Radiation damage in single-particle cryo-electron microscopy: effects of dose and dose rate

In Situ Liquid Cell Transmission Electron Microscopy Study of Studtite Particle Formation and Growth via Electron Beam Radiolysis

This study presents in situ observations of studtite (UO2O2(H2O)2·2H2O) crystal growth utilizing liquid phase transmission electron microscopy (LP-TEM). Studtite was precipitated from a uranyl nitrate hexahydrate solution using hydrogen peroxide formed by the radiolysis of water in the TEM electron beam. The hydrogen peroxide (H2O2) concentration, directly controlled by the electron beam current, was varied to create local environments of low and high concentrations to compare the impact of the supersaturation ratio on the nucleation and growth mechanisms of studtite particles. The subsequent growth mechanisms were observed in real time by TEM and scanning TEM imaging. After the initial precipitation reaction, a post-mortem TEM analysis was performed on the samples to obtain high-resolution TEM images and selected area electron diffraction patterns to investigate crystallinity as well as energy-dispersive X-ray spectroscopy spectra to ensure that studtite was produced. The results reveal that studtite particles form through various mechanisms based on the concentration ratio of uranyl to H2O2 and that studtite is initially produced through an amorphous intermediary prior to formation of the crystalline material commonly reported in the literature.

Cryo-electron ptychography: Applications and potential in biological characterisation

There is a clear need for developments in characterisation techniques that provide detailed information about structure-function relationships in biology. Using electron microscopy to achieve high resolution while maintaining a broad field of view remains a challenge, particularly for radiation-sensitive specimens where the signal-to-noise ratio required to maintain structural integrity is limited by low electron fluence. In this review, we explore the potential of cryogenic electron ptychography as an alternative method for characterising biological systems under low-fluence conditions. Using this method with increased information content from multiple sampled regions of interest potentially allows 3D reconstruction with far fewer particles than required in conventional cryo-electron microscopy. This is important for achieving higher resolution in systems where distributions of homogeneous single particles are difficult to obtain. We discuss the progress, limitations, and potential areas for future development of this approach for both single particle analysis and applications to heterogeneous large objects.

Dynamic light scattering and transmission electron microscopy in drug delivery: a roadmap for correct characterization of nanoparticles and interpretation of results

In this focus article, we provide a scrutinizing analysis of transmission electron microscopy (TEM) and dynamic light scattering (DLS) as the two common methods to study the sizes of nanoparticles with focus on the application in pharmaceutics and drug delivery. Control over the size and shape of nanoparticles is one of the key factors for many biomedical systems. Particle size will substantially affect their permeation through biological membranes. For example, an enhanced permeation and retention effect requires a very narrow range of sizes of nanoparticles (50-200 nm) and even a minor deviation from these values will substantially affect the delivery of drug nanocarriers to the tumour. However, amazingly a great number of research papers in pharmaceutics and drug delivery report a striking difference in nanoparticle size measured by the two most popular experimental techniques (TEM and DLS). In some cases, this difference was reported to be 200-300%, raising the question of which size measurement result is more trustworthy. In this focus article, we primarily focus on the physical aspects that are responsible for the routinely observed mismatch between TEM and DLS results. Some of these factors such as concentration and angle dependencies are commonly underestimated and misinterpreted. We convincingly show that correctly used experimental procedures and a thorough analysis of results generated using both methods can eliminate the DLS and TEM data mismatch completely or will make the results much closer to each other. Also, we provide a clear roadmap for drug delivery and pharmaceutical researchers to conduct reliable DLS measurements.

Raimond B. G. Ravelli (25 March 1968-30 June 2023)

Raimond B. G. Ravelli is remembered.

Temporal dynamics of charge buildup in cryo-electron microscopy

It is well known that insulating samples can accumulate electric charges from exposure to an electron beam. How the accumulation of charge affects imaging parameters and sample stability in transmission electron microscopy is poorly understood. To quantify these effects, it is important to know how the charge is distributed within the sample and how it builds up over time. In the present study, we determine the spatial distribution and temporal dynamics of charge accumulation on vitreous ice samples with embedded proteins through a combination of modeling and Fresnel diffraction experiments. Our data reveal a rapid evolution of the charge state on ice upon initial exposure to the electron beam accompanied by charge gradients at the interfaces between ice and carbon films. We demonstrate that ice film movement and charge state variations occur upon electron beam exposure and are dose-rate dependent. Both affect the image defocus through a combination of sample height changes and lensing effects. Our results may be used as a guide to improve sample preparation, data collection, and data processing for imaging of dose-sensitive samples.

Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination

To understand the dynamic structure-function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.

