Development Of Super-resolution Microscopy Research Articles

Aggregation-induced emission luminogens for super-resolution imaging

Over the past three decades, humanity has successfully surpassed Abbe's diffraction limit through the development of super-resolution microscopy (SRM), which leads to an increasing demand for specialized fluorescent molecules. The concept of aggregation-induced emission (AIE) has emerged as a powerful tool in fluorescence imaging since its inception in 2001. While thousands of distinctive AIE-based fluorescent molecules have been extensively utilized, their application in SRM was not explored until 2013. Although fewer than one hundred works on AIE and SRM have been published so far, this field is experiencing rapid growth. This review provides a comprehensive summary of advancements made by these intersecting domains over the last decade. The recent research is outlined, and four future directions are highlighted to guide the design of high-quality AIE-based probes for SRM applications that can further advance and promote this exciting area of research.

Quantitative Single-Molecule Localization Microscopy.

Super-resolution fluorescence microscopy allows the investigation of cellular structures at nanoscale resolution using light. Current developments in super-resolution microscopy have focused on reliable quantification of the underlying biological data. In this review, we first describe the basic principles of super-resolution microscopy techniques such as stimulated emission depletion (STED) microscopy and single-molecule localization microscopy (SMLM), and then give a broad overview of methodological developments to quantify super-resolution data, particularly those geared toward SMLM data. We cover commonly used techniques such as spatial point pattern analysis, colocalization, and protein copy number quantification but also describe more advanced techniques such as structural modeling, single-particle tracking, and biosensing. Finally, we provide an outlook on exciting new research directions to which quantitative super-resolution microscopy might be applied.

Novel imaging methods and force probes for molecular mechanobiology of cytoskeleton and adhesion.

Detection and conversion of mechanical forces into biochemical signals is known as mechanotransduction. From cells to tissues, mechanotransduction regulates migration, proliferation, and differentiation in processes such as immune responses, development, and cancer progression. Mechanosensitive structures such as integrin adhesions, the actin cortex, ion channels, caveolae, and the nucleus sense and transmit forces. In vitro approaches showed that mechanosensing is based on force-dependent protein deformations and reorganizations. However, the mechanisms in cells remained unclear since cell imaging techniques lacked molecular resolution. Thanks to recent developments in super-resolution microscopy (SRM) and molecular force sensors, it is possible to obtain molecular insight of mechanosensing in live cells. We discuss how understanding of molecular mechanotransduction was revolutionized by these innovative approaches, focusing on integrin adhesions, actin structures, and the plasma membrane.

Immune cells-derived exosomes: A promising strategy for COVID-19 treatment.

Immune cells-derived exosomes: A promising strategy for COVID-19 treatment.

Correlative Live-Cell and Super-Resolution Imaging to Link Presynaptic Molecular Organisation With Function.

Information transfer at synapses occurs when vesicles fuse with the plasma membrane to release neurotransmitters, which then bind to receptors at the postsynaptic membrane. The process of neurotransmitter release varies dramatically between different synapses, but little is known about how this heterogeneity emerges. The development of super-resolution microscopy has revealed that synaptic proteins are precisely organised within and between the two parts of the synapse and that this precise spatiotemporal organisation fine-tunes neurotransmission. However, it remains unclear if variability in release probability could be attributed to the nanoscale organisation of one or several proteins of the release machinery. To begin to address this question, we have developed a pipeline for correlative functional and super-resolution microscopy, taking advantage of recent technological advancements enabling multicolour imaging. Here we demonstrate the combination of live imaging of SypHy-RGECO, a unique dual reporter that simultaneously measures presynaptic calcium influx and neurotransmitter release, with post hoc immunolabelling and multicolour single molecule localisation microscopy, to investigate the structure-function relationship at individual presynaptic boutons.

Multi-target and fast DNA-paint imaging of neuronal tissue using exchange paint and artificial neural networks

The dense nanoscale morphology and arrangement of proteins within the synapse of neuronal tissue was difficult to visualize until the development of superresolution microscopy. Here, we show the application of multi-target DNA-PAINT in semi-thin (400 nm) brain sections of the medial nucleus of the trapezoid body (MNTB) from rat tissue. Four targets were imaged in situ to visualize the organization of calyces of Held presynapses, proteins within the active zone, and the postsynaptic principal cells with its postsynaptic density.

Transient Fluorescence Labeling: Low Affinity-High Benefits.

