PhD applications - idil 2025 mirrored doctoral contracts

SUBJECT A - Life & Environmental Sciences, Science and Technology

Impact of the structure of biosourced gels on their ability to encapsulate and release therapeutic molecules in the colon

Student profile :

M2 or engineering degree in biochemistry, physical chemistry or materials science. Plus: interest or skills in soft matter physics.

Skills in enzymology and physical chemistry.

Good interpersonal skills for teamwork. Good laboratory practices.

Writing skills, written and spoken scientific English, autonomy, curiosity, rigor and dynamism.

Experience in a research laboratory may be an asset, but is not required to apply.

TOPIC B - Information, Structures and Systems

Dynamic monitoring of encapsulation and release of bioactive molecules in and from a biosourced gel bead.

Student profile :

M2 or engineering degree in physics, physical chemistry or materials science. Knowledge of soft matter physics is a plus.

Good interpersonal skills for teamwork. Good laboratory practices.

Writing skills, written and spoken scientific English

Autonomy, curiosity, rigor and dynamism.

Experience in a research laboratory may be an asset, but is not required to apply.

Project summary:

The aim of the VEBIOCOL project is to characterize the potential of feruloylated arabinoxylan (AXf) gels, the main non-starch polysaccharides found in cereals, as targeted delivery vehicles for local oral treatment of the colon. These biopolymers are resistant to the digestive fluids and enzymes of the human gastrointestinal tract, and are degraded in the colon by the glycosyl hydrolases of the microbiota. The project evaluates the encapsulation and bioactive molecule release capacities of AXf gels under static in vitro digestive conditions simulating the different compartments of the gastrointestinal tract, up to the colon.this study is based on an interdisciplinary approach combining biochemistry and physics, enabling an integrated, multi-scale analysis of the "molecular structure/properties/functionalities" continuum of the gels.

Thesis 1 integrates various AXf molecular structures and aims to use biochemical and rheological approaches to understand the links between molecular structure, architecture, properties and functionality of gels.

The physical approach of thesis 2, based on the mapping of molecular and fluorescence dynamics with spatial and temporal resolutions adapted to the scale of a millimetric gel bead, aims to measure and model the coupled kinetics of polymers and molecules to be encapsulated during the encapsulation and release stages.

The same compounds will be used in both theses (AXf, model media of the gastrointestinal tract and colon, and bioactive proteins), enabling a constant and relevant dialogue between the two teams. The synergy between the two theses will enable us to identify the parameters required for optimized, targeted delivery of bioactive molecules (in this case, immunomodulating dairy proteins) to the colon.

SUBJECT A - Life and Environmental Sciences, Science and Technology

Influence of the urban environment on the circadian rhythms of wild chickadees and mice

Student profile :

We are looking for a highly motivated individual who wishes to undertake a study straddling ecology and physiology. The person should have skills in animal physiology, behavior and ecology, as well as in combining field and laboratory work. Previous experience of fieldwork with wild animals is desirable, as is a good command of statistical tools.

SUBJECT B - Chemical and Biological Sciences for Health

Influence of nocturnal exposure to artificial light on
the circadian pacemaker in laboratory mice

Student profile :

The candidate will have a Master's degree in Neuroscience or Physiology, with a good grounding in molecular biology, and a willingness to work with live animals (animal experimentation clearance would be an advantage). Fluency in English (B2) is required to work in an international environment.

Project summary:

The extension of human activities into the nighttime arena raises both public health issues (such as anxiety-depressive, metabolic and cardiovascular disorders linked in particular to night-time work) and ecological issues (disturbance of numerous wild animal species, particularly in large, ever-expanding urban centers).

The origin of these disorders lies in the fact that human beings and wild animals possess an autonomous rhythmicity, long shaped over the course of evolution, in line with our planet's 24-hour rotation period. These circadian clocks are robust, but perhaps not completely rigid... offering the possibility of adapting natural rhythms to the functioning of our modern societies. To understand whether and how such adaptations are possible, and whether it is possible
to help people in a state of disorder, we first need to study the extent to which our clocks and those of animals can be modulated. We are therefore proposing two theses which will look at the physiological and behavioural impact of disruptions to the day-night cycle, and the mechanisms involved at brain level, in order to estimate to what extent these effects could be reversible, and how.

In the first thesis, we'll be looking at the impact of altered day-night cycles on the behavior and physiology of two widespread wildlife species (the house mouse and the great tit).

In the second thesis, we will focus specifically on the suprachiasmatic nuclei, the cerebral seat of our internal clock. We will investigate their modularity in the brains of laboratory mice, in the face of physiological and pathological perturbations.