High-resolution ptychographic imaging enabled by high-speed multi-pass scanning

As a coherent diffraction imaging technique, ptychography provides high-spatial resolution beyond Rayleigh's criterion of the focusing optics, but it is also sensitively affected by the decoherence coming from the spatial and temporal variations in the experiment. Here we show that high-speed ptychographic data acquisition with short exposure can effectively reduce the impact from experimental variations. To reach a cumulative dose required for a given resolution, we further demonstrate that a continuous multi-pass scan via high-speed ptychography can achieve high-resolution imaging. This low-dose scan strategy is shown to be more dose-efficient, and has potential for radiation-sensitive sample studies and time-resolved imaging.

Gold nanomaterials and their potential use as cryo-electron tomography labels

Rapid advances in cryo-electron tomography (cryo-ET) are driving a revolution in cellular structural biology. However, unambiguous identification of specific biomolecules within cellular tomograms remains challenging. Overcoming this obstacle and reliably identifying targets in the crowded cellular environment is of major importance for the understanding of cellular function and is a pre-requisite for high-resolution structural analysis. The use of highly-specific, readily visualised and adjustable labels would help mitigate this issue, improving both data quality and sample throughput. While progress has been made in cryo-CLEM and in the development of cloneable high-density tags, technical issues persist and a robust 'cryo-GFP' remains elusive. Readily-synthesized gold nanomaterials conjugated to small 'affinity modules' may represent a solution. The synthesis of materials including gold nanoclusters (AuNCs) and gold nanoparticles (AuNPs) is increasingly well understood and is now within the capabilities of non-specialist laboratories. The remarkable chemical and photophysical properties of <3nm diameter nanomaterials and their emergence as tools with widespread biomedical application presents significant opportunities to the cryo-microscopy community. In this review, we will outline developments in the synthesis, functionalisation and labelling uses of both AuNPs and AuNCs in cryo-ET, while discussing their potential as multi-modal probes for cryo-CLEM.

A case for glycerol as an acceptable additive for single-particle cryoEM samples

Buffer-composition and sample-preparation guidelines for cryo-electron microscopy are geared towards maximizing imaging contrast and reducing electron-beam-induced motion. These pursuits often involve the minimization or the complete removal of additives that are commonly used to facilitate proper protein folding and minimize aggregation. Among these admonished additives is glycerol, a widely used osmolyte that aids protein stability. In this work, it is shown that the inclusion of glycerol does not preclude high-resolution structure determination by cryoEM, as demonstrated by an ∼2.3 Å resolution reconstruction of mouse apoferritin (∼500 kDa) and an ∼3.3 Å resolution reconstruction of rabbit muscle aldolase (∼160 kDa) in the presence of 20%(v/v) glycerol. While it was found that generating thin ice that is amenable to high-resolution imaging requires long blot times, the addition of glycerol did not result in increased beam-induced motion or an inability to pick particles. Overall, these findings indicate that glycerol should not be discounted as a cryoEM sample-buffer additive, particularly for large, fragile complexes that are prone to disassembly or aggregation upon its removal.

Single-particle cryo-EM: alternative schemes to improve dose efficiency

Imaging of biomolecules by ionizing radiation, such as electrons, causes radiation damage which introduces structural and compositional changes of the specimen. The total number of high-energy electrons per surface area that can be used for imaging in cryogenic electron microscopy (cryo-EM) is severely restricted due to radiation damage, resulting in low signal-to-noise ratios (SNR). High resolution details are dampened by the transfer function of the microscope and detector, and are the first to be lost as radiation damage alters the individual molecules which are presumed to be identical during averaging. As a consequence, radiation damage puts a limit on the particle size and sample heterogeneity with which electron microscopy (EM) can deal. Since a transmission EM (TEM) image is formed from the scattering process of the electron by the specimen interaction potential, radiation damage is inevitable. However, we can aim to maximize the information transfer for a given dose and increase the SNR by finding alternatives to the conventional phase-contrast cryo-EM techniques. Here some alternative transmission electron microscopy techniques are reviewed, including phase plate, multi-pass transmission electron microscopy, off-axis holography, ptychography and a quantum sorter. Their prospects for providing more or complementary structural information within the limited lifetime of the sample are discussed.

Towards Visual Proteomics at High Resolution

Traditionally, structural biologists approach the complexity of cellular proteomes in a reductionist manner. Proteomes are fractionated, their molecular components purified and studied one-by-one using the experimental methods for structure determination at their disposal. Visual proteomics aims at obtaining a holistic picture of cellular proteomes by studying them in situ, ideally in unperturbed cellular environments. The method that enables doing this at highest resolution is cryo-electron tomography. It allows to visualize cellular landscapes with molecular resolution generating maps or atlases revealing the interaction networks which underlie cellular functions in health and in disease states. Current implementations of cryo ET do not yet realize the full potential of the method in terms of resolution and interpretability. To this end, further improvements in technology and methodology are needed. This review describes the state of the art as well as measures which we expect will help overcoming current limitations.

