Biology subjects

Laborde, A.

Publications and source records attributed to Laborde, A..

10 recordsLinked to original sources

bioRxiv2025

Sardine: a modular framework for developing data acquisition and near real-time analysis applications

We present Sardine, a software framework built with.NET to control experimental setups through the reliable execution of dynamic networks of independent modules, where each module can interface with a hardware device (e.g., camera, motor) or represent an operation over data (e.g., image filter, data stream). The Sardine framework delivers robust fault-tolerant hardware control and eliminates downstream delays by implementing dedicated data processing queues for each module. Any.NET class can be seamlessly adapted into a Sardine module, enabling effortless integration with existing codebases. Sardines modular architecture ensures flexibility to accommodate changes in experimental paradigms, simplifying the adaptation of essential features, such as swapping hardware components or redefining the logic of their interactions. The core of Sardine is a novel aggregation system that connects modules in two layers, designed to streamline complex workflows such as those in microscopy applications. The first layer (link layer) enables concurrent operations between modules, such as synchronizing a camera module with a stage controller or a laser module, while maintaining a dependency tree to ensure devices operate as intended. For example, in an imaging experiment, Sardine oversees individual module malfunctions, such as a camera failure or stage misalignment, gracefully handling errors and dynamically restoring functionality to impacted network segments to minimize disruption. The second layer (data layer) facilitates the transmission of information across modules by associating them with operations that produce, consume, or transform data. In an imaging context, this could involve processing raw image data from a camera module, passing it through a real-time analysis module for feature detection, and forwarding the results to a visualization module for immediate feedback. This two-layer architecture ensures seamless data flow and robust error handling, making Sardine ideal for dynamic and complex experimental setups. Sardine also integrates logging, a metadata collection system, and tools to create graphical applications.

neuroscience↗

bioRxiv2024

Megabouts: a flexible pipeline for zebrafish locomotion analysis

Accurate quantification of animal behavior is crucial for advancing neuroscience and for defining reliable physiological markers. We introduce Megabouts (megabouts.ai), a software package standardizing zebrafish larvae locomotion analysis across experimental setups. Its flexibility, achieved with a Transformer neural network, allows the classification of actions regardless of tracking methods or frame rates. We demonstrate Megabouts ability to quantify sensorimotor transformations and enhance sensitivity to drug-induced phenotypes through high-throughput, high-resolution behavioral analysis.

animal behavior and cognition↗

bioRxiv2024

Neutrophil immune profile controls spinal cord regeneration in zebrafish

Spinal cord injury triggers a strong innate inflammatory response in both non-regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet, their role in the repair process, particularly in a regenerative context, remains largely unknown. Here, we show that, following rapid recruitment to the injured spinal cord, neutrophils mostly reverse migrate throughout the zebrafish body. In addition, promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil-specific RNA-seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf- expression in macrophage/microglia populations. Conversely, blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether, these findings provide new insights into the role of neutrophils in spinal cord regeneration, emphasizing the significant impact of their immune profile on the outcome of the repair process. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/576035v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@6153f1org.highwire.dtl.DTLVardef@1ce09faorg.highwire.dtl.DTLVardef@1f11187org.highwire.dtl.DTLVardef@1b5c152_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2023

Parallel on-chip micropipettes enabling quantitative multiplexed characterization of vesicle mechanics and cell aggregates rheology

Micropipette aspiration (MPA) is one of the gold standards to quantify biological samples mechanical properties, which are crucial from the cell membrane scale to the multicellular tissue. However, relying on the manipulation of individual home-made glass pipettes, MPA suffers from low throughput and difficult automation. Here, we introduce the sliding insert micropipette aspiration (SIMPA) method, that permits parallelization and automation, thanks to the insertion of tubular pipettes, obtained by photolithography, within microfluidic channels. We show its application both at the lipid bilayer level, by probing vesicles to measure membrane bending and stretching moduli, and at the tissue level by quantifying the viscoelasticity of 3D cell aggregates. This approach opens the way to high-throughput, quantitative mechanical testing of many types of biological samples, from vesicles and individual cells to cell aggregates and explants, under dynamic physico-chemical stimuli.

