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Genome-wide association for agro-morphological traits in a triploid banana population with large chromosome rearrangements
No full textAll phenotypic and genotypic data underlying this study are available from the following CIRAD Dataverse repository: https://doi.org/10.18167/DVN1/FTM7GC, including the vcf file ‘Genotyping_1129hybrids_200Ksnps.vcf.gz’, the pedigree information and BLUPs for all traits in ‘Phenotyping_2727hybrids_24traits.tsv’, and GWAS summary statistics for the K and Kc in archives ‘GWAS_summary_stats_K_model.tar.gz’ and ‘GWAS_summary_stats_Kc_model.tar.gz’, respectively. The vcf file is also available on the exploration and visualization tool Gigwa: https://gigwa.cgiar.org/gigwa/?module=GWAS_agromorphotraits. The Illumina data of the progenies are available in the SRA database (PRJNA1106767).International audienceBanana breeding is hampered by the very low fertility of domesticated bananas and the lack of knowledge about the genetic determinism of agronomic traits. We analysed a breeding population of 2723 triploid hybrids resulting from crosses between diploid and tetraploid Musa acuminata parents, which was evaluated over three successive crop cycles for 24 traits relating to yield components and plant, bunch, and fruit architectures. A subset of 1129 individuals was genotyped by sequencing, revealing 205 612 single-nucleotide polymorphisms (SNPs). Most parents were heterozygous for one or several large reciprocal chromosomal translocations, which are known to impact recombination and chromosomal segregation. We applied two linear mixed models to detect associations between markers and traits: (i) a standard model with a kinship calculated using all SNPs and (ii) a model with chromosome-specific kinships that aims at recovering statistical power at alleles carried by long non-recombined haplotypic segments. For 23 of the 24 traits, we identified one to five significant quantitative trait loci (QTLs) for which the origin of favourable alleles could often be determined amongst the main ancestral contributors to banana cultivars. Several QTLs, located in the rearranged regions, were only detected using the second model. The resulting QTL landscape represents an important resource to support breeding programmes. The proposed strategy for recovering power at SNPs carried by long non-recombined rearranged haplotypic segments is an important methodological advance for future association studies in banana and other species affected by chromosomal rearrangements
Antibody-secreting cell repertoires hold high-affinity anti-rocuronium specificities that can induce anaphylaxis in vivo
No full textInternational audienceBackgroundNeuromuscular blocking agents (NMBA) are muscle relaxants used to assist mechanical ventilation but lead in 1/10,000 anesthesia to severe acute hypersensitivity reactions i.e., anaphylaxis. Incidences vary between types of NMBAs. Rocuronium, a widely used non-depolarizing aminosteroid NMBA, induces among the highest anaphylaxis rates. Rocuronium-induced anaphylaxis is proposed to rely on pre-existing rocuronium-binding antibodies, but no such antibodies have ever been identified.ObjectivesIdentify rocuronium-specific antibody repertoires from plasma cells or plasmablasts of rocuronium-immunized mice, and determine the affinities, structures and anaphylactogenic potential of these antibodies for rocuronium.MethodsHerein, we engrafted rocuronium onto carrier proteins allowing immunization of mice against rocuronium, screening for rocuronium-specific antibody responses, and sorting of rocuronium-specific plasma cells using droplet microfluidics coupled to single-cell antibody gene (VH and VL) sequencing.ResultsThe two different repertoires of >500 VH-VL pairs were oligoclonal, comprised of three major clonal families, and displayed convergence. Expressed as human IgG1, these antibodies demonstrated subnanomolar affinities for rocuronium with families either monospecific for rocuronium or cross-reactive only for closely-related NMBAs. Expressed as human IgE, they triggered human mast cell and basophil activation, and severe passive systemic anaphylaxis in mice humanized for the IgE receptor FcεRI. Co-crystal structures between rocuronium and antibody representatives of three different VH-VL families revealed distinct interaction modes with, however, the ammonium group involved systematically in the binding interface.ConclusionsThis work identifies the epitopes of antibody reactivity to rocuronium, demonstrates anaphylactogenic potential of anti-rocuronium IgE and establishes the first mouse model of NMBA anaphylaxis
The afterlife effects of leaf and root litter traits on soil N cycling
No full textInternational audienceLitter nitrogen (N) release during decomposition crucially influences ecosystem N cycling and the amount of N available to plants and other soil organisms. However, the role of initial litter traits in affecting patterns of temporal N release from litters and determining the fate of N in the soil is still poorly understood.Here, we measured litter N release during the 12-month decomposition of 15N-labelled leaf and root litters of 12 common Mediterranean herbaceous species. We further traced the fate of N during decomposition of the litters into the soil and measured the inorganic N content in the soil solution as well as total N in the particulate (POM) and mineral-associated organic matter (MAOM) fractions at the end of the incubation.While most litters exhibited a very rapid initial N release, they were also quite variable in their N dynamics. As