ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging

Single-molecule lipid biosensors mitigate inhibition of endogenous effector proteins

Genetically encoded lipid biosensors uniquely provide real time, spatially resolved kinetic data for lipid dynamics in living cells. Despite clear strengths, these tools have significant drawbacks; most notably, lipid molecules bound to biosensors cannot engage with effectors, potentially inhibiting signaling. Here, we show that although PI 3-kinase (PI3K)-mediated activation of AKT is not significantly reduced in a cell population transfected with a PH-AKT1 PIP3/PI(3,4)P2 biosensor, single cells expressing PH-AKT at visible levels have reduced activation. Tagging endogenous AKT1 with neonGreen reveals its EGF-mediated translocation to the plasma membrane. Co-transfection with the PH-AKT1 or other PIP3 biosensors eliminates this translocation, despite robust recruitment of the biosensors. Inhibition is even observed with PI(3,4)P2-selective biosensor. However, expressing lipid biosensors at low levels, comparable with those of endogenous AKT, produced no such inhibition. Helpfully, these single-molecule biosensors revealed improved dynamic range and kinetic fidelity compared with overexpressed biosensor. This approach represents a noninvasive way to probe spatiotemporal dynamics of PI3K signaling in living cells.

RNA-binding proteins and glycoRNAs form domains on the cell surface for cell-penetrating peptide entry

The composition and organization of the cell surface determine how cells interact with their environment. Traditionally, glycosylated transmembrane proteins were thought to be the major constituents of the external surface of the plasma membrane. Here, we provide evidence that a group of RNA-binding proteins (RBPs) is present on the surface of living cells. These cell-surface RBPs (csRBPs) precisely organize into well-defined nanoclusters enriched for multiple RBPs and glycoRNAs, and their clustering can be disrupted by extracellular RNase addition. These glycoRNA-csRBP clusters further serve as sites of cell-surface interaction for the cell-penetrating peptide trans-activator of transcription (TAT). Removal of RNA from the cell surface, or loss of RNA-binding activity by TAT, causes defects in TAT cell internalization. Together, we provide evidence of an expanded view of the cell surface by positioning glycoRNA-csRBP clusters as a regulator of communication between cells and the extracellular environment.

Super-resolution of nodal and paranodal disruption in anti-pan-neurofascin-associated autoimmune nodopathy

Introduction

In autoimmune nodopathies, autoantibodies target the nodes of Ranvier, impairing saltatory nerve conduction. Understanding the impact of autoantibody binding on protein assembly is crucial for gaining insights into the pathogenicity of different autoantibodies. We investigated nodal, paranodal, and cytoskeletal axonal proteins in teased fibers from a sural nerve biopsy of a patient with anti-pan-neurofascin autoantibodies. Conventional diagnostic tools, including fluorescence microscopy, often miss subtle alterations at the ultrastructural level.

Methods

We utilized direct stochastic optical reconstruction microscopy (dSTORM), a super-resolution fluorescence imaging technique, to assess the nanoscale architecture of nodal, paranodal, and cytoskeletal axonal proteins.

Result

While conventional fluorescence microscopy revealed severe paranodal and nodal damage in 14% of the nodes, with 86% appearing normal at first glance, the super-resolved images revealed a decreased neurofascin-155 and Caspr-1 density, but preserved colocalization of these adhesion proteins in paranodes that initially seemed normal. At the nodes, sodium channel density and distribution remained intact, but neurofascin-186 density was reduced. Axonal beta-IV spectrin was altered only in severely damaged nodes. This indicates that axonal integrity is largely preserved, with a potentially reversible decrease in paranodal and nodal adhesion proteins in patients with nodopathy revealing subtle alterations in nodal integrity that are not apparent with conventional imaging.

Discussion

These likely reversible changes may explain the rapid recovery seen in patients with anti-pan-neurofascin autoantibodies following autoantibody depletion. Conversely, the small percentage of severely and axonally damaged nodes may account for the residual symptoms experienced by most patients.

Nanosized core-shell bio-hybrid microgels and their internal structure

Microgels are versatile materials with applications across biomedicine, materials science, and beyond. Their controllable size and composition enables tailoring specific properties, yet characterizing their internal structures on the nanoscale remains challenging. Super-resolution fluorescence microscopy (SRFM) effectively analyzes sub-μm structures, including microgels, offering a tool for investigating more complex systems such as core-shell microgels. Understanding their internal structure, in particular interpenetration at the soft-soft interface between core and shell and accessibility for guest molecules, is vital for rationally designing predictable functionalities. This study examines the core-shell morphology and the accessibility for guest molecules of bio-hybrid DNA-poly(N-isopropylmethacrylamide) microgels at three stages of shell polymerization using SRFM. Covalent fluorescence labeling probes the core polymer, co-polymerized with N,N'-bis(acryloyl)cystamine, which provides visual insight into core and shell compartmentalization. The results demonstrate core polymer interpenetration into the shell without compromising its original structure, and additionally allow us to determine the size- and hydrophobicity dependent accessibility of the microgel core. This, offering new perspectives on the internal architecture of core-shell microgels, contributes to the in-depth understanding of their complex behavior, potentially guiding the rational design of new microgel drug delivery systems, taking into account the complex interplay of polarity, size and charge of guest molecules.

SynPull: An advanced method for studying neurodegeneration-related aggregates in synaptosomes using super-resolution microscopy

Synaptic dysfunction is a primary hallmark of both Alzheimer's and Parkinson's disease, leading to cognitive and behavioral decline. While alpha-synuclein, beta-amyloid, and tau are involved in the physiological functioning of synapses, their pathological aggregation has been linked to synaptopathology. The methodology for studying the small-soluble protein aggregates formed by these proteins is limited. Here we describe SynPull, a method combining single-molecule pull-down, super-resolution microscopy, and advanced computational analyses to characterize the protein aggregates in human and mouse synaptosomes. We show that AT8-positive tau aggregates are the predominant aggregate type in synaptosomes from postmortem Alzheimer's disease brain, although the aggregate size does not change in disease. Meanwhile, the relatively smaller amount of alpha-synuclein and beta-amyloid aggregates found in the synapses are larger than the extra-synaptic ones. Collectively, these results show the utility of SynPull to study pathological aggregates in neurodegeneration, elucidating the disease mechanisms causing synaptic dysfunction.

Single-molecule electrochemical imaging of 'split waves' in the electrocatalytic (EC') mechanism

We describe a single-molecule electrochemical imaging strategy to study the electrocatalytic (EC') mechanism. Using the fluorescent molecule ATTO647N at extremely low concentrations as the substrate, we confirmed its catalytic reduction to a nonfluorescent form in the presence of the mediator phenazine methosulfate (PMS) by imaging and counting fluorescent molecules. Conventional electrochemical current in cyclic voltammetry would not have allowed us to infer the existence of an EC' process or the PMS-mediated ATTO647N reduction. Additionally, we observed shifts in the catalytic reduction potential of ATTO647N at various mediator concentrations, which agree with the theoretical predictions by Savéant. Our work offers a new perspective on connecting single-molecule EC' behaviors with the conventional ensemble EC' mechanism, both practically and theoretically.

Super-Resolution Fluorescence Imaging Reveals the Mechanism of NRP1 Clustering on Non-Small-Cell Lung Cancer Membranes

Neuropilin 1 (NRP1) is upregulated in various types of malignant tumors, especially non-small-cell lung cancer (NSCLC). However, the precise mechanisms for membrane localization and regulation are not fully understood. Observations from super-resolution microscopy have revealed that NRP1 tends to form nanoscale clusters on the cell membrane, with these clusters varying significantly in size and density across different regions. Further research has shown that stimulation by hepatocyte growth factor (HGF) can reorganize the distribution of NRP1, reducing the number of small clusters while promoting the formation of larger ones. This suggests a propensity for internalization after activation. Additionally, dual-color dSTORM imaging has demonstrated a certain degree of colocalization between NRP1 and c-MET, indicating that c-MET plays an important role in stabilizing NRP1 clusters. This study provides new insights into the mechanism behind NRP1's clustered distribution on cell membranes and paves the way for developing more effective therapeutic strategies targeting NRP1 within tumors.

