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Identification des interactions entre les protéines et les excipients afin d'élucider les propriétés de la solution et les processus de stabilisation dans les formulations biothérapeutiques à haute concentration
No full textHigh-concentration monoclonal antibody (mAb) formulations are essential for subcutaneous administration, as they allow a high therapeutic dose to be administered in small volumes. However, at concentrations above 100 mg/mL, mAbs tend to reversibly self-associate into transient oligomers, leading to a sharp increase in viscosity. This complicates the manufacture, handling, and injection of the treatment and can compromise its stability and efficacy. To limit these effects, excipients, typically amino acids, sugars, or surfactants, are added. These reduce protein-protein interactions and ensure the stability of the mAb. However, their selection remains largely empirical, as their impact on self-association and viscosity remains poorly understood.During this study, an IgG evaluated in clinical trials by Sanofi was used as a model. A set of complementary NMR methods was optimized with the aim of detecting mAb:mAb and mAb:excipient interactions under standard formulation conditions. These methods included analysis of ¹H signals from the mAb in the presence of nine different excipients, pulsed field gradient (PFG-NMR) experiments, chemical shift perturbation (CSP) analysis, saturation transfer (STD-NMR) experiments, and transverse relaxation (R2) measurements. In addition, the macroscopic viscosity of the samples was measured by rheometry, and the size distribution of mAb clusters was analyzed by dynamic light scattering (DLS). This analysis was complicated by exchanges between monomers and clusters, confirming the limited ability of DLS to describe the distribution of mAb species at high concentrations. Furthermore, the interaction parameters deduced from low-concentration analyses (kD) did not allow the viscosity at high concentrations to be predicted. However, NMR analyses made it possible to link the macroscopic viscosity measured by rheometry with the molecular interactions of the mAb. The 1D ¹H NMR intensities proved to be very sensitive to reversible oligomerization of the mAb. After correction for viscosity (measured by rheometry), a significant loss of NMR signal was observed above 50 mg/mL, indicating the formation of transient oligomers (or clusters). Among the nine excipients tested, arginine and lysine significantly reduced the loss of NMR signal, and therefore the reversible oligomerization of the mAb. Most excipients reduced macroscopic viscosity, with arginine and lysine again being the most effective. R2 analysis and CSPs showed that arginine, lysine, and sucrose interact most strongly with the surface of the mAb, while glycine and surfactants show weaker interactions, mainly detected in the presence of clusters. STD-NMR proved to be particularly sensitive to the reversible oligomeric state of the mAb and detected strong interactions with lysine, while measurements in the presence of proline showed low reproducibility. Overall, this work shows that NMR is suitable for studying weak interactions in concentrated mAb solutions. The data indicate that viscosity depends not only on the degree of mAb self-association, but also on the nature of the transient interactions between different clusters. mAb-excipient interactions may contribute to the regulation of the interaction network formed by the mAb, but cannot alone determine macroscopic viscosity. The mechanistic description of mAb self-assembly and the role of excipients by NMR helps to rationalize the molecular determinants of viscosity.Les formulations d'anticorps monoclonaux (mAb) à haute concentration sont essentielles pour l'administration sous-cutanée, car elles permettent d'administrer une forte dose thérapeutique dans de faibles volumes. Toutefois, à des concentrations supérieures à 100 mg/mL, les mAb ont tendance à s'auto-associer de façon réversible en oligomères transitoires, entraînant une forte augmentation de la viscosité. Cela complique la fabrication, la manipulation et l'injection du traitement et peut en compromettre la stabilité et l'efficacité. Pour limiter ces effets, des excipients, typiquement des acides aminés, des sucres ou des tensioactifs, sont ajoutés. Ils permettent de réduire les interactions protéine-protéine et d'assurer la stabilité du mAb. Cependant, leur sélection reste largement empirique, car leur impact sur l'auto-association et la viscosité demeure mal élucidé. Au cours de cette étude, une IgG évaluée lors d'essais cliniques par Sanofi a été utilisée comme modèle. Un ensemble de méthodes RMN complémentaires a été optimisé dans le but de détecter les interactions mAb :mAb et mAb :excipients dans des conditions standard de formulation. Ces méthodes incluent une analyse des signaux ¹H du mAb en présence de neuf excipients différents, des expériences à gradient de champ pulsé (PFG-RMN), une analyse des perturbations de déplacement chimique (CSP), des expériences de transfert de saturation (STD-RMN) et des mesures de relaxation transverse (R2). De manière complémentaire, la viscosité macroscopique des échantillons a été mesurée par rhéométrie, et la distribution en taille des oligomères de mAb a été analysée par diffusion dynamique de la lumière (DLS). Cette analyse s'est avérée complexifiée par les échanges entre monomères et clusters, confirmant la faible capacité de la DLS à décrire la distribution des espèces de mAb à haute concentration. De plus, les paramètres d'interaction déduits des analyses à faible concentration (kD) n'ont pas permis de prédire la viscosité à haute concentration. Cependant, les analyses par RMN ont permis de relier la viscosité macroscopique mesurée par rhéométrie avec les interactions moléculaires du mAb. Les intensités RMN 1D ¹H se sont révélées très sensibles à l'oligomérisation réversible du mAb. Après correction par la viscosité (mesurée par rhéométrie), une forte perte de signal RMN