Spectral Unmixing: Analysis of Performance in the Olfactory Bulb In Vivo

Background: The generation of transgenic mice expressing combinations of fluorescent proteins has greatly aided the reporting of activity and identification of specific neuronal populations. Methods capable of separating multiple overlapping fluorescence emission spectra, deep in the living brain, with high sensitivity and temporal resolution are therefore required. Here, we investigate to what extent spectral unmixing addresses these issues. Methodology/Principal Findings: Using fluorescence resonance energy transfer (FRET)-based reporters, and two-photon laser scanning microscopy with synchronous multichannel detection, we report that spectral unmixing consistently improved FRET signal amplitude, both in vitro and in vivo. Our approach allows us to detect odor-evoked FRET transients 180-250 mm deep in the brain, the first demonstration of in vivo spectral imaging and unmixing of FRET signals at depths greater than a few tens of micrometer. Furthermore, we determine the reporter efficiency threshold for which FRET detection is improved by spectral unmixing. Conclusions/Significance: Our method allows the detection of small spectral variations in depth in the living brain, which is essential for imaging efficiently transgenic animals expressing combination of multiple fluorescent proteins

Simulation of Astrocytic Calcium Dynamics in Lattice Light Sheet Microscopy Images

International audienceAstrocytes regulate neuronal information processing through a variety of spatio-temporal calcium signals. Advances in calcium imaging started to reveal astrocytic activities, but the complexity of the recorded data strongly call for computational analysis tools. Their development is hindered by the lack of reliable annotations that are essential for their evaluation and for the design of learning-based methods. To overcome the labeling problem, we present a framework to simulate realistic astrocytic calcium signals in 3D+time lattice light sheet microscopy (LLSM) images by closely modeling calcium kinetics in real astrocytes

Plasmodesmata act as unconventional membrane contact sites regulating intercellular molecular exchange in plants

Funding: This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (projects 772103-BRIDGING to E.M.B. and 101001097-LIPIDEV to Y.J.), the National Agency for Research (grants ANR-18-CE13-0016 STAYING-TIGHT to E.M.B. and Y.J., ANR-2020-CE20-0002 3C TomFruit Growth to E.M.B., ANR-21-CE13-0016-01 DIVCON to A.T. and E.M.B., and ANR-18-CE13-0025-02 caLIPSO to Y.J.), the Human Frontier Science Program (project RGP0002/2020 to E.M.B.), the French Government in the framework of the IdEX Bordeaux University “Investments for the Future” program/GPR Bordeaux Plant Sciences (E.M.B.), the Swiss National Science Foundation (project 31003A_179159 to M.B.), Research Foundation-Flanders grant G002121N to E.R., the HORIZON-MSCA-2023-PF-01 project 101152141-BRACTION to Y.L., and Projet Emergents FlowValve University of Bordeaux to M.S.Membrane contact sites (MCSs) are fundamental for intracellular communication, but their role in intercellular communication remains unexplored. We show that in plants, plasmodesmata communication bridges function as atypical endoplasmic reticulum (ER)-plasma membrane (PM) tubular MCSs, operating at cell-cell interfaces. Similar to other MCSs, ER-PM apposition is controlled by a protein-lipid tethering complex, but uniquely, this serves intercellular communication. Combining high-resolution microscopy, molecular dynamics, and pharmacological and genetic approaches, we show that cell-cell trafficking is modulated through the combined action of multiple C2 domains transmembrane domain proteins (MCTPs) 3, 4, and 6 ER-PM tethers and phosphatidylinositol-4-phosphate (PI4P) lipid. Graded PI4P amounts regulate MCTP docking to the PM, their plasmodesmata localization, and cell-cell permeability. SAC7, an ER-localized PI4P-phosphatase, regulates MCTP4 accumulation at plasmodesmata and modulates cell-cell trafficking capacity in a cell-type-specific manner. Our findings expand MCS functions in information transmission from intracellular to intercellular cellular activities.Peer reviewe

Understanding the nervous system: Lessons from Frontiers in Neurophotonics

The Frontiers in Neurophotonics Symposium is a biennial event that brings together neurobiologists and physicists/engineers who share interest in the development of leading-edge photonics-based approaches to understand and manipulate the nervous system, from its individual molecular components to complex networks in the intact brain. In this Community paper, we highlight several topics that have been featured at the symposium that took place in October 2022 in Québec City, Canada

Approches intégrées de construction et d’analyse des modèles de systèmes pétroliers : apports pour l’exploration pétrolière