Bayesian Inference of Binding Kinetics from Fluorescence Time Series

The study of binding kinetics via the analysis of fluorescence time traces is often confounded by measurement noise and photophysics. Although photoblinking can be mitigated by using labels less likely to photoswitch, photobleaching generally cannot be eliminated. Current methods for measuring binding and unbinding rates are therefore limited by concurrent photobleaching events. Here, we propose a method to infer binding and unbinding rates alongside photobleaching rates using fluorescence intensity traces. Our approach is a two-stage process involving analyzing individual regions of interest (ROIs) with a Hidden Markov Model to infer the fluorescence intensity levels of each trace. We then use the inferred intensity level state trajectory from all ROIs to infer kinetic rates. Our method has several advantages, including the ability to analyze noisy traces, account for the presence of photobleaching events, and provide uncertainties associated with the inferred binding kinetics. We demonstrate the effectiveness and reliability of our method through simulations and data from DNA origami binding experiments.

Microfluidics-Driven Manufacturing and Multiscale Analytical Characterization of Nanoparticle-Vesicle Hybrids

Coating synthetic nanoparticles (NPs) with lipid membranes is a promising approach to enhance the performance of nanomaterials in various biological applications, including therapeutic delivery to target organs. Current methods for achieving this coating often rely on bulk approaches which can result in low efficiency and poor reproducibility. Continuous processes coupled with quality control represent an attractive strategy to manufacture products with consistent attributes and high yields. Here, this concept is implemented by developing an acoustic microfluidic device together with an analytical platform to prepare nanoparticle-vesicle hybrids and quantitatively characterize the nanoparticle coverage using fluorescence-based techniques at different levels of resolution. With this approach polymethyl methacrylate (PMMA) nanoparticles are successfully coated with liposomes and extracellular vesicles (EVs), achieving a high encapsulation efficiency of 70%. Moreover, the approach enables the identification of design rules to control the efficiency of encapsulation by tuning various operational parameters and material properties, including buffer composition, nanoparticle/vesicle ratio, and vesicle rigidity.

Neural network-assisted localization of clustered point spread functions in single-molecule localization microscopy

Single-molecule localization microscopy (SMLM), which has revolutionized nanoscale imaging, faces challenges in densely labelled samples due to fluorophore clustering, leading to compromised localization accuracy. In this paper, we propose a novel convolutional neural network (CNN)-assisted approach to address the issue of locating the clustered fluorophores. Our CNN is trained on a diverse data set of simulated SMLM images where it learns to predict point spread function (PSF) locations by generating Gaussian blobs as output. Through rigorous evaluation, we demonstrate significant improvements in PSF localization accuracy, especially in densely labelled samples where traditional methods struggle. In addition, we employ blob detection as a post-processing technique to refine the predicted PSF locations and enhance localization precision. Our study underscores the efficacy of CNN in addressing clustering challenges in SMLM, thereby advancing spatial resolution and enabling deeper insights into complex biological structures.

Trans-synaptic molecular context of NMDA receptor nanodomains

Tight coordination of the spatial relationships between protein complexes is required for cellular function. In neuronal synapses, many proteins responsible for neurotransmission organize into subsynaptic nanoclusters whose trans-cellular alignment modulates synaptic signal propagation. However, the spatial relationships between these proteins and NMDA receptors (NMDARs), which are required for learning and memory, remain undefined. Here, we mapped the relationship of key NMDAR subunits to reference proteins in the active zone and postsynaptic density using multiplexed super-resolution DNA-PAINT microscopy. GluN2A and GluN2B subunits formed nanoclusters with diverse configurations that, surprisingly, were not localized near presynaptic vesicle release sites marked by Munc13-1. Despite this, we found a subset of release sites was enriched with NMDARs, and modeling of glutamate release and receptor activation in measured synapses indicated this nanotopography promotes NMDAR activation. This subset of release sites was internally denser with Munc13-1, aligned with abundant PSD-95, and associated closely with specific NMDAR nanodomains. Further, NMDAR activation drove rapid reorganization of this release site/receptor relationship, suggesting a structural mechanism for tuning NMDAR-mediated synaptic transmission. This work reveals a new principle regulating NMDAR signaling and suggests that synaptic functional architecture depends on the assembly of and trans-cellular spatial relationships between multiprotein nanodomains.

Super-resolution imaging of proteins inside live mammalian cells with mLIVE-PAINT

Super-resolution microscopy has revolutionized biological imaging, enabling the visualization of structures at the nanometer length scale. Its application in live cells, however, has remained challenging. To address this, we adapted LIVE-PAINT, an approach we established in yeast, for application in live mammalian cells. Using the 101A/101B coiled-coil peptide pair as a peptide-based targeting system, we successfully demonstrate the super-resolution imaging of two distinct proteins in mammalian cells, one localized in the nucleus, and the second in the cytoplasm. This study highlights the versatility of LIVE-PAINT, suggesting its potential for live-cell super-resolution imaging across a range of protein targets in mammalian cells. We name the mammalian cell version of our original method mLIVE-PAINT.

Nuclear blebs are associated with destabilized chromatin-packing domains

Disrupted nuclear shape is associated with multiple pathological processes including premature aging disorders, cancer-relevant chromosomal rearrangements and DNA damage. Nuclear blebs (i.e. herniations of the nuclear envelope) can be induced by (1) nuclear compression, (2) nuclear migration (e.g. cancer metastasis), (3) actin contraction, (4) lamin mutation or depletion, and (5) heterochromatin enzyme inhibition. Recent work has shown that chromatin transformation is a hallmark of bleb formation, but the transformation of higher-order structures in blebs is not well understood. As higher-order chromatin has been shown to assemble into nanoscopic packing domains, we investigated whether (1) packing domain organization is altered within nuclear blebs and (2) whether alteration in packing domain structure contributed to bleb formation. Using dual-partial wave spectroscopic microscopy, we show that chromatin-packing domains within blebs are transformed both by B-type lamin depletion and the inhibition of heterochromatin enzymes compared to what is seen in the nuclear body. Pairing these results with single-molecule localization microscopy of constitutive heterochromatin, we show fragmentation of nanoscopic heterochromatin domains within bleb domains. Overall, these findings indicate that chromatin within blebs is associated with a fragmented higher-order chromatin structure.

Visualizing PIEZO1 Localization and Activity in hiPSC-Derived Single Cells and Organoids with HaloTag Technology

PIEZO1 is critical to numerous physiological processes, transducing diverse mechanical stimuli into electrical and chemical signals. Recent studies underscore the importance of visualizing endogenous PIEZO1 activity and localization to understand its functional roles. To enable physiologically and clinically relevant studies on human PIEZO1, we genetically engineered human induced pluripotent stem cells (hiPSCs) to express a HaloTag fused to endogenous PIEZO1. Combined with advanced imaging, our chemogenetic platform allows precise visualization of PIEZO1 localization dynamics in various cell types. Furthermore, the PIEZO1-HaloTag hiPSC technology facilitates the non-invasive monitoring of channel activity across diverse cell types using Ca2+-sensitive HaloTag ligands, achieving temporal resolution approaching that of patch clamp electrophysiology. Finally, we used lightsheet imaging of hiPSC-derived neural organoids to achieve molecular scale imaging of PIEZO1 in three-dimensional tissue organoids. Our advances offer a novel platform for studying PIEZO1 mechanotransduction in human cells and tissues, with potential for elucidating disease mechanisms and targeted therapeutic development.

