Biomimetic 3D Materials for More Predictive Intestinal Toxicity Testing
Assessing the toxicity of chemical substances to human health requires reliable experimental models that accurately reflect human physiology. The intestine represents a major interface between the human body and its environment, yet current cellular models fail to fully reproduce its structural organization and physical properties. This PhD project aims to develop advanced intestinal models using three-dimensional biomimetic materials (BAM). Through 3D printing technologies, these materials will reproduce key architectural features of the intestine, including its crypts and villi. An innovative, patented coating, whose mechanical properties can be tuned independently of scaffold geometry, will mimic essential characteristics of the intestinal extracellular matrix. Intestinal organoid-derived cells will be cultured on these scaffolds to develop models that more closely resemble human intestinal physiology. The project will investigate how microenvironmental geometry and stiffness influence intestinal cell organization, differentiation, and function. The resulting models will then be exposed to reference chemicals with known toxicological effects. Cellular responses will be analyzed and compared with those obtained using conventional culture models. The objective is to determine whether better reproducing the intestinal microenvironment can improve the sensitivity, reproducibility, and physiological relevance of toxicity testing. This interdisciplinary project will combine biomaterials engineering, cell biology, mechanobiology, and toxicology. Ultimately, these advanced intestinal models could also contribute to reducing the reliance on animal experimentation.
Optimization of CotA bacterial laccases (Bacillus subtilis) and their Pseudomonas homologs for the biodegradation of PFAS under biofilm growth conditions: an integrated approach combining enzyme engineering and microbial ecophysiology
PFAS comprise a family of more than 6,000 virtually indestructible fluorinated compounds that are now subject to European regulations. Existing treatment processes are costly, energy-intensive, or waste-generating, and biological approaches face a major hurdle: effectively defluorinating PFOA and PFOS quickly and at high concentrations remains impossible to date. Among the candidate enzymes, laccases stand out: functioning in the open air, they break down PFOA in the presence of mediators. However, the literature remains dominated by fungal enzymes, which are effective in acidic environments, whereas the water to be treated is neutral to basic. The project therefore focuses on the CotA laccase from Bacillus subtilis—which is heat-stable, active in basic environments, naturally bound to the spore, and easily optimizable—as well as on Pseudomonas strains capable of forming pollutant-tolerant biofilms. During sessile growth, the biofilm matrix traps PFAS, protects the enzyme, and creates conditions favorable for co-metabolism. Since this approach has never been quantified, it opens up an unexplored scientific niche.
Conformational dynamics of single molecules using atomic force microscopy
Molecular biology emerged in the 1940s with the goal of understanding biological activity at the molecular level. Since the discovery of the DNA double helix, structural biology has focused primarily on determining the precise atomic structure of molecules. However, conventional high-resolution techniques such as cryo-electron microscopy or X-ray crystallography provide only static snapshots. Although nuclear magnetic resonance and computer simulations incorporate the dynamic dimension, no experimental method allows for the direct observation of a single, isolated molecular structure.
The major challenge currently facing the field is therefore to precisely link structural dynamics to biological function. To achieve this, integrated structural biology now combines several experimental approaches, chemical data, and computational tools. In this context, high-speed atomic force microscopy stands out by enabling the direct, time-resolved visualization of macromolecular motion. Nevertheless, the link between the topography obtained through this dynamic microscopy and the underlying atomic structures has yet to be fully exploited.
This research project therefore aims to use the computational pipeline called AFM-Assembly to translate dynamic microscopy data into structural information. The work will involve adapting and optimizing this set of algorithms—which have already been validated on static images—to process large sets of dynamic data. The selected candidate will be responsible for modifying the code for this pipeline, which runs on Linux, requiring a basic understanding of Shell and C programming. Finally, the study will rely on high-performance computers as well as experimental data that is either already available or acquired in collaboration with specialists in Marseille.
Molecular Mechanisms of IRE1a Regulation in Stress Signaling
The endoplasmic reticulum supports the biogenesis and maturation of approximately one-third of the human proteome, including most secreted proteins and many membrane proteins. The accumulation of improperly folded proteins can activate the stress sensor IRE1a, initiating adaptive stress response (UPR). Dysregulation of this response is implicated in several diseases, including cancer and metabolic disorders. IRE1a also responds to changes in membrane lipids, but the underlying molecular mechanisms remain poorly understood. This PhD project aims to understand how the membrane environment influences IRE1a structure and dynamics. It will focus on its membrane-spanning region and the flexible linker connecting it to the signaling domains. The work will involve producing protein fragments and studying them in membranes with controlled lipid compositions. Solution and solid-state nuclear magnetic resonance (NMR) spectroscopy will provide atomic-level information about these regions. Complementary biochemical and biophysical approaches will characterize their self-association and interactions with lipids. The aim is to identify how lipids affect the organization of the membrane-spanning region and the mobility of the flexible linker. Studying fragments containing both regions will help test how these effects are transmitted between them. The results will provide a structural basis for understanding IRE1a regulation and its role in stress responses.