Correlative Super-Resolution Microscopy: New Dimensions and New Opportunities

Advancing biosensing through super-resolution fluorescence microscopy

Advancement of super-resolution fluorescence microscopy (SRM) has recently allowed applications to the biosensing by offering significant advantages over conventional methods. Its nanoscale spatial resolution and single-molecule sensitivity allow visualization and quantification of biomolecular targets without the need of signal amplification steps typically required in traditional biosensing methods. Moreover, recent innovations in probe design and imaging protocols have expanded SRM capabilities to enable dynamic biosensing in living cells, revealing molecular processes in their native cellular contexts. In this review, we discuss these applications of various SRM techniques to biosensing by highlighting their unique capabilities in providing spatial distribution information and high molecular sensitivity. We address several challenges that must be overcome for the broader application of SRM-based biosensing. Finally, we discuss perspectives on future directions for advancing this field towards practical applications.

Engineering ultrasmall gold nanoclusters: tailored optical modulation for phototherapeutic and multimodal biomedical applications

Ultrasmall gold nanoclusters (Au NCs) with core sizes below 2 nm exhibit distinctive physicochemical properties and hold remarkable promise in a variety of biomedical applications. Through precise synthesis and surface engineering, Au NCs can be endowed with high quantum yields, excellent stability, and favorable biocompatibility. Recent studies have demonstrated the versatility of Au NCs in imaging modalities-ranging from fluorescence and Raman to photoacoustics-as well as in light-driven therapeutics such as photodynamic therapy (PDT) and photothermal therapy (PTT). This review provides an overview of Au NC design strategies, highlighting ligand-assisted synthesis and supramolecular self-assembly for optimizing optical features and biological performance. Representative biomedical applications in optical imaging, biosensing, and phototherapy are summarized to illustrate the multifaceted benefits of Au NCs in disease diagnosis and treatment. Finally, challenges related to large-scale production, long-term biosafety, and clinical translation are discussed, along with future perspectives on leveraging Au NCs for next-generation theranostic platforms.

Nanogold-albumin conjugates: transformative approaches for next-generation cancer therapy and diagnostics

Nanogold-albumin conjugates have garnered significant attention as a highly adaptable theranostic platform, capable of delivering a wide range of therapeutics, from small-molecule drugs to larger biomolecules, while offering promising applications for monitoring and managing cancer. The remarkable theranostic capabilities of these conjugates stem from the combined strengths of gold and albumin, which provide low toxicity, a large surface area, customizable surface chemistry, and unique optical properties, all contributing to their potential in cancer therapy. This review delves into the design and development of two primary types of nanogold-albumin conjugate: supramolecular albumin-coated gold nanoparticles (GNP-BSA/HSA) and albumin-templated ultra-small gold nanoclusters (GNC-BSA/HSA). Each strategy offers distinct advantages, enabling the fine-tuning of conjugate properties to optimize therapeutic delivery and facilitate cancer-specific bio-sensing. The integration of gold and albumin further improves biocompatibility, extends circulation time, and enhances tumor targeting, making these conjugates an attractive option for cancer treatment. The review also focuses on the refinement of surface chemistry to achieve precise targeting of cancer cells, as well as the challenges and future prospects for advancing nanogold-albumin systems in clinical applications.

Oxygen-excluded nanoimaging of polymer blend films

Polymer blend films exhibit unique properties and have applications in various fields. However, understanding their nanoscale structures and polymer component distributions remains a challenge. To address this limitation, we have developed a super-resolution fluorescence microscopy-based technique called oxygen-excluded nanoimaging. By using point accumulation for imaging in nanoscale topography with sulfonate-based dye molecules, we achieved nanoscale imaging of polymer blend films while specifically labeling non-oxygen domains and excluding oxygen-containing domains. This selectivity is attributed to the electrostatic repulsion between the negatively charged sulfonate groups in the dye molecules and the oxygen atoms in the polymer side chains. We demonstrate the applicability of oxygen-excluded nanoimaging to various polymer blend films, enabling domain identification and visualization of nanoscale structures. Our oxygen-excluded nanoimaging technique provides unique insights into the complex phase separation behavior of polymer blends at the nanoscale, opening possibilities for the nanoscale characterization of a wide range of materials beyond polymer blends.

Lipid-Directed Covalent Labeling of Plasma Membranes for Long-Term Imaging, Barcoding and Manipulation of Cells

Fluorescent probes for cell plasma membranes (PM) generally exploit a noncovalent labeling mechanism, which constitutes a fundamental limitation in multiple bioimaging applications. Here, we report a concept of lipid-directed covalent labeling of PM, which exploits transient binding to the lipid membrane surface generating a high local dye concentration, thus favoring covalent ligation to random proximal membrane proteins. This concept yielded fluorescent probes for PM called MemGraft, which are built of a dye (cyanine Cy3 or Cy5) bearing a low-affinity membrane anchor and a reactive group: an activated ester or a maleimide. In contrast to specially designed control dyes and commercial Cy3-based labels of amino or thiol groups, MemGraft probes stain efficiently PM, revealing the crucial role of the membrane anchor combined with optimal reactivity of the activated ester or the maleimide. MemGraft probes overcome existing limitations of noncovalent probes, which makes them compatible with cell fixation, permeabilization, trypsinization, and the presence of serum. The latter allows long-term cell tracking and video imaging of cell PM dynamics without the signs of phototoxicity. The covalent strategy also enables staining and long-term tracking of cocultured cells labeled in different colors without exchange of probes. Moreover, the combination of MemGraft-Cy3 and MemGraft-Cy5 probes at different ratios enabled long-term cell barcoding in at least 5 color codes, important for tracking and visualizing multiple populations of cells. Ultimately, we found that the MemGraft strategy enables efficient biotinylation of the cell surface, opening the path to cell surface engineering and cell manipulation.

