Biology subjects

Prevedel, R.

Publications and source records attributed to Prevedel, R..

At least 19 recordsLinked to original sources

bioRxiv2026

A mobile optical coherence microscope for studying aquatic organisms in- and outside the laboratory

High-resolution, three-dimensional imaging of live organisms has largely depended on laboratory-bound microscopes, limiting quantitative analysis of morphology and dynamics to species that survive transport and thrive under lab-controlled conditions. Here we present a mobile optical coherence microscopy (OCM) platform that overcomes this constraint, delivering [~]2.5 {micro}m axial resolution, label-free, volumetric imaging of live aquatic organisms in both laboratory and remote field environments. We demonstrate the platform across a broad range of aquatic organisms from the lab and field, spanning multiple phyla - including cnidarians, poriferans, annelids, arthropods and echinoderms - resolving internal anatomy, tissue boundaries and organismal morphology at micrometer scale without fixation, fluorescent labeling, or specialized sample preparation. High-speed acquisition, with up to 250 kHz A-line rate and 7.7 Hz volume rate, further enabled morphodynamic imaging of live biological processes, including cellular aggregate motility, embryonic cell division, and organ-level peristaltic dynamics in intact, living animals. To demonstrate field deployability, the platform was operated during the EMBL TREC pan-European expedition, enabling on-site, label-free imaging of marine organisms and plankton immediately upon collection. By decoupling high-resolution volumetric imaging from fixed laboratory settings, mobile OCM opens a path toward field-ready quantitative morphological and dynamic phenotyping of aquatic life.

bioengineering↗

bioRxiv2026

An ancient monoaminergic signaling system coordinates contractility in a nerveless sponge

Chemical neurotransmission was a key animal innovation, enabling multicellular coordination of physiology and locomotion. Sponges are early-diverging animals that lack neurons and muscles, yet still coordinate contraction and relaxation of their filter-feeding water canals. Here, we show that Spongilla lacustris synthesizes the monoamines tryptamine, phenethylamine, and tyramine to elicit distinct canal behaviors. We identify previously uncharacterized decarboxylases and vesicular transporters coexpressed in secretory neuroid and metabolic cells. Using phosphoproteomics and label-free 3D imaging, we show that tryptamine activates GPCR signaling and Rho GTPases, remodeling adhesion and actomyosin networks in contractile canal epithelia to drive localized constrictions and whole-body deflations. Together, these findings define an ancestral monoaminergic system linking secretory and contractile cell types that predate neurons and was later elaborated for neuromodulation of synaptic transmission.

evolutionary biology↗

bioRxiv2025

Bridging Light and Sound: a Spironaphtopyran-Rhodamine Dyad with High-Contrast Photoswitching Between Fluorescence and Photoacoustic Signal.

Fluorescence and photoacoustic imaging are complementary modalities that provide distinct advantages for biological imaging: fluorescence microscopy offers high sensitivity and resolution, while photoacoustic imaging enables deeper penetration in complex tissue. Leveraging the strengths of both modalities through optically switchable contrast agents can offer enhanced imaging contrast and facilitate dual-modality imaging. Here, we report a photoswitchable probe capable of toggling between high fluorescence and high photoacoustic signal upon illumination, exploiting Forster Resonance Energy Transfer (FRET). We engineer novel spironaphtopyran photoswitches which undergo reversible photoisomerization between absorbing and non-absorbing states. Their photoswitching properties were systematically characterized, establishing structure-properties relationships, and providing the first photoacoustic investigation into this class of compounds. The best-performing switch was incorporated into a FRET dyad with a rhodamine fluorophore, which exhibits robust, reversible switching between fluorescent and photoacoustic-dominant states with excellent contrast in vitro, establishing a foundation for multimodal imaging probes with promising potential for dynamic correlative imaging.

biochemistry↗

bioRxiv2025

Critical phenomenon underlies de novo luminogenesis during mammalian follicle development

