ED Sciences Chimiques
Fluorescent Polypeptide Nanoparticles Synthesized by Ring-Opening Polymerization-Induced Self-Assembly of N-Carboxyanhydrides
by Amin EL JARROUDI HAMMOU (Institut des Sciences Moléculaires)
The defense will take place at 9h00 - Amphithéâtre Adolphe Pacault Centre de Recherche Paul Pascal, 115 Avenue du Dr Albert Schweitzer, 33600 Pessac
in front of the jury composed of
- Chloé GRAZON - Chargée de recherche - CNRS / Université de Bordeaux / LCPO / Bordeaux INP - Directeur de these
- Silvia MARCHESAN - Full professor - Université de Trieste - Rapporteur
- Guillaume DELAITTRE - Full professor - Université Heinrich Heine de Düsseldorf - Rapporteur
- Colin BONDUELLE - Directeur de recherche - CNRS / Université de Bordeaux / LCPO / Bordeaux INP - CoDirecteur de these
- Emilie POUGET - Directrice de recherche - CNRS / Institut de Chimie et de Biologie des Membranes et des Nano-objets (CBMN) - Examinateur
- Diana CIUCULSECU PRADINES - Maîtresse de conférences - Université de Toulouse / UMR 5623 SOFTMAT - Examinateur
This PhD work focuses on the development of functional and fluorescent polypeptide nanoparticles using aqueous ring-opening polymerization-induced self-assembly (ROPISA). While fluorescent nanoparticles are promising tools for bioimaging and biosensing, most currently available systems are based on non-biodegradable materials. Polypeptides therefore represent an attractive alternative owing to their intrinsic biocompatibility and biodegradability. First, a propargyl-functionalized N-carboxyanhydride (PLG-NCA) was synthesized and investigated for its polymerization. A one-pot strategy combining ROPISA with copper-catalyzed azide–alkyne cycloaddition (CuAAC), termed Click'n ROPISA, was subsequently developed for the direct synthesis of fluorescent nanoparticles. Using a poly(ethylene glycol) macroinitiator and various azide-functionalized dyes, fluorescent nanoparticles spanning from blue to red emission range were successfully obtained. FRET was demonstrated between green donor nanoparticles and red acceptors. In addition, the red-emitting nanoparticles exhibited high volumetric brightness, exceeding that of commercial red-emitting quantum dots. The thesis then investigates fully pepeptide nanoparticles using poly(glutamic acid) as a polyelectrolyte macroinitiator for the polymerization of hydrophobic NCAs. Their morphology was modulated by varying the nature and concentration of the added salts, providing access to different nano-object morphologies, ranging from elongated to spherical structures. Fully polypeptide fluorescent nanoparticles were also obtained by combining this polyelectrolyte macroinitiator with a fluorescent NCA. Finally, oligonucleotides were investigated as macroinitiators, potentially extending the scope of ROPISA toward the development of biohybrid polypeptide nanoparticles. Overall, this work expands the scope of aqueous ROPISA toward the synthesis of functional and fluorescent polypeptide nanoparticles and demonstrates its versatility for accessing nano-objects with tunable composition, morphology, and optical properties. These nanoparticles provide promising platforms for biosensing and bioimaging applications, particularly in contexts requiring high fluorescence brightness and single-particle resolution.
