Biology subjects

Weber, B.

Publications and source records attributed to Weber, B..

At least 19 recordsLinked to original sources

bioRxiv2026

PURELIGHT: a quantitative photon-counting framework unifying intensity and lifetime imaging at video rate across detector technologies

Quantitative fluorescence microscopy requires photon-efficiency, speed and accurate intensity and lifetime measurements. Time-correlated single-photon counting (TCSPC) simultaneously captures intensity and lifetime, but photon pile-up distorts both signals at high count rates, preventing fast acquisitions. Existing corrections discard photons, distort intensity, or require specialized detectors. Here we introduce PURELIGHT, an integrated hardware and software framework that simultaneously recovers undistorted intensities and lifetimes at count rates far beyond conventional pile-up limits. PURELIGHT works with hybrid photodetectors, silicon photomultipliers and photomultiplier tubes while retaining over three times more photons than alternative approaches. Using two-photon imaging, we showcase PURELIGHT's superior accuracy and spatial contrast, demonstrating video-rate subcellular lifetime imaging in awake mice, a unique lifetime-calibrated ratiometric modality and crosstalk-free temporal multiplexing. By removing the limits that have confined TCSPC to low-signal applications, PURELIGHT promotes the adoption of quantitative, photon-efficient microscopy across the life sciences.

neuroscience↗

bioRxiv2026

A longitudinal two-photon imaging platform for focal astrocyte ablation in vivo

Investigating the consequences of astrocyte loss in the intact brain is both important and challenging. As integral components of the neuro-glia-vascular unit, astrocytes are involved in a variety of brain processes including water homeostasis, metabolic supply, regulation of cerebral blood flow, and coordination of neuronal circuit activity. Astrocyte impairment has been associated with numerous neurological disorders. However, experimental models combining focal astrocyte ablation with longitudinal in vivo imaging in the intact adult brain have been lacking, limiting efforts to define the causal contribution of astrocyte loss to central nervous system (CNS) pathology and repair. Here, we present an in vivo model of antibody-mediated astrocyte ablation that enables longitudinal imaging and detailed investigation of ensuing cellular responses. It integrates focal induction of aquaporin-4 antibody-mediated astrocyte loss, chronic in vivo two-photon imaging, genetically encoded sensors, and reporter mouse lines. This advancement allows visualization and quantification of cellular and subcellular events in living organisms during lesion progression and recovery. It overcomes many longstanding limitations of previous models that are either constrained by non-specific hypoxic or mechanical tissue damage or require sacrificing animals at discrete time points, hindering the ability to monitor dynamic biological processes over time. In contrast, the selective targeting of astrocytes prevents the formation of the glial border, enabling the investigation of CNS response in a scar-free environment. Overall, this new approach represents a significant technical advancement, enabling comprehensive longitudinal studies of CNS responses to astrocyte loss, thus opening new avenues for understanding astrocytopathy-driven pathology, evaluating therapeutic interventions, and promoting translational research.

neuroscience↗

bioRxiv2026

Brain pericytes exhibit spatially organized and dynamically regulated molecular heterogeneity

Brain capillary pericytes are essential components of the neurovascular unit, yet the extent of their molecular heterogeneity within intact vascular networks remains poorly understood. Here, we combined spatial imaging with reanalysis of independent single-cell transcriptomic datasets to investigate the molecular organization of adult mouse brain pericytes. We identified spatial organization of pericyte molecular heterogeneity associated with anatomical region and position within the vascular network, including recurrent differences in ACE2, CASQ2, Igf2, and OPN expression. Moreover, pericyte molecular phenotypes varied with aging, acute ischemia, and circadian phase. Notably, light-dark phase emerged as a major axis of transcriptional variation, with pericytes exhibiting distinct circadian phase-associated molecular states. Together, these data demonstrate that adult brain pericytes exhibit spatially organized and dynamically regulated molecular heterogeneity associated with vascular and physiological context.

neuroscience↗

bioRxiv2026

A recent domestication event in Penicillium biforme, independent of the emblematic cheese mold P. camemberti