Numerical tools for petroleum system modeling and forward stratigraphic modeling were designed to account for complex processes responsible for hydrocarbon accumulations in petroleum reservoirs. These processes, which extended to new mechanisms and gained details with increasing understanding, involve several geoscience disciplines making difficult the building of models consistent with both data and knowledge. The work performed during this Ph.D. aims at making basin modeling more accessible to geoscientists first by making easier the integration of geological concepts and available data during the process of model building and then by improving quality of forecasts and of risk quantification through sensitivity and risk analysis on maps. In a first section, two methods designed for better and easier estimation of the thermal history and of the distribution of marine organic matter in sedimentary basins are presented. They are based on a similar procedure which uses local data and regional knowledge to assess these two key aspects of petroleum system exploration. An optimization loop is initially performed on input parameters to fit on local data before extrapolating the results to basin scale under the constraint of the regional geological information. Both approaches were patented (Ducros, 2012; Ducros et Chauveau, 2015). The basin of Berkine in Algeria, for which an important set of thermal data is available, was used as an application case study for the method designed for estimating thermal history. The Western Canadian Sedimentary Basin, known for its production of unconventionals, was used for illustrating the estimation of the distribution of organic matter. The second part of the work is dedicated to a new methodology for sensitivity and risk analysis on maps. It is built on a proxy-model of the simulator behavior in the uncertain space to save time during the sampling phase required for providing statistical results. It also uses a principal component analysis to reduce the space dimension when dealing with maps. The approach is illustrated on two case studies: one using a forward stratigraphic model for assessing the position of petroleum reservoirs and one on a petroleum system modeling tool for assessing the maturity of a source-rock in the Levant Basin. These new tools strengthen the integration of data coming from different disciplines to produce more consistent and robust results. They make easier the interpretation of risk analysis provided on a format compatible with classical methods of risk assessment in petroleum exploration such as CRS mapping. The results of this work emphasize the role of these tools for making the link between the different disciplines of geosciences to provide consistent and predictive results. They also give access to powerful risk mapping that can be part of a more general framework, called Common Risk Segment Mapping, used for risks assessment in petroleum exploration.Les outils numériques de modélisation des bassins sédimentaires et des systèmes pétroliers prennent en compte des processus naturels chaque fois plus nombreux et font intervenir une grande variété de disciplines des géosciences. C’est pourquoi il est ardu de construire des modèles qui soient cohérents avec l’ensemble des données disponibles et l’ensemble des connaissances géologiques. Les travaux réalisés dans cette thèse de doctorat visent à rendre ces outils de modélisation plus accessibles d’une part en facilitant la construction des modèles numériques par l’intégration simultanée et automatique des concepts géologiques et des données et d’autre part en donnant accès à l’interprétation des risques d’exploration sous forme de cartes. Pour répondre au premier objectif, deux méthodes ont été mises au point afin de faciliter et d’améliorer la détermination de l’histoire thermique des bassins sédimentaires et de la distribution régionale de la matière organique. Elles se basent sur une même procédure d’exploitation des mesures locales et de l’information géologique régionale pour mieux estimer ces aspects clés pour l’exploration des systèmes pétroliers. Une optimisation des paramètres de modélisation est d’abord réalisée afin de reproduire les données locales avant d’extrapoler les résultats à l’échelle du bassin via l’utilisation des données géologiques. Les deux approches ont été valorisées chacune par le dépôt d’un brevet (Ducros, 2012 ; Ducros et Chauveau, 2015). Elles sont illustrées pour l’une sur le cas du bassin de Berkine, où l’on dispose d’une importante base de données thermiques, et pour l’autre sur le bassin Ouest-Canadien, objet d’une intense exploration des hydrocarbures de roche-mère. La deuxième partie des travaux a porté sur la mise au point et l’application d’une méthode d’analyse de sensibilité et de risques sous forme de cartes. Elle s’appuie sur une approche d’approximation de la réponse d’un simulateur sur l’ensemble de l’espace d’incertitude afin de réduire le temps d’échantillonnage nécessaire à l’estimation des risques et sur une analyse en composantes principales permettant de réduire la dimension des résultats à traiter. La méthode est illustrée sur deux exemples d’application : le premier utilise un outil de modélisation stratigraphique pour l’estimation de la position des réservoirs pétroliers dans un bassin sédimentaire et le deuxième montre comment peut-être déterminé le risque sur la maturité de la roche-mère. Ces nouveaux outils renforcent les liens entre les différentes disciplines des géosciences afin de produire des résultats plus cohérents et plus prédictifs. Ils facilitent également l’accès à des analyses d’incertitudes et de risques qui permettent des interprétations cartographiques puissantes, en lien avec les techniques courantes d’appréciation des risques d’exploration (CRS mapping)

Integrated approach for building and analyzing petroleum system models : new insights for petroleum exploration

