Biology subjects

Leterrier, C.

Publications and source records attributed to Leterrier, C..

At least 19 recordsLinked to original sources

bioRxiv2026

VLab4Mic: prediction of structural resolvability in super-resolution microscopy

Determining whether a microscopy experiment can resolve a specific feature of a protein assembly remains difficult because researchers must balance imaging modality, labelling strategy, and probe choice. We present VLab4Mic, a simulation platform that predicts structural resolvability before experiments. Starting from atomic models from the PDB or AlphaFold predictions, VLab4Mic places antibodies, nanobodies, chemical linkers, or fluorescent proteins on epitopes, applies stochastic labelling and steric constraints, and generates virtual samples for widefield, confocal, AiryScan, Stimulated Emission Depletion (STED), and Single-Molecule Localisation Microscopy (SMLM). Simulations of nuclear pore complexes agree with experimental data across all five modalities. In case studies, HIV capsid appearance depended strongly on orientation, and STED and SMLM separated domed from flat clathrin lattices where confocal and AiryScan did not. VLab4Mic therefore lets researchers judge which biological questions a given imaging configuration can answer before spending time tuning parameters at the microscope.

bioinformatics↗

bioRxiv2026

Direct labeling of microtubule turnover reveals in-lattice repair and stabilization patterns in developing neurons

The microtubule cytoskeleton is the backbone of neuronal morphogenesis, driving the development of the dendrites and axon, and supporting trafficking to distant compartments. How neuronal microtubules are maintained and renewed in the face of this dynamic endeavor and long-term commitment remains unclear. Recently, in-lattice repair has emerged as an alternative mechanism of microtubule renewal that could allow for continuity of the existing network and for the emergence of cell polarity. Here, we directly assessed microtubule turnover using microinjection of labeled tubulin in cultured hippocampal neurons that exhibit well defined stages of development and polarization during the first 24 hours in culture. Sizeable tubulin integration was visible minutes after microinjection, indicating fast turnover of microtubules in developing neurons. Once it appeared, a longer neurite that would become the nascent axon showed decreased turnover, both for its acetylated and non-acetylated populations of microtubules. Combining microinjection with expansion microscopy allowed us to visualize tubulin integration sites along single microtubules, unambiguously demonstrating the existence of in-lattice integration along neurites. In thick neurites, we observed preferential integration within non-acetylated cortical microtubules, but in-lattice integration sites were also visible in the deeper core bundles of acetylated microtubules. Overall, our results link previous observations of microtubule stabilization patterns in developing neurons to their actual turnover. Mapping these patterns of turnover strengthens the notion that microtubules establish an organized network that participates in axon emergence and the establishment of neuronal polarity.

cell biology↗

bioRxiv2025

Presynaptic Actin Nanostructures: A Reproducibility Case Study

In an effort to assess the reproducibility of bioimage analyses in current publications, we took part in a Global BioImage Analysts Society (GloBIAS) initiative to try and reproduce results from published articles. We attempted to reproduce core findings from the work of Bingham et al., which investigates the actin organisation in presynaptic structures by using diffraction-limited and super-resolution microscopy. While the original paper unveiled clear biological insight, it lacked sufficient detail in the bioimage analysis methodological approach, limiting the depth of reproducibility we could achieve. Through frequent contacts with the corresponding author, we managed to replicate qualitative aspects of the analysis of actin nanostructures in bead-induced presynapses. We performed image reconstruction from super-resolution microscopy data, automatic image registration and visual inspection, followed by manual annotation of structures of interest in [~]35 images. Our experience with this exercise highlights the importance of transparent data sharing and accessibility, as well as the need to adhere to bioimage analysis standards that ensure the reproducibility of nowadays complex biological image analysis studies. It also shows how crucial interdisciplinary collaboration is, since many biology labs are simply unaware of these standards, which are often easy to implement and would likely be widely adopted if their value was better understood or known.

neuroscience↗

bioRxiv2025

Non-synaptic exocytosis along the axon shaft and its regulation by the submembrane periodic skeleton

