Biology subjects

Pages, S.

Publications and source records attributed to Pages, S..

14 recordsLinked to original sources

bioRxiv2025

CleLight: A scalable 3D histology pipeline for mappingneurodegenerative and psychiatric pathology in archivalhuman brains

Mesoscopic brain imaging, enabled by advances in tissue clearing, light-sheet microscopy, and large-scale image processing, allows detailed analysis of cellular and molecular architecture across whole neural circuits. However, applying these methods to postmortem human brain tissue is hindered by strong autofluorescence, high tissue density, and fixation-induced damage. We introduce CleLight, a light-enhanced clearing method that increases tissue transparency while quenching autofluorescence. Combined with complementary chemical treatments, CleLight supports multiplexed immunolabeling and high-resolution imaging of centimeter-thick, formalin-fixed, paraffin-embedded human brain sections. It is compatible with a wide range of antibodies and fluorescent dyes, enabling the visualization of physiological and pathological features across diverse CNS regions in healthy and diseased samples. CleLight offers a simple, robust, and scalable workflow for clearing, deep labeling, and volumetric imaging of human brain tissue. Its compatibility with conventional histology and archival material makes it well suited for organ-wide pathological studies in large patient cohorts and historical brain collections.

neuroscience↗

bioRxiv2025

Pleiotropic role of PAX cyclolipopeptides in the Xenorhabdus bacterium mutualistically associated with entomopathogenic nematodes

Xenorhabdus is an entomopathogenic bacterium involved in a mutualistic relationship with Steinernema nematodes. Xenorhabdus produces a multitude of specialized metabolites by Non-Ribosomal Peptide Synthetases (NRPSs) pathways to mediate bacterial-nematode- insect interactions. PAX cyclolipopeptides are a family of NRP-type molecules whose ecological role remains poorly understood. In this study, the pleiotropic role of PAX peptides in the life cycle of Xenorhabdus nematophila has been investigated. By mass spectrometry analysis, we first demonstrated that PAX peptides were detected from the pathogenic stage up to the necrotrophic stage. We discovered that the bromothymol blue adsorption phenotype historically used to discriminate Xenorhabdus variants was associated with the presence of PAX peptides. We found that PAX peptides were positively involved in biofilm formation and negatively involved in swimming motility. PAX peptides were also shown to promote in vivo the production of infective Steinernema juveniles, suggesting their involvement in the mutualistic relationship between Xenorhabdus and its nematode partner. Finally, we showed that the paxTABC cluster as well as PAX peptide production was conserved across the whole Xenorhabdus genus except in Xenorhabdus poinarii and Xenorhabdus ishibashii. This work has revealed multiple new ecological roles for NRP-type peptides. ImportanceXenorhabdus bacteria are models of particular interest for their mutualistic relationship with Steinernema nematodes and their ability to produce a wide range of natural NRP-type bioactive metabolites. These compounds are mostly studied for their medical or industrial applications, but their ecological role is poorly understood. This study provides a dynamic characterization of PAX cyclolipopeptide presence during Xenorhabdus nematophila life cycle, as well as confirmation of their production by 7 different strains within the Xenorhabdus genus. We revealed new multiple functions for PAX peptides in biofilm formation, swimming motility and juvenile nematode production. A deeper understanding of how PAX peptides interact with the nematode host would provide a better insight into the role of these cyclolipopeptides in bacterial-nematode mutualism.

microbiology↗

bioRxiv2024

Repetitive sensory stimulation potentiates and recruits sensory-evoked cortical population activity