Finally, the two theses will converge in a final chapter in which we will use the lessons learned from our work on laboratory mice to describe, in an unprecedented way, the brain mechanisms at work in our two wild species. This project, which concerns biology and health as well as ecology and evolution, will enable the two directors involved, Xavier Bonnefont (IGF, CBS2) and Samuel Caro (CEFE, GAIA), to initiate a brand-new collaboration and pool their respective expertise on biological rhythms for the first time. These two theses not only address
complementary questions, but are also interdependent, enabling the two thesis students to work hand in hand to advance this integrative and innovative project.

TOPIC A - Human Movement Sciences

The value of haptic feedback in learning to use the hand for diagnostic and therapeutic purposes

Student profile :

Training or professional activity as a caregiver (Medical, Paramedical, Manual Therapy), Master's degree (Research, Pedagogy, Human Sciences), experience desired (clinical examination skills, internship or experience in a care service), interpersonal skills, written and oral writing skills (French and English), adaptability, availability.

TOPIC B - Information, Structures and Systems

Design of a flexible haptic sensor for monitoring hand pressure during palpatory examinations

Desired student profile: Engineering school or Master's degree (applied physics, electronics, mechatronics, applied mathematics), excellent interpersonal skills, good written and oral communication skills (French and English), adaptability, experience desirable (project internship on medical applications and/or AI).

Project summary:

The reform of medical studies in France, with the introduction of Objective Structured Clinical Examinations (OSCE), underlines the need to standardize the learning of clinical skills. Palpatory examination, an essential component of clinical examination, is based on haptic perception. The learner assesses the biomechanical properties of tissues by interpreting tactile and proprioceptive information perceived with his or her hands.

Today, learning to palpate is mainly based on a "journeyman" approach, with no standardized framework or suitable teaching aids to structure instruction. Modernizing training in the sense of touch is therefore a major educational challenge. Objective monitoring of the pressure exerted by the hand on tissues would enable learners to assess their clinical skills by comparing them with those of experienced clinicians. Further down the line, it will be possible to improve the accuracy of research in clinical practice for diagnostic (i.e., measuring spasticity) and therapeutic (i.e., effectiveness of a manual medicine technique) purposes.

The HAPTIMED (HAPTique MEDical) project proposes an interdisciplinary approach combining motion sciences, flexible electronics and artificial intelligence to design an innovative pedagogical tool dedicated to learning clinical palpation. The aim is to monitor the manual gestures made during palpatory examinations using a haptic glove equipped with flexible electronic sensors, capable of recording the pressure exerted by the clinician's hand on the anatomical structures being tested. A machine learning algorithm, trained on haptic data labeled by expert clinicians, will analyze these signals to provide individualized pedagogical feedback (practical recommendation).

The project is based on two mirror theses and a transversal axis:

The first thesis aims to standardize the palpatory examination. Analysis of manual clinical gestures will enable objective criteria of haptic competence to be defined and pedagogical feedback to be adapted.

The second concerns the design of a haptic glove suitable for monitoring the pressure exerted by the hand on the anatomical structures under test.

These two aspects are consolidated by a transversal axis of uncertainty management based on the formalism of belief function theory. The modeling of a digital twin of haptic perception represents a significant advance in medical education. This innovative device will accelerate and optimize the acquisition of the sense of touch in care, objectively assess clinical skills through touch, and ensure longitudinal monitoring of the learning curve. HAPTIMED will make it possible to draw up evidence-based teaching recommendations, contributing directly to the standardization of OSCEs.

SUBJECT A - Chemical Sciences

Design and chemical synthesis of mono- and multi-capped RNAs.

Student profile :

The ideal candidate will have a solid background in organic synthesis and a proven interest in nucleic acid chemistry and/or life sciences.

SUBJECT B - Biological Sciences for Health

Customized RNA capping and expression solutions for targeted gene therapy

Student profile :

RNA biology: in particular RNA extraction, mRNA purification

Mass spectrometry and analytical chemistry: knowledge of sample preparation and LC-MS/MS, analysis of mass spectrometry data

Synthetic and molecular biology: knowledge/skills in epitranscriptomics would be a plus

Cell culture and transfection: mammalian cell culture, electroporation, RNA delivery

Interdisciplinary and collaborative work: team spirit, willingness to collaborate between biology and chemistry

Project summary:

In recent years, RNA has attracted growing interest in therapeutic research, notably for vaccine development, cell reprogramming and protein production. Although mRNA vaccines have proved effective, safe and versatile, their stability remains a challenge compared to DNA-based alternatives. To improve this stability and enhance ribosome engagement, RNA is chemically modified via epitranscriptomics, a process that regulates post-transcriptional gene expression and key biological functions. These modifications fall into two categories: cap modifications and internal modifications, with the mRNA cap playing a crucial role in translation initiation. For example, the 5′ N7-methylguanosine (m7G) cap interacts with translation initiation factors, influencing mRNA stability and translation. In addition, modifications such as 2′-O-methylation (2′OMe) and N6-methyladenosine (m6A) at the 5′ untranslated region (5′ UTR) further modulate translation and decapping activity. The diversity of cap modifications across cell types offers an opportunity for targeted gene expression, potentially improving RNA-based therapies.

