Single-Molecule Localization Microscopy and Tracking with a Fluorescent Mechanosensitive Probe

A milestone in optical imaging of mechanical forces in cells has been the development of the family of flipper fluorescent probes able to report membrane tension noninvasively in living cells through their fluorescence lifetime. The specifically designed Flipper-CF3 probe with an engineered inherent blinking mechanism was recently introduced for super-resolution fluorescence microscopy of lipid ordered membranes but was too dim to be detected in lipid disordered membranes at the single-molecule level (García-Calvo, J. J. Am. Chem. Soc. 2020, 142(28), 12034-12038). We show here that the original and commercially available probe Flipper-TR is compatible with single-molecule based super-resolution imaging and resolves both liquid ordered and liquid disordered membranes of giant unilamellar vesicles below the diffraction limit. Single probe molecules were additionally tracked in lipid bilayers, enabling to distinguish membranes of varying composition from the diffusion coefficient of the probe. Differences in brightness between Flipper-CF3 and Flipper-TR originate in their steady-state absorption and fluorescence properties. The general compatibility of the Flipper-TR scaffold with single-molecule detection is further shown in super-resolution experiments with targetable Flipper-TR derivatives.

Recent advances in super-resolution optical imaging based on aggregation-induced emission

Super-resolution imaging has rapidly emerged as an optical microscopy technique, offering advantages of high optical resolution over the past two decades; achieving improved imaging resolution requires significant efforts in developing super-resolution imaging agents characterized by high brightness, high contrast and high sensitivity to fluorescence switching. Apart from technical requirements in optical systems and algorithms, super-resolution imaging relies on fluorescent dyes with special photophysical or photochemical properties. The concept of aggregation-induced emission (AIE) was proposed in 2001, coinciding with unprecedented advancements and innovations in super-resolution imaging technology. AIE probes offer many advantages, including high brightness in the aggregated state, low background signal, a larger Stokes shift, ultra-high photostability, and excellent biocompatibility, making them highly promising for applications in super-resolution imaging. In this review, we summarize the progress in implementation methods and provide insights into the mechanism of AIE-based super-resolution imaging, including fluorescence switching resulting from photochemically-converted aggregation-induced emission, electrostatically controlled aggregation-induced emission and specific binding-regulated aggregation-induced emission. Particularly, the aggregation-induced emission principle has been proposed to achieve spontaneous fluorescence switching, expanding the selection and application scenarios of super-resolution imaging probes. By combining the aggregation-induced emission principle and specific molecular design, we offer some comprehensive insights to facilitate the applications of AIEgens (AIE-active molecules) in super-resolution imaging.

Nanoscale imaging of tumor cell exosomes by expansion single molecule localization microscopy (ExSMLM)

Tumor cell exosomes play a very important role in the process of tumor cell proliferation and metastasis. However, due to the nanoscale size and high heterogeneity of exosomes, in-depth understanding of their appearance and biological characteristics is still lacking. Expansion microscopy (ExM) is a method that embeds biological samples in a swellable gel to physically magnify the samples to improve the imaging resolution. Before the emergence of ExM, scientists had invented several super-resolution imaging techniques that could break the diffraction limit. Among them, single molecule localization microscopy (SMLM) usually has the best spatial resolution (20-50 nm). However, considering the small size of exosomes (30-150 nm), the resolution of SMLM is still not high enough for detailed imaging of exosomes. Hence, we propose a tumor cell exosomes imaging method that combines ExM and SMLM (i.e. Expansion SMLM, denoted as ExSMLM), which can realize the expansion and super-resolution imaging of tumor cell exosomes. In this technique, immunofluorescence was first performed to fluorescently label the protein markers on the exosomes, then the exosomes were polymerized into a swellable polyelectrolyte gel. The electrolytic nature of the gel made the fluorescently labeled exosomes undergo isotropic linear physical expansion. The expansion factor obtained in the experiment was about 4.6. Finally, SMLM imaging of the expanded exosomes was performed. Owing to the improved resolution of ExSMLM, nanoscale substructures of closely packed proteins were observed on single exosomes, which has never been achieved before. With such a high resolution, ExSMLM would have a great potential in detailed investigation of exosomes and exosome-related biological processes.

