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Biology subjects

Deschamps, J.

Publications and source records attributed to Deschamps, J..

At least 19 recordsLinked to original sources

Super-resolution mapping of platelet α-granules uncovers non-polarized secretion and differential retention of von Willebrand Factor and thrombospondin-1

Platelet -granules contain hundreds of bioactive proteins that regulate thrombosis, inflammation and tissue repair. The interplay between -granule secretion and platelet biomechanics is central to platelet function but remains incompletely understood. Here we combined complementary super-resolution microscopy methods, computational image simulations and quantitative single-cell analysis to investigate -granule nanoscale organization and secretion in tandem with cytoskeletal remodeling in spreading human platelets. We show that P-selectin, thrombospondin-1 (TSP1) and von Willebrand factor (VWF) occupy distinct subgranular domains and that apparent co-localization strongly depends on imaging resolution. We identify ring-like P-selectin staining as a robust signature of intact -granules and demonstrate that -granule secretion in spreading platelets was confined to the platelet cell body rather than the actively remodeling periphery. Quantitative assessment at the single-cell level showed that degranulation coincided with transitions from filopodia-rich to lamellipodial morphologies. Comparisons across adhesive substrates and perturbations by soluble agonists indicated that these processes are coordinated through overlapping signaling networks rather than direct local coupling. Analysis of secreted cargo revealed distinct extracellular fates despite no evidence for polarized secretion. TSP1 accumulated beneath platelets within diffusion barrier-restricted membrane pockets and around platelets following matrix binding, whereas VWF remained predominantly tethered to platelet membranes and formed short VWF strings. Together, our findings redefine the organization and release of platelet -granules, demonstrate an absence of secretion polarity, and establish cargo-specific retention mechanisms that may influence platelet signaling and thrombus architecture.

cell biology↗

AI4Life Open Calls and Public Challenges: why, how, and what we have learned.

Within AI4Life, we ran three Open Calls and three Public Challenges (2023-2025), supporting 22 bioimage analysis projects from 151 applications and engaging 225 challenge participants, with the aim of applying FAIR deep learning in the life sciences. Our experience offers a view of the current state of bioimage analysis, the landscape of available tools, as well as the existing gaps between method developers, tool producers and potential users. It highlights that even after careful selection for AI-ready projects, most still require substantial effort to apply deep learning, and that the field still relies heavily on established, well-rounded methods to solve common problems. We come to the conclusion that for scientific AI in biology, the rate-limiting step is not methods and models but data, annotations, and shared infrastructure underneath them.

bioinformatics↗

Complementary killing activities of Pbunavirus LS1 and Bruynoghevirus LUZ24 phages on planktonic and sessile Pseudomonas aeruginosa PAO1 derivatives

Four P. aeruginosa phages active against a representative panel of strains, and with complementary spectra of action were chosen with the goal of using them for phage therapy. Two of them were myoviruses belonging to the Pbunavirus LS1 species, and two were podoviruses belonging to the Bruynoghevirus LUZ24 species. In order to better apprehend the interactions of these phages with their P. aeruginosa host bacteria, we undertook the characterization of their bacterial receptors, using a PAO1 derivative as a recipient strain. Whereas the receptor of the P. LS1 phage Ab27 had already been characterized as the O-antigen chain of the lipopolysaccharides, no information was available at the onset of this work on the receptor used by the phages of the B. LUZ24 species. We show that the surface polysaccharide Psl is this receptor. Psl stands for polysaccharide synthesis locus, and it is an important component of the biofilm matrix in a large panel of P. aeruginosa strains, including PAO1. Remarkably, the B. LUZ24 phages were more active against PAO1 in minimal medium compared to rich medium. Consistently, this was correlated with larger amounts of Psl bound at the bacterial surface during exponential growth in the minimal medium compared to the rich medium. Biofilms formed on a medical intubation device, as well as in in 96-well plates, were degraded to different extent by the two phage species: biofilms grown for 7 hours on tubing device were degraded more efficiently by the B. LUZ24 than the P. LS1 phage, whereas mature biofilms (16 hours) formed in 96-well plates were degraded more rapidly by P. LS1 than by B. LUZ24 phage. The frequency of genetic mutants resisting to each phage were determined in liquid medium by a fluctuation assay and found in the range of 10-5 to 10-6 per generation. Interestingly, most of the P. LS1 resisting mutants were more sensitive to the B. LUZ24 phage. We conclude that the combination of the four selected phages has very promising properties, which should be relevant in the framework of phage therapy.

