A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy

Smart sensing hydrogel actuators conferred by MXene gradient arrangement

Smart sensing and excellent actuation abilities of natural organisms have driven scientists to develop bionic soft-bodied robots. However, most conventional robots suffer from poor electrical conductivity, limiting their application in real-time sensing and actuation. Here, we report a novel strategy to enhance the electrical conductivity of hydrogels that integrated actuation and strain-sensing functions for bioinspired self-sensing soft actuators. Conductive hydrogels were synthesized in situ by copolymerizing MXene nanosheets with thermosensitive N-isopropylacrylamide and acrylamide under a direct current electric field. The resulting hydrogels exhibited high electrical conductivity (2.11 mS/cm), good sensitivity with a gauge factor of 4.79 and long-term stability. The developed hydrogels demonstrated remarkable capabilities in detecting human motions at subtle strains such as facial expressions and large strains such as knee bending. Additionally, the hydrogel electrode patch was capable of monitoring physiological signals. Furthermore, the developed hydrogel showed good thermally induced actuation effects when the temperature was higher than 30 °C. Overall, this work provided new insights for the design of sensory materials with integrated self-sensing and actuation capabilities, which would pave the way for the development of high-performance conductive soft materials for intelligent soft robots and automated machinery.

Accelerated protein retention expansion microscopy using microwave radiation

Protein retention expansion microscopy (ExM) retains fluorescent signals in fixed tissue and isotropically expands the tissue to allow nanoscale (<70 nm) resolution on diffraction-limited confocal microscopes. Despite the numerous advantages of ExM, the protocol is time-consuming. Here, we adapted an ExM protocol to vibratome-sectioned brain tissue of Xenopus laevis tadpoles and implemented a microwave (M/W)-assisted protocol (M/WExM) to reduce the workflow from days to hours. Our M/WExM protocol maintains the superior resolution of the original ExM protocol and yields a higher magnitude of expansion, suggesting that M/W radiation may also facilitate the expansion process. We then adapted the M/W protocol to the whole-mount brain of Drosophila melanogaster fruit flies, and successfully reduced the processing time of a widely used Drosophila IHC-ExM protocol from 6 to 2 days. This demonstrates that with appropriate adjustment of M/W parameters, this protocol can be readily adapted to different organisms and tissue types to greatly increase the efficiency of ExM experiments.

Derivative Technologies of Expansion Microscopy and Applications in Biomedicine

Expansion microscopy (ExM) is an innovative super-resolution imaging technique that utilizes physical expansion to magnify biological samples, facilitating the visualization of cellular structures that are challenging to observe using traditional optical microscopes. The fundamental principle of ExM revolves around employing a specialized hydrogel to uniformly expand biological samples, thereby achieving super-resolution imaging under conventional optical imaging conditions. This technology finds application not only in various biological samples such as cells and tissue sections, but also enables super-resolution imaging of large biological molecules including proteins, nucleic acids, and metabolite molecules. In recent years, numerous researchers have delved into ExM, resulting in the continuous development of a range of derivative technologies that optimize experimental protocols and broaden practical application fields. This article presents a comprehensive review of these derivative technologies, highlighting the utilization of ExM for anchoring nucleic acids, proteins, and other biological molecules, as well as its applications in biomedicine. Furthermore, this review offers insights into the future development prospects of ExM technology.

Single-shot 20-fold expansion microscopy

Expansion microscopy (ExM) is in increasingly widespread use throughout biology because its isotropic physical magnification enables nanoimaging on conventional microscopes. To date, ExM methods either expand specimens to a limited range (~4-10× linearly) or achieve larger expansion factors through iterating the expansion process a second time (~15-20× linearly). Here, we present an ExM protocol that achieves ~20× expansion (yielding <20-nm resolution on a conventional microscope) in a single expansion step, achieving the performance of iterative expansion with the simplicity of a single-shot protocol. This protocol, which we call 20ExM, supports postexpansion staining for brain tissue, which can facilitate biomolecular labeling. 20ExM may find utility in many areas of biological investigation requiring high-resolution imaging.

One-step nanoscale expansion microscopy reveals individual protein shapes

The attainable resolution of fluorescence microscopy has reached the subnanometer range, but this technique still fails to image the morphology of single proteins or small molecular complexes. Here, we expand the specimens at least tenfold, label them with conventional fluorophores and image them with conventional light microscopes, acquiring videos in which we analyze fluorescence fluctuations. One-step nanoscale expansion (ONE) microscopy enables the visualization of the shapes of individual membrane and soluble proteins, achieving around 1-nm resolution. We show that conformational changes are readily observable, such as those undergone by the ~17-kDa protein calmodulin upon Ca2+ binding. ONE is also applied to clinical samples, analyzing the morphology of protein aggregates in cerebrospinal fluid from persons with Parkinson disease, potentially aiding disease diagnosis. This technology bridges the gap between high-resolution structural biology techniques and light microscopy, providing new avenues for discoveries in biology and medicine.

