Oskar Bordeaux
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Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology
No full textBackground: Plant and soil microbiomes can interfere with pathogen life cycles, but their influence on disease epidemiology remains understudied. Here, we analyzed the relationships between plant and soil microbiomes and longterm epidemiological records of grapevine downy mildew, a major disease caused by the oomycete Plasmopara viticola. Results: We found that certain microbial taxa were consistently more abundant in plots with lower disease incidence and severity and that the microbial community composition could predict disease incidence and severity. Microbial diversity was not strongly linked to epidemiological records, suggesting that disease incidence and severity is more related to the abundance of specific microbial taxa. These key taxa were identified in the topsoil, where the pathogen's oospores overwinter, and in the phyllosphere, where zoospores infect leaves. By contrast, the leaf endosphere, where the pathogen's mycelium develops, contained few taxa of interest. Surprisingly, the soil microbiota was a better predictor of disease incidence and severity than the leaf microbiota, suggesting that the soil microbiome could be a key indicator of the dynamics of this primarily aerial disease. Conclusion: Our study integrates long-term epidemiological data with microbiome profiles of healthy plants to reveal fungi and bacteria relevant for the biocontrol of grapevine downy mildew. The resulting database provides a valuable resource for designing microbial consortia with potential biocontrol activity. The framework can be applied to other crop systems to guide the development of biocontrol strategies and reduce pesticide use in agriculture.Cultivating the grapevine without pesticides : towards agroecological wine-producing socio-ecosystem
Combination of metabolomics and machine learning to unravel environmental drivers of spatial heterogeneity of microbial metabolome assemblage in aquatic periphyton : The COMBO project
No full textFreshwater periphyton, playing a key role in ecosystem functions and services, are increasingly used in ecotoxicology to better understand the link between chemical exposure and ecosystem disturbance. To this end, one key challenge is to understand better how environmental conditions interact and modulate the community dynamics in situ. In this context, this project aims to gain understanding of the spatial heterogeneity of the natural periphyton metabolome assembly under various environmental conditions through the implementation of statistic and predictive meta-metabolomics approach. This attempts to characterize the assembling rules (stockastic vs deterministic) of metabolomes in periphyton and to identify the main environmental driving forces of meta-metabolome assemblages that contributes to its spatial heterogeneity. To do so, autochthonous periphytons were collected in 100 sites widely distributed in France encompassing various water physico-chemistry and chemical/ecological status (water agency data). The photosynthetic yield of the periphyton was characterized in situ in parallel of the measurement of the water physico-chemistry (nutrients, micropollutants) by the water agency. Physico-chemical results confirmed the heterogeneity between the sites. The global biomass parameters (e.g. proteins) will be soon characterized while untargeted metametabolomics based on LC-HRMS is ongoing. Those metametabolomics data will provide a comprehensive picture of the chemical landscape of the periphyton, potentially highlighting the existence of a core meta-metabolome. Then meta-community ecology metrics (α/β diversity) will be used to define assembling mechanisms. In parallel, statistics and machine-learning will be implemented in order to identify features or groups of features that can predict specific environmental conditions and water quality status. In addition, by linking metabolites to biomass or photosynthesis, COMBO would support the discovery of predictive effect biomarkers at the community level that may have impair ecosystem functions. Overall, this knowledge will support the translation of metametabolome responses of periphyton to chemical stress under controlled conditions into real applications for biomonitoring purposes
Reconstructing community dynamics from limited observations
No full textEcosystems tend to fluctuate around stable equilibria in response to internal dynamics and environmental factors. Occasionally, they enter an unstable tipping region and collapse into an alternative stable state. Our understanding of how ecological communities vary over time and respond to perturbations depends on our ability to quantify and predict these dynamics. However, the scarcity of long, dense time series data poses a severe bottleneck for characterising community dynamics using existing methods. We overcome this limitation by combining information across multiple short time series using Bayesian inference. By decomposing dynamics into deterministic and stochastic components using Gaussian process priors, we predict stable and tipping regions along the community landscape and quantify resilience while addressing uncertainty. After validation with simulated and real ecological time series, we use the model to question common assumptions underlying classical potential analysis and re-evaluate the stability of previously proposed "tipping elements" in the human gut microbiota