microbiology↗

CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies

Cell cycle progression, migration, and proliferation shape development and regeneration, but simultaneous live-cell imaging remains challenging as conventional fluorescent cell cycle indicators (FUCCI) monopolize the green and red channels used by most structural and functional biosensors. To overcome this, we integrated a spectrally re-engineered FUCCI variant, open-source analysis software, and four-color human stem cell reporter lines into CALIPERS: a method for Cell-cycle-Aware Live-cell Imaging in Phenotyping and Regeneration Studies.

bioengineering↗

FeatureForest: the power of foundation models, theusability of random forests

Once the work at the microscope is done, biological discoveries rely heavily on proper downstream analysis. This often amounts to first segmenting the biological objects of interest in the image before performing a quantitative analysis. Deep-learning (DL) is nowadays ubiquitous in such segmentation tasks. However, DL can be cumbersome to apply, as it often requires large amount of manual labeling to produce ground-truth data, and expert knowledge to train the models from scratch. Nonetheless, the performance of large foundation models, although trained on natural images, are improving on scientific images with every new model released. They, however, require either manual prompting or tedious post-processing to selectively segment the biological objects of interest. Classical machine learning algorithms, such as random forest classifiers, on the other hand, are well-established, easy to train, and often yield results of sufficient quality for downstream processing tasks, hence their continued popularity. Unfortunately, they are limited to objects with distinct, well-defined textures compared to their environment. This generally limits their usefulness to structures easy to recognize. Here, we present FeatureForest, an open-source tool that leverages the feature embeddings of large foundation models to train a random forest classifier, thereby providing users with a rapid way of semantically segmenting complex images using only a few labeling strokes. We demonstrate the improvement in performance over a variety of datasets, including large and complex volumetric electron microscopy stacks. Our implementation is available in napari, currently integrates four foundation models, and can easily be extended to any new model once they become available.

bioinformatics↗

Hijacking and Integration of Algal Plastids andMitochondria in a Polar Planktonic Host

In oceanic plankton, various host organisms are capable of engulfing and temporarily integrating microalgae (photosymbiosis) or just their photosynthetic plastids (kleptoplastidy) as a solar-powered energy source. These cellular interactions can be considered to be representative of evolutionary steps in plastid acquisition in eukaryotes, but the underlying cellular mechanisms and dynamics are not fully understood. Here, we studied a kleptoplastidic dinoflagellate (RSD: Ross Sea Dinoflagellate), which is known to steal plastids of the microalga Phaeocystis antarctica. We tracked the morphology and activity of stolen plastids over several months by combining multimodal subcellular imaging and photophysiology. Upon integration inside a host vacuole, the volume of plastids and pyrenoids significantly increased and photosynthetic activity was boosted along with carbon fixation and transfer to the host. This may be supported by the retention of a 50-fold larger algal nucleus for [~]1 week. Once the algal nucleus was lost, there was a decrease in plastid volume and photosynthesis, but plastids were still beneficial for the host after > 2 months. Unlike other kleptoplastidic interactions, we showed that the algal mitochondrion was also stolen and retained for several months, transforming into an extensive network in close proximity with plastids. This highlights a new strategy in plankton along the continuum of plastid symbioses where both the energy-producing plastid and mitochondrion of a microalga are hijacked for several months by a host. This symbiosis that we found to be widely-distributed in polar regions suggests that plastid-mitochondrion interaction may have played a role in the evolution of plastid acquisition.

ecology↗

Anti-S-layer monoclonal antibodies impact Clostridioides difficile physiology

Clostridioides difficile (C. difficile), a gram-positive anaerobic and spore-forming bacterium, is the leading cause of nosocomial antibiotic-associated diarrhea in adults and is characterized by high levels of recurrence and mortality. Surface-layer Protein A (SlpA), the most expressed protein on bacterial surface, plays a crucial role in the early stages of infection although its role in C. difficile physiology is yet to be fully understood. Anti-S-layer antibodies have been identified in the sera of convalescent patients and correlate with improved outcome of C. difficile infection (CDI). However, the precise mechanisms of how anti-S-layer antibodies can confer protection to the host remain unknown. In this study, we report the first monoclonal antibodies (mAbs) targeting S-layer of the reference strain 630. Characterization of these mAbs unravels important roles for S-layer protein in growth, toxin secretion, and biofilm formation with, surprisingly, opposite effects of different anti-SlpA mAbs on these functions. One anti-SlpA mAb impaired C. difficile growth and restored sensitivity to lysozyme-induced lysis. These findings suggest that anti-S-layer antibody responses may include protective and detrimental effects for the host and provide important insights for designing adequate S-layer-targeting therapeutics.