such they differed in the quantity and temporal patterns of N release, the accumulation of inorganic N in the soil solution, as well as in the incorporation of N in stable soil organic matter (SOM) fractions during decomposition. This variability was driven by differences in initial litter chemistry, particularly N, but also P and Mn, and litter C leachate concentrations. These and other traits (including water-soluble compounds and lignin concentrations) explained up to 81% of the variance in N release rate, 48% for N accumulation in the soil solution, 57% for N entering the soil POM and 55% for MAOM fraction.Synthesis. We identified litter traits and litter types (root versus leaf) with afterlife effects on N cycling in soils and important implications for ecosystem functioning. Highly decomposable litters (typically high N; including most leaf litters) generally support a fast N release through mineralization, thereby the immediate supply of N to plants, but also potentially higher losses from the system, and long-term storage as MAOM-N, likely within microbial resynthesis products. In contrast, poorly decomposable litters (typically low N; including most root litters) promote longer and weaker N release and foster N retention via lower N losses and increased POM-N formation
L'économie à l'ère de la science ouverte : un nouvel élan pour la reproductibilité
No full textLa crise de la reproductibilité, révélée par Ioannidis (2005) et confirmée par de nombreuses études, a intensifié les préoccupations sur la fiabilité des résultats scientifiques. Bien que l'économie affiche un taux de réplication supérieur à d'autres disciplines, elle reste exposée aux biais de publication, au p-hacking et à l'effet-tiroir, compromettant la crédibilité des conclusions. La science ouverte apparaît comme une réponse méthodologique et institutionnelle à ces défis. Nous explorons trois leviers d'amélioration : (1) l'accès libre aux publications, données et codes, (2) le pré-enregistrement et les registered reports, qui limitent la flexibilité analytique et les biais de sélection, et (3) la réplication systématique des études, clé de la validation scientifique. En analysant leurs mécanismes, avantages et défis, nous mettons en lumière leur impact sur la fiabilité des recherches en économie et au-delà. L'essor de ces pratiques marque un tournant vers une science plus robuste et cumulative, mais leur adoption requiert une évolution des incitations académiques, un soutien institutionnel et un engagement collectif en faveur de la reproductibilité
Economic Principles in Cell Biology
No full textInternational audienceHow can a cell maintain itself as a living being? Living cells, shaped by billions of years of evolution, have developed many ways to adapt to their environment, e.g. by regulation of gene expression. But the rules of physics and chemistry enforce certain boundaries on what cells can achieve and how they can allocate their own resources. Shaped by evolution, cells "do certain things right", and our goal is to uncover some of the governing principles.In our open textbook - to which anyone can contribute - we give an overview of established approaches to "cellular economics", from descriptions of simple metabolic systems to cell growth, variability, and dynamic behaviour.For more information, please see our website https://principlescellphysiology.org/book-economic-principles
LIMAQUA : African interdisciplinary laboratory in sustainable, nutrition-sensitive marine aquaculture
No full textOne Ocean Science Congress, Nice, FRA, 03-/06/2025 - 06/06/2025Over the past three decades, global capture fisheries production has remained relatively unchanged, while aquaculture production has strongly increased to satisfy the demands of a growing world population. Since 2022, aquaculture production has surpassed that of capture fisheries. Although the environmental performance of aquaculture has shown positive trends over the last 20 years, further research is necessary to address its sustainability challenges, such as reducing the use of marine resources in aquafeeds, limiting habitat degradation, and improving disease management.Research in aquaculture has traditionally focused on enhancing the growth and health of farmed species, rather than addressing human nutrition concerns. Nutrition-sensitive aquaculture proposes a new paradigm that moves beyond merely producing aquatic foods to fostering well-being. This involves promoting diversification and sustainable intensification of aquaculture production, investigating a wider range of aquatic species and their dietary contributions to prioritize nutrient-rich alternatives that improve dietary diversity, and encouraging nutrition-enhancing aquaculture feeding practices, among other strategies.Based in South Africa, the International Joint Laboratory LIMAQUA?lima means ?to cultivate' in Xhosa, a language spoken in Southern Africa?conducts an interdisciplinary research and training programme to tackle nutritional and sustainability challenges of marine aquaculture, contributing to food and nutrition security, poverty alleviation, and income creation in the region. LIMAQUA brings together a team of scientists specializing in biology, biotechnology, socioeconomics, food science and human nutrition. The research and training activities are grounded in the sustainability science approach?an inter- and transdisciplinary approach co-constructed with academic, governmental, private sector, and civil society actors. Specifically, LIMAQUA focuses on i) developing sustainable marine aquaculture practices for target species, including research on culture technologies, sustainable nutrition, welfare and health of farmed organisms (One Health approach), and aquaculture-environment interactions; ii) adopting an integrated approach to marine aquaculture development; iii) creating aquaculture-based food and nutritional products; iv) providing capacity-building and training; and v) fostering collaborations within Africa.This presentation will examine examples of research activities undertaken within the framework of LIMAQUA. This includes the development of integrated multitrophic aquaculture systems, assessments of social acceptability of aquaculture development, and evaluations of the nutrient supply from local aquaculture production, highlighting sustainable and nutrition-sensitive approaches in marine aquaculture