Domestication of molds for cheese production has repeatedly shaped Penicillium fungi, most notably giving rise to the emblematic P. camemberti lineage, derived from P. biforme. Here, we identified a new P. biforme lineage, named cheesy, likely selected from P. biforme for food fermentation, including cheese and sausage production. This lineage exhibits evidence of a severe bottleneck, with little nucleotide polymorphism and a single mating type. The cheesy lineage has evolved advantageous traits for cheesemaking: compared to other P. biforme strains and its wild relative P. fuscoglaucum, it displays faster growth on cheese, galactose and lactose media, higher sporulation and germination rates on cheese, elevated lipolytic activity, enhanced inhibition capacities, and produced specific volatile organic compounds. Additionally, P. camemberti and P. biforme cheesy differ in their content of Starship mobile elements, acquired through horizontal transfers. These elements carry cargo genes potentially relevant for adaptation to cheese. Notably, the cheesy lineage has acquired a 20 kb Starship element (Rattus), nested within a much larger 160 kb Starship (Bilge), and carrying cargo genes with predicted functions involved in antagonistic interactions among micro-organisms. SignificanceO_LIWe identified a new Penicillium biforme lineage, named cheesy, which was likely selected from P. biforme for food fermentation (cheese and sausage), genetically and phenotypically different from the emblematic P. camemberti lineage. This lineage suffered from a severe bottleneck, displaying very little nucleotide polymorphism and a single mating type. C_LIO_LIThis newly identified lineage has evolved advantageous traits for cheesemaking; compared to other P. biforme strains and its wild relative P. fuscoglaucum, it displayed faster growth on cheese, galactose and lactose media, higher sporulation and germination rates on cheese, higher lipolytic activity, better inhibition capacities and specific volatile organic compounds. C_LIO_LIPenicillium camemberti and P. biforme cheesy also differed by their content in Starship mobile elements, acquired through horizontal transfers, and carrying cargo genes potentially relevant for adaptation to cheese. C_LIO_LINotably, the cheesy lineage has acquired a specific 20 kb Starship nested within a much larger 160 kb Starship, and likely involved in antagonistic interactions. C_LI

evolutionary biology↗

bioRxiv2026

Opportunistic neuronal fuelling

Neurons can utilize either glucose or lactate, yet fuel selection during periods of activity remains unresolved. By combining optical monitoring of cytosolic pyruvate and NADH with mathematical modelling, we systematically evaluated mitochondrial fuelling in cultured neurons and acute brain slices. Under substrate concentrations typical of resting brain tissue, neurons rely almost exclusively on glucose, with a minor contribution from pyruvate. However, when extracellular lactate rises to levels mimicking tissue activity, glycolysis is inhibited and lactate becomes a major substrate, irrespective of ongoing neuronal activity. Ultimately, neuronal fuel selection is dictated not by internal energy demand, but by extracellular lactate availability, which fluctuates with local glial metabolism and systemic states such as exercise. These findings redefine our understanding of short-term metabolic flexibility in the brain and underscore the significant yet understudied role of extracellular pyruvate.

physiology↗

bioRxiv2026

Developmental Trajectory of Synaptic Remodeling in the Mouse Prefrontal Cortex

The prefrontal cortex (PFC) is a heteromodal association area critical for higher-order cognitive functions. Its protracted maturation extends through adolescence into early adulthood, a period characterized by extensive remodeling of neuronal networks and synaptic architecture. This heightened plasticity supports the refinement of prefrontal circuits necessary to meet the evolving cognitive and behavioral demands of this developmental transition. However, the extended maturation window also increases vulnerability to environmental perturbations, which can lead to lasting synaptic and cognitive impairments. Despite widespread use of developmental disruption models during adolescence, a systematic characterization of synaptic dynamics during normal PFC maturation is lacking. Here, we combined longitudinal in vivo two-photon imaging of dendritic spines with cross-sectional quantification of excitatory and inhibitory synapses, and microglia-mediated synaptic engulfment, in mice from juvenile to adult stages. This integrated approach provides a comprehensive reference atlas of normal prefrontal synaptic maturation, offering a framework for interpreting alterations to synapses in models of developmental disturbance.

neuroscience↗

bioRxiv2026

Adolescent Astrocyte Dysregulation Impairs Prefrontal Interneuron Maturation and Adult Cognition

