Biology subjects

Boccara, C.

Publications and source records attributed to Boccara, C..

8 recordsLinked to original sources

bioRxiv2026

Nyx: a flexible framework for sleep scoring across species, lifespan and modalities

Sleep is a key factor in almost every physiological process, yet scoring tools lag behind innovations in basic to clinical research. New automated algorithms are trained on narrow datasets, typically healthy adult mouse or human, and fail to generalise, leaving labs to fall back on slow, laborious, and often poorly reproducible manual scoring. Here we introduce Nyx, an unsupervised framework built on principal component analysis that flexibly clusters epochs into sleep states, akin to how spike-sorting algorithms cluster single-neuron activity. Validated on about 8,000 hours spanning 19 independent datasets, it generalises across species, lifespan, recording modalities, and altered sleep architectures, matching human inter-scorer agreement. Beyond this, Nyx opens new ground for modern sleep research: classifying NREM subtypes in rodents, revealing states that cut across canonical boundaries in non-mammalian species, and enabling real-time, closed-loop manipulation. Distributed as an open-source package with a graphical user interface, Nyx offers an accessible, explainable framework built to scale with the pace of innovation itself.

neuroscience↗

bioRxiv2026

The scaling behavior of hippocampal activity in sleep/rest predicts spatial memory performance

In the hippocampus, reactivation of spatial memories during sleep enhances consolidation and recall. However, network dynamics may independently influence memory retention. We applied the Phenomenological Renormalization Group to CA1 neuronal activity in rats during sleep/rest epochs surrounding a spatial learning task. The scaling exponent of activity variance (), assessed either before or after learning, predicted subsequent recall performance independently of reactivation. The prediction model was transferable across subjects, suggesting that it is a robust biomarker of learning ability. Single-cell features, such as burst propensity and intrinsic timescales, correlated with and memory, predicted retention even when controlling for these factors. Our results identified a link between scale-free circuit dynamics and memory stabilization, suggesting that the tuning of the underlying dynamical regime near criticality is a key determinant of memory longevity. Targeted modulation of these collective states could offer new avenues for memory enhancement.

neuroscience↗

bioRxiv2025

Mechanisms of sexually dimorphic adipose tissue remodelling upon prolonged breastfeeding

Early developmental cues exert lasting influence on the adipose tissue function and the metabolic health throughout adulthood. In mice, adipose tissue remodelling during the weaning transition programs long-term tissue plasticity, setting its capacity for expansion and thermogenesis in response to environmental stimuli. However, the mechanisms driving this remodelling, and the role of weaning-associated dietary changes in this process, are unknown. Here, we characterise the emergence of sexually dimorphic patterns of adipose tissue distribution and function during the post-weaning period. As subcutaneous adipocytes acquire a white phenotype, the tissue microenvironment undergoes a coordinated remodelling, including reduced innervation and an increase in immune cell content. Using a model of prolonged breastfeeding, we show that it promotes adipose tissue expansion through sex-dependent mechanisms, stimulating progenitor proliferation in males and adipocyte hypertrophy in females. In males, this is accompanied by accelerated tissue whitening, which we link to enhanced clearance of extracellular noradrenaline by mature adipocytes. Our findings reveal sex- and diet-dependent mechanisms governing adipose tissue maturation and highlight how early life nutritional cues shape the microenvironment and function of mature adipocytes. Highlights- The peri-weaning period associates with sexually dimorphic remodelling of the adipose tissue - Whitening of the adipose tissue associates with immune infiltration and decrease innervation in both sexes - Prolonged breastfeeding prevents drop in proliferation in males - Whitening is accelerated in males during prolonged breastfeeding

physiology↗

bioRxiv2022

Label-free virus-antibody interaction monitoring in real-time by common-path interferometry

Viruses can affect all life forms, raising concerns about virus detection and quantification of small nanoparticles. In this paper we use a label-free, full-field, incoherently illuminated common path interferometric method to detect, track, and quantify biotic nanoparticles. The detection consists of amplifying the light scattered by single nanoparticles in the sample solution. Then, the use of single-particle tracking analysis is used to monitor the change in particle diffusive mobility. With this approach, the recognition signature of T5 phages with purified antibodies targeting the major capsid protein is detected in a few minutes. We also tracked the interaction between SPP1 phages and physiological non-purified serum-containing multiples antibodies molecules. The first interactions occur after around one minute, and the recognition signature is detectable after minutes. In addition, we have been able to differentiate two populations of similar size of empty and full (encapsulating DNA) capsids of T5 in a heterogeneous solution demonstrating the robustness of this label-free detection approach. Furthermore, by combining the diffusion coefficient to the number of tracked particles, we were able to estimate the affinity of the virus-antibodies reaction.

biophysics↗

bioRxiv2021

Dynamic Cell Imaging: application to the diatom Phaeodactylum tricornutum under environmental stresses

