PhD scholarship In vitro digestion / peptide processing by the intestinal epithelium / absorption

ESR 4: PhD scholarship In vitro digestion / peptide processing by the intestinal epithelium / absorption

Host organisation: INRAE – STLO (Science & Technology of Milk and Eggs), Rennes, France

Recruited education level: Academic, Master degree

Area/topic: In vitro food digestion, mass spectrometry, cell cultures, ex vivo models of absorption (Ussing chambers)

Position: PhD Candidate – MSCA fellow part of MSCA-DN project ALLPreT No 101072377

Application deadline: 28 November 2022

Planned start date: March 2023

Do you want to contribute to the development of new tools for the prediction of allergenicity of novel foods and food proteins and enable the production of new and safe food for the future?

If you have knowledge within the area of allergy, immunology, biostatistics, and/or protein-chemistry as well as have experience working with in silico, in vitro or in vivo models and are looking for a PhD fellowship opportunity to put your skills into practice, you have it right here.

As part of the ALLPreT project and as our new colleague in INRAE Rennes, you will be part of dynamic and highly ambitious research and innovation environments with many national and international collaborators from both academia and industries.

Project description:

The objectives of the ESR 4 project aims to contribute to developing the allergenicity toolbox, identification of intrinsic properties of allergenic/non-allergenic proteins and to measure the effect of matrix and digestion on allergenicity. The activities will contribute to:

  • To optimize the INFOGEST digestion model with brush border enzymes by preparing vesicles from pig intestinal mucosa scrapes.
  • To quantify markers (alkaline phosphatase, DPPIV enzyme activity) released by brush border vesicles.
  • To perform gastrointestinal digestions on legume proteins obtained from ESR3 using the optimized INFOGEST method.
  • To investigate in Ussing chambers how the peptide patterns released by the INFOGEST model is modified by intestinal cell enzymes and the consequences on peptide absorption.
  • To identify IgE binding epitopes (obtained from ESR3) in the protein domains resistant to digestion using LC-MS.
  • To determine the effect of food structure and matrix on epitope resistance to digestion (INFOGEST) and LC-MS.
  • To characterize lipid composition of legumes using TLC and GC-MS to elucidate the role of lipids in matrix on digestion and allergenicity

Scientific work and aspects will include: An improved, physiological relevant gastrointestinal digestion model with brush border enzymes to elucidate the effect of digestion on relevant IgE binding epitopes to better predict allergenicity. In addition, more insights on the role of lipids, food structure and matrix on stability of allergic/non-allergenic proteins and IgE binding epitopes.

The training programme will include: Training on in vitro digestion models, isolation of brush border enzymes, enzyme activation assay, Using chamber and cell culture, LC-MS analysis, statistical analysis.

Responsibilities and tasks

For this project, we seek a highly motivated food biochemist/nutritionist or equivalent background who will contribute to the objectives of the project by:

1) optimising the international consensus digestion protocol developed by COST Action INFOGEST, by incorporating brush border enzymes into the model;

2) investigating the effect of processing and food matrix on digestion and

3) standardizing the method for determining digestion kinetics and end points (ESR4).


We are looking for a team player with the motivation and drive needed for making a difference that matters. You should have a critical mindset, be curious and eager to learn. As you will join international teams, a good command of written and spoken English is necessary.

Your CV comprises a Master’s degree (or equivalent) in food biochemistry, nutrition or a related field;  as well as:

  • Preferably experience with in vitro digestion, cell culturing, LC-MS, Ussing chambers

According to the rules for MSCA doctoral networks, applicants should not have resided or worked in France for more than 12 out of the last 36 months.

We offer

  • A position part of an innovative and international EU funded Marie Skłodowska-Curie Doctoral-Network (project ALLPreT - No 101072377)
  • you will take part in all training, networking, and collaborative tasks offered by the ALLPreT project, which include developing technical and soft skills (organisation of meetings, grant writing, presentation for different audiences, etc.)
  • External stays, including two secondments are a mandatory part of your new PhD fellowship position, where university of Leeds, for 6 months, to learn to work with intestinal epithelium in Ussing chamber to measure digestion by brush border enzymes, and Roquette Freres SA, for 2 months, to learn techniques and methodologies to characterize plant proteins and to learn how to work in a commercial setting will be the hosting instituations.

Terms of Employment: 3 years full time position (39h/week). Your gross salary will be in line with the collective labour agreement of the INREA, which will be an indicative gross salary of 3000 Euro a month, and compensation package will comply with the MSCA-ITN programme regulations for early stage researchers (ESR).

For further information: Didier Dupont,

Information on the organization/department:

INRAE is a public French research organisation employing some 12,000 people and has among its strategic interests the impact of food on human health and well-being. It is ranked 2nd in the world and 1st in Europe for publications in agricultural sciences and plant and animal sciences. INRAE Rennes, localized in a mid-size city with more than 70,000 students, is the largest research unit at INRAE involved on milk and egg science and technology. It is a joint research unit between INRAE and l’Institut Agro that gives PhD degrees. The research group led by Dr Didier Dupont (Highly Cited Researcher 2020, 2021) has published more than 150 papers on food digestion over the last 10 years being one of the most productive in the world on that topic. The group is at the edge of the international network INFOGEST on food digestion and has all the most up-to-date technologies to investigate food digestion (dynamic simulators, cell cultures, mass spec, pig facilities). It gathers 25-30 people in a very friendly atmosphere.

Application procedure uitklapper, klik om te openen

Candidates can apply for a position using the 'apply now' button

Your complete online application must be submitted no later than 28 November, 2022.

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please use the apply now button, fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

  • A letter motivating the application (cover letter)
  • Curriculum vitae
  • Letters of recommendation by former supervisors

You may apply before obtai­ning your master's degree but cannot begin before having received it.

Applications received after the deadline will not be considered.

All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.

Please note, candidates can apply to max two ESR positions.

Information on the ALLPreT project

Introducing novel foods, such as insects, will strongly contribute to the security and stainability of our food supply. However, these novel foods must be safe (EU regulation 2015/2283). Allergenicity assessment is an essential part of the safety assessment of novel foods. Unfortunately, current methods to assess de novo allergenicity lack predictive power and are not validated. Consequently, food producers and risk assessors struggle with allergenicity assessment, slowing the introduction of novel foods into our food supply. Enabling the safe introduction of novel foods while protecting humans from unacceptable food allergy risks calls for a multidisciplinary approach. The ALLPreT consortium is a highly multidisciplinary group of experts from universities, research institutes, hospitals, patient organisations, and industry arising from the EU COST Action ImpARAS (Improved Allergenicity Risk Assessment Strategy). This puts them in an ideal position to consolidate their previous collaboration and establish an innovative doctoral training network in this area. The overall goal of ALLPreT is to train the next generation of scientists who can tackle the shortcomings in the current food allergy assessment of novel food products. ALLPreT will train 10 PhD students in the core aspects of food allergy risk assessment, immunology, protein chemistry, bioinformatics, in vitro/in vivo/in silico model development and complementary “soft” skills to deliver well-educated young scientists, with a unique position within the EU labour market. The PhD students will explore the new field of research on de novo sensitisation by novel foods and develop a toolbox of in vitro/in vivo/in silico allergenicity prediction tools that are scientifically sound, validated, and easily usable by industry and food safety authorities. This toolbox will contribute to fast and accurate safety assessment, thereby speeding up safety approval and market uptake of novel foods. Read more at

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