ED Sciences Chimiques
Microfluidic approaches for the sorting and morpho-mechanical caracterisation of cellular aggregates
by Léon REMBOTTE (Centre de Recherche Paul Pascal)
The defense will take place at 14h00 - Amphithéâtre Centre de Recherche Paul Pascal 115 avenue du Docteur Albert Schweitzer Pessac 33600
in front of the jury composed of
- Jean-Christophe BARET - Professeur - Centre de Recherche Paul Pascal - CoDirecteur de these
- Charles BAROUD - Professeur - Ecole polytechnique - Rapporteur
- Pierre NASSOY - Directeur de recherche - Laboratoire Photonique, Numérique et Nanosciences - CoDirecteur de these
- Jean-François JOANNY - Professeur - Collège de France - Examinateur
- Claire WILHELM - Directrice de recherche - Institut Curie - Rapporteur
- Pierre JOSEPH - Directeur de recherche - LAAS-CNRS - Examinateur
- Diego BARESCH - Chargé de recherche - Institut de Mécanique et d'Ingénierie - Examinateur
- Cécile ZAKRI - Professeure - Centre de Recherche Paul Pascal - Examinateur
Cell aggregates, such as spheroids and organoids, are increasingly used in laboratories to replicate biological tissues. Typically comprising a few thousand cells, they exhibit an intermediate level of complexity between conventional cell cultures and animal models, and offer promising perspectives for both fundamental and applied research, particularly in the field of personalised medicine. However, their use remains limited by high experimental variability and by the lack of standardised analysis methods. In this context, this doctoral work aimed to develop automated approaches for the characterisation of large populations of cell aggregates. First, I adapted the principles of flow cytometry to the sorting of cell aggregates, based on real-time image analysis and encapsulation in millimetric droplets manipulated by acoustic radiation force. The cytometer thus designed is capable of measuring morphological and phenotypic properties within populations of several hundred aggregates, and of isolating subpopulations with homogeneous properties. This approach paves the way for more reproducible and statistically robust characterisation protocols for the study of spheroids and organoids. I then investigated the mechanisms of self-organisation of hiPSC cysts. These aggregates consist of a spherical epithelial cell monolayer enclosing a central cavity called a lumen, and are considered as models of embryos at the epiblast stage. Since these fragile samples cannot be imaged over long periods, I developed an on-chip cytometry method using automated confocal imaging, which enabled the analysis of hundreds of cysts at different stages of growth, from lumen formation to epithelial stratification. This revealed scaling laws of the self-organisation of hiPSC cysts and highlighted the key stages of their development, interpreted from a geometric and mechanical perspective. Finally, I characterised the mechanical properties of cysts through micropipette aspiration experiments, a technique historically dedicated to single cells and more recently adapted to multicellular aggregates. In particular, I studied cyst rupture under extreme deformations and explored the possibility of extending these analyses towards high-throughput deformability cytometry, in order to generalise the measurement of their mechanical properties. In this thesis, I thus introduced new methods for the manipulation and characterisation of multicellular aggregates, contributing to the standardisation of their large-scale study.
ED Sciences et environnements
Investigating spatial synchrony in European eel population dynamics and providing new tools to support the management of the species
by Mathilde BENEZECH (EABX - Écosystèmes aquatiques et changements globaux)
The defense will take place at 14h00 - Amphithéâtre INRAE, 50 Avenue de Verdun, 33610 Cestas
in front of the jury composed of
- Hilaire DROUINEAU - Ingénieur de recherche - Université de Bordeaux - Directeur de these
- Stéphanie MAHEVAS - Directrice de recherche - IFREMER - Rapporteur
- Estibaliz DIAZ - Chercheuse senior - AZTI - Examinateur
- Clara ULRICH - Directrice de recherche - IFREMER - Rapporteur
- Jean-Christophe POGGIALE - Professeur - Université Aix-Marseille - Examinateur
The European eel (Anguilla anguilla) is a catadromous fish that spawns in the Sargasso Sea and grows in the continental waters of Europe and North Africa. This species has been in decline since the 1980s, and no signs of recovery have been observed to date, despite the implementation of management measures. The assessment and management of this species face various challenges, such as (i) its wide distribution area involving a multitude of stakeholders, (ii) its complex life cycle, which is disurpted by various components of global change, and (iii) the spatial variability of its life history traits. The aim of this work is to improve understanding of the spatial dynamics of the European eel population in Europe during its continental phase in order to strengthen scientific expertise on the stock, on which its management and conservation are based. More specifically, we seek to study the spatio-temporal variations in the abundance and life history traits of the species, looking for potential spatial synchrony that could shed light on the causes of these variations. Changes in recruitment distribution and biomass in Europe are studied using time series analysis methods. Correlation analyses are conducted between biological data (spatial distribution, biomass) and environmental or anthropogenic data. An increase in the proportion of recruits arriving in the British Isles has been identified in recent years. For yellow and silver eels, differences are observed between the southernmost and northernmost regions. These results suggest that changes in ocean currents could alter the drift of larvae in the short term, while variations in ocean conditions could affect their long-term survival. For yellow and silver eels, correlations between biomass and temperature or climate indices suggest the influence of environmental conditions. In a context of global change, where the climate is likely to be disrupted, this highlights the challenges that eel conservation will face. This exploratory analysis is followed by the introduction of mechanistic links between the different continental stages (glass, yellow and silver eels, escapement) through the development of a spatial population dynamics model at the scale of species management units in France, Spain, and Portugal. The specific features of this model are (i) the integration of all continental stages through a homogeneous mechanistic approach, and (ii) its broad spatial coverage (international) while maintaining the spatial scale used in management, allowing for the spatial variability of life history traits and anthropogenic pressures to be taken into account. This model is a preliminary tool for integrating the spatial dimension into the study of population dynamics in a consistent manner and improving scientific advice on the stock. At the French level, the development of short-term recruitment forecasting models and their comparison using a multicriteria approach are proposed in order to provide a specific tool for estimating glass eel catch possibilities. The work carried out demonstrates the need to continue the efforts already underway to improve and standardize data collection. The contributions of this study are based both on the development of new statistical tools for studying the population dynamics of the species and on the information provided by the use of these tools. This work presents a homogeneous tool for large-scale spatial integration and constitutes preliminary work with the aim of achieving a spatial assessment of the population status.