Super-resolution microscopy for structural biology.

Recent years have witnessed significant advances in overcoming the resolution limits of traditional optical imaging, particularly in fluorescence-based super-resolution microscopy. In contrast, label-free super-resolution microscopy eliminates the need for sample staining, offering broader applicability. However, most label-free methods often rely on saturation effects or nonlinearity, which limits their applicability. Here, we have developed a reflection label-free super-resolution confocal optical microscopy technique based on super-resolution focusing. Illuminating a conventional objective lens with a hollow beam generates a super-resolution focal spot at its front focal plane. By utilizing the confocal configuration, the same objective lens is used to collect the reflected and scattered light. Experiments demonstrate that the proposed label-free super-resolution confocal microscope resolves a grating with a pitch of 160 nm and a line width of 80 nm. This technology has potential applications in biological and non-biological microscopy.

Supramolecular fibers are prominent structures in biology and chemistry. A quantitative understanding of molecular exchange pathways in these one-dimensional aggregates was obtained by a combination of super-resolution stochastic optical reconstruction microscopy and stochastic simulation. The potential of this methodology is demonstrated with a set of well-defined synthetic building blocks that self-assemble into supramolecular fibrils. Previous ensemble measurements hid all molecular phenomena underpinning monomer exchange, but the molecular pathway determined from single-aggregate studies revealed unexpected homogeneous exchange along the polymer backbone. These results pave the way for experimental investigation of the structure and exchange pathways of synthetic and natural supramolecular fibers.

Stress granules (SGs) are cytoplasmic messenger ribonucleoprotein granules transiently formed in stressed mammalian cells. Although SG components have been well characterized, detailed insights into the molecular behavior inside SGs remain unresolved. We investigated nanoscale dynamics and localization of endogenous mRNAs in SGs combining single mRNA tracking and super-resolution localization microscopy. First, we developed a methodology for tracking single mRNAs within SGs, revealing that although mRNAs in SGs are mainly stationary (∼40%), they also move in a confined (∼25%) or freely diffusing (∼35%) manner. Second, the super-resolution localization microscopy showed that the mRNAs in SGs are heterogeneously distributed and partially form high-density clusters. Third, we simultaneously performed single mRNA tracking and super-resolution microscopy in SGs, demonstrating that single mRNA trajectories are mainly found around high-density clusters. Finally, a quantitative analysis of mRNA localization and dynamics during stress removal was conducted using live super-resolution imaging and single-molecule tracking. These results suggest that SGs have a highly organized structure that enables dynamic regulation of the mRNAs at the nanoscale, which is responsible for the ordered formation and the wide variety of functions of SGs.

The presentation gives and overviews of two super-resolution fluorescence microscopy techniques are presented which are inspired by single-molecule spectroscopy. The first is Superresolution Optical Fluctuation Imaging (SOFI), which converts temporal intensity fluctuations of emitters into an enhanced spatial resolution of an image. Besides providing higher resolution, SOFI is also very efficient in suppressing any background or auto-fluorescence, increases image contrast, and allows for recording three-dimensional images (z-sectioning) with a wide field microscope. The fundamental principles behind SOFI as well as several applications for super-resolved, three-dimensional cell imaging will be presented.The second technique is Metal-Induced Energy-Transfer Imaging. When placing a fluorescent molecule close to a metal, its fluorescence properties change dramatically. In particular, one observes a strongly modified lifetime of its excited state (Purcell effect). We call this effect metal-induced energy transfer or MIET. The MIET-coupling between an excited emitter and a metal film is strongly dependent on the emitter's distance from the metal. We have used this effect for mapping the basal membrane of live cells with an axial accuracy of ∼3 nm. The method is easy to implement and does not require any change to a conventional fluorescence lifetime microscope; it can be applied to any biological system of interest, and is compatible with most other super-resolution microscopy techniques which enhance the lateral resolution of imaging. Moreover, it is even applicable to localizing individual molecules, thus offering the prospect of using single-molecule localization microscopy for structural studies of biomolecules and biomolecular complexes.

Achieving a spatial resolution that is not limited by the diffraction of light, recent developments of super-resolution fluorescence microscopy techniques allow the observation of many biological structures not resolvable in conventional fluorescence microscopy. New advances in these techniques now give them the ability to image three-dimensional (3D) structures, measure interactions by multicolor colocalization, and record dynamic processes in living cells at the nanometer scale. It is anticipated that super-resolution fluorescence microscopy will become a widely used tool for cell and tissue imaging to provide previously unobserved details of biological structures and processes.