Fluorescent labeling is an established method for visualizing cellular structures and dynamics. The fundamental diffraction limit in image resolution was recently bypassed with the development of super-resolution microscopy. Notably, both localization microscopy and stimulated emission depletion (STED) microscopy impose tight restrictions on the physico-chemical properties of labels. One of them—the requirement for high photostability—can be satisfied by transiently interacting labels: a constant supply of transient labels from a medium replenishes the loss in the signal caused by photobleaching. Moreover, exchangeable tags are less likely to hinder the intrinsic dynamics and cellular functions of labeled molecules. Low-affinity labels may be used both for fixed and living cells in a range of nanoscopy modalities. Nevertheless, the design of optimal labeling and imaging protocols with these novel tags remains tricky. In this review, we highlight the pros and cons of a wide variety of transiently interacting labels. We further discuss the state of the art and future perspectives of low-affinity labeling methods.

Can Developments in Tissue Optical Clearing Aid Super-Resolution Microscopy Imaging?

The rapid development of super-resolution microscopy (SRM) techniques opens new avenues to examine cell and tissue details at a nanometer scale. Due to compatibility with specific labelling approaches, in vivo imaging and the relative ease of sample preparation, SRM appears to be a valuable alternative to laborious electron microscopy techniques. SRM, however, is not free from drawbacks, with the rapid quenching of the fluorescence signal, sensitivity to spherical aberrations and light scattering that typically limits imaging depth up to few micrometers being the most pronounced ones. Recently presented and robustly optimized sets of tissue optical clearing (TOC) techniques turn biological specimens transparent, which greatly increases the tissue thickness that is available for imaging without loss of resolution. Hence, SRM and TOC are naturally synergistic techniques, and a proper combination of these might promptly reveal the three-dimensional structure of entire organs with nanometer resolution. As such, an effort to introduce large-scale volumetric SRM has already started; in this review, we discuss TOC approaches that might be favorable during the preparation of SRM samples. Thus, special emphasis is put on TOC methods that enhance the preservation of fluorescence intensity, offer the homogenous distribution of molecular probes, and vastly decrease spherical aberrations. Finally, we review examples of studies in which both SRM and TOC were successfully applied to study biological systems.

Visualizing Synaptic Multi-Protein Patterns of Neuronal Tissue With DNA-Assisted Single-Molecule Localization Microscopy.

The development of super-resolution microscopy (SRM) has widened our understanding of biomolecular structure and function in biological materials. Imaging multiple targets within a single area would elucidate their spatial localization relative to the cell matrix and neighboring biomolecules, revealing multi-protein macromolecular structures and their functional co-dependencies. SRM methods are, however, limited to the number of suitable fluorophores that can be imaged during a single acquisition as well as the loss of antigens during antibody washing and restaining for organic dye multiplexing. We report the visualization of multiple protein targets within the pre- and postsynapse in 350–400 nm thick neuronal tissue sections using DNA-assisted single-molecule localization microscopy (SMLM). In a single labeling step, antibodies conjugated with short DNA oligonucleotides visualized multiple targets by sequential exchange of fluorophore-labeled complementary oligonucleotides present in the imaging buffer. This approach avoids potential effects on structural integrity when using multiple rounds of immunolabeling and eliminates chromatic aberration, because all targets are imaged using a single excitation laser wavelength. This method proved robust for multi-target imaging in semi-thin tissue sections with a lateral resolution better than 25 nm, paving the way toward structural cell biology with single-molecule SRM.

The role of the membrane-associated periodic skeleton in axons.

The identification of the membrane periodic skeleton (MPS), composed of a periodic lattice of actin rings interconnected by spectrin tetramers, was enabled by the development of super-resolution microscopy, and brought a new exciting perspective to our view of neuronal biology. This exquisite cytoskeleton arrangement plays an important role on mechanisms regulating neuronal (dys)function. The MPS was initially thought to provide mainly for axonal mechanical stability. Since its discovery, the importance of the MPS in multiple aspects of neuronal biology has, however, emerged. These comprise its capacity to act as a signaling platform, regulate axon diameter-with important consequences on the efficiency of axonal transport and electrophysiological properties- participate in the assembly and function of the axon initial segment, and control axon microtubule stability. Recently, MPS disassembly has also surfaced as an early player in the course of axon degeneration. Here, we will discuss the current knowledge on the role of the MPS in axonal physiology and disease.

Structural and Functional Modulation of Perineuronal Nets: In Search of Important Players with Highlight on Tenascins.