Les outils numériques de modélisation des bassins sédimentaires et des systèmes pétroliers prennent en compte des processus naturels chaque fois plus nombreux et font intervenir une grande variété de disciplines des géosciences. C’est pourquoi il est ardu de construire des modèles qui soient cohérents avec l’ensemble des données disponibles et l’ensemble des connaissances géologiques. Les travaux réalisés dans cette thèse de doctorat visent à rendre ces outils de modélisation plus accessibles d’une part en facilitant la construction des modèles numériques par l’intégration simultanée et automatique des concepts géologiques et des données et d’autre part en donnant accès à l’interprétation des risques d’exploration sous forme de cartes. Pour répondre au premier objectif, deux méthodes ont été mises au point afin de faciliter et d’améliorer la détermination de l’histoire thermique des bassins sédimentaires et de la distribution régionale de la matière organique. Elles se basent sur une même procédure d’exploitation des mesures locales et de l’information géologique régionale pour mieux estimer ces aspects clés pour l’exploration des systèmes pétroliers. Une optimisation des paramètres de modélisation est d’abord réalisée afin de reproduire les données locales avant d’extrapoler les résultats à l’échelle du bassin via l’utilisation des données géologiques. Les deux approches ont été valorisées chacune par le dépôt d’un brevet (Ducros, 2012 ; Ducros et Chauveau, 2015). Elles sont illustrées pour l’une sur le cas du bassin de Berkine, où l’on dispose d’une importante base de données thermiques, et pour l’autre sur le bassin Ouest-Canadien, objet d’une intense exploration des hydrocarbures de roche-mère. La deuxième partie des travaux a porté sur la mise au point et l’application d’une méthode d’analyse de sensibilité et de risques sous forme de cartes. Elle s’appuie sur une approche d’approximation de la réponse d’un simulateur sur l’ensemble de l’espace d’incertitude afin de réduire le temps d’échantillonnage nécessaire à l’estimation des risques et sur une analyse en composantes principales permettant de réduire la dimension des résultats à traiter. La méthode est illustrée sur deux exemples d’application : le premier utilise un outil de modélisation stratigraphique pour l’estimation de la position des réservoirs pétroliers dans un bassin sédimentaire et le deuxième montre comment peut-être déterminé le risque sur la maturité de la roche-mère. Ces nouveaux outils renforcent les liens entre les différentes disciplines des géosciences afin de produire des résultats plus cohérents et plus prédictifs. Ils facilitent également l’accès à des analyses d’incertitudes et de risques qui permettent des interprétations cartographiques puissantes, en lien avec les techniques courantes d’appréciation des risques d’exploration (CRS mapping).Numerical tools for petroleum system modeling and forward stratigraphic modeling were designed to account for complex processes responsible for hydrocarbon accumulations in petroleum reservoirs. These processes, which extended to new mechanisms and gained details with increasing understanding, involve several geoscience disciplines making difficult the building of models consistent with both data and knowledge. The work performed during this Ph.D. aims at making basin modeling more accessible to geoscientists first by making easier the integration of geological concepts and available data during the process of model building and then by improving quality of forecasts and of risk quantification through sensitivity and risk analysis on maps. In a first section, two methods designed for better and easier estimation of the thermal history and of the distribution of marine organic matter in sedimentary basins are presented. They are based on a similar procedure which uses local data and regional knowledge to assess these two key aspects of petroleum system exploration. An optimization loop is initially performed on input parameters to fit on local data before extrapolating the results to basin scale under the constraint of the regional geological information. Both approaches were patented (Ducros, 2012; Ducros et Chauveau, 2015). The basin of Berkine in Algeria, for which an important set of thermal data is available, was used as an application case study for the method designed for estimating thermal history. The Western Canadian Sedimentary Basin, known for its production of unconventionals, was used for illustrating the estimation of the distribution of organic matter. The second part of the work is dedicated to a new methodology for sensitivity and risk analysis on maps. It is built on a proxy-model of the simulator behavior in the uncertain space to save time during the sampling phase required for providing statistical results. It also uses a principal component analysis to reduce the space dimension when dealing with maps. The approach is illustrated on two case studies: one using a forward stratigraphic model for assessing the position of petroleum reservoirs and one on a petroleum system modeling tool for assessing the maturity of a source-rock in the Levant Basin. These new tools strengthen the integration of data coming from different disciplines to produce more consistent and robust results. They make easier the interpretation of risk analysis provided on a format compatible with classical methods of risk assessment in petroleum exploration such as CRS mapping. The results of this work emphasize the role of these tools for making the link between the different disciplines of geosciences to provide consistent and predictive results. They also give access to powerful risk mapping that can be part of a more general framework, called Common Risk Segment Mapping, used for risks assessment in petroleum exploration

Map-based uncertainty analysis for exploration using basin modeling and machine learning techniques applied to the Levant Basin petroleum systems, Eastern Mediterranean

International audienceThe Levant Basin of the East-Mediterranean region contains a biogenic petroleum system and possibly an underlying thermogenic system. The application of a new map-based uncertainty and sensitivity analysis that integrates a large set of geological parameters demonstrates that a connection between an Upper Cretaceous thermogenic petroleum system and the shallower Oligo-Miocene reservoirs is highly possible in the southern part of the basin (offshore Israel and southern Lebanon) where hydrocarbon fluids are generated from the Campanian source rock and charge the overlying Oligo-Miocene reservoir interval through faults. Estimates of volumes of expelled hydrocarbons combined with regional analysis of the Eocene top seal integrity indicates that the most prospective zones correspond to the southern offshore Lebanon and offshore Israel. In the northern part of the Levant Basin (offshore central and northern Lebanon), petroleum fluids potentially generated by the Campanian source rocks remain trapped under the Eocene seal or they migrate towards the margins of the basin. Our approach is based on applications of machine learning techniques and robust statistical analyses to petroleum systems modeling, focusing on spatial uncertainty analysis. It may be used on similar frontier or emerging hydrocarbon provinces to help de-risking the petroleum systems