Single-molecule localization microscopy (SMLM) enables volumetric nanoscopy by retrieving 3D molecular positions from engineered 2D fluorescence patterns. However, achieving nanoscale resolution over large axial ranges in complex samples remains challenging due to optical aberrations and overlapping signals from high-density molecules. Here, we introduce LUNAR, a self-supervised neural-physics framework that overcomes those limitations by jointly optimizing a physical imaging model and a deep neural network. This strategy allows LUNAR to precisely infer 3D molecular positions, photon counts, and aberrations directly from raw, high-density data without prior calibration. Through simulations and experiments, we demonstrate that LUNAR achieves superior robustness and accuracy across diverse imaging conditions, consistently outperforming existing methods. We showcase its capabilities through whole-cell nanoscopy of mitochondria, nuclear pores, and neuronal cytoskeletons at large imaging depths. By uniting deep learning with physical modeling, LUNAR provides a calibration-free solution for aberration-robust 3D SMLM and establishes a general framework for adaptive, data-driven microscopy.

Submerged cultures of undifferentiated or transformed epithelial cells are widely used in respiratory research due to their ease of use and scalability. However, these systems fail to capture the cellular diversity of the human airway epithelium. Here, we describe a submerged differentiation model using cryopreserved human nasal epithelial cells obtained via minimally invasive brushings. By targeting Notch and BMP signaling with small molecule inhibitors, we differentiate these cells into complex epithelial cultures containing basal, secretory, and ciliated cell types on standard plastic cultureware. This method supports scalable culture of both 2D epithelial monolayers and 3D organoids and is applied to disease modeling in primary ciliary dyskinesia, cystic fibrosis, and respiratory syncytial virus infection. The resulting system enables scalable assessment of disease-relevant epithelial functions in respiratory research.

Microtubule organization depends on cell type and function. Microtubule networks of many differentiated cell types, such as epithelial cells, are poorly understood due to their complexity and high density. Here, we used expansion microscopy to visualize and quantitatively map the three-dimensional organization of the microtubule network in human airway multiciliated cells. In these cells, most apical and apicobasal microtubules nucleate and anchor at the basal foot, a part of the ciliary basal body. A small subset of stable microtubules is detached from basal bodies and forms an apical crescent. By combining expansion microscopy with a newly developed averaging tool for multichannel volumetric data, we generated a high-resolution 3D map of the basal body. We delineated the position of structural components and proteins involved in microtubule nucleation and anchoring, uncovering some interesting differences with centrioles of dividing cells. γ-TuRC, its binding partners NEDD1 and augmin/HAUS, and centriolar appendage proteins ninein and AKNA localize to the basal foot. Functional analyses demonstrated that NEDD1 is essential for basal foot-dependent microtubule organization. Our data reveal the distinct architecture of microtubule-organizing centers responsible for the formation of dense microtubule arrays in multiciliated cells.

Abscission is the last step of cell division. It separates the two sister cells and consists of cutting the cytoplasmic bridge. Abscission is mediated by the ESCRT membrane remodeling machinery, which also triggers the severing of a thick bundle of microtubules. Here, we show that rather than being passive actors in abscission, microtubules control abscission speed. Using mouse embryonic stem cells, which transition from slow to fast abscission during exit from naive pluripotency, we investigate the molecular mechanism for the regulation of abscission dynamics and identify crosstalk between Aurora B activity and microtubule stability. We demonstrate that naive stem cells maintain high Aurora B activity on the bridge after cytokinesis. This high Aurora B activity leads to transient microtubule stabilization that delays abscission by decreasing MCAK recruitment to the midbody. In turn, stable microtubules promote the activity of Aurora B. Overall, our data demonstrate that Aurora B-dependent microtubule stability controls abscission dynamics.