Assessing Antigen Presentation on the Surface of Plasmodium falciparum-Infected Erythrocytes by Photoactivated Localization Microscopy (PALM)

Super-resolution microscopy in the form of photoactivated localization microscopy (PALM) offers the possibility of counting single molecules in a cell, a cellular compartment or a molecular complex. PALM can, therefore, underpin molecular and biochemical processes with a numeric and stoichiometric understanding of the interacting players. Here, we introduce the physical principles underlying PALM and provide a step-by-step protocol of how to apply PALM to questions related to the biology and pathophysiology of P. falciparum and other malaria parasites.

Neurophotonic tools for microscopic measurements and manipulation: status report

Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.

Directed evolution approaches for optogenetic tool development

Photoswitchable proteins enable specific molecular events occurring in complex biological settings to be probed in a rapid and reversible fashion. Recent progress in the development of photoswitchable proteins as components of optogenetic tools has been greatly facilitated by directed evolution approaches in vitro, in bacteria, or in yeast. We review these developments and suggest future directions for this rapidly advancing field.

The Benefits of Unnatural Amino Acid Incorporation as Protein Labels for Single Molecule Localization Microscopy

Single Molecule Localization Microscopy (SMLM) is an imaging method that allows for the visualization of structures smaller than the diffraction limit of light (~200 nm). This is achieved through techniques such as stochastic optical reconstruction microscopy (STORM) and photoactivated localization microscopy (PALM). A large part of obtaining ideal imaging of single molecules is the choice of the right fluorescent label. An upcoming field of protein labeling is incorporating unnatural amino acids (UAAs) with an attached fluorescent dye for precise localization and visualization of individual molecules. For this technique, fluorescent probes are conjugated to UAAs and are introduced into the protein of interest (POI) as a label. Here we contrast this labeling method with other commonly used protein-based labeling methods such as fluorescent proteins (FPs) or self-labeling tags such as Halotag, SNAP-tags, and CLIP-tags, and highlight the benefits and shortcomings of the site-specific incorporation of UAAs coupled with fluorescent dyes in SMLM.

FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy

Single-molecule localization microscopy (SMLM) is a powerful tool for studying intracellular structure and macromolecular organization at the nanoscale. The increasingly massive pointillistic data sets generated by SMLM require the development of new and highly efficient quantification tools. Here we present FOCAL3D, an accurate, flexible and exceedingly fast (scaling linearly with the number of localizations) density-based algorithm for quantifying spatial clustering in large 3D SMLM data sets. Unlike DBSCAN, which is perhaps the most commonly employed density-based clustering algorithm, an optimum set of parameters for FOCAL3D may be objectively determined. We initially validate the performance of FOCAL3D on simulated datasets at varying noise levels and for a range of cluster sizes. These simulated datasets are used to illustrate the parametric insensitivity of the algorithm, in contrast to DBSCAN, and clustering metrics such as the F1 and Silhouette score indicate that FOCAL3D is highly accurate, even in the presence of significant background noise and mixed populations of variable sized clusters, once optimized. We then apply FOCAL3D to 3D astigmatic dSTORM images of the nuclear pore complex (NPC) in human osteosaracoma cells, illustrating both the validity of the parameter optimization and the ability of the algorithm to accurately cluster complex, heterogeneous 3D clusters in a biological dataset. FOCAL3D is provided as an open source software package written in Python.

We have developed an accurate, highly-efficient and flexible algorithm for quantifying spatial clustering in large, 3-dimensional single-molecule localization microscopy (SMLM) datasets. Our method, FOCAL3D, is provided as an open-source software package written in Python. FOCAL3D scales linearly with the number of localizations and the algorithmic parameters may be systematically optimized so that the resulting analysis is insensitive to variation over a range of parameter choices. We initially validate the performance and parametric insensitivity of FOCAL3D on simulated datasets, then apply the algorithm to 3-dimensional, astigmatic dSTORM images of the nuclear pore complex in human osteosarcoma cells.