Recent advances in microscopy techniques enabled nanoscale discoveries in biology. In particular, electron microscopy reveals important cellular structures with nanometer resolution, yet it is hard, and sometimes impossible to resolve specific protein localizations. Super-resolution fluorescence microscopy techniques developed over the recent years allow for protein-specific localization with ~ 20 nm precision are overcoming this limitation, yet it remains challenging to place those in cells without a reference frame. Correlative light and electron microscopy (CLEM) approaches have been developed to place the fluorescence image in the context of a cellular structure. However, combining imaging methods such as super resolution microscopy and transmission electron microscopy necessitates a correlation using fiducial markers to locate the fluorescence on the structures visible in electron microscopy, with a measurable precision. Here, we investigated different fiducial markers for super-resolution CLEM (sCLEM) by evaluating their shape, intensity, stability and compatibility with photoactivatable fluorescent proteins as well as the electron density. We further carefully determined limitations of correlation accuracy. We found that spectrally-shifted FluoSpheres are well suited as fiducial markers for correlating single-molecule localization microscopy with transmission electron microscopy.

The first section of this chapter concerns scattering factors for the diffraction of electrons by crystalline solids. An explanation of the theory of scattering by a perfect crystal is followed by a discussion of the kinematical, two-beam and phase-grating approximations. Relativistic and absorption effects are considered. Extensive tables of atomic scattering amplitudes for electrons for neutral and ionized atoms are presented. The second section of the chapter briefly discusses the parameterization of electron atomic scattering factors. Tables of useful parameters as a function of accelerating voltage and elastic atomic scattering factors for neutral atoms are given. Complex scattering factors for the diffraction of electrons by gases are discussed in the third section of the chapter. This section includes tables of scattering factors of interest for gas-phase electron diffraction from atoms and molecules in the keV energy region. In addition to the tables and a description of their uses, a discussion of the theoretical uncertainties related to the material in the tables is also provided. The tables give scattering factors for elastic and inelastic scattering from free atoms. The theory of molecular scattering based on these atomic quantities is also discussed. Electron energy-loss spectroscopy on solids is discussed in the fourth section of the chapter. Topics covered include: the use of electron beams; single and multiple scattering; the classification of the different excitations in a spectrum; instrumentation; and the excitation spectra of valence and core electrons. The fifth section of the chapter describes oriented texture patterns. Lamellar and fibre texture patterns are discussed and applications to metals and organic materials are mentioned. The computation of dynamic wave amplitudes in then described in the sixth section of the chapter. This section deals first with the multislice method. The numerical procedure is outlined and factors that influence the choice of thickness of the slice are discussed. Two checks that can be performed during a multislice calculation are noted. The Bloch-wave method is then described. The use of Bloch waves to describe electron diffraction and electron imaging in thin crystals is outlined together with the concept of the dispersion surface. These emerge as natural solutions of the Schrodinger equation with a periodic optical potential to generate the elastic scattering and also the loss of intensity from the coherent wave field due to thermal diffuse and inelastic scattering. The Bloch-wave approach is a useful complement to the multislice method and provides a clear picture of wave propagation in perfect and imperfect crystals. In the seventh section of the chapter, the measurement of structure factors and the determination of crystal thickness by electron diffraction are described. The use of convergent-beam electron diffraction to obtain integrated intensities is discussed and the relationship between intensity features and the dispersion surface is explained. The last section of the chapter concerns crystal-structure determination by high-resolution microscopy. This technique allows the arrangement of atomic columns in thin crystals to be observed directly. The resolution of the best instruments is now slightly below 0.1 nm. The images usually show a projection through a slice of crystal about 20 nm thick, however tomographic (three-dimensional) reconstruction is now possible at nanometre resolution. The images show the host of microphases, grain boundaries, twins, line and planar defects which broad-beam methods, such as X-ray diffraction, provide the average scattering from. These defects often control the properties of crystals, engineering materials and electronic devices. Individual nanostructures, such as carbon nanotubes and catalyst particles, may be imaged at atomic resolution. Fine twinning, polytypes, intergrowth of oxide phases etc. can be identified, and increasingly the detailed atomic structure of defects (such as oxide, superconductor and semiconductor interfaces) is being determined. Substitutional dopant atoms have recently been imaged for the first time. In biology the method is limited by radiation damage; however by summing many images of identical randomly oriented macromolecules, tomographic density maps can be reconstructed at subnanometre resolution from hydrated proteins which cannot be crystallized (e.g. membrane proteins). This section reviews the theoretical principles of high-resolution electron microscopy, including few-beam and structure image formation, effects of electron-optical lens aberrations, partial coherence, resolution-limiting factors, image-simulation methods, dynamical effects, and a summary of super-resolution schemes. Keywords: absorption; atomic scattering amplitudes; atomic scattering factors; Bethe theory; Bloch-wave method; core-electron spectroscopy; core-loss spectroscopy; crystal thickness; crystalline solids; dielectric description; dynamical diffraction; dynamical wave amplitudes; EELS; elastic scattering; electron diffraction; electron energy-loss spectroscopy; electron microscopy; electrons; free-electron gas; high-resolution electron microscopy; HREM; hyper-resolution; inelastic scattering; lamellar textures; lattice-fringe images; molecular scattering factors; multiple scattering; multislice method; oriented texture patterns; plasmons; real solids; relativistic effects; STEM; scanning transmission electron microscopes; scattering factors; solid-state effects; spectrometers; structure factors; surface plasmons; texture; wave amplitudes; X-ray diffraction