ED Sciences de la Vie et de la Santé
Microenvironment in skin cancer : Role of Telocytes in the physiopathology of cutaneous Squamous Cell Carcinoma
by Julie CLACHET (BoRdeaux Institute of onCology)
The defense will take place at 14h00 - Amphithéâtre 2, Rue du Dr Hoffmann Martinot, Bâtiment Bordeaux Biologie Santé, 33000, Bordeaux
in front of the jury composed of
- Muriel CARIO - Chargée de recherche - CHU / Université de Bordeaux / BoRdeaux Institute of onCology - Directeur de these
- Véronique BRAUD - Directrice de recherche - CNRS / Institut de Pharmacologie Moléculaire et Cellulaire-UMR7275 - Rapporteur
- Stéphane DEDIEU - Professeur des universités - Université de Reims Champagne-Ardenne - Rapporteur
- Katia BONIFACE - Professeure des universités - Université de Bordeaux - Examinateur
- Julien ABLAIN - Chargé de recherche - INSERM / Cancer Research Center of Lyon - Examinateur
Cutaneous squamous cell carcinoma (cSCC) represents one of the most prevalent cancers globally. Although cSCC is often preceded by pre-cancerous lesions (actinic keratosis, AK), accurately predicting their progression remains challenging. They result from solar exposure, affecting the superficial part of the skin: the epidermis. UVs radiation induces mutations in epidermal cells, but these changes can extend into the dermis, where critical cellular components reside. Notably, telocytes (TCs), a recently identified cell type distinct from fibroblasts, undergo modifications concurrent with dermal structural alterations. These cells are characterized by a particular morphology with extensions reaching hundreds of micrometers in length called telopodes. This feature enables telocytes to interact with a wide variety of cell types (immune, stromal, and endothelial cells) and their presence across most tissues forms a structural network. They are often described as nurse cells due to their close contact with stem cells, and their decrease seems to correlate with diseases such as fibrosis. Similar alterations have also been reported in tumoral contexts, particularly in the colon and breast, as well as peritumoral regions. While the literature has established the essential role of fibroblasts in cancer progression, the role of telocytes remains unexplored. The present thesis explores the role of TCs in the pathophysiology of cutaneous squamous cell carcinoma, from precancerous lesions to invasion. First, immunofluorescence analysis of patient samples revealed a disruption of the CD34+ stromal network, corresponding to TCs, surrounding skin appendages. This altered network was already present in some actinic keratoses and confirmed in in situ cSCC. To define TC cellular identity and distinguish them from fibroblasts, a comparative proteomics approach identified CD10 as a distinct marker highlighting differences between TCs and fibroblasts. Combining CD10 and CD34 substantially simplifies TC identification in situ. Functionally, our in vitro coculture models demonstrate that tumor cells induce a phenotypic transition in TCs, characterized by a loss of dendricity, downregulation of CD34 and upregulation of CD10. This morphological and secretory shift reflects their phenotypic conversion into a cancer-associated fibroblast-like phenotype (CD10+ CAFs), endowed with pro-tumoral and immunomodulatory properties that support tumor progression. Finally, an exploratory proteomic profiling following UV-A irradiation revealed the induction of a cellular stress signature, opening promising avenues to investigate the role of TCs in photo-induced stromal alterations. In conclusion, this work uncovers a novel source of CAFs, arising from TCs at early stages of cutaneous carcinogenesis. TCs represent both a promising biomarker for predicting AK progression into cSCC, and a new therapeutic target for cSCC prevention.
ED Sciences Physiques et de l'Ingénieur
Exploring 2P imaging in the NIR-IIb window with individual carbon nanotubes
by Nasim AKHTAR (Laboratoire Photonique, Numérique & Nanosciences)
The defense will take place at h00 - Amphithéâtre A. DUCASSE LP2N – Institut d'Optique d'Aquitaine, Amphithéâtre A. DUCASSE, Rue François Mitterrand, 33400 Talence, France
in front of the jury composed of
- Laurent COGNET - Directeur de recherche - CNRS / LP2N / Université de Bordeaux - Directeur de these
- Chiara STRINGARI - Directrice de recherche - CNRS / LOB / École Polytechnique - Rapporteur
- Nicolas IZARD - Chargé de recherche - CNRS / L2C / Université de Montpellier - Rapporteur
- Stéphane BANCELIN - Chargé de recherche - CNRS / LP2N / Université de Bordeaux - CoDirecteur de these
- Claire LEFORT - Chargée de recherche - CNRS / Institut XLIM / Université de Limoges - Examinateur
- Lionel CANIONI - Professeur des universités - Université de Bordeaux / ICMCB - Examinateur