The extracellular matrix (ECM) of the brain plays a crucial role in providing optimal conditions for neuronal function. Interactions between neurons and a specialized form of ECM, perineuronal nets (PNN), are considered a key mechanism for the regulation of brain plasticity. Such an assembly of interconnected structural and regulatory molecules has a prominent role in the control of synaptic plasticity. In this review, we discuss novel ways of studying the interplay between PNN and its regulatory components, particularly tenascins, in the processes of synaptic plasticity, mechanotransduction, and neurogenesis. Since enhanced neuronal activity promotes PNN degradation, it is possible to study PNN remodeling as a dynamical change in the expression and organization of its constituents that is reflected in its ultrastructure. The discovery of these subtle modifications is enabled by the development of super-resolution microscopy and advanced methods of image analysis.

Single-Protein Tracking to Study Protein Interactions During Integrin-Based Migration.

Cell migration is a complex biophysical process which involves the coordination of molecular assemblies including integrin-dependent adhesions, signaling networks andforce-generating cytoskeletal structures incorporating bothactin polymerization and myosin activity. During the last decades, proteomic studies have generated impressive protein-protein interaction maps, although the subcellular location, duration, strength, sequence, and nature of these interactions are still concealed. In this chapter we describe how recent developments in superresolution microscopy (SRM) and single-protein tracking (SPT) start to unravel protein interactions and actions in subcellular molecular assemblies driving cell migration.

Super-resolution microscopy and its applications in neuroscience

Optical microscopy promises researchers to see most tiny substances directly. However, the resolution of conventional microscopy is restricted by the diffraction limit. This makes it a challenge to observe subcellular processes happened in nanoscale. The development of super-resolution microscopy provides a solution to this challenge. Here, we briefly review several commonly used super-resolution techniques, explicating their basic principles and applications in biological science, especially in neuroscience. In addition, characteristics and limitations of each technique are compared to provide a guidance for biologists to choose the most suitable tool.

Dendritic Actin Cytoskeleton: Structure, Functions, and Regulations.

Actin is a versatile and ubiquitous cytoskeletal protein that plays a major role in both the establishment and the maintenance of neuronal polarity. For a long time, the most prominent roles that were attributed to actin in neurons were the movement of growth cones, polarized cargo sorting at the axon initial segment, and the dynamic plasticity of dendritic spines, since those compartments contain large accumulations of actin filaments (F-actin) that can be readily visualized using electron- and fluorescence microscopy. With the development of super-resolution microscopy in the past few years, previously unknown structures of the actin cytoskeleton have been uncovered: a periodic lattice consisting of actin and spectrin seems to pervade not only the whole axon, but also dendrites and even the necks of dendritic spines. Apart from that striking feature, patches of F-actin and deep actin filament bundles have been described along the lengths of neurites. So far, research has been focused on the specific roles of actin in the axon, while it is becoming more and more apparent that in the dendrite, actin is not only confined to dendritic spines, but serves many additional and important functions. In this review, we focus on recent developments regarding the role of actin in dendrite morphology, the regulation of actin dynamics by internal and external factors, and the role of F-actin in dendritic protein trafficking.

Live-cell super-resolution imaging of intrinsically fast moving flagellates*This article belongs to the special issue: Emerging Leaders, which features invited work from the best early-career researchers working within the scope of J Phys D. This project is part of the Journal of Physics series’ 50th anniversary celebrations in 2017. Susanne Fenz was selected by the Editorial Board of J Phys D

Recent developments in super-resolution microscopy make it possible to resolve structures in biological cells at a spatial resolution of a few nm and observe dynamical processes with a temporal resolution of ms to μs. However, the optimal structural resolution requires repeated illumination cycles and is thus limited to chemically fixed cells. For live cell applications substantial improvement over classical Abbe-limited imaging can already be obtained in adherent or slow moving cells. Nonetheless, a large group of cells are fast moving and thus could not yet be addressed with live cell super-resolution microscopy. These include flagellate pathogens like African trypanosomes, the causative agents of sleeping sickness in humans and nagana in livestock.Here, we present an embedding method based on a in situ forming cytocompatible UV-crosslinked hydrogel. The fast cross-linking hydrogel immobilizes trypanosomes efficiently to allow microscopy on the nanoscale. We characterized both the trypanosomes and the hydrogel with respect to their autofluorescence properties and found them suitable for single-molecule fluorescence microscopy (SMFM). As a proof of principle, SMFM was applied to super-resolve a structure inside the living trypanosome. We present an image of a flagellar axoneme component recorded by using the intrinsic blinking behavior of eYFP.