Spectrally Resolved Single-Molecule Orientation Imaging Reveals a Direct Correspondence between the Polarity and Microviscosity Experienced by Nile Red in Supported Lipid Bilayer Membranes

Molecular-level interactions among lipids, cholesterol, and water dictate the nanoscale membrane organization of lipid bilayers into liquid-ordered (Lo) and liquid-disordered (Ld) phases, characterized by different polarities and orders. Generally, solvatochromic dyes easily discriminate polarity difference between Lo and Ld phases, whereas molecular flippers and rotors show distinct photophysics depending on the membrane order. Despite progress in single-molecule spectral imaging and single-molecule orientation mapping, direct experimental proof linking polarity with microviscosity sensed by the same probe eludes us. Here, we demonstrate spectrally resolved single-molecule orientation localization microscopy to connect nanoscopic localization of a probe on a bilayer membrane with its emission spectra, three-dimensional dipole orientation, and rotational constraint offered by the local microenvironment and highlight the excellent correspondence between the polarity and order experienced by the same probe. This technique has the potential to address nanoscale heterogeneity and dynamics, especially in biology and material sciences.

Artificial Intelligence-Empowered Spectroscopic Single Molecule Localization Microscopy

Spectroscopic single-molecule localization microscopy (SMLM) has revolutionized the visualization and analysis of molecular structures and dynamics at the nanoscale level. The technique of combining high spatial resolution of SMLM with spectral information, enables multicolor super-resolution imaging and provides insights into the local chemical environment of individual molecules. However, spectroscopic SMLM faces significant challenges, including limited spectral resolution and compromised localization precision because of signal splitting and the difficulties in analyzing complex, multidimensional datasets, that limit its application in studying intricate biological systems and materials. The recent integration of artificial intelligence (AI) with spectroscopic SMLM has emerged as a powerful approach for addressing these challenges. Here, it is reviewed how AI-based methods applied to spectroscopic SMLM enhance and expand the capabilities of these applications. Recent advancements in AI-driven data analysis for spectroscopic SMLM, including improved spectral classification, localization precision, and extraction of rich spectral information from unmodified point-spread functions are discussed, further examining their applications in biological studies, materials science, and single-molecule reaction analysis, which highlight how AI provides new insights into molecular behavior and interactions. The AI-empowered approach adds new dimensions of information and provides new opportunities and insights into the nanoscale world of rapidly evolving field of spectroscopic SMLM.

Nanoscale single-vesicle analysis: High-throughput approaches through AI-enhanced super-resolution image analysis

The analysis of membrane vesicles at the nanoscale level is crucial for advancing the understanding of intercellular communication and its implications for health and disease. Despite their significance, the nanoscale analysis of vesicles at the single particle level faces challenges owing to their small size and the complexity of biological fluids. This new vesicle analysis tool leverages the single-molecule sensitivity of super-resolution microscopy (SRM) and the high-throughput analysis capability of deep-learning algorithms. By comparing classical clustering methods (k-means, DBSCAN, and SR-Tesseler) with deep-learning-based approaches (YOLO, DETR, Deformable DETR, and Faster R-CNN) for the analysis of super-resolution fluorescence images of exosomes, we identified the deep-learning algorithm, Deformable DETR, as the most effective. It showed superior accuracy and a reduced processing time for detecting individual vesicles from SRM images. Our findings demonstrate that image-based deep-learning-enhanced methods from SRM images significantly outperform traditional coordinate-based clustering techniques in identifying individual vesicles and resolving the challenges related to misidentification and computational demands. Moreover, the application of the combined Deformable DETR and ConvNeXt-S algorithms to differently labeled exosomes revealed its capability to differentiate between them, indicating its potential to dissect the heterogeneity of vesicle populations. This breakthrough in vesicle analysis suggests a paradigm shift towards the integration of AI into super-resolution imaging, which is promising for unlocking new frontiers in vesicle biology, disease diagnostics, and the development of vesicle-based therapeutics.

Lanthanide ion-doped upconversion nanoparticles for low-energy super-resolution applications

Energy-intensive technologies and high-precision research require energy-efficient techniques and materials. Lens-based optical microscopy technology is useful for low-energy applications in the life sciences and other fields of technology, but standard techniques cannot achieve applications at the nanoscale because of light diffraction. Far-field super-resolution techniques have broken beyond the light diffraction limit, enabling 3D applications down to the molecular scale and striving to reduce energy use. Typically targeted super-resolution techniques have achieved high resolution, but the high light intensity needed to outperform competing optical transitions in nanomaterials may result in photo-damage and high energy consumption. Great efforts have been made in the development of nanomaterials to improve the resolution and efficiency of these techniques toward low-energy super-resolution applications. Lanthanide ion-doped upconversion nanoparticles that exhibit multiple long-lived excited energy states and emit upconversion luminescence have enabled the development of targeted super-resolution techniques that need low-intensity light. The use of lanthanide ion-doped upconversion nanoparticles in these techniques for emerging low-energy super-resolution applications will have a significant impact on life sciences and other areas of technology. In this review, we describe the dynamics of lanthanide ion-doped upconversion nanoparticles for super-resolution under low-intensity light and their use in targeted super-resolution techniques. We highlight low-energy super-resolution applications of lanthanide ion-doped upconversion nanoparticles, as well as the related research directions and challenges. Our aim is to analyze targeted super-resolution techniques using lanthanide ion-doped upconversion nanoparticles, emphasizing fundamental mechanisms governing transitions in lanthanide ions to surpass the diffraction limit with low-intensity light, and exploring their implications for low-energy nanoscale applications.

