Single Molecule Counting using STORM/PALM

Nanoscopic imaging techniques provide a powerful set of tools for static and dynamic fluorescence microscopy below the diffraction limit of light. Among these super-resolution techniques, photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) are based on the detection of single fluorophores, whose signals are localized with great precision. The strength of single-molecule approaches lies in their high localization accuracy and their molecular specificity and in the development of multicolor approaches, three-dimensional imaging, and the quantification of absolute molecule numbers. These capabilities make PALM and STORM imaging ideally suited to visualize the ultrastructures of synapses, to track the movements of synaptic components, and to quantify the molecular plasticity at synapses.Key wordsActive zone (AZ)Dendritic spineGluA1 (AMPA receptor subunit GluR1)GluN2B (NMDA receptor subunit NR2B)Photoactivated localization microscopy (PALM)Postsynaptic density (PSD)Stochastic optical reconstruction microscopy (STORM)

ABSTRACTMycoplasmas are the smallest free-living organisms. These bacteria are important models for both fundamental and synthetic biology, owing to their highly reduced genomes. They are also relevant in the medical and veterinary fields, as they are pathogenic to both humans and most livestock species. Mycoplasma cells have minute sizes, often in the 300- to 800-nm range. As these dimensions are close to the diffraction limit of visible light, fluorescence imaging in mycoplasmas is often poorly informative. Recently developed superresolution imaging techniques can break this diffraction limit, improving the imaging resolution by an order of magnitude and offering a new nanoscale vision of the organization of these bacteria. These techniques have, however, not been applied to mycoplasmas before. Here, we describe an efficient and reliable protocol to perform single-molecule localization microscopy (SMLM) imaging in mycoplasmas. We provide a polyvalent transposon-based system to express the photoconvertible fluorescent protein mEos3.2, enabling photo-activated localization microscopy (PALM) in most Mycoplasma species. We also describe the application of direct stochastic optical reconstruction microscopy (dSTORM). We showcase the potential of these techniques by studying the subcellular localization of two proteins of interest. Our work highlights the benefits of state-of-the-art microscopy techniques for mycoplasmology and provides an incentive to further the development of SMLM strategies to study these organisms in the future.IMPORTANCE Mycoplasmas are important models in biology, as well as highly problematic pathogens in the medical and veterinary fields. The very small sizes of these bacteria, well below a micron, limits the usefulness of traditional fluorescence imaging methods, as their resolution limit is similar to the dimensions of the cells. Here, to bypass this issue, we established a set of state-of-the-art superresolution microscopy techniques in a wide range of Mycoplasma species. We describe two strategies: PALM, based on the expression of a specific photoconvertible fluorescent protein, and dSTORM, based on fluorophore-coupled antibody labeling. With these methods, we successfully performed single-molecule imaging of proteins of interest at the surface of the cells and in the cytoplasm, at lateral resolutions well below 50 nm. Our work paves the way toward a better understanding of mycoplasma biology through imaging of subcellular structures at the nanometer scale.

The combination of optical sectioning provided by a two-photon temporal focusing with lateral super resolution provided by PALM enables imaging of protein distributions in cells with a lateral localization precision better than 20 nm at multi ple imaging planes over an axial range of 10μm in both mitochondrially labeled fixed cells, and in the membranes of living S2 Drosophila cells. The present super-resolution techniques, such as photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM), do not allow imaging of whole cells and organelles that are typically up to 15 μm deep into the cell, because they are limited to an imaging depth of order to of a fraction of the wavelength. The two photon temporal focusing provides the optical sectioning necessary for a 3D super resolution technique.

The Drosophila melanogaster brain comprises different neuronal cell types that interconnect with precise patterns of synaptic connections. These patterns are essential for the normal function of the brain. To understand the connectivity patterns requires characterizing them at single-cell resolution, for which a fluorescence microscope becomes an indispensable tool. Additionally, because the neurons connect at the nanoscale, the investigation often demands super-resolution microscopy. Here, we adopt one super-resolution microscopy technique, called stochastic optical reconstruction microscopy (STORM), improving the lateral and axial resolution to ∼20 nm. This article extensively describes our methods along with considerations for sample preparation of neurons in vitro and in vivo, conjugation of dyes to antibodies, immunofluorescence labeling, and acquisition and processing of STORM data. With these tools and techniques, we open up the potential to investigate cell-cell interactions using STORM in the Drosophila nervous system. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparation of Drosophila primary neuronal culture and embryonic fillets Basic Protocol 2: Immunofluorescence labeling of samples Basic Protocol 3: Single-molecule fluorescence imaging Basic Protocol 4: Localization and visualization of single-molecule data Supporting Protocol: Conjugation of antibodies with STORM-compatible dyes.

