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Effects of climate on the phenology of Annona senegalensis Pers. (Annonaceae) and the distribution of associated insects in Burkina Faso
No full textInternational audienceClimate change and global warming in the Sahelian region cause dramatic drought and advancing of the desert. This phenomenon could affect the plant survival and community composition, but even for surviving plants, it could affect their phenology and the insect community associated with them. In a space‐for‐time approach, we studied the case of Annona senegalensis Pers. (Annonaceae), a common shrub in tropical areas, to determine the impact of climate change on its phenology and the insects associated with its flowers and fruits. We determined the phenology phases of Annona senegalensis during a 1‐year period and assessed the abundance and diversity of insects in the Sudanian and the Sudano‐Sahelian climatic zones of Burkina Faso. Temperature, rainfall and relative humidity were recorded during 12 months in two sites per zone. Leafing of Annona senegalensis lasted 10 months in the Sudanian zone, flowering and fruiting were 3 months long. In the Sudano‐Sahelian zone, leafing lasted 8 months while flowering and fruiting were 3 and 4 months long, respectively. A total of 10,040 insects belonging to 48 species were collected in the two climatic zones. Forty‐six species were found in the Sudanian zone while 25 species were recorded in the Sudano‐Sahelian one. The variations in the plant phenology and the insect community were mainly due to the variation in rainfall across both climatic zones. Our results emphasize that advancing of the desert due to climate change could not only affect the survival of plants but for resistant species it also affect their interactions with insects and the whole insect community associated
Typologie des digestats « Ferti-Dig » : de l’établissement des classes aux effets sur les agroécosystèmes
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Inférence statistique multi-omique de l'hétérogénéité cellulaire - COBICA 2024
No full textInternational audienceCellular heterogeneity in biological tissues reflects progression of disease state and is therefore a key indicator for improved diagnostic and prognosis. The cellular composition of tissues is difficult to assess and quantify from bulk molecular profiles, with all cells present in the tissue contributing to the recorded signals. Cell deconvolution is a common approach to unravel the heterogeneous molecular profiles observed in bulk tissues, by inferring the underlying relative abundance of individual cell types using one or more omics data, such as RNA-seq gene expressions or DNA methylation rates.So far, cellular deconvolution assumes that bulk omic profiles result from weighted sums of so-called signature cell-specific omic profiles, weights being the unknown proportions of those cell types. Consistently, most statistical methods used for cellular deconvolution are based on extensions of the Ordinary Least Squares (OLS) optimization algorithm, under nonnegativity and sum-to-one constraints on those unknown mixing coefficients. Using OLS implicitly assumes independence, homoscedasticity and normality of the residual errors, required to guarantee optimal and unbiased estimations. In cellular deconvolution applied to bulk molecular profile, all three assumptions are highly questionable. Indeed, strong violations of those assumptions may be due to the instrinsic nature of omics data, RNA-seq data being overdispersed read counts and DNA methylation rates being percentages for example, or to the dependence structure induced by the gene regulatory network, some key genes being more influent on deconvolution accuracy than others.The goal of this work is to provide a well defined statistical framework that respects the inherent characteristics of biological data for deconvolution, using multi-omic data.Multi-omic data integration for cellular deconvolution aims at leveraging mutually dependent viewpoints on cellular heterogeneity. The general statistical framework we propose is especially designed for integration of two frequently used omic data types for cell deconvolution mentioned previously, RNA-seq gene expression data, for which a constrained negative binomial regression model is assumed, and DNA methylation rates, using a constrained beta regression model. Many simultaneous optimization strategies are considered, either based on constrained and weighted maximum likelihood, weights being introduced to strengthen the influence of some genes based on their specific combination of signature expressions and DNA-methyation rates, or on gene selection.An extensive comparative study of cell deconvolution performance with leading single or multi-omic methods is conducted on benchmark data, created for a data challenge and using 9 cell types commonly found in PDAC (pancreatic cancer). Results confirm both the gain in a multi-omic integration approach and in the use of ad-hoc probability distributions for each omic data type. Additional improvements based on dependence models between approximation errors by the two omic data types for each gene are finally discussed
Exogenous carbon addition soil mediated phosphorus dynamics under eight years continuous input of swine manure in a wheat-rice rotation
