Development of High Spectral Resolution Coherent Raman Microscopy for Deciphering Biomineralisation Pathways in Corals

**Development of High spectral resolution Coherent Raman microscopy for deciphering Biomineralisation Pathways in Corals**:

- Réf **ABG-131726**
- Sujet de Thèse
- 06/05/2025
- Autre financement public
- Institut Fresnel
- Lieu de travail- MARSEILLE - Provence-Alpes-Côte d'Azur - France
- Intitulé du sujet- Development of High spectral resolution Coherent Raman microscopy for deciphering Biomineralisation Pathways in Corals
- Champs scientifiques- Physique
- Mots clés- optique non linéaire, microscopie, biominéralisation

**Description du sujet**:
**Scientific context**
- At Fresnel Institute, we are addressing these questions by developing novel optical applied to the biomineralisation question. They respectively allow us to provide structural chemical information (optical coherent Raman, Figure 1f), at a high resolution and high sensitivity level. Furthermore, we exploit the capability of these instruments to image well-defined regions, representative of the early stage of biomineralisation, i.e., where the temporal imprint of the biomineral formation and growth is clearly visible. This PhD thesis project aims at focusing on the development of coherent Raman microscopy, which will be further applied on coral species samples, ideally _in vivo_.

**Coherent Raman microscopy**
- Amorphous calcium carbonate precursors present vibrational signatures, which are significantly different from their crystalline counterparts. They also vary as a function of their exact chemical composition, making them invaluable tools to progress on some of the major biomineralisation questions listed above. In order to image the amorphous to crystalline transition, Raman coherent microscopy is used at Institut Fresnel, based on an in-house developed set-up. It is based on a 4-waves mixing, in which two photons interact with the vibration of the targeted molecules. This imaging modality is fast, efficient and highly-spatially resolved, making it compatible with _in vivo_ studies. However, the need to produce short laser pulses to activate the non-linear process results in a spectral broadening, limiting the spectral resolution. It makes the fine identification and characterization of the amorphous and crystalline phases difficult and limited.

**PhD Thesis objectives**
- The PhD Thesis project is structured along two main objectives. First, the student will build an optical line allowing the increase of the spectral resolution. The approach is based on « spectral focusing » [3]: two laser pulses will be temporally stretched thanks to optical gratings and temporally recombined at the sample. This high-spectral resolution microscope will be tested and quantified on well-known samples. Second, the method will be applied to shed new light on the biomineralisation mechanisms occurring in corals samples. To reach this aim, post mortem and alive samples will be investigated. Thanks to collaboration with the team of Sylvie Tambutté at the Monaco Scientific Center, the student will have access to a unique set of samples, in which the early growth front is easily accessible with optical approaches including Coherent Raman microscopy. The experiments will allow to evidence the occurrence and transformation of different calcareous amorphous precursors in time and 3D space and to understand the role of the different compounds of the organic tissue in the building of the hard tissue. If successful, the in vivo experiments will be further conducted under different non-optimal growth conditions. Additional characterizations will be performed with electron microscopy and Raman spectroscopy. Finally the chemical results will be confronted to the physical results (x-ray diffraction) for a full description of the physico-chemical growth mechanism in corals.

**Prise de fonction**:

- 01/10/2025

**Nature du financement**:

- Autre financement public

**Précisions sur le financement**:

- MITI

**Présentation établissement et labo d'accueil**:

- Institut Fresnel

Depuis sa création en 2000, l’Institut Fresnel n’a cessé de croitre et d’affirmer son rayonnement scientifique dans des sujets très variés autour de la physique des ondes. Plus récemment, le laboratoire a élargi son périmètre scientifique vers la biologie, la biophysique et le biomédical, en fort lien avec l’imagerie.
Les thèmes de recherche du laboratoire couvrent aujourd’hui quatre grands axes : modélisation et simulation électromagnétiques, nanophotonique et composants optiques, traitement de l’information et ondes aléatoires et, enfin, imagerie avancée et vivant. Les synergies entre ces axes sont importantes et donnent naissance à des projets innovants, souvent aux frontières entre plusieurs disciplines. Ces projets peuvent être aussi bien fondamentaux qu’appliqués avec un fort potentiel d’innovation, que le laboratoire accompagne au travers de plusieurs plateformes technologiques.
Le laboratoire est aujourd’hui soutenu par les établissements de tutelle, Aix-Marseille Université, CNRS et