Despite their therapeutic potential, the application of modified caps is limited by challenges related to synthetic methods. Current in vitro approaches to preparing capped mRNAs rely on co-transcriptional incorporation of capping analogues or post-transcriptional enzymatic capping, but these methods remain limited in the types of modifications that can be integrated. Recent advances in tri- and tetranucleotide capping analogues have enabled direct incorporation of modified caps, but these techniques are still limited.

To overcome these limitations, we have developed a strategy for incorporating both natural and unnatural chemical modifications into the 5′ end of mRNA. This modular approach, combining chemistry and enzymology, enables systematic screening of cap modifications to assess their impact on properties such as mRNA stability and translational capacity. This project aims to bring together the expertise of the IBMM and IRCM teams to develop solutions tailored to gene expression in specific cell subtypes with optimal efficiency, thus providing innovative tools for RNA-based therapeutic strategies. Objectives include the synthesis of natural and multi-capped oligonucleotides, the detailed profiling of capping modifications in immune cells, and the development of a screening method to identify the best performing capped oligonucleotides for specific cell subtypes.

SUBJECT A - Chemical and Biological Sciences for Health

Engineering and assembly of signal transduction biohybrids integrating cellular biosensors with functional biopolymers

Student profile :

This PhD contract focuses on the development of bacterial biosensors and the assembly of biohybrid systems capable of responding to stimuli modulated by radio frequency (RF). The ideal candidate will have a Master's degree in bioengineering, molecular biology, synthetic biology or biophysics, with a strong interest in interdisciplinary research.

The PhD project involves engineering bacterial strains with custom biosensors, optimizing polymer-bacteria interfaces and integrating biohybrids into electrogenetic platforms. The student will gain expertise in synthetic biology, microbiology and advanced microscopy, and work closely with IES's electronics partner on device integration and validation.

TOPIC B - Information, Structures and Systems

Development and validation of conductive biopolymers for RFID interaction and integration with biohybrids

Student profile :

This position involves the design and characterization of conductive polymers for integration with biological systems. The ideal candidate will have a Master's degree (M.Sc., École d'Ingénieur) with a specialization in electronics (from direct currents to radio frequencies), materials science or applied physics, with a strong interest in biosensors and biomedical applications.

The work will involve developing conductive polymers (COPs) responsive to environmental and radiofrequency (RF)-induced stimuli, designing new protocols for their electrical characterization (from kHz to GHz) and collaborating on their integration into functional bacterial biohybrids. The student will have access to state-of-the-art platforms for microfluidics and wireless system prototyping, and will interact regularly with the CBS biology team.

Project summary:

The mirror doctoral project, BIOREACH, explores the design of bioelectronic systems capable of remote sensing and response, integrating genetically modified bacteria with conductive organic polymers (COPs). These electrogenetic biohybrids aim to revolutionize biomedical technologies by enabling two-way communication for therapeutic and diagnostic applications. This innovative initiative addresses the limitations of current cell control methods, such as optogenetics and sonogenetics, by exploiting RF technology, which offers deeper tissue penetration and non-invasive external control. It is based on biohybrids equipped with electroconductive biopolymers coupled to biosensors embedded in bacterial frames reprogrammed for signal integration and transmission.

BIOREACH illustrates an interdisciplinary synergy, combining expertise in biophysics, synthetic biology, soft matter and electronics. The project brings together two leading research groups: the Synthetic Biology team at the Centre de Biologie Structurale (CBS), specializing in biohybrid engineering, and the RFID and Flexible Electronics team at theInstitut d'Électronique et des Systèmes (IES), renowned for its expertise in microtechnology and wireless communication. Their collaboration covers the design of biocompatible conductive polymers, bacterial biosensors and functional biohybrids, while developing innovative methodologies for electrical characterization and system integration.

Two complementary PhD projects form the basis of BIOREACH. The first involves engineering bacteria with biosensors capable of responding to signals induced by COPs, enabling precise control of cellular functions. The second develops new COPs with adjustable properties, capable of interacting with electromagnetic waves and triggering cellular responses. Both projects emphasize strong interaction between biology and electronics, fostering advanced interdisciplinary training through international collaborations, including joint internships at the University of Tokyo.