The prefrontal cortex (PFC), a brain region critical for executive and cognitive functions, is characterized by its protracted maturation extending through adolescence until early adulthood. During adolescence, the PFC undergoes substantial rearrangements, creating a window of heightened plasticity allowing experience-dependent refinement of neural networks. While this extended plasticity supports the development of higher-order cognitive functions, it also confers increased vulnerability to environmental and biological perturbations that can disrupt circuit development and contribute to cognitive and behavioral impairments relevant to psychiatric disorders. Astrocytes are central regulators of brain homeostasis and actively participate in developmental processes that shape postnatal brain maturation. Although astrocyte dysfunction has been increasingly linked to psychiatric pathophysiology, it remains unknown whether aberrant astrocyte activity can directly influence PFC development and cognitive maturation. Here, using selective modulation of astrocyte activity during defined developmental windows in the PFC, we show that abnormal astrocyte activity during adolescence induces transient synaptic loss through enhanced microglial phagocytosis, produces long-lasting alterations in fast-spiking parvalbumin (PV) interneurons, and results in persistent deficits in PFC-dependent behaviors. Together, these findings provide causal evidence that disrupted astrocyte function during adolescent PFC maturation can lead to persistent neuronal and cognitive deficits with relevance to major psychiatric disorders.

neuroscience↗

bioRxiv2026

Common, species-specific, and accession-specific responses of foliar phytohormones and morphological traits to drought and herbivory

BackgroundPlants are exposed to various environmental challenges. With ongoing climate change, droughts and insect outbreaks are expected to become more frequent. Thus, a better understanding is needed of how different plant species respond to such single and combined challenges. This study investigated common versus species-specific responses to environmental challenges in three perennial plant species of different growth forms and whether responses differ intraspecifically among accessions. Clones of different accessions of the herbaceous species Tanacetum vulgare, the woody vine Solanum dulcamara, and the tree Populus nigra were subjected to similar control, herbivory, drought, and combined (drought and herbivory) treatments for the same periods. After the exposure, concentrations of foliar phytohormones and various morphological traits were measured. ResultsAcross all species, several foliar phytohormones and one of ten morphological traits responded consistently to the environmental challenges. Jasmonoyl-isoleucine was induced by herbivory and the combined treatment, abscisic acid (ABA) by drought and the combined treatment, and indole acetic acid by the combined treatment in all species. Root mass remained unchanged in all species. However, structural equation models (SEMs) revealed a shared regulatory pathway across species in which ABA connected treatment and root mass, indicating a common hormonal response potentially linking challenges to growth responses. Despite these common patterns, species-specific responses were pronounced. In P. nigra, a unique induction of salicylic acid was found under the combined treatment, while aboveground mass and root-shoot ratio remained unaffected by any treatment, in contrast to the other two species. Species-specific SEMs further indicated distinct phytohormone-mediated pathways underlying morphological variation. Phenotypic plasticity reflected these species-specific patterns, with none of the phytohormones or morphological traits exhibiting uniform plasticity across species. Intraspecific variation further shaped responses, as phytohormone and morphological trait plasticity depended on accession, indicating substantial accession-specific plant responses. ConclusionsOur results indicate that some responses to comparable challenges may be conserved across species, while others are species-specific. The combined treatment elicited the most pronounced responses, and such complex responses may become more frequent under current global change. Our study highlights that comprehensive understanding of plant responses requires systematic comparisons at both interspecific and intraspecific scales.

ecology↗

bioRxiv2026

Latitudinal diversity gradients and selective microbialexchange at the Atlantic ocean-air interface

Microbial communities at the ocean-atmosphere interface play a vital role in nutrient, aerosol, and water cycling, yet their large-scale biogeography remains scarcely studied. Here we assessed microbial cell abundance and community structure in air and surface ocean samples along a 14,400 km transect from the polar circle to the equator. Air and surface ocean microbiomes were taxonomically distinct across the North East Atlantic. The microbiome in the air had a lower local community richness compared to the surface ocean, yet was more diverse across larger geographical scales. Our results suggest that terrestrial-derived air masses affected air and surface ocean communities. Air microbial communities showed a latitudinal diversity gradient with richness and cell abundance increasing from the polar circle to the equator. We observed an exchange of microbial lineages between ocean and air, however, most lineages were confined to one realm, suggesting lineage-selective aerosolization and deposition of microbial cells.