biophysics↗

bioRxiv2023

An easy-to-use microfluidic mechano-chemostat for tissues and organisms reveals that confined growth is accompanied with increased macromolecular crowding

Conventional culture conditions are oftentimes insufficient to study tissues, organisms, or 3D multicellular assemblies. They lack both dynamic chemical and mechanical control over the microenvironment. While specific microfluidic devices have been developed to address chemical control, they are often hard to use and do not allow the control of compressive forces. Here, we present a set of microfluidic devices which all rely on the use of sliding elements consisting of microfabricated rods that can be inserted inside a microfluidic device. Sliding elements enable the creation of reconfigurable sealed culture chambers for the study of whole organisms or model micro-tissues. By confining the micro-tissues, we studied the biophysical impact of growth-induced pressure and showed that this mechanical stress is associated with an increase in macromolecular crowding, shedding light on this understudied type of mechanical stress. Our mechano-chemostat is an easy-to-use microfluidic device that allows the long-term culture of biological samples and can be used to study both the impact of specific conditions as well as the consequences of mechanical compression.

biophysics↗

bioRxiv2023

Dimensionality reduction reveals separate translation and rotation populations in the zebrafish hindbrain

In many brain areas, neuronal activity is associated with a variety of behavioral and environmental variables. In particular, neuronal responses in the zebrafish hindbrain relate to oculomotor and swimming variables, as well as sensory information. However, the precise functional organization of the neurons has been difficult to unravel since neuronal responses are heterogeneous. Here we used dimensionality reduction methods on neuronal population data to reveal the role of the hindbrain in visually-driven oculomotor behavior and swimming. We imaged neuronal activity in zebrafish expressing GCaMP6s in the nucleus of almost all neurons, while monitoring the behavioral response to gratings that rotated with different speeds. We then used reduced-rank regression, a method that condenses the sensory and motor variables into a smaller number of features, to predict the fluorescence traces of all ROIs (regions of interest). Despite the potential complexity of the visuo-motor transformation, our analysis revealed that the bulk of population activity can be explained by only two features. Based on the contribution of these features to each ROIs activity, ROIs formed three clusters. One cluster was related to vergent movements and swimming, whereas the other two clusters related to leftward and rightward rotation. Voxels corresponding to these clusters were segregated anatomically, with leftward and rightward rotation clusters located selectively to the left and right hemispheres, respectively. Just as described in many cortical areas, our analysis revealed that single neuron complexity co-exists with a simpler population-level description, thereby providing insights into the organization of visuo-motor transformations in the hindbrain.

neuroscience↗

bioRxiv2022

The Adaptor Protein 2 (AP2) complex modulates habituation and behavioral selection across multiple pathways and time windows

Animals constantly perceive and integrate information across sensory modalities, and their nervous systems must select behavioral responses appropriate to the current situation and prior experience. Genetic factors supporting this behavioral flexibility are often disrupted in neuropsychiatric conditions, and our previous work revealed the disease-associated ap2s1 gene critically supports habituation learning in acoustically-evoked escape behavior of zebrafish. ap2s1 encodes a subunit of the AP2 endocytosis adaptor complex and has been linked to autism spectrum disorder, though its mechanism and direct behavioral importance have not been established. Here, we show that multiple subunits of the AP2 complex regulate acoustically-evoked behavior selection and habituation learning. Furthermore, ap2s1 biases the choice between distinct escape behaviors in sensory modality-specific manners, and more broadly regulates action selection across different sensory contexts. Using tissue-specific and inducible transgenic rescue, we demonstrate that the AP2 complex functions acutely and in the nervous system to modulate acoustically-evoked habituation learning, suggesting several spatially and/or temporally distinct mechanisms through which AP2 regulates different aspects of escape behavior selection and performance. Altogether, we demonstrate that the AP2 complex coordinates action selection across stimulus modalities and contexts, providing a new vertebrate model for the role of ap2s1 in human conditions including autism spectrum disorder. SIGNIFICANCE STATEMENTThe AP2S1 gene has been linked to learning disabilities and autism spectrum disorders (ASD), though the mechanisms underlying its impact on human behavior are unknown. We explored how, when, and where this gene regulates vertebrate behavior, developing a zebrafish model to identify the roles and mechanisms through which ap2s1 modulates behavior. We find that ap2s1 regulates simple acoustically-evoked learning, as well as how individuals bias behavioral choice in a wide variety of contexts. We show that ap2s1 acts at multiple distinct time periods and locations both within and outside of neuronal tissues, revealing the diverse mechanisms and pathways through which it modulates vertebrate behavior.