An Overview of Microcrystal Electron Diffraction (MicroED)

The bedrock of drug discovery and a key tool for understanding cellular function and drug mechanisms of action is the structure determination of chemical compounds, peptides, and proteins. The development of new structure characterization tools, particularly those that fill critical gaps in existing methods, presents important steps forward for structural biology and drug discovery. The emergence of microcrystal electron diffraction (MicroED) expands the application of cryo-electron microscopy to include samples ranging from small molecules and membrane proteins to even large protein complexes using crystals that are one-billionth the size of those required for X-ray crystallography. This review outlines the conception, achievements, and exciting future trajectories for MicroED, an important addition to the existing biophysical toolkit.

Understanding the invisible hands of sample preparation for cryo-EM

Cryo-electron microscopy (cryo-EM) is rapidly becoming an attractive method in the field of structural biology. With the exploding popularity of cryo-EM, sample preparation must evolve to prevent congestion in the workflow. The dire need for improved microscopy samples has led to a diversification of methods. This Review aims to categorize and explain the principles behind various techniques in the preparation of vitrified samples for the electron microscope. Various aspects and challenges in the workflow are discussed, from sample optimization and carriers to deposition and vitrification. Reliable and versatile specimen preparation remains a challenge, and we hope to give guidelines and posit future directions for improvement.

[Progress in filters for denoising cryo-electron microscopy images]

Cryo-electron microscopy (cryo-EM) imaging has the unique potential to bridge the gap between cellular and molecular biology. Therefore, cryo-EM three-dimensional (3D) reconstruction has been rapidly developed in recent several years and applied widely in life science research to reveal the structures of large macromolecular assemblies and cellular complexes, which is critical to understanding their functions at all scales. Although the technical breakthrough in recent years, for example, the introduction of the direct detection device (DDD) camera and the development of cryo-EM software tools, made the three cryo-EM pioneers share the 2017 Nobel Prize, several bottleneck problems still exist that hamper the further increase of the resolution of single-particle reconstruction and hold back the application of in situ subnanometer structure determination by cryo-tomography. Radiation damage is still the key limiting factor in cryo-EM. In order to minimize the radiation damage and preserve as much resolution as possible, the imaging conditions of a low dose and weak contrast make cryo-EM images extremely noisy with very low signal-to-noise ratios (SNR), generally about 0.1. The high noise will obscure the fine details in cryo-EM images or reconstructed maps. Thus, a method to reduce the level of noise and improve the resolution has become an important issue. In this paper, we systematically reviewed and compared some robust filters in the cryo-EM field of two aspects, single-particle analysis (SPA) and cryo-electron tomography (cryo-ET), and especially studied their applications, such as, 3D reconstruction, visualization, structural analysis, and interpretation. Conventional approaches to noise reduction in cryo-EM imaging include the use of Gaussian, median, and bilateral filters, among other means. A Gaussian filter selects an appropriate filter kernel to conduct spatial convolution with a noisy image. Although noise with larger standard deviations in cryo-EM images can be suppressed and satisfactory performance is achieved in certain cases, this filter also blurs the images and over-smooths small-scale image features. This is especially detrimental when precise quantitative information needs to be extracted. Unlike a Gaussian filter, a median filter is based on the order statistics of the image and selects the median intensity in a window of the adjacent pixels to denoise the image. Although this filter is robust to outliers, it suffers from aliasing problems that possibly result in incorrect information for cryo-EM structure interpretation. A bilateral filter is a nonlinear filter that performs spatial weighted averaging and is more selective in the pixels allowing to contribute to the weighted sum, excluding the high frequency noise from the smoothing process. Thus, this filter can be used to smooth out noise while maintaining the edge details, which is similar to an anisotropic diffusion filter, and distinct from a Gaussian filter but its utility will be limited when the SNR of a cryo-EM image is very low. Generally, spatial filtering methods have the disadvantage of losing image resolution when reducing noise. A wavelet transform can exploit the wavelet's natural ability to separate a signal from noise at multiple image scales to allow for joint resolution in both the spatial and frequency domains, and thus has the potential to outperform existing methods. The modified wavelet shrinkage filter we developed can offer a remarkable improvement in image quality with a good compromise between detail preservation and noise smoothing. We expect that our review study on different filters can provide benefits to cryo-EM applications and the interpretation of biological structures.

Imaging and 3D Reconstruction of De Novo Peptide Capsids

Nanoscale systems encapsulating biomacromolecules hold promise for cell and gene therapies. Common issues hampering progress include polydispersity, heterogeneity in size and shape, agglomeration, and poor stability. Much attention is given to the search of novel designs. However, reliable protocols for the validation of encapsulating systems in the continuum of their physicochemical properties, from design to ultrastructure, are lacking. Herein, we report electron microscopy protocols for biologically functional shell-like peptide capsids, which exhibit the physical characteristics of viruses including folding-mediated self-assembly, hollow shell morphology, and uniformity in size.