a été observée au-delà de 50 mg/mL, ce qui indique la formation d'oligomères transitoires (ou clusters). Parmi les neuf excipients testés, l'arginine et la lysine réduisent de manière significative la perte de signal RMN, et donc l'oligomérisation réversible du mAb. La majorité des excipients permettent de diminuer la viscosité macroscopique, les plus efficaces étant là encore l'arginine et la lysine. L'analyse R2 et les CSP ont montré que l'arginine, la lysine et le sucrose interagissent le plus fortement avec la surface du mAb, tandis que la glycine et les surfactants montrent des interactions plus faibles, essentiellement détectées en présence de clusters. Les STD-RMN se sont révélées particulièrement sensibles à l'état oligomérique du mAb et ont détecté de fortes interactions avec la lysine, tandis que les mesures en présence de proline ont montré une faible reproductibilité. Globalement, ce travail montre que la RMN est adaptée à l'étude des interactions faibles dans des solutions concentrées de mAb. Les données indiquent que la viscosité dépend non seulement du degré d'auto-association du mAb, mais aussi de la nature des interactions transitoires entre les différents clusters. Les interactions mAb-excipients peuvent contribuer à la régulation du réseau d'interactions formé par le mAb, mais ne peuvent à elles seules déterminer la viscosité macroscopique. La description mécanistique de l'auto-assemblage du mAb et du rôle des excipients par la RMN contribue à rationaliser les déterminants moléculaires de la viscosité
Inlining as a space optimization: a simple time- and space-invariant implementation of the weak lambda-calculus
No full textA multiscale coupled PDE model of host-microbiota interaction: application to colonic mucosal barrier dynamics
No full textThis study presents a multiscale mathematical model based on a system of coupled Partial Differential Equations (PDEs) that integrates microbial dynamics with the host's colonic structure, emphasizing the accurate modeling of the mucosal barrier effect. This coupled colon-crypt model is designed to investigate complex interactions between the gut microbiota and host defense mechanisms under healthy and perturbed conditions. Validation against previous models and literature data confirms that the model accurately captures the dynamics of the intestinal crypt, cellular composition, and the distinct structural behaviors of the inner (hard) and outer (soft) mucus layers.This work provides a mathematically grounded and computationally tractable platform for studying colonic mucosal function and its alteration under pathological conditions, and constitutes a step towards patient-specific in silico modeling
Low temperature brine formation by serpentinization on asteroid (162173) Ryugu
No full textInternational audienceSecondary mineral prevalence in Ryugu samples, similar to primitive carbonaceous-Ivuna type (CI) chondrites, suggests that aqueous alteration was a key factor in its formation. However, this general consensus masks our limited understanding of the specific mechanisms and environmental conditions involved in water-rock interactions on primitive asteroids. Highresolution cathodoluminescence (CL) analysis of the ubiquitous dolomite crystals in Ryugu samples reveals concentric epitaxial overgrowths with varying levels of Mn 2+ -activated luminescence. CL panchromatic images and spectral deconvolution provide compelling evidence for the evolution of aqueous fluids toward highly saturated brines. Given the close association of dolomite with widespread intergrowths of serpentine and saponite in the matrix, we propose that brine formation occurs as a byproduct of serpentinization. Unlike large-scale evaporation or freezing, this process can locally cause the hydrothermal fluid to dry out, significantly increasing its salinity over time. This leads to the sporadic precipitation of an evaporite mineral sequence, with dolomite forming at an early stage. This serpentinizationdriven brine formation model offers a convincing alternative to a purely prograde alteration history for Ryugu. It may also provide a better explanation for the alteration processes of Bennu and other CI chondrite parent bodies
Observations of AGN-driven feedback: dynamics and ionization of the filaments in M87
No full textInternational audienceWe present a comprehensive kinematic and ionization analysis of the warm ionized filaments ( K) in M87, the central galaxy of the Virgo cluster, using new integral field spectroscopy from MEGARA (Multi-Espectrógrafo en GTC de Alta Resolución para Astronomía, GTC) and SITELLE (Spectromètre Imageur à Transformée de Fourier pour l'Etude en Long et en Large de raies d'Emission, CFHT). MEGARA targets the southeastern (SE) filaments (3 kpc from the nucleus) coincident with the only known molecular gas clump, and the far eastern (FE) filament (15 kpc), spatially isolated within an old radio lobe. SITELLE fully maps the filaments, offering the first complete views of their kinematics and excitation. Combined with archival ALMA (Atacama Large Millimeter Array), MUSE (Multi-Unit Spectroscopic Explorer), and Chandra data, these observations offer a multiphase view of gas dynamics. The filaments display complex motions inconsistent with simple rotation. Velocity structure functions (VSFs) of the warm and cold gas in the central and SE filaments show consistent steep slopes (> 2/3) and flattening on small scales of a few hundred parsecs, possibly suggesting energy injection from Type Ia supernovae, though interpretation is method-limited. The FE filament shows lower VSF amplitude, suggesting less active driving. ALMA CO emission is cospatial and kinematically aligned with the ionized gas, the latter showing broader velocity dispersions. Ionization diagnostics indicate AGN (active galactic nucleus)-related processes (e.g. shocks) dominate, with higher energy excitation near the radio lobes and (lower energy) fossil feedback signatures in the FE filament. Finally, the filaments follow the same strong H–X-ray surface brightness correlation seen in other clusters, supporting local thermal coupling between phases. However, the FE filament deviates from this trend, possibly due to uplift from past AGN outbursts or limitations in the analysis method