This project will produce major breakthroughs, including programmable biohybrid systems for real-time monitoring and therapy, high-impact publications and patentable innovations. Beyond biomedical applications, BIOREACH will train its PhD students in cutting-edge skills at the interface between biology and electronics, preparing them for leadership roles in academia and industry. This partnership not only enriches the training of students, but also establishes a solid and lasting collaboration between CBS andIES, paving the way for innovative advances in remotely accessible biohybrid technologies.

SUBJECT A - Life and Environmental Sciences, Science and Technology

Isotopic composition of collagen extracted from archaeological artifacts from the western Mediterranean basin

Student profile :

Prerequisites :

The candidate must hold a Master 2 (or engineering degree) in biogeochemistry, bioarchaeology, paleoclimatology, paleoenvironments, continental surface geosciences, environmental sciences or related disciplines. Profiles with dual or interdisciplinary skills in these fields are particularly welcome.

A solid command of stable isotope geochemistry is required, particularly as applied to organic matrices.

Skills required:

• Theoretical mastery of isotope fractionation, particularly of carbon and nitrogen isotopes in the living world (fauna/flora).
• Proficiency in data processing and statistical tools (R, SIAR, SIBER).
• Autonomy, creativity and the ability to commit to an ambitious research project.
• Ability to work as part of a team in an interdisciplinary environment (archaeology, bioarchaeology, geochemistry).
• Respect and benevolence towards the work environment and colleagues.
• Collaborative spirit and openness to diverse scientific approaches.
• Interest in fieldwork and openness to international collaboration.
• Motivation to publish in peer-reviewed scientific journals.

Appreciated skills :

• Experience in collagen extraction from biological remains.
• A good knowledge of the stable isotopes of sulfur, oxygen and hydrogen.
• Theoretical and/or practical knowledge of isotope ratio mass spectrometry techniques - Knowledge of GC-IRMS - AMS (radiocarbon ¹⁴C) .
• Sample preparation skills for isotopic analysis (collagen, lipids, etc.).
• Experience or theoretical knowledge of archaeological protein analysis (ZooMS, CSIA-AA) .
• Good level of scientific English (written and spoken)

We are looking for someone who is curious and open to the world, with a strong humanist dimension, capable of bringing a fresh perspective to the interdisciplinary nature of the project. An altruistic person, respectful of the values of collaboration and sharing, who can integrate the project into a network of international collaborations.

SUBJECT B - Chemical Sciences

Chiral mass spectrometry analysis for archaeology

Student profile :

Prerequisites :

Graduate/future graduate of a Master 2 (or engineer) in analytical sciences.

The candidate must have a sound knowledge of mass spectrometry and separative techniques.

Profile required:

Knowledge/experience in high-resolution mass spectrometry, tandem mass spectrometry and ion mobility, as well as in separative techniques such as liquid chromatography and capillary electrophoresis, are required to develop analytical methods for peptide/protein characterization.

Knowledge of peptide and protein chemistry will be an asset, particularly for sample conditioning. Experience in protein analysis using proteomic strategies will be appreciated.

The ability to work independently, creativity and the motivation to take on complex scientific challenges as part of a multidisciplinary project are expected.

Project summary:

Collagen chirality alteration, a result of amino acid epimerization from the L to the D form over time, has significant perspectives in bioarchaeology. This project explores the potential of chiral analyses by mass spectrometry to analyze collagen in archaeological remains, aiming to refine dating techniques and improve our understanding of preservation processes.

The analytical strategy represents a major challenge. Indeed, the determination of the configuration of stereogenic centers constitutes the highest level of characterization for an organic molecule. In order to tackle such demanding structural identification level of the biomolecules of interest (collagen proteins), we aim at implementing fragmentation experiments in high resolution tandem mass spectrometry (HR-MS/MS) coupled to liquid chromatography (LC) and ion mobility (IM-MS) on non-covalent diastereoisomeric species generated in the gas phase between a metal and the chiral peptide issued from trypticn digestion of extracted collagen samples. Such LC-IM-HR-MS/MS method development will
be carried out on modern samples to study abundant and non-precious collagen material.

Our approach integrates collagen extraction, purification, and isotopic analyses (¹³C, ¹⁵N, 34S) to assess environmental and climate changes and agriculture and farming practices in Holocene Human Societies of the Western Mediterranean Basin. The method is validated using reference samples of known age, establishing a robust framework for applying amino acid epimerization as a chronological tool. By combining chiral analysis with 14C dating and multi-isotopic data, we propose a multi-parameter model that enhances the accuracy of organic material dating's and paleo-ecological and paleo-climate indicators; the method
also creates a counterbalance to 14C dating and all the risks that this method brings.

Beyond archaeology, this research has broader applications in analytical chemistry and life sciences, where amino acid epimerization serves as a biomarker for tissue aging. This interdisciplinary approach thus provides an innovative pathway for studying protein longevity, with potential technological transfer to biomedicine and conservation sciences.