microbiology↗

bioRxiv2026

Streak-Aware Localization Microscopy Enables High-Throughput Brain Imaging Across Platforms

Optical, ultrasound, and optoacoustic localization microscopy based on microparticle tracking has enabled surpassing the resolution limits imposed by ultrasound diffraction and optical diffusion in tissues. However, its reliance on high-speed (kilohertz) data acquisition systems for precise emitter localization and tracking substantially increases methodological complexity and data storage demands, limiting scalability and applicability beyond specialized benchtop platforms. Here, we present streak-aware localization microscopy (SALM) that employs localization- and tracking-free deep learning model to convert motion-blurred streaks originating from low frame rate recordings of flowing emitters into super-resolved structural and functional readouts. In optical implementations, SALM exploits streaks captured by low-speed cameras to recover capillary-level cerebrovascular maps across a variety of benchtop, miniaturized, and second near-infrared preclinical imaging platforms, achieving over 30-fold reduction in the reconstruction time compared to conventional localization pipelines. We further introduce three coded excitation strategies that embed finer time-varying vectorial flow signatures into individual streaks, enabling single-frame velocimetry and video-rate hemodynamic imaging. Extending SALM to ultrasound imaging enables high-fidelity vascular imaging with centimeter-scale penetration in rhesus macaque and rat brains while reducing plane-wave compounding frame rates by up to one order of magnitude. By overcoming long-standing trade-offs between spatiotemporal resolution and hardware complexity, SALM offers a flexible and scalable framework for next-generation super-resolution microscopy.

neuroscience↗

bioRxiv2026

Photoreceptors have a dual dependency on both aerobic glycolysis and OXPHOS and diverge metabolically from other retinal neurons

The retina metabolizes glucose into lactate, a hallmark of aerobic glycolysis known as the Warburg effect. Although evidence points to rod photoreceptors as the primary source of aerobic glycolysis, a comparison of the energy metabolism in different retinal neurons has yet to be performed. We combined two-photon fluorescence lifetime imaging of biosensors with pharmacological protocols to analyse metabolic dynamics in healthy and diseased photoreceptors and in inner retinal neurons. Our data reveal distinct metabolic profiles among retinal neurons, identify rods as the drivers of aerobic glycolysis, demonstrate that inner retinal neurons rely on oxidative phosphorylation, show that rods need both glycolysis and oxidative phosphorylation to maintain ATP levels, and suggest that rods can metabolize lactate. A mutation causing retinitis pigmentosa increases lactate production in rods but changes the energy metabolism only subtly otherwise. Our results improve the understanding of retinal physiology and are relevant for pathologies involving imbalanced energy metabolism.

neuroscience↗

bioRxiv2026

Reprogrammed neutrophils with impaired transit mechanics drive multi-organ capillary stalling after stroke

Beyond the focal brain lesion, stroke causes systemic complications including cardiac failure, pneumonia, renal injury, and sustained immune dysfunction. The source of this multiorgan vulnerability remains unresolved. By imaging over 16,000 vessels of healthy, inflamed and ischemic brains, we identify a circulating neutrophil subpopulation reprogrammed by stroke into a pathological stalling phenotype, occluding capillaries in the brain, heart, kidneys, retina and lungs. Combining transcriptomics, genetic models, integrated microfluidics, cell mechanics assays, and in vivo imaging, we show that this subpopulation exhibits an atypical morphology, increased actin polymerization, and heightened adhesion that impair transit through capillary networks. This phenotype is present in patients with stroke, transmissible by adoptive transfer, and selectively sensitive to inhibition of the Src-family kinase Fgr. Both pharmacological and genetic inactivation of Fgr normalize neutrophil adhesion, reduce capillary stalls, and improve neurological recovery after stroke. These findings identify immune cell transit failure as a systemic driver of post-stroke pathology and a therapeutic target to improve both cerebral and multiorgan outcomes.

neuroscience↗

bioRxiv2026

Dryland soil rewetting induces strong VOC emissions with potential to form ozone and aerosols