Devenir des pesticides dans les paysages agricoles Méditerranéens : Analyse et modélisation du rôle des infrastructures
No full textSoil secrets and tree tales: an in-depth comparison of carbon storage in mixed and pure stands of pine and birch
No full textInternational audienceWith climate change intensifying droughts, pest outbreaks and fire risks, forest management practices are increasingly focused on stabilizing soil carbon (C) stocks, which are essential for long-term ecosystem productivity and climate change mitigation. Planting more species-rich forests has been proposed as a potential solution, but the impact of species selection and planting density on carbon stocks remains largely unknown, particularly in mixed-species plantations, where local water availability plays a key role. In this study, our objective was to examine the effects of tree diversity, water availability, and tree density on carbon stocks and fluxes. Using a 10-year-old tree diversity experiment, we investigated how pure monocultures of pine (Pinus pinaster) and birch (Betula pendula), as well as mixed pine-birch stands, influence carbon dynamics under contrasting water conditions and different tree densities. Our results indicated that tree species mixtures slightly increased total C stocks, primarily through enhanced soil C storage due to niche partitioning and greater root turnover. However, pine monocultures showed higher aboveground biomass productivity than birch monocultures and mixed stands, regardless of water availability. Overall, increased soil moisture enhanced both tree biomass and soil carbon stocks, especially in mixed stands, likely by alleviating drought stress for birch. In contrast, higher water availability accelerated litter decomposition, reducing C stocks in the litter layer. Tree density was a key driver of C storage, with denser stands of pine monocultures showing increased aboveground biomass but reduced understory C stocks. These findings highlight the context-dependent benefits of mixed stands: while species mixtures can enhance soil C storage and adaptability to drought, they may be inferior to pine monocultures in aboveground C storage, at least under the specific environmental conditions and temporal scale covered by our study. This study underscores the need for site-specific forest management strategies that balance productivity and C sequestration goals, offering guidance for climate change mitigation through alternative planting schemes adjusting tree density and species composition while maintaining ecosystem services.</div
Médiation équine : état des lieux et défis pour l'avenir
No full textInternational audienceLa médiation équine est un secteur en plein développement en France, porté majoritairement par des femmes installées depuis moins de dix ans, souvent en cumul d’activités. Les pratiques sont très diverses : types de structures, profils des bénéficiaires, équidés mobilisés et modalités d’intervention. Les difficultés les plus fréquemment évoquées concernent la viabilité économique, le soin et le renouvellement de la cavalerie, ainsi qu’un manque de reconnaissance institutionnelle. La formation continue est jugée essentielle, avec une préférence pour le présentiel et les ateliers pratiques. Les professionnels expriment un fort intérêt pour la recherche, notamment sur les effets de la médiation, la relation humain-animal et le bien-être équin. Cette étude dresse un premier état des lieux utile pour structurer et accompagner ce secteur en pleine évolution
Impact de la représentation cartographique de l'incertitude pour la prise de décision : le cas de la prise en compte de la qualité des sols dans l'aménagement du territoire
No full textAccurate and spatially explicit information is essential for more informed spatial planning decisions. However, this information comes with significant uncertainty which is often poorly communicated. While map producers have primarily focused on quantifying uncertainty, they have largely overlooked end-users' needs and preferences regarding its representation. As a result, users struggle to interpret and incorporate this information into their decision-making, frequently leading to its disregard.In this thesis, we took the example of a soil quality map produced using Digital Soil Mapping techniques, and followed its entire lifecycle, from the initial spatial predictive mapping to its use in land planning decisions. Along the way, we developed and implemented specific methodologies to improve the map from an end-user’s point of view. To improve the relevance of the map for local decision making, we tried to reduce the uncertainty by increasing the size of the soil dataset used to calibrate the DSM model. To improve map integrity, we performed an uncertainty analysis that included not only the mapping errors but also the