neuroscience↗

bioRxiv2021

Structural and functional organization of visual responses in the inferior olive of larval zebrafish

The olivo-cerebellar system plays an important role in vertebrate sensorimotor control. According to a classical theory of cerebellar cortex, the inferior olive (IO) provides Purkinje cells with error information which drives motor learning in the cerebellum. Here we investigate the sensory representations in the IO of larval zebrafish and their spatial organization. Using single-cell labeling of genetically identified IO neurons we find that they can be divided into at least two distinct groups based on their spatial location, dendritic morphology, and axonal projection patterns. In the same genetically targeted population, we recorded calcium activity in response to a set of visual stimuli using 2-photon imaging. We found that most IO neurons showed direction selective and binocular responses to visual stimuli and that functional properties were spatially organized within the IO. Light-sheet functional imaging that allowed for simultaneous activity recordings at the soma and axonal level revealed tight coupling between soma location, axonal projections and functional properties of IO neurons. Taken together, our results suggest that anatomically-defined classes of inferior olive neurons correspond to distinct functional types, and that topographic connections between IO and cerebellum contribute to organization of the cerebellum into distinct functional zones.

neuroscience↗

bioRxiv2021

Scalable Batch Fabrication of Ultrathin Flexible Neural Probes using Bioresorbable Silk Layer

Flexible deep brain probes have been the focus of many research works and aims at achieving better compliance with the surrounding brain tissue while maintaining minimal rejection. Strategies have been explored to find the best way to implant a flexible probe in the brain, while maintaining its flexibility once positioned in the cortex. Here, we present a novel and versatile scalable batch fabrication approach to deliver ultra-thin and flexible penetrating neural probe consisting of a silk-parylene bilayer. The biodegradable silk layer provides a temporary and programmable stiffener to ensure ease of insertion of the ultrathin parylene-based flexible devices. The innovative and yet robust batch fabrication technology allows complete design freedom of the neural probe in terms of materials, size, shape and thickness. These results provide a novel technological solution for implanting ultra-flexible and ultrathin devices, which possesses great potential for brain research.

bioengineering↗

bioRxiv2021

Microwell array-based opto-electrochemical detections revealing co-adaptation of rheological properties and oxygen metabolism in budding yeast

Microdevices composed of microwell arrays integrating nanoelectrodes (OptoElecWell) were developed to achieve dual high-resolution optical and electrochemical detections on single Saccharomyces cerevisiae budding yeast cells. Each array consists in 1.6 x 105 microwells of 8 {micro}m diameter and 5 {micro}m height, with a platinum nanoring electrode for in-situ electrochemistry, all integrated on a transparent thin wafer for further high-resolution live-cell imaging. After optimizing the filling rate, 32% of cells were effectively trapped within microwells. This allowed to analyse S. cerevisiae metabolisms associated with basal respiration while simultaneously measuring optically other cellular parameters. In this study, we focused on the impact of glucose concentration on respiration and intracellular rheology. We found that while oxygen uptake rate decreased with increasing glucose concentration, diffusion of tracer nanoparticles increased. Our OptoElecWell based respiration methodology provided similar results compared to the commercial gold-standard Seahorse XF analyser, while using 20 times lesser biological samples, paving the way to achieve single cell metabolomics. In addition, it facilitates an optical route to monitor the contents within single cells. The proposed device, in combination with the dual detection analysis, opens up new avenues for measuring cellular metabolism, and relating it to various cellular physiological and rheological indicators at single cell level.

biophysics↗