Mature chromatin packing domains persist after RAD21 depletion in 3D

Understanding chromatin organization requires integrating measurements of genome connectivity and physical structure. It is well established that cohesin is essential for TAD and loop connectivity features in Hi-C, but the corresponding change in physical structure has not been studied using electron microscopy. Pairing chromatin scanning transmission electron tomography with multiomic analysis and single-molecule localization microscopy, we study the role of cohesin in regulating the conformationally defined chromatin nanoscopic packing domains. Our results indicate that packing domains are not physical manifestation of TADs. Using electron microscopy, we found that only 20% of packing domains are lost upon RAD21 depletion. The effect of RAD21 depletion is restricted to small, poorly packed (nascent) packing domains. In addition, we present evidence that cohesin-mediated loop extrusion generates nascent domains that undergo maturation through nucleosome posttranslational modifications. Our results demonstrate that a 3D genomic structure, composed of packing domains, is generated through cohesin activity and nucleosome modifications.

Visualization of Mechanical Force Regulation of Exosome Secretion Using High Time-Spatial Resolution Imaging

Exosomes are small endosome-derived extracellular vesicles that participate in cell-cell communication, particularly in the context of tumorigenesis, and their secretion is influenced by the tumor microenvironment. While previous studies suggest that mechanical forces may enhance exosome release, the direct relationship between these forces and exosome secretion needs to be further characterized. Here, we utilized dual-color CD63 reporter-based high-speed live-cell imaging to visualize how mechanical forces influence exosome release in situ. Through live-cell tracking, we observed the dynamic fusion of multivesicular bodies (MVBs) with the plasma membrane (PM) to release exosomes at the single-vesicle level. More importantly, we directly detected a real-time stimulatory effect of mechanical forces on exosome release, with a bulk release of exosomes occurring under mechanical pressure stimulation. Furthermore, we identified mechanical force-induced actin rearrangement as a crucial determinant of exosome release. Our findings provide direct insights into the role of mechanical forces in exosome release and lay the groundwork for developing potential strategies to target disease-derived exosomes from their source.

Lipidic folding pathway of α-Synuclein via a toxic oligomer

Aggregation intermediates play a pivotal role in the assembly of amyloid fibrils, which are central to the pathogenesis of neurodegenerative diseases. The structures of filamentous intermediates and mature fibrils are now efficiently determined by single-particle cryo-electron microscopy. By contrast, smaller pre-fibrillar α-Synuclein (αS) oligomers, crucial for initiating amyloidogenesis, remain largely uncharacterized. We report an atomic-resolution structural characterization of a toxic pre-fibrillar aggregation intermediate (I1) on pathway to the formation of lipidic fibrils, which incorporate lipid molecules on protofilament surfaces during fibril growth on membranes. Super-resolution microscopy reveals a tetrameric state, providing insights into the early oligomeric assembly. Time resolved nuclear magnetic resonance (NMR) measurements uncover a structural reorganization essential for the transition of I1 to mature lipidic L2 fibrils. The reorganization involves the transformation of anti-parallel β-strands during the pre-fibrillar I1 state into a β-arc characteristic of amyloid fibrils. This structural reconfiguration occurs in a conserved structural kernel shared by a vast number of αS-fibril polymorphs including extracted fibrils from Parkinson's and Lewy Body Dementia patients. Consistent with reports of anti-parallel β-strands being a defining feature of toxic αS pre-fibrillar intermediates, I1 impacts viability of neuroblasts and disrupts cell membranes, resulting in an increased calcium influx. Our results integrate the occurrence of anti-parallel β-strands as salient features of toxic oligomers with their significant role in the amyloid fibril assembly pathway. These structural insights have implications for the development of therapies and biomarkers.

Optimized molecule detection in localization microscopy with selected false positive probability

Single-molecule localization microscopy (SMLM) allows imaging beyond the diffraction limit. Detection of molecules is a crucial initial step in SMLM. False positive detections, which are not quantitatively controlled in current methods, are a source of artifacts that affect the entire SMLM analysis pipeline. Furthermore, current methods lack standardization, which hinders reproducibility. Here, we present an optimized molecule detection method which combines probabilistic thresholding with theoretically optimal filtering. The probabilistic thresholding enables control over false positive detections while optimal filtering minimizes false negatives. A theoretically optimal Poisson matched filter is used as a performance benchmark to evaluate existing filtering methods. Overall, our approach allows the detection of molecules in a robust, single-parameter and user-unbiased manner. This will minimize artifacts and enable data reproducibility in SMLM.

Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system

In single cells, variably sized nanoscale chromatin structures are observed, but it is unknown whether these form a cohesive framework that regulates RNA transcription. Here, we demonstrate that the human genome is an emergent, self-assembling, reinforcement learning system. Conformationally defined heterogeneous, nanoscopic packing domains form by the interplay of transcription, nucleosome remodeling, and loop extrusion. We show that packing domains are not topologically associated domains. Instead, packing domains exist across a structure-function life cycle that couples heterochromatin and transcription in situ, explaining how heterochromatin enzyme inhibition can produce a paradoxical decrease in transcription by destabilizing domain cores. Applied to development and aging, we show the pairing of heterochromatin and transcription at myogenic genes that could be disrupted by nuclear swelling. In sum, packing domains represent a foundation to explore the interactions of chromatin and transcription at the single-cell level in human health.

Proteolethargy is a pathogenic mechanism in chronic disease

The pathogenic mechanisms of many diseases are well understood at the molecular level, but there are prevalent syndromes associated with pathogenic signaling, such as diabetes and chronic inflammation, where our understanding is more limited. Here, we report that pathogenic signaling suppresses the mobility of a spectrum of proteins that play essential roles in cellular functions known to be dysregulated in these chronic diseases. The reduced protein mobility, which we call proteolethargy, was linked to cysteine residues in the affected proteins and signaling-related increases in excess reactive oxygen species. Diverse pathogenic stimuli, including hyperglycemia, dyslipidemia, and inflammation, produce similar reduced protein mobility phenotypes. We propose that proteolethargy is an overlooked cellular mechanism that may account for various pathogenic features of diverse chronic diseases.

Single molecule Lipid Biosensors Mitigate Inhibition of Endogenous Effector Proteins

Genetically encoded lipid biosensors uniquely provide real time, spatially resolved kinetic data for lipid dynamics in living cells. Despite clear strengths, these tools have significant drawbacks; most notably, lipid molecules bound to biosensors cannot engage with effectors, potentially inhibiting signaling. Here, we show that although PI 3-kinase (PI3K)-mediated activation of Akt is not significantly reduced in a cell population transfected with a PH-Akt1 PIP3/PI(3,4)P2 biosensor, single cells expressing PH-Akt at visible levels have reduced activation. Tagging endogenous AKT1 with neonGreen reveals its EGF-mediated translocation to the plasma membrane. Co-transfection with the PH-Akt1 or other PIP3 biosensors eliminates this translocation, despite robust recruitment of the biosensors. Inhibition is even observed with PI(3,4)P2-selective biosensor. However, expressing lipid biosensors at low levels, comparable with those of endogenous AKT, produced no such inhibition. Helpfully, these single-molecule biosensors revealed improved dynamic range and kinetic fidelity compared with over-expressed biosensor. This approach represents a non-invasive way to probe spatiotemporal dynamics of PI3K signaling in living cells.