Fluorescent Membrane Tension Probes for Super-Resolution Microscopy: Combining Mechanosensitive Cascade Switching with Dynamic-Covalent Ketone Chemistry

We report the design, synthesis, and evaluation of fluorescent flipper probes for single-molecule super-resolution imaging of membrane tension in living cells. Reversible switching from bright-state ketones to dark-state hydrates, hemiacetals, and hemithioacetals is demonstrated for twisted and planarized mechanophores in solution and membranes. Broadband femtosecond fluorescence up-conversion spectroscopy evinces ultrafast chalcogen-bonding cascade switching in the excited state in solution. According to fluorescence lifetime imaging microscopy, the new flippers image membrane tension in live cells with record red shifts and photostability. Single-molecule localization microscopy with the new tension probes resolves membranes well below the diffraction limit.

Turn-on mode fluorescent diarylethenes: effect of electron-donating and electron-withdrawing substituents on photoswitching performance†

Diarylethene derivatives having benzothiophene S,S-dioxide groups undergo turn-on mode fluorescence photoswitching. For the practical application to super-resolution fluorescence microscopy, photoswitchable fluorescent molecules are desired to be resistant against photodegradation. Here we synthesized turn-on mode fluorescent diarylethenes having electron-withdrawing (trifluoromethyl or nitro) or electron-donating (methyl, methoxy, or dimethylamino) substituents on phenyl rings at 6- and 6'-positions of the benzothiophene S,S-dioxide groups and examined the effect of the substituents on the photoswitchiing performance. The derivatives having electron-donating substituents showed significant bathochromic shifts of the absorption and fluorescence spectra. The cycloreversion quantum yield was increased by introducing electron-withdrawing substituents, while it was decreased by the electron-donating ones. Introduction of electron-donating substituents was found to remarkably improve the fatigue resistance of the fluorescent diarylethene under continuous ultraviolet (UV) irradiation. Such highly fatigue-resistant fluorescent diarylethenes are useful for super-resolution fluorescence imaging or single-molecule fluorescence tracking.

Single-molecule imaging reveals the oligomeric state of functional TNFα-induced plasma membrane TNFR1 clusters in cells

Ligand-induced tumor necrosis factor receptor 1 (TNFR1) activation controls nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) signaling, cell proliferation, programmed cell death, and survival and is crucially involved in inflammation, autoimmune disorders, and cancer progression. Despite the relevance of TNFR1 clustering for signaling, oligomerization of ligand-free and ligand-activated TNFR1 remains controversial. At present, models range from ligand-independent receptor predimerization to ligand-induced oligomerization. Here, we used quantitative, single-molecule superresolution microscopy to study TNFR1 assembly directly in native cellular settings and at physiological cell surface abundance. In the absence of its ligand TNFα, TNFR1 assembled into monomeric and dimeric receptor units. Upon binding of TNFα, TNFR1 clustered predominantly not only into trimers but also into higher-order oligomers. A functional mutation in the preligand assembly domain of TNFR1 resulted in only monomeric TNFR1, which exhibited impaired ligand binding. In contrast, a form of TNFR1 with a mutation in the ligand-binding CRD2 subdomain retained the monomer-to-dimer ratio of the unliganded wild-type TNFR1 but exhibited no ligand binding. These results underscore the importance of ligand-independent TNFR1 dimerization in NF-κB signaling.

The first example of “turn-off” red fluorescence photoswitching for the representatives of nitrile-rich negative photochromes

The first example of reversible fluorescence photoswitching by visible light was shown for the representatives of negative photochromes containing a nitrile-rich acceptor.

Optical super-resolution microscopy unravels the molecular composition of functional protein complexes

Optical super-resolution microscopy has revolutionized our understanding of cell biology. Next to visualizing cellular structures with near-molecular spatial resolution, an additional benefit is the molecular characterization of biomolecular complexes directly in an intact cell. Single-molecule localization microscopy, as one technology out of the toolbox of super-resolution methods, generates images by detecting the position of single fluorophore labels and is particularly suited for molecular quantification. We review imaging and analysis methods employing single-molecule localization microscopy and extract molecule numbers.

