Oskar Bordeaux
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Nitrogen nutrition impacts grapevine esca leaf symptom incidence, physiology, and metabolism
No full textNitrogen plays a crucial role in plant growth and defence mechanisms, yet its role in plant–pathogen interactions is complex and remains largely unexplored, especially in perennial crops. This study aimed to investigate the effects of controlled nitrogen nutrition levels on disease incidence, fungal communities, and plant physiology and metabolism. Esca is a widespread grapevine vascular disease affecting physiology, xylem integrity, and metabolism. Naturally infected Vitis vinifera L. cv. Sauvignon blanc were subjected to three ammonium nitrate treatments across three seasons, resulting in reduced esca incidence under nitrogen deficiency compared with medium nutrition levels, while excess nitrogen had no significant impact. Nitrogen treatments significantly impacted vine physiology and leaf metabolites, but did not affect fungal wood communities. Nitrogen deficiency significantly reduced stem diameter, photosynthesis, and leaf area, probably decreasing whole-plant transpiration, while excess nitrogen increased these factors, suggesting a key role for plant transpiration in esca incidence. Additionally, nitrogen deficiency led to significantly higher production of phenylpropanoids, particularly flavonoids, in leaf metabolomes compared with the medium level. These findings highlight the pivotal role of nitrogen in the development of esca through alterations in vine morphology, physiology, and metabolism. Fertilization practices may be crucial in the management of plant diseases.Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovationMetaboHUB National Infrastructure of metabolomics and fluxomicsPlateforme d'Innovation " Forêt-Bois-Fibre-Biomasse du Futur
Forest biodiversity and structure modulate human health benefits and risks
No full textThe benefits and risks of forests to human health are widely recognized. Yet, variation across forest types and their ecological characteristics driving health effects remain underexplored. Based on a continental-scale, interdisciplinary empirical database from 164 European forest stands, we constructed a Bayesian Belief Network to quantify seven causal pathways relating distinct forest types to physical and mental health. These forest–health pathways included mental well-being via visual or auditory stimuli, thermal comfort, polyphenol content of medicinal plants, mushrooms and nutrition, air quality, and ticks and Lyme disease. Results show that forests consistently provide net health benefits regardless of their ecological characteristics. Forest canopy density and tree species diversity emerge as key drivers, but their effect size and directionality are strongly pathway-dependent. Changes in forest canopy density can generate trade-offs. For example, forests optimized for heat buffering and air pollution mitigation may compromise medicinal plant yield and enhance Lyme disease prevalence. Tree diversity effects were weaker but more uniformly positive. Therefore, forest management should account for such trade-offs to tailor forest biodiversity and functioning to local public health priorities
Artificial intelligence: the human response to approach the complexity of big data in biology
No full textSince the late 2010s, artificial intelligence (AI), encompassing machine learning and propelled by deep learning, has transformed life science resear c h. It has become a crucial tool for ad v ancing the computational anal ysis of biological pr ocesses, the discov er y of natural products, and the study of ecosystem dynamics. This re vie w explores how the rapid increase in high-throughput omics data acquisition has dri v en the need for AI-based analysis in life sciences, with a particular focus on plant sciences, animal sciences, and microbiology. We highlight the role of omics-based predictive analytics in systems biology and innov ati v e AI-based anal ytical approaches for gaining deeper insights into comple x biolo gical systems. F inally, w e discuss the importance of FAIR (finda b le, accessib le, inter opera b le, r eusa b le) principles for omics data, as well as the future challenges and opportunities presented by the increasing use of AI in life sciences.Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovationNext generation metabolomics and fluxomics, from population to single cellsMetaboHUB National Infrastructure of metabolomics and fluxomicsCentre français de phénomique végétal
The Effect of Augmented Reality on Involuntary Autobiographical Memory
Get PDFWe know little about the impact of augmented reality (AR) on human cognition, particularly regarding involuntary autobiographical memory (IAM). IAMs are spontaneous recollections of personal events, ubiquitous in daily life but under-researched in both psychology and human-computer interaction. We first discuss the potential opportunities and risks of replacing conventional displays with AR to increase the likelihood of IAMs. We then report on a study investigating whether stimuli displayed on the same mobile device using video-see-through AR are more likely to resurface than those shown with a simple 3D viewer. We found that AR elicits approximately twice as many IAMs in controlled settings with immediate re-exposure to contextual cues, but no measurable effect was found in everyday settings with delayed re-exposure. Therefore, AR can enhance IAMs, but its effects may be modest and short-lived in most cases. Nevertheless, future studies could reveal stronger effects of AR in other settings. Supplementary material is available at osf.io/gscpv/. © 2025 Copyright held by the owner/author(s)
