Services déconcentrés d'appui à la recherche Ile-de-France-Jouy-en-Josas-Antony

Accounting for the variability of hydrological processes and climate conditions between catchments and within catchments remains a challenge in rainfall–runoff modelling. Among the many approaches developed over the past decades, multi-model approaches provide a way to consider the uncertainty linked to the choice of model structure and its parameter estimates. Semi-distributed approaches make it possible to account explicitly for spatial variability while maintaining a limited level of complexity. However, these two approaches have rarely been used together. Such a combination would allow us to take advantage of both methods. The aim of this work is to answer the following question: what is the possible contribution of a multi-model approach within a variable spatial framework compared to lumped single models for streamflow simulation? To this end, a set of 121 catchments with limited anthropogenic influence in France was assembled, with precipitation, potential evapotranspiration, and streamflow data at the hourly time step over the period 1998–2018. The semi-distribution set-up was kept simple by considering a single downstream catchment defined by an outlet and one or more upstream sub-catchments. The multi-model approach was implemented with 13 rainfall–runoff model structures, three objective functions, and two spatial frameworks, for a total of 78 distinct modelling options. A simple averaging method was used to combine the various simulated streamflow at the outlet of the catchments and sub-catchments. The lumped model with the highest efficiency score over the whole catchment set was taken as the benchmark for model evaluation. Overall, the semi-distributed multi-model approach yields better performance than the different lumped models considered individually. The gain is mainly brought about by the multi-model set-up, with the spatial framework providing a benefit on a more occasional basis. These results, based on a large catchment set, evince the benefits of using a multi-model approach in a variable spatial framework to simulate streamflow.

In endangered species, it is critical to analyse the level at which populations interact (i.e. dispersal) as well as the levels of inbreeding and local adaptation to set up conservation policies. These parameters were investigated in the endangered species Parnassia palustris living in contrasted habitats. We analysed population structure in 14 populations of northern France for isozymes, cpDNA markers and phenotypic traits related to fitness. Within population genetic diversity and inbreeding coefficients were not correlated to population size. Populations seem not to have undergone severe recent bottleneck. Conversely to pollen migration, seed migration seems limited at a regional scale, which could prevent colonization of new sites even if suitable habitats appear. Finally, the habitat type affects neither within-population genetic diversity nor genetic and phenotypic differentiation among populations. Thus, even if unnoticed local adaptation to habitats exists, it does not influence gene flow between populations.

Abstract Background and aims Faecalibacterium prausnitzii , a highly abundant bacterium in the human gut microbiota, has been linked to overall health and is decreased in several pathological conditions, such as Inflammatory Bowel Disease (IBD). F. prausnitzii has shown anti-inflammatory properties in human and mouse models, notably through the induction of IL-10 signaling. Here, we investigated which cell types from human blood and intestinal tissue are responsible for producing IL-10 induced by F. prausnitzii , and providing the first mechanistic insights. Methods Immune cells isolated from human blood and intestinal lamina propria of patients with IBD and non-inflamed controls, were stimulated with either F. prausnitzii EXL01 strain or Escherichia coli lipopolysaccharide (LPS) and analysed by Legendplex, ELISA, flow cytometry, RNA-sequencing (RNAseq), and Seahorse technology. Results F. prausnitzii EXL01 strain induced the direct and dose-dependent production of IL-10 in CD14 + monocytes from the systemic circulation and intestinal tissue of IBD patients and non-inflamed controls, without inducing a pro-inflammatory response as compared to LPS stimulation. RNAseq analysis corroborated these results and revealed that F. prausnitzii EXL01 strain differentially affects cell energy metabolism compared to LPS. The anti-inflammatory response induced by F. prausnitzii in monocytes was dependent on mitochondrial respiration. Conclusion F. prausnitzii induces an anti-inflammatory response and rewires energy metabolism in human monocytes, which might explain its beneficial impact on intestinal inflammation and human health in general. These results provide new insight into the mechanisms underlying the anti-inflammatory effects of F. prausnitzii and are crucial for a better understanding of its potential use in the treatment of IBD.

Abstract Increasing evidence suggests that the human blood hosts microbes including bacteria and eukaryotic viruses, which could have important implications for health. Bacteriophages of the blood are challenging to study and have been overlooked, but could translocate to this environment from different body-sites. We thus developed specific virome protocols and analysis methods to study the viral communities of blood samples obtained from healthy individuals and Crohn’s disease (CD) patients. We uncovered a diverse viral community in the human blood, dominated by phages infecting Pseudomonadota bacteria. We found that an important fraction of those phages overlaps with the gut virome, consolidating the idea that gut phages can translocate to the blood. Strikingly, viral communities of the blood were different between CD patients and healthy individuals, revealing a new signature of disease. This was not the case for fecal viral communities. Collectively, these results advance our knowledge of the microorganisms present in the human blood and pave the way for further studies of this environment in the context of disease.