Sensory experience and learning are thought to be associated with plasticity of neocortical circuits. Repetitive sensory stimulation can induce long-term potentiation (LTP) of cortical excitatory synapses in anesthetized mice; however, it is unclear if these phenomena are associated with sustained changes in activity during wakefulness. Here we used time-lapse, calcium imaging of layer (L) 2/3 neurons in the primary somatosensory cortex (S1), in awake male mice, to assess the effects of a bout of rhythmic whisker stimulation (RWS) at a frequency by which rodents sample objects. We found that RWS induced a 1h-increase in whisker-evoked L2/3 neuronal activity. This was not observed for whiskers functionally connected to distant cortical columns. We also found that RWS altered whether individual neurons encoded subsequent stimulus representation by either being recruited or suppressed. Vasoactive intestinal-peptide-expressing (VIP) interneurons, which promote plasticity through disinhibition of pyramidal neurons, were found to exclusively elevate activity during RWS. These findings indicate that cortical neurons representation of sensory input can be modulated over hours through repetitive sensory stimulation, which may be gated by activation of disinhibitory circuits. SIGNIFICANCE STATEMENTSensory experience and learning are thought to be associated with the plasticity of cortical synaptic circuits. Here, we tested how repeated sensory stimulation changes subsequent sensory-evoked responses, using the mouse somatosensory cortex as a model. This cortical area processes, among others, sensory information from the whiskers. We found that rhythmic whisker stimulation potentiated excitatory neuronal activity for an hour, and identified a disinhibitory interneuron-mediated mechanism that could gate this plasticity. This work increases our understanding of sensory learning and experience-dependent plasticity processes by demonstrating that cortical representations of sensory input are dynamic and are effectively modulated by repeated sensory stimulation.

neuroscience↗

bioRxiv2024

CellSeg3D: self-supervised 3D cell segmentation for microscopy

Understanding the complex three-dimensional structure of cells is crucial across many disciplines in biology and especially in neuroscience. Here, we introduce a set of models including a 3D transformer (SwinUNetR) and a novel 3D self-supervised learning method (WNet3D) designed to address the inherent complexity of generating 3D ground truth data and quantifying nuclei in 3D volumes. We developed a Python package called CellSeg3D that provides access to these models in Jupyter Notebooks and in a napari GUI plugin. Recognizing the scarcity of high-quality 3D ground truth data, we created a fully human-annotated mesoSPIM dataset to advance evaluation and benchmarking in the field. To assess model performance, we benchmarked our approach across four diverse datasets: the newly developed mesoSPIM dataset, a 3D platynereis-ISH-Nuclei confocal dataset, a separate 3D Platynereis-Nuclei light-sheet dataset, and a challenging and densely packed Mouse-Skull-Nuclei confocal dataset. We demonstrate that our self-supervised model, WNet3D - trained without any ground truth labels - achieves performance on par with state-of-the-art supervised methods, paving the way for broader applications in label-scarce biological contexts.

cell biology↗

bioRxiv2023

Higher-order thalamocortical projections selectively control excitability via NMDAR and mGluRI-mediated mechanisms.

The apical dendrites of layer (L) 2/3 pyramidal neurons in the mouse somatosensory cortex integrate synaptic input from long-range projections. Among those, inputs from the higher-order thalamic posteromedial nucleus may facilitate sensory-evoked cortical activity, but it remains elusive how this role emerges. Here we show using ex vivo dendritic recordings that these projections provide dense synaptic input to broad tufted neurons residing predominantly in L2 and cooperate with other inputs to produce NMDA spikes. They have the unique capacity to block two-pore domain potassium leak channels via group 1 metabotropic glutamate receptor (mGluRI) signaling, which increases excitability. Slender tufted L2/3 neurons and other long-range projections fail to invoke these mechanisms. In vivo imaging of calcium signals confirms the presence of mGluRI-dependent modulation of feedback-mediated spiking in L2. Our results imply that higher-order thalamocortical projections regulate neuronal excitability in a cell type and input-selective manner through fast NMDAR and mGluRI-dependent mechanisms.

neuroscience↗

bioRxiv2023

Efficient image analysis for large-scale next generation histopathology using pAPRica