Multiphoton microscopy, including two-photon (2P) and three-photon (3P) fluorescence microscopy, is widely used to visualize in vivo and ex vivo tissue morphology and physiology at cellular and subcellular resolution deep within scattering tissue with minimal invasiveness. Its depth advantage arises from the combination of nonlinear excitation confinement and long-wavelength near-infrared (NIR) excitation. The 1700 nm excitation window is particularly attractive because it provides a favorable trade-off between reduced tissue scattering and absorption, thereby enabling deeper light penetration in biological tissue. While 3P microscopy at 1700 nm using red fluorophores is increasingly used for deep-tissue imaging, the corresponding use of 2P excitation at the same excitation wavelength remains much less explored because suitable fluorophores with strong 2P responses are scarce. In this thesis, we investigated single-walled carbon nanotubes (SWCNTs) as NIR fluorescent probes for 2P microscopy in the 1700 nm spectral region. A tunable femtosecond source operating from 1630 to 1700 nm was characterized and used to study the 2P fluorescence properties of pristine, chirality-sorted, and oxygen-functionalized SWCNTs. Oxygen-functionalized (6,5) SWCNTs exhibited a very large 2P action cross-section reaching (57.1 ± 2.1) × 10^3 GM at 1640 nm, more than three times that of pristine (6,5) SWCNTs under the same conditions. Their red-shifted color center fluorescence near 1140 nm was then used in a custom-built multiphoton microscope to detect and spectroscopically characterize individual nanotubes. To our knowledge, this constitutes the first demonstration of single-particle fluorescence imaging using 2P excitation in the 1700 nm spectral region. A second objective was to determine how the performance of 2P, 3P, and 4P microscopy evolves with imaging depth at a common excitation wavelength in the 1700 nm. A combined analytical and Monte Carlo framework was developed that includes excitation attenuation, absolute multiphoton fluorescence generation, out-of-focus background, wavelength-dependent fluorescence transport and collection, and detector contribution. After validation against published deep-brain imaging results in the 1300nm window, the model was applied to gray matter, white matter, rat liver, and human skin. The calculations show that increasing the nonlinear excitation order does not necessarily increase the accessible imaging depth. Although 3P provides stronger intrinsic background suppression, its practical depth can become limited by the decreasing focal fluorescence signal and detector contribution before its theoretical background limit is reached; this effect is even more pronounced for 4P. The crossover between these regimes depends on pulse energy, repetition rate, tissue optical properties, fluorophore performance, and detection conditions. Lower pulse energies and higher repetition rates favor 2P and potentially faster acquisition, whereas increasing pulse energy makes 3P progressively more advantageous; 4P becomes favorable only at substantially larger pulse energies in the present model.
ED Sciences et environnements
Mapping forest regrowth in Equatorial Africa using synthetic aperture Radar
by Solène RENAUDINEAU (ISPA - Interaction Sol-Plante-Atmosphère)
The defense will take place at 9h00 - Salle conférence ISPA 71, Avenue Edouard Bourlaux 33140 Villenave d'Ornon
in front of the jury composed of
- Frédéric FRAPPART - Directeur de recherche - INRAE / Université de Bordeaux - Directeur de these
- Nicolas BAGHDADI - Directeur de recherche - INRAE / Université de Montpellier - Rapporteur
- Valéry GOND - Directeur de recherche - CIRAD / AgroParisTech - Rapporteur
- Annabel PORTé - Directrice de recherche - INRAE / Université de Bordeaux - Examinateur
- Marie PARRENS - Maîtresse de conférences - Ecole ingénieur de Purpan - Examinateur
- Emmanuel ROUX - Chargé de recherche - IRD / Université de Montpellier - Examinateur
- Marc PEAUCELLE - Chargé de recherche - INRAE / Université de Bordeaux - CoDirecteur de these
Climate change, driven by human activities, is prompting scientists and policymakers to focus on carbon sinks. Among them, tropical forests play a central role. While the Amazon, the world's largest tropical forest, may have reached its carbon‑saturation point, this is not the case for the second‑largest tropical forest, which is located in Africa. Although this forest is essential for climate regulation and biodiversity conservation, it remains poorly studied and is threatened by climate change and increasing anthropogenic pressure. Shifting (itinerant) agriculture is one of the main drivers of deforestation in this region. Paradoxically, it also promotes natural regeneration in the form of secondary forests, which now account for roughly 70 % of tropical forest cover. To better monitor the evolution of these ecosystems, many projects have been launched. The very definition of “forest” varies from country to country, and these areas are often difficult to access; remote sensing therefore appears as a promising technology. The wide variety of freely available sensors enables the monitoring of forest structure. Although they do not measure biomass (and thus carbon stock) directly, these sensors can serve as proxies, provided that field data are available to calibrate the relationships. This thesis therefore aims to exploit these sensors to estimate the biomass of secondary forests in equatorial Africa. Field measurements were carried out to develop allometric relationships linking forest age to biomass. A subsequent study evaluated the use of globally available land‑cover maps to determine the age of secondary forests. Finally, a new detection method based on radar time‑series was explored to locate these forests. Understanding how the radar signal evolves over time opens new perspectives, especially with the forthcoming satellite missions.