Admixture is an evolutionary process that enables short-term adaptation. The Creole cattle from Guadeloupe is a tropically adapted breed. Its three-way admixture and long-term isolation offer a unique opportunity for understanding the genetic determinants of adaptive admixture in livestock. Here, we sequenced 23 Creole cattle from Guadeloupe (GUA) and combined our data with sequenced genomes of 99 cattle from 25 breeds representative of European, African and indicine groups to provide the most detailed exploration, to date, of patterns of genetic variation and to detect selection signatures in this population. We detect 17 228 983 single nucleotide polymorphisms (SNPs) and we confirmed the higher level of African and indicine ancestries, compared to the European ancestry, in the GUA genome. We show that, unlike Criollo cattle, GUA population originates directly from West Africa with indicine ancestry inherited via West African ancestors. We relied on consistency of signals across various methods based on excess of haplotype homozygosity, differences in allele frequencies and excess ⁄ deficiency of local ancestry to identify five strong candidate regions showing an excess of indicine ancestry. These encompass immune-, heat-tolerance- and physical exercise-related genes. Moreover, we found that a previously identified horn-related gene, RXFP2 is under strong selective pressure in GUA genome likely owing to human-driven (socio-cultural) pressure. Our study highlights the role played by population admixture for driving rapid adaptive response to local environmental constraints.

Tenacibaculum maritimum is a devastating bacterial pathogen affecting a large variety of marine fish species. It is responsible for significant economic losses in aquaculture farms worldwide. Different typing methods have been proposed to analyze bacterial diversity and population structure. Serological heterogeneity has been observed and up to four different serotypes have been described so far. However, the underlying molecular factors remain unknown. By combining conventional serotyping and genome-wide association study, we identified the genomic loci likely involved in the O-antigen biosynthesis. This finding allowed the development of a robust multiplex PCR-based serotyping scheme able to detect subgroups within each serotype and therefore performs better than conventional serotyping. This scheme was successfully applied to a large number of isolates from worldwide origin and retrieved from a large variety of fish species. No obvious correlations were observed between the mPCR-based serotype and the host species or the geographic origin of the isolates. Strikingly, the distribution of mPCR-based serotypes does not follow the core-genome phylogeny. Nevertheless, this simple and cost-effective mPCR-based serotyping method could be useful for different applications such as population structure analysis, disease surveillance, vaccine formulation and efficacy follow-up.

International audience

Il ne semble pas y avoir consensus pour dire si le monde traverse aujourd’hui une crise sans précédent ou non. Quoi qu’il en soit, il reste un nombre de situations inacceptables et des améliorations urgentes sont à réaliser. Le monde est un organisme complexe qui souffre de nombreuses crises : crise économique et financière, crise environnementale, de l’agriculture, crise sanitaire, crise des valeurs. Face à une crise systémique comme celle-ci la réponse doit être globale. Comment les géosynthétiques et la société internationale des géosynthétiques (International Geosynthetics Society, IGS) peuvent-ils contribuer à résoudre ces crises et apporter leur contribution à la guérison du monde ? Les solutions technologiques sont le plus souvent mises en exergue. Elles ne seront pas suffisantes. Quelles valeurs pouvons-nous attendre de l’IGS 35 ans après sa création ? L’objectif de la lecture Giroud, dans une version en français et raccourcie ici est de mettre en évidence ces différentes contributions pour apporter de l’eau de qualité à tous, nourrir le monde, protéger notre environnement, atténuer ou anticiper les catastrophes naturelles, apporter des solutions économiques et connecter les hommes pour les aider à vivre ensemble selon les valeurs humaines universelles.