The large size of imaging datasets generated by next-generation histology methods limits the adoption of those approaches in research and the clinic. We propose pAPRica (pipelines for Adaptive Particle Representation image compositing and analysis), a framework based on the Adaptive Particle Representation (APR) to enable efficient analysis of large microscopy datasets, scalable up to petascale on a regular workstation. pAPRica includes stitching, merging, segmentation, registration, and mapping to an atlas as well as visualization of the large 3D image data, achieving 100+ fold speedup in computation and commensurate data-size reduction.

bioinformatics↗

bioRxiv2021

Mosquito excreta reveals circulation of West Nile virus and its underlying ecosystem

Emerging and endemic mosquito-borne viruses can be difficult to detect and monitor because they often cause asymptomatic infections in human or vertebrate animals or cause nonspecific febrile illness with a short recovery waiting period. Cases detection in vertebrate hosts can be complemented by entomological surveillance, but this method is not adapted to low infection rates in mosquito populations that typically occur in low or non-endemic areas. We identified West Nile Virus circulation in Camargue, a wetland area in South of France, using a cost effective innovative xenomonitoring method based on the molecular detection of virus in excreta from trapped mosquitoes. We also succeeded at identifying the mosquito community diversity dynamic on several sampling sites, together with the vertebrate hosts on which they fed prior to be captured using amplicon-based metagenomic on mosquito excreta without processing any mosquito. Mosquito excreta-based virus surveillance can be considered as a cost-effective and non-invasive strategy that offers the additional asset to reveal the ecological network underlying arbovirus circulation.

ecology↗

bioRxiv2021

Molecular and functional characterization of the mouse intracardiac nervous system

BackgroundThe intracardiac nervous system (ICNS) refers to clusters of neurons, located within the heart, which participate to the neuronal regulation of cardiac functions and which are involved in the initiation of cardiac arrhythmias. Therefore, deciphering its role in cardiac physiology and physiopathology is mandatory. ObjectiveThe aim of this study is to provide a phenotypic, electrophysiological and pharmacological characterization of the mouse ICNS, which is still poorly characterized. MethodsGlobal cardiac innervation and phenotypic diversity were investigated using immunohistochemistry on cleared murine heart and on tissue sections. Patch clamp technique was used for electrophysiological and pharmacological characterization of isolated mouse intracardiac neurons. ResultsWe have identified the expression of seven distinct neuronal markers within mouse ICNS, thus proving the neurochemical diversity of this network. Of note, it was the first time that the existence of neurons expressing the calcium binding protein calbindin, the neuropeptide Y (NPY) and the cocain and amphetamine regulated transcript (CART) peptide, was described in the mouse. Electrophysiological studies also revealed the existence of four different neuronal populations based on their electrical behavior. Finally, we showed that these neurons can be modulated by several neuromodulators. ConclusionThis study showed that mouse ICNS presents a molecular and functional complexity similar to other species, and is therefore a suitable model to decipher the role of individual neuronal subtypes regarding the modulation of cardiac function and the initiation of cardiac arrhythmias.

physiology↗

bioRxiv2020

An increase in dendritic plateau potentials is associated with experience-dependent cortical map reorganization

The organization of sensory maps in the cerebral cortex depends on experience, which drives homeostatic and long-term synaptic plasticity of cortico-cortical circuits. In the mouse primary somatosensory cortex (S1) afferents from the higher-order, posterior medial thalamic nucleus (POm) gate synaptic plasticity in layer (L) 2/3 pyramidal neurons via disinhibition and the production of dendritic plateau potentials. Here we address whether these thalamocortically mediated responses play a role in whisker map plasticity in S1. We find that trimming all but two whiskers causes a partial fusion of the representations of the two spared whiskers, concomitantly with an increase in the occurrence of POm-driven, N-methyl-D-aspartate receptor (NMDAR)-dependent plateau potentials. Blocking the plateau potentials restores the archetypical organization of the sensory map. Our results reveal a novel mechanism for experience-dependent cortical map plasticity in which higher-order thalamocortically mediated plateau potentials facilitate the fusion of normally segregated cortical representations.

