2020-06-Offer for a Thesis Allowance - Subject: Development of a new methodology for cell surface molecular fingerprinting of pathogens using innovative mass spectrometry techniques and bioconjugated metal nanoparticles labelling.

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Offer for a Thesis AllowanceSubject: Development of a new methodology for cell surface molecular fingerprinting of pathogens using innovative mass spectrometry techniques and bioconjugated metal nanoparticles labelling

Scientific context

Essential in the cycling of many elements, the microbes also play key roles in digestive, metabolic and immune functions, which are mainly beneficial but sometimes harmful (pathogenic bacteria). In this latter case, they constitute serious issues in public health and in many industrial sectors (food spoilage, ventilation systems, corrosion of pipes ...) as their selected genetic features and biochemical abilities make them dangerous for human health. In fact, it is estimated that approximately 1400 pathogens can cause human diseases and pathogenic bacteria alone are etiological agents of 350 million cases of foodborne diseases. Salmonella sp., Campylobacter sp., and pathogenic Escherichia coli (PEC) are among the most common foodborne pathogens that affect millions of people annually – sometimes with severe and fatal outcomes. Particularly, PEC are associated with unpasteurized milk, undercooked meat and fresh fruits and vegetables. In this context, the accurate identification and the complete characterization of pathogens, especially PEC ones involved in food diseases, is of primary importance.

The frontier between pathogenic and non-pathogenic PEC strains is connected to the molecular variability of a little set of molecules mainly coming from the cell surface (adhesins). The precise molecular characterization of PEC pathogens surface adhesins is essential to determine the full pathogenic picture of strains.

Keywords: ToF-SIMS, gold nanoparticles, bacteria, intimins, Auger spectroscopy


Missions and activities

The PhD will be focused on the development of a new method based on the precise molecular characterization of intimins (a cell surface membrane protein) and more generally cell surface proteins, using Time-of-Flight Secondary Ions Mass Spectrometry (ToF-SIMS), equipped with one of the two copies in France of a secondary mass fragmentation analyzer (Tandem MS), an innovative system particularly adapted to the analysis of complex biological molecules. Moreover, on the basis of the well-known Metal-assisted mechanism, we will use gold nanoparticles to tag the bacteria surface and enhance the detected signals. The interactions of bacteria and gold nanoparticles will also be characterized by Auger spectroscopy and single particle ICP-MS (SP-ICPMS) technique.


The main objectives of the PhD are :

  • Molecular characterization of commercial and laboratory constructed recombinant intimin variants by ToF-SIMS Tandem MS.
  • Synthesis of different types of functionalized and bioconjugated gold nanoparticles
  • Culture of wild-type and intimin-producing E. coli strains.
  • Molecular characterization of bacteria surface by ToF-SIMS Tandem MS.
  • Labelling of cell surface with functionalized gold nanoparticles and ToF-SIMS characterization.

Work plan

Year 1
Construction of plasmids and purification of recombinant intimin variants. ToF-SIMS reference data bank of recombinant Intimins. Gold nanoparticles synthesis and bioconjugation. ToF-SIMS reference of functionalized gold nanoparticles.

Year 2
Construction of intimin-producing E. coli strains. Labelling of gold nanoparticles on cells surface. Molecular detection and characterization of cell surface intimins by ToF-SIMS Tandem MS, SP-ICPMS experiments and Auger spectroscopy analyses.

Year 3
Refinement of cells surface molecular fingerprinting and experimental conditions. Valorization of the work (publications, communication). PhD Manuscript writing.


Literature References

  • Prakash et al., J. Microbiol. 47, 98–108, (2007).
  • Manaļ¬, M., Int. J. Food Microbiol., 31, 45–58, (1996).
  • Castro-Escarpulli et al., Archives of Clinical Microbiology 7, (2015).
  • Fratamico et al.,  Frontiers in Microbiology 7 (2016).
  • McWilliams et al., Microbiology Spectrum 2, no3, (2014).
  • Soulé et al. Langmuir 32, no 39, 10073-82 (2016)
  • Faucher et al. , Journal of Trace Elements in Medicine and Biology 47, 70-78, (2018).


Working conditions

Hosting laboratory: The Institute of Analytical Sciences and Physico-Chemistry for Environment and Materials (IPREM) is a Joint Research Unit CNRS / UPPA (UMR 5254).

Laboratory expertise: IPREM members are interested in the development of fundamental knowledge in physico-chemistry, analytical chemistry and microbiology, in relation to applications concerning the structure of living beings, the management of the environment and the functional properties of different classes of materials. Their skills are based on analytical strategies, modeling, physico-chemical approaches, fine studies of structures and reactivity, development, characterization and implementation at different scales, with applications in many industrial sectors both at national and international levels.

Localisation: Université de Pau et des Pays de l’Adour (France)

PhD supervisor: Joachim Allouche
PhD co-supervisor: Cécile Courrèges

Starting date: October 1st, 2020

Length: 3 years

Employer: UPPA, doctoral school ED 211 Doctoral School of Exact Sciences and their Applications

Gross monthly salary: 1878 €, including 32h of teaching activities, each year (UPPA doctoral contract, according to E2S UPPA project)


Required skills and competences - Who can apply ?

The candidate has the following skills and expertise:

  • An excellent academic background in Universities and/or Engineering schools, level master degree.
  • Good knowledge in physico-chemistry, analytical techniques and microbiology. Knowledge in gold and metal nanoparticles synthesis by soft chemistry, bacteria culture and mass spectrometry will be highly appreciated.
  • Autonomy, dynamism, creativity, good communication skills.
  • The candidate should have a strong predilection for laboratory work. Team working abilities are highly appreciated.
  • English proficiency is mandatory. A good level in French will be appreciated.
  • Good bibliographic and writing integration skills
  • The candidate must be passionate for identifying solutions to environment related concerns and for multidisciplinary research.
  • A previous experience would be a plus.


Application - Evaluation criteria

Selection process step:

  • Establishment of the selection comittee
  • Evaluation of the applicants files
  • Interview with the selected candidates and ranking

Application files will be evaluated based on the following criteria:

  • Candidate's motivation, scientific maturity and curiosity
  • Candidate's basic knowledge and experimental skills
  • Academic results : grades and ranking in M1 and M2 ; steadiness in the academic background
  • English language proficiency
  • Oral and written communication skills
  • Candidate’s ability to present her/his work and results
  • Professional experience (e.g. Work experience similar to an internship in a laboratory – or likewise, any previously achieved research work, reports, publications ...)

Application file composition and submission deadline

Application must be written in English and sent to the following email addresses:
(nicolas.beaudoin @ univ-pau.fr)  joachim.allouche @ univ-pau.fr and cecile.courreges @ univ-pau.fr
with the title “Doctoral application”, and the following documents attached (altogether, in a single pdf file):

  • CV (max 2 pages) including the publication list when applicable
  • Cover letter detailing the candidate's motivations (max 2 pages)
  • Copy of your Master diploma (or equivalent) and transcripts (marks and ranking)
  • Any letter of recommendation
  • Contact details ( Name and e-mail addresses) of 2 referees (including the Master thesis supervisor)


Submission deadline : July 20th, 2020