Expansion and Light-Sheet Microscopy for Nanoscale 3D Imaging

Expansion Microscopy (ExM) and Light-Sheet Fluorescence Microscopy (LSFM) are forefront imaging techniques that enable high-resolution visualization of biological specimens. ExM enhances nanoscale investigation using conventional fluorescence microscopes, while LSFM offers rapid, minimally invasive imaging over large volumes. This review explores the joint advancements of ExM and LSFM, focusing on the excellent performance of the integrated modality obtained from the combination of the two, which is refer to as ExLSFM. In doing so, the chemical processes required for ExM, the tailored optical setup of LSFM for examining expanded samples, and the adjustments in sample preparation for accurate data collection are emphasized. It is delve into various specimen types studied using this integrated method and assess its potential for future applications. The goal of this literature review is to enrich the comprehension of ExM and LSFM, encouraging their wider use and ongoing development, looking forward to the upcoming challenges, and anticipating innovations in these imaging techniques.

Nanoscale volumetric fluorescence imaging via photochemical sectioning

Optical nanoscopy of intact biological specimens has been transformed by recent advancements in hydrogel-based tissue clearing and expansion, enabling the imaging of cellular and subcellular structures with molecular contrast. However, existing high-resolution fluorescence microscopes have limited imaging depth, which prevents the study of whole-mount specimens without physical sectioning. To address this challenge, we developed "photochemical sectioning," a spatially precise, light-based sample sectioning process. By combining photochemical sectioning with volumetric lattice light-sheet imaging and petabyte-scale computation, we imaged and reconstructed axons and myelination sheaths across entire mouse olfactory bulbs at nanoscale resolution. An olfactory-bulb-wide analysis of myelinated and unmyelinated axons revealed distinctive patterns of axon degeneration and de-/dysmyelination in the neurodegenerative mouse, highlighting the potential for peta- to exabyte-scale super-resolution studies using this approach.

On-demand expansion fluorescence and photoacoustic microscopy (ExFLPAM)

Expansion microscopy (ExM) is a promising technology that enables nanoscale imaging on conventional optical microscopes by physically magnifying the specimens. Here, we report the development of a strategy that enables i) on-demand labeling of subcellular organelles in live cells for ExM through transfection of fluorescent proteins that are well-retained during the expansion procedure; and ii) non-fluorescent chromogenic color-development towards efficient bright-field and photoacoustic imaging in both planar and volumetric formats, which is applicable to both cultured cells and biological tissues. Compared to the conventional ExM methods, our strategy provides an expanded toolkit, which we term as expansion fluorescence and photoacoustic microscopy (ExFLPAM), by allowing on-demand fluorescent protein labeling of cultured cells, as well as non-fluorescent absorption contrast-imaging of biological samples.

Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics

A technique capable of label-free detection, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of native biomolecules in intact specimens. However, MSI has often been precluded from single-cell applications due to the spatial resolution limit set forth by the physical and instrumental constraints of the method. By taking advantage of the reversible interaction between the analytes and a superabsorbent hydrogel, we have developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome the spatial resolution limits of modern mass spectrometers. With GAMSI, we show that the spatial resolution of MALDI-MSI can be enhanced ~3-6-fold to the sub-micrometer level without changing the existing mass spectrometry hardware or analysis pipeline. This approach will vastly enhance the accessibility of MSI-based spatial analysis at the cellular scale.

Expanding boundaries - a cell biologist's guide to expansion microscopy

Expansion microscopy (ExM) is a revolutionary novel approach to increase resolution in light microscopy. In contrast to super-resolution microscopy methods that rely on sophisticated technological advances, including novel instrumentation, ExM instead is entirely based on sample preparation. In ExM, labeled target molecules in fixed cells are anchored in a hydrogel, which is then physically enlarged by osmotic swelling. The isotropic swelling of the hydrogel pulls the labels apart from one another, and their relative organization can thus be resolved using conventional microscopes even if it was below the diffraction limit of light beforehand. As ExM can additionally benefit from the technical resolution enhancements achieved by super-resolution microscopy, it can reach into the nanometer range of resolution with an astoundingly low degree of error induced by distortion during the physical expansion process. Because the underlying chemistry is well understood and the technique is based on a relatively simple procedure, ExM is easily reproducible in non-expert laboratories and has quickly been adopted to address an ever-expanding spectrum of problems across the life sciences. In this Review, we provide an overview of this rapidly expanding new field, summarize the most important insights gained so far and attempt to offer an outlook on future developments.