Super-resolution imaging and estimation of protein copy numbers at single synapses with DNA-point accumulation for imaging in nanoscale topography

In the brain, the strength of each individual synapse is defined by the complement of proteins present or the "local proteome." Activity-dependent changes in synaptic strength are the result of changes in this local proteome and posttranslational protein modifications. Although most synaptic proteins have been identified, we still know little about protein copy numbers in individual synapses and variations between synapses. We use DNA-point accumulation for imaging in nanoscale topography as a single-molecule super-resolution imaging technique to visualize and quantify protein copy numbers in single synapses. The imaging technique provides near-molecular spatial resolution, is unaffected by photobleaching, enables imaging of large field of views, and provides quantitative molecular information. We demonstrate these benefits by accessing copy numbers of surface AMPA-type receptors at single synapses of rat hippocampal neurons along dendritic segments.

Synthetic and genetic dimers as quantification ruler for single-molecule counting with PALM

How membrane proteins oligomerize determines their function. Superresolution microscopy can report on protein clustering and extract quantitative molecular information. Here, we evaluate the blinking kinetics of four photoactivatable fluorescent proteins for quantitative single-molecule microscopy. We identified mEos3.2 and mMaple3 to be suitable for molecular quantification through blinking histogram analysis. We designed synthetic and genetic dimers of mEos3.2 as well as fusion proteins of monomeric and dimeric membrane proteins as reference structures, and we demonstrate their versatile use for quantitative superresolution imaging in vitro and in situ. We further found that the blinking behavior of mEos3.2 and mMaple3 is modified by a reducing agent, offering the possibility to adjust blinking parameters according to experimental needs.

Visualizing ubiquitination in mammalian cells

Covalent modification of proteins with ubiquitin is essential for the majority of biological processes in mammalian cells. Numerous proteins are conjugated with single or multiple ubiquitin molecules or chains in a dynamic fashion, often determining protein half-lives, localization or function. Experimental approaches to study ubiquitination have been dominated by genetic and biochemical analysis of enzyme structure-function relationships, reaction mechanisms and physiological relevance. Here, we provide an overview of recent developments in microscopy-based imaging of ubiquitination, available reagents and technologies. We discuss the progress in direct and indirect imaging of differentially linked ubiquitin chains in fixed and living cells using confocal fluorescence microscopy and super-resolution microscopy, illustrated by the role of ubiquitin in antibacterial autophagy and pro-inflammatory signalling. Finally, we speculate on future developments and forecast a transition from qualitative to quantitative super-resolution approaches to understand fundamental aspects of ubiquitination and the formation and distribution of functional E3 ligase protein complexes in their native environment.

A Method to Visualize the Nanoscopic Morphology of Astrocytes In Vitro and In Situ

In recent years it has become apparent that astroglia are not only essential players in brain development, homeostasis, and metabolic support but are also important for the formation and regulation of synaptic circuits. Fine astrocytic processes that can be found in the vicinity of synapses undergo considerable structural plasticity associated with age- and use-dependent changes in neural circuitries. However, due to the extraordinary complex, essentially nanoscopic morphology of astroglia, the underlying cellular mechanisms remain poorly understood.Here we detail a super-resolution microscopy approach, based on the single-molecule localisation microscopy (SMLM) technique direct stochastic optical reconstruction microscopy (dSTORM) to visualize astroglial morphology on the nanoscale. This approach enables visualization of key morphological changes that occur in nanoscopic astrocyte processes, whose characteristic size falls below the diffraction limit of conventional optical microscopy.

Unusual fluorescent photoswitching of imidazole derivatives: the role of molecular conformation and twist angle controlled organic solid state fluorescence

Triphenylamine-imidazole molecules exhibited unprecedented light induced fluorescence switching via conformational change.