Single-Molecule Spectroscopy and Super-Resolution Mapping of Physicochemical Parameters in Living Cells

By superlocalizing the positions of millions of single molecules over many camera frames, a class of super-resolution fluorescence microscopy methods known as single-molecule localization microscopy (SMLM) has revolutionized how we understand subcellular structures over the past decade. In this review, we highlight emerging studies that transcend the outstanding structural (shape) information offered by SMLM to extract and map physicochemical parameters in living mammalian cells at single-molecule and super-resolution levels. By encoding/decoding high-dimensional information-such as emission and excitation spectra, motion, polarization, fluorescence lifetime, and beyond-for every molecule, and mass accumulating these measurements for millions of molecules, such multidimensional and multifunctional super-resolution approaches open new windows into intracellular architectures and dynamics, as well as their underlying biophysical rules, far beyond the diffraction limit.

Enhanced optical imaging and fluorescent labeling for visualizing drug molecules within living organisms

The visualization of drugs in living systems has become key techniques in modern therapeutics. Recent advancements in optical imaging technologies and molecular design strategies have revolutionized drug visualization. At the subcellular level, super-resolution microscopy has allowed exploration of the molecular landscape within individual cells and the cellular response to drugs. Moving beyond subcellular imaging, researchers have integrated multiple modes, like optical near-infrared II imaging, to study the complex spatiotemporal interactions between drugs and their surroundings. By combining these visualization approaches, researchers gain supplementary information on physiological parameters, metabolic activity, and tissue composition, leading to a comprehensive understanding of drug behavior. This review focuses on cutting-edge technologies in drug visualization, particularly fluorescence imaging, and the main types of fluorescent molecules used. Additionally, we discuss current challenges and prospects in targeted drug research, emphasizing the importance of multidisciplinary cooperation in advancing drug visualization. With the integration of advanced imaging technology and molecular design, drug visualization has the potential to redefine our understanding of pharmacology, enabling the analysis of drug micro-dynamics in subcellular environments from new perspectives and deepening pharmacological research to the levels of the cell and organelles.

High throughput spectrally resolved super-resolution fluorescence microscopy with improved photon usage

Single-molecule localization microscopy (SMLM), a type of super-resolution fluorescence microscopy, has become a strong technique in the toolbox of chemists, biologists, physicists, and engineers in recent years for its unique ability to resolve characteristic features at the nanoscopic level. It drastically improves the resolution of optical microscopes beyond the diffraction limit, with which previously unresolvable structures can now be studied. Spectrally resolved super-resolution fluorescence microscopy via multiplexing of different fluorophores is one of the greatest advancements among SMLM techniques. However, current spectrally resolved SMLM (SR-SMLM) methodologies present low spatial resolution due to loss of photons, low throughput due to spectral interferences, or require complex optical systems. Here, we overcome these drawbacks by developing a SR-SMLM methodology using a color glass filter. It enables high throughput and improved photon usage for hyperspectral imaging at the nanoscopic level. Our methodology can readily distinguish fluorophores of close spectral emission and achieves sub-10 nm localization and sub-5 nm spectral precisions.

Harnessing atomic force microscopy-based single-cell analysis to advance physical oncology

Single-cell analysis is an emerging and promising frontier in the field of life sciences, which is expected to facilitate the exploration of fundamental laws of physiological and pathological processes. Single-cell analysis allows experimental access to cell-to-cell heterogeneity to reveal the distinctive behaviors of individual cells, offering novel opportunities to dissect the complexity of severe human diseases such as cancers. Among the single-cell analysis tools, atomic force microscopy (AFM) is a powerful and versatile one which is able to nondestructively image the fine topographies and quantitatively measure multiple mechanical properties of single living cancer cells in their native states under aqueous conditions with unprecedented spatiotemporal resolution. Over the past few decades, AFM has been widely utilized to detect the structural and mechanical behaviors of individual cancer cells during the process of tumor formation, invasion, and metastasis, yielding numerous unique insights into tumor pathogenesis from the biomechanical perspective and contributing much to the field of cancer mechanobiology. Here, the achievements of AFM-based analysis of single cancer cells to advance physical oncology are comprehensively summarized, and challenges and future perspectives are also discussed. RESEARCH HIGHLIGHTS: Achievements of AFM in characterizing the structural and mechanical behaviors of single cancer cells are summarized, and future directions are discussed. AFM is not only capable of visualizing cellular fine structures, but can also measure multiple cellular mechanical properties as well as cell-generated mechanical forces. There is still plenty of room for harnessing AFM-based single-cell analysis to advance physical oncology.

Correlative super-resolution bright-field and fluorescence imaging by microsphere assisted microscopy

The resolution of fluorescence imaging has been significantly enhanced with the development of super-resolution imaging techniques, surpassing the diffraction limit and reaching sub-diffraction scales of tens of nanometers. However, the resolution of the bright-field images of cells is restricted by the diffraction limit, leading to a significant gap between the resolutions of fluorescence and bright-field imaging, which hinders the research of the precise distribution of intracellular nanostructures. A microsphere superlens offers a promising solution by providing label-free super-resolution imaging capabilities compatible with fluorescence super-resolution imaging. In this study, we used microsphere superlenses to simultaneously enhance the resolution of bright-field and fluorescence imaging, achieving correlated super-resolution bright-field and fluorescence imaging. Compared to conventional bright-field images, we improved the imaging resolution from λ/1.3 to λ/4.2. A correlative super-resolution of mouse skeletal muscle cells was achieved, enabling the clear observation of the precise distribution of nanoparticles in mouse skeletal muscle cells. Furthermore, microsphere superlenses inherit the advantages of optical imaging, which is expected to enable the capturing of ultrafast biological activity within living cells with extremely high temporal resolutions.