A key process during mammalian folliculogenesis is the formation of a fluid-filled antrum around the oocyte. While it is known that the antrum is critical for oocyte maturation and the eventual ovulation, the detailed process underlying de novo luminogenesis remains poorly understood. In this study, we investigated the spatiotemporal dynamics of lumen growth and the cellular mechanism driving this process, using advanced microscopy, molecular perturbations and computational modelling. We found that in secondary follicles, the interstitial gaps exist in a near-critical regime, characterised by a highly dynamic and interconnected fluid network with gap size obeying a power-law distribution. Above a critical size of 180 m, we observed an onset of cell death and the emergence of a stably growing dominant fluid cavity resembling phase separation. By modelling the granulosa cells and the interstitial fluid as a binary fluid, we reproduced the near-critical and phase-separated regimes and found that a spatial gradient of cell-fluid interfacial tension, as observed experimentally, is sufficient to robustly maintain the secondary follicles in a near-critical state. Reducing cell-fluid interfacial tension globally by weakening the cell-cell adhesion between granulosa cells leads to fragmentation of fluid and growth arrest of the dominant cavity, as predicted by the model. Importantly, perturbing the critical state in secondary follicles leads to impaired follicle growth. Altogether, our study reveals how collective spatiotemporal regulation of cell junction mechanics and cell death can contribute to the effective transition between distinct regimes of fluids, which are indispensable for functional maturation of follicles.

developmental biology↗

bioRxiv2025

Centrosome Softening As A Mechanical Adaptation For Mitosis

Centrosomes are microtubule-organizing centers important for mitotic spindle assembly and chromosome segregation. During mitosis, centrosomes are exposed to mechanical forces via the microtubules they nucleate, yet the material properties underlying their response to these forces remain poorly understood. In this study, we systematically probed the mechanical behavior of C. elegans centrosomes, both in vitro and in vivo. Using microtubule perturbations and quantitative live cell imaging, we found that centrosomes become increasingly deformed during mitosis. Centrosome deformation is independent of cortical pulling forces but instead results from microtubule polymerization within the pericentriolar material. This deformation impacts centrosome size: as microtubule number decreases with cell volume in early cleavage divisions, centrosome size scales proportionately. To directly measure centrosome elasticity, we employed atomic force microscopy (AFM) on isolated centrosomes in vitro and Brillouin light scattering microscopy in developing embryos in vivo. Both approaches revealed that centrosomes progressively soften during mitosis. Theoretical modeling predicts that softening serves to dampen spindle force fluctuations, helping to protect kinetochore-microtubule interactions and safeguarding chromosome segregation. Further, softening may enhance centrosomal microtubule nucleation capacity, facilitating mitotic spindle assembly, particularly in large early embryonic cells. We propose that centrosome softening is a mechanical adaptation for mitosis that couples microtubule number to centrosome size through force-dependent deformation. This optimally balances two mitotic requirements: the need for robust microtubule nucleation and the ability to withstand spindle forces, thereby ensuring accurate cell division.

cell biology↗

bioRxiv2025

Column-Like Subnetwork Reconstruction in Motor Cortex from Graph-Based 3D High-Density Two-Photon Calcium Imaging

How precise 3D interactions among cortical neurons underlie layer-specific computations remains elusive. We developed a graph-framework to infer functional connectivity from fast volumetric two-photon Ca2+ imaging in the awake mouse primary motor cortex. By converting deconvolved traces into binary spike trains, removing population bursts, and applying an adaptive, layer-specific statistical threshold, we reconstructed a directed, weighted network of [~]1,000 neurons. Decomposition into strongly connected components revealed [~]10-cell subnetworks, predominantly in layer II/III but often bridging to layer Va. Across six 20-min recordings, we found that (1) layer II/III dominates connectivity, (2) feedback (Va[->]II/III) links are more numerous and stronger than the feed-forward (II/III[->]Va) ones, and (3) information flows in [≤] 6 synapses. We uncovered seven geometrical and dynamical motifs--ranging from compact columns to elongated diagonals--each with characteristic event sizes and durations. These findings reveal diverse, column-like microcircuits in M1 with a net ascending flow, suggesting that such subnetworks form elemental processing modules for motor control.

