Biology subjects

Robert, P.

Publications and source records attributed to Robert, P..

14 recordsLinked to original sources

bioRxiv2026

Surprise gates two distinct mechanisms to support memorability in music

Music is a uniquely memorable human creation that, when skillfully composed, can persist in individual memory (as in e.g., earworms) and cultural transmission (e.g. global hits or anthems). While both acoustic and statistical properties are known to influence a songs memorability, the neural mechanisms that facilitate the engramming of certain musical sequences remain unclear. Current theories suggest that memory systems function as predictive internal models, enhancing learning when expectations are violated. Yet expected stimuli, by aligning with and reinforcing prior knowledge, also enhance memorability. How these two opposing processes arise from the brains sensitivity to statistical regularities, especially in naturalistic sequences, is not well understood. Here, we leveraged musics intrinsic balance between expectancy and surprise, and examined the neural correlates of minutes-scale memorability using intracranial EEG recordings from nine patients with epilepsy performing a musical memory task. Quantifying the statistical surprise of each musical excerpt with PolyRNN, a polyphonic model of musical expectations, we uncovered a U-shaped relationship between musical surprise and memory performance: both highly expected and highly surprising melodies led to greater memorability. While neural pattern similarity between song repetitions was enhanced for low-surprise stimuli, high-surprise stimuli enhanced neural pattern separability in medial temporal regions, each mediating memorability in distinguishable ways. These findings reveal complementary neural mechanisms through which statistical structure shapes musical sequence memory, clarifying how the brain encodes complex, ecologically valid stimuli.

neuroscience↗

bioRxiv2026

Antibody maturation in germinal centers selects mutants based on BCR-antigen bond mechanical resistance

Antibody maturation in germinal centers (GCs) is traditionally viewed as a process that enhances antigen-binding affinity of B cell receptors (BCR). However, recent studies challenge this paradigm, revealing no systematic antibody affinity improvement during GC selection. Here, we investigate whether mechanical resistance of antibody-antigen bonds, rather than affinity, is the selective parameter driving GC maturation. Using biolayer interferometry measurements for assessing affinity and laminar flow chamber for mechanical resistance, we analyzed three lineages of mouse antibodies generated after immunization with ovalbumin. While affinity changes were heterogeneous, ranging from gains to losses across lineages, mechanical resistance consistently increased after maturation. Bond lifetimes under physiological forces (10-70 pN) converged to similar values across lineages, suggesting a selective pressure for mechanical stability. Functionally, NK cell activation in a surrogate in vitro ADCC assay correlated with bond lifetimes under force, but not with affinity. This indicates that lymphocytes are sensitive to the mechanical stability of antibody-antigen interactions, which may underlie GC selection. Our findings reconcile antibody maturation with the idea of enhanced binding, while aligning with the role of mechanical forces in B cell signaling and antigen uptake. These insights provide a framework for understanding GC biology and may inform the design of therapeutic antibodies.

immunology↗

bioRxiv2025

A Quest for a Histaminergic or Orexinergic Biomarker for Sudden Infant Death Syndrome

AimsThis study aimed to investigate the role of the Hypocretin/Orexin (Ox) and Histamine (HA) systems--two key regulators of wakefulness --in sudden infant death syndrome (SIDS), a condition characterized by impaired arousal responses during sleep. MethodsCerebrospinal fluid (CSF) Ox levels were measured in 61 healthy controls, 70 Sudden Unexpected Death Infants (SUDI) (38 SIDS cases and 32 explained deaths (ED). HA and its metabolite, tele-methylhistamine (t-MeHA), were analysed in an additional 46 SUDI (34 SIDS, 12 ED) and 42 controls. Immunocytochemistry was performed on hypothalamic tissue from 11 SIDS and 13 ED cases to assess the number of Ox and HA neurons, using markers for Orexin-A and histidine decarboxylase (HDC), respectively. ResultsOverall CSF Ox levels did not differ significantly between groups. However, while an age-related decline in Ox levels was observed in controls (0-2 vs. 2-6 months), this pattern was absent in deceased infants, resulting in relatively higher Ox concentrations in the 2-6 month age group. HA and t-MeHA levels were significantly elevated in both SIDS and ED cases, likely due to postmortem release. Immunohistochemical analysis revealed an increased number of Ox-immunoreactive neurons in the rostral and caudal dorsolateral hypothalamus in SIDS cases compared to EDs. No differences were observed in the number or morphology of HA neurons. ConclusionFindings suggest increased Ox activity in SIDS cases, potentially reflecting repeated exposure to stress or hypoxia prior to death. In contrast, HA neurons do not appear to play a role in the pathophysiology of SIDS. Further research is needed to identify more specific biomarkers for assessing SIDS risk.

