HAL Portal ESPCI (Ecole Supérieure de Physique et de Chimie Industrielles)
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Repeated losses of self-fertility shaped heterozygosity and polyploidy in yeast evolution
No full textEvolutionary transitions in mating strategy have profound consequences for genetic variation and adaptation. In Saccharomyces cerevisiae, mating-type switching is a central feature of the life cycle that enables homothallism, i.e., mating between mitotic descendants of the same haploid cell. Yet heterothallic isolates that have lost this ability are found across diverse niches, indicating that this trait is polymorphic. Here we experimentally characterized loss of mating-type switching in a representative panel of strains. Analysis of 117 telomere- to-telomere genome assemblies revealed multiple independent loss-of-function mutations in the Ho endonuclease gene and structural variants in the silent HML and HMR cassettes, the three loci essential for switching. We estimated that at least 13 independent transitions from homothallism to heterothallism have occurred in the species history. Analysis of the HO genotype of 2,915 strains show that at least 27% are heterothallic. We found that heterothallism is strongly associated with polyploidy and elevated genome-wide heterozygosity, although the strength of these associations varies between populations. Heterothallic isolates are most prevalent in domesticated and clinical clades, consistent with an origin linked to human-associated environments. However, they are also found, though less frequently, in natural niches. Signatures of recombination in HO sequences suggest that outcrossing contributed to the ecological and geographical distribution of the trait. Our findings reveal that mating-type switching has undergone repeated losses in S. cerevisiae evolution, with major consequences for genome architecture and ecological diversification. Significance Statement Mating-type switching evolved multiple times in yeasts, enabling haploid selfing, which became a key feature of their life cycles. We show that this trait has been lost repeatedly in the history of Saccharomyces cerevisiae , producing heterothallic isolates that cannot switch mating type. Analysis of thousands of genomes reveals that these losses involve multiple mutations in the Ho endonuclease and structural changes in the silent mating-type cassettes. Heterothallism is associated with polyploidy and increased genome-wide heterozygosity. It is more frequent in domesticated and clinical lineages, but also occurs in natural ecological niches. Our findings illustrate how repeated changes in a single life-history trait can reshape genome architecture and highlight the dynamic interplay between genetics, environment, and evolution in a model eukaryote
Probing the Microscopic Origin of Toughness in Multiple Polymer Networks
No full textMultiple polymer networks, such as double-network elastomers comprising a sacrificial and a matrix network, exhibit exceptional mechanical resilience, commonly attributed to the formation of an extended damage zone before a crack can grow. However, the microscopic mechanisms underlying their toughness remain poorly understood. Here, we combine advanced light scattering methods and molecular dynamics simulations to explore the microscopic relaxation dynamics and stress redistribution at the polymer strand scale of single-network and double-network elastomers under uni-axial loading. Dynamic light scattering experiments show that microscopic rearrangements and bond-breaking events are localized near the crack tip in single networks, readily causing the crack to advance. In contrast, double networks exhibit delocalized microscopic rearrangements well ahead of and not directly correlated with crack propagation, enabling the dissipation of energy over broader regions and timescales. Numerical simulations of the damage zone show that bond breaking in the matrix network of double networks leads to widespread stress redistribution, mitigating catastrophic damage localization. This enhanced ability to redistribute stress in a non-local manner allows a much larger extension before localized macroscopic failure occurs, explaining the superior toughness of double networks. Our findings identify early, delocalized bond-breaking events combined with more efficient dissipation pathways through enhanced microscopic rearrangements as the key microscopic mechanisms responsible for the outstanding toughness and extensibility of multiple elastomer networks
Universal features of autocatalytic systems
No full textAutocatalytic networks are prevalent in nature, from the metabolism of single cells to the food webs of ecosystems. Inspired by the universal constructor model introduced by von Neumman, we study universal features of these networks, which are shared by all self-replicating living systems. Minimal autocatalytic subnetworks or cores are an example of such universal properties because they should be present in all autocatalytic networks. These autocatalytic cores are topological structures which can be identified based only considerations of stoichiometry. We then establish a connection between this stoichiometric analysis of autocatalytic networks and von Neumann model of a growing economy, of which Leontief model is a particular case. Finally, we show how these ideas provide a new path into the modeling of cell metabolism
Self-Supervised Z-Slice Augmentation for 3D Bio-Imaging via Knowledge Distillation
No full textThree-dimensional biological microscopy has significantly advanced our understanding of complex biological structures. However, limitations due to microscopy techniques, sample properties or phototoxicity often result in poor z-resolution, hindering accurate cellular measurements. Here, we introduce ZAugNet, a fast, accurate, and self-supervised deep learning method for enhancing z-resolution in biological images. By performing nonlinear interpolation between consecutive slices, ZAugNet effectively doubles resolution with each iteration. Compared on several microscopy modalities and biological objects, it outperforms competing methods on most metrics. Our method leverages a generative adversarial network (GAN) architecture combined with knowledge distillation to maximize prediction speed without compromising accuracy. We also developed ZAugNet+, an extended version enabling continuous interpolation at arbitrary distances, making it particularly useful for datasets with nonuniform slice spacing. Both ZAugNet and ZAugNet+ provide high-performance, scalable z-slice augmentation solutions for large-scale 3D imaging. They are available as open-source frameworks in PyTorch, with an intuitive Colab notebook interface for easy access by the scientific community
