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QuaDS Qualitative/Quantitative Description Statistics
No full textQuaDS(Quantitative/Qualitative Description Statistics) is a pipeline tailored to describe a factor (a qualitative variable of of interest) in heterogeneous datasets consisting of qualitative and quantitative variables. This pipeline separately analyses the variables related to the factor using appropriate statistical tests. The QuaDS pipeline offers an interactive visualisation that describes the factor. Several parameters can be defined by the user to ensure the most personalized results based on their data
Flower strips in winter reduce barley yellow dwarf virus incidence in cereal crops
No full textInternational audienceMost studies that have explored the effect of biological control in maintaining pest populations at acceptable levels have focused on the ability of natural enemies to reduce pest abundances. The reduction in pest populations induced by natural enemies, however, is rarely studied in association with the incidence of viruses transmitted by pests, as well as its impact on crop damage and yield. Here, we performed large-scale winter field monitoring to assess the direct and indirect effects (via arthropod natural enemies) of flower strips along cereal crop margins, on (i) cereal aphid abundance, (ii) the incidence of barley yellow dwarf viruses (BYDVs) transmitted by aphids in autumn and winter, (iii) crop damage, and (iv) crop yield. In 28 cereal fields (over 2 years), we used a paired experimental design to compare a cereal field edge directly adjacent to a flower strip with an opposite (at least 50 m apart) cereal field edge adjacent to a grassy margin. Our results highlight that winter flower strips favoured the activity of ground arthropod predators in the adjacent cereal field but not aphid parasitism rate in winter. Parasitism rate only increased with the complexity of the surrounding landscape. Our results also showed that flower strips reduced both vector abundance and virus incidence in the adjacent cereal field in winter but did not affect virus symptom levels or yields. Damages were low and yield remained high in our study, which may encourage farmers to stop insecticides during the autumn-winter. This study provides a first example of how flower strips along field edges can decrease the incidence of a vector-borne virus in winter and could be used as a strategy to promote more sustainable agriculture
Isolation, Identification, and Characterization of Bacillus cereus Group Bacteria Isolated from the Dairy Farm Environment and Raw Milk in Tunisia
No full textInternational audienceMembers of the Bacillus cereus group are well-known opportunistic foodborne pathogens. In this study, the prevalence, hemolytic activity, antimicrobial resistance profile, virulence factor genes, genetic diversity by enterobacterial repetitive intergenic consensus (ERIC)-polymerase chain reaction (PCR) genotyping, and adhesion potential were investigated in isolates from a Tunisian dairy farm environment and raw milk. A total of 200 samples, including bedding, feces, feed, liquid manure, and raw bovine milk, were examined. Based on PCR test targeting sspE gene, 59 isolates were detected. The prevalence of B. cereus group isolates in bedding, feces, liquid manure, feed, and raw milk was 48%, 37.8%, 20%, 17.1%, and 12.5%, respectively. Out of the tested strains, 81.4% showed β-hemolytic on blood agar plates. An antimicrobial resistance test against 11 antibiotics showed that more than 50% of the isolates were resistant to ampicillin and novobiocin, while a high sensitivity to other antibiotics tested was observed in most isolates. The distribution of enterotoxigenic genes showed that 8.5% and 67.8% of isolates carried hblABCD and nheABC, respectively. In addition, the detection rate of cytotoxin K (cytk), enterotoxin T (bceT), and ces genes was 72.9%, 64.4%, and 5.1%, respectively. ERIC-PCR fingerprinting genotype analysis allowed discriminating 40 different profiles. The adhesion potential of B. cereus group on stainless steel showed that all isolates were able to adhere at various levels, from 1.5 ± 0.3 to 5.1 ± 0.1 log colony-forming unit (CFU)/cm2 for vegetative cells and from 2.6 ± 0.4 to 5.7 ± 0.3 log CFU/cm2 for spores. An important finding of the study is useful for updating the knowledge of the contamination status of B. cereus group in Tunisia, at the dairy farm level
Digestibilité réelle de protéines animale et végétale : comparaison des mesures obtenues in vitro vs. in vivo