Biogenic volatile organic compounds (VOCs) significantly influence atmospheric chemistry, yet the importance of microbial VOC emissions remains understudied. We investigate petrichor VOC emissions, the characteristic scent following rainfall after prolonged drought, in an aridity gradient across Israel, by simulating soil rewetting events. Rewetting triggered strong VOC fluxes (1-3.5 nmol m-2 s-1 ground area) dominated by sesquiterpenes and benzenoids, with emission patterns linked to climatic regions, soil aridity, and microbial community composition. Petrichor consisted of a complex bouquet of 58 VOCs, and the initial VOC burst resembled the CO2 pulse of the Birch effect. Petrichor emissions showed ozone and secondary organic aerosol formation potentials comparable in magnitude to those estimated for anthropogenic VOC sources in Israel. Despite compositional differences, emissions were of similar magnitudes across the aridity gradient. Given that drylands cover nearly half of Earths terrestrial surface and are expanding, these episodic microbial VOC emissions may represent a significant, previously overlooked source of reactive carbon with potential implications for regional and global atmospheric chemistry.

microbiology↗

bioRxiv2025

Pial collaterals propagate neurovascular responses across functional units

Neurovascular coupling refers to the regulation of cerebral blood flow in response to neuronal activity, a process forming the basis for multiple functional neuroimaging techniques. However, the mechanisms that coordinate neurovascular responses across distinct cortical arterial territories remain poorly understood. Here we show that pial collaterals, arterio-arterial connections traditionally considered dormant under physiological conditions, serve as active conduits that propagate neurovascular signals between adjacent cortical territories and functional units. We demonstrate that neuronal activity in the somatosensory cortex triggers direct vascular signaling via endothelial Kir2.1 channels through pial collaterals, synchronizing blood flow responses beyond the activated area. The loss of pial collaterals abolished inter-territorial coupling without affecting local neurovascular responses. These results reveal that pial collaterals are critical regulators of cerebral perfusion.

neuroscience↗

bioRxiv2025

Compartmentalized above- and belowground defenses in Tanacetum vulgare are tailored to localized antagonists

Specialized metabolites, specially terpenoids, play a key role in plant defense. However, how terpenoid diversity governs inducible chemistry and root architectural development remain poorly understood. We used a combination of high-throughput root phenotyping and targeted metabolite profiling to examine three leaf terpenoid chemotypes of common tansy (Tanacetum vulgare). Using a phenotyping platform, we tested whether (i) root-chewing wireworms induce root terpenoids locally and alter shoot terpenoids systemically, (ii) phloem-feeding aphids elicit chemotype-dependent responses, and (iii) chemotypes differ in root-system development. After root establishment, the plants were exposed to wireworms (Agriotes spp.) and aphids (Macrosiphoniella tanacetaria), both separately and together, and were then monitored for 60 days. The chemotypes differed in inducible chemistry and root architecture. Chemotype 1 developed the fastest-growing root systems and the highest root:shoot ratios. Wireworms increased stored root sesquiterpenoid levels by more than twofold in chemotypes 1 and 2, whereas chemotype 3 was largely unresponsive. Aphids didn t alter root terpenoids, but significantly increased leaf monoterpenoid emissions in chemotype 1 without affecting stored pools. Therefore, storage and emission were decoupled and depended on both organ and chemotype. Our analysis reveals a compartmentalized, chemotype-specific defense strategy in tansy, highlighting the coordinated regulation of the root system and inducible chemistry. HighlightIn Tanacetum vulgare, wireworms boost root sesquiterpenoids and aphids elevate leaf monoterpenoid emissions; chemotype governs terpenoid defense and root system architecture.

plant biology↗

bioRxiv2025

Volatile cues from pathogenic, mutualistic and saprotrophic fungi cause specific, fungus-dependent responses in poplar

