Institut de Biologie de l'École Normale Supérieure

Abstract Sensory operators are classically modeled using small circuits involving canonical computations, such as energy extraction and gain control. Notwithstanding their utility, circuit models do not provide a unified framework encompassing the variety of effects observed experimentally. We develop a novel, alternative framework that recasts sensory operators in the language of intrinsic geometry. We start from a plausible representation of perceptual processes that is akin to measuring distances over a sensory manifold. We show that this representation is sufficiently expressive to capture a wide range of empirical effects associated with elementary sensory computations. The resulting geometrical framework offers a new perspective on state-of-the-art empirical descriptors of sensory behavior, such as first-order and second-order perceptual kernels. For example, it relates these descriptors to notions of flatness and curvature in perceptual space.

ABSTRACT Cross-kingdom RNA interference (ckRNAi) is emerging as a mode of inter-organismal gene regulation, yet mechanistic examples in plant–metazoan interactions remain limited. Here, we demonstrate miRNA-driven ckRNAi in the nematode–plant pathosystem. Root-knot nematodes are among the most destructive plant pathogens, reprogramming root tissues to develop into galls containing multinucleated, hypermetabolic giant feeding cells essential for parasitism. AGO1-associated small-RNA immunoprecipitation (AGO1-RIP) from tomato galls revealed the selective in planta loading of 10 M. incognita miRNAs into host AGO1. Integrating degradome profiling, target prediction, and dual-luciferase reporter assays, we validated miRNA-directed silencing of nine tomato transcripts by four secreted nematode miRNAs. These targets map to major pathway classes involved in immune signaling, metabolic regulation, and cellular reprogramming linked to feeding-site establishment. Functional analyses further show that the nematode-secreted miR-2b is enhances giant feeding cell development. Comparative AGO1-RIP in Arabidopsis thaliana identified a conserved subset of AGO1-loaded nematode miRNAs, including miR-2b and miR-100, consistent with shared small-RNA effectors across hosts. Finally, the overlap between AGO1-loaded miRNA families and helminth secreted small-RNA repertoires supports evolutionary convergence on RNA-based virulence strategies. Collectively, our findings establish miRNA-mediated ckRNAi as a mechanistic component of plant–root-knot nematode interactions and provide a framework for leveraging RNA-based vulnerabilities for nematode control.

Abstract Malaria affects almost 263 million people worldwide, most of whom live in sub-Saharan countries. In a strategy to reduce malaria-related mortality and limit transmission, diagnosis in endemic areas needs to be immediately available on the field, easy to perform and cheap. Therefore, it currently heavily relies on microscopic examination of blood smears. However, several studies comparing the sensitivity of this approach with qPCR, considered as the most sensitive method albeit not available on the field, found that up to half of the infected population failed to be detected by microscopy alone because no visible parasites could be found in blood smears. These so-called submicroscopic infections pose a diagnostic challenge, yet represent a huge reservoir for malaria transmission. In this study, we hypothesized that qPCR results could be predicted by deep learning from subtle cell signals present in thin blood smear images, even in the absence of visible parasites, making a sensitive diagnostic directly available on the field using a microscope and a smartphone. To test this hypothesis, we acquired a large smartphone-based blood smear images dataset from samples tested both for microscopy and qPCR. We then focused exclusively on these “negative” slides from the microscopic diagnostic point of view, among which half were qPCR positive. A range of standard deep learning models were evaluated to best predict the qPCR result from these microscopy images, using various backbones along with various aggregation functions at the slide level, from a simple vote to Multiple Instance Learning with attention. Our results show that the qPCR results can be predicted from parasite free blood smear images with 62.00% (±2.5 on 4-folds) accuracy and reaching 67.2 % (±9.6 on 4-folds) in sensitivity. We then used generative models to investigate the subtle morphological variations occurring in red blood cells that may contribute to predicting malaria infection in the absence of parasites. Leveraging thin blood smear and portable deep learning, we established the first proof of concept that the qPCR sensitivity can be approached through the detection of submicroscopic infections directly on the field without additional infrastructure and thus could significantly improve malaria surveillance and elimination efforts.