neuroscience↗

bioRxiv2025

The Cell Wall Controls Stem Cell Fate in the Arabidopsis Shoot Apical Meristem

At the basis of plant developmental plasticity are continuously active pluripotent stem cells, which fuel the life-long post-embryonic formation of new organs. Since plant cells are encased in cell walls and thus immotile, their individual fate-specification program is dependent on their relative position within the organism. It is assumed that the cell wall and its mechanical properties are under surveillance, linking cell wall state to intracellular gene-regulatory networks. However, the role of these cell wall signalling pathways in plant development and the contribution of cell wall properties to cell behaviour and identity are unclear. Here, we show that control of cell wall properties is essential for the perpetuation of stem cell populations and pattering in the shoot apical meristems. The expression of pectin methylesterases (PMEs), which modify homogalacturonan methylesterification and thereby modulate cell wall mechanics, is maintained at low levels in stem cells by the stem cell specifying transcription factor WUS. Low PME expression is required for stemness, auxin patterning and stem cell-specific mechanical properties. Conversely, WUS depletion reduces wall stiffness in the meristem centre, reinforcing its role in maintaining mechanical homeostasis. Together, our findings show that WUS-mediated control of cell wall-modifying enzymes is essential for sustaining stem cell identity and SAM organization. These results demonstrat that the plant cell wall is not only involved in cell differentiation, but also exerts feedback control on developmental transitions, contributing to our understanding how the immediate physical environment is able to guide cell fate decisions in plants.

plant biology↗

bioRxiv2025

Central infusion of prostaglandin E2 reveals a unified representation of sickness in the mouse insular cortex

During infections, vertebrates develop stereotypic symptoms such as elevated body temperature, reduced appetite, and lethargy. These changes, collectively known as sickness syndrome, are orchestrated by the brain in response to immune mediators released during systemic inflammation. While the roles of subcortical regions, including the hypothalamus and brainstem nuclei, in regulating sickness symptoms are well established, the contribution of the neocortex to the encoding and modulation of the sick state remains less well understood. We examined the neuronal correlates of sickness in the neocortex of awake mice following a single intracerebroventricular (i.c.v.) injection of prostaglandin E2 (PGE2), a well-characterized mediator of sickness. Behavioral analysis revealed that PGE2 elicited a rapid and robust sickness response, characterized by fever, slower locomotion, quiescence, anorexia, and eye squinting. Whole-brain Fos mapping showed that PGE2 generates a distinct neural activation pattern encompassing much of the interoceptive network. Electrophysiological recordings using Neuropixel probes in awake mice together with dimensionality reduction and decoding analysis revealed that neuronal population dynamics in the insular cortex (IC) and the primary somatosensory cortex (SSp), two regions involved in body state representation, encode sickness-related information, such as body temperature, walking velocity, grooming, and eye squinting. However, unlike SSp, ongoing neuronal activity in IC exhibited a better decoding performance for an integrated measure of sickness rather than individual symptoms. Together, these results suggest that PGE2 induces a coordinated physiological and behavioral response akin to a sick state, which is preferentially encoded in the IC.

neuroscience↗

bioRxiv2024

Highly dynamic mechanical transitions in embryonic cell populations during Drosophila gastrulation