Façade maritime : Atlantique (Aquitaine), Rapport de prospection inventaire (2024), commune de Soulac-sur-Mer (Gironde), OA 5324
No full textPairing energy crops and root biostimulants for phytomanaging a former landfill
No full textPhytomanagement of contaminated soils is increasingly valued both to produce biomass for the bioenergy sector and as nature-based soil remediation option. However, degraded soil conditions may hinder energy crop growth. Biostimulants and micro-organisms could boost crop yield and phytomanagement performance but field-based evidences remain scarce. This study aimed at determining the shoot dry weight (SDW) yield, metal uptake and decrease in soil contaminants for Cannabis sativa, Sorghum bicolor, and Miscanthus × giganteus at a former landfill mainly contaminated by Cu, Zn and PCBs. The 3-year field trial, carried out in a randomized block design, consisted in control plots (C) and plots amended by humic substances paired with mycorrhizal fungi (Hs+M). The technosol exhibited high topsoil stoniness due to abundant debris and an unfavorable sandy-loam texture. SDW yields and metal concentrations (ICP -OES) were measured annually. Sorghum produced the highest SDW yields (3-year average: 20 Mg DW ha -¹) and responded best to the Hs+M treatment (+16 %-35 %). Treatment did not influence shoot metal concentrations, which tended to decrease over the years. However, higher SDW yields of sorghum increased its shoot Cu and Zn removals (+ 60 % and 46 %-65 % vs. control plants, respectively). Over the three years, shoot Cu uptake was similar for Hs+M sorghum and C hemp. DTPA-extractable soil metals did not change, final soil PCB concentrations as well. Consequently, crops studied would not promote environmental pollutant dispersion. Sorghum paired with the Hs+M treatment was the most promising option, maximizing biomass yield and gradual stripping of bioavailable soil Cu and Zn.</div
Contribution of the total papilla preservation technique to the regeneration of an infra-bony defect: about a clinical case
No full textLa maladie parodontale touche environ 60% de la population adulte dentée mondiale. Des séquelles, telles que les lésions infra-osseuses, peuvent être présentes et susceptibles de compromettre, à court, moyen ou long terme, le pronostic des dents restantes. Afin de traiter ces défauts infra-osseux, différents lambeaux et techniques de régénération parodontale sont disponibles dans notre arsenal thérapeutique, chacun ayant ses indications selon la morphologie du défaut. À travers un cas clinique, nous présenterons le lambeau de préservation papillaire total, décrit pour la première fois en 2015 par les équipes des docteurs Aslan et Buduneli. Un point sur la littérature sera également abordé dans la discussion. L'utilisation du lambeau de préservation papillaire total dans le cadre du cas clinique est justifiée, ses indications sont précisées, ainsi que son apport dans la régénération parodontale d'un défaut infra-osseux.Periodontal disease affects approximately 60% of the world's dentate adult population. Sequelae, such as infra-bony lesions, may be present and could compromise the prognosis of the remaining teeth in the short, medium, or long term. To treat these infra-bony defects, various flap techniques and periodontal regeneration methods are available in our therapeutic arsenal, each with its specific indications depending on the defect's morphology. Through a clinical case, we will present the Total Papilla Preservation Flap, first described in 2015 by the teams of Drs. Aslan and Buduneli. A review of the literature will also be included in the discussion. The use of the Total Papilla Preservation Flap in this clinical case is justified, its indications are clarified, as well as its contribution to the periodontal regeneration of an infra-bony defect
Comparative study of the multi-allergenic screening tests PHADIATOP and SX01 in the screening of respiratory, ENT and ophthalmic allergies
No full textIntroduction : les allergies causées par les pneumallergènes sont parmi les maladies chroniques les plus fréquentes au monde, elles pourraient toucher 50% de la population mondiale d’ici 2050. Ce sont également des maladies largement sous diagnostiquées. Le dosage PHADIATOP® (ThermoFischer) est un test de dépistage multi-allergénique (mélange d’allergènes extraits), considéré comme référence en Europe. Sa spécificité et sa sensibilité sont supérieures à 80-90%, ce qui en fait une bonne première approche diagnostique de l'allergie respiratoire pour le médecin sans compétence allergologique. Nous avons comparé les performances du PHADIATOP avec celles d’un autre test de dépistage multi-allergénique : le Sx01 (Hycor), nouveau sur le marché, composé d’allergènes moléculaires modulables par le biologiste. Matériel Et Méthodes : nous avons effectué une étude observationnelle rétrospective transversale : Dans un premier temps, les sérums de patients ayant effectué un test PHADIATOP® au CHU de Bordeaux durant la période d’inclusion ont été testés avec le test Sx01 pour comparer leur performances diagnostiques biologiques. Dans un deuxième temps, un recueil clinique a été effectué sur l’ensemble des sérums analysés pour comparer leurs performances diagnostiques cliniques. Résultats : nous avons retrouvé de très bonnes performances pour le test Sx01, qui