Intracellular Delivery of Membrane Impermeable Photostable Fluorescent Probes into Living Cells for Super-Resolution Microscopy

Super-Resolution Microscopy and FIB-SEM Imaging Reveal Parental Centriole-Derived, Hybrid Cilium in Mammalian Multiciliated Cells.

The regulated release of neurotransmitter occurs via the fusion of synaptic vesicles (SVs) at specialized regions of the presynaptic membrane called active zones (AZs). These regions are defined by a cytoskeletal matrix assembled at AZs (CAZ), which functions to direct SVs toward docking and fusion sites and supports their maturation into the readily releasable pool. In addition, CAZ proteins localize voltage-gated Ca(2+) channels at SV release sites, bringing the fusion machinery in close proximity to the calcium source. Proteins of the CAZ therefore ensure that vesicle fusion is temporally and spatially organized, allowing for the precise and reliable release of neurotransmitter. Importantly, AZs are highly dynamic structures, supporting presynaptic remodeling, changes in neurotransmitter release efficacy, and thus presynaptic forms of plasticity. In this review, we discuss recent advances in the study of active zones, highlighting how the CAZ molecularly defines sites of neurotransmitter release, endocytic zones, and the integrity of synapses.

High-resolution studies in structural biology are often limited by the challenges of crystallization and low contrast in the cellular native environment. The exquisite labeling specificity of fluorescence microscopy gets around these issues and allows superresolution microscopy, but to date, these works have used chemically fixed samples. To establish light microscopy as a workhorse in structural biology, two main requirements must be fulfilled: near-native sample preservation and near-atomic optical resolution. Here, we introduce single-particle cryogenic light microscopy (spCryo-LM) as a technique that satisfies these key criteria. We adapt established protocols from cryogenic electron microscopy (Cryo-EM) for shock-freezing samples and use a high-vacuum cryogenic shuttle system to transfer them in and out of a liquid-helium cryostat that houses a superresolution fluorescence microscope. By exploiting the enhanced photophysics at low temperature, angstrom precision can be achieved in localizing several fluorophores attached to proteins separated by a few hundred nanometers. We present various characterization studies on vitreous ice, single-molecule photoblinking behavior, and the effects of laser intensity and benchmark our method by resolving the heptameric membrane protein alpha-hemolysin in a synthetic lipid membrane. Additionally, we report on the technique's capability to resolve membrane proteins in their native cellular membrane environment. spCryo-LM enables structural studies of proteins in their native environment without chemical fixation or protein isolation, and can be integrated with other superresolution or spectroscopic techniques. We believe our approach establishes light microscopy as a powerful tool in structural biology and sets the stage for correlative microscopy with Cryo-EM and related techniques.

Caveolae are plasma membrane invaginations whose formation requires caveolin-1 (Cav1), the adaptor protein polymerase I, and the transcript release factor (PTRF or CAVIN1). Caveolae have an important role in cell functioning, signaling, and disease. In the absence of CAVIN1/PTRF, Cav1 forms non-caveolar membrane domains called scaffolds. In this work, we train machine learning models to automatically distinguish between caveolae and scaffolds from single molecule localization microscopy (SMLM) data. We apply machine and deep learning algorithms to discriminate biological structures from SMLM data. Our work is the first that is leveraging machine and deep learning approaches to automatically identifying biological structures from SMLM data. In particular, we develop and compare three binary classification methods to identify whether or not a given 3D cluster of Cav1 proteins is a caveolae. The first uses a random forest classifier applied to 28 hand-picked features, the second uses a convolutional neural net (CNN) applied to a projection of the point clouds onto three planes, and the third uses a PointNet model, a recent development that can directly take point clouds as its input. We validate our methods on a dataset of super-resolution microscopy images of PC3 prostate cancer cells labeled for Cav1. Specifically, we have images from two cell populations: 10 PC3 and 10 CAVIN1/PTRF-transfected PC3 cells (PC3-PTRF cells) that form caveolae. We obtained a balanced set of 1714 different cellular structures. Our results show that both the random forest on hand selected features and the deep learning approach achieve high accuracy in distinguishing the intrinsic features of the caveolae and non-caveolae biological structures. More specifically, both random forest and deep CNN classifiers achieve classification accuracy reaching 94% on our test set, while the PointNet model only reached 83% accuracy. We also discuss the pros and cons of the different approaches. Additional information about individual files is in the accompanying CSV file (item_metadata.csv). This dataset was originally deposited in the Simon Fraser University institutional repository.