neuroscience↗

bioRxiv2025

Bivalency of natalizumab promotes inhibition of dynamic VLA-4 adhesion beyond affinity gain

Natalizumab, a monoclonal IgG4 antibody used in the treatment of multiple sclerosis (MS), inhibits VLA-4 binding to VCAM-1, thereby reducing leukocyte recruitment to inflamed tissues. The intricate mechanisms underlying these effects remain unclear, particularly concerning the heavy-chain shuffling of IgG4. We conducted an in vitro study to quantify the impact of bivalent IgG and monovalent Fab forms of natalizumab on the capture and migration of human primary memory T lymphocytes under shear stress, using VCAM-1 and SDF-1-coated surfaces. IgG natalizumab at concentrations near its cell surface EC50 showed significant of capture and resistance of adherent cells to shear stress, whereas significantly higher doses of Fab natalizumab, up to 100-fold greater than its cell surface EC50, were needed to achieve similar effects. These findings highlight that receptor occupancy alone may not adequately predict the functional outcomes of inhibitor antibodies. For optimal therapeutic effect, inhibition of cell-surface adhesion may require specific kinetic and geometric binding properties of antibodies.

immunology↗

bioRxiv2024

Multi-stream predictions in human auditory cortex during natural music listening

Musical expectations shape how we perceive and process music, yet current computational models are limited to monophonic or simplified stimuli. The study of the neural processes underlying musical expectations in real-world music therefore requires significant advances in our statistical modeling of these stimuli. We present PolyRNN, a recurrent neural network designed to model expectations in naturalistic, polyphonic music. We recorded neurophysiological activity non invasively (MEG) and within the human brain (intracranial EEG) while participants listened to naturally expressive piano recordings. The musical expectations estimated by the model are encoded in evoked P2- and P3-like components in auditory regions. Comparing PolyRNN to a state-of-the-art generative music model, we show that piano roll representations are best suited to represent expectations in polyphonic contexts. Overall, our approach provides a new way to capture the musical expectations emerging from natural music listening, and enables the study of predictive processes in more ecologically valid settings.

neuroscience↗

bioRxiv2024

ClassiCOL: LC-MS/MS analysis for ancient species Classification via Collagen peptide ambiguation

LC-MS/MS extends on the MALDI-TOF ZooMS approach by providing fragmentation spectra for each peptide. However, ancient bone samples generate sparse datasets containing only a few collagen proteins, rendering target-decoy strategies unusable and increasing uncertainty in peptide annotation. ClassiCOL embraces and even extends this ambiguity using a novel isoBLAST approach. The exhaustive set of potential peptide candidates created in this way is then used to retain or reject different potential paths at each taxonomic branching point down to the taxonomic level attainable with the sample information, always allowing for potential mixtures in the process. As an end point, all considered ambiguity is graphically represented with a clear prioritization of the species in the sample. Using public as well as in-house data, we demonstrate the performance of this universal postprocessing approach on different instruments and explore the possibility of identifying genetic as well as sample mixtures. Diet reconstruction from 40,000 year old cave hyena coprolites illustrates the exciting potential of this approach. TeaserClassiCOL is a postprocessing tool that allows for more accurate species classification from LC-MS/MS measurements of collagen.

bioinformatics↗

bioRxiv2024

Decoupling individual host response and immune cell engager cytotoxic potency

Immune cell engagers are molecular agents, usually antibody-based constructs, engineered to recruit immune cells against cancer cells and kill them. They represent a versatile and powerful tool for cancer immunotherapy. Despite the multiplication of new engagers tested and accepted in the clinics, how molecular and cellular parameters influence their action is poorly understood. In particular, disentangling the respective role of host immune cells and engager biophysical characteristics is needed to improve their design and efficiency. Focusing here on harnessing antibody dependent Natural Killer cell cytotoxicity, we measure the efficiency of 6 original bispecific antibodies (bsAb), associating an anti-HER2 nanobody and an anti-CD16 nanobody. In vitro cytotoxicity data using primary human NK cells on different target cell lines exposing different antigen densities were collected, exhibiting a wide range of bsAb dose response. In order to rationalize our observations, we introduce a simple multiscale model, postulating that the density of bsAb bridging the two cells is the main parameter triggering the cytotoxic response. We introduce two new microscopic parameters: the surface cooperativity describing bsAb affinity at the bridging step and the threshold of bridge density determining the donor-dependent response. Both parameters permit to rank Abs and donors and to predict bsAb potency as a function of antibodies bulk affinities and receptor surface densities on cells. Our approach thus provides a general way to decouple donor response from immune engagers characteristics, rationalizing the landscape of molecule design.