Photoswitchable Fluorescent Diarylethene Derivatives with Thiophene 1,1-Dioxide Groups: Effect of Alkyl Substituents at the Reactive Carbons

Photoswitching and fluorescent properties of sulfone derivatives of 1,2-bis(2-alkyl-4-methyl-5-phenyl-3-thienyl)perfluorocyclopentene, 1–5, having methyl, ethyl, n-propyl, i-propyl, and i-butyl substituents at the reactive carbons (2- and 2′-positions) of the thiophene 1,1-dioxide rings were studied. Diarylethenes 1–5 underwent isomerization reactions between open-ring and closed-ring forms upon alternate irradiation with ultraviolet (UV) and visible light and showed fluorescence in the closed-ring forms. The alkyl substitution at the reactive carbons affects the fluorescent property of the closed-ring isomers. The closed-ring isomers 2b–5b with ethyl, n-propyl, i-propyl, and i-butyl substituents show higher fluorescence quantum yields than 1b with methyl substituents. In polar solvents, the fluorescence quantum yield of 1b markedly decreases, while 2b–5b maintain the relatively high fluorescence quantum yields. Although the cycloreversion quantum yields of the derivatives with methyl, ethyl, n-propyl, and i-propyl substituents are quite low and in the order of 10⁻⁵, introduction of i-butyl substituents was found to increase the yield up to the order of 10⁻³. These results indicate that appropriate alkyl substitution at the reactive carbons is indispensable for properly controlling the photoswitching and fluorescent properties of the photoswitchable fluorescent diarylethenes, which are potentially applicable to super-resolution fluorescence microscopies.

Quantitative microscopy based on single-molecule fluorescence

Quantitative microscopy is needed to understand reactions or phenomena carried out by biological molecules such as enzymes, receptors, and membrane-localized proteins. Counting the biomolecules of interest in single organelles or cellular compartments is critical in these approaches. In this brief perspective, we focus on the development of quantitative fluorescence microscopies that measure the precise copy numbers of proteins in cellular organelles or purified samples. We introduce recent improvements in quantitative microscopies to overcome undercounting or overcounting errors in certain conditions. We conclude by discussing biological applications.

Single-Molecule Localization Microscopy in Eukaryotes

Super-resolution fluorescence imaging by photoactivation or photoswitching of single fluorophores and position determination (single-molecule localization microscopy, SMLM) provides microscopic images with subdiffraction spatial resolution. This technology has enabled new insights into how proteins are organized in a cellular context, with a spatial resolution approaching virtually the molecular level. A unique strength of SMLM is that it delivers molecule-resolved information, along with super-resolved images of cellular structures. This allows quantitative access to cellular structures, for example, how proteins are distributed and organized and how they interact with other biomolecules. Ultimately, it is even possible to determine protein numbers in cells and the number of subunits in a protein complex. SMLM thus has the potential to pave the way toward a better understanding of how cells function at the molecular level. In this review, we describe how SMLM has contributed new knowledge in eukaryotic biology, and we specifically focus on quantitative biological data extracted from SMLM images.

Molecule Counts in Localization Microscopy with Organic Fluorophores

Single-molecule localization microscopy (SMLM) can be used to count fluorescently labeled molecules even when they are not individually resolved. We demonstrate SMLM molecule counting for nucleic acids labeled with the organic fluorophore Alexa Fluor 647 and imaged under photoswitching conditions. From the observed distributions of the number of fluorophore blinking events, we extract the number of fluorophores per spot using a statistical model. We validate the molecule counting method for single Alexa Fluor 647 fluorophores, and for trimers of Alexa Fluor 647 constructed on a DNA origami structure. This simple counting strategy enables quantitative super-resolution imaging with organic fluorophores.

Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins: The Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells

Despite their small size and the lack of compartmentalization, bacteria exhibit a striking degree of cellular organization, both in time and space. During the last decade, a group of new microscopy techniques emerged, termed super-resolution microscopy or nanoscopy, which facilitate visualizing the organization of proteins in bacteria at the nanoscale. Single-molecule localization microscopy (SMLM) is especially well suited to reveal a wide range of new information regarding protein organization, interaction, and dynamics in single bacterial cells. Recent developments in click chemistry facilitate the visualization of bacterial chromatin with a resolution of ~20 nm, providing valuable information about the ultrastructure of bacterial nucleoids, especially at short generation times. In this chapter, we describe a simple-to-realize protocol that allows determining precise structural information of bacterial nucleoids in fixed cells, using direct stochastic optical reconstruction microscopy (dSTORM). In combination with quantitative photoactivated localization microscopy (PALM), the spatial relationship of proteins with the bacterial chromosome can be studied. The position of a protein of interest with respect to the nucleoids and the cell cylinder can be visualized by super-resolving the membrane using point accumulation for imaging in nanoscale topography (PAINT). The combination of the different SMLM techniques in a sequential workflow maximizes the information that can be extracted from single cells, while maintaining optimal imaging conditions for each technique.