Electron Beam-Induced Transformation in High-Density Amorphous Ices

Amorphous ice is commonly used as a noncrystalline matrix for protecting sensitive biological samples in cryogenic electron microscopy (cryo-EM). The amorphization process of water is complex, and at least two amorphous states of different densities are known to exist, high- and low-density amorphous ices (HDA and LDA). These forms are considered to be the counterparts of two distinct liquid states, namely, high- and low-density liquid water. Herein, we investigate the HDA to LDA transition using electron diffraction and cryo-EM. The observed phase transition is induced by the impact of electrons, and we discuss two different mechanisms, namely, local heating and beam-induced motion of water molecules. The temperature increase is estimated by comparison with X-ray scattering experiments on identically prepared samples. Our results suggest that HDA, under the conditions used in our cryo-EM measurements, is locally heated above its glass-transition temperature.

Beyond protein structure determination with MicroED

Microcrystal electron diffraction (MicroED) was first coined and developed in 2013 at the Janelia Research Campus as a new modality in electron cryomicroscopy (cryoEM). Since then, MicroED has not only made important contributions in pushing the resolution limits of cryoEM protein structure characterization but also of peptides, small-organic and inorganic molecules, and natural-products that have resisted structure determination by other methods. This review showcases important recent developments in MicroED, highlighting the importance of the technique in fields of studies beyond protein structure determination where MicroED is beginning to have paradigm shifting roles.

Cryo-FIB preparation of whole cells and tissue for cryo-TEM: use of high-pressure frozen specimens in tubes and planchets

The desire to study macromolecular complexes within their cellular context requires the ability to produce thin samples suitable for cryo‐TEM (cryo‐transmission electron microscope) investigations. In this paper, we discuss two similar approaches, which were developed independently in Utrecht (the Netherlands) and Albany (USA). The methods are particularly suitable for both tissue samples and cell suspensions prepared by a high‐pressure freezer (HPF). The workflows are explained with particular attention to potential pitfalls, while underlying principles are highlighted (‘why to do so’). Although both workflows function with a high success rate, full execution requires considerable experience and remains demanding. In addition, throughput is low. We hope to encourage other research groups worldwide to take on the challenge of improving the HPF– cryo‐FIB‐SEM – cryo‐TEM workflow. We discuss a number of suggestions to this end.

Lay Description

Life is ultimately dictated by the interaction of molecules in our bodies. Highly complex equipment is being used and further developed to study these interactions. The present paper describes methods to prepare small, very thin lamellae (area of 5×5 µm², thickness 50–300 nm) of a cell to be studied in a cryo‐transmission electron microscope (cryo‐TEM). Special care must be taken to preserve the natural state of molecules in their natural environment. In the case of cryo‐TEM, the samples must be frozen and kept frozen to be compatible with the vacuum conditions in the microscope. The frozen condition imposes technical challenges which are addressed. Two approaches to obtain the thin lamellae are described. Both make use of a focused ion beam (FIB) microscope. The FIB allows removal of material with nanometre precision by focusing a beam of ionised atoms (gallium ions) onto the sample. Careful control of the FIB allows cutting out of the required thin lamellae. In both strategies, the thin lamellae remain attached to the original sample, and the ensemble of sample with section and sample holder is transported from the FIB microscope to the TEM while being kept frozen.

Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose

Both high resolution and high precision are required to quantitatively determine the atomic structure of complex nanostructured materials. However, for conventional imaging methods in scanning transmission electron microscopy (STEM), atomic resolution with picometer precision cannot usually be achieved for weakly-scattering samples or radiation-sensitive materials, such as 2D materials. Here, we demonstrate low-dose, sub-angstrom resolution imaging with picometer precision using mixed-state electron ptychography. We show that correctly accounting for the partial coherence of the electron beam is a prerequisite for high-quality structural reconstructions due to the intrinsic partial coherence of the electron beam. The mixed-state reconstruction gains importance especially when simultaneously pursuing high resolution, high precision and large field-of-view imaging. Compared with conventional atomic-resolution STEM imaging techniques, the mixed-state ptychographic approach simultaneously provides a four-times-faster acquisition, with double the information limit at the same dose, or up to a fifty-fold reduction in dose at the same resolution.

With conventional scanning transmission electron microscopy, some sensitive materials are difficult to image with atomic resolution. The authors present a method of mixed-state electron ptychography that enables picometer precision with fast acquisition and low dosage.

Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials

Despite significant advances in resolution, the potential for cryo-electron microscopy (EM) to be used in determining the structures of protein-drug complexes remains unrealized. Determination of accurate structures and coordination of bound ligands necessitates simultaneous fitting of the models into the density envelopes, exhaustive sampling of the ligand geometries, and, most importantly, concomitant rearrangements in the side chains to optimize the binding energy changes. In this article, we present a flexible-fitting pipeline where molecular dynamics flexible fitting (MDFF) is used to refine structures of protein-ligand complexes from 3 to 5 Å electron density data. Enhanced sampling is employed to explore the binding pocket rearrangements. To provide a model that can accurately describe the conformational dynamics of the chemically diverse set of small-molecule drugs inside MDFF, we use QM/MM and neural-network potential (NNP)/MM models of protein-ligand complexes, where the ligand is represented using the QM or NNP model, and the protein is represented using established molecular mechanical force fields (e.g., CHARMM). This pipeline offers structures commensurate to or better than recently submitted high-resolution cryo-EM or X-ray models, even when given medium to low-resolution data as input. The use of the NNPs makes the algorithm more robust to the choice of search models, offering a radius of convergence of 6.5 Å for ligand structure determination. The quality of the predicted structures was also judged by density functional theory calculations of ligand strain energy. This strain potential energy is found to systematically decrease with better fitting to density and improved ligand coordination, indicating correct binding interactions. A computationally inexpensive protocol for computing strain energy is reported as part of the model analysis protocol that monitors both the ligand fit as well as model quality.

Preparation of Proteins and Macromolecular Assemblies for Cryo-electron Microscopy

Cryo-electron microscopy has become popular as the penultimate step on the road to structure determination for many proteins and macromolecular assemblies. The process of obtaining high-resolution images of a purified biomolecular complex in an electron microscope often follows a long, and in many cases exhaustive screening process in which many iterative rounds of protein purification are employed and the sample preparation procedure progressively re-evaluated in order to improve the distribution of particles visualized under the electron microscope, and thus maximize the opportunity for high-resolution structure determination. Typically, negative stain electron microscopy is employed to obtain a preliminary assessment of the sample quality, followed by cryo-EM which first requires the identification of optimal vitrification conditions. The original methods for frozen-hydrated specimen preparation developed over 40 years ago still enjoy widespread use today, although recent developments have set the scene for a future where more systematic and high-throughput approaches to the preparation of vitrified biomolecular complexes may be routinely employed. Here we summarize current approaches and ongoing innovations for the preparation of frozen-hydrated single particle specimens for cryo-EM, highlighting some of the commonly encountered problems and approaches that may help overcome these.

A novel nondestructive diagnostic method for mega-electron-volt ultrafast electron diffraction

A real-time, nondestructive, Bragg-diffracted electron beam energy, energy-spread and spatial-pointing jitter monitor is experimentally verified by encoding the electron beam energy and spatial-pointing jitter information into the mega-electron-volt ultrafast electron diffraction pattern. The shot-to-shot fluctuation of the diffraction pattern is then decomposed to two basic modes, i.e., the distance between the Bragg peaks as well as its variation (radial mode) and the overall lateral shift of the whole pattern (drift mode). Since these two modes are completely decoupled, the Bragg-diffraction method can simultaneously measure the shot-to-shot energy fluctuation from the radial mode with 2·10⁻⁴ precision and spatial-pointing jitter from the drift mode having wide measurement span covering energy jitter range from 10⁻⁴ to 10⁻¹. The key advantage of this method is that it allows us to extract the electron beam energy spread concurrently with the ongoing experiment and enables online optimization of the electron beam especially for future high charge single-shot ultrafast electron diffraction (UED) and ultrafast electron microscopy (UEM) experiments. Furthermore, real-time energy measurement enables the filtering process to remove off-energy shots, improving the resolution of time-resolved UED. As a result, this method can be applied to the entire UED user community, beyond the traditional electron beam diagnostics of accelerators used by accelerator physicists.

An ImageJ tool for simplified post-treatment of TEM phase contrast images (SPCI)

Tools for taking advantage of phase-contrast in transmission electron microscopy are of great interest for both biological and material sciences studies as shown by the recent use of phase plates and the development of holography. Nevertheless, these tools most often require highly qualified experts and access to advanced equipment that can only be considered after preliminary investigations. Here we propose to address this issue by the development of an ImageJ plugin that allow the retrieval of a phase image by simple numerical treatment applied to two defocused images. This treatment based on Tikhonov regularization requires the adjustment of a single parameter. Moreover, it is possible to use this approach on one-image. Although in that case the retrieved image gives only qualitative information, it is able to enhance the image contrast appropriately. This can be of interest for specimens producing low contrast images under the electron microscopes, such as some frozen hydrated biological samples or those sensible to electron radiation unsuitable for holographic studies.