Microtubules play an essential role in many cellular functions, in part by serving as tracks for intracellular transport by kinesin and dynein. The ability of microtubules to fulfill this role fundamentally depends on the fact that they are polar, with motors moving along them toward either their plus or minus end. Given that the microtubule cytoskeleton adopts a variety of specialized architectures in different cell types, it is important to map precisely how microtubules are oriented and organized in these cells. To this end, motor-PAINT has been developed, but in its current implementation, it relies on total internal reflection fluorescence (TIRF) microscopy and is thus restricted to imaging microtubules in a thin section of the cell immediately adjacent to the coverslip. Here, we report a variant of motor-PAINT that uses lattice light-sheet microscopy to overcome this, allowing for the mapping of microtubule organization and orientation in three-dimensional samples. We describe the necessary steps to purify, label, use, and image kinesin motors for motor-PAINT and outline the analysis pipeline used to visualize the resulting data. The method described here can be used in the future to study the microtubule cytoskeleton in (thick) polarized cells such as intestinal epithelial cells.

γ-Tubulin ring complex (γ-TuRC) is the major microtubule-nucleating factor. After nucleation, microtubules can be released from γ-TuRC and stabilized by other proteins, such as CAMSAPs, but the biochemical cross-talk between minus-end regulation pathways is poorly understood. Here we reconstituted this process in vitro using purified components. We found that all CAMSAPs could bind to the minus ends of γ-TuRC-attached microtubules. CAMSAP2 and CAMSAP3, which decorate and stabilize growing minus ends but not the minus-end tracking protein CAMSAP1, induced microtubule release from γ-TuRC. CDK5RAP2, a γ-TuRC-interactor, and CLASP2, a regulator of microtubule growth, strongly stimulated γ-TuRC-dependent microtubule nucleation, but only CDK5RAP2 suppressed CAMSAP binding to γ-TuRC-anchored minus ends and their release. CDK5RAP2 also improved selectivity of γ-tubulin-containing complexes for 13- rather than 14-protofilament microtubules in microtubule-capping assays. Knockout and overexpression experiments in cells showed that CDK5RAP2 inhibits the formation of CAMSAP2-bound microtubules detached from the microtubule-organizing centre. We conclude that CAMSAPs can release newly nucleated microtubules from γ-TuRC, whereas nucleation-promoting factors can differentially regulate this process.

BACKGROUND: The first evidence of micro- and nanoplastic (MNP) exposure in the human placenta s emerging. However, toxicity of MNPs in the placenta, specifically environmentally relevant particles, remain unclear. OBJECTIVES: We examined the transport, uptake, and toxicity of pristine and experimentally weathered MNPs in nonsyncytialized and syncytialized BeWo b30 choriocarcinoma cells. METHODS: We performed untargeted chemical characterization of pristine and weathered MNPs using liquid chromatography high-resolution mass spectrometry to evaluate compositional differences following particle weathering. We investigated cellular internalization of pristine and weathered polystyrene (PS; 0.05-10 mu m) and high-density polyethylene (HDPE; 0-80 mu m) particles using high-resolution confocal imaging and three-dimensional rendering. We investigated the influence, of particle coating with human plasma on the cellular transport of PS particles using a transwell setup and examined the influence of acute MNP exposure on cell viability, damage to the plasma membrane, and expression of genes involved in steroidogenesis. RESULTS: Chemical characterization of MNPs showed a significantly higher number of unique features in pristine particles in comparison with weathered particles. Size-dependent placental uptake of pristine and weathered MNPs was observed in both placental cell types after 24 h exposure. Cellular transport was limited and size-dependent and was not influenced by particle coating with human plasma. None of the MNPs affected cell viability. Damage to the plasma membrane was observed only for 0.05 mu m PS particles in the nonsyncytialized cells at the highest concentration tested (100 (mu g/mL). Modest down-regulation of hsd17b1 was observed in syncytialized cells exposed to pristine MNPs. DISCUSSION: Our results suggest that pristine and weathered MNPs are internalized and translocated in placental cells in vitro. Effects on gene expression observed upon pristine PS and HDPE particle exposure warrant further examination. More in-depth investigations are needed to better understand the potential health risks of MNP and chemicals associated with them under environmentally relevant exposure scenarios.