Unveiling the cell biology of hippocampal neurons with dendritic axon origin

In mammalian axon-carrying-dendrite (AcD) neurons, the axon emanates from a basal dendrite, instead of the soma, to create a privileged route for action potential generation at the axon initial segment (AIS). However, it is unclear how such unusual morphology is established and whether the structure and function of the AIS in AcD neurons are preserved. By using dissociated hippocampal cultures as a model, we show that the development of AcD morphology can occur prior to synaptogenesis and independently of the in vivo environment. A single precursor neurite first gives rise to the axon and then to the AcD. The AIS possesses a similar cytoskeletal architecture as the soma-derived AIS and similarly functions as a trafficking barrier to retain axon-specific molecular composition. However, it does not undergo homeostatic plasticity, contains lesser cisternal organelles, and receives fewer inhibitory inputs. Our findings reveal insights into AcD neuron biology and underscore AIS structural differences based on axon onset.

Long-Term Single-Molecule Tracking in Living Cells using Weak-Affinity Protein Labeling

Single-particle tracking (SPT) has become a powerful tool to monitor the dynamics of membrane proteins in living cells. However, permanent labeling strategies for SPT suffer from photobleaching as a major limitation, restricting observation times, and obstructing the study of long-term cellular processes within single living cells. Here, we use exchangeable HaloTag Ligands (xHTLs) as an easy-to-apply labeling approach for live-cell SPT and demonstrate extended observation times of individual living cells of up to 30 minutes. Using the xHTL/HaloTag7 labeling system, we measure the ligand-induced activation kinetics of the epidermal growth factor receptor (EGFR) in single living cells. We generate spatial maps of receptor diffusion in cells, report non-uniform distributions of receptor mobility, and the formation of spatially confined 'hot spots' of EGFR activation. Furthermore, we measured the mobility of an ER-luminal protein in living cells and found diffusion coefficients that correlated with the ER nano-structure. This approach represents a general strategy to monitor protein mobility in a functional context and for extended observation times in single living cells.

Super-resolution imaging reveals the role of DDR1 cluster in NSCLC proliferation

Discoidin domain receptor 1 (DDR1), a transmembrane protein, is crucial in tumor development. Prior studies have demonstrated a significant correlation between protein cluster distribution on the cell membrane and tumor evolution. However, the precise spatial distribution characteristics of DDR1 on cell membranes and their impact on tumor development remain unclear. In this study, we conducted gene expression analysis to investigate DDR1 expression in non-small cell lung cancer (NSCLC) and its association with patient prognosis. We also employed direct stochastic optical reconstruction microscopy (dSTORM) imaging to examine DDR1's spatial distribution in NSCLC cells and tissues. Our findings indicate that DDR1 forms larger, tighter, and more abundant clusters in cancer cells and tissues compared to their normal counterparts. Notably, we observed that the enhanced aggregation of DDR1 clusters increased the likelihood of interaction with SRC, thereby activating the SRC-STAT3 signaling pathway in NSCLC cells and promoting cell proliferation. This study provides novel insights into the role of DDR1 aggregation in tumor proliferation, confirms DDR1 as a potential tumor marker, and serves as a valuable resource for future drug development.

Importin subunit beta-1 mediates ERK5 nuclear translocation, and its inhibition synergizes with ERK5 kinase inhibitors in reducing cancer cell proliferation

The mitogen-activated protein kinase (MAPK) extracellular signal-regulated kinase 5 (ERK5) is emerging as a promising target in cancer. Indeed, alterations of the MEK5/ERK5 pathway are present in many types of cancer, including melanoma. One of the key events in MAPK signalling is MAPK nuclear translocation and its subsequent regulation of gene expression. Likewise, the effects of ERK5 in supporting cancer cell proliferation have been linked to its nuclear localization. Despite many processes regulating ERK5 nuclear translocation having been determined, the nuclear transporters involved have not yet been identified. Here, we investigated the role of importin subunit alpha (α importin) and importin subunit beta-1 (importin β1) in ERK5 nuclear shuttling to identify additional targets for cancer treatment. Either importin β1 knockdown or the α/β1 importin inhibitor ivermectin reduced the nuclear amount of overexpressed and endogenous ERK5 in HEK293T and A375 melanoma cells, respectively. These results were confirmed in single-molecule microscopy in HeLa cells. Moreover, immunofluorescence analysis showed that ivermectin impairs epidermal growth factor (EGF)-induced ERK5 nuclear shuttling in HeLa cells. Both co-immunoprecipitation experiments and proximity ligation assay provided evidence that ERK5 and importin β1 interact and that this interaction is further induced by EGF administration and prevented by ivermectin treatment. The combination of ivermectin and the ERK5 inhibitor AX15836 synergistically reduced cell viability and colony formation ability in A375 and HeLa cells and was more effective than single treatments in preventing the growth of A375 and HeLa spheroids. The increased reduction of cell viability upon the same combination was also observed in patient-derived metastatic melanoma cells. The combination of ivermectin and ERK5 inhibitors other than AX15836 provided similar effects on cell viability. The identification of importin β1 as the nuclear transporter of ERK5 may be exploited for additional ERK5-inhibiting strategies for cancer therapy.

Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells

Pioneer transcription factors (PTFs) possess the unique capability to access closed chromatin regions and initiate cell fate changes, yet the underlying mechanisms remain elusive. Here, we characterized the single-molecule dynamics of PTFs targeting chromatin in living cells, revealing a notable 'confined target search' mechanism. PTFs such as FOXA1, FOXA2, SOX2, OCT4 and KLF4 sampled chromatin more frequently than non-PTF MYC, alternating between fast free diffusion in the nucleus and slower confined diffusion within mesoscale zones. Super-resolved microscopy showed closed chromatin organized as mesoscale nucleosome-dense domains, confining FOXA2 diffusion locally and enriching its binding. We pinpointed specific histone-interacting disordered regions, distinct from DNA-binding domains, crucial for confined target search kinetics and pioneer activity within closed chromatin. Fusion to other factors enhanced pioneer activity. Kinetic simulations suggested that transient confinement could increase target association rate by shortening search time and binding repeatedly. Our findings illuminate how PTFs recognize and exploit closed chromatin organization to access targets, revealing a pivotal aspect of gene regulation.

Analysis of Adherence Junctions in Rhinovirus-Infected Airway Epithelial Cells

The airway mucosal epithelium is the main gateway of entry for numerous human respiratory viruses, including human influenza virus, respiratory syncytial virus (RSV), coronavirus, and rhinoviruses (RV). For respiratory viruses to perpetuate infection, they must be able to traverse the airway mucosal epithelium and then spread into distal sites of the respiratory tract and lung parenchyma. However, this cellular interface has evolved well-developed apical junctional complexes (AJCs), including tight and adherens junctions, that bridge adjacent epithelial cells together. The resulting structure not only provides a strong physical barrier but also plays an active role in preventing and/or limiting the spread and dissemination of viral pathogens. Respiratory viruses, such as RVs, have been shown to target various components of these AJCs, either directly or indirectly, thus facilitating paracellular viral penetration, resulting in airway epithelial barrier dysfunction. Disruption of these AJCs may also result in unintended contact with hidden viral receptors, further enabling viral infection of the airway epithelium. Here we describe the various models of RV-infected airway epithelial cells and the methods used for the characterization and analysis of AJCs following RV infection.