Combining single-molecule and expansion microscopy in fission yeast to visualize protein structures at the nanostructural level

In this work, we have developed an expansion microscopy (ExM) protocol that combines ExM with photoactivated localization microscopy (ExPALM) for yeast cell imaging, and report a robust protocol for single-molecule and expansion microscopy of fission yeast, abbreviated as SExY. Our optimized SExY protocol retains about 50% of the fluorescent protein signal, doubling the amount obtained compared to the original protein retention ExM (proExM) protocol. It allows for a fivefold, highly isotropic expansion of fission yeast cells, which we carefully controlled while optimizing protein yield. We demonstrate the SExY method on several exemplary molecular targets and explicitly introduce low-abundant protein targets (e.g. nuclear proteins such as cbp1 and mis16, and the centromere-specific histone protein cnp1). The SExY protocol optimizations increasing protein yield could be beneficial for many studies, when targeting low abundance proteins, or for studies that rely on genetic labelling for various reasons (e.g. for proteins that cannot be easily targeted by extrinsic staining or in case artefacts introduced by unspecific staining interfere with data quality).

Percolation-induced gel-gel phase separation in a dilute polymer network

Cosmic large-scale structures, animal flocks and living tissues can be considered non-equilibrium organized systems created by dissipative processes. Replicating such properties in artificial systems is still difficult. Herein we report a dissipative network formation process in a dilute polymer-water mixture that leads to percolation-induced gel-gel phase separation. The dilute system, which forms a monophase structure at the percolation threshold, spontaneously separates into two co-continuous gel phases with a submillimetre scale (a dilute-percolated gel) during the deswelling process after the completion of the gelation reaction. The dilute-percolated gel, which contains 99% water, exhibits unexpected hydrophobicity and induces the development of adipose-like tissues in subcutaneous tissues. These findings support the development of dissipative structures with advanced functionalities for distinct applications, ranging from physical chemistry to tissue engineering.

iU-ExM: nanoscopy of organelles and tissues with iterative ultrastructure expansion microscopy

Expansion microscopy (ExM) is a highly effective technique for super-resolution fluorescence microscopy that enables imaging of biological samples beyond the diffraction limit with conventional fluorescence microscopes. Despite the development of several enhanced protocols, ExM has not yet demonstrated the ability to achieve the precision of nanoscopy techniques such as Single Molecule Localization Microscopy (SMLM). Here, to address this limitation, we have developed an iterative ultrastructure expansion microscopy (iU-ExM) approach that achieves SMLM-level resolution. With iU-ExM, it is now possible to visualize the molecular architecture of gold-standard samples, such as the eight-fold symmetry of nuclear pores or the molecular organization of the conoid in Apicomplexa. With its wide-ranging applications, from isolated organelles to cells and tissue, iU-ExM opens new super-resolution avenues for scientists studying biological structures and functions.

Microscale visualization of cellular features in adult macaque visual cortex

Expansion microscopy and light sheet imaging enable fine-scale resolution of intracellular features that comprise neural circuits. Most current techniques visualize sparsely distributed features across whole brains or densely distributed features within individual brain regions. Here, we visualize dense distributions of immunolabeled proteins across early visual cortical areas in adult macaque monkeys. This process may be combined with multiphoton or magnetic resonance imaging to produce multimodal atlases in large, gyrencephalic brains.

Atmospheric-moisture-induced polyacrylate hydrogels for hybrid passive cooling

Heat stress is being exacerbated by global warming, jeopardizing human and social sustainability. As a result, reliable and energy-efficient cooling methods are highly sought-after. Here, we report a polyacrylate film fabricated by self-moisture-absorbing hygroscopic hydrogel for efficient hybrid passive cooling. Using one of the lowest-cost industrial materials (e.g., sodium polyacrylate), we demonstrate radiative cooling by reducing solar heating with high solar reflectance (0.93) while maximizing thermal emission with high mid-infrared emittance (0.99). Importantly, the manufacturing process utilizes only atmospheric moisture and requires no additional chemicals or energy consumption, making it a completely green process. Under sunlight illumination of 800 W m-2, the surface temperature of the film was reduced by 5 °C under a partly cloudy sky observed at Buffalo, NY. Combined with its hygroscopic feature, this film can simultaneously introduce evaporative cooling that is independent of access to the clear sky. The hybrid passive cooling approach is projected to decrease global carbon emissions by 118.4 billion kg/year compared to current air-conditioning facilities powered by electricity. Given its low-cost raw materials and excellent molding feature, the film can be manufactured through simple and cost-effective roll-to-roll processes, making it suitable for future building construction and personal thermal management needs.