No full textInternational audienceIntroduction et but de l’étudeAvec l’arrivée de nouvelles sources protéiques, il est important de pouvoir évaluer leur qualité nutritionnelle, dépendant en partie de leur digestibilité. Bien que la FAO recommande de l’évaluer in vivo (FAO, 2013), une méthodologie in vitro de référence est nécessaire pour des raisons éthiques et économiques. Il existe unconsensus international pour le protocole de digestion in vitro (INFOGEST), mais pas encore pour la digestibilité in vitro des protéines. Après digestion in vitro, la fraction digestible doit être séparée de la fraction non digestible, la phase d’absorption n’étant pas reproduite. De plus, une correction doit être apportée pour soustraire la part d’azote (N) endogène digestible, provenant des enzymes et de leur autolyse. L’objectif de l'étude a été de comparer entre elles deux méthodes de fractionnement des digestats de deux protéines alimentaires (animale et végétale) marquées au 15N, et de comparer leur digestibilité réelle obtenues in vitro et chez l’Homme .Matériel et méthodesDe la caséine micellaire et des fèves, marquées au 15N, ont été intégrées, à deux taux protéiques (5,2 et 8,5%), dans des repas tels qu’administrés dans des études cliniques et, ont été digérés suivant le protocole in vitro INFOGEST. En fin de phase intestinale, deux méthodes de fractionnement ont été testées : ajoutd’acide sulfosalicylique [(ASS) (4,5% ; m/v)] ou de méthanol (80%, v/v) puis centrifugation (4000 ou 2000g, 10 min, 4°C). La distribution de taille des peptides dans les fractions surnageantes (dites digestibles) a été évaluée par chromatographie d’exclusion stérique (Superdex® Peptides 10/300 GL) et le seuil de coupure (95% des peptides solubles en dessous de ce seuil) déterminé. Pour chaque échantillon, l’N alimentaire et endogène a été quantifié dans le surnageant et le culot de centrifugation grâce à un analyseur élémentaire couplé à un spectromètre de masse à ratio isotopique. La digestibilité réelle des protéines a été définie directement en mesurant l’N alimentaire digestible dans le surnageant ou indirectement via la mesure de l’N alimentaire non digestible dans le culot. Les écarts absolus (en point de %) entre les valeurs in vivo et in vitro ont été analysés par ANOVA à 4 facteurs (teneur en protéines, fraction, protéine et précipitant). Les seuils de coupure ont été analysés par ANOVA à 2 facteurs (protéine et précipitant). Les résultats sont présentés sous forme de moyenne et écart-type.Résultats et analyse statistiqueLe seuil de coupure ne différait pas significativement entre le méthanol et l'ASS (p>0.05), mais différait significativement (p<0.05) selon la protéine (caséine : 4,2±1,4 kDa ; fève : 2,5±0,3 kDa). Ce seuil est au-delà de ce qui est absorbable physiologiquement (< 1-0.5 kDa), mais ceci peut être justifié au vu de l’absence de peptidases dans le protocole in vitro. Les valeurs de digestibilité réelle mesurées dans le culot étaient très proches des valeurs in vivo (caséine : 94%, fèves : 84%), avec des écarts absolus faibles (2±1) et non différents entre précipitants (p>0.05). Les mesures dans le surnageant étaient significativement plus éloignées des valeurs cibles que les mesures faites dans le culot, et elles étaient plusélevées pour l’ASS par rapport au méthanol (12,7±12,9 vs. 10,5±6,5). L’N endogène représentait 18±3% à 26±3% de l’N total du culot et du surnageant, respectivement, mettant en évidence la nécessité d’une correction, sans laquelle il y aurait une surestimation de digestibilité. L’N endogène mis en oeuvre se retrouvait, en fin de digestion, à 74±7% dans le surnageant , probablement en raison de l’autolyse des enzymes.ConclusionCette étude montre qu’il est possible d'estimer in vitro la digestibilité réelle des protéines, à condition qu’une correction soit apportée pour ne tenir compte que de l’N alimentaire. Les deux méthodes de fractionnement se sont avérées équivalentes pour prédire la digestibilité réelle, à condition qu'elle soit évaluée dans le culot. Il sera important de poursuivre les comparaisons sur d’autres protéines alimentaireset de définir le blanc le plus adéquat pour corriger la digestibilité in vitro des protéines, en l’absence de protéines marquées au 15N
Spectrométries IR et Raman pour l’agrophotonique : innovations en suivi environnemental et sélection génétique
No full textNational audienceLa spectrométrie portable et miniaturisée (proche et moyen infrarouge, Raman), couplée à des modèles chimiométriques performants, offre des potentialités pour la détection sélective de polluants agricoles et la caractérisation des acides gras en aquaculture et aviculture, avec des mesures rapides, fiables et applicables à la sélection génétique et à l’agro-industrie