Development of flexible nanoporous gold electrodes for the detection of glucose
Get PDFThe development of implantable glucose sensors is of significant interest in the management of diabetes. This work focuses on developing an implantable, biocompatible nanoporous gold electrode prototype based on Kapton® for the subcutaneous detection of glucose. The electrodes were first modified with a layer containing glucose oxidase and Os(2,2′-bipyridine) 2 Cl⋅PVI (Os(bpy) 2 Cl PVI). An additional polymeric layer containing poly (2-methacryloyloxyethyl phosphorylcholine-co-glycidyl methacrylate) was then added to reduce biofouling and foreign body reaction effects. The modified electrode had a V MAX of 211 ± 13 μA cm -2 and a K Mapp of 6.1 ± 0.8 mM in pseudo physiological conditions, with a linear detection range from 1 to 4 mM and a sensitivity of 28.6 ± 2.1 μA cm -2 mM -1 . In artificial plasma, the response of the sensor was saturated at 3 mM, with a V MAX of 113 ± 10 μA cm -2 and a K Mapp of 2.1 ± 0.4 mM with a linear detection range from 1 to 2.5 mM and a sensitivity of 14.6 ± 3.3 μA cm -2 mM -1 . Mechanical stress testing demonstrated that there was a 40 % reduction of the redox polymer coverage after 320 deformation events, however the catalytic activity was still detectable after 160 events. Minimal cytotoxicity effects of the electrodes were observed. When subcutaneously implanted the electrodes showed fairly good mechanical stability after one week and detachment of the metallic layer on some electrodes after 21 days, probably due to electrode bending. A limited foreign body reaction was observed. These results indicated that the electrodes could be implanted for a period of up to 1 week
An ecosystem for producing and sharing metadata within the web of FAIR Data
No full textBackground Descriptive metadata are vital for reporting, discovering, leveraging, and mobilizing research datasets. However, resolving metadata issues as part of a data management plan can be complex for data producers. To organize and document data, various descriptive metadata must be created. Furthermore, when sharing data, it is important to ensure metadata interoperability in line with FAIR (Findable, Accessible, Interoperable, Reusable) principles. Given the practical nature of these challenges, there is a need for management tools that can assist data managers effectively. Additionally, these tools should meet the needs of data producers and be user-friendly, requiring minimal training. Results We developed Maggot (Metadata Aggregation on Data Storage), a web-based tool to locally manage a data catalog using high-level metadata. The main goal was to facilitate easy data dissemination and deposition in data repositories. With Maggot, users can easily generate and attach high-level metadata to datasets, allowing for seamless sharing in a collaborative environment. This approach aligns with many data management plans as it effectively addresses challenges related to data organization, documentation, storage, and the sharing of metadata based on FAIR principles within and beyond the collaborative group. Furthermore, Maggot enables metadata crosswalks (i.e., generated metadata can be converted to the schema used by a specific data repository or be exported using a format suitable for data collection by third-party applications). Conclusion The primary purpose of Maggot is to streamline the collection of high-level metadata using carefully chosen schemas and standards. Additionally, it simplifies data accessibility via metadata, typically a requirement for publicly funded projects. As a result, Maggot can be utilized to promote effective local management with the goal of facilitating data sharing while adhering to the FAIR principles. Furthermore, it can contribute to the preparation of the future EOSC FAIR Web of Data within the European Open Science Cloud framework.Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovationProjet vin authenticité en RM
Toxicol Anal Clin
No full textBackground: New psychoactive drugs appeared in Reunion Island beginning in 2016, principally synthetic cannabinoids such as “tabac chimique”. We described the clinical features of twelve hospitalizations during 2023–2024 requiring admission to intensive care unit for suspected psychoactive drug intoxication with atypical clinical presentation for synthetic cannabinoids, including a morphine-like toxidrome. Results: Over a ten-month period, twelve patients aged from 21 to 43 years required treatment in the intensive care unit with a suspected psychoactive drug intoxication. The main cause of intensive care unit admission was a profound coma with early acute respiratory failure. All patients except one developed acute respiratory distress syndrome, with six being severe and ten requiring intubation with mechanical ventilation. Four patients experienced hemodynamic shock. Five exhibited acute heart failure, with three requiring inotropic drugs. Five patients developed acute renal failure and one patient developed acute liver failure. Most of the patients confirmed inhaling “tabac chimique”. Two blood and urine samples were positive for the novel synthetic opioid Protonitazene, one was associated with a novel synthetic cannabinoid. Another analysis was positive for a metamphetamine analogue. Conclusions: Inhalation of new psychoactive substances including novel synthetic opioids can lead to severe organ failure with a life-threatening prognosis, with neurological and respiratory failure initially, followed by early acute cardiac failure. © 2025 The Author