New technologies are ready to revolutionize glomerular imaging and significantly improve or replace immunofluorescence and electron microscopy, which have driven research and diagnosis of glomerular diseases for over 50 years. Advanced forms of transmission and scanning electron microscopy have revealed the detailed spatial relationships of the glomerular basement membrane, podocytes, and endothelial cells. These may be overshadowed by super resolution microscopy (SRM), which combines the advantages of immunofluorescence and electron microscopy, offers high resolution identification of specific molecules, and images large, physiologically relevant volumes of the glomerulus. Rapidity, ease of use and low cost with some types of SRM make them potentially suitable for routine diagnosis. SRM visualizes structures below the classical diffraction limit of conventional light microscopy by adding a time variable to either the illumination of the specimen, or to the fluorescence signal emitted by it. Ensemble techniques vary illumination and include Structured Illumination Microscopy (SIM) and Stimulation Emission Depletion Microscopy (STED). Single molecule localization techniques vary the light emission by fluorescence labels in the specimen, and include Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM). Technologies such as expansion microscopy and genetic labeling can also create effective super resolution imaging by non-optical, specialized preparation techniques. All technologies require dark field fluorescence and some require computer image analysis and reconstruction. Replicating successful application in other areas of biology, SIM, STED, and STORM have visualized normal and nephrotic disease podocytes, and have confirmed their appearances to be similar to those seen by electron microscopy, but with added new information on cell configuration and protein localization. STORM has also localized podocyte cytoskeleton and adhesion proteins, and glomerular basement membrane proteins at a resolution never before possible. These pioneering efforts show the promise of super resolution microscopy, and lay the groundwork for future study and new diagnostic tools for glomerular diseases.

The structure of the centrosome was resolved by EM many years ago to reveal a pair of centrioles embedded in a dense network of proteins. More recently, the molecular composition of the centrosome was catalogued by mass spectroscopy and many novel components were identified. Determining precisely where a novel component localizes to within the centrosome remains a challenge, and until now it has required the use of immuno-EM. This technique is both time-consuming and unreliable, as it often fails due to problems with antigen accessibility. We have investigated the use of two nanoscopic techniques, photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), as alternative techniques for localizing centrosomal proteins. The localization of a known centrosomal component, the distal appendage protein Cep164 was investigated by direct STORM (dSTORM) and resolved with a high spatial resolution. We further validated the use of nanoscopic PALM imaging by showing that the previously uncharacterized centrosomal protein CCDC123 (Cep123) localizes to the distal appendages, forming ring-like structures with a diameter of 500 nm. Our results demonstrate that both PALM and STORM imaging have great potential as alternatives to immuno-EM.

Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (tThresh and dThresh) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and allows a variety of quantitative measurements tailored to specific needs of different biological systems.

Conventional microscopy techniques, namely, the confocal microscope or deconvolution processes, are resolution limited to approximately 200-250 nm by the diffraction properties of light as developed by Ernst Abbe in 1873. This diffraction limit is appreciably above the size of most multi-protein complexes, which are typically 20-50 nm in diameter. In the mid-2000s, biophysicists moved beyond the diffraction barrier by structuring the illumination pattern and then applying mathematical principles and algorithms to allow a resolution of approximately 100 nm, sufficient to address protein subcellular co-localization questions. This "breaking" of the diffraction barrier, affording resolution beyond 200 nm, is termed super-resolution microscopy. More recent approaches include single-molecule localization (such as photoactivated localization microscopy (PALM)/stochastic optical reconstruction microscopy (STORM)) and point spread function engineering (such as stimulated emission depletion (STED) microscopy). In this review, we explain basic principles behind currently commercialized super-resolution setups and address advantages and considerations in applying these techniques to protein co-localization in biological systems.