Single-molecule orientation-localization microscopy: Applications and approaches

Single-molecule orientation-localization microscopy (SMOLM) builds upon super-resolved localization microscopy by imaging orientations and rotational dynamics of individual molecules in addition to their positions. This added dimensionality provides unparalleled insights into nanoscale biophysical and biochemical processes, including the organization of actin networks, movement of molecular motors, conformations of DNA strands, growth and remodeling of amyloid aggregates, and composition changes within lipid membranes. In this review, we discuss recent innovations in SMOLM and cover three key aspects: (1) biophysical insights enabled by labeling strategies that endow fluorescent probes to bind to targets with orientation specificity; (2) advanced imaging techniques that leverage the physics of light-matter interactions and estimation theory to encode orientation information with high fidelity into microscope images; and (3) computational methods that ensure accurate and precise data analysis and interpretation, even in the presence of severe shot noise. Additionally, we compare labeling approaches, imaging hardware, and publicly available analysis software to aid the community in choosing the best SMOLM implementation for their specific biophysical application. Finally, we highlight future directions for SMOLM, such as the development of probes with improved photostability and specificity, the design of “smart” adaptive hardware, and the use of advanced computational approaches to handle large, complex datasets. This review underscores the significant current and potential impact of SMOLM in deepening our understanding of molecular dynamics, paving the way for future breakthroughs in the fields of biophysics, biochemistry, and materials science.

Targeted Photoactivatable Green-Emitting BODIPY Based on Directed Photooxidation-Induced Activation and its Application to Live Dynamic Super-Resolution Microscopy

Photoactivatable fluorescent probes are valuable tools in bioimaging for tracking cells down to single molecules and for single molecule localization microscopy. For the latter application, green emitting dyes are in demand. We herein developed an efficient green-emitting photoactivatable furanyl-BODIPY (PFB) and we established a new mechanism of photoactivation called Directed Photooxidation Induced Activation (DPIA) where the furan is photo-oxidized in a directed manner by the singlet oxygen produced by the probe. The efficient photoconverter (93-fold fluorescence enhancement at 510 nm, 49 % yield conversion) is functionalizable and allowed targeting of several subcellular structures and organelles, which were photoactivated in live cells. Finally, we demonstrated the potential of PFB in super-resolution imaging by performing PhotoActivated Localization Microscopy (PALM) in live cells.

DNA Hybridization Kinetics Observed at the Single-Molecule Level Using Graphene Near-Field Effects

We present the development of an advanced sensing platform using a monolayer of graphene functionalized with fluorophore-labeled DNA hairpins to detect the kinetics of single hairpins during the hybridization reaction. The near-field photonic effects of graphene induce a distance-dependent quenching effect on the attached fluorescent labels, resulting in distinct optical signals in response to axial displacements resulting from DNA hybridization. Employing a wide-field Total Internal Reflection Fluorescence (TIRF) optical setup coupled with a sensitive Electron-Multiplying Charge-Coupled Device (EM-CCD) camera, we successfully detected fluorescent signals of individual or a low number of individual DNA hairpins within a low-concentration environment DNA target (tDNA). These signals were used to determine the optical setup's Point Spread Function (PSF) in a novel approach to super-resolution reconstruction. Combining these techniques, the subpixel localization of single hairpin molecules and their respective intensity profiles were extracted, enabling a kinetic assessment of individual DNA hairpins, with estimated unfolding times of approximately 7 s. Observations of kinetic phenomena unveiled intermediate partially hybridized states, extending the time required to unfold the hairpin probes by more than a factor of 2. Furthermore, a developed semiempirical model allowed the conversion of fluorescent signals into fluorophore-graphene distances. At the nanometer scale, we observed a step-like unfolding process characterized by intermittent metastates of unfolding and static periods, which can be attributed to nucleation events in some cases. Our graphene-based sensing platform and optical methodologies can be adopted for further research into the kinetics of different biomolecules under diverse environmental conditions.

Superresolution Imaging Reveals the Spatial Organization of CD81 Microdomains in Regulating Membrane Signaling on Jurkat T Cell Microvilli

Tetraspanin proteins are closely associated with high-curvature membrane structures and play key roles in organizing membrane domains and regulating membrane signaling in immune cells. However, their specific roles in regulating T cell membrane signaling, particularly within the microvilli often characteristic of these cells, remain poorly understood. Here, we used Jurkat T cells as a model system and investigated CD81 as a member of the tetraspanin family. Using total internal reflection fluorescence (TIRF) microscopy and structured illumination microscopy (SIM), we identified an enrichment of the tetraspanin CD81 microdomains along the actin-rich membrane microvilli. At the distal end of the microvilli, SIM images revealed the spatial colocalization of CD81 with T cell receptors (TCR) and CD63, implying a potential role for CD81 in regulating TCR signaling in conjunction with CD63. Spatial analysis of CD81 and CD63 microdomains from the dual-color SIM data revealed their preference for associating with each other. Cluster analysis of direct stochastic optical reconstruction microscopy (dSTORM) data revealed that in vitro T cell activation results in reduced domain sizes and increased domain separation of CD81. These findings provide visual evidence of the spatial organization and rearrangement of CD81 on the T cell microvilli, highlighting its potential role in signal regulation on specialized membrane protrusions.

COBRA-LIKE4 modulates cellulose synthase velocity and facilitates cellulose deposition in the secondary cell wall

Cellulose is a critical component of secondary cell walls (CWs) and woody tissues of plants. Cellulose synthase (CESA) complexes (CSCs) produce cellulose as they move within the plasma membrane, extruding glucan chains into the CW that coalesce and often crystallize into cellulose fibrils. Here we examine COBRA-LIKE4 (COBL4), a GPI-anchored protein on the outer leaflet of the plasma membrane that is required for normal cellulose deposition in secondary CWs. Characterization of the Arabidopsis (Arabidopsis thaliana) cobl4 mutant alleles called irregular xylem6, irx6-2 and irx6-3, showed reduced α-cellulose content and lower crystallinity, supporting a role for COBL4 in maintaining cellulose quantity and quality. In live-cell imaging, mNeon Green-tagged CESA7 moved in the plasma membrane at higher speeds in the irx6-2 background compared to wild-type. To test conservation of COBL4 function between herbaceous and woody plants, poplar (Populus trichocarpa) COBL4 homologs PtCOBL4a and PtCOBL4b were transformed into, and rescued, the Arabidopsis irx6 mutants. Using the Arabidopsis secondary CW-inducible VND7-GR system to study poplar COBL4 dynamics, YFP-tagged PtCOBL4a localized to the plasma membrane in regions of high cellulose deposition in secondary CW bands. As predicted for a lipid-linked protein, COBL4 was more mobile in the plane of the plasma membrane than CESA7 or a control plasma membrane marker. Following programmed cell death, COBL4 anchored to the secondary CW bands. These data support a role for COBL4 as a modulator of cellulose organization in the secondary CW, influencing cellulose production, and CSC velocity at the plasma membrane.

KARR-seq reveals cellular higher-order RNA structures and RNA-RNA interactions

RNA fate and function are affected by their structures and interactomes. However, how RNA and RNA-binding proteins (RBPs) assemble into higher-order structures and how RNA molecules may interact with each other to facilitate functions remain largely unknown. Here we present KARR-seq, which uses N3-kethoxal labeling and multifunctional chemical crosslinkers to covalently trap and determine RNA-RNA interactions and higher-order RNA structures inside cells, independent of local protein binding to RNA. KARR-seq depicts higher-order RNA structure and detects widespread intermolecular RNA-RNA interactions with high sensitivity and accuracy. Using KARR-seq, we show that translation represses mRNA compaction under native and stress conditions. We determined the higher-order RNA structures of respiratory syncytial virus (RSV) and vesicular stomatitis virus (VSV) and identified RNA-RNA interactions between the viruses and the host RNAs that potentially regulate viral replication.