3D d STORM Imaging of Fixed Brain Tissue

Central nervous system tissue contains a high density of synapses each composed of an intricate molecular machinery mediating precise transmission of information. Deciphering the molecular nanostructure of pre- and postsynaptic specializations within such a complex tissue architecture poses a particular challenge for light microscopy. Here, we describe two approaches suitable to examine the molecular nanostructure of synapses at 20-30 nm lateral and 50-70 nm axial resolution within an area of 500 μm × 500 μm and a depth of 0.6 μm to several micrometers. We employ single-molecule localization microscopy (SMLM) on immunolabeled fixed brain tissue slices. tomoSTORM utilizes array tomography to achieve SMLM in 40 nm thick resin-embedded sections. dSTORM of cryo-sectioned slices uses optical sectioning in 0.1-4 μm thick hydrated sections. Both approaches deliver 3D nanolocalization of two or more labeled proteins within a defined tissue volume. We review sample preparation, data acquisition, analysis, and interpretation.

Quantitative Single-Molecule Localization Microscopy (qSMLM) of Membrane Proteins Based on Kinetic Analysis of Fluorophore Blinking Cycles

Photoswitchable or photoactivatable fluorophores are the key in single-molecule localization microscopy. Next to providing fluorescence images with subdiffraction spatial resolution, additional information is available from observing single fluorophores over time. This includes the characteristic photophysical phenomenon of "blinking" that is exhibited by single fluorescent proteins or fluorophores and follows well-defined kinetic laws. Analyzing the kinetics of "blinking" allows determining the number of fluorophores in a multi-molecular complex. As such, quantitative information at the molecular level can be extracted, representing a tremendously useful extension of single-molecule super-resolution microscopy. This concept is in particular useful to study homo- and heterooligomeric signaling protein complexes in the plasma membrane of an intact cell with molecular resolution. Here, we provide an experimental framework for deciphering the stoichiometry of membrane proteins on the basis of SMLM and photoswitching statistics.

Model-independent counting of molecules in single-molecule localization microscopy

Most biomolecular processes rely on tightly controlled stoichiometries, from the formation of molecular assemblies to cellular signaling. Single-molecule localization micro-scopy studies of fluorophore blinking offer a promising route to probe oligomeric states. Here we show that the distribution of the number of blinking events assumes a universal functional form, independent of photophysics, under relatively mild assumptions. The number of photophysical states, the kinetics of interconversion, and the fraction of active fluorophores enter as two or three constants. This essentially model-independent formulation allows us to determine molecule counts from fluorophore blinking statistics. The formulas hold even if the fluorophores have many different yet unresolved dark states, as long as there is only a single fluorescent state, or if there are different yet unresolvable fluorescent states, as long as there is only a single dark state. We demonstrate the practical applicability of this approach by quantifying the oligomerization states of membrane proteins tagged with the mEos2 fluorescent protein. We find that the model parameters, obtained by likelihood maximization, are transferable. With the counting statistics being independent of the detailed photophysics and its parameters being transferable, the method should be robust and broadly applicable to counting colocalized molecules in vivo and in vitro.