neuroscience↗

bioRxiv2019

Partner-specific induction of Spodoptera frugiperda immune genes in response to the entomopathogenic nematobacterial complex Steinernema carpocapsae-Xenorhabdus nematophila

The Steinernema carpocapsae-Xenorhabdus nematophila association is a nematobacterial complex (NBC) used in biological control of insect crop pests. The ability of this dual pathogen to infest and kill an insect strongly depends on the dialogue between the hosts immune system and each partner of the complex. Even though this dialogue has been extensively studied from the two partners points of view in several insect models, still little is known about the structure and the molecular aspects of the insects immune response to the dual infection. Here, we used the lepidopteran pest Spodoptera frugiperda as a model to analyze the respective impact of each NBC partner in the spatiotemporal immune responses that are induced after infestation. To this aim, we first analyzed the expression variations of the insects immune genes in the fat bodies and hemocytes of infested larvae by using previously obtained RNAseq data. We then selected representative immune genes for RT-qPCR investigations of the temporal variations of their expressions after infestation and of their induction levels after independent injections of each partner. We found that the fat body and the hemocytes both produce potent and stable immune responses to the infestation by the NBC, which correspond to combinations of bacterium- and nematode-induced ones. Consistent with the nature of each pathogen, we showed that X. nematophila mainly induces genes classically involved in antibacterial responses, whereas S. carpocapsae is responsible for the induction of lectins and of genes expected to be involved in melanization and cellular encapsulation. In addition, we found that two clusters of unknown genes dramatically induced by the NBC also present partner-specific induction profiles, which paves the way for their functional characterization. Finally, we discuss putative relationships between the variations of the expression of some immune genes and the NBCs immunosuppressive strategies.\n\nAuthor summaryEntomopathogenic nematodes (EPNs) are living in the soil and prey upon insect larvae. They enter the insect by the natural orifices, and reach the hemocoel through the intestinal epithelium. There, they release their symbiotic bacteria that will develop within the insect and eventually kill it. Nematodes can then feed and reproduce on the insect cadaver. By using transcriptomic approaches, we previously showed that Lepidoptera larvae (caterpillars of the fall armyworm Spodoptera frugiperda) produce a strong immune response in reaction to infestation by EPNs. However, we do not know if this immune reaction is triggered by the nematode itself -Steinernema carpacapsae - or its symbiotic bacteria - Xenorhabdus nematophila. To answer this question, we present in this work a careful annotation of immunity genes in S. frugiperda and surveyed their activation by quantitative PCR in reaction to an injection of the bacteria alone, the axenic nematode or the associated complex. We found that the immune genes are selectively activated by either the bacteria or the nematode and we discuss the implication of which pathway are involved in the defense against various pathogens. We also show that a cluster of newly discovered genes, present only in Lepidoptera, is activated by the nematode only and could represent nematicide genes.

immunology↗

bioRxiv2019

Dynamic encoding of perceptual features in primary somatosensory cortex upon reversal learning

Neurons in primary sensory cortex encode a variety of stimulus features upon perceptual learning. However, it is unclear whether the acquired stimulus selectivity remains stable when the same input is perceived in a different context. Here, we monitored the activity of individual neurons in the mouse primary somatosensory cortex in a reward-based texture discrimination task. We tracked their stimulus selectivity before and after changing reward contingencies, which allowed us to identify various classes of neurons. We found neurons that stably represented a texture or the upcoming behavioral choice, but the majority was dynamic. Among those, a subpopulation of neurons regained selectivity contingent on stimulus-value. These value-sensitive neurons forecasted the onset of learning by displaying a distinct and transient increase in activity, depending on past behavioral experience. Thus, stimulus selectivity of excitatory neurons during perceptual learning is dynamic and largely relies on behavioral contingencies, even in primary sensory cortex.