Unlocking Intracellular Protein Delivery by Harnessing Polymersomes Synthesized at Microliter Volumes using Photo-PISA

Efficient delivery of therapeutic proteins and vaccine antigens to intracellular targets is challenging due to generally poor cell membrane permeation and endolysosomal entrapment causing degradation. Herein, these challenges are addressed by developing an oxygen-tolerant photoinitiated polymerization-induced self-assembly (Photo-PISA) process, allowing for the microliter-scale (10 µL) synthesis of protein-loaded polymersomes directly in 1536-well plates. High-resolution techniques capable of analysis at a single particle level are employed to analyze protein encapsulation and release mechanisms. Using confocal microscopy and super-resolution stochastic optical reconstruction microscopy (STORM) imaging, their ability to deliver proteins into the cytosol following endosomal escape is subsequently visualized. Lastly, the adaptability of these polymersomes is exploited to encapsulate and deliver a prototype vaccine antigen, demonstrating its ability to activate antigen-presenting cells and support antigen cross-presentation for applications in subunit vaccines and cancer immunotherapy. This combination of ultralow volume synthesis and efficient intracellular delivery holds significant promise for unlocking the high throughput screening of a broad range of otherwise cost-prohibitive or early-stage therapeutic protein and vaccine antigen candidates that can be difficult to obtain in large quantities. The versatility of this platform for rapid screening of intracellular protein delivery can result in significant advancements across the fields of nanomedicine and biomedical engineering.

ULM-MbCNRT: In Vivo Ultrafast Ultrasound Localization Microscopy by Combining Multibranch CNN and Recursive Transformer

Ultrasound localization microscopy (ULM) overcomes the acoustic diffraction limit by localizing tiny microbubbles (MBs), thus enabling the microvascular to be rendered at subwavelength resolution. Nevertheless, to obtain such superior spatial resolution, it is necessary to spend tens of seconds gathering numerous ultrasound (US) frames to accumulate the MB events required, resulting in ULM imaging still suffering from tradeoffs between imaging quality, data acquisition time, and data processing speed. In this article, we present a new deep learning (DL) framework combining multibranch convolutional neural network (CNN) and recursive transformer (RT), termed ULM-MbCNRT, that is capable of reconstructing a super-resolution (SR) image directly from a temporal mean low-resolution image generated by averaging much fewer raw US frames, i.e., implement an ultrafast ULM imaging. To evaluate the performance of ULM-MbCNRT, a series of numerical simulations and in vivo experiments are carried out. Numerical simulation results indicate that ULM-MbCNRT achieves high-quality ULM imaging with ~10-fold reduction in data acquisition time and ~130-fold reduction in computation time compared to the previous DL method (e.g., the modified subpixel CNN, ULM-mSPCN). For the in vivo experiments, when comparing to the ULM-mSPCN, ULM-MbCNRT allows ~37-fold reduction in data acquisition time (~0.8 s) and ~2134-fold reduction in computation time (~0.87 s) without sacrificing spatial resolution. It implies that ultrafast ULM imaging holds promise for observing rapid biological activity in vivo, potentially improving the diagnosis and monitoring of clinical conditions.

FERONIA adjusts CC1 phosphorylation to control microtubule array behavior in response to salt stress

Cell wall remodeling is important for plants to adapt to environmental stress. Under salt stress, cortical microtubules undergo a depolymerization-reassembly process to promote the biosynthesis of stress-adaptive cellulose, but the regulatory mechanisms underlying this process are still largely unknown. In this study, we reveal that FERONIA (FER), a potential cell wall sensor, interacts with COMPANION OF CELLULOSE SYNTHASE1 (CC1) and its closest homolog, CC2, two proteins that are required for cortical microtubule reassembly under salt stress. Biochemical data indicate that FER phosphorylates CC1 on multiple residues in its second and third hydrophobic microtubule-binding regions and that these phosphorylations modulate CC1 trafficking and affect the ability of CC1 to engage with microtubules. Furthermore, CC1 phosphorylation level is altered upon exposure to salt stress, which coincides with the changes of microtubule organization. Together, our study outlines an important intracellular mechanism that maintains microtubule arrays during salt exposure in plant cells.

The Rho effector ARHGAP18 coordinates a Hippo pathway feedback loop through YAP and Merlin to regulate the cytoskeleton and epithelial cell polarity

The organization of the cell's cytoskeletal filaments is coordinated through a complex symphony of signaling cascades originating from internal and external cues. Two major actin regulatory pathways are signal transduction through Rho family GTPases and growth and proliferation signaling through the Hippo pathway. These two pathways act to define the actin cytoskeleton, controlling foundational cellular attributes such as morphology and polarity. In this study, we use human epithelial cells to investigate the interplay between the Hippo and Rho Family signaling pathways, which have predominantly been characterized as independent actin regulatory mechanisms. We identify that the RhoA effector, ARHGAP18, forms a complex with the Hippo pathway transcription factor YAP to address a long-standing enigma in the field. Using super resolution STORM microscopy, we characterize the changes in the actin cytoskeleton, on the single filament level, that arise from CRISPR/Cas9 knockout of ARHGAP18. We report that the loss of ARHGAP18 results in alterations of the cell that derive from both aberrant RhoA signaling and inappropriate nuclear localization of YAP. These findings indicate that the Hippo and Rho family GTPase signaling cascades are coordinated in their temporal and spatial control of the actin cytoskeleton.

Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet

Multi-target single-molecule super-resolution fluorescence microscopy offers a powerful means of understanding the distributions and interplay between multiple subcellular structures at the nanoscale. However, single-molecule super-resolution imaging of whole mammalian cells is often hampered by high fluorescence background and slow acquisition speeds, especially when imaging multiple targets in 3D. In this work, we have mitigated these issues by developing a steerable, dithered, single-objective tilted light sheet for optical sectioning to reduce fluorescence background and a pipeline for 3D nanoprinting microfluidic systems for reflection of the light sheet into the sample. This easily adaptable microfluidic fabrication pipeline allows for the incorporation of reflective optics into microfluidic channels without disrupting efficient and automated solution exchange. We combine these innovations with point spread function engineering for nanoscale localization of individual molecules in 3D, deep learning for analysis of overlapping emitters, active 3D stabilization for drift correction and long-term imaging, and Exchange-PAINT for sequential multi-target imaging without chromatic offsets. We then demonstrate that this platform, termed soTILT3D, enables whole-cell multi-target 3D single-molecule super-resolution imaging with improved precision and imaging speed.

nanoFeatures: a cross-platform application to characterize nanoparticles from super-resolution microscopy images

Super-resolution microscopy and Single-Molecule Localization Microscopy (SMLM) are powerful tools to characterize synthetic nanomaterials used for many applications such as drug delivery. In the last decade, imaging techniques like STORM, PALM, and PAINT have been used to study nanoparticle size, structure, and composition. While imaging has progressed significantly, image analysis has often not advanced accordingly and many studies remain limited to qualitative and semi-quantitative analyses. Therefore, it is imperative to have a robust and accurate method to analyze SMLM images of nanoparticles and extract quantitative features from them. Here, we introduce nanoFeatures, a cross-platform Matlab-based app for the automatic and quantitative analysis of super-resolution images. nanoFeatures makes use of clustering algorithms to identify nanoparticles from the raw data (localization list) and extract quantitative information about size, shape, and molecular abundance at the single-particle and single-molecule levels. Moreover, it applies a series of quality controls, increasing data quality and avoiding artifacts. nanoFeatures, thanks to its intuitive interface, is also accessible to non-experts and will facilitate analysis of super-resolution microscopy for materials scientists and nanotechnologies. This easy accessibility to expansive feature characterization at the single particle level will bring us one step closer to understanding the relationship between nanostructure features and their efficiency (https://github.com/n4nlab/nanoFeatures).