errors conveyed by the soil quality indicator. To improve the intelligibility of map uncertainty representations, we tested both spatial aggregations of predicted maps using an agglomerative clustering algorithm and an alternative visualisation technique involving a coincident representation of uncertainty using glyphs. Ultimately, we conducted an experiment involving 283 end-users of soil maps using a web-based survey to identify their preferences regarding the representation of uncertain soil quality information, and assess the impact of map features on their decision-making. Our main findings were that 1) increasing the size of the calibration datasets significantly reduced the uncertainties of the DSM products involved in the production of the soil quality map, but resulted in only a moderate reduction in the uncertainty of the final soil quality map, 2) errors affecting the definition of the soil quality indicators made a small but non-negligible contribution to the overall uncertainty of the soil quality map, 3) agglomerative clustering outperformed other spatial aggregation techniques in reducing uncertainty while preserving the representation of fine soil variation, 4) end-users tend to prefer moderately aggregated map products over traditional raster DSM products and uncertainty representations by separate maps over coincident representations, 5) decision-making was significantly hindered when uncertainty values exceeded a given threshold, 6) there were clear differences in the factors influencing decision making depending on whether the decision was to authorise soil sealing or to protect against sealing. The findings of this thesis allowed us to formulate recommendations for soil map production that better accounts for uncertainty. We hope that these recommendations will assist map-makers in meeting end-users' needs, and that it will contribute to a more effective use of environmental maps in policy-making.Une information spatiale précise est essentielle pour informer les décisions d’aménagement du territoire. Cependant, cette information s’accompagne d’une incertitude élevée qui est souvent mal communiquée. Jusqu’à maintenant, les producteurs de cartes se sont principalement focalisés sur la quantification de cette incertitude, et ont largement négligé les besoins et préférences des utilisateurs quant à sa représentation. En conséquence, les utilisateurs peinent à interpréter et à intégrer cette information dans leur prise de décision, et tendent à simplement l’ignorer.Dans cette thèse, nous sommes partis de l’exemple d’une carte de qualité des sols produite par cartographie des sols par modélisation statistique (CSMS), et avons suivi tout son cycle de vie, depuis la spatialisation de l’information, jusqu’à son utilisation dans les décisions d’aménagement du territoire. Tout au long de ce processus, nous avons développé et mis en œuvre des méthodologies spécifiques visant à améliorer la carte du point de vue des utilisateurs. Afin d’accroître la pertinence de la carte pour la prise de décision locale, nous avons cherché à réduire l’incertitude en augmentant la taille du jeu de données pédologiques utilisé pour calibrer le modèle de CSMS. Pour améliorer l’intégrité de la carte, nous avons réalisé une analyse d’incertitude prenant en compte non seulement les erreurs de cartographie, mais aussi celles associées à l’indicateur de qualité des sols. Pour améliorer l’intelligibilité des représentations de l’incertitude, nous avons testé d’une part l’agrégation spatiale des cartes prédictives à l’aide d’un algorithme de clustering agglomératif, et d’autre part une visualisation alternative impliquant une représentation coïncidente de l’incertitude à l’aide de glyphes. Enfin, nous avons mené une expérience auprès de 283 utilisateurs de cartes des sols via une enquête en ligne afin d’identifier leurs préférences en matière de représentation de l’incertitude et d’évaluer l’impact des caractéristiques des cartes sur leurs décisions.Nos principaux résultats sont les suivants. (1) L’augmentation de la taille des jeux de données de calibration a permis de réduire significativement les incertitudes des produits DSM impliqués dans la production de la carte de qualité des sols, mais n’a entraîné qu’une diminution modérée de l’incertitude de la carte finale. (2) Les erreurs affectant la définition des indicateurs de qualité des sols ont contribué de manière faible mais non négligeable à l’incertitude globale de la carte. (3) L’algorithme de clustering agglomératif s’est révélé plus performant que d’autres techniques d’agrégation spatiale pour réduire l’incertitude tout en préservant la représentation des variations fines des sols. (4) Les utilisateurs ont tendance à préférer des cartes modérément agrégées aux produits raster traditionnels, ainsi qu’une représentation de l’incertitude sur des cartes distinctes plutôt qu’une représentation coïncidente. (5) La prise de décision est significativement entravée lorsque les valeurs d’incertitude dépassent un certain seuil. (6) Des différences nettes existent dans les facteurs influençant la prise de décision selon qu’il s’agit d’autoriser l’imperméabilisation des sols ou de protéger un sol contre cette imperméabilisation.Les résultats de cette thèse nous ont permis de formuler des recommandations pour une production de cartes des sols tenant mieux compte de leur incertitude. Nous espérons que ces recommandations aideront les cartographes à répondre aux attentes des utilisateurs, et qu’elles contribueront à une utilisation plus efficace des cartes environnementales dans l’élaboration des politiques publiques