Insulin secretion in pancreatic β-cells is regulated by cortical complexes that are enriched at the sites of adhesion to extracellular matrix facing the vasculature. Many components of these complexes, including Bassoon, RIM, ELKS and liprins, are shared with neuronal synapses. Here, we show that insulin secretion sites also contain non-neuronal proteins LL5β and KANK1, which in migrating cells organize exocytotic machinery in the vicinity of integrin-based adhesions. Depletion of LL5β or focal adhesion disassembly triggered by myosin II inhibition perturbed the clustering of secretory complexes and attenuated the first wave of insulin release. While previous analyses in vitro and in neurons suggested that secretory machinery might assemble through liquid-liquid phase separation, analysis of endogenously labeled ELKS in pancreatic islets indicated that its dynamics is inconsistent with such a scenario. Instead, fluorescence recovery after photobleaching and single molecule imaging showed that ELKS turnover is driven by binding and unbinding to low-mobility scaffolds. Both the scaffold movements and ELKS exchange were stimulated by glucose treatment. Our findings help to explain how integrin-based adhesions control spatial organization of glucose-stimulated insulin release.

γ-tubulin ring complex (γ-TuRC) is the major microtubule-nucleating factor. After nucleation, microtubules can be released from γ-TuRC and stabilized by other proteins, such as CAMSAPs, but the biochemical cross-talk between minus-end regulation pathways is poorly understood. Here, we reconstituted this process in vitro using purified components. We found that all CAMSAP proteins could bind to the minus-ends of γ-TuRC-attached microtubules. CAMSAP2 and CAMSAP3, which decorate and stabilize growing minus ends, but not the minus-end tracking protein CAMSAP1 induced microtubule release from γ-TuRC. CDK5RAP2, a γ-TuRC-interactor, and CLASP2, a regulator of microtubule growth, stimulated γ-TuRC-dependent microtubule nucleation, but only CDK5RAP2 inhibited CAMSAP-driven microtubule detachment by suppressing CAMSAP binding to γ-TuRC-anchored minus ends. CDK5RAP2 also improved γ-TuRC selectivity for 13-rather than 14-protofilament microtubules in microtubule-capping assays. Our results support a model whereby CAMSAPs exploit an imperfect attachment between γ-TuRC and the nucleated microtubule to promote minus-end elongation and release, whereas CDK5RAP2 improves the fit between γ-TuRC and 13-protofilament microtubules and enhances nucleation.

Introducing hierarchical porosity to zeolites is vital for providing molecular access to microporous domains. Yet, the dynamics of meso- and macropore formation has remained elusive and pore space ill-characterized by a lack of (in situ) microscopic tools sensitive to nanoporosity. Here, we probe hierarchical porosity formation within a zeolite ZSM-5 crystal in real-time by in situ fluorescence microscopy during desilication. In addition, we introduce small-angle X-ray scattering microscopy as novel characterization tool to map intracrystal meso- and macropore properties. It is shown that hierarchical porosity formation initiates at the crystal surface and propagates to the crystal core via a pore front with decreasing rate. Also, hierarchical porosity only establishes in specific (segments of) subunits which constitute ZSM-5. Such space-dependent meso- and macroporosity implies local discrepancies in diffusion, performance and deactivation behaviors even within a zeolite crystal.

ABSTRACTDegradation of aggregates by selective autophagy is important as damaged proteins may impose a threat to cellular homeostasis. Although the core components of the autophagy machinery are well-characterized, the spatiotemporal regulation of many selective autophagy processes, including aggrephagy, remains largely unexplored. Furthermore, because most live-cell imaging studies have so far focused on starvation-induced autophagy, little is known about the dynamics of aggrephagy. Here, we describe the development and application of the mKeima-PIM assay, which enables live-cell observation of autophagic turnover and degradation of inducible protein aggregates in conjunction with key autophagy players. This allowed us to quantify the relative timing and duration of different steps of aggrephagy and revealed the short-lived nature of the autophagosome. The assay furthermore showed the spatial distribution of omegasome formation, highlighting that autophagy initiation is directly instructed by the cargo. Moreover, we found that nascent autophagosomes mostly remain immobile until acidification occurs. Thus, our assay provides new insights into the spatiotemporal regulation and dynamics of aggrephagy.