Opinion and report of the French Agency for Food, Environmental and Occupational Health and Safety (ANSES) relating to an analysis of the health risks associated with exposure to caterpillars with stinging hairs and the development of management recommendations
No full textXavier Bailly et Elsa Jourdain ne sont pas auteurs mais relecteurs du rapportInternational audienceSeveral species of Lepidoptera with caterpillars bearing urticating hairs are increasing their range in metropolitan France from year to year, such as the pine processionary (Thaumetopoea pityocampa Denis et Schiffermüller 1775) whose presence was historically limited to the south of France, and which is gradually being observed in the north and at higher altitudes. The procession period also seems to be appearing earlier. Climate change could have an impact on the range and phenology of this species, as well as other species of Lepidoptera with caterpillar bearing urticating hairs. Urticating caterpillars, which can trigger diffuse urticariform papules and allergic reactions for human people through contact with the skin, mucous membranes or inhalation, represent a health issue. These caterpillars also cause a health risk for animals and can have an impact on plants due to the resulting defoliation. This risk assessment therefore focused on the risk posed by these urticating caterpillars in areas where they have been established for a long time as well as in areas where they currently do not occur but could be colonized in the short or medium terms. One of the outputs of the evaluation consisted in identifying 55 different species of Lepidoptera with urticating caterpillars, for metropolitan France, but also for the overseas regions, based on the review by Kawamoto and Kumada (1984) and the GBIF database. In addition, detailed sheets for the well‐known species were drawn up, describing in particular their range, their phenology and the period when the urticating stages occur. A literature review as well as data from poison control centres and the analysis of the results of two surveys (of three associations of dermatologists/allergists and of occupational populations at risk) allowed to characterize the contexts of exposure and the human populations at risk. Concerning animal health, in addition to an epidemioclinical description based on the literature, data from veterinary poison control centres were analyzed in the specific case of dog exposure to the pine processionary between 1999 and 2021 in metropolitan french territory. Given the impact of these species of Lepidoptera on ecosystems, due to the defoliation they induce, this scientific opinion investigated the impact of these species on ecosystem services. The socio‐economic impacts of defoliations and risk management measures implemented in the event of an outbreak were studied based on a literature review and simulations for forest recreation. To represent risk for the whole metropolitan France territory, three risk maps of the human population exposure to the pine processionary, the oak processionary and the brown‐tail moth were designed at municipality level. A multi‐criteria analysis was undertaken to characterize danger (urticating caterpillars) and vulnerability of human populations. Then, the municipalities were ranked according to their level of danger and vulnerability. As a result, municipalities have been classified into 5 danger classes and 5 vulnerability classes. Based on a risk matrix with levels of hazard (abscissa axis) and levels of vulnerability (ordinate axis), 5 levels of risk were finally defined and the 34,816 municipalities of metropolitan France were classified according to their level of risk
A robust workflow to benchmark deconvolution of multi-omic data
No full textInternational audienceBackground: Tumour heterogeneity significantly affects cancer progression and therapeutic response, yet quantifying it from bulk molecular data remains challenging. Deconvolution algorithms, which estimate cell type proportions in bulk samples, offer a potential solution. However, there is no consensus on the optimal algorithm for transcriptomic or methylomic data.Results: Here, we present an unbiased evaluation framework for the first comprehensive comparison of deconvolution algorithms across both omic types, including reference-based and -free approaches. Our evaluation covers raw performance, stability, and computational efficiency under varying conditions, such as gene dependencies, missing or additional cell types and diverse sample compositions. We apply this framework across multiple benchmark datasets, including a novel multi-omics dataset generated specifically for this study. To ensure transparency and re-usability, we have designed a reproducible workflow using containerization and publicly available code.Conclusions: Our results highlight the strengths and limitations of various algorithms, and provides practical guidance for selecting the best method based on data type and analysis context. This benchmark sets a new standard for evaluating deconvolution methods and analysing tumour heterogeneity
