNRS UMR brings together world-class fundamental research and applied research with an interdisciplinary mission. An example of the dynamism of the Institut Langevin and its unique ecosystem is the creation of 14 startups since 2009 and seven granted patent applications in 2016 alone.

Attracting exceptional scientist in the fields of waves and imaging, the Institut Langevin, which has around 130 members, assembles a unique combination of expertise on wave manipulation, including acoustics, optic, and electromagnetic waves, from fundamental research to industrial applications. The Institut Langevin is structured in four research axes : waves in complex media, wave physics for medicine and biology, non-conventional imaging and sensing, and subwavelength physics. Due to the interdisciplinary nature of the institute, most researchers develop activities in more than one of these themes.

Site web :
https://www.upto.paris/

Profil du candidat

We are looking for candidates with a Masters diploma in physics or biophysics. The applicant must have a good knowledge of optics, photonics and microscopy, and have some experimental research experience. Knowledge in fluid dynamics and statistical physics is also highly appreciated, as well as notions in biology. Besides experimental experience, the candidate must be familiar with programming and numerical methods in Matlab, Python or similar languages, and be confortable with numerical simulations. The candidate must be able to work in a diverse team, both culturally and scientifically ; must possess initiative and curiosity, as well as decent communication skills.

Date limite de candidature
28/02/2018

Date de début de thèse
01/09/2018

Eléments à fournir pour la candidature

Applications must be submitted on the UPtoPARIS
More information is available in the "How to apply" section of the website.





ÉCOLE SUPÉRIEURE DE PHYSIQUE ET DE CHIMIE INDUSTRIELLES DE LA VILLE DE PARIS
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