Axon formation critically relies on local microtubule remodeling and marks the first step in establishing neuronal polarity. However, the function of the microtubule-organizing centrosomes during the onset of axon formation is still under debate. Here, we demonstrate that centrosomes play an essential role in controlling axon formation in human-induced pluripotent stem cell (iPSC)-derived neurons. Depleting centrioles, the core components of centrosomes, in unpolarized human neuronal stem cells results in various axon developmental defects at later stages, including immature action potential firing, mislocalization of axonal microtubule-associated Trim46 proteins, suppressed expression of growth cone proteins, and affected growth cone morphologies. Live-cell imaging of microtubules reveals that centriole loss impairs axonal microtubule reorganization toward the unique parallel plus-end out microtubule bundles during early development. We propose that centrosomes mediate microtubule remodeling during early axon development in human iPSC-derived neurons, thereby laying the foundation for further axon development and function.

Zeolith-Katalysatoren zeigen oft stark verwachsene Strukturen, die auf der Mikroskala als “Blume” oder “Sonne” erscheinen. Mithilfe von Röntgenkleinwinkelstreuung und In-situ-Fluoreszenzmikroskopie zeigen Bert M. Weckhuysen et al. in ihrer Zuschrift auf S. 13922, dass sich die Porosität nur in bestimmten Segmenten der Zeolithe ausbildet, was zu starken lokalen Unterschieden in der Leistung und im Deaktivierungsverhalten führen kann. Die gelbe Sonne erinnert an das Symbol der Universität Utrecht, an der die Arbeit durchgeführt wurde.

Microtubules are dynamic cytoskeletal polymers that spontaneously switch between phases of growth and shrinkage. The probability of transitioning from growth to shrinkage, termed catastrophe, increases with microtubule age, but the underlying mechanisms are poorly understood. Here, we set out to test whether microtubule lattice defects formed during polymerization can affect growth at the plus end. To generate microtubules with lattice defects, we used microtubule-stabilizing agents that promote formation of polymers with different protofilament numbers. By employing different agents during nucleation of stable microtubule seeds and subsequent polymerization phase, we could reproducibly induce switches in protofilament number. Such switches led to frequent catastrophes, which were not observed when microtubules were grown in the same conditions but without a protofilament number mismatch. Microtubule severing at the site of the defect was sufficient to suppress catastrophes. We conclude that structural defects within microtubule lattice can affect the dynamic state of the plus end.

The neuronal microtubule cytoskeleton underlies the polarization and proper functioning of neurons, amongst others by providing tracks for motor proteins that drive intracellular transport. Different subsets of neuronal microtubules, varying in composition, stability, and motor preference, are known to exist, but the high density of microtubules has so far precluded mapping their relative abundance and three-dimensional organization. Here, we use different super-resolution techniques (STED, Expansion Microscopy) to explore the nanoscale organization of the neuronal microtubule network in rat hippocampal neurons. This revealed that in dendrites acetylated microtubules are enriched in the core of the dendritic shaft, while tyrosinated microtubules are enriched near the plasma membrane, thus forming a shell around the acetylated microtubules. Moreover, using a novel analysis pipeline we quantified the absolute number of acetylated and tyrosinated microtubules within dendrites and found that they account for 65–75% and ~20–30% of all microtubules, respectively, leaving only few microtubules that do not fall in either category. Because these different microtubule subtypes facilitate different motor proteins, these novel insights help to understand the spatial regulation of intracellular transport.