microbiology↗

Multi-scale transcriptome unveils spatial organisation and temporal dynamics of Bacillus subtilis biofilms

Bacillus subtilis has been extensively used to study the molecular mechanisms behind the development and dispersal of surface bacterial multicellular communities. Well-structured spatially organised communities (colony, pellicle, and submerged biofilm) share some similarities, but also display considerable differences at the structural, chemical and biological levels. To unveil the spatial transcriptional heterogeneity between the different communities, we analysed by RNA-seq nine spatio-physiological populations selected from planktonic and spatially organised communities. This led to a global landscape characterisation of gene expression profiles uncovering genes specifically expressed in each compartmental population. From this mesoscale analysis and using fluorescent transcriptional reporter fusions, 17 genes were selected and their patterns of expression reported at single cell scale with time-lapse confocal laser scanning microscopy (CLSM). Derived kymographs allowed to emphasise spectacular mosaic gene expression patterns within a biofilm. A special emphasis on oppositely regulated carbon metabolism genes (gapA and gapB) permitted to pinpoint the coexistence of spatially segregated bacteria under either glycolytic or gluconeogenic regime in a same biofilm population. Altogether, this study gives novel insights on the development and dispersal of B. subtilis surface-associated communities.

microbiology↗

Extracellular succinate induces spatially organized biofilm formation in Clostridioides difficile

Clostridioides difficile is the major cause of nosocomial diarrhea, which are associated with gut microbiome dysbiosis. Biofilms of C. difficile have been progressively linked to the pathogenesis of this bacterium and the recurrences of its infections. Though the number of conditions in which C. difficile biofilms are being produced is increasing, little is known about how and when biofilms are formed in the gut. Here we report that succinate, a metabolite abundantly produced by the dysbiotic gut microbiota, induces in vitro biofilm formation of C. difficile strains. We characterized the morphology and spatial composition of succinate-induced biofilms, and compared to non-induced or deoxycholate-induced biofilms, biofilms induced by succinate are significantly thicker, structurally more complex, and poorer in proteins and exopolysaccharides (EPS). We then applied transcriptomics and genetics to characterize the early stages of succinate-induced biofilm formation and we showed that succinate-induced biofilm results from major metabolic shifts and cell-wall composition changes. Similar to deoxycholate-induced biofilms, biofilms induced by succinate depend on the presence of a rapidly metabolized sugar. Finally, although succinate can be consumed by the bacteria, we found that the extracellular succinate is in fact responsible for the induction of biofilm formation through complex regulation involving global metabolic regulators and the osmotic stress response. In the context of human gut dysbiosis, succinate can limit bacterial infections through the control of innate immune responses. Collectively, our results suggest that succinate is an intestinal signal which can drive the biofilm formation and persistence of C. difficile in the gut and increase the risk of relapse.

microbiology↗

Comparative genome analysis of Enterococcus cecorum reveals intercontinental spread of a lineage of clinical poultry isolates.

Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering, mortality, and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last ten years in 16 French broiler farms. Comparative genomics, genome-wide association study, and measured susceptibility to serum, biofilm forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate origin of the isolates or phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster in few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCEEnterococcus cecorum is an important pathogen in poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first dataset on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage probably also circulating elsewhere and which should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum-related diseases.