Abstract African swine fever virus (ASFV) causes a highly lethal disease in pigs and represents a significant threat to the global pork industry due to the lack of effective vaccines or treatments. Despite intensive research, many ASFV proteins remain uncharacterized. This study aimed to elucidate the functions of two ASFV proteins, MGF360-21R and A151R, through comprehensive analysis of their interactions with host proteins. Using affinity purification-mass spectrometry and yeast two-hybrid screening approaches, we identified the host protein barrier- to-autointegration factor 1 (BANF1) as a key interactor of both viral proteins. Biochemical and colocalization assays confirmed these interactions and demonstrated that MGF360-21R and A151R expression leads to cytoplasmic relocalization of BANF1. Functionally, BANF1 silencing significantly reduced ASFV replication, indicating its proviral role. Given BANF1’s established function in regulating the cGAS/STING-dependent type I interferon (IFN-I) response, we postulated that A151R and MGF360-21R could inhibit this pathway. Using different strategies, we showed that both A151R and MGF360-21R did indeed inhibit IFN-I induction. Generation of ASFV deficient of A151R or MGF360-21R showed that both mutant viruses enhanced the host IFN response in primary porcine macrophages compared to wild-type virus. However, their capacity to inhibit this pathway could occur through mechanisms independent of BANF1. Proteomic analysis of BANF1 interactors during ASFV infection highlighted potentially roles in chromatin remodeling, nuclear transport, and innate immune response pathways. Altogether, our data provide new insights into ASFV-host interactions, identifying BANF1 as an important new host factor required for replication and uncovering novel functions for A151R and MGF360-21R. Author Summary African swine fever virus (ASFV) is a highly contagious and deadly disease affecting pigs worldwide, for which there are currently no effective vaccines or treatments. Despite extensive research, many ASFV proteins remain poorly understood. Our study investigated two ASFV proteins, MGF360-21R and A151R, to better understand their functions and interactions with host proteins. Using proteomic approaches, we found both these viral proteins interact with a host protein called barrier-to-autointegration factor 1 (BANF1). Importantly, BANF1 silencing significantly reduced ASFV replication, indicating its important role in the viral life cycle. We also showed that MGF360-21R and A151R help the virus evade the immune system by blocking the production of interferons, which are key defensive molecules against viral infections. However, this immune evasion does not seem to depend on their interaction with BANF1. Additionally, our analysis of BANF1’s interactions during ASFV infection revealed potential roles in chromatin remodeling, nuclear transport, and the innate immune response. These findings provide new insights into how ASFV interacts with its host and highlight BANF1 as a critical factor in viral replication and immune evasion. Our work contributes to a better understanding of ASFV and could pave the way for developing more effective strategies to fight this virus.

An international educational initiative to facilitate the exposure of geosynthetics to undergraduate civil engineering students has been conducted by the International Geosynthetics Society (IGS) for over a decade. Geosynthetics is a comparatively new topic within geotechnical engineering and, consequently, has only been sporadically introduced into undergraduate Civil Engineering curricula. In particular, geotechnical engineering professors themselves may have not been exposed to the basics of geosynthetics to be able to comfortably transfer such knowledge to their students. As part of this educational program, civil engineering professors are invited to take a course on geosynthetics, for which they receive fellowships covering their expenses. The course also includes complementary components such as a workshop consisting of practical demonstrations, pedagogical material, and technical documents. Implementation of the program involves multiple parties, including the IGS, its national chapters, and geosynthetics industry, who are allotted the responsibilities of supporting the program instructors, offering practical project-oriented input. This paper describes the course structure, the educational tools employed, the impact on the program caused by the pandemic, and results from feedback surveys that assessed how the knowledge on geosynthetics acquired by the participants was transferred to their students in terms of new courses on geosynthetics, inclusion of geosynthetics topics in existing undergraduate disciplines, etc. Emphasis is given on the experience of the Brazilian Chapter of IGS, which has already conducted programs. The educational outcomes of the programs currently offered are being evaluated and they suggest excellent acceptance of the course by participants and undergraduate students at the universities.

International audience

Abstract Background: Technological advances and decreasing costs have led to the rise of increasingly dense genotyping data, making feasible the identification of potential causal or candidate markers. Custom genotyping chips, which represent a cost-effective strategy to combine medium-density genotypes with a custom genotype panel, can capitalize on these candidates to potentially yield improved accuracy and interpretability in genomic prediction. A particularly promising model to this end is BayesR, which divides markers into four effect size classes (null, small, medium, and large). The flexibility of BayesR has been shown to yield accurate predictions and promise for quantitative trait loci (QTL) mapping in real data applications, but an extensive benchmarking in simulated data is currently lacking.Results: Based on a set of real genotypes, we generated simulated data under a variety of genetic architectures, phenotype heritabilities, and polygenic variances, and we evaluated the impact of excluding (50k genotype data) or including (50k custom genotype data) causal markers among the genotypes. We define several statistical criteria for QTL mapping using BayesR output (maximum a posteriori rule, non-null maximum a posteriori rule, posterior variance, weighted cumulative inclusion probability), including several based on sliding windows rather than individual markers to account for linkage disequilibrium. We compare and contrast these statistics and their ability to accurately prioritize known causal markers. Overall, we confirm the strong predictive performance for BayesR in moderately to highly heritable traits, particularly for 50k custom data; in cases of low heritability or weak linkage disequilibrium with the causal marker in 50k genotypes, QTL mapping is a challenge, regardless of the criterion used.Conclusion: BayesR is a promising approach to simultaneously obtain accurate predictions and interpretable classifications of SNPs into effect size classes. Although QTL mapping is unsurprisingly easiest for highly heritable phenotypes and large QTLs, we illustrated the performance of BayesR in a variety of simulation scenarios, and compared the advantages and limitations of each. Among those considered, the weighted cumulative inclusion probability appears to provide the best mapping results, even under less favorable conditions. Finally, we quantify the advantage that can be gained by incorporating causal mutations on a custom genotyping chip.