Computational Study of Heme b 595 to Heme d Electron Transfer in E. coli Cytochrome bd -I Oxidase
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Leveraging Computer Vision for Efficient and Scalable Biodiversity Monitoring in Marine Ecosystems: A Multi-Year Study on 3 Ecologically Important Fishes
No full textMarine environments face multiple threats, including climate change, overfishing, and shoreline artificialisation leading to a great loss of biodiversity. Therefore, fast and efficient biodiversity assessments are crucial to understand the current and future state of marine ecosystems. Traditionally, underwater visual censuses (UVCs) have served as the primary method for assessing biodiversity, with divers recording species presence, abundance, and other biological indicators along fixed transects. In this study, we collected video transects recorded by camera-equipped divers, resulting in 41h of video footage that enhanced the data collection but also increasing the volume of material requiring tedious manual analysis. This manual analysis of video footage is in a lot of cases financially and logistically unfeasible. Here, we present a comprehensive multi-year computer-vision-based pipeline applied to all recorded video transects to extract ecological information on three ecologically and economically important species (Epinephelus marginatus, Sciaena umbra and Diplodus vulgaris). Using a fully automated computer vision pipeline that enables researchers rapid and less-biased data extraction from large datasets, we confirmed known depth and substrate preferences of the three target species. Additionally, we identified seasonal variations in D. vulgaris that may be disrupted by climate change. Our results demonstrate that computer-vision enables rapid and less-biased data extraction from large datasets, facilitating efficient biodiversity monitoring. We anticipate that this study will serve as a foundation to expand computer-vision applications to other marine regions, species, and environmental scenarios. Increased efficiency in data processing will make more frequent and extensive biodiversity assessments possible, strengthening conservation efforts through improved ecological insights
Unlocking research on rhizodeposition: a step-by-step guide for producing, sampling and analyzing
No full textRhizodeposits, i.e. the organic materials released by living roots into the soil, play a major role in plant interactions with their biotic and abiotic environment. However, our understanding of rhizodeposition processes has remained limited due to the methodological challenges associated with the collection and analysis of rhizodeposits. Here, we aimed to synthesize knowledge from the various fields of expertise required for studying rhizodeposition, in order to support the scientific community in making informed methodological choices and to ensure the robustness and comparability of studies. In particular, we developed an open-access decision support tool (CARROT: Collecting and Analyzing Rhizodeposits: Reviewing and Optimizing Tool), using existing literature and practical expertise from the interdisciplinary network RhizosPHARE. This tool has been designed to help newcomers and specialists in the field i) to quickly identify the most appropriate methodological option(s) in terms of plant growth conditions, sample collection and sample analysis according to their scientific question and their experimental constraints, ii) to get practical recommendation about each method, and iii) to get a direct access to additional information and references. As part of these guidelines, we also suggest a standardized protocol for collecting root exudates from hydroponically grown plants to characterize their composition. Together with the CARROT tool, this protocol paves the way towards establishing consistent, standardized methods for characterizing rhizodeposition and its impact in the plant-soil system
Microbiome metabolic modeling as a tool for innovation in fermented foods
No full textInternational audienceAt the crossroads of a growing interest in fermented foods as part of a healthy, sustainable diet and advances in multi-omics technologies stands the need for developing new types of fermented foods while improving traditional ones. The scientific path toward these challenges lies in our capacity to rationalize and predict microbial interactions. For this, genome or metagenome-scale metabolic modeling represents a promising approach. We assess its benefits and limits through rare examples in the field of food microbiomes and advocate for community-level metabolic engineering as the superior strategy. We underline their power as a cornerstone in comprehensive and rational strategies for optimization of microbial consortia assembly, whether they are used in bottom-up or top-down approaches. We raise the challenges and bottlenecks of integrating the dynamics of microbial communities and present how we foresee their potential for shaping the future of fermented foods and regulatory science, bridging gaps between knowledge and innovation
Two-Pion Exchange Contributions to the Nucleon-Nucleon Interaction from the Roper Resonance
No full textInternational audienceWe derive the long-range components of the nucleon-nucleon (NN) two-pion-exchange potential with an intermediate Roper resonance. Leading-order interactions in heavy-baryon chiral perturbation theory are considered. NN phase shifts with orbital angular momentum are calculated in first-order perturbation theory and compared to those obtained without the Roper resonance. We show that the Roper contribution is sizeable for waves and improves the description of phase shifts for all the partial waves slightly. We also discuss the role of the Roper resonance in the NN interaction in the framework of resonance saturation