Imagining the future of optical microscopy: everything, everywhere, all at once

The optical microscope has revolutionized biology since at least the 17th Century. Since then, it has progressed from a largely observational tool to a powerful bioanalytical platform. However, realizing its full potential to study live specimens is hindered by a daunting array of technical challenges. Here, we delve into the current state of live imaging to explore the barriers that must be overcome and the possibilities that lie ahead. We venture to envision a future where we can visualize and study everything, everywhere, all at once - from the intricate inner workings of a single cell to the dynamic interplay across entire organisms, and a world where scientists could access the necessary microscopy technologies anywhere.

Big data in contemporary electron microscopy: challenges and opportunities in data transfer, compute and management

The second decade of the twenty-first century witnessed a new challenge in the handling of microscopy data. Big data, data deluge, large data, data compliance, data analytics, data integrity, data interoperability, data retention and data lifecycle are terms that have introduced themselves to the electron microscopy sciences. This is largely attributed to the booming development of new microscopy hardware tools. As a result, large digital image files with an average size of one terabyte within one single acquisition session is not uncommon nowadays, especially in the field of cryogenic electron microscopy. This brings along numerous challenges in data transfer, compute and management. In this review, we will discuss in detail the current state of international knowledge on big data in contemporary electron microscopy and how big data can be transferred, computed and managed efficiently and sustainably. Workflows, solutions, approaches and suggestions will be provided, with the example of the latest experiences in Australia. Finally, important principles such as data integrity, data lifetime and the FAIR and CARE principles will be considered.

Advanced imaging techniques for tracking drug dynamics at the subcellular level

Optical microscopes are an important imaging tool that have effectively advanced the development of modern biomedicine. In recent years, super-resolution microscopy (SRM) has become one of the most popular techniques in the life sciences, especially in the field of living cell imaging. SRM has been used to solve many problems in basic biological research and has great potential in clinical application. In particular, the use of SRM to study drug delivery and kinetics at the subcellular level enables researchers to better study drugs' mechanisms of action and to assess the efficacy of their targets in vivo. The purpose of this paper is to review the recent advances in SRM and to highlight some of its applications in assessing subcellular drug dynamics.

The power of super-resolution microscopy in modern biomedical science

Super-resolution microscopy (SRM) technology that breaks the diffraction limit has revolutionized the field of cell biology since its appearance, which enables researchers to visualize cellular structures with nanometric resolution, multiple colors and single-molecule sensitivity. With the flourishing development of hardware and the availability of novel fluorescent probes, the impact of SRM has already gone beyond cell biology and extended to nanomedicine, material science and nanotechnology, and remarkably boosted important breakthroughs in these fields. In this review, we will mainly highlight the power of SRM in modern biomedical science, discussing how these SRM techniques revolutionize the way we understand cell structures, biomaterials assembly and how assembled biomaterials interact with cellular organelles, and finally their promotion to the clinical pre-diagnosis. Moreover, we also provide an outlook on the current technical challenges and future improvement direction of SRM. We hope this review can provide useful information, inspire new ideas and propel the development both from the perspective of SRM techniques and from the perspective of SRM's applications.

Correlative Multi-Modal Microscopy: A Novel Pipeline for Optimizing Fluorescence Microscopy Resolutions in Biological Applications

The modern fluorescence microscope is the convergence point of technologies with different performances in terms of statistical sampling, number of simultaneously analyzed signals, and spatial resolution. However, the best results are usually obtained by maximizing only one of these parameters and finding a compromise for the others, a limitation that can become particularly significant when applied to cell biology and that can reduce the spreading of novel optical microscopy tools among research laboratories. Super resolution microscopy and, in particular, molecular localization-based approaches provide a spatial resolution and a molecular localization precision able to explore the scale of macromolecular complexes in situ. However, its use is limited to restricted regions, and consequently few cells, and frequently no more than one or two parameters. Correlative microscopy, obtained by the fusion of different optical technologies, can consequently surpass this barrier by merging results from different spatial scales. We discuss here the use of an acquisition and analysis correlative microscopy pipeline to obtain high statistical sampling, high content, and maximum spatial resolution by combining widefield, confocal, and molecular localization microscopy.

Integrated multimodality microscope for accurate and efficient target-guided cryo-lamellae preparation

Cryo-electron tomography (cryo-ET) is a revolutionary technique for resolving the structure of subcellular organelles and macromolecular complexes in their cellular context. However, the application of the cryo-ET is hampered by the sample preparation step. Performing cryo-focused ion beam milling at an arbitrary position on the sample is inefficient, and the target of interest is not guaranteed to be preserved when thinning the cell from several micrometers to less than 300 nm thick. Here, we report a cryogenic correlated light, ion and electron microscopy (cryo-CLIEM) technique that is capable of preparing cryo-lamellae under the guidance of three-dimensional confocal imaging. Moreover, we demonstrate a workflow to preselect and preserve nanoscale target regions inside the finished cryo-lamellae. By successfully preparing cryo-lamellae that contain a single centriole or contact sites between subcellular organelles, we show that this approach is generally applicable, and shall help in innovating more applications of cryo-ET.

Visualizing extracellular vesicle biogenesis in gram-positive bacteria using super-resolution microscopy

BACKGROUND

Recently, bacterial extracellular vesicles (EVs) have been considered to play crucial roles in various biological processes and have great potential for developing cancer therapeutics and biomedicine. However, studies on bacterial EVs have mainly focused on outer membrane vesicles released from gram-negative bacteria since the outermost peptidoglycan layer in gram-positive bacteria is thought to preclude the release of EVs as a physical barrier.