The "Bioproductions (B-BEST): Biomass, Biotechnologies, and Sustainable Technologies for Chemistry and Fuels" research program is part of the national acceleration strategy "Bio-based Products and Industrial Biotechnologies - Sustainable Fuels" under the France 2030 plan. Co-led by INRAE and IFPEN, this program supports the transition from a petrochemical economy to bio-based products and services by aiming to better understand and utilise biomass to produce bio-based products and sustainable fuels. A secondary objective is to establish common practices for bio-refineries, which are currently not implemented at national level, thereby limiting the efficiency and reproducibility of developments. To address these issues, the Galaxy-BioProd project aims to develop a centralised portal providing standardised digital tools and resources to simplify, connect and accelerate industrial biotechnology projects. The tools and pipelines are developed by the members of the project. Based on the Galaxy environment and adhering to FAIR principles, the B-BEST Galaxy lab deployed on usegalaxy.fr offers an accessible and unified platform that can serve various communities in the fields of synthetic biology, biocatalysis and industrial biotechnology. Seventeen tools ranging from synthetic biology to Life Cycle Analysis are currently under development and will be deployed on B-BEST lab of usegalaxy.fr. Galaxy-BioProd project is part of the PEPR Bioproductions (B-BEST) program , supported by the France 2030 investment plan and co-led by INRAE and IFPEN [ANR-22-PEBB-0008] .

Raw data for the paper titled "TLR7/8 agonist 3M-052 formulated in micelles induces local Type I IFN response and antiviral immunity in zebrafish larvae". https://doi.org/10.3389/fimmu.2026.1834678 Data contains .lif files containing the raw images used for analysis as well as excel files containing the raw data collected for use in graphs.

Raw data for the paper titled "TLR7/8 agonist 3M-052 formulated in micelles induces local Type I IFN response and antiviral immunity in zebrafish larvae". https://doi.org/10.3389/fimmu.2026.1834678 Data contains .lif files containing the raw images used for analysis as well as excel files containing the raw data collected for use in graphs.

433 MB full UHGG gut .syldb consumed at runtime by the in-browser sylph profiler. cite : UHGG catalog — Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature Biotechnology 39, 105–114 (2021). https://www.nature.com/articles/s41587-020-0603-3

433 MB full UHGG gut .syldb consumed at runtime by the in-browser sylph profiler. cite : UHGG catalog — Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature Biotechnology 39, 105–114 (2021). https://www.nature.com/articles/s41587-020-0603-3

BACKGROUND: Gut microbiota and their metabolites play a key role in digestive dysimmunity and tolerance breakdown, leading to pathologies such as food protein-induced enterocolitis syndrome (FPIES). This study aimed to compare both the gut and salivary microbiota over time between the allergic and tolerant patients and the matched controls. METHODS: Faecal and salivary samples were collected longitudinally from FPIES allergic patients on an elimination diet, and after their natural tolerance acquisition, and from matched controls (1:1 ratio). 16S rRNA gene sequencing and biostatistical analyses (ALDEx2, ANCOM-BC, DESeq2, LEfSe, and MaAsLIN2) were used to compare microbiota composition between groups. The measurement of faecal short-chain fatty acids (SCFAs) using gas chromatography evaluated the gut microbiota functions. RESULTS: Thirty-eight allergic patients were included (median age: 1.3 years), and 22 became tolerant over time. Allergic patients exhibited lower gut and salivary alpha-diversities, and several different genera (12 in stools, including less Ruminococcus, and 2 in saliva), and higher relative abundance of acetate than the controls. With tolerance acquisition, faecal alpha-diversities partially increased, whereas SCFAs normalised. Ultimately, there were more differences in faecal and salivary microbiota in allergic patients versus after tolerance acquisition (i.e., more Blautia, Ruminococcus, Faecalibacterium, Prevotella-9, and less Escherichia-Shigella in tolerant patients) than between the controls over time. CONCLUSION: The faecal and salivary dysbiosis observed in allergic patients with FPIES partially resolved after tolerance acquisition. Understanding the underlying mechanisms of dysbiosis is crucial to prevent and help manage FPIES. A prolonged follow-up could determine whether dysbiosis resolution may be complete, and whether this early infancy dysbiosis has long-term consequences on health.

Additional file 4. PCoA representation of the resistome according to stage (A) and feed form (B), based on Bray-Curtis distances of Hellinger transformed normalized read counts (counts per million).

Additional file 3. PERMANOVA analysis of resistome (antimicrobial resistance gene abundance) according to stage.