Single-Molecule Localization Microscopy allows for the analysis of cancer metastasis-specific miRNA distribution on the nanoscale

We describe a novel approach for the detection of small non-coding RNAs in single cells by Single-Molecule Localization Microscopy (SMLM). We used a modified SMLM–setup and applied this instrument in a first proof-of-principle concept to human cancer cell lines. Our method is able to visualize single microRNA (miR)-molecules in fixed cells with a localization accuracy of 10–15 nm, and is able to quantify and analyse clustering and localization in particular subcellular sites, including exosomes. We compared the metastasis-site derived (SW620) and primary site derived (SW480) human colorectal cancer (CRC) cell lines, and (as a proof of principle) evaluated the metastasis relevant miR-31 as a first example. We observed that the subcellular distribution of miR-31 molecules in both cell lines was very heterogeneous with the largest subpopulation of optically acquired weakly metastatic cells characterized by a low number of miR-31 molecules, as opposed to a significantly higher number in the majority of the highly metastatic cells.

Furthermore, the highly metastatic cells had significantly more miR-31-molecules in the extracellular space, which were visualized to co-localize with exosomes in significantly higher numbers. From this study, we conclude that miRs are not only aberrantly expressed and regulated, but also differentially compartmentalized in cells with different metastatic potential. Taken together, this novel approach, by providing single molecule images of miRNAs in cellulo can be used as a powerful supplementary tool in the analysis of miRNA function and behaviour and has far reaching potential in defining metastasis-critical subpopulations within a given heterogeneous cancer cell population.

Extracting quantitative information from single-molecule super-resolution imaging data with LAMA - LocAlization Microscopy Analyzer

Super-resolution fluorescence microscopy revolutionizes cell biology research and provides novel insights on how proteins are organized at the nanoscale and in the cellular context. In order to extract a maximum of information, specialized tools for image analysis are necessary. Here, we introduce the LocAlization Microscopy Analyzer (LAMA), a comprehensive software tool that extracts quantitative information from single-molecule super-resolution imaging data. LAMA allows characterizing cellular structures by their size, shape, intensity, distribution, as well as the degree of colocalization with other structures. LAMA is freely available, platform-independent and designed to provide direct access to individual analysis of super-resolution data.

Single-particle tracking uncovers dynamics of glutamate-induced retrograde transport of NF-κB p65 in living neurons

Retrograde transport of NF-κB from the synapse to the nucleus in neurons is mediated by the dynein/dynactin motor complex and can be triggered by synaptic activation. The caliber of axons is highly variable ranging down to 100 nm, aggravating the investigation of transport processes in neurites of living neurons using conventional light microscopy. We quantified for the first time the transport of the NF-κB subunit p65 using high-density single-particle tracking in combination with photoactivatable fluorescent proteins in living mouse hippocampal neurons. We detected an increase of the mean diffusion coefficient ([Formula: see text]) in neurites from [Formula: see text] to [Formula: see text] after stimulation with glutamate. We further observed that the relative amount of retrogradely transported p65 molecules is increased after stimulation. Glutamate treatment resulted in an increase of the mean retrograde velocity from [Formula: see text] to [Formula: see text], whereas a velocity increase from [Formula: see text] to [Formula: see text] was observed for anterogradely transported p65. This study demonstrates for the first time that glutamate stimulation leads to an increased mobility of single NF-κB p65 molecules in neurites of living hippocampal neurons.

Biased signalling is an essential feature of TLR4 in glioma cells

A distinct feature of the Toll-like receptor 4 (TLR4) is its ability to trigger both MyD88-dependent and MyD88-independent signalling, culminating in activation of pro-inflammatory NF-κB and/or the antiviral IRF3. Although TLR4 agonists (lipopolysaccharides; LPSs) derived from different bacterial species have different endotoxic activity, the impact of LPS chemotype on the downstream signalling is not fully understood. Notably, different TLR4 agonists exhibit anti-tumoural activity in animal models of glioma, but the underlying molecular mechanisms are largely unknown. Thus, we investigated the impact of LPS chemotype on the signalling events in the human glioma cell line U251. We found that LPS of Escherichia coli origin (LPS_EC) leads to NF-κB-biased downstream signalling compared to Salmonella minnesota-derived LPS (LPS_SM). Exposure of U251 cells to LPS_EC resulted in faster nuclear translocation of the NF-κB subunit p65, higher NF-κB-activity and expression of its targets genes, and higher amount of secreted IL-6 compared to LPS_SM. Using super-resolution microscopy we showed that the biased agonism of TLR4 in glioma cells is neither a result of differential regulation of receptor density nor of formation of higher order oligomers. Consistent with previous reports, LPS_EC-mediated NF-κB activation led to significantly increased U251 proliferation, whereas LPS_SM-induced IRF3 activity negatively influenced their invasiveness. Finally, treatment with methyl-β-cyclodextrin (MCD) selectively increased LPS_SM-induced nuclear translocation of p65 and NF-κB activity without affecting IRF3. Our data may explain how TLR4 agonists differently affect glioma cell proliferation and migration.