Long-Axial-Range Double-Helix Point Spread Functions for 3D Volumetric Super-Resolution Imaging

Single-molecule localization microscopy (SMLM) is a powerful tool for observing structures beyond the diffraction limit of light. Combining SMLM with engineered point spread functions (PSFs) enables 3D imaging over an extended axial range, as has been demonstrated for super-resolution imaging of various cellular structures. However, super-resolving structures in 3D in thick samples, such as whole mammalian cells, remains challenging as it typically requires acquisition and postprocessing stitching of multiple slices to cover the entire sample volume or more complex analysis of the data. Here, we demonstrate how the imaging and analysis workflows can be simplified by 3D single-molecule super-resolution imaging with long-axial-range double-helix (DH)-PSFs. First, we experimentally benchmark the localization precisions of short- and long-axial-range DH-PSFs at different signal-to-background ratios by imaging fluorescent beads. The performance of the DH-PSFs in terms of achievable resolution and imaging speed was then quantified for 3D single-molecule super-resolution imaging of mammalian cells by DNA-PAINT imaging of nuclear lamina protein lamin B1 in U-2 OS cells. Furthermore, we demonstrate how the use of a deep-learning-based algorithm allows the localization of dense emitters, drastically improving the achievable imaging speed and resolution. Our data demonstrate that using long-axial-range DH-PSFs offers stitching-free, 3D super-resolution imaging of whole mammalian cells, simplifying the experimental and analysis procedures for obtaining volumetric nanoscale structural information.

Discovery of Antinociceptive α9α10 Nicotinic Acetylcholine Receptor Antagonists by Stable Receptor Expression

Chronic neuropathic pain is an increasingly prevalent societal issue that responds poorly to existing therapeutic strategies. The α9α10 nicotinic acetylcholine receptor (nAChR) has emerged as a potential target to treat neuropathic pain. However, challenges in expressing functional α9α10 nAChRs in mammalian cell lines have slowed the discovery of α9α10 ligands and studies into the relationship between α9α10 nAChRs and neuropathic pain. Here, we develop a cell line in the HEK293 background that stably expresses functional α9α10 nAChRs. By also developing cell lines expressing only α9 and α10 subunits, we identify distinct receptor pharmacology between homomeric α9 or α10 and heteromeric α9α10 nAChRs. Moreover, we demonstrate that incubation with nAChR ligands differentially regulates the expression of α9- or α10-containing nAChRs, suggesting a possible mechanism by which ligands may modify receptor composition and trafficking in α9- and α10-expressing cells. We then apply our α9α10 cell line in a screen of FDA-approved and investigational drugs to identify α9α10 ligands that provide new tools to probe α9α10 nAChR function. We demonstrate that one compound from this screen, diphenidol, possesses antinociceptive activity in a murine model of neuropathic pain. These results expand our understanding of α9α10 receptor pharmacology and provide new starting points for developing efficacious neuropathic pain treatments.

Reorganization of the flagellum scaffolding induces a sperm standstill during fertilization

Mammalian sperm delve into the female reproductive tract to fertilize the female gamete. The available information about how sperm regulate their motility during the final journey to the fertilization site is extremely limited. In this work, we investigated the structural and functional changes in the sperm flagellum after acrosomal exocytosis (AE) and during the interaction with the eggs. The evidence demonstrates that the double helix actin network surrounding the mitochondrial sheath of the midpiece undergoes structural changes prior to the motility cessation. This structural modification is accompanied by a decrease in diameter of the midpiece and is driven by intracellular calcium changes that occur concomitant with a reorganization of the actin helicoidal cortex. Midpiece contraction occurs in a subset of cells that undergo AE, and live-cell imaging during in vitro fertilization showed that the midpiece contraction is required for motility cessation after fusion is initiated. These findings provide the first evidence of the F-actin network's role in regulating sperm motility, adapting its function to meet specific cellular requirements during fertilization, and highlighting the broader significance of understanding sperm motility.

ASC specks as a single-molecule fluid biomarker of inflammation in neurodegenerative diseases

Immunotherapeutic strategies for Alzheimer's and Parkinson's disease would be facilitated by better measures of inflammation. Here we established an ultra-sensitive single-molecule pull-down immunoassay combined with direct stochastic optical reconstruction microscopy (dSTORM) to measure the number, size and shape of individual extracellular inflammasome ASC specks. We assayed human post-mortem brain, serum and cerebrospinal fluid of patients with Parkinson's and Alzheimer's as well as healthy elderly. The number of ASC specks increased and showed altered morphology in the blood of early-stage Parkinson's and Alzheimer's patients compared to controls, mimicking those found in the brain and cerebrospinal fluid. In serum samples we also measured the number of Aβ, p-tau and α-syn aggregates and formed a composite biomarker of (ASC + p-tau)/Aβ and (ASC + α-syn)/Aβ ratios that distinguished age-matched healthy controls from patients with early-stage Alzheimer's with AUC of 92% and early-stage Parkinson's with AUC of 97%. Our findings confirm ASC specks as a fluid candidate biomarker of inflammation for neurodegenerative diseases with blood being the main focus for further development as convenient sample for diagnostics and clinical trials.

The polyadenylase PAPI is required for virulence plasmid maintenance in pathogenic bacteria

Many species of pathogenic bacteria harbor critical plasmid-encoded virulence factors, and yet the regulation of plasmid replication is often poorly understood despite playing a critical role in plasmid-encoded gene expression. Human pathogenic Yersinia, including the plague agent Y. pestis and its close relative Y. pseudotuberculosis, require the type III secretion system (T3SS) virulence factor to subvert host defense mechanisms and colonize host tissues. The Yersinia T3SS is encoded on the IncFII plasmid for Y ersinia virulence (pYV). Several layers of gene regulation enables a large increase in expression of Yersinia T3SS genes at mammalian body temperature. Surprisingly, T3SS expression is also controlled at the level of gene dosage. The number of pYV molecules relative to the number of chromosomes per cell, referred to as plasmid copy number, increases with temperature. The ability to increase and maintain elevated pYV plasmid copy number, and therefore T3SS gene dosage, at 37°C is important for Yersinia virulence. In addition, pYV is highly stable in Yersinia at all temperatures, despite being dispensable for growth outside the host. Yet how Yersinia reinforces elevated plasmid replication and plasmid stability remains unclear. In this study, we show that the chromosomal gene pcnB encoding the polyadenylase PAP I is required for regulation of pYV plasmid copy number (PCN), maintenance of pYV in the bacterial population outside the host, robust T3SS activity, and Yersinia virulence in a mouse infection model. Likewise, pcnB/PAP I is also required for robust expression of the Shigella flexneri virulence plasmid-encoded T3SS. Furthermore, Yersinia and Shigella pcnB/PAP I is required for maintaining normal PCN of model antimicrobial resistance (AMR) plasmids whose replication is regulated by sRNA, thereby increasing antibiotic resistance by ten-fold. These data suggest that pcnB/PAP I contributes to the spread and stabilization of virulence and AMR plasmids in bacterial pathogens, and is essential in maintaining the gene dosage required to mediate plasmid-encoded traits. Importantly pcnB/PAP I has been bioinformatically identified in many species of bacteria despite being studied in only a few species to date. Our work highlights the potential importance of pcnB/PAP I in antibiotic resistance, and shows for the first time that pcnB/PAP I reinforces PCN and virulence plasmid stability in natural pathogenic hosts with a direct impact on bacterial virulence.

Nanoscopic visualization of microgel-immobilized cytochrome P450 enzymes and their local activity

Microgels provide a controlled microenvironment for enzymes, protecting them from degradation while enhancing stability and activity. Their customizable and biocompatible structure allows for targeted delivery and controlled release, making them ideal for transporting and preserving enzyme function in various applications. For such applications, detailed knowledge of the distribution of enzymes and their activity within the microgels is essential. We present a combination of different localization-based super-resolution fluorescence microscopy measurements to localise single Cytochrome P450 BM3 enzymes and compare their local catalytic activity.