Motor recovery through perineuronal net modulation in a Parkinson’s disease mouse model
No full textInternational audiencePerineuronal nets are specialized extracellular matrix structures forming preferentially around parvalbumin interneurons to regulate plasticity. While cortical perineuronal nets have been implicated in sensory plasticity and memory modulation, perineuronal nets of the primary motor cortex have been largely overlooked. We found that transient reduction of primary motor cortex perineuronal nets by ChABC treatment in otherwise healthy adult mice resulted in temporary deficits in motor function. In a mouse model of Parkinson's disease based on unilateral 6-hydroxydopamine lesions of the midbrain, perineuronal net levels were decreased in both primary motor cortex hemispheres 2 weeks post-lesion, yet returned to baseline within 5 weeks. We discovered that subsequent transient reduction of primary motor cortex perineuronal nets through ChABC treatment could unlock motor recovery when coupled with motor stimulation. This recovery was associated with a bilateral increase in perineuronal-net-enwrapped parvalbumin interneurons and a rebalancing of parvalbumin cell soma excitatory synaptic markers. These findings reveal distinct roles of perineuronal net plasticity – first in response to the initial midbrain lesion and then during rescue after ChABC treatment – suggesting that primary motor cortex perineuronal nets play a nuanced role in regulating motor function. This duality positions perineuronal nets as potential therapeutic targets for motor rehabilitation strategies in Parkinson's disease
A diffusion model for light scattering in ejecta
No full textInternational audienceWe derive a diffusion equation for light scattering from ejecta produced by extreme shocks on metallic samples. This model is easier to handle than a more conventional model based on the Radiative Transfer Equation (RTE) and is a relevant tool to analyze spectrograms obtained from Photon Doppler Velocimetry measurements in the deep multiple scattering regime. We also determine the limits of validity of the diffusive model compared to the RTE, based on a detailed analysis of various ejecta properties in configurations with increasing complexity
A spin-state switchable MOF-based film for visual DMSO vapor sensing
No full textInternational audienceThe design of new colorimetric sensors for the detection of volatile organic compounds (VOCs) is of high interest due to the health issues they can induce. In this study, we report the fabrication of a film composed of the spin crossover complex [Fe(Sal 2 trien)]NO 3 embedded within metal-organic framework nanocrystals. This composite material demonstrates a selective and reversible colorimetric response to dimethyl sulfoxide (DMSO) vapor exposure at room temperature, which is attributed to a spin state switching from high-spin (HS) to low-spin (LS) of the Fe(III) centers upon DMSO adsorption (down to 15 ppm V ). This work highlights the potential of integrating spin crossover complexes into MOFs to develop colorimetric and reusable VOC vapor sensors
Une expérience modèle de la propagation d’ondes dans les artères
No full textOndes guidées; GAPSUS - Acoustique Physique, Sous-Marine et Ultra-SonoreNational audienceNous proposons une expérience minimale reproduisant la propagation d’ondes dans les artères. Nous étudions un guide d’onde fluide présentant une paroi souple faite d’un élastomère déformable et incompressible qui imite les propriétés des tissus biologiques. Nous obtenons la relation de dispersion des ondes guidées, mettant en évidence le rôle clé de la différence de pression entre l’eau contenue dans le guide et le milieu ambient. En prenant en compte la rhéologie et la grande déformation statique de la paroi, nous montrons que la pression imposée modifie la relation de dispersion à la fois en créant une tension, orthogonale à la direction de propagation, et une courbure, qui rigidifie la paroi. Nous montrons enfin comment ces résultats peuvent être interprétés dans le contexte biologique, en établissant le lien entre nos mesures et la vitesses de l’onde de pouls
Contrôle du champ acoustique engendré par un laser
No full textUltrasons laser, interaction son-lumière; GAPSUS - Acoustique Physique, Sous-Marine et Ultra-SonoreNational audienceLes techniques ultrasons laser offrent un outil unique pour générer et détecter sans contact des ondes élastiques guidées dans les solides. Grâce à l'identification des modes guidés ainsi mesurés, il est possible d'évaluer de manière non destructive les propriétés mécaniques des matériaux. Les méthodes classiques reposent sur l'utilisation d'un faisceau laser focalisé. Une telle source excite généralement plusieurs modes, avec un niveau d'énergie qui est limité par le seuil d'ablation afin d'éviter tout endommagement du matériau. En conséquence, ces modes risquent d'être en deçà du niveau de bruit et impossible à séparer et à identifier. Une solution pour s'affranchir de cette limitation est le façonnage de la source laser afin d’engendrer un mode choisi. Pour cela, nous proposons d'assurer l’excitation par une source laser continue modulée en intensité à une fréquence voulue et de contrôler le nombre d’onde engendré par la source à l'aide d'un modulateur spatial de lumière (SLM). Ainsi, il est possible de sélectionner sur les courbes de dispersions le ou les couple(s) (fréquence, nombre d’onde) que l’on souhaite étudier. Dans cette présentation, nous nous intéresserons notamment à l’étude de l’anisotropie dans des plaques d’acier à l’aide de ce dispositif. Nous démontrerons également expérimentalement la génération sélective de modes particuliers
Caractérisation de Cibles et de la Micro-architecture de Milieux Désordonnés
No full textOndes en milieu hétérogène; GAPSUS - Acoustique Physique, Sous-Marine et Ultra-SonoreNational audienceJe présenterai une méthode matricielle pour identifier et localiser des objets non-ponctuels enfouis dans un milieu désordonné. Cette méthode est basée sur une connaissance préalable de l'objet cible en mesurant préalablement sa matrice de réflexion dans un milieu homogène. Un filtre optimal associé à cette cible peut alors être construit, permettant d'obtenir sa position même en présence de diffusion multiple. Je présenterai des résultats obtenus en acoustique pour des billes d'acier enfouies dans du sable à une distance de quelques libre parcours moyen de diffusion. Par ailleurs, cet opérateur peut être utilisé pour identifier la micro-architecture d'un matériau. J'illustrerai cette application par l'étude des fibres d'un muscle, pour lequel il est possible d'obtenir la taille et orientation caractéristiques des fibres localement