No full textInternational audienceThe study investigated the prolonged impact of swine manure application on soil inorganic phosphorus (P) fractions over an 8-year continuous, randomized field trial involving rotating wheat (wet conditions) and rice (flooded conditions) crops. The trial comprised six treatments: triplicate control plots receiving only chemical fertilizers, and triplicate plots receiving chemical fertilizers and/or swine manure ranging from 150 to 1200 kg P2O5 ha- 1. The continuous application of swine manure increased soil P content and availability. Initially, P primarily accumulated in the soil as Fe-P during the first four years of manure application, transitioning to Ca8-P over the following four years. The main driver of these changes in P fractions was soil total organic carbon (TOC) was identified as the main driver of these changes in P fractions, contributing 31.5% to the observed variations. TOC increased steadily throughout the trial, with a faster rising in years 1-4 compared to years 4-8. Laboratoryscale soil incubation experiments were conducted, involving the addition of glucose or cellulose as exogenous carbon sources to test their effects on soil P dynamics and mitigate environmental damage from P leaching. The addition of cellulose to soil that had received high quantities of swine manure for eight years resulted in increased the moderately labile and moderately resistant organic P fractions while decreasing the Ca8-P and Olsen-P fractions. This promoted adsorption of high-activity inorganic P to organic matter, consequently limiting the accumulation of Ca8-P. The long-term application of swine manure altered soil P fractions and enhances P lability, enhancing P lability and availability. This study identified an optimized the risk of leaching of labile P from soil under a fertilization regime applying 10,300 kg ha- 1 yr- 1 swine manure. To further mitigate the risk of P leaching, the inclusion of additional cellulose-based organic matter (e.g., straw) in swine manure fertilization regimes is recommended
Identification of soil‐related professional profiles for the future from a survey of European stakeholders
No full textInternational audienceCurrent and future stakeholders and decision‐makers involved in agricultural soil management need to develop soil‐related skills to meet the challenges of food security and global change in the coming decades. The aim of this study was to identify professional profiles related to the management, conservation and restoration of agricultural soils on the basis of a European stakeholder survey and to relate these profiles to specific and generic skills. Stakeholders from 24 European countries, selected by the national hubs of the European Joint Programme on agricultural soil management, were invited to propose soil‐related professional profiles that they considered important to develop over the next 20 years. They were then asked to identify up to 15 specific or generic skills that they considered necessary for each profile. In total, 299 stakeholders proposed 1–3 professional profiles each, in 20 languages, for a total of 786 profiles ranging from the bachelor to doctoral level. After translation into English and grouping by expertise, 60 profiles were identified and classified as ‘traditional’, ‘specialised’ or ‘innovative’. Innovative profiles were related to the inclusion of soil in fields that do not currently provide soil‐related education (e.g., communication, mediation, economics, law, land‐use planning, architecture, data science). Correspondence analysis based on the number of times a skill was considered necessary for a given profile led to the grouping of the 60 initial profiles into 10 clusters of profiles that required similar skills: these 10 clusters of profiles were described, and their necessary skills were identified. The clusters illustrate the need to broaden the scope of soil science and the variety of professions that can address soil‐related issues and require knowledge about soils. Ultimately, this list of soil‐related professional profiles and their necessary skills could help revise existing higher‐education curricula or create new curricula
Peptide bonds cleaved by pepsin are affected by the morphology of heat-induced ovalbumin aggregates
No full textInternational audienceThe study aimed to assess the extent to which protein aggregation, and even the modality of aggregation, can affect gastric digestion, down to the nature of the hydrolyzed peptide bonds. By controlling pH and ionic strength during heating, linear or spherical ovalbumin (OVA) aggregates were prepared, then digested with pepsin.Statistical analysis characterized the peptide bonds specifically hydrolyzed versus those not hydrolyzed for a given condition, based on a detailed description of all these bonds. Aggregation limits pepsin access to buried regions of native OVA, but some cleavage sites specific to aggregates reflect specific hydrolysis pathways due to the denaturation-aggregation process. Cleavage sites specific to linear aggregates indicate greater denaturation compared to spherical aggregates, consistent with theoretical models of heat-induced aggregation of OVA. Thus, the peptides released during the gastric phase may vary depending on the aggregation modality. Precisely tuned aggregation may therefore allow subtle control of the digestion process
Selection of soil health indicators for modelling soil functions to promote smart urban planning