Neuronal communication relies on signaling molecules transferred via exo- and endocytosis throughout the brain. Historically, studies have focused on vesicle exo- and endocytosis and their release machinery at synapses, and much less is known about non-synaptic exocytosis. If and how vesicles can access the plasma membrane along the axonal shaft, overcoming the insulating layer of the membrane-associated periodic scaffold, remains unclear. Here, we used fast live-cell imaging of mature cultured hippocampal neurons expressing the vamp2-pHluorin reporter to map sponta-neous exocytosis along axons. We detected non-synaptic exocytic events along the axon shaft that concentrated at the axon initial segment. Perturbation of the membrane-associated actin-spectrin skeleton revealed its role in regulating shaft exocytosis, similarly to its recently demonstrated role in shaping axonal endocytosis. To visualize the nanoscale arrangement of exocytic locations, we developed a novel correlative live-cell/two - color, single-molecule localization microscopy (SMLM) approach. We observed that regions of exocytosis are devoid of the submembrane spectrin mesh, with these spectrin-free areas being spatially separated from the spectrin clearings that contain clathrin-coated pits. Overall, our work reveals a new process of spontaneous exocytosis along the axon shaft, and how the axonal submem-brane skeleton shapes a heterogeneous landscape that uniquely segregates vesicular trafficking events.

cell biology↗

bioRxiv2025

Extracting biological structure and heterogeneity from the nano to the macro scale

Fluorescence microscopy is an essential tool in biology. It has revealed great variability at multiple scales, in macromolecular complexes, cells, and organisms. Understanding this variability will reveal the mechanisms by which genetically or biochemically identical systems adopt different biological states. Achieving this requires the ability to extract both the underlying biological structure and how it varies across the population. Currently the field lacks general techniques to deal with arbitrary structures and different types of variability. Here we present SQUASSH, a new convolutional neural network-based approach to freely fit structural models to fluorescence microscopy data that simultaneously quantifies variability to reveal correlations, dynamics, and systematic distortions. SQUASSH is highly versatile: it accommodates diverse imaging modalities at length scales from nm to mm. This approach opens up applications such as imaging nanoscale macromolecular structures, revealing patterns in shape changes from organelle to tissue scale, and characterizing systems biology of dynamical processes.

cell biology↗

bioRxiv2024

Structural Repetition Detector: multi-scale quantitative mapping of molecular complexes through microscopy

From molecules to organelles, cells exhibit recurring structural motifs across multiple scales. Understanding these structures provides insights into their functional roles. While super-resolution microscopy can visualise such patterns, manual detection in large datasets is challenging and biased. We present the Structural Repetition Detector (SReD), an unsupervised computational framework that identifies repetitive biological structures by exploiting local texture repetition. SReD formulates structure detection as a similarity-matching problem between local image regions. It detects recurring patterns without prior knowledge or constraints on the imaging modality. We demonstrate SReDs capabilities on various fluorescence microscopy images. Quantitative analyses of three datasets highlight SReDs utility: estimating the periodicity of spectrin rings in neurons, detecting HIV-1 viral assembly, and evaluating microtubule dynamics modulated by EB3. Our open-source ImageJ and Fiji plugin enables unbiased analysis of repetitive structures across imaging modalities in diverse biological contexts.

cell biology↗

bioRxiv2024

Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model

Chemical synapses are fundamental units for the transmission of information throughout the nervous system. The cyto-skeleton allows to build, maintain and transform both pre- and postsynaptic contacts, yet its organization and the role of its unique synaptic nanostructures are still poorly understood. Here we present a presynapse-on-glass model where presynaptic specializations are robustly induced along the axons of cultured neurons by micropatterned dots of neuroligin, allowing the controlled orientation and easy optical visualization of functional induced presynapses. We demonstrate the relevance and usefulness of this presynapse-on-glass model for the study of presynaptic actin architecture, showing that a majority of induced presynapses are enriched in actin, with this enrichment being correlated to higher synaptic cycling activity. We confirm our previous results on bead-induced presynapses by identifying the same distinct actin nanostructures with-in presynapses: corrals, rails and mesh. Furthermore, we leverage the controlled orientation of the presynapse-on-glass model, visualizing the arrangement of these actin structures relative to the active zone nanoclusters using multicolor 3D Single Molecule Localization Microscopy (SMLM), and relative to the sub-diffractive localization exocytic events using a correlative live-cell and SMLM approach.