genomics↗

MicroFPGA: an affordable FPGA platform for microscope control

Modern microscopy relies increasingly on microscope automation to improve throughput, ensure reproducibility or observe rare events. Automation requires in particular computer control of the important elements of the microscope. Furthermore, optical elements that are usually fixed or manually movable can be placed on electronically-controllable elements. In most cases, a central electronics board is necessary to generate the control signals they require and to communicate with the computer. Fur such tasks, Arduino microcontrollers are widely used due to their low cost and programming entry barrier. However, they are limiting in their performance for applications that require high-speed or multiple parallel processes. Field programmable gate arrays (FPGA) are the perfect technology for high-speed microscope control, as they are capable of processing signals in parallel and with high temporal precision. While plummeting price made the technology available to consumers, a major hurdle remains the complex languages used to configure them. In this work, we used an affordable FPGA, delivered with an open-source and friendly-to-use programming language, to create a versatile microscope control platform called MicroFPGA. It is capable of synchronously triggering cameras and multiple lasers following complex patterns, as well as generating various signals used to control microscope elements such as filter wheels, servomotor stages, flip-mirrors, laser power or acoustooptic modulators. MicroFPGA is open-source and we provide online Micro-Manager, Java, Python and LabVIEW libraries, together with blueprints and tutorials.

biophysics↗

Labkit: Labeling and Segmentation Toolkit for Big Image Data

We present LO_SCPLOWABKITC_SCPLOW, a user-friendly Fiji plugin for the segmentation of microscopy image data. It offers easy to use manual and automated image segmentation routines that can be rapidly applied to single- and multi-channel images as well as to timelapse movies in 2D or 3D. LO_SCPLOWABKITC_SCPLOW is specifically designed to work efficiently on big image data and enables users of consumer laptops to conveniently work with multiple-terabyte images. This efficiency is achieved by using ImgLib2 and BigDataViewer as the foundation of our software. Furthermore, memory efficient and fast random forest based pixel classification inspired by the Waikato Environment for Knowledge Analysis (Weka) is implemented. Optionally we harness the power of graphics processing units (GPU) to gain additional runtime performance. LO_SCPLOWABKITC_SCPLOW is easy to install on virtually all laptops and workstations. Additionally, LO_SCPLOWABKITC_SCPLOW is compatible with high performance computing (HPC) clusters for distributed processing of big image data. The ability to use pixel classifiers trained in LO_SCPLOWABKITC_SCPLOW via the ImageJ macro language enables our users to integrate this functionality as a processing step in automated image processing workflows. Last but not least, LO_SCPLOWABKITC_SCPLOW comes with rich online resources such as tutorials and examples that will help users to familiarize themselves with available features and how to best use LO_SCPLOWABKITC_SCPLOW in a number of practical real-world use-cases.

bioinformatics↗

Photon-free (s)CMOS camera characterization for artifact reduction in high- and super-resolution microscopy

Modern implementations of widefield fluorescence microscopy often rely on sCMOS cameras, but this camera architecture inherently features pixel-to-pixel variations. Such variations lead to image artifacts and render quantitative image interpretation difficult. Although a variety of algorithmic corrections exists, they require a thorough characterization of the camera, which typically is not easy to access or perform. Here, we developed a fully automated pipeline for camera characterization based solely on thermally generated signal, and implemented it in the popular open-source software Micro-Manager and ImageJ/Fiji. Besides supplying the conventional camera maps of noise, offset and gain, our pipeline also gives access to dark current and thermal noise as functions of the exposure time. This allowed us to avoid structural bias in single-molecule localization microscopy (SMLM), which without correction is substantial even for scientific-grade, cooled cameras. In addition, our approach enables high-quality 3D super-resolution as well as live-cell time-lapse microscopy with cheap, industry-grade cameras. As our approach for camera characterization does not require any user interventions or additional hardware implementations, numerous correction algorithms demanding camera characterization become easily applicable.

biophysics↗

Direct Supercritical Angle Localization Microscopy for Nanometer 3D Superresolution

3D single molecule localization microscopy (SMLM) is an emerging superresolution method for structural cell biology, as it allows probing precise positions of proteins in cellular structures. Supercritical angle fluorescence strongly depends on the z-position of the fluorophore and can be used for z localization in a method called supercritical angle localization microscopy (SALM). Here, we realize the full potential of SALM by directly splitting supercritical and undercritical emission, using an ultra-high NA objective, and applying new fitting routines to extract precise intensities of single emitters, resulting in a four-fold improved z-resolution compared to the state of the art. We demonstrate nanometer isotropic localization precision on DNA origami structures, and on clathrin coated vesicles and microtubules in cells, illustrating the potential of SALM for cell biology.

