ED Sciences de la Vie et de la Santé
The investigation of songbirds' cortical-basal ganglia neural sleep dynamics through an Open Science-inspired computational framework
by Eduarda GERVINI ZAMPIERI CENTENO (Institut des Maladies Neurodégénératives)
The defense will take place at 14h00 - Amphi Centre Broca Nouvelle - Aquitaine 146 Rue Léo Saignat, 33076 Bordeaux
in front of the jury composed of
- Arthur LEBLOIS - Chargé de recherche - Université de Bordeaux - Directeur de these
- Camille MAUMET - Chargée de recherche - Centre Inria de l'Université de Rennes - Rapporteur
- Daniela VALLENTIN - Directrice de recherche - Max Planck Institute for Biological Intelligence - Rapporteur
- Nicolas ROUGIER - Directeur de recherche - Centre Inria de l'Université de Bordeaux - Examinateur
- Andrew DAVISON - Chargé de recherche - Institut des Neurosciences Paris‑Saclay - Examinateur
- Lisa ROUX - Directrice de recherche - IINS Bordeaux - Examinateur
As neuroscience incorporates big data and advanced technologies, it becomes crucial to prioritise data management, reproducibility, and resource sharing. Open Science (OS) offers a framework to fulfil these objectives. Our project utilizes OS principles to explore the neural mechanisms underlying vocal learning in songbirds—a well-established model for studying speech learning. Similar to how humans learn how to speak, birdsong acquisition relies on a long trial-and-error auditory-feedback-dependent process engaging cortical and subcortical areas in the brain. Mastering such a complex sensorimotor skill is no small feat, and songbirds have a dedicated brain circuitry for acquiring songs, which includes a cortical-basal-ganglia (CBG) loop homologous to that found in mammals. Several studies have demonstrated how this CBG loop is necessary for song acquisition and plasticity. However, the process through which learning is consolidated within this loop remains unknown. We know that successful song learning depends on sleep and that, during the night, oscillatory activity emerges and neural activity related to singing is replayed in parts of the song circuitry. Could neural oscillations and replays underlie song consolidation in the avian CBG loop? Drawing from the understanding of how synchronised oscillatory activity in the hippocampal-cortical network facilitates the transfer and consolidation of memories, we used Neuropixel 1.0 probes in the avian CBG loop to explore whether similar neural mechanisms can be observed, suggesting participation in song consolidation. To efficiently handle our high-yield and multiplexed datasets (electrophysiology, behaviour, and histology), we first built the necessary computational infrastructure with standardised (meta)data management and sharing protocols, automated spike sorting, and data-tailored visualisation and analysis tools. Then, we applied this toolset to sleep recordings from seven birds and were the first to identify that avian CBG-loop cortical areas exhibit higher local field coherence, neural firing variability, and spike-to-field entrainment during slow wave sleep, as compared to the basal ganglia, which instead had a more desynchronised and uncoordinated profile.
Spatial and temporal variability of temperature at local scale in the context of climate change. Impact on vine development and grape ripening.
by Laure DE RESSEGUIER (Ecophysiologie et Génomique Fonctionnelle de la Vigne)
The defense will take place at 9h30 - Amphithéatre Institut des sciences de la vigne et du vin. 210 Chem. de Leysotte, 33140 Villenave-d'Ornon
in front of the jury composed of
- Cornelis VAN LEEUWEN - Professeur - Bordeaux Sciences Agro - Directeur de these
- Hans Reiner SCHULTZ - Professor - Hochschule Geisenheim University - Rapporteur
- Guillaume CHARRIER - Chargé de recherche - INRAE UMR PIAF 547 - Rapporteur
- Valérie BONNARDOT - Maîtresse de conférences - Université Rennes 2 - Examinateur
- Bénédicte WENDEN - Chargée de recherche - INRAE UMR1332 Biologie du Fruit et Pathologie - Examinateur
- Queiróz JORGE - Professeur - Université de Porto - Examinateur
Considering the sensitivity of grapevines to environmental factors, in particular soil and climate, and the challenges raised by climate change, it is important to study the spatial distribution of climate and its interactions with the plant at the scale of wine-growing regions. One of the main components of terroir, which characterises the interactions between human factors, vines and the physical parameters of the environment, is temperature. This factor affects photosynthesis and therefore the production of biomass, but also the grape composition and wine typicity. To characterise terroir, the wine-growing territory scale is relevant, as these are contiguous areas where collective decisions and actions are built, allowing processes of adaptation to climate change to be defined. The first objective of this research was to characterise the spatial and temporal variability of temperature at different scales, from the wine-growing region down to the vineyard plot, using physical geography approaches. The environmental factors and weather conditions that influence this distribution were identified. A second objective was to characterise the grapevine response in terms of phenology. This was carried out through observations and phenological modelling based on temperature data, in order to predict the key stages of vine development (budburst, flowering, veraison and a proxy for grape maturity), at local scale. These models were parameterised and evaluated under current and future climatic conditions in Saint-Émilion, Pomerol and surrounding appellations. One of the visible effects of climate change is the rising sugar concentration in grapes, which leads to higher alcohol content in wines. While this has occasionally led to more consistent ripening in late-ripening areas that have historically struggled to produce quality wines, in other areas, over-ripening can lead to unbalanced wines that fail consumer expectations. A third objective of this research was to evaluate the influence and relative importance of several abiotic factors of the terroir (temperature, vine water and nitrogen status) and two biotic factors (berry weight and the timing of phenology) that influence the dynamics of sugar accumulation at local scale. This work improves our knowledge of terroir and provides the wine industry with information and tools to optimise vineyard management, training systems, and adaptation of plant material to the local terroir characteristics. It is also a useful tool to anticipate the necessary adaptations in the context of climate change.