During animal development, the acquisition of three-dimensional morphology is a direct consequence of the dynamic interaction between cellular forces and the mechanical properties of cells and their environment. While the generation and transmission of cellular forces has been widely explored, less is known about the dynamic changes in cell mechanical properties during morphogenesis. Here, we characterise and spatially map in three dimensions the dynamics of cell mechanical properties during Drosophila gastrulation utilising line-scan Brillouin microscopy. We find that cells in the embryo undergo rapid and spatially varying changes in their mechanical properties and that these differ in cell populations with different fates and behaviours. We identify microtubules as potential effectors of cell mechanics in this system, and corroborate our experimental findings with a physical model that underscores the role of localised and dynamic changes in mechanical properties to facilitate tissue folding. Our work provides the first spatio-temporal description of the evolving mechanical properties of cell populations during morphogenesis, and highlights the potential of Brillouin microscopy in studying the dynamic changes in cell shape behaviours and cell mechanical properties simultaneously in different cell populations in an intact organism.

biophysics↗

bioRxiv2024

Chemigenetic far-red labels and Ca2+ indicators optimized for photoacoustic imaging.

Photoacoustic imaging is an emerging modality with significant promise for biomedical applications such as neuroimaging, owing to its capability to capture large fields of view, deep inside complex scattering tissue. However, the widespread adoption of this technique has been hindered by a lack of suitable molecular reporters for this modality. In this work, we introduce chemigenetic labels and calcium sensors specifically tailored for photoacoustic imaging, using a combination of synthetic dyes and HaloTag-based self-labelling proteins. We rationally design and engineer far-red "acoustogenic" dyes, showing high photoacoustic turn-ons upon binding to HaloTag, and develop a suite of tunable calcium indicators based on these scaffolds. These first-generation photoacoustic reporters show excellent performance in tissue-mimicking phantoms, with the best variants outperforming existing sensors in terms of signal intensity, sensitivity and photostability. We demonstrate the application of these ligands for labelling HaloTag-expressing neurons in mouse brain tissue, producing strong, specifically targeted photoacoustic signal, and provide a first example of in vivo labelling with these chemigenetic photoacoustic probes. Together, this work establishes a new approach for the design of photoacoustic reporters, paving the way towards deep tissue functional imaging.

biochemistry↗

bioRxiv2023

An interplay of HSP-proteostasis, biomechanics and ECM-cell junctions ensures C. elegans astroglial architecture

Tissue integrity is sensitive to temperature, tension, age and is sustained throughout life by adaptive cell-autonomous or extrinsic mechanisms. Safeguarding the remarkably-complex architectures of neurons and glia ensures age-dependent, functional circuit integrity. Here we report mechanisms sustaining integrity of the C. elegans astrocyte-like CEPsh glia. We combine large-scale genetics with manipulation of genes, cells, and their environment, with quantitative imaging of cellular, subcellular features and material properties of tissues and extracellular matrix (ECM). We identify mutants with age-progressive, environment-dependent defects in glial architecture, consequent disruption of axons, synapses, and aging. Functional loss of epithelial Hsp70/Hsc70-cochaperone BAG2 causes ECM disruption, altered animal biomechanics, and hypersensitivity of glial cells to environmental temperature and mechanics. Glial-cell junctions ensure ECM-CEPsh glia-epithelia association. Modifying glial junctions or ECM mechanics safeguards glial integrity against disrupted BAG2-proteostasis. Overall, we present a finely-regulated interplay of proteostasis-ECM and cell junctions with conserved components that ensures age-progressively the robustness of glial architecture.

cell biology↗

bioRxiv2023

Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response

A hallmark of animals is the coordination of whole-body movement. Neurons and muscles are central to this, yet coordinated movements also exist in sponges that lack these cell types. Sponges are sessile animals with a complex canal system for filter-feeding. They undergo whole-body movements resembling "contractions" that lead to canal closure and water expulsion. Here, we combine 3D optical coherence microscopy, pharmacology, and functional proteomics to elucidate anatomy, molecular physiology, and control of these movements. We find them driven by the relaxation of actomyosin stress fibers in epithelial canal cells, which leads to whole-body deflation via collapse of the incurrent and expansion of the excurrent system, controlled by an Akt/NO/PKG/A pathway. A concomitant increase in reactive oxygen species and secretion of proteinases and cytokines indicate an inflammation-like state reminiscent of vascular endothelial cells experiencing oscillatory shear stress. This suggests an ancient relaxant-inflammatory response of perturbed fluid-carrying systems in animals. HighlightsO_LISponge deflation is driven by tension release in actomyosin stress fibers of epithelial pinacocytes C_LIO_LIAkt kinase/Nitric oxide/Protein kinase G/A regulate actomyosin relaxation C_LIO_LIAgitation-induced deflation coincides with an inflammatory state C_LIO_LIThe sponge relaxant-inflammatory response is evolutionary related to similar responses in the vertebrate vascular system C_LI