RESULTS

Here, we examined the ultrastructural organization of the EV produced by gram-positive bacteria using super-resolution stochastic optical reconstruction microscopy (STORM) at the nanoscale, which has not been resolved using conventional microscopy. Based on the super-resolution images of EVs, we propose three major mechanisms of EV biogenesis, i.e., membrane blebbing (mechanisms 1 and 2) or explosive cell lysis (mechanism 3), which are different from the mechanisms in gram-negative bacteria, despite some similarities.

CONCLUSIONS

These findings highlight the significant role of cell wall degradation in regulating various mechanisms of EV biogenesis and call for a reassessment of previously unresolved EV biogenesis in gram-positive bacteria.

Calcite-Assisted Localization and Kinetics (CLocK) Microscopy

Localization-based super-resolution imaging techniques have improved the spatial resolution of optical microscopy well below the diffraction limit, yet encoding additional information into super-resolved images, such as anisotropy and orientation, remains a challenge. Here we introduce calcite-assisted localization and kinetics (CLocK) microscopy, a multiparameter super-resolution imaging technique easily integrated into any existing optical microscope setup at low cost and with straightforward analysis. By placing a rotating calcite crystal in the infinity space of an optical microscope, CLocK microscopy provides immediate polarization and orientation information while maintaining the ability to localize an emitter/scatterer with <10 nm resolution. Further, kinetic information an order of magnitude shorter than the integration time of the camera is encoded in the unique point spread function of a CLocK image, allowing for new mechanistic insight into dynamic processes such as single-nanoparticle dissolution and single-molecule surface-enhanced Raman scattering.

Quantification of mechanical stimuli inducing nucleoplasmic translocation of YAP and its distribution mechanism using an AFM-dSTORM coupled technique

Cells can regulate a variety of behaviors by sensing mechanical signals, including growth, differentiation, apoptosis and so on. Yes-associated protein (YAP) is a mechanically sensitive protein that can be used as an indicator of mechanosignaling transduction. Unlike macroscopic statistical analysis, single-cell analysis is more demanding and challenging in terms of mechanistic regulation. Here, we quantified the location, amplitude and duration of single-cell mechanical stimulation by precise mechanical modulation, and simultaneously observed the mechanical force induced YAP nuclear and cytoplasmic distribution translocation using the AFM-dSTORM coupled techniques. Additionally, we investigated the regulation of YAP translocation according to the physical factors (cytoskeletal destruction and osmotic pressure) and biochemical factors (nuclear active transport protein inhibiter and starvation). Our study revealed that mechanical signals were transferred from the cytoskeleton to the nucleus through the synergistic action of microfilaments and microtubules, and then induced YAP translocation from the nucleus to the cytoplasm under the cooperation of nuclear export proteins. This conclusion deepens the understanding of the signaling pathway by which mechanical signals are transmitted from the plasma membrane to the cytoplasm and then to the nucleus to determine the cell's fate.

Cell membrane sample preparation method of combined AFM and dSTORM analysis

A major role of cell membranes is to provide an ideal environment for the constituent proteins to perform their biological functions. A deep understanding of the membrane proteins assembly process under physiological conditions is quite important to elucidate both the structure and the function of the cell membranes. Along these lines, in this work, a complete workflow of the cell membrane sample preparation and the correlated AFM and dSTORM imaging analysis methods are presented. A specially designed, angle-controlled sample preparation device was used to prepare the cell membrane samples. The correlated distributions of the specific membrane proteins with the topography of the cytoplasmic side of the cell membranes can be obtained by performing correlative AFM and dSTORM measurements. These methods are ideal for systematically studying the structure of the cell membranes. The proposed method of the sample characterization was not only limited to the measurement of the cell membrane but also can be applied for both biological tissue section analysis and detection.

Optimising correlative super resolution and atomic force microscopies for investigating the cellular cytoskeleton

Correlative imaging methods can provide greater information for investigations of cellular ultra-structure, with separate analysis methods complementing each other’s strengths and covering for deficiencies. Here we present a method for correlative applications of super resolution and atomic force microscopies, optimising the sample preparation for correlative imaging of the cellular cytoskeleton in COS-7 cells. This optimisation determined the order of permeabilisation and fixation, the concentration of Triton X-100 surfactant used and time required for sufficient removal of the cellular membrane while maintaining the microtubule network. Correlative SMLM/AFM imaging revealed the different information that can be obtained through each microscopy. The widths of microtubules and microtubule clusters were determined from both AFM height measurements and Gaussian fitting of SMLM intensity cross sections, these were then compared to determine the orientation of microtubules within larger microtubule bundles. The ordering of microtubules at intersections was determined from the AFM height profiles as each microtubule crosses the other. The combination of both microtubule diameter measurements enabled greater information on their structure to be found than either measurement could individually.

Microbiota in Tumors: From Understanding to Application

Microbes with complex functions have been found to be a potential component in tumor microenvironments. Due to their low biomass and other obstacles, intratumor microbiota is poorly understood. Mucosal sites and normal adjacent tissues are important sources of intratumor microbiota, while hematogenous spread also leads to the invasion of microbes. Intratumor microbiota affects the progression of tumors through several mechanisms, such as DNA damage, activation of oncogenic pathways, induction of immunosuppression, and metabolization of drugs. Notably, in different types of tumors, the composition and abundance of intratumor microbiota are highly heterogeneous and may play different roles in the progression of tumors. Because of the concern in this field, several techniques such as omics and immunological methods have been used to study intratumor microbiota. Here, recent progress in this field is reviewed, including the potential sources of intratumor microbiota, their functions and related mechanisms, and their heterogeneity. Techniques that can be used to study intratumor microbiota are also discussed. Moreover, research is summarized into the development of strategies that can be used in antitumor treatment and prospects for possible future research in this field.