Nanofluidic and monolithic environmental cells for cryogenic microscopy

We present a device capable of combining nanofluidics and cryogenic transmission electron microscopy (cryo-TEM) to allow inspection of water-soluble samples under near-native conditions. The devices can be produced in a multitude of designs, but as a general rule, they consist of channels or chambers enclosed between two electron-transparent silicon nitride windows. With the appropriate design, those devices can allow screening of multiple samples in parallel and remove the interaction between the sample and the environment (no air-water interface). We demonstrate channel sizes from 80 to 500 nm in height and widths from 100 to 2000 μm. The presented fabrication flow allows producing hollow devices on a single wafer eliminating the need of aligning or bonding two half-cavities from separate wafers, which provides additional resistance to thermal stress. Taking advantage of a single-step through-membrane exposure with a 100 keV electron beam, we introduced arrays of thin (10-15 nm) electron-transparent silicon nitride membrane windows aligned between top and bottom (200-250 nm) carrier membranes. Importantly, the final devices are compatible with standard TEM holders. Furthermore, they are compatible with rapid freezing of samples, which is crucial for the formation of vitreous water, hence avoiding the formation of crystalline ice, that is detrimental for TEM imaging. To demonstrate the potential of this technology, we tested those devices in imaging experiments verifying their applicability for cryo-TEM applications and proved that vitreous water could be prepared through conventional plunge freezing of the chips.

Single-particle reconstruction statistics: a diagnostic tool in solving biomolecular structures by cryo-EM

In single-particle analysis (SPA), the aim is to obtain a 3D reconstruction of a biological molecule from 2D electron micrographs to the highest level of detail or resolution as possible. Current practice is to collect large volumes of data, hoping to reach high-resolution maps through sheer numbers. However, adding more particles from a specific data set eventually leads to diminishing improvements in resolution. Understanding what these resolution limits are and how to deal with them are important in optimization and automation of SPA. This study revisits the theory of 3D reconstruction and demonstrates how the associated statistics can provide a diagnostic tool to improve SPA. Small numbers of images already give sufficient information on micrograph quality and the amount of data required to reach high resolution. Such feedback allows the microscopist to improve sample-preparation and imaging parameters before committing to extensive data collection. Once a larger data set is available, a B factor can be determined describing the suppression of the signal owing to one or more causes, such as specimen movement, radiation damage, alignment inaccuracy and structural variation. Insight into the causes of signal suppression can then guide the user to consider appropriate actions to obtain better reconstructions.

Manipulating and monitoring nanoparticles in micellar thin film superstructures

Understanding the dynamics of discrete self-assembled structures under influence of external triggers is of interest to harvest the potential of nano- and mesoscale materials. In particular, controlling the hierarchical organization of (macro)molecular and nanoparticle building blocks in monolayer superstructures is of paramount importance for tuning properties and characteristics. Here we show how the electron beam in cryo-transmission electron microscopy can be exploited to induce and follow local migration of building blocks and global migration of micellar aggregates inside micrometer-sized superstructures. We employ stroboscopic exposure to heat up and convert the vitrified superstructure into a liquid-like thin film under cryogenic conditions, resulting in controlled evaporation of water that finally leads to rupture of the micelle-containing superstructure. Micelle-embedded nanoparticles prove a powerful tool to study the complex hierarchically built-up superstructures, and to visualize both global movement of individual dendrimicelles and local migration of nanoparticles inside the micellar core during the exposure series.

Understanding how nanoparticle superstructures respond to external stimuli is of importance to their potential application. Here, the authors demonstrate the use of cryo-transmission electron microscopy for monitoring and manipulating movement within nanoparticle-loaded dendrimicelle superstructure thin films upon irradiation with an electron beam.

Considerations for imaging thick, low contrast, and beam sensitive samples with liquid cell transmission electron microscopy

Transmission electron microscopy of whole cells is hindered by the inherently large thickness and low atomic contrast intrinsic of cellular material. Liquid cell transmission electron microscopy allows samples to remain in their native hydrated state and may permit visualizing cellular dynamics in-situ. However, imaging biological cells with this approach remains challenging and identifying an optimal imaging regime using empirical data would help foster new advancements in the field. Recent questions about the role of the electron beam inducing morphological changes or damaging cellular structure and function necessitates further investigation of electron beam-cell interactions, but such comparisons are complicated by variability in imaging techniques used across various studies currently present in literature. The necessity for using low electron fluxes while imaging biological samples requires finding an imaging strategy which produces the strongest contrast and signal to noise ratio for the electron flux used. Here, we experimentally measure and evaluate signal to noise ratios and damage mechanisms between liquid and cryogenic samples of intact cells using multiple electron imaging modalities all on the same instrument and with equivalent beam parameters to standardize the comparison. We also discuss considerations for optimal electron microscopy imaging conditions for future studies on whole cells within liquid environments.