neuroscience↗

bioRxiv2024

Spectrin condensates provide a nidus for assembling the periodic axonal structure

Coordinated assembly of individual components into higher-order structures is a defining theme in biology, but underlying principles are not well-understood. In neurons, /{beta} spectrins, adducin, and actinfilaments assemble into a lattice wrapping underneath the axonal plasma membrane, but mechanistic events leading to this periodic axonal structure (PAS) are unclear. Visualizing PAS components in axons as they develop, we found focal patches in distal axons containing spectrins and adducin (but sparse actin filaments) with biophysical properties reminiscent of biomolecular condensation. Overexpressing spectrin-repeats - constituents of /{beta}-spectrins - in heterologous cells triggered condensate formation, and preventing association of {beta}II-spectrin with actin-filaments/membranes also facilitated condensation. Finally, overexpressing condensate-triggering spectrin repeats in neurons before PAS establishment disrupted the lattice, presumably by competing with innate assembly, supporting a functional role for biomolecular condensation. We propose a condensation-assembly model where PAS components form focal phase-separated condensates that eventually unfurl into a stable lattice-structure by associating with subplasmalemmal actin. By providing local depots of assembly parts, biomolecular condensation may play a wider role in the construction of intricate cytoskeletal structures.

cell biology↗

bioRxiv2023

Surpassing Challenges in Structured-Illumination Microscopy with FlexSIM

Super-resolution structured-illumination microscopy (SIM) is a powerful technique that allows one to surpass the diffraction limit by up to a factor two. Yet, its practical use is hampered by its sensitivity to imaging conditions which makes it prone to reconstruction artifacts. In this work, we present FlexSIM, a flexible SIM reconstruction method capable to handle highly challenging data. Specifically, we demonstrate the ability of FlexSIM to deal with the distortion of patterns, the high level of noise encountered in live imaging, as well as out-of-focus fluorescence. Moreover, we show that FlexSIM achieves state-of-the-art performance over a variety of open SIM datasets.

biophysics↗

bioRxiv2023

The actin-spectrin submembrane scaffold restricts endocytosis along proximal axons

Neuronal clathrin-mediated endocytosis has unique features in compartments such as dendrites and presynaptic boutons, but how membrane and extracellular components are internalized along the axon shaft remains poorly known. Here we focused on clathrin-coated structures and endocytosis along the axon initial segment (AIS), and their relationship to the periodic actin-spectrin scaffold that lines the axonal plasma membrane. Super-resolution optical microscopy, platinum replica electron microscopy, and their correlative combination on cultured hippocampal neurons reveal that in the AIS, clathrin-coated pits form on bare membrane patches, [~]300 nm circular areas devoid of spectrin mesh and lined by actin filaments we termed "clearings". In fibroblasts and the proximal axon of neurons, spectrin depletion and drug-induced scaffold disorganization increase clathrin-coated pit formation. However, the presence of clathrin-coated pits at the AIS is not directly linked to actual endocytosis: using cargo uptake and live-cell imaging experiments, we find that most AIS clathrin-coated pits are long-lived and immobile within the spectrin mesh clearings. Direct perturbation of the spectrin scaffold as well as elevated neuronal activity could induce endocytosis downstream of clathrin pit formation, showing that spectrin clearings are structures responsible for regulated endocytosis at the AIS.

cell biology↗

bioRxiv2023

pHusion: A robust and versatile toolset for automated detection and analysis of exocytosis

Exocytosis is a fundamental process used by eukaryotic cells to regulate the composition of the plasma membrane and facilitate cell-cell communication. To investigate the role exocytosis plays in neuronal morphogenesis, previously we developed computational tools with a graphical user interface (GUI) to enable the automatic detection and analysis of exocytic events (ADAE GUI) from fluorescence timelapse images. Though these tools have proven useful, we found that the code was brittle and not easily adapted to different experimental conditions. Here, we have developed and validated a robust and versatile toolkit, named pHusion, for the analysis of exocytosis written in ImageTank, a graphical programming language that combines image visualization and numerical methods. We tested this method using a variety of imaging modalities and pH-sensitive fluorophores, diverse cell types, and various exocytic markers to generate a flexible and intuitive package. Using pHusion, we show that VAMP3-mediated exocytosis occurs 30-times more frequently in melanoma cells compared with primary oligodendrocytes, that VAMP2-mediated fusion events in mature rat hippocampal neurons are longer lasting than those in immature murine cortical neurons, and that exocytic events are clustered in space yet random in time in developing cortical neurons. Summary StatementExocytosis is an essential process by which cells change shape, alter membrane composition, and communicate with other cells. Though all eukaryotic cells carry out exocytosis, the regulation of vesicle fusion, the cargo of vesicles, and the role exocytosis plays in cell fate differ greatly across cell types. Here, we developed a flexible and robust set of tools to enable automatic identification and analysis of exocytic events across a wide range of cell types, vesicle types, and imaging conditions.