New PALM-compatible integration vectors for use in the Gram-positive model bacterium Bacillus subtilis

Improvements in super-resolution and single-molecule techniques, along with the development of new fluorescent proteins and labeling methods, have allowed super-resolution imaging of bacterial cells. Cloning vectors are important tools for engineering fluorescent fusions and perform efficient labeling. Here, we report the construction of four photoactivated localization microscopy (PALM)-compatible integration plasmids for the Gram-positive model organism Bacillus subtilis. These plasmids carry genes encoding either the photoswitchable green fluorescent protein dronPA or the photoactivatable red fluorescent protein PAmCherry1, codon-optimized or not for expression in B. subtilis. For fast and flexible cloning, multiple cloning sites were added at both the C-terminal and the N-terminal ends of the fluorescent protein genes. The plasmids replicate in Escherichia coli and allow integration at the ectopic amyE or thrC loci of B. subtilis via double homologous recombination, for stable chromosomal insertions of single copy number dronPA and PAmCherry1 fusions, respectively. Two-color imaging is accessible with the simultaneous use of both vectors. Insertion of the LacI repressor gene under control of a constitutive promoter in each plasmid yielded four derivative vectors that, combined with an array of lacO operator sites, allow fluorescent repressor-operator system localization studies. We demonstrated the effective photoactivation of the LacI-dronPA and LacI-PAmCherry1 fusions, and used them to report with nanoscale precision bacteriophage SPP1 DNA within infected B. subtilis cells, both live and fixed, as proof of concept. Our integration vectors provide a convenient and versatile workflow for qualitative and quantitative, single- and dual-color PALM studies in B. subtilis.

IMPORTANCE

Super-resolution microscopy techniques allow localization of proteins and cellular components in prokaryotic and eukaryotic cells with unprecedented spatial resolution. Plasmids remain a powerful approach to clone fluorescent protein fusions in bacterial cells. In the current work, we expanded the toolbox of vectors available to engineer the Gram-positive model organism Bacillus subtilis for PALM studies. Four integrative vectors in total, two carrying the gene encoding the photoswitchable green fluorescent protein dronPA and two carrying the gene encoding the photoactivatable red fluorescent protein PAmCherry1, were constructed and tested by generating translational fusions to the LacI repressor. The LacI fluorescent fusions successfully reported the subcellular localization of viral DNA in infected B. subtilis cells, either live or upon fixation, by PALM. Our dronPA and PAmCherry1 integration vectors expand the genetic toolbox for single-molecule localization microscopy studies in B. subtilis.

Correlative super-resolution microscopy with deep UV reactivation

Correlative super-resolution microscopy has the potential to accurately visualize and validate new biological structures past the diffraction limit. However, combining different super-resolution modalities, such as deterministic stimulated emission depletion (STED) and stochastic single-molecule localization microscopy (SMLM), is a challenging endeavour. For correlative STED and SMLM, the following poses a significant challenge: (1) the photobleaching of the fluorophores in STED; (2) the subsequent reactivation of the fluorophores for SMLM and (3) finding the right fluorochrome and imaging buffer for both imaging modalities. Here, we highlight how the deep ultraviolet (DBUE) wavelengths of the Mercury (Hg) arc lamp can help recover STED bleaching and allow for the reactivation of single molecules for SMLM imaging. We also show that Alexa Fluor 594 and the commercially available Prolong Diamond to be excellent fluorophores and imaging media for correlative STED and SMLM.

Revealing Spatial Molecular Heterogeneity of High-Density Biofunctionalized Surfaces Using DNA-PAINT

The quantification and control of molecular densities and distributions on biofunctionalized surfaces are key for enabling reproducible functions in biosciences. Here, we describe an analysis methodology for quantifying the density and spatial distribution of high-density biofunctionalized surfaces, with densities in the order of 102-105 biomolecules per μm2 area, in a short measurement time. The methodology is based on single-molecule DNA-PAINT imaging combined with simulation models that compensate for lifetime and spatial undersampling effects, resulting in three distinct molecule counting methods and a statistical test for spatial distribution. The analysis methodology is exemplified for a surface with ssDNA affinity binder molecules coupled to a PLL-g-PEG antifouling coating. The results provide insights into the biofunctionalization efficiency, yield, and homogeneity. Furthermore, the data reveal that heterogeneity is inherent to the biofunctionalization process and shed light on the underlying molecular mechanisms. We envision that DNA-PAINT imaging with the developed analysis framework will become a versatile tool to study spatial heterogeneity of densely biofunctionalized surfaces for a wide range of applications.

Point-Spread Function Deformations Unlock 3D Localization Microscopy on Spherical Nanoparticles

Nanoparticles (NPs) have proven their applicability in biosensing, drug delivery, and photothermal therapy, but their performance depends critically on the distribution and number of functional groups on their surface. When studying surface functionalization using super-resolution microscopy, the NP modifies the fluorophore's point-spread function (PSF). This leads to systematic mislocalizations in conventional analyses employing Gaussian PSFs. Here, we address this shortcoming by deriving the analytical PSF model for a fluorophore near a spherical NP. Its calculation is four orders of magnitude faster than numerical approaches and thus feasible for direct use in localization algorithms. We fit this model to individual 2D images from DNA-PAINT experiments on DNA-coated gold NPs and demonstrate extraction of the 3D positions of functional groups with <5 nm precision, revealing inhomogeneous surface coverage. Our method is exact, fast, accessible, and poised to become the standard in super-resolution imaging of NPs for biosensing and drug delivery applications.

DivIVA controls the dynamics of septum splitting and cell elongation in Streptococcus pneumoniae

Bacterial shape and division rely on the dynamics of cell wall assembly, which involves regulated synthesis and cleavage of the peptidoglycan. In ovococci, these processes are coordinated within an annular mid-cell region with nanometric dimensions. More precisely, the cross-wall synthesized by the divisome is split to generate a lateral wall, whose expansion is insured by the insertion of the so-called peripheral peptidoglycan by the elongasome. Septum cleavage and peripheral peptidoglycan synthesis are, thus, crucial remodeling events for ovococcal cell division and elongation. The structural DivIVA protein has long been known as a major regulator of these processes, but its mode of action remains unknown. Here, we integrate click chemistry-based peptidoglycan labeling, direct stochastic optical reconstruction microscopy, and in silico modeling, as well as epifluorescence and stimulated emission depletion microscopy to investigate the role of DivIVA in Streptococcus pneumoniae cell morphogenesis. Our work reveals two distinct phases of peptidoglycan remodeling during the cell cycle that are differentially controlled by DivIVA. In particular, we show that DivIVA ensures homogeneous septum cleavage and peripheral peptidoglycan synthesis around the division site and their maintenance throughout the cell cycle. Our data additionally suggest that DivIVA impacts the contribution of the elongasome and class A penicillin-binding proteins to cell elongation. We also report the position of DivIVA on either side of the septum, consistent with its known affinity for negatively curved membranes. Finally, we take the opportunity provided by these new observations to propose hypotheses for the mechanism of action of this key morphogenetic protein.IMPORTANCEThis study sheds light on fundamental processes governing bacterial growth and division, using integrated click chemistry, advanced microscopy, and computational modeling approaches. It addresses cell wall synthesis mechanisms in the opportunistic human pathogen Streptococcus pneumoniae, responsible for a range of illnesses (otitis, pneumonia, meningitis, septicemia) and for one million deaths every year worldwide. This bacterium belongs to the morphological group of ovococci, which includes many streptococcal and enterococcal pathogens. In this study, we have dissected the function of DivIVA, which is a structural protein involved in cell division, morphogenesis, and chromosome partitioning in Gram-positive bacteria. This work unveils the role of DivIVA in the orchestration of cell division and elongation along the pneumococcal cell cycle. It not only enhances our understanding of how ovoid bacteria proliferate but also offers the opportunity to consider how DivIVA might serve as a scaffold and sensor for particular membrane regions, thereby participating in various cell cycle processes.