Genetically encodable fluorescent protein markers in advanced optical imaging

Optical fluorescence microscopy plays a pivotal role in the exploration of biological structure and dynamics, especially on live specimens. Progress in the field relies, on the one hand, on technical advances in imaging and data processing and, on the other hand, on progress in fluorescent marker technologies. Among these, genetically encodable fluorescent proteins (FPs) are invaluable tools, as they allow facile labeling of live cells, tissues or organisms, as these produce the FP markers all by themselves after introduction of a suitable gene. Here we cover FP markers from the GFP family of proteins as well as tetrapyrrole-binding proteins, which further complement the FP toolbox in important ways. A broad range of FP variants have been endowed, by using protein engineering, with photophysical properties that are essential for specific fluorescence microscopy techniques, notably those offering nanoscale image resolution. We briefly introduce various advanced imaging methods and show how they utilize the distinct properties of the FP markers in exciting imaging applications, with the aim to guide researchers toward the design of powerful imaging experiments that are optimally suited to address their biological questions.

Combining multiple fluorescence imaging techniques in biology: when one microscope is not enough

While fluorescence microscopy has proven to be an exceedingly useful tool in bioscience, it is difficult to offer simultaneous high resolution, fast speed, large volume, and good biocompatibility in a single imaging technique. Thus, when determining the image data required to quantitatively test a complex biological hypothesis, it often becomes evident that multiple imaging techniques are necessary. Recent years have seen an explosion in development of novel fluorescence microscopy techniques, each of which features a unique suite of capabilities. In this Technical Perspective, we highlight recent studies to illustrate the benefits, and often the necessity, of combining multiple fluorescence microscopy modalities. We provide guidance in choosing optimal technique combinations to effectively address a biological question. Ultimately, we aim to promote a more well-rounded approach in designing fluorescence microscopy experiments, leading to more robust quantitative insight.

Near-infrared excitation/emission microscopy with lanthanide-based nanoparticles

Near-infrared optical imaging offers some advantages over conventional imaging, such as deeper tissue penetration, low or no autofluorescence, and reduced tissue scattering. Lanthanide-doped nanoparticles (LnNPs) have become a trend in the field of photoactive nanomaterials for optical imaging due to their unique optical features and because they can use NIR light as excitation and/or emission light. This review is focused on NaREF₄ NPs and offers an overview of the state-of-the-art investigation in their use as luminophores in optical microscopy, time-resolved imaging, and super-resolution nanoscopy based on, or applied to, LnNPs. Secondly, whenever LnNPs are combined with other nanomaterial or nanoparticle to afford nanohybrids, the characterization of their physical and chemical properties is of current interest. In this context, the latest trends in optical microscopy and their future perspectives are discussed.

Bleaching-Resistant Super-Resolution Fluorescence Microscopy

Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.

Super-Resolution Microscopy for Structural Cell Biology

Super-resolution microscopy techniques, and specifically single-molecule localization microscopy (SMLM), are approaching nanometer resolution inside cells and thus have great potential to complement structural biology techniques such as electron microscopy for structural cell biology. In this review, we introduce the different flavors of super-resolution microscopy, with a special emphasis on SMLM and MINFLUX (minimal photon flux). We summarize recent technical developments that pushed these localization-based techniques to structural scales and review the experimental conditions that are key to obtaining data of the highest quality. Furthermore, we give an overview of different analysis methods and highlight studies that used SMLM to gain structural insights into biologically relevant molecular machines. Ultimately, we give our perspective on what is needed to push the resolution of these techniques even further and to apply them to investigating dynamic structural rearrangements in living cells. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Recent Developments in Correlative Super-Resolution Fluorescence Microscopy and Electron Microscopy

The recently developed correlative super-resolution fluorescence microscopy (SRM) and electron microscopy (EM) is a hybrid technique that simultaneously obtains the spatial locations of specific molecules with SRM and the context of the cellular ultrastructure by EM. Although the combination of SRM and EM remains challenging owing to the incompatibility of samples prepared for these techniques, the increasing research attention on these methods has led to drastic improvements in their performances and resulted in wide applications. Here, we review the development of correlative SRM and EM (sCLEM) with a focus on the correlation of EM with different SRM techniques. We discuss the limitations of the integration of these two microscopy techniques and how these challenges can be addressed to improve the quality of correlative images. Finally, we address possible future improvements and advances in the continued development and wide application of sCLEM approaches.

Scalable Characterization of 2D Gallium-Intercalated Epitaxial Graphene

Scalable synthesis of two-dimensional gallium (2D-Ga) covered by graphene layers was recently realized through confinement heteroepitaxy using silicon carbide substrates. However, the thickness, uniformity, and area coverage of the 2D-Ga heterostructures have not previously been studied with high-spatial resolution techniques. In this work, we resolve and measure the 2D-Ga heterostructure thicknesses using scanning electron microscopy (SEM). Utilizing multiple correlative methods, we find that SEM image contrast is directly related to the presence of uniform bilayer Ga at the interface and a variation of the number of graphene layers. We also investigate the origin of SEM contrast using both experimental measurements and theoretical calculations of the surface potentials. We find that a carbon buffer layer is detached due to the gallium intercalation, which increases the surface potential as an indication of the 2D-Ga presence. We then scale up the heterostructure characterization over a few-square millimeter area by segmenting SEM images, each acquired with nanometer-scale in-plane resolution. This work leverages the spectroscopic imaging capabilities of SEM that allows high-spatial resolution imaging for tracking intercalants, identifying relative surface potentials, determining the number of 2D layers, and further characterizing scalability and uniformity of low-dimensional materials.