Localization based super-resolution microscopy techniques require precise drift correction methods because the achieved spatial resolution is close to both the mechanical and optical performance limits of modern light microscopes. Multi-color imaging methods require corrections in addition to those dealing with drift due to the static, but spatially-dependent, chromatic offset between images. We present computer simulations to quantify this effect, which is primarily caused by the high-NA objectives used in super-resolution microscopy. Although the chromatic offset in well corrected systems is only a fraction of an optical wavelength in magnitude (<50 nm) and thus negligible in traditional diffraction limited imaging, we show that object colocalization by multi-color super-resolution methods is impossible without appropriate image correction. The simulated data are in excellent agreement with experiments using fluorescent beads excited and localized at multiple wavelengths. Finally we present a rigorous and practical calibration protocol to correct for chromatic optical offset, and demonstrate its efficacy for the imaging of transferrin receptor protein colocalization in HeLa cells using two-color direct stochastic optical reconstruction microscopy (dSTORM).

Superresolution microscopy offers the advantage of imaging biological structures within cells at the nano-scale. Here we apply two superresolution microscopy techniques, specifically 3D structured illumination microscopy (3D-SIM) and direct stochastic optical reconstruction microscopy (dSTORM), a type of single molecule localisation microscopy, to localise IRSp53 protein and its I-BAR domain in relation to F-actin within filopodia. IRSp53 generates dynamic (extending and retracting) filopodia 300 nm wide with a distinct gap between IRSp53 and F-actin. By contrast, protrusions induced by the I-BAR domain alone are non-dynamic measuring between 100–200 nm in width and exhibit a comparatively closer localisation of the I-BAR domain with the F-actin. The data suggest that IRSp53 membrane localisation is spatially segregated to the lateral edges of filopodia, in contrast to the I-BAR domain is uniformly distributed throughout the membranes of protrusions. Modeling of fluorescence recovery after photobleaching (FRAP) data suggests that a greater proportion of I-BAR domain is associated with membranes when compared to full length IRSp53. The significance of this new data relates to the role filopodia play in cell migration and its importance to cancer.

Gene expression is dynamic and heterogeneous across all cell types. It serves several fundamental functions such as adaptation for changing environment and developing tissue specific phenotype and functionality during development and in adult organism. Control of gene expression mostly occurs at the transcription stage. Two main factors that regulate transcription in high eukaryotes are chromatin organization and transcription factor (TF) protein dynamics. Until recently they were mostly studied by methods that are performed in vitro or/and require ensemble averaging. We have been contributing to a development of new single molecule imaging methods that allow quantifying chromatin organization and TF dynamics in vivo and at single cell/single molecule level. Here we present our methodological developments and apply them to study how chromatin organization and TF dynamics regulate transcription. On the technical side of the study we, first, developed a method of imaging DNA with enhanced resolution in living cells. Super-resolution (SR) point localization based microscopy allows visualizing sub-diffraction organization of cellular structures and their dynamics in vivo. However, until recently almost exclusively proteins were imaged in SR microscopy. We found photoswitching conditions to image with stochastic optical reconstruction microscopy (STORM) DNA directly using the site-specific DNA –binding dye Picogreen (Chapter 2). We achieved a resolution of 50-70 nm which is 5 fold better than conventional microscopy. Due to the excellent dye preservation we were able to do time lapse SR imaging. This study was a first demonstration of using a site-specific dye for STORM SR imaging in living cells. Photoswitching principle used in SR microscopy can be applied to single molecule (SM) tracking. It provides up to 1000x increase in density of trajectories compared to classic SM tracking. Initially, photoactivatable (PA) fusion proteins were used for high density SR based tracking. However, PA proteins are relatively dim and there is a limited choice of them. We demonstrated a new approach to SR based high density tracking by using organic dyes’ photoswitching to track proteins (Chapter 4). We showed that different dyes can be photoswitched in similar live-cell compatible media on membrane and in different organelles. Together with orthogonal protein labelling schemes this allows us to perform multicolour high density tracking across different compartments. This approach gives flexibility of labelling and increased track length compared to PA-FP SR based tracking. In a separate study, using tracking we developed algorithm which can account for long-living molecules in live cell SR imaging and allows us to correct clustering artefacts (Chapter 5). [...]