Design of compact ultrafast microscopes for single- and multi-shot imaging with MeV electrons

Ultrafast high-energy electron microscopy, taking advantage of strong interaction of electrons with matter while minimizing space charge problems, can be used to address a wide range of grand challenges in basics energy sciences. However, MeV-electron lenses are inherently bulky and expensive, preventing them from acceptance in a broad scientific community. In this article, we report our novel design of a compact, low-cost imaging-lens system for MeV-electrons based on quadrupole multiplets, including triplet, quadruplet and quintuplet, both symmetric and asymmetric. We compare optical performance of quadrupole-based condenser, objective and projector lenses with that of the traditional round-lenses and discuss the strategy for their practical use in constructing MeV-electron microscopes for high spatial and temporal resolution single- and multi-shot imaging. Combining the compound electron-optical system with a photocathode radiofrequency (RF) gun, such a MeV electron microscope can be fit into a small-sized laboratory for ultrafast observations and measurements.

Approaches to altering particle distributions in cryo-electron microscopy sample preparation

Cryo-electron microscopy (cryo-EM) can now be used to determine high-resolution structural information on a diverse range of biological specimens. Recent advances have been driven primarily by developments in microscopes and detectors, and through advances in image-processing software. However, for many single-particle cryo-EM projects, major bottlenecks currently remain at the sample-preparation stage; obtaining cryo-EM grids of sufficient quality for high-resolution single-particle analysis can require the careful optimization of many variables. Common hurdles to overcome include problems associated with the sample itself (buffer components, labile complexes), sample distribution (obtaining the correct concentration, affinity for the support film), preferred orientation, and poor reproducibility of the grid-making process within and between batches. This review outlines a number of methodologies used within the electron-microscopy community to address these challenges, providing a range of approaches which may aid in obtaining optimal grids for high-resolution data collection.

Cryo-electron tomography: an ideal method to study membrane-associated proteins

Cryo-electron tomography (cryo-ET) is a three-dimensional imaging technique that makes it possible to analyse the structure of complex and dynamic biological assemblies in their native conditions. The latest technological and image processing developments demonstrate that it is possible to obtain structural information at nanometre resolution. The sample preparation required for the cryo-ET technique does not require the isolation of a protein and other macromolecular complexes from its native environment. Therefore, cryo-ET is emerging as an important tool to study the structure of membrane-associated proteins including pores.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.

In Situ Atomic-Scale Observation of Droplet Coalescence Driven Nucleation and Growth at Liquid/Solid Interfaces

Unraveling dynamical processes of liquid droplets at liquid/solid interfaces and the interfacial ordering is critical to understanding solidification, liquid-phase epitaxial growth, wetting, liquid-phase joining, crystal growth, and lubrication processes, all of which are linked to different important applications in material science. In this work, we observe direct in situ atomic-scale behavior of Bi droplets segregated on SrBi₂Ta₂O₉ by using aberration-corrected transmission electron microscopy and demonstrate ordered interface and surface structures for the droplets on the oxide at the atomic scale and unravel a nucleation mechanism involving droplet coalescence at the liquid/solid interface. We identify a critical diameter of the formed nanocrystal in stabilizing the crystalline phase and reveal lattice-induced fast crystallization of the droplet at the initial stage of the coalescence of the nanocrystal with the droplet. Further sequential observations show the stepped coalescence and growth mechanism of the nanocrystals at the atomic scale. These results offer insights into the dynamic process at liquid/solid interfaces, which may have implications for many functionalities of materials and their applications.

The advent of structural biology in situ by single particle cryo-electron tomography

Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ. Here we review the development of SPT, highlighting its applications and identifying areas of ongoing development.

Quantitative Analysis of Electron Beam Damage in Organic Thin Films

In transmission electron microscopy (TEM) the interaction of an electron beam with polymers such as P3HT:PCBM photovoltaic nanocomposites results in electron beam damage, which is the most important factor limiting acquisition of structural or chemical data at high spatial resolution. Beam effects can vary depending on parameters such as electron dose rate, temperature during imaging, and the presence of water and oxygen in the sample. Furthermore, beam damage will occur at different length scales. To assess beam damage at the angstrom scale, we followed the intensity of P3HT and PCBM diffraction rings as a function of accumulated electron dose by acquiring dose series and varying the electron dose rate, sample preparation, and the temperature during acquisition. From this, we calculated a critical dose for diffraction experiments. In imaging mode, thin film deformation was assessed using the normalized cross-correlation coefficient, while mass loss was determined via changes in average intensity and standard deviation, also varying electron dose rate, sample preparation, and temperature during acquisition. The understanding of beam damage and the determination of critical electron doses provides a framework for future experiments to maximize the information content during the acquisition of images and diffraction patterns with (cryogenic) transmission electron microscopy.