neuroscience↗

bioRxiv2019

rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing

BackgroundMicrobiome composition is frequently studied by the amplification and high-throughput sequencing of specific molecular markers (metabarcoding). Various hypervariable regions of the 16S rRNA gene are classically used to estimate bacterial diversity, but other universal bacterial markers with a finer taxonomic resolution could be employed. We compared specificity and sensitivity between a portion of the rpoB gene and the V3V4 hypervariable region of the 16S rRNA gene.\n\nResultsWe first designed universal primers for rpoB suitable for use with Illumina sequencing-based technology and constructed a reference rpoB database of 45,000 sequences. The rpoB and V3V4 markers were amplified and sequenced from (i) a mock community of 19 bacterial strains from both Gram-negative and Gram-positive lineages; (ii) bacterial assemblages associated with entomopathogenic nematodes. In metabarcoding analyses of mock communities with two analytical pipelines (FROGS and DADA2), the estimated diversity captured with the rpoB marker resembled the expected composition of these mock communities more closely than that captured with V3V4. The rpoB marker had a higher level of taxonomic affiliation, a higher sensitivity (detection of all the species present in the mock communities), and a higher specificity (low rates of spurious OTU detection) than V3V4. We applied both primers to infective juveniles of the nematode Steinernema glaseri. Both markers showed the bacterial community associated with this nematode to be of low diversity (< 50 OTUs), but only rpoB reliably detected the symbiotic bacterium Xenorhabdus poinarii.\n\nConclusionsOur results confirm that different microbiota composition data may be obtained with different markers. We found that rpoB was a highly appropriate marker for assessing the taxonomic structure of mock communities and the nematode microbiota. Further studies on other ecosystems should be considered to evaluate the universal usefulness of the rpoB marker. Our data highlight two crucial elements that should be taken into account to ensure more reliable and accurate descriptions of microbial diversity in high-throughput amplicon sequencing analyses: i) the need to include mock communities as controls; ii) the advantages of using a multigenic approach including at least one housekeeping gene (rpoB is a good candidate) and one variable region of the 16S rRNA gene.

microbiology↗

bioRxiv2019

The mesoSPIM initiative: open-source light-sheet mesoscopes for imaging in cleared tissue

Over the course of the past decade, tissue clearing methods have reached a high level of sophistication with a wide variety of approaches now available1. To image large cleared samples, light-sheet microscopes have proven to be ideal due to their excellent optical sectioning capability in transparent tissue2. Such instruments have recently seen extensive technological and commercial development. However, despite this progress, the community is lacking instruments capable of exploring large samples with near-isotropic resolution within minutes. Here, we introduce the mesoscale selective plane-illumination microscopy (mesoSPIM) initiative, an open-hardware project that provides researchers with instructions and software to easily build and operate light-sheet microscopes for centimeter-sized cleared samples (http://www.mesospim.org).\n\nA wide range of commercial light-sheet microscopes have ...

neuroscience↗

bioRxiv2019

Photorhabdus Dam methyltransferase overexpression impairs virulence of the nemato-bacterial complex in insects

Photorhabdus luminescens is an entomopathogenic bacterium found in symbiosis with the nematode Heterorhabditis. Dam DNA methylation is involved in the pathogenicity of many bacteria, including P. luminescens, whereas studies about the role of bacterial DNA methylation during symbiosis are scarce. The aim of this study was to determine the role of Dam DNA methylation in P. luminescens symbiosis with H. bacteriophora. We constructed a strain overexpressing dam by inserting an additional copy of the dam gene under the control of a constitutive promoter in the chromosome of P. luminescens and then achieved association between this recombinant strain and nematodes. The dam overexpressing strain was able to feed the nematode in vitro and in vivo similarly as a control strain, and to re-associate with Infective Juvenile (IJ) stages in the insect. No difference in the amount of emerging IJs from the cadaver was observed between the two strains. Compared to the nematode in symbiosis with the control strain, a significant increase in LT50 was observed during insect infestation with the nematode associated with the dam overexpressing strain. These results suggest that the P. luminescens Dam plays a role in the pathogenicity of the nemato-bacterial complex.

microbiology↗