Super-resolution microscopy enables imaging of structures smaller than the diffraction limit. Single-molecule localization microscopy methods, such as photoactivation localization microscopy and stochastic optical reconstruction microscopy, reconstruct images by plotting the centroids of fluorescent point sources from a series of frames in which only a few molecules are fluorescing at a time. These approaches require simpler instrumentation than methods that depend on structured illumination and thus are becoming widespread. The functionalized rhodamine derivative reported in this paper spontaneously converts between a bright and dark state due to pH-dependent cyclization. At pH 7, less than 0.5% of the dye molecules are fluorescent at any given time. Blinking occurs on time scales of seconds to minutes and can therefore be used for single-molecule localization microscopy without sample treatment or activation. The dye is bright and straightforward to use, and it is easy to synthesize and functionalize. Thus, it has potential to become a new and powerful addition to the toolset for super-resolution imaging.

Nanoprocessing with nanojoule near-infrared femtosecond laser pulses

The ultimate resolution limit of an imaging system is a long-standing puzzle that originated from the 18th century. Although many heuristic resolution criteria have been proposed after the discovery of Abbe's diffraction limit, the exact characterization of the resolution limit is still unknown. In this thesis, we aim to provide a rigorous mathematical theory for the resolution limits in various setups. Specifically, we define and quantitatively characterize the computational resolution limits for number detection and location recovery in the deconvolution problem, the one-dimensional and multi-dimensional line spectral estimation problems, and the imaging problem with multi-illumination. The results explicitly elucidate the dependence of each computational resolution limit on the cutoff frequency, signal-to-noise ratio, sparsity of the source, and illumination pattern. In contrast to the classical resolution limits that are only related to the cutoff frequency, our characterizations highlight the importance of all the aforementioned factors to the super-resolution problem and thus are more applicable to modern super-resolution algorithms whose performances are highly related to the signal-to-noise ratio. Moreover, our results indicate that there are phase transitions in these reconstruction problems. We derive number detection and location recovery algorithms and numerically confirm the predicted phase transition phenomenons. Finally, we propose a fast algorithm for super-resolving point sources with a cluster structure.

The theoretical aspects of the light scattering on the statistical irregularities of the planar optical waveguide are described. The analysis of direct and inverse light scattering problems is accomplished. The theoretical investigation predicts: the lateral resolution can attain approximately 20 nm and the vertical resolution (in rms height) can attain approximately 1 angstrom. The limiting lateral resolution is a approximately 15-times less than Abbe's diffraction limit. Thus the superresolution may be accomplished by the waveguide optical microscopy (WOM). The increasing of WOM's resolution depends on a-priori information of the irregularities and on a sufficiently high signal-to-noise ratio. A possible using of WOM for bioecological researchers has been mentioned.

Superresolution methods in digital holographic microscopy provide a useful tool to overcome the Abbe's diffraction limit when using modest microscope lenses. The process improves the cutoff frequency of the microscope lens by means of the generation of a synthetic aperture based on time multiplexing and using 3 main stages: optical coding, optical decoding, and digital postprocessing. After the whole process, a superresolved image is obtained by Fourier transformation of the synthetic aperture.

In 1928 E H Synge proposed that Abbe's diffraction limit, which restricts the resolution of classical optical microscopy to about half the wavelength of light, could be overcome by near-field microscopy. If an aperture (of subwavelength dimension) in a metal sheet was scanned close to an object, a super-resolved image could be obtained from the light passing through it.

Time domain two-dimensional infrared (2DIR) spectroscopy extends the capabilities of traditional infrared spectroscopy by revealing information on vibrational modes' anharmonicities, couplings, and energy transfer processes, making it a powerful tool for studying fast dynamic processes. Recent advancements in mid-IR laser technology and detection methods have significantly improved the resolution and acquisition rate of 2DIR spectroscopy. Despite these exciting developments, 2DIR spectroscopy remains limited by Abbe's diffraction limit, which restricts its spatial resolution. Aimed to address this challenge, the integration of action-based detection methods, notably the atomic force microscope (AFM)-based photothermal detection, offers a promising solution. AFM-2DIR spectroscopy combines the high spatial resolution of AFM with the richness of molecular insights of 2DIR, allowing nanoscale analysis of heterogeneous samples. This new type of technique would open avenues for investigating complex molecular systems, surface phenomena, and nanostructures with unprecedented spatial precision, offering potential for research in chemistry, materials science, bio-macromolecules, and nanotechnology for the chemical physics community.