No full textInternational audienceThe contribution of soil health to global health receives a growing interest, especially in urban environment. Therefore, there is a true need to develop methods to evaluate ecological functions provided by urban soils in order to promote smart urban planning. This work aims first at identifying relevant soil indicators based either on in situ description, in situ measurement or lab analysis. Then, 9 soil functions and sub-functions were selected to meet the main expectations regarding soil health in urban contexts. A crucial step of the present research was then to select adequate indicators for each soil function and then to create adapted reference frameworks; they were in the form of 4 classes with scores ranging from 0 to 3. All the reference frameworks were developed to evaluate soil indicators in order to score soil functions, either by using existing scientific or technical standards or references or based on the expertise of the co-authors. Our model was later tested on an original database of 109 different urban soils located in 7 cities of Western Europe and under various land uses. The scores calculated for 8 soil functions of 109 soils followed a Gaussian distribution. The scoring successfully expressed the strong contrasts between the various soils; the lowest scores were calculated for sealed soils and soils located in urban brownfields, whereas the highest were found for soils located in city parks or urban agriculture. Despite requiring a soil expertise, the proposed approach is easy to implement and could help reveal their true potential of urban soils in order to promote smart urban planning and enhance their contribution to global health
Communautés de pratique, plasticité des usages et nouveaux patrimoines sociaux. Pour une grille d’analyse prospective appliquée au végétal urbain à Angers
No full textInternational audienceL’originalité de ce chapitre réside dans la lecture de l’innovation sociale urbaine à travers la plasticité des usages. Cette dernière est abordée ici comme co-évolution et non comme un tournant disruptif par rapport à l’héritage passé. Les communautés de pratique réinterprètent ces héritages pour mieux répondre à leurs besoins dans de nouveaux contextes, ici le renouvellement urbain. Le processus de patrimonialisation résulte de la capacité de ces communautés à entrer en interaction sociale et à redéployer les ressources existantes de manière inédite. Il est éminemment social dans son fondement. Partant d’une conceptualisation de ce processus de patrimonialisation sociale, l’objectif de ce chapitre est d’aboutir à une grille d’analyse prospective pour l’action publique encore peu initiée à ces nouvelles formes patrimoniales
Face au changement climatique, quelles stratégies d’atténuation et d’adaptation pour les productions avicoles ?
No full textCet article a pour origine une synthèse réalisée dans le cadre du World’s Poultry Congress (Collinet al., 2022).International audiencePoultry meat and eggs are major sources of animal protein for human consumption worldwide. Their production has increased rapidly in recent decades. However, poultry production is vulnerable to climate change, in particular to global warming and its direct and indirect consequences. To cope with this, it is necessary to implement adaptation strategies at the animal level, in particular by improving the resilience of the animals; these strategies require, on the one hand, a better understanding of the physiology of the birds (thermoregulation, efficiency for meat and egg production, etc.) and, on the other hand, the search for innovations in relation to nutrition, health, early reprogramming or genetics (integration of new adaptive traits in selection strategies). Solutions also need to be found at the production systems level to take into account the changes in the geographical distribution of diseases linked to climate change and to introduce mitigation practices to reduce energy consumption and greenhouse gas emissions. Interdisciplinary research focusing on genetics, technical methods (such as early thermal programming), engineering solutions, nutritional innovations and new breeding strategies is being developed. These strategies consider the growing social demand for ethical animal production in the perspectives of the “One Health” and “One Welfare” concepts and limit the feed-food competition in the context of climate change. This review illustrates through a few examples the levers of improvement and combined adaptive strategies that can be considered to make poultry production systems more resilient in the context of climate change.La viande de volaille et les œufs sont des sources principales de protéines animales pour l’alimentation humaine dans le monde. Leur pro-duction a augmenté rapidement au cours des dernières décennies. Cependant, les productions avicoles sont vulnérables au changement climatique, en particulier au réchauffement de la planète et à ses conséquences directes et indirectes. Pour y faire face, il est nécessaire de mettre en place des stratégies d’adaptation des animaux, en particulier en améliorant leur résilience. Ces stratégies nécessitent d’une part de mieux comprendre la physiologie des oiseaux (thermorégulation, efficacité pour la production de viande et d’œufs...) et d’autre part de rechercher des innovations en lien avec la nutrition, la santé, la reprogrammation précoce ou encore la génétique (intégration de nouveaux caractères adaptatifs dans les stratégies de sélection). Il faut également trouver des solutions au niveau des systèmes de production, par exemple en prenant en compte les aires de répartition géographique des maladies liées au changement climatique et en introduisant des pratiques d’atténuation pour réduire les consommations d’énergie et les émissions de gaz à effet de serre. Des recherches interdiscipli-naires axées sur la génétique, les méthodes techniques (telles que la programmation thermique précoce), les solutions d’ingénierie, des innovations nutritionnelles et de nouvelles stratégies d’élevage agroécologiques sont ainsi développées. Ces stratégies tiennent compte de la demande sociale croissante en faveur de productions animales éthiques dans les perspectives d’une seule santé (« One Health ») et d’un seul bien-être (« One Welfare ») et visent à limiter la concurrence entre l’homme et les animaux pour les ressources alimentaires. Cette revue illustre par quelques exemples les leviers d’amélioration et de stratégies adaptatives envisageables pour rendre les animaux et les systèmes de production avicole plus résilients dans le contexte du changement climatique