This is the first study to propose a combined approach for predicting NB in ICU patients with suspected AMI. When AMI is highly suspected, surgical exploration should be considered in patients presenting with signs of gastrointestinal injury in a context of fluid removal or renal replacement therapy, as these findings are strongly suggestive of necrotic bowel.

Laboratory mutation accumulation experiments allow the assessment of spontaneous mutation rates and patterns with minimal selection. Here, we aimed to study the accumulation and fate of mutations in natural populations, in a spatial context. The nematode Caenorhabditis elegans is particularly suited for such endeavor, as it reproduces almost exclusively by selfing. We analyzed the evolution of clonal C. elegans genotypes along a 300-m long stream bank in the Santeuil wood (France), based on short-read whole-genome sequencing of individuals collected between 2009 and 2022. We followed along years two distinct clones (isotypes), composed of individuals only differing by recent mutations. Recombination was scarce. A temporal signal was detected: strains from earlier years were found close to inner nodes of the tree, while recent ones were found on outer tips. This signal allowed us to estimate a substitution rate of 4 to 5x10-8 mutations per base pair per year. Based on the spontaneous mutation rate per generation in laboratory lines, we estimated that C. elegans locally undergoes around 25 effective generations per year, which can be used to calibrate divergence times among and within species. Mutation densities were higher on the X chromosome, on chromosome arms, and in non-exonic regions. We detected a high transition-to-transversion ratio, not observed in C. elegans laboratory mutation accumulation lines. Finally, using these recent mutations, we detected a spatio-temporal pattern within the field site, indicating limited dispersal at the scale of 100 meters within 10 years.

Background. Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual generations. A polyploid transcriptionally active somatic macronucleus (MAC) develops at each sexual generation from a copy of the MIC through programmed DNA elimination (PDE) of > 30% of germline DNA. PDE requires the domesticated PiggyMac (Pgm) transposase. Assembly of Paramecium germline genomes has presented an enormous challenge owing to the difficulty of MIC isolation. Results. We report chromosome-scale short-read MIC assemblies for 7 species from the P. aurelia species complex. We discovered a novel clade of Helitrons, with 9-10 kb transposase ORFs under purifying selection, that have remained active in all P. aurelia lineages. A long-read assembly for P. tetraurelia together with a genetic linkage map provided a nearly telomere-to-telomere assembly. Conclusions. The genome consists of tiny (300 kb to 1.2 Mb) and numerous (~160) germline chromosomes with the highest recombination rate ever reported for a eukaryote (420 cM/Mb). The ends of the chromosomes consist of Helitrons inserted in telomeric C4A2 repeats, forming a distinct genomic compartment that is eliminated very early during MAC development in a Pgm-independent manner.

The central Arctic is experiencing warming up to four times faster than the global average. This Arctic amplification is accompanied by large deviations in climate projections, making anticipation of high-impact, near-term regional biodiversity and climate change difficult. Several atmospheric processes contribute simultaneously to Arctic amplification and biodiversity change yet remain largely unstudied, not least because of the difficulty to access the central Arctic Ocean and conduct year-round studies. This article introduces the near- to mid-term objectives of the Tara Polar Station scoping group on “atmosphere-biosphere interactions,” with a focus on identifying and quantifying the origin and genetic composition of local and long-range transported biogenic particles that can impact biodiversity and cloud formation, the role of the stratified boundary layer on vertical fluxes of cloud seeds, bioaerosols and nutrients, and the impact of clouds on atmospheric light transmission. The Tara Polar Station is a fortified research vessel built to drift in the Arctic sea ice throughout the next 20 years in ten Tara Polaris expeditions, each lasting one and a half years. The platform allows for year-round interdisciplinary studies targeted at understanding the central Arctic Ocean ecosystem functioning, biodiversity, and climate change at the ocean-ice-atmosphere nexus. This scoping group will deploy novel and automated instruments for in situ, real-time vertical and remote sensing observations of aerosols, clouds, and radiation. The link between the biosphere and atmosphere will be investigated specifically through bio- and chemo-molecular sampling of air, clouds, ice, and water. We expect the early Tara Polaris expeditions to deliver insights that can be implemented into models for improved scenarios of Arctic change, in particular for the next few decades when we expect a regime shift in summer sea-ice presence.