molecular biology↗

bioRxiv2023

Deep intravital brain tumor imaging enabled by tailored three-photon microscopy and analysis

Intravital two-photon microscopy has emerged as a powerful technology to study brain tumor biology and its temporal dynamics, including invasion, proliferation and therapeutic resistance in the superficial layers of the mouse cortex. However, intravital microscopy of deeper cortical layers and especially the subcortical white matter, an important route of glioblastoma invasion and recurrence, has not yet been feasible due to low signal-to-noise ratios, missing spatiotemporal resolution and the inability to delineate myelinated axonal tracts. Here, we present a tailored intravital microscopy and artificial intelligence-based analysis methodology and workflow that enables routine deep imaging of glioblastoma over extended time periods, named Deep3P. We show that three-photon microscopy, adaptive optics, as well as customized deep learning-based denoising and machine learning segmentation together allow for deep brain intravital investigation of tumor biology up to 1.2 mm depth. Leveraging this approach, we find that perivascular invasion is a preferred invasion route into the corpus callosum as compared to intracortical glioblastoma invasion and uncover two vascular mechanisms of glioblastoma migration in the white matter. Furthermore, we can define an imaging biomarker of white matter disruption during early glioblastoma colonization. Taken together, Deep3P allows for an efficient and non-invasive investigation of brain tumor biology and its tumor microenvironment in unprecedented deep white and gray matter of the living mouse, opening up novel opportunities for studying the neuroscience of brain tumors and other model systems.

cancer biology↗

bioRxiv2023

Thermogenetic control of Ca2+ levels in cells and tissues

Virtually all major processes in cells and tissues are regulated by calcium ions (Ca2+). Understanding the influence of Ca2+ on cell function requires technologies that allow for non-invasive manipulation of intracellular calcium levels including the formation of calcium patterns, ideally in a way that is expandable to intact organisms. The currently existing tools for optical and optogenetic Ca2+ manipulation are limited with respect to response time, and tissue penetration depth. Here we present Genetically Encoded Calcium Controller (GECCO), a system for thermogenetic Ca2+ manipulation based on snake TRP channels optically controlled by infrared illumination. GECCO is functional in animal and plant cells and allows studying how cells decode different profiles of Ca2+ signals. GECCO enabled the shaping of insulin release from {beta}-cells, the identification of drugs that potentiate Ca2+-induced insulin release, and the generation of synthetic Ca2+ signatures in plants.

synthetic biology↗

bioRxiv2022

Pulsed stimulated Brillouin microscopy enables high-sensitivity mechanical imaging of live and fragile biological specimens