Expansion microscopy using a single anchor molecule for high-yield multiplexed imaging of proteins and RNAs

Expansion microscopy (ExM), by physically enlarging specimens in an isotropic fashion, enables nanoimaging on standard light microscopes. Key to existing ExM protocols is the equipping of different kinds of molecules, with different kinds of anchoring moieties, so they can all be pulled apart from each other by polymer swelling. Here we present a multifunctional anchor, an acrylate epoxide, that enables proteins and RNAs to be equipped with anchors in a single experimental step. This reagent simplifies ExM protocols and reduces cost (by 2-10-fold for a typical multiplexed ExM experiment) compared to previous strategies for equipping RNAs with anchors. We show that this united ExM (uniExM) protocol can be used to preserve and visualize RNA transcripts, proteins in biologically relevant ultrastructures, and sets of RNA transcripts in patient-derived xenograft (PDX) cancer tissues and may support the visualization of other kinds of biomolecular species as well. uniExM may find many uses in the simple, multimodal nanoscale analysis of cells and tissues.

Iterative immunostaining combined with expansion microscopy and image processing reveals nanoscopic network organization of nuclear lamina

Investigation of nuclear lamina architecture relies on superresolved microscopy. However, epitope accessibility, labeling density, and detection precision of individual molecules pose challenges within the molecularly crowded nucleus. We developed iterative indirect immunofluorescence (IT-IF) staining approach combined with expansion microscopy (ExM) and structured illumination microscopy to improve superresolution microscopy of subnuclear nanostructures like lamins. We prove that ExM is applicable in analyzing highly compacted nuclear multiprotein complexes such as viral capsids and provide technical improvements to ExM method including three-dimensional-printed gel casting equipment. We show that in comparison with conventional immunostaining, IT-IF results in a higher signal-to-background ratio and a mean fluorescence intensity by improving the labeling density. Moreover, we present a signal-processing pipeline for noise estimation, denoising, and deblurring to aid in quantitative image analyses and provide this platform for the microscopy imaging community. Finally, we show the potential of signal-resolved IT-IF in quantitative superresolution ExM imaging of nuclear lamina and reveal nanoscopic details of the lamin network organization-a prerequisite for studying intranuclear structural coregulation of cell function and fate.

Expansion microscopy: A chemical approach for super-resolution microscopy

Super-resolution microscopy is a series of imaging techniques that bypass the diffraction limit of resolution. Since the 1990s, optical approaches, such as single-molecular localization microscopy, have allowed us to visualize biological samples from the sub-organelle to the molecular level. Recently, a chemical approach called expansion microscopy emerged as a new trend in super-resolution microscopy. It physically enlarges cells and tissues, which leads to an increase in the effective resolution of any microscope by the length expansion factor. Compared with optical approaches, expansion microscopy has a lower cost and higher imaging depth but requires a more complex procedure. The integration of expansion microscopy and advanced microscopes significantly pushed forward the boundary of super-resolution microscopy. This review covers the current state of the art in expansion microscopy, including the latest methods and their applications, as well as challenges and opportunities for future research.

All-Covalent Nuclease-Resistant and Hydrogel-Tethered DNA Hairpin Probes Map pN Cell Traction Forces

Cells sense and respond to the physical properties of their environment through receptor-mediated signaling, a process known as mechanotransduction, which can modulate critical cellular functions such as proliferation, differentiation, and survival. At the molecular level, cell adhesion receptors, such as integrins, transmit piconewton (pN)-scale forces to the extracellular matrix, and the magnitude of the force plays a critical role in cell signaling. The most sensitive approach to measuring integrin forces involves DNA hairpin-based sensors, which are used to quantify and map forces in living cells. Despite the broad use of DNA hairpin sensors to study a variety of mechanotransduction processes, these sensors are typically anchored to rigid glass slides, which are orders of magnitude stiffer than the extracellular matrix and hence modulate native biological responses. Here, we have developed nuclease-resistant DNA hairpin probes that are all covalently tethered to PEG hydrogels to image cell traction forces on physiologically relevant substrate stiffness. Using HeLa cells as a model cell line, we show that the molecular forces transmitted by integrins are highly sensitive to the bulk modulus of the substrate, and cells cultured on the 6 and 13 kPa gels produced a greater number of hairpin unfolding events compared to the 2 kPa substrates. Tension signals are spatially colocalized with pY118-paxillin, confirming focal adhesion-mediated probe opening. Additionally, we found that integrin forces are greater than 5.8 pN but less than 19 pN on 13 kPa gels. This work provides a general strategy to integrate molecular tension probes into hydrogels, which can better mimic in vivo mechanotransduction.

Gel-assisted mass spectrometry imaging

Compatible with label-free detection and quantification, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of biomolecules in intact specimens. Yet, the spatial resolution of MSI is limited by the method's physical and instrumental constraints, which often preclude it from single-cell and subcellular applications. By taking advantage of the reversible interaction of analytes with superabsorbent hydrogels, we developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome these limits. With GAMSI, the spatial resolution of lipid and protein MALDI-MSI can be enhanced severalfold without changing the existing mass spectrometry hardware and analysis pipeline. This approach will further enhance the accessibility to (sub)cellular-scale MALDI-MSI-based spatial omics.