biophysics↗

bioRxiv2023

Auditory hemispheric asymmetry as a specialization for actions and objects

What is the function of auditory hemispheric asymmetry? We propose that the identification of sound sources relies on two complementary and perceptually relevant acoustic invariants -- actions and objects -- that are processed asymmetrically and sufficient to model and categorize any sound. We observed that environmental sounds are an independent combination of purely temporal and spectral acoustic modulations. Behaviorally, discrimination of actions relied on temporal modulations, while discrimination of objects relied on spectral modulations. Functional magnetic resonance imaging data showed that actions and objects are respectively decoded in the left and right hemispheres, in bilateral superior temporal and left inferior frontal regions. This asymmetry reffects a generic differential processing -- through differential neural sensitivity to temporal and spectral modulations present in all environmental sounds -- that supports the efficient categorization of actions and objects. These results provide an ecologically valid framework of the functional role of auditory brain asymmetry.

neuroscience↗

bioRxiv2022

Mechanical forces impair antigen discrimination by reducing differences in T cell receptor off-rates

T cells use their T cell receptors (TCRs) to discriminate between lower-affinity self and higher-affinity foreign peptide major-histocompatibility-complexes (pMHCs) based on the TCR/pMHC off-rate. It is now appreciated that T cells generate mechanical forces during this process but how force impacts the TCR/pMHC off-rate remains unclear. Here, we measured the effect of mechanical force on the off-rate of multiple TCR/pMHC interactions. Unexpectedly, we found that lower-affinity pMHCs with faster solution off-rates were more resistant to mechanical force (weak slip or catch bonds) than higher-affinity interactions (strong slip bonds), and this was confirmed by molecular dynamic simulations. Consistent with these findings, we show that the best characterized catch-bond, involving the OT-I TCR, has a low affinity and an exceptionally fast solution off-rate. Our findings imply that reducing forces on the TCR/pMHC interaction improves antigen discrimination and we suggest this new force-shielding role for the adhesion receptors CD2 and LFA-1. One sentence summaryMechanical forces disproportionately accelerate the off-rates of higher-affinity antigens reducing T cell antigen discrimination

immunology↗

bioRxiv2020

Simulating the outcome of amyloid treatments in Alzheimer's Disease from multi-modal imaging and clinical data

In this study we investigate a novel quantitative instrument for the development of intervention strategies for disease modifying drugs in Alzheimers disease. Our framework is based on the modeling of the spatio-temporal dynamics governing the joint evolution of imaging and clinical biomarkers along the history of the disease, and allows the simulation of the effect of intervention time and drug dosage on the biomarkers progression. When applied to multi-modal imaging and clinical data from the Alzheimers Disease Neuroimaging Initiative our method enables to generate hypothetical scenarios of amyloid lowering interventions. The results quantify the crucial role of intervention time, and provide a theoretical justification for testing amyloid modifying drugs in the pre-clinical stage. Our experimental simulations are compatible with the outcomes observed in past clinical trials, and suggest that anti-amyloid treatments should be administered at least 7 years earlier than what is currently being done in order to obtain statistically powered improvement of clinical endpoints.

bioinformatics↗

bioRxiv2020

The study of the determinants controlling Arpp19 phosphatase-inhibitory activity reveals a new Arpp19/PP2A-B55 feedback loop

Arpp19 is a potent inhibitor of PP2A-B55 that regulates this phosphatase to ensure the stable phosphorylation of mitotic/meiotic substrates. At G2-M, Arpp19 is phosphorylated by Greatwall on S67. This phosphorylated Arpp19 form displays a high affinity to PP2A-B55 and a slow dephosphorylation rate, acting as an "unfair" competitor of PP2A-B55 substrates. The molecular determinants conferring slow dephosphorylation kinetics to S67 are unknown. PKA also phosphorylates Arpp19. This phosphorylation performed on S109 is essential to maintain prophase I-arrest in Xenopus oocytes although the underlying signaling mechanism is elusive. Here, we characterized the molecular determinants conferring slow dephosphorylation to S67 and controlling PP2A-B55 inhibitory activity of Arpp19. Moreover, we showed that phospho-S109 restricts S67 phosphorylation by increasing its catalysis by PP2A-B55. Finally, we discovered a double feed-back loop between these two phospho-sites which is essential to coordinate the temporal pattern of Arpp19-dependent PP2A-B55 inhibition and Cyclin B/Cdk1 activation during cell division.

