Subject

Recent advances in next-generation sequencing (NGS) technologies and computational methods are revolutionizing scientific research in the field of public health as well as emerging infectious diseases (EID). NGS has become an essential tool for the molecular characterization of viral communities that could help determine the origin of epidemics and discover new pathogens. Performing an enrichment step that focuses on one or more pathogens allows for optimal sequencing. However, hybridization capture, which is widely used, is not only laborious (>2-3 days of work) and expensive because it requires the design and synthesis of thousands of primers or hybridization probes, but it also requires quantities of DNA. In addition, this approach can often produce inconsistent results and lack of homogeneity of coverage at the target region. Droplet microfluidics is an alternative approach that allows targeting of fragments of interest by encapsulating an independent amplification and identification reaction (PCR or other equivalent systems such as RPA and/or CRISPR/Cas13a) in millions of microscopic droplets. Targeted enrichment is then achieved by sorting these droplets. Currently, droplets are generated by microfluidic arrays and sorted with a fluorescence-activated cell sorter (FACS). However, the arrays require a complex laboratory environment and FACS is an expensive instrument that can damage droplets.
It is now possible to generate millions of droplets at once by spreading the stock solution on microstructured plates (microplates). The roughness of these microplates destabilizes the liquid film of stock solution, which forms a very large number of microdroplets. However, these plates are not compatible with FACS, and droplet sorting is currently impossible. However, acoustic tweezers allow the manipulation of micro-objects (such as cells or microdroplets) without contact, but they have not been tested for target enrichment of DNA in droplets. This postdoctoral project proposes to generate the droplets using a microstructured wafer (microplate) and then sort them using an acoustic tweezer. It is articulated in three axes:

Objectives of this project:
1. Use microplates to generate millions of droplets in seconds without any pumps.
2. Use micro acoustic tweezers to extract individual millimeter droplets from plates.
3. Develop and validate one-pot detection systems based on the combination of RPA and CRISPR/cas13a in these microdroplets.
This post-doctoral fellowship will be carried out at the Pasteur Institute of Paris in the EPVO unit and in collaboration with the University of Lille with the team of Pr Michael Baudoin.

Skills needed:

- We are looking for candidates motivated by a multidisciplinary work at the interface between physics
(acoustics, microfluidics), biology and chemistry.
- A strong background in physics and/or biology and/or experimental chemistry is required and a
experience in clean room microfabrication would be a big plus.
- Finally, basic theoretical knowledge in wave physics (especially acoustics)
and/or microfluidics would be appreciated.

Contact:

NICOLA BERTHET, RESEARCHER
INSTITUT PASTEUR - EPVO. UNIT 25 RUE DU DOCTEUR
ROUX. 75724 PARIS
EMAIL: NICOLAS.BERTHET@PASTEUR.FR
HTTPS://RESEARCH.PASTEUR.FR/FR/MEMBER/NICOLASBERTHET/

MICHAEL BAUDOIN, PROFESSOR
INSTITUT UNIVERSITAIRE DE FRANCE
UNIVERSITY OF LILLE, IEMN LABORATORY
EMAIL: MICHAEL.BAUDOIN@UNIV-LILLE.FR
HTTPS://PRO.UNIV-LILLE.FR/EN/MICHAEL-BAUDOIN

Start date:as soon as possible

Duration 18 months

Primary location:
Institut Pasteur - Unit EPVO. 25 rue du docteur Roux. 75724 Paris with
assignments at IEMN, Avenue Poincaré, 59652 Villeneuve d'Ascq

Contact: Michael Baudoin MICHAEL.BAUDOIN@UNIV-LILLE.FR

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