Photo-expansion microscopy enables super-resolution imaging of cells embedded in 3D hydrogels

Hydrogels are extensively used as tunable, biomimetic three-dimensional cell culture matrices, but optically deep, high-resolution images are often difficult to obtain, limiting nanoscale quantification of cell-matrix interactions and outside-in signalling. Here we present photopolymerized hydrogels for expansion microscopy that enable optical clearance and tunable ×4.6-6.7 homogeneous expansion of not only monolayer cell cultures and tissue sections, but cells embedded within hydrogels. The photopolymerized hydrogels for expansion microscopy formulation relies on a rapid photoinitiated thiol/acrylate mixed-mode polymerization that is not inhibited by oxygen and decouples monomer diffusion from polymerization, which is particularly beneficial when expanding cells embedded within hydrogels. Using this technology, we visualize human mesenchymal stem cells and their interactions with nascently deposited proteins at <120 nm resolution when cultured in proteolytically degradable synthetic polyethylene glycol hydrogels. Results support the notion that focal adhesion maturation requires cellular fibronectin deposition; nuclear deformation precedes cellular spreading; and human mesenchymal stem cells display cell-surface metalloproteinases for matrix remodelling.

Fluorescence Microscopy in Adeno-Associated Virus Research

Research on adeno-associated virus (AAV) and its recombinant vectors as well as on fluorescence microscopy imaging is rapidly progressing driven by clinical applications and new technologies, respectively. The topics converge, since high and super-resolution microscopes facilitate the study of spatial and temporal aspects of cellular virus biology. Labeling methods also evolve and diversify. We review these interdisciplinary developments and provide information on the technologies used and the biological knowledge gained. The emphasis lies on the visualization of AAV proteins by chemical fluorophores, protein fusions and antibodies as well as on methods for the detection of adeno-associated viral DNA. We add a short overview of fluorescent microscope techniques and their advantages and challenges in detecting AAV.

[Closer to the native architecture of the cell using Cryo-ExM]

Most cellular imaging techniques, such as light or electron microscopy, require that the biological sample is first fixed by chemical cross-linking agents. This necessary step is also known to damage molecular nanostructures or even sub-cellular organization. To overcome this problem, another fixation approach was invented more than 40 years ago, which consists in cryo-fixing biological samples, thus allowing to preserve their native state. However, this method has been scarcely used in light microscopy due to the complexity of its implementation. In this review, we present a recently developed super-resolution method called expansion microscopy, which, when coupled with cryo-fixation, allows to visualize at a nanometric resolution the cell architecture as close as possible to its native state.

Current Progress in Expansion Microscopy: Chemical Strategies and Applications

Expansion microscopy (ExM) is a newly developed super-resolution technique, allowing visualization of biological targets at nanoscale resolution on conventional fluorescence microscopes. Since its introduction in 2015, many efforts have been dedicated to broaden its application range or increase the resolution that can be achieved. As a consequence, recent years have witnessed remarkable advances in ExM. This review summarizes recent progress in ExM, with the focus on the chemical aspects of the method, from chemistries for biomolecule grafting to polymer synthesis and the impact on biological analysis. The combination of ExM with other microscopy techniques, in search of additional resolution improvement, is also discussed. In addition, we compare pre- and postexpansion labeling strategies and discuss the impact of fixation methods on ultrastructure preservation. We conclude this review with a perspective on existing challenges and future directions. We believe that this review will provide a comprehensive understanding of ExM and facilitate its usage and further development.

Molecular Resolution Mapping of Erythrocyte Cytoskeleton by Ultrastructure Expansion Single-Molecule Localization Microscopy

The combination of expansion microscopy and single-molecule localization microscopy has the potential to approach the molecular resolution. However, this combination meets challenges due to the hydrogel shrinkage in the presence of imaging buffer. Here, a method of ultrastructure expansion single-molecule localization microscopy (U-ExSMLM) based on skillfully adhering the gel onto poly-l-lysine (pLL)-coated coverslip is developed to prevent lateral shrinkage of the hydrogel. U-ExSMLM is then applied to dissect the membrane cytoskeleton organization of human erythrocytes at molecular resolution. The resolved nanoscale spatial distributions of cytoskeleton proteins, including the N/C-termini of β-spectrin, protein 4.1, and tropomodulin, show good agreement with the acknowledged model of erythrocyte cytoskeleton structure, demonstrating the reliability of U-ExSMLM. Furthermore, the concentration of pLL is adjusted to preserve the physiological biconcave morphology of erythrocytes, and it is found that the spectrin cytoskeleton in the dimple regions has lower density and larger length than that in the rim regions, which provides the direct evidence for cytoskeleton asymmetry in human erythrocytes. Therefore, the integrated method offers future opportunities to study the ultrastructure of membrane cytoskeleton at molecular resolution.