cell biology↗

bioRxiv2023

Microtubules under mechanical pressure can breach dense actin networks

The crosstalk between actin network and microtubules is key to the establishment of cell polarity. It ensures that the asymmetry of actin architec ture along cell periphery directs the organization of microtubules in cell interior. In particular, the way the two networks are physically inter-twined regulates the spatial organization and the distribution of forces in the microtubule network. While their biochemical crosstalk is getting uncovered, their mechanical crosstalk is still poorly understood. Here we designed an in vitro reconstitution assay to study the physical interaction between dynamic microtubules with various structures made of actin fil aments. We found that microtubules can align and move by their polymerization force along linear bundles of actin filaments. But they cannot enter dense and branched actin meshworks, such as those found in the lamellipodium along cell periphery. However, when microtubules are immobilized, by their crosslinking with actin structures or others means, the force of polymerization builds up pressure in the microtubules that is sufficient to allow them to breach and penetrate these dense actin meshworks. This mechanism may explain the final progression of microtubules up to cell periphery through the denser parts of the actin network.

biophysics↗

bioRxiv2023

Robust and fast multicolor Single Molecule Localization Microscopy using spectral separation and demixing

Single Molecule Localization Microscopy (SMLM) is a straightforward approach to reach sub-50 nm resolution using techniques such as Stochastic Optical Reconstruction Microscopy (STORM) or DNA-Point Accumulation for Imaging in Nanoscale Topography (PAINT), and to resolve the arrangement of cellular components in their native environment. However, SMLM acquisitions are slow, particularly for multicolor experiments where channels are usually acquired in sequence. In this work, we evaluate two approaches to speed-up multicolor SMLM using a module splitting the fluorescence emission toward two cameras: simultaneous 2-color PAINT (S2C-PAINT) that images spectrally-separated red and far-red imager strands on each camera, and spectral demixing STORM (SD-STORM) that uses spectrally-close far-red fluorophores imaged on both cameras before assigning each localization to a channel by demixing. For each approach, we carefully evaluate the crosstalk between channels using three types of samples: DNA origami nanorulers of different sizes, single-target labeled cells, or cells labeled for multiple targets. We then devise experiments to assess how crosstalk can potentially affect the detection of biologically-relevant subdiffraction patterns. Finally, we show how these approaches can be combined with astigmatism to obtain three-dimensional data, and how SD-STORM can be extended three-color imaging, making spectral separation and demixing attractive options for robust and versatile multicolor SMLM investigations.

cell biology↗

bioRxiv2022

Distinct nano-structures support a multifunctional role of actin at presynapses

Synapses are the nexus of signal transmission in the nervous system. Despite decades of work, the architecture of the actin cytoskeleton that concentrates at presynapses remain poorly known, hindering our comprehensive understanding of its roles in presynaptic physiology. In this work, we take advantage of a validated model of bead-induced presynapses to measure and visualize isolated presynaptic actin by diffraction-limited and super-resolution microscopy. We first identify a major population of actin-enriched presynapses that concentrates more presynaptic components, and shows higher synaptic vesicle cycling than their non-enriched counterparts. Using pharmacological perturbations, we determine that an optimal amount of actin is necessary for this effect of actin enrichment. Modulation of this effect by actin nucleation inhibitors indicates its dependance on distinct presynaptic actin assemblies. Using Single Molecule Localization Microscopy (SMLM), we directly visualize these nano-structures in isolated presynapses, defining an actin mesh at the active zone, actin rails between the active zone and deeper reserve pools, and actin corrals around the whole presynaptic compartment. We finally show that these three types of presynaptic actin nano-structures are differentially affected by actin nucleation inhibitors, consistent with their effect on presynaptic component concentration and on synaptic vesicle cycling.