Plants are exposed to complex interactions with belowground organisms, yet how they differentiate between mutualistic and pathogenic fungi before physical contact remains largely unknown. We exposed the roots of young Populus x canescens to volatile organic compounds (VOCs) emitted by either a pathogenic (Heterobasidion annosum), a saprotrophic (Postia placenta), or an ectomycorrhizal (Laccaria bicolor) fungus. VOC analysis of the shared rhizosphere headspace and leaf emissions revealed that poplar plants could perceive and respond to fungal identity solely through airborne cues. The root-zone headspace contained fungus-specific sesquiterpene fingerprints that remained similar after three and six weeks of co-cultivation: Pathogen-derived VOCs induced constant high sesquiterpene emissions from the root-zone, whereas mycorrhiza caused low but targeted emissions of specific sesquiterpenes. In contrast, saprotrophic VOCs caused a temporal shift in root-zone VOC pattern, with increased sesquiterpene emissions after six weeks. Fungal VOC exposure also altered leaf VOC emissions, enriching alkanes, esters and monoterpenes. Initially, leaf VOC emissions were fungal lifestyle-specific but they converged over time, indicating systemic signal integration of belowground signals. These findings demonstrate that trees can discriminate "friend-versus-foe" through VOCs alone, extending pattern-recognition theory beyond contact-dependent cues. Multivariate analyses suggested organ-specific chemical strategies: roots function as chemosensors decoding fungal volatilomes, while systemic adjustments shape aboveground VOC profiles. Understanding the plant response to fungal VOCs may offer potential for developing early pathogen diagnostics and further elucidate the volatile-mediated plant-fungal interactions.

plant biology↗

bioRxiv2025

Lipid monolayers adsorbing mRNA as models for mRNA enclosed in lipid nanoparticles for transfection

In lipid-based mRNA pharmaceuticals applicable for vaccination, cancer therapy, and other types of therapeutics, the negatively charged RNA is embedded in nanoparticles containing positively charged or ionizable lipids. The local cohesion at the lipid-RNA interface plays an important role for the stability and biological activity of the resulting nanoparticles. Ions and other buffer components in the RNAs immediate surroundings may affect RNA stability against hydrolysis and its binding strength to the oppositely charged lipid layers, which is relevant for release after cellular uptake and endosomal processing. Here, we use Langmuir monolayers at the air/water interface as well-defined experimental models to study the local molecular organization of mRNA adsorbed to lipid layers. Binding of mRNA in the presence of monovalent and divalent ions from the aqueous phase to monolayers consisting of cationic transfection lipids and zwitterionic phospholipids is investigated with synchrotron-based x-ray fluorescence and scattering techniques. The experiments provide detailed insights into the structure of the adsorbed layers as well as the fractions of all molecular moieties contributing to the interfacial electrostatic balance, specifically phosphates from RNA, phosphates from phospholipids in the monolayer, and elemental counterions. The mRNA forms discrete electron-dense layers tightly bound to the lipid membrane, where cationic ions accumulate at the interface together with the mRNA. This leads to an excess of anionic nucleotides relative to cationic lipids at the interface, which is more pronounced in the presence of divalent compared to monovalent cations. The quantitative information on local interfacial moieties obtained here may constitute a valuable basis for the evaluation of quality aspects of nanoparticles comprising mRNA in the bulk phase.

biophysics↗

bioRxiv2025

In Vivo Network-Level Cerebrovascular Mapping Reveals the Impact of Flow Topology on Capillary Stalls After Stroke

Cerebral microvasculature is essential for brain function, but how flow and large-scale connectivity contribute to its resilience or failure remains poorly understood. To address this, we developed OMNIMap, a framework for mesoscale in vivo mapping of functional microvascular networks, capturing flow dynamics and connectivity across thousands of capillaries. OMNIMap integrates extended-focus optical coherence microscopy and learning-based segmentation with global vessel-graph optimization to resolve artery-vein classification and branching order, linking capillary flow and stalls to broader network context. Applied to over 40,000 capillaries in the mouse cortex before and after ischemic stroke, we observe heterogeneous vulnerability patterns: while most capillaries stall or reduce flow after arterial occlusion, some experience accelerated flow. Further analysis revealed that stall-prone flow topology subtypes were less prevalent than their robust counterparts. Notably, the overall distribution of these subtypes remains largely preserved after stroke, revealing a previously unrecognized, system-level organizing principle that alleviates the impact of individual capillary stalls to maintain network-level perfusion.

neuroscience↗