Ultrastructure expansion microscopy reveals the cellular architecture of budding and fission yeast

The budding and fission yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have served as invaluable model organisms to study conserved fundamental cellular processes. Although super-resolution microscopy has in recent years paved the way to a better understanding of the spatial organization of molecules in cells, its wide use in yeasts has remained limited due to the specific know-how and instrumentation required, contrasted with the relative ease of endogenous tagging and live-cell fluorescence microscopy. To facilitate super-resolution microscopy in yeasts, we have extended the ultrastructure expansion microscopy (U-ExM) method to both S. cerevisiae and S. pombe, enabling a 4-fold isotropic expansion. We demonstrate that U-ExM allows imaging of the microtubule cytoskeleton and its associated spindle pole body, notably unveiling the Sfi1p–Cdc31p spatial organization on the appendage bridge structure. In S. pombe, we validate the method by monitoring the homeostatic regulation of nuclear pore complex number through the cell cycle. Combined with NHS-ester pan-labelling, which provides a global cellular context, U-ExM reveals the subcellular organization of these two yeast models and provides a powerful new method to augment the already extensive yeast toolbox.

This article has an associated First Person interview with Kerstin Hinterndorfer and Felix Mikus, two of the joint first authors of the paper.

Hydrogel-Based, Dynamically Tunable Plasmonic Metasurfaces with Nanoscale Resolution

Flat metasurfaces with subwavelength meta-atoms can be designed to manipulate the electromagnetic parameters of incident light and enable unusual light-matter interactions. Although hydrogel-based metasurfaces have the potential to control optical properties dynamically in response to environmental conditions, the pattern resolution of these surfaces has been limited to microscale features or larger, limiting capabilities at the nanoscale, and precluding effective use in metamaterials. This paper reports a general approach to developing tunable plasmonic metasurfaces with hydrogel meta-atoms at the subwavelength scale. Periodic arrays of hydrogel nanodots with continuously tunable diameters are fabricated on silver substrates, resulting in humidity-responsive surface plasmon polaritons (SPPs) at the nanostructure-metal interfaces. The peaks of the SPPs are controlled reversibly by absorbing or releasing water within the hydrogel matrix, the matrix-generated plasmonic color rendering in the visible spectrum. This work demonstrates that metasurfaces designed with these spatially patterned nanodots of varying sizes benefit applications in anti-counterfeiting and generate multicolored displays with single-nanodot resolution. Furthermore, this work shows system versatility exhibited by broadband beam-steering on a phase modulator consisting of hydrogel supercell units in which the size variations of constituent hydrogel nanostructures engineer the wavefront of reflected light from the metasurface.

Improved Dye Survival in Expansion Microscopy through Stabilizer-Conjugated Linkers

Expansion microscopy (ExM) has been widely used to detect biomolecules in cultured cells and tissue samples due to its enablement of super resolution imaging with conventional microscopes, via physical expansion of samples. However, reaction conditions inherent to the process bring about strong fluorescent signal loss during polymerization and digestion and thus limit the brightness of the signal obtained post expansion. Here, we explore the impact of stabilizer-containing organic fluorophores in ExM, as a mitigation strategy for this radical-induced dye degradation. Through direct conjugation of 4-nitrophenylalanine (NPA) to our previously developed trifunctional reagents, we validate and demonstrate that these multifunctional linkers enable visualization of different organelles with improved fluorescent intensity, owning to protection of the dyes to radical induced degradation as well as to photoprotection upon imaging. At this point, we cannot disentangle the relative contribution of both mechanisms. Furthermore, we report anchoring linkers that allow straightforward application of NPA or Trolox to commercially available fluorophore-conjugated antibodies. We show that these anchoring linkers enable complete retention of biological targets while increasing fluorophore photostability. Our results provide guidance in exploring these stabilizer-modified agents in ExM and methods for increased signal survival through the polymerization steps of the ExM protocols.

Lipid Expansion Microscopy

Strategies to visualize cellular membranes with light microscopy are restricted by the diffraction limit of light, which far exceeds the dimensions of lipid bilayers. Here, we describe a method for super-resolution imaging of metabolically labeled phospholipids within cellular membranes. Guided by the principles of expansion microscopy, we develop an all-small molecule approach that enables direct chemical anchoring of bioorthogonally labeled phospholipids into a hydrogel network and is capable of super-resolution imaging of cellular membranes. We apply this method, termed lipid expansion microscopy (LExM), to visualize organelle membranes with precision, including a unique class of membrane-bound structures known as nuclear invaginations. Compatible with standard confocal microscopes, LExM will be widely applicable for super-resolution imaging of phospholipids and cellular membranes in numerous physiological contexts.