C3-O-05Electron Cryo-Tomography ofThermoplasma acidophilumwith Volta Phase Plate

Last year, the Nobel Chemistry Award was given to three physicists working on the development of superresolution microscopy. During the last decade, the diffraction limit of resolution was beautifully overcome by manipulating the on/off switching of fluorophores, or by saturation of fluorescence emission, resulting in resolution below 100 nm. Nevertheless, fluorescence exhibits intrinsic photobleaching issue. Therefore, it will be more than desirable to develop superresolution imaging modality based on an alternative contrast agent without bleaching, such as scattering. It is known that plasmonic nanoparticles exhibit extraordinarily strong scattering due to surface plasmon resonance (SPR). To our knowledge, neither saturation, nor switching of scattering from SPR structures has been reported, but there are plenty of reports on saturable absorption of plasmonic nanoparticles embedded in dielectric matrix. Since scattering and absorption are related to the real and imaginary parts of electric susceptibility, respectively, we expect to find saturable scattering with plasmonic particles.

C4-O-01Super-resolution imaging based on nonlinearities of plasmonic scattering

Last year, the Nobel Chemistry Award was given to three physicists working on the development of superresolution microscopy. During the last decade, the diffraction limit of resolution was beautifully overcome by manipulating the on/off switching of fluorophores, or by saturation of fluorescence emission, resulting in resolution below 100 nm. Nevertheless, fluorescence exhibits intrinsic photobleaching issue. Therefore, it will be more than desirable to develop superresolution imaging modality based on an alternative contrast agent without bleaching, such as scattering. It is known that plasmonic nanoparticles exhibit extraordinarily strong scattering due to surface plasmon resonance (SPR). To our knowledge, neither saturation, nor switching of scattering from SPR structures has been reported, but there are plenty of reports on saturable absorption of plasmonic nanoparticles embedded in dielectric matrix. Since scattering and absorption are related to the real and imaginary parts of electric susceptibility, respectively, we expect to find saturable scattering with plasmonic particles.

Generating the best superresolution microscopy data: Finding the right tool for the right job

Superresolution microscopy has recently been making headlines again, not least because it was the breakthrough that spurred Eric Betzig, Stefan Hell, and William Moerner to be awarded the Nobel Prize for Chemistry in 2014. The number of superresolution technologies keeps increasing, along with an alphabet soup of acronyms that includes SIM, SPIM, STED, PALM, and STORM. It is difficult enough for the microscopy experts to keep up, but even more challenging for the average biologist, particularly when they are looking for more from their data than a standard or confocal microscope can offer. When faced with the array of possible techniques, how does one decide which technique is going to get the results needed for that next major publication? In this webinar we will discuss the newest developments in superresolution microscopy and provide practical advice on obtaining the best imaging results. Our panelists, including 2014 Nobel Prize winner Eric Betzig, will help you find the right tool to answer your biological question. You will also hear case studies about how superresolution microscopy data has made the difference between acceptance and rejection of key papers by scientific journals.

Dances with Membranes: Breakthroughs from Super-resolution Imaging.

Biological membrane organization mediates numerous cellular functions and has also been connected with an immense number of human diseases. However, until recently, experimental methodologies have been unable to directly visualize the nanoscale details of biological membranes, particularly in intact living cells. Numerous models explaining membrane organization have been proposed, but testing those models has required indirect methods; the desire to directly image proteins and lipids in living cell membranes is a strong motivation for the advancement of technology. The development of super-resolution microscopy has provided powerful tools for quantification of membrane organization at the level of individual proteins and lipids, and many of these tools are compatible with living cells. Previously inaccessible questions are now being addressed, and the field of membrane biology is developing rapidly. This chapter discusses how the development of super-resolution microscopy has led to fundamental advances in the field of biological membrane organization. We summarize the history and some models explaining how proteins are organized in cell membranes, and give an overview of various super-resolution techniques and methods of quantifying super-resolution data. We discuss the application of super-resolution techniques to membrane biology in general, and also with specific reference to the fields of actin and actin-binding proteins, virus infection, mitochondria, immune cell biology, and phosphoinositide signaling. Finally, we present our hopes and expectations for the future of super-resolution microscopy in the field of membrane biology.

Super-resolution imaging of nuclear bodies by STED microscopy.

The sizes of nuclear bodies and other nuclear structures are normally no more than a few hundred nanometers. This size is below the resolution limit of light microscopy and thus requires electron microscopy for direct observation. Recent developments in super-resolution microscopy have extended the resolution of light microscopy to beyond 100 nm. Here, we describe a super-resolution technique, gated STED, for the analysis of the structure of nuclear bodies, with emphasis on the sample preparation and other technical tips that are important to obtain high-quality super-resolution images.