The regenerative soundscapes of Burck Wood (Bordeaux Métropole): The emergence of an anthropo-biophonic indicator in an urban environment
No full textEn ville, le défi climatique n’est pas dissociable de la question écologique du paysage. À ce titre, l’écologie sonore paysagère développée par Raymond Murray Schafer prend tout son sens dans le partage territorial sonore entre humains et non-humains. Depuis les années 1970, Schafer a réveillé notre écoute du monde sonore entre vivant et non-vivant ; le processus même de perception du sonore et son intégration dans le rapport ordinaire à l’environnement portent un nom : le paysage sonore. Afin de saisir toute la dynamique spatiale de ce partage territorial des sources sonores humaines et non humaines, nous proposons ici une approche paysagère d’appréhension sonore des qualités humaines et non humaines de l’environnement vécu – telles que définies par Bernie Krause (2016) – le spectre de présence, approche actuellement testée sur les zones calmes – bois, forêts, parcs et jardins – de la métropole bordelaise. Cette méthode de relevé et d’analyse du paysage sonore urbain permet de prendre un « instantané » des effets anthropophoniques de l’urbanisation galopante et du changement climatique. Elle constitue un outil de diagnostic ambiantal des « sanctuaires sonores » au sein de la ville, à créer ou à préserver pour répondre au besoin d’acclimatation de l’habitant des villes en situation de stress environnemental. À terme, ce modèle d’analyse ambiantale est voué à évoluer vers un outil d’observation et de qualification des ambiances sonores, capable d’étudier le devenir et l’utilisation de ces « zones calmes » face aux réponses urbaines au changement climatique.In cities, climate change cannot be dissociated from the environmental question of the landscape. In this respect, the sound ecology of the landscape developed by Raymond Murray Schafer takes on its full meaning in the territorial sound experience shared by humans and non-humans. Since the 1970s Schäfer has raised awareness of the world of sound shared by the human and non-human features of the environment; the very process of perceiving sound and including it in our ordinary relationship with the environment has a name: soundscape. In order to capture all the spatial dynamics of this territorial sharing of human and non-human sound sources, we propose to apprehend the biophonic and anthropophonic qualities of the experienced environment—as defined by Bernie Krause (2016)—through the landscape and the spectrum of presence; an approach currently being tested in quiet areas such as woods, forests, parks and gardens in the metropolitan area of Bordeaux. This method of surveying and analysing the urban soundscape provides a ‘snapshot’ of the anthropophonic effects of rapid urbanisation and climate change. It provides a tool for conducting an ambient diagnostic of ‘sound sanctuaries’ within the city that need to be preserved or created to meet the acclimatisation needs of urban dwellers in situations of environmental stress. Eventually, the intention is for this ambient analytical model to evolve into a tool for observing and qualifying sound environments to study the potential status and use of these ‘quiet zones’ in the face of urban responses to climate change
Appl Neuropsychol Adult
No full textBackgroundVirtual technologies (VR) could respond to several challenges in Unilateral Spatial Neglect (USN) assessment, particularly the lack of sensitivity and ecological validity of traditional paper-and-pencil tests. A scoping review was conducted to explore current trends in this area.MethodsPubMed, EMBASE, PsycINFO, Web of Science, IEEE, ACM, and the Cochrane Library were systematically searched for VR USN assessment. The Joanna Briggs Institute methodological guidelines for scoping reviews were used to inform our methodology.ResultsThirty-one publications were included. There were two populations: healthy adults (n = 349) and post-stroke individuals (n = 903). A classification based on tasks and type of interaction used was proposed. Correlations with paper and pencil tests (PPTs) were often significant when the task structure was similar to PPTs but was lacking for activities with more dynamic components. The ecological validity of the tasks was assessed in comparison with the Catherine Bergego Scale (n = 4) and a real-world navigation task (n = 1). Using VR, USN disorders have been characterized using a wide range of indicators.ConclusionsFew studies have addressed ecological validity, yet the use of VR in the assessment of the USN in this scoping review shows an undeniable contribution compared to traditional pencil-paper tests, especially for capturing the patient's behavior toward the far extrapersonal space, essential in daily life