Microtubules are dynamic cytoskeletal polymers that spontaneously switch between phases of growth and shrinkage. The probability of transitioning from growth to shrinkage, termed catastrophe, increases with microtubule age, but the underlying mechanisms are poorly understood. Here, we set out to test whether microtubule lattice defects formed during polymerization can affect growth at the plus end. To generate microtubules with lattice defects, we used microtubule-stabilizing agents that promote formation of polymers with different protofilament numbers. By employing different agents during nucleation of stable microtubule seeds and the subsequent polymerization phase, we could reproducibly induce switches in protofilament number and induce stable lattice defects. Such drug-induced defects led to frequent catastrophes, which were not observed when microtubules were grown in the same conditions but without a protofilament number mismatch. Microtubule severing at the site of the defect was sufficient to suppress catastrophes. We conclude that structural defects within the microtubule lattice can exert effects that can propagate over long distances and affect the dynamic state of the microtubule end.

Bunyaviruses have a genome that is divided over multiple segments. Genome segmentation complicates the generation of progeny virus, since each newly formed virus particle should preferably contain a full set of genome segments in order to disseminate efficiently within and between hosts. Here, we combine immunofluorescence and fluorescence in situ hybridization techniques to simultaneously visualize bunyavirus progeny virions and their genomic content at single-molecule resolution in the context of singly infected cells. Using Rift Valley fever virus and Schmallenberg virus as prototype tri-segmented bunyaviruses, we show that bunyavirus genome packaging is influenced by the intracellular viral genome content of individual cells, which results in greatly variable packaging efficiencies within a cell population. We further show that bunyavirus genome packaging is more efficient in insect cells compared to mammalian cells and provide new insights on the possibility that incomplete particles may contribute to bunyavirus spread as well.

Single-molecule localization microscopy (SMLM) enables fluorescent microscopy with nanometric resolution. While localizing molecules close to the coverslip is relatively straightforward using high numerical aperture (NA) oil immersion (OI) objectives, optical aberrations impede SMLM deeper in watery samples. Adaptive optics (AO) with a deformable mirror (DM) can be used to correct such aberrations and to induce precise levels of astigmatism to encode the z-position of molecules. Alternatively, the use of water immersion (WI) objectives might be sufficient to limit the most dominant aberrations. Here we compare SMLM at various depths using either WI or OI with or without AO. In addition, we compare the performance of a cylindrical lens and a DM for astigmatism-based z-encoding. We find that OI combined with adaptive optics improves localization precision beyond the performance of WI-based imaging and enables deep (>10 µm) 3D localization.

Intracellular transport relies on multiple kinesins, but it is poorly understood which kinesins are present on particular cargos, what their contributions are and whether they act simultaneously on the same cargo. Here, we show that Rab6-positive secretory vesicles are transported from the Golgi apparatus to the cell periphery by kinesin-1 KIF5B and kinesin-3 KIF13B, which determine the location of secretion events. KIF5B plays a dominant role, whereas KIF13B helps Rab6 vesicles to reach freshly polymerized microtubule ends, to which KIF5B binds poorly, likely because its cofactors, MAP7-family proteins, are slow in populating these ends. Sub-pixel localization demonstrated that during microtubule plus-end directed transport, both kinesins localize to the vesicle front and can be engaged on the same vesicle. When vesicles reverse direction, KIF13B relocates to the middle of the vesicle, while KIF5B shifts to the back, suggesting that KIF5B but not KIF13B undergoes a tug-of-war with a minus-end directed motor.

Expansion microscopy (ExM) is a recently introduced technique that enables high-resolution imaging with conventional microscopes by using physical expansion of samples. While this technique does not require a complicated microscope setup (like in STED or STORM microscopy), sample preparation and handling require additional attention. Here we describe a workflow for imaging of the neuronal microtubule network with minimal artifacts and sample perturbations. We demonstrate that the use of custom-printed mounting chambers simplifies sample handling and facilitates stable imaging of the sample. In addition, refractive index matching between the sample and the objective greatly improves signal retention deeper in thick samples. To accurately determine the precise expansion factor and determine sample distortion, we describe how samples can be compared using STED and ExM. Together, these procedures enabled us to better resolve different microtubule subsets in neuronal soma and dendrites.