Development of a New Approach for Low-Laser-Power Super-Resolution Fluorescence Imaging

The development of super-resolution fluorescence microscopy over the past decade has drastically improved the resolution of light microscopy to ∼10 nm. Stochastic optical reconstruction microscopy (STORM) can be used to achieve subdiffraction-limit resolution by sequentially imaging and localizing individual fluorophores. In principle, the super-resolution of STORM can be obtained by high-accuracy localization of photoswitchable fluorophores, which require fast photoswitching and bright fluorescence intensity from a single emitter. It is known that the switching rate of photoswitchable fluorophores depends on the laser power─a high laser power being required for the enhancement of imaging resolution. However, high laser power is usually harmful to biological specimens and limits the imaging time because of its photobleaching effects and high phototoxicity. In this study, we attempted to overcome this problem by improving the STORM resolution at a lower laser power. Through the quantitative analysis of the photoswitching behavior of single fluorophores under different laser power conditions, we developed a new approach to achieve super-resolution fluorescence images at a laser power 10 times lower than had previously been reported. This approach is expected to play an increasingly significant role in super-resolution imaging of power-sensitive samples.

Research fronts of Chemical Biology

Over the past decades, researchers have witnessed substantially increasing and ever-growing interests and efforts in Chemical Biology studies, thanks to the development of genome and epi-genome sequencing (revealing potential drug targets), synthetic chemistry (producing new medicines), bioorthogonal chemistry (chemistry in living systems) and high-throughput screening technologies (in vitro cell systems, protein binding assays and phenotypic assays). This report presents literature search results for current research in Chemical Biology, to explore basic principles, summarize recent advances, identify key challenges, and provide suggestions for future research (with a focus on Chemical Biology in the context of human health and diseases). Chemical Biology research can positively contribute to delivering a better understanding of the molecular and cellular mechanisms that accompany pathology underlying diseases, as well as developing improved methods for diagnosis, drug discovery, and therapeutic delivery. While much progress has been made, as shown in this report, there are still further needs and opportunities. For instance, pressing challenges still exist in selecting appropriate targets in biological systems and adopting more rational design strategies for the development of innovative and sustainable diagnostic technologies and medical treatments. Therefore, more than ever, researchers from different disciplines need to collaborate to address the challenges in Chemical Biology.

Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples

Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses-bacteriophages and archaeal viruses-influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage-host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth's ecosystems.

Dopamine-Mediated Biomineralization of Calcium Phosphate as a Strategy to Facilely Synthesize Functionalized Hybrids

Organic-inorganic hybrid materials have been considered to be promising carriers or immobilization matrixes for biomolecules due to their high efficiency and significantly enhanced activities and stabilities of biomolecules. Here, the well-defined dopamine/calcium phosphate organic-inorganic hybrids (DACaPMFs) are fabricated via one-pot dopamine-mediated biomineralization, and their structure and properties are also characterized. Direct stochastic optical reconstruction microscopy (dSTORM) is first used to probe the distribution of organic components in these hybrids. Combined with spectroscopic data, the direct observation of dopamine in the hybrids helps to understand the formation of a physical chemistry mechanism of the biomineralization. The obtained DACaPMFs with multiple-level pores allow the loading of doxorubicin with a high loading efficiency and a pH-responsive property. Furthermore, thrombin is entrapped by the hybrids to prove the controlled release. It is expected that such organic-inorganic hybrid materials may hold great promise for application in drug delivery as well as scaffold materials in bone tissue engineering and hemostatic material.

Correlative Light-Environmental Scanning Electron Microscopy of Plasma Membrane Efflux Carriers of Plant Hormone Auxin

Fluorescence light microscopy provided convincing evidence for the domain organization of plant plasma membrane (PM) proteins. Both peripheral and integral PM proteins show an inhomogeneous distribution within the PM. However, the size of PM nanodomains and protein clusters is too small to accurately determine their dimensions and nano-organization using routine confocal fluorescence microscopy and super-resolution methods. To overcome this limitation, we have developed a novel correlative light electron microscopy method (CLEM) using total internal reflection fluorescence microscopy (TIRFM) and advanced environmental scanning electron microscopy (A-ESEM). Using this technique, we determined the number of auxin efflux carriers from the PINFORMED (PIN) family (NtPIN3b-GFP) within PM nanodomains of tobacco cell PM ghosts. Protoplasts were attached to coverslips and immunostained with anti-GFP primary antibody and secondary antibody conjugated to fluorochrome and gold nanoparticles. After imaging the nanodomains within the PM with TIRFM, the samples were imaged with A-ESEM without further processing, and quantification of the average number of molecules within the nanodomain was performed. Without requiring any post-fixation and coating procedures, this method allows to study details of the organization of auxin carriers and other plant PM proteins.

Single Molecules Are Your Quanta: A Bottom-Up Approach toward Multidimensional Super-resolution Microscopy

The rise of single-molecule localization microscopy (SMLM) and related super-resolution methods over the past 15 years has revolutionized how we study biological and materials systems. In this Perspective, we reflect on the underlying philosophy of how diffraction-unlimited pictures containing rich spatial and functional information may gradually emerge through the local accumulation of single-molecule measurements. Starting with the basic concepts, we analyze the uniqueness of and opportunities in building up the final picture one molecule at a time. After brief introductions to the more established multicolor and three-dimensional measurements, we highlight emerging efforts to extend SMLM to new dimensions and functionalities as fluorescence polarization, emission spectra, and molecular motions, and discuss rising opportunities and future directions. With single molecules as our quanta, the bottom-up accumulation approach provides a powerful conduit for multidimensional microscopy at the nanoscale.