est non inférieur au test PHADIATOP®, avec comparativement une sensibilité de 85,96%, une spécificité de 98,09%, une valeur prédictive positive de 94,23% et une valeur prédictive négative de 95,06% (p < 0,01). Les discordances portaient principalement sur la sensibilisation aux moisissures. Comparativement à la clinique, nous avons retrouvé respectivement pour PHADIATOP® et Sx01 une sensibilité de 88,46% et 97,87%, une spécificité de 94,96% et 95,14%, une valeur prédictive positive de 86,79% et 86,79% et une valeur prédictive négative de 95,65% et 99,28% (p < 0,01). Conclusion : cette étude de comparaison des performances diagnostiques biologiques et cliniques des tests PHADIATOP® et Sx01 montre des résultats très prometteurs pour le Sx01 en termes de performance diagnostique, ce qui en ferait un très bon test de dépistage. De plus, il présente des caractéristiques techniques rendant son utilisation particulièrement intéressante, notamment la possibilité de s’adapter aux allergènes selon leur répartition territoriale.Introduction: allergies caused by pneumallergens are among the most common chronic diseases in the world, they could affect 50% of the world population by 2050. They are also largely underdiagnosed diseases. The PHADIATOP® assay (ThermoFischer) is a multi-allergenic screening test (mixture of extract allergens), considered a reference in Europe. Its specificity and sensitivity are greater than 80-90%, which makes it a good first diagnostic approach to respiratory allergy for doctors without allergological expertise. We compared the performances of PHADIATOP with those of another multi-allergenic screening test: Sx01 (Hycor), new on the market, composed of molecular allergens that can be modulated by the biologist. Material and methods: we carried out a retrospective, cross-sectional observational study. Firstly, sera from patients who performed a PHADIATOP® test at Bordeaux University Hospital during the inclusion period were tested with the Sx01 test to compare their biological diagnostic performance. Secondly, a clinical collection was carried out on all the sera analyzed to compare their clinical diagnostic performances. Results: we found very good performance for the Sx01 test, which is non-inferior to the PHADIATOP® test, with comparatively a sensitivity of 85.96%, a specificity of 98.09%, a positive predictive value of 94.23% and a negative predictive value of 95.06% (p < 0.01). The discrepancies mainly concerned mold sensitization. In the complementary clinical study, we found respectively for PHADIATOP® and Sx01 a sensitivity of 88.46% and 97.87%, a specificity of 94.96% and 95.14%, a positive predictive value of 86.79% and 86.79% and a negative predictive value of 95.65% and 99.28% (p < 0.01). Conclusion: this comparison study of the biological and clinical diagnostic performances of the PHADIATOP® and Sx01 tests shows very promising results for Sx01 in terms of diagnostic performance, which would make it a very good screening test. In addition, it has technical characteristics making its use particularly interesting, in particular the possibility of adapting to allergens according to their territorial distribution
GrAuFlow: A snakemake workflow for pangenome graph augmentation using short read data
No full textPangenome graphs are gaining popularity in genomic analysis as they address the bias introduced by using a single reference genome in population variant analyses. However, with the constant acquisition of new sequencing data, it is essential to update these graphs to incorporate new genomic resources. When new fully sequenced genomes are available, reconstructing the graph is often the most convenient method. In the case of small sequences, such as those from amplicon sequencing, augmenting the graph may be more straightforward, as only a small portion of the graph will be modified. In this study, we are interested in augmenting a graph with fragmented genomes assembled from short reads. This data represents a valuable resource of genetic diversity that is not currently utilized in graphs, where use of T2T genomes are recommended.In this context, we are developing a workflow called GrAuFlow (Graph Augmentation Workflow) using the Snakemake workflow manager (Mölder et al, 2021). First, GrAuFlow performs an assembly of Illumina short read data using the SPAdes assembly toolkit ( Prjibelski et al, 2020), retaining only contigs that pass stringent quality filters. Then, contigs are fractioned in long reads sequence like and mapped onto the graph using different tools: Palss (Denti et al, 2025) , GraphAligner ( Rautiainen et al, 2020) and SVArp (Soylev et al, 2024), before graph augmentation with vg augment (Garrison etal, 2018). GrAuFlow then extracts structural variants (SV) from the different strategies to retain only well supported with a minimal length. Finally, SVs are compared to modify the graph only with those that show consistent variants across all graph augmentation tools. To test our approach, we use Zymoseptoria tritici, a fungal pathogen responsible for septoria tritici blotch of wheat.Based on graphs generated by Minigraph and Minigraph-Cactus using 8 genomes of Zymoseptoria tritici, we validate that short-reads data could be useful to add new information in pangenome graph. Nevertheless, this approach is limited to medium-size variants. Structural variants that are not easilyassembled due to repeat contents or complex events may not be detected, which makes this approach interesting for enriching specific loci of interest