Constraining the water budget of an agricultural headwater catchment using flux tower, satellite-based evapotranspiration, and a semi-distributed hydrological model
No full textInternational audienc
Insect visitors of green fruits of Annona senegalensis Pers. (Annonaceae) and their potential role in the plant fruiting
No full textInternational audienceAnnona senegalensis is a multipurpose wild shrub mainly used for food and traditional medicine by local people in tropical African. During its fruiting period, especially at the green fruit stage, this plant harbors an important community of insects such as various ant species (Formicidae) and the planthopper Hilda undata Walker (Tettigometridae). This study aimed at understanding the role of ants on Annona senegalensis during the fruiting period. Insect visitors of green fruits of Annona senegalensis were collected randomly on 30 green fruits from 30 plants per site, at four sites across the Sudanian and Sudano-Sahelian climatic zones of Burkina Faso, from June to July 2020. The behavior of insects was observed in the field. HPLC analyses of sugar profiles of the extrafloral nectar of green fruits, ants and Hilda undata were carried out in the laboratory to determine whether ants were feeding on green fruit nectar and Hilda undata honeydew. Ants were the most recorded visiting insect group, representing up to 95% of the insects observed on the fruit and the most frequently encountered species were Trichomyrmex abyssinicus Forel, Crematogaster sp., Messor galla Mayr, Brachyponera sennaarensis Mayr and the planthopper Hilda undata. Coleoptera, Diptera, Hemiptera, Hymenoptera and Lepidoptera were recorded. Behavioural observations and HPLC analyses showed that ants consumed extrafloral nectar of green fruits and the Hilda undata honeydew. Ants protect the green fruits and Hilda undata from pests. This study is the first report highlighting mutualistic interactions between Annona senegalensis, ants and Hilda undata
Decoding the sugar-strigolactone crosstalk: new frontier in plant growth and stress resilience
No full textInternational audiencePlants continuously integrate metabolic and hormonal signals to coordinate growth, development, and responses to environmental stimuli. Among these signals, sugars and strigolactones (SLs) have emerged as central regulators. Beyond serving as metabolic fuels, sugars act as signaling molecules that govern key developmental transitions and stress responses. SLs, a relatively recent addition to the phytohormone family, play pivotal roles in shaping plant architecture, modulating resource allocation, and facilitating environmental adaptation. While the individual signaling functions of sugars and SLs are well documented, their crosstalk remains an emerging and largely underexplored area of plant biology. This review synthesizes current knowledge on both the independent and interactive roles of sugar and SL signaling across critical developmental processes, including seed germination, hypocotyl elongation, root and shoot architecture, flowering, senescence and plant responses to abiotic and biotic stress. By analyzing antagonistic and synergistic interactions, we identify several potential integrative hubs where metabolic and hormonal signals converge to finetune the final decision. Notably, the nodal roles of BRC1 (BRANCHED1/TEOSINTE BRANCHED1),(FT (FLOWERING LOCUS T), in mediating sugar-SL crosstalk in shoot branching, flowering, respectively, are highlighted. We also explore how sugar-SL interplay influences seed germination and plant adaptation to environmental stresses through shared regulators such as TOR (Target of Rapamycin) kinase, SnRK1 (Sucrose non-fermenting-1 Related Kinase 1), and SMXLs (Suppressor of MAX2-Like proteins). Understanding these interactions not only deepens our knowledge of fundamental plant biology but also offers new insights for improving the performance and resilience of crop and horticultural species