biophysics↗

EMU: reconfigurable graphical user interfaces for Micro-Manager

Advanced light microscopy methods are becoming increasingly popular in biological research. Their ease of use depends, besides experimental aspects, on intuitive user interfaces. The open-source software Micro-Manager offers a universal interface for microscope control but requires implementing plugins to further tailor it to specific systems. Since even similar devices can have different Micro-Manager properties (such as power percentage versus absolute power), transferring user interfaces to other systems is usually very restricted. We developed Easier Micro-Manager User interface (EMU), a Micro-Manager plugin, to simplify building flexible and reconfigurable user interfaces. EMU offers a choice of interfaces that are rapidly ready to use thanks to an intuitive configuration menu. In particular, the configuration menu allows mapping device properties to the various functions of the interface in a few clicks. Exchanging or adding new devices to the microscope no longer requires rewriting code. The EMU framework also simplifies implementing a new interface by providing the configuration and device interaction mechanisms. The user interface can be built by using a drag-and-drop tool in ones favorite Java development environment and writing a few lines of code for compatibility with EMU. Micro-Manager users now have a powerful tool to improve the user experience on their instruments. EMU interfaces can be easily transferred to new microscopes and shared with other research groups. In the future, newly developed interfaces will be added to EMU to benefit the whole community.

bioinformatics↗

A cost-efficient open source laser engine for microscopy

Scientific-grade lasers are costly components of modern microscopes. For high-power applications, such as single-molecule localization microscopy, their price can become prohibitive. Here, we present an open-source high-power laser engine that can be built for a fraction of the cost. It uses affordable, yet powerful laser diodes at wavelengths of 405 nm, 488 nm and 640 nm and optionally a 561 nm diode-pumped solid-state laser. The light is delivered to the microscope via an agitated multimode fiber in order to suppress speckles. We provide the part lists, CAD files and detailed descriptions, allowing any research group to build their own laser engine.

biophysics↗

Whole-head recording of chemosensory activity in the marine annelid Platynereis dumerilii

Chemical detection is key to various behaviours in both marine and terrestrial animals. Marine species, though highly diverse, have been underrepresented so far in studies on chemosensory systems, and our knowledge mostly concerns the detection of airborne cues. A broader comparative approach is therefore desirable. Marine annelid worms with their rich behavioural repertoire represent attractive models for chemosensory studies. Here, we study the marine worm Platynereis dumerilii to provide the first comprehensive study of head chemosensory organ physiology in an annelid. By combining microfluidics and calcium imaging, we record neuronal activity in the entire head of early juveniles upon chemical stimulation. We find that Platynereis uses four types of organs to detect stimuli such as alcohols, esters, amino acids and sugars. Antennae, but not nuchal organs or palps as generally hypothesised in annelids, are the main chemosensory organs. We report chemically-evoked activity in possible downstream brain regions including the mushroom bodies, which are anatomically and molecularly similar to insect mushroom bodies. We conclude that chemosensation is a major sensory modality for marine annelids, and propose early Platynereis juveniles as a model to study annelid chemosensory systems.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC=\"FIGDIR/small/391920_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (74K):\norg.highwire.dtl.DTLVardef@4384corg.highwire.dtl.DTLVardef@10c2563org.highwire.dtl.DTLVardef@6a8a32org.highwire.dtl.DTLVardef@96f06c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

Systematic analysis of the molecular architecture of endocytosis reveals a nanoscale actin nucleation template that drives efficient vesicle formation

Clathrin-mediated endocytosis is an essential cellular function in all eukaryotes that is driven by a self-assembled macromolecular machine of over 50 different proteins in tens to hundreds of copies. How these proteins are organized to produce endocytic vesicles with high precision and efficiency is not understood. Here, we developed high-throughput superresolution microscopy to reconstruct the nanoscale structural organization of 23 endocytic proteins from over 100,000 endocytic sites in yeast. We found that proteins assemble by radially-ordered recruitment according to function. WASP family proteins form a circular nano-scale template on the membrane to spatially control actin nucleation during vesicle formation. Mathematical modeling of actin polymerization showed that this WASP nano-template creates sufficient force for membrane invagination and substantially increases the efficiency of endocytosis. Such nanoscale pre-patterning of actin nucleation may represent a general design principle for directional force generation in membrane remodeling processes such as during cell migration and division.

cell biology↗