Nanoscale fluorescence imaging of biological ultrastructure via molecular anchoring and physical expansion

Nanoscale imaging of biological samples can provide rich morphological and mechanistic information about biological functions and dysfunctions at the subcellular and molecular level. Expansion microscopy (ExM) is a recently developed nanoscale fluorescence imaging method that takes advantage of physical enlargement of biological samples. In ExM, preserved cells and tissues are embedded in a swellable hydrogel, to which the molecules and fluorescent tags in the samples are anchored. When the hydrogel swells several-fold, the effective resolution of the sample images can be improved accordingly via physical separation of the retained molecules and fluorescent tags. In this review, we focus on the early conception and development of ExM from a biochemical and materials perspective. We first examine the general workflow as well as the numerous variations of ExM developed to retain and visualize a broad range of biomolecules, such as proteins, nucleic acids, and membranous structures. We then describe a number of inherent challenges facing ExM, including those associated with expansion isotropy and labeling density, as well as the ongoing effort to address these limitations. Finally, we discuss the prospect and possibility of pushing the resolution and accuracy of ExM to the single-molecule scale and beyond.

Use of red, far-red, and near-infrared light in imaging of yeasts and filamentous fungi

Abstract

While phototoxicity can be a useful therapeutic modality not only for eliminating malignant cells but also in treating fungal infections, mycologists aiming to observe morphological changes or molecular events in fungi, especially when long observation periods or high light fluxes are warranted, encounter problems owed to altered regulatory pathways or even cell death caused by various photosensing mechanisms. Consequently, the ever expanding repertoire of visible fluorescent protein toolboxes and high-resolution microscopy methods designed to investigate fungi in vitro and in vivo need to comply with an additional requirement: to decrease the unwanted side effects of illumination. In addition to optimizing exposure, an obvious solution is red-shifted illumination, which, however, does not come without compromises. This review summarizes the interactions of fungi with light and the various molecular biology and technology approaches developed for exploring their functions on the molecular, cellular, and in vivo microscopic levels, and outlines the progress towards reducing phototoxicity through applying far-red and near-infrared light.

Key points

• Fungal biological processes alter upon illumination, also under the microscope

• Red shifted fluorescent protein toolboxes decrease interference by illumination

• Innovations like two-photon, lightsheet, and near IR microscopy reduce phototoxicity

Expansion microscopy with ninefold swelling (NIFS) hydrogel permits cellular ultrastructure imaging on conventional microscope

Superresolution microscopy enables probing of cellular ultrastructures. However, its widespread applications are limited by the need for expensive machinery, specific hardware, and sophisticated data processing. Expansion microscopy (ExM) improves the resolution of conventional microscopy by physically expanding biological specimens before imaging and currently provides ~70-nm resolution, which still lags behind that of modern superresolution microscopy (~30 nm). Here, we demonstrate a ninefold swelling (NIFS) hydrogel, that can reduce ExM resolution to 31 nm when using regular traditional microscopy. We also design a detachable chip that integrates all the experimental operations to facilitate the maximal reproducibility of this high-resolution imaging technology. We demonstrate this technique on the superimaging of nuclear pore complex and clathrin-coated pits, whose structures can hardly be resolved by conventional microscopy. The method presented here offers a universal platform with superresolution imaging to unveil cellular ultrastructural details using standard conventional laboratory microscopes.

Virus morphology: Insights from super-resolution fluorescence microscopy

As epitomised by the COVID-19 pandemic, diseases caused by viruses are one of the greatest health and economic burdens to human society. Viruses are 'nanostructures', and their small size (typically less than 200 nm in diameter) can make it challenging to obtain images of their morphology and structure. Recent advances in fluorescence microscopy have given rise to super-resolution techniques, which have enabled the structure of viruses to be visualised directly at a resolution in the order of 20 nm. This mini-review discusses how recent state-of-the-art super-resolution imaging technologies are providing new nanoscale insights into virus structure.

Cell-based biocomposite engineering directed by polymers

Biological cells such as bacterial, fungal, and mammalian cells always exploit sophisticated chemistries and exquisite micro- and nano-structures to execute life activities, providing numerous templates for engineering bioactive and biomorphic materials, devices, and systems. To transform biological cells into functional biocomposites, polymer-directed cell surface engineering and intracellular functionalization have been developed over the past two decades. Polymeric materials can be easily adopted by various cells through polymer grafting or in situ hydrogelation and can successfully bridge cells with other functional materials as interfacial layers, thus achieving the manufacture of advanced biocomposites through bioaugmentation of living cells and transformation of cells into templated materials. This review article summarizes the recent progress in the design and construction of cell-based biocomposites by polymer-directed strategies. Furthermore, the applications of cell-based biocomposites in broad fields such as cell research, biomedicine, and bioenergy are discussed. Last, we provide personal perspectives on challenges and future trends in this interdisciplinary area.