developmental biology↗

bioRxiv2020

CD8 co-receptor enhances T cell activation without any effect on initial attachment

The scanning of surrounding tissues by T lymphocytes to detect cognate antigen is a highly demanding process that requires high rapidity, sensitivity and specificity. Co-receptors such as CD8 are known to increase detection performance, but the exact mechanism of this role remains incompletely understood. Here, we used interference reflection microscopy to image the initial spreading of 1G4 receptor transfected CD8+ and CD8- Jurkat cells dropped on surfaces exposing five cognate antigens of varying activating power, and we used a laminar flow chamber to measure the influence of CD8 on the kinetics of bond formation and rupture between cell-born T cell receptors (TCRs) and peptide-exposing major histocompatibility complex antigens (pMHCs) at the single molecule level. It is concluded that CD8 did not influence TCR-pMHC interaction during the first seconds following cell surface encounter, but it promoted the spreading responses during the first minutes, thus suggesting that CD8 was involved in early activation rather than binding. In addition, presented results were quantitatively compared with a recent report on the cell-free interaction between the same ligand-receptor couples : it is concluded that bond formation was strongly impaired by cell molecular environment, while bond rupture was comparable in both systems. Results from this and previous reports were used to propose a quantitative scheme of the strategy used by T lymphocytes to scan foreign surfaces. It is suggested that the understanding of the strategy used by cells to perform their basic functions may be a prerequisite to understand the function of molecular networks revealed by high throughput methods.

immunology↗

bioRxiv2020

Intrinsic defects in lymph node stromal cells underpin poor germinal center responses during aging

The failure to generate enduring humoral immunity after vaccination is a hallmark of advancing age. This can be attributed to a reduction in the germinal center response, which generates long-lived antibody-secreting cells that provide protection against (re)infection. Despite intensive investigation into the effect of age on the lymphoid compartment, the primary cellular defect that causes impaired germinal centers in aging has not been identified. Herein we demonstrate that aging reduces the capacity of germinal center-associated stromal cells to respond to vaccination. Heterochronic parabiosis and mathematical modeling demonstrate that a poor stromal cell response limits the size of the germinal center. This study reveals that age-associated defects in stromal cells are a significant barrier to efficacious vaccine responses in older individuals.

immunology↗

bioRxiv2018

Nanobody-antigen catch-bond reveals NK cell mechanosensitivity

Antibodies are key tools in biomedical research and medicine. Their binding properties are classically measured in solution and characterized by an affinity. However, in physiological conditions, antibodies can bridge an immune effector cell and an antigen presenting cell, implying that mechanical forces apply to the bonds. For example, in antibody-dependent cell cytotoxicity, a major mode of action of therapeutic monoclonal antibodies, the Fab domains bind the antigens on the target cell, while the Fc domain binds to the activating receptor CD16 (also known as FcgRIII) of an immune effector cell, in a quasi bi-dimensional environment (2D). Therefore, there is a strong need to investigating antigen/antibody binding under force (2D), to better understand and predict antibody activity in vivo. We used two anti-CD16 nanobodies targeting two different epitopes and laminar flow chamber assay to measure the association and dissociation of single bonds formed between microsphere-bound CD16 antigens and surface-bound anti-CD16 nanobodies (or single domain antibodies), simulating 2D encounters. The two nanobodies exhibit similar 2D association kinetics, characterized by a strong dependence on the molecular encounter duration. However, their 2D dissociation kinetics strongly differ as a function of applied force: one exhibits a slip bond behaviour where off-rate increases with force; the other exhibits a catch bond behaviour with off-rate decreasing with force. This is the first time, to our knowledge, that catch bond behaviour was reported for antigen-antibody bond. We further exploit this property to show how Natural Killer cells spread differentially on surfaces coated with these molecules, revealing NK cells mechanosensitivity. Our results may also have strong implications for the design of efficient bispecific antibodies for therapeutic applications.

biophysics↗