The dynamic movement of cell organelles is an important and poorly understood component of cellular organisation and metabolism. In this work we present a non-invasive non-destructive method (Dynamic Cell Imaging, DCI) based on light scattering and interferometry to monitor dynamic events within photosynthetic cells using the diatom Phaeodactylum tricornutum as a model system. For this monitoring we acquire few seconds movies of the signals that are related to the motion of dynamic structures within the cell (denoted scatterers), followed by a statistical analysis of each pixel time series. Illuminating P.tricornutum with LEDs of different wavelengths associated to short pulsed or continuous-wave modes of illumination revealed that dynamic movements depend on chloroplast activity, in agreement with the reduction in the number of pixels with dynamic behaviour after addition of photosystemII inhibitors. We studied P. tricornutum under two environmentally relevant stresses, iron and phosphate deficiency. The major dynamic sites were located within lipid droplets and chloroplast envelope membranes. By comparing standard deviation and cumulative sum analysis of the time series, we showed that within the droplets two types of scatterer movement could be observed: random motions (Brownian type) but also anomalous movements corresponding to a drift which may relate to molecular fluxes within a cell. The method appears valuable for studying the effects of various environments on a large variety of microalgae in the laboratory as well as in natural aquatic environments. HIGHLIGHTsLight scattering an alternative to fluorescence to rapidly evidence dynamic processes. Lipid droplets the major metabolic active sites under stress A non-destructive visualisation method for laboratory microalgae and aquatic samples.. SIGNIFICANCE STATEMENTLight scattering could be an alternative to fluorescence techniques to study dynamic processes within photosynthetic cells. We used a method combining light scattering and interferometry to analyse movements of intracellular scatterers in the marine diatom Phaedactylum tricornutum under two environmentally relevant stresses, iron and phosphate deficiency. Lipid droplets were the major active sites under stress. The method which is rapid and non destructive can be broadly expanded to study other microalgae and their stress responses, in the laboratory and in aquatic environments.

microbiology↗

bioRxiv2021

Angular and Linear Speed Cells in the Parahippocampal Circuits

An essential role of the hippocampal region is to integrate information to compute and update representations. How this transpires is highly debated. Many theories hinge on the integration of self-motion signals and the existence of continuous attractor networks (CAN). CAN models hypothesise that neurons coding for navigational correlates - such as position and direction - receive inputs from cells conjunctively coding for position, direction and self-motion. As yet, such conjunctive coding had not been found in the hippocampal region. Here, we report neurons coding for angular and linear velocity, distributed across the medial entorhinal cortex, the presubiculum and the parasubiculum. These self-motion neurons often conjunctively encoded position and/or direction, yet lacked a structured organisation, calling for the revision of current CAN models. These results offer insights as to how linear/angular speed - derivative in time of position/direction - may allow the updating of spatial representations, possibly uncovering a generalised algorithm to update any representation.

neuroscience↗

bioRxiv2020

Full-field optical coherence tomography for the diagnosis of giant cell arteritis

Histopathological examination of temporal artery biopsy (TAB) remains the gold standard for the diagnosis of giant cell arteritis (GCA) but is associated with essential limitations that emphasize the need for an upgraded pathological process. This study pioneered the use of full-field optical coherence tomography (FF-OCT) for rapid and automated on-site pathological diagnosis of GCA. Sixteen TABs (12 negative and 4 positive for GCA) were selected according to major histopathological criteria of GCA following hematoxylin-eosin-saffron-staining for subsequent acquisition with FF-OCT to compare structural modifications of the artery cell wall and thickness of each tunica. Gabor filtering of FF-OCT images was then used to compute TAB orientation maps and validate a potential automated analysis of TAB sections. FF-OCT allowed both qualitative and quantitative visualization of the main structures of the temporal artery wall, from the internal elastic lamina to the vasa vasorum and red blood cells, unveiling a significant correlation with conventional histology. FF-OCT imaging of GCA TABs revealed destruction of the media with distinct remodeling of the whole arterial wall into a denser reticular fibrous neo-intima, which is distinctive of GCA pathogenesis and accessible through automated Gabor filtering. Rapid on-site FF-OCT TAB acquisition makes it possible to identify some characteristic pathological lesions of GCA within a few minutes, paving the way for potential machine intelligence-based or even non-invasive diagnosis of GCA.View Full Text

pathology↗

bioRxiv2018

Pkd2l1 is required for mechanoception in cerebrospinal fluid-contacting neurons and maintenance of spine curvature

Flow of cerebrospinal fluid (CSF) may contribute to spine morphogenesis, as mutations affecting both cilia motility and CSF flow lead to scoliosis1. However, the mechanisms underlying detection of the CSF flow in the central canal of the spinal cord remain elusive. Here we used full-field optical coherence tomography (FF-OCT) and bead tracking to demonstrate that CSF flows bidirectionally along the antero-posterior axis in the central canal of zebrafish embryos. In the zebrafish mutant cfap298tm304, previously known as kurly, reduction of cilia motility slows transport down the length of central canal. To investigate downstream mechanisms that could transduce CSF flow, we performed calcium imaging in sensory neurons contacting the CSF (CSF-cNs) and found that disruption in cilia motility impaired the activity of CSF-cNs. CSF-cNs across species express the transient receptor potential channel PKD2L1, also known as TRPP3, which contributes to CSF-cN chemosensory properties. Using calcium imaging and whole-cell patch clamp recordings, we found that the loss of the Pkd2l1 channel in pkd2l1 mutant embryos also abolished CSF-cN activity. Whole-cell recordings further demonstrated that opening of a single channel is sufficient to trigger action potentials in wild type CSF-cNs. Recording from isolated cells in vitro, we showed that CSF-cNs are mechanosensory cells that respond to pressure in a Pkd2l1-dependent manner. Interestingly, adult pkd2l1 mutant zebrafish develop an exaggerated spine curvature, reminiscent of kyphosis in humans. Our study indicates that CSF-cNs are mechanosensory cells whose spontaneous activity reflects CSF flow in vivo. Furthermore, Pkd2l1 in CSF-cNs contributes to the maintenance of the natural curvature of the spine.

neuroscience↗