Towards a Comprehensive Optical Connectome at Single Synapse Resolution via Expansion Microscopy

Mapping and determining the molecular identity of individual synapses is a crucial step towards the comprehensive reconstruction of neuronal circuits. Throughout the history of neuroscience, microscopy has been a key technology for mapping brain circuits. However, subdiffraction size and high density of synapses in brain tissue make this process extremely challenging. Electron microscopy (EM), with its nanoscale resolution, offers one approach to this challenge yet comes with many practical limitations, and to date has only been used in very small samples such as C. elegans, tadpole larvae, fruit fly brain, or very small pieces of mammalian brain tissue. Moreover, EM datasets require tedious data tracing. Light microscopy in combination with tissue expansion via physical magnification-known as expansion microscopy (ExM)-offers an alternative approach to this problem. ExM enables nanoscale imaging of large biological samples, which in combination with multicolor neuronal and synaptic labeling offers the unprecedented capability to trace and map entire neuronal circuits in fully automated mode. Recent advances in new methods for synaptic staining as well as new types of optical molecular probes with superior stability, specificity, and brightness provide new modalities for studying brain circuits. Here we review advanced methods and molecular probes for fluorescence staining of the synapses in the brain that are compatible with currently available expansion microscopy techniques. In particular, we will describe genetically encoded probes for synaptic labeling in mice, zebrafish, Drosophila fruit flies, and C. elegans, which enable the visualization of post-synaptic scaffolds and receptors, presynaptic terminals and vesicles, and even a snapshot of the synaptic activity itself. We will address current methods for applying these probes in ExM experiments, as well as appropriate vectors for the delivery of these molecular constructs. In addition, we offer experimental considerations and limitations for using each of these tools as well as our perspective on emerging tools.

Cellular transformers for targeted therapy

Employing natural cells as drug carriers has been a hotspot in recent years, attributing to their biocompatibility and inherent dynamic properties. In the earlier stage, cells were mainly used as vehicles by virtue of their lipid-delimited compartmentalized structures and native membrane proteins. The scope emphasis was 'what cell displays' instead of 'how cell changes'. More recently, the dynamic behaviours, such as changes in surface protein patterns, morphologies, polarities and in-situ generation of therapeutics, of natural cells have drawn more attention for developing advanced drug delivery systems by fully taking advantage of these processes. In this review, we revolve around the dynamic cellular transformation behaviours which facilitate targeted therapy. Cellular deformation in geometry shape, spitting smaller vesicles, activation of antigen present cells, polarization between distinct phenotypes, local production of therapeutics, and hybridization with synthetic materials are involved. Other than focusing on the traditional delivery of concrete cargoes, more functional 'handles' that are derived from the cells themselves are introduced, such as information exchange, cellular communication and interactions between cell and extracellular environment.

RNA Structures and Their Role in Selective Genome Packaging

To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution.

Tetra-gel enables superior accuracy in combined super-resolution imaging and expansion microscopy

The accuracy of expansion microscopy (ExM) depends on the structural preservation of samples embedded in a hydrogel. However, it has been unknown to what extent gel embedding alters the molecular positions of individual labeled sites. Here, we quantified the accuracy of gel embedding by using stochastic optical reconstruction microscopy (STORM) to image DNA origami with well-defined structures. We found that embedding in hydrogels based on polyacrylamide, the most widely used chemistry in ExM, resulted in random displacements of labeled sites with a standard deviation of ~ 16 nm. In contrast, we found that embedding in tetra-gel, a hydrogel that does not depend on free-radical chain-growth polymerization, preserved labeled sites with a standard deviation of less than 5 nm. By combining tetra-gel ExM with STORM, we were able to resolve 11-nm structural features without the loss in accuracy seen with polyacrylamide gels. Our study thus provides direct measurements of the single-molecule distortions resulting from hydrogel embedding, and presents a way to improve super-resolution microscopy through combination with tetra-gel ExM.

Studying SARS-CoV-2 with Fluorescence Microscopy

The COVID-19 pandemic caused by SARS-CoV-2 coronavirus deeply affected the world community. It gave a strong impetus to the development of not only approaches to diagnostics and therapy, but also fundamental research of the molecular biology of this virus. Fluorescence microscopy is a powerful technology enabling detailed investigation of virus-cell interactions in fixed and live samples with high specificity. While spatial resolution of conventional fluorescence microscopy is not sufficient to resolve all virus-related structures, super-resolution fluorescence microscopy can solve this problem. In this paper, we review the use of fluorescence microscopy to study SARS-CoV-2 and related viruses. The prospects for the application of the recently developed advanced methods of fluorescence labeling and microscopy-which in our opinion can provide important information about the molecular biology of SARS-CoV-2-are discussed.