Correlative Super-Resolution and Atomic Force Microscopy of DNA Nanostructures and Characterization of Addressable Site Defects

To bring real-world applications of DNA nanostructures to fruition, advanced microscopy techniques are needed to shed light on factors limiting the availability of addressable sites. Correlative microscopy, where two or more microscopies are combined to characterize the same sample, is an approach to overcome the limitations of individual techniques, yet it has seen limited use for DNA nanotechnology. We have developed an accessible strategy for high resolution, correlative DNA-based points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution and atomic force microscopy (AFM) of DNA nanostructures, enabled by a simple and robust method to selectively bind DNA origami to cover glass. Using this technique, we examined addressable "docking" sites on DNA origami to distinguish between two defect scenarios-structurally incorporated but inactive docking sites, and unincorporated docking sites. We found that over 75% of defective docking sites were incorporated but inactive, suggesting unincorporated strands played a minor role in limiting the availability of addressable sites. We further explored the effects of strand purification, UV irradiation, and photooxidation on availability, providing insight on potential sources of defects and pathways toward improving the fidelity of DNA nanostructures.

Long-term switching of single photochromic triads based on dithienylcyclopentene and fluorophores at cryogenic temperatures

Photochromic molecules can be reversibly converted between two bistable forms by light. These systems have been intensively studied for applications as molecular memories, sensing devices, or super-resolution optical microscopy. Here, we study the long-term switching behavior of single photochromic triads under oxygen-free conditions at 10 K. The triads consist of a photochromic unit that is covalently linked to two strong fluorophores that were employed for monitoring the light-induced conversions of the switch via changes in the fluorescence intensity from the fluorophores. As dyes we use either perylene bisimide or boron-dipyrromethen, and as photochromic switch we use dithienylcyclopentene (DCP). Both types of triads showed high fatigue resistance allowing for up to 6000 switching cycles of a single triad corresponding to time durations in the order of 80 min without deterioration. Long-term analysis of the switching cycles reveals that the probability that an intensity change in the emission from the dyes can be assigned to an externally stimulated conversion of the DCP (rather than to stochastic blinking of the dye molecules) amounts to 0.7 ± 0.1 for both types of triads. This number is far too low for optical data storage using single triads and implications concerning the miniaturization of optical memories based on such systems will be discussed. Yet, together with the high fatigue resistance, this number is encouraging for applications in super-resolution optical microscopy on frozen biological samples.

The nanoscale molecular morphology of docked exocytic dense-core vesicles in neuroendocrine cells

Rab-GTPases and their interacting partners are key regulators of secretory vesicle trafficking, docking, and fusion to the plasma membrane in neurons and neuroendocrine cells. Where and how these proteins are positioned and organized with respect to the vesicle and plasma membrane are unknown. Here, we use correlative super-resolution light and platinum replica electron microscopy to map Rab-GTPases (Rab27a and Rab3a) and their effectors (Granuphilin-a, Rabphilin3a, and Rim2) at the nanoscale in 2D. Next, we apply a targetable genetically-encoded electron microscopy labeling method that uses histidine based affinity-tags and metal-binding gold-nanoparticles to determine the 3D axial location of these exocytic proteins and two SNARE proteins (Syntaxin1A and SNAP25) using electron tomography. Rab proteins are distributed across the entire surface and t-SNARE proteins at the base of docked vesicles. We propose that the circumferential distribution of Rabs and Rab-effectors could aid in the efficient transport, capture, docking, and rapid fusion of calcium-triggered exocytic vesicles in excitable cells.

ML-SIM: universal reconstruction of structured illumination microscopy images using transfer learning

Structured illumination microscopy (SIM) has become an important technique for optical super-resolution imaging because it allows a doubling of image resolution at speeds compatible with live-cell imaging. However, the reconstruction of SIM images is often slow, prone to artefacts, and requires multiple parameter adjustments to reflect different hardware or experimental conditions. Here, we introduce a versatile reconstruction method, ML-SIM, which makes use of transfer learning to obtain a parameter-free model that generalises beyond the task of reconstructing data recorded by a specific imaging system for a specific sample type. We demonstrate the generality of the model and the high quality of the obtained reconstructions by application of ML-SIM on raw data obtained for multiple sample types acquired on distinct SIM microscopes. ML-SIM is an end-to-end deep residual neural network that is trained on an auxiliary domain consisting of simulated images, but is transferable to the target task of reconstructing experimental SIM images. By generating the training data to reflect challenging imaging conditions encountered in real systems, ML-SIM becomes robust to noise and irregularities in the illumination patterns of the raw SIM input frames. Since ML-SIM does not require the acquisition of experimental training data, the method can be efficiently adapted to any specific experimental SIM implementation. We compare the reconstruction quality enabled by ML-SIM with current state-of-the-art SIM reconstruction methods and demonstrate advantages in terms of generality and robustness to noise for both simulated and experimental inputs, thus making ML-SIM a useful alternative to traditional methods for challenging imaging conditions. Additionally, reconstruction of a SIM stack is accomplished in less than 200 ms on a modern graphics processing unit, enabling future applications for real-time imaging. Source code and ready-to-use software for the method are available at http://ML-SIM.github.io.

Cryogenic Super-Resolution Fluorescence and Electron Microscopy Correlated at the Nanoscale

We review the emerging method of super-resolved cryogenic correlative light and electron microscopy (srCryoCLEM). Super-resolution (SR) fluorescence microscopy and cryogenic electron tomography (CET) are both powerful techniques for observing subcellular organization, but each approach has unique limitations. The combination of the two brings the single-molecule sensitivity and specificity of SR to the detailed cellular context and molecular scale resolution of CET. The resulting correlative data is more informative than the sum of its parts. The correlative images can be used to pinpoint the positions of fluorescently labeled proteins in the high-resolution context of CET with nanometer-scale precision and/or to identify proteins in electron-dense structures. The execution of srCryoCLEM is challenging and the approach is best described as a method that is still in its infancy with numerous technical challenges. In this review, we describe state-of-the-art srCryoCLEM experiments, discuss the most pressing challenges, and give a brief outlook on future applications.