Brillouin microscopy is an emerging optical elastography technique capable of assessing mechanical properties of biological samples in a 3D, all-optical and hence non-contact fashion. The typically weak Brillouin scattering signal can be substantially enhanced via a stimulated photon-phonon process, which improves the signal-to-background ratio (SBR) as well as provides higher spectral resolution. However, current implementations of stimulated Brillouin spectroscopy (SBS) require high pump powers, which prohibit applications in many areas of biology, especially when studying photosensitive samples, or when live-imaging in 3D and/or over extended time periods. Here, we present a pulsed SBS scheme that takes full advantage of the non-linearity of the pump-probe interaction in SBS. In particular, we show that through quasi-pulsing and diligent optimization of signal detection parameters, the required pump laser power can be decreased ~20-fold without affecting the signal levels or spectral precision. Moreover, we devise a custom analysis approach that facilitates the analysis of complex, multi-peaked Brillouin spectra in order to harness the high spectral resolution of SBS for the specific identification of biomechanical components inside the point-spread function of the microscope. We then demonstrate the low-phototoxicity and high-specificity of our pulsed SBS approach by imaging sensitive single cells, zebrafish larvae, and mouse embryos as well as adult C. elegans with sub-cellular detail. Furthermore, our method permits observing the mechanics of organoids and C. elegans embryos over time. We expect that the substantially lower photo-burden and improved SBR of pulsed SBS will facilitate studying biomechanics in 3D at high spatio-temporal resolution in living biological specimens in a non-invasive manner, opening up exciting new possibilities for the field of mechanobiology.

bioengineering↗

bioRxiv2022

Effective sound localization coding by noisy populations of mouse inferior colliculus neurons revealed by fast volumetric imaging

Sound location coding has been extensively studied at the central nucleus of the mammalian inferior colliculus (CNIC), supporting a population code. However, this population code has not been extensively characterized on the single-trial level with simultaneous recordings or at other anatomical regions like the dorsal cortex of inferior colliculus (DCIC), which is relevant for learning-induced experience dependent plasticity. To address these knowledge gaps, here we made in two complementary ways large-scale recordings of DCIC populations from awake mice in response to sounds delivered from 13 different frontal horizontal locations (azimuths): volumetric two-photon calcium imaging with [~]700 cells simultaneously recorded at a relatively low temporal resolution, and high-density single-unit extracellular recordings with [~]20 cells simultaneously recorded at a high temporal resolution. Independent of the method, the recorded DCIC population responses revealed substantial trial-to-trial variation (neuronal noise) which was significantly correlated across pairs of neurons (noise correlations) in the passively listening condition. Nevertheless, decoding analysis supported that these noisy response patterns encode sound location on the single-trial basis, reaching errors that match the discrimination ability of mice. The detected noise correlations contributed to minimize the error of the DCIC population code of sound azimuth. Altogether these findings point out that DCIC can encode sound location in a similar format to what has been proposed for CNIC, opening exciting questions about how noise correlations could shape this code in the context of cortico-collicular input and experience dependent plasticity.

neuroscience↗

bioRxiv2022

An oblique plane microscope for mesoscopic imaging of freely moving organisms with cellular resolution

Several important questions in biology require non-invasive and three-dimensional imaging techniques with appropriate spatiotemporal resolution that permit live organisms to move in an unconstrained fashion over an extended field-of-view. While selective-plane illumination microscopy (SPIM) has emerged as a powerful method to observe live biological specimens at high spatio-temporal resolution, typical implementations often necessitate constraining sample mounting or lack the required volumetric speed. Here, we report on an open-top, dual-objective oblique plane microscope (OPM) capable of observing millimeter sized, freely moving animals at cellular resolution. We demonstrate the capabilities of our mesoscopic OPM (MesOPM) by imaging the behavioural dynamics of the sea anemone Nematostella vectensis over 1.56 x 1.56 x 0.25 mm at 1.5 x 2.8 x 5.3{micro}m resolution and 0.5Hz volume rate.

bioengineering↗

bioRxiv2022

High-resolution line-scan Brillouin microscopy for live-imaging of mechanical properties during embryo development

Brillouin microscopy (BM) can be used to assess the mechanical properties of biological samples in a 3D, all-optical, and hence non-contact fashion, but its weak signals require long imaging times and illumination dosages harmful to living organisms. Here, we present a line-scanning Brillouin microscope optimized for fast and high-resolution live-imaging of dynamic biological processes with low photo-toxicity. In combination with fluorescence light-sheet imaging, we demonstrate the capabilities of our microscope to visualize the mechanical properties of cells and tissues over space and time in living model organisms such as fruit flies, ascidians, and mouse embryos.

bioengineering↗