Nanoscopic Visualization of Soft Matter Using Fluorescent Diarylethene Photoswitches

The in situ imaging of soft matter is of paramount importance for a detailed understanding of functionality on the nanoscopic scale. Although super-resolution fluorescence microscopy methods with their unprecedented imaging capabilities have revolutionized research in the life sciences, this potential has been far less exploited in materials science. One of the main obstacles for a more universal application of super-resolved fluorescence microscopy methods is the limitation of readily available suitable dyes to overcome the diffraction limit. Here, we report a novel diarylethene-based photoswitch with a highly fluorescent closed and a nonfluorescent open form. Its photophysical properties, switching behavior, and high photostability make the dye an ideal candidate for photoactivation localization microscopy (PALM). It is capable of resolving apolar structures with an accuracy far beyond the diffraction limit of optical light in cylindrical micelles formed by amphiphilic block copolymers.

Single cell super-resolution imaging of E. coli OmpR during environmental stress

Two-component signaling systems are a major strategy employed by bacteria, and to some extent, yeast and plants, to respond to environmental stress. The EnvZ/OmpR system in E. coli responds to osmotic and acid stress and is responsible for regulating the protein composition of the outer membrane. EnvZ is a histidine kinase located in the inner membrane. Upon activation, it is autophosphorylated by ATP and subsequently, it activates OmpR. Phosphorylated OmpR binds with high affinity to the regulatory regions of the ompF and ompC porin genes to regulate their transcription. We set out to visualize these two-components in single bacterial cells during different environmental stress conditions and to examine the subsequent modifications to the bacterial nucleoid as a result. We created a chromosomally-encoded, active, fluorescent OmpR-PAmCherry fusion protein and compared its expression levels with RNA polymerase. Quantitative western blotting had indicated that these two proteins were expressed at similar levels. From our images, it is evident that OmpR is significantly less abundant compared to RNA polymerase. In cross-sectional axial images, we observed OmpR molecules closely juxtaposed near the inner membrane during acidic and hyposomotic growth. In acidic conditions, the chromosome was compacted. Surprisingly, under acidic conditions, we also observed evidence of a spatial correlation between the DNA and the inner membrane, suggesting a mechanical link through an active DNA-OmpR-EnvZ complex. This work represents the first direct visualization of a response regulator with respect to the bacterial chromosome.

Molecular architecture of native fibronectin fibrils

Fibronectin fibrils within the extracellular matrix play central roles in physiological and pathological processes, yet many structural details about their hierarchical and molecular assembly remain unknown. Here we combine site-specific protein labelling with single-molecule localization by stepwise photobleaching or direct stochastic optical reconstruction microscopy (dSTORM), and determine the relative positions of various labelled sites within native matrix fibrils. Single end-labelled fibronectin molecules in fibrils display an average end-to-end distance of ∼133 nm. Sampling of site-specific antibody epitopes along the thinnest fibrils (protofibrils) shows periodic punctate label patterns with ∼95 nm repeats and alternating N- and C-terminal regions. These measurements suggest an antiparallel 30–40 nm overlap between N-termini, suggesting that the first five type I modules bind type III modules of the adjacent molecule. Thicker fibres show random bundling of protofibrils without a well-defined line-up. This super-resolution microscopy approach can be applied to other fibrillar protein assemblies of unknown structure.

Fibronectin fibres are an important component of the extracellular matrix, supporting cell adhesion, growth and migration. Here the authors combine site-specific protein labelling with single-molecule localization microscopy to provide detailed insights into the molecular organization of native fibronectin fibrils.