neuroscience↗

bioRxiv2022

High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation

In recent years, the development of new image analysis approaches has highlighted the possibility of recovering superresolution information from short sequences of wide-field images. Our recently developed method, SRRF (Super-Resolution Radial Fluctuations), enables long-term live-cell imaging beyond the resolution limit without specialized hardware. Here, we present eSRRF (enhanced-SRRF), a significant improvement over our initial method, enhancing image fidelity to the underlying structure and resolution. Especially, eSRRF uses automated data-driven parameter optimization, including an estimation of the number of frames necessary for optimal reconstruction. We demonstrate the improved fidelity of the images reconstructed with eSRRF and highlight its versatility and ease of use over a wide range of microscopy techniques and biological systems. We also extend eSRRF to 3D super-resolution microscopy by combining it with multi-focus microscopy (MFM), obtaining volumetric super-resolution imaging of live cells with acquisition speed of ~1 volume/second.

biophysics↗

bioRxiv2021

ShareLoc - an open platform for sharing localization microscopy data

Novel insights and more powerful analytical tools can emerge from the reanalysis of existing data sets, especially via machine learning methods. Despite the widespread use of single molecule localization microscopy (SMLM) for super-resolution bioimaging, the underlying data are often not publicly accessible. We developed ShareLoc (https://shareloc.xyz), an open platform designed to enable sharing, easy visualization and reanalysis of SMLM data. We discuss its features and show how data sharing can improve the performance and robustness of SMLM image reconstruction by deep learning.

bioinformatics↗

bioRxiv2021

Microbiota and stress: a loop that impacts memory

Chronic stress and the gut microbiota appear to comprise a feed-forward loop, which contributes to the development of depressive disorders. Evidence suggests that memory can also be impaired by either chronic stress or microbiota imbalance. However, it remains to be established whether these could be a part of an integrated loop model and be responsible for memory impairments. To shed light on this, we used a two-pronged approach in Japanese quail: first stress-induced alterations in gut microbiota were characterized, then we tested whether this altered microbiota could affect brain and memory function when transferred to a germ-free host. The cecal microbiota of chronically stressed quails was found to be significantly different from that of unstressed individuals with lower and {beta} diversities and increased Bacteroidetes abundance largely represented by the Alistipes genus, a well-known stress target in rodents and humans. The transfer of this altered microbiota into germ-free quails decreased their spatial and cue-based memory abilities as previously demonstrated in the stressed donors. The recipients also displayed increased anxiety-like behavior, reduced basal plasma corticosterone levels and differential gene expression in the brain. Furthermore, cecal microbiota transfer from a chronically stressed individual was sufficient to mimic the adverse impact of chronic stress on memory in recipient hosts and this action may be related to the Alistipes genus. Our results provide evidence of a feed-forward loop system linking the microbiota-gut-brain axis to stress and memory function and suggest that maintaining a healthy microbiota could help alleviate memory impairments linked to chronic stress.

animal behavior and cognition↗

bioRxiv2021

Training level reveals a dynamic dialogue between stress and memory systems in birds

It is now well-accepted that memory is a dynamic process, and that stress and training level may influence which memory system an individual engages when solving a task. In this work, we investigated whether and how chronic stress impacts spatial and cue-based memories according to training level. To that aim, control and chronically stressed Japanese quail were trained in a task that could be solved using spatial and cue-based memory and tested for their memory performances after 5 and 15 training days (initial training and overtraining, respectively) and following an emotional challenge (exposure to an open field). While chronic stress negatively impacted spatial memory in chronically stressed birds after initial training, this impact was lowered after overtraining compared to control quail. Interestingly, the emotional challenge reinstated the differences in performance between the two groups, revealing that chronic stress/overtraining did not eliminate spatial memory. Differences caused by previous stressors can re-emerge depending on the more immediate psychological state of the individual. Contrary to spatial memory, cue-based memory was not impaired in any test occasion, confirming that this form of memory is resistant to chronic stress. Altogether these findings reveal a dynamic dialogue between stress, training, and memory systems in birds.

animal behavior and cognition↗