Non-contact luminescence lifetime cryothermometry for macromolecular crystallography

Temperature is a very important parameter when aiming to minimize radiation damage to biological samples during experiments that utilize intense ionizing radiation. A novel technique for remote, non-contact, in situ monitoring of the protein crystal temperature has been developed for the new I23 beamline at the Diamond Light Source, a facility dedicated to macromolecular crystallography (MX) with long-wavelength X-rays. The temperature is derived from the temperature-dependent decay time constant of luminescence from a minuscule scintillation sensor (<0.05 mm3) located in very close proximity to the sample under test. In this work the underlying principle of cryogenic luminescence lifetime thermometry is presented, the features of the detection method and the choice of temperature sensor are discussed, and it is demonstrated how the temperature monitoring system was integrated within the viewing system of the endstation used for the visualization of protein crystals. The thermometry system was characterized using a Bi4Ge3O12 crystal scintillator that exhibits good responsivity of the decay time constant as a function of temperature over a wide range (8-270 K). The scintillation sensor was calibrated and the uncertainty of the temperature measurements over the primary operation temperature range of the beamline (30-150 K) was assessed to be ±1.6 K. It has been shown that the temperature of the sample holder, measured using the luminescence sensor, agrees well with the expected value. The technique was applied to characterize the thermal performance of different sample mounts that have been used in MX experiments at the I23 beamline. The thickness of the mount is shown to have the greatest impact upon the temperature distribution across the sample mount. Altogether, these tests and findings demonstrate the usefulness of the thermometry system in highlighting the challenges that remain to be addressed for the in-vacuum MX experiment to become a reliable and indispensable tool for structural biology.

Enhanced thermal stability of a polymer solar cell blend induced by electron beam irradiation in the transmission electron microscope

We show by in situ microscopy that the effects of electron beam irradiation during transmission electron microscopy can be used to lock microstructural features and enhance the structural thermal stability of a nanostructured polymer:fullerene blend. Polymer:fullerene bulk-heterojunction thin films show great promise for use as active layers in organic solar cells but their low thermal stability is a hindrance. Lack of thermal stability complicates manufacturing and influences the lifetime of devices. To investigate how electron irradiation affects the thermal stability of polymer:fullerene films, a model bulk-heterojunction film based on a thiophene-quinoxaline copolymer and a fullerene derivative was heat-treated in-situ in a transmission electron microscope. In areas of the film that exposed to the electron beam the nanostructure of the film remained stable, while the nanostructure in areas not exposed to the electron beam underwent large phase separation and nucleation of fullerene crystals. UV-vis spectroscopy shows that the polymer:fullerene films are stable for electron doses up to 2000kGy.

Effects of radiation damage in studies of protein-DNA complexes by cryo-EM

Nucleic acids are responsible for the storage, transfer and realization of genetic information in the cell, which provides correct development and functioning of organisms. DNA interaction with ligands ensures the safety of this information. Over the past 10 years, advances in electron microscopy and image processing allowed to obtain the structures of key DNA-protein complexes with resolution below 4Å. However, radiation damage is a limiting factor to the potentially attainable resolution in cryo-EM. The prospect and limitations of studying protein-DNA complex interactions using cryo-electron microscopy are discussed here. We reviewed the ways to minimize radiation damage in biological specimens and the possibilities of using radiation damage (so-called 'bubblegrams') to obtain additional structural information.

Enhanced thermal stability of a polymer solar cell blend induced by electron beam irradiation in the transmission electron microscope

We show by in situ microscopy that the effects of electron beam irradiation during transmission electron microscopy can be used to lock microstructural features and enhance the structural thermal stability of a nanostructured polymer:fullerene blend. Polymer:fullerene bulk-heterojunction thin films show great promise for use as active layers in organic solar cells but their low thermal stability is a hindrance. Lack of thermal stability complicates manufacturing and influences the lifetime of devices. To investigate how electron irradiation affects the thermal stability of polymer:fullerene films, a model bulk-heterojunction film based on a thiophene-quinoxaline copolymer and a fullerene derivative was heat-treated in-situ in a transmission electron microscope. In areas of the film that exposed to the electron beam the nanostructure of the film remained stable, while the nanostructure in areas not exposed to the electron beam underwent large phase separation and nucleation of fullerene crystals. UV-vis spectroscopy shows that the polymer:fullerene films are stable for electron doses up to 2000kGy.

Damage-free vibrational spectroscopy of biological materials in the electron microscope

Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof' electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies <1 eV can be ‘safely' investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ∼10 nm, simultaneously combined with imaging in the electron microscope.

Use of electron microscopy to determine morphology, or find where functionally significant biomolecules are located with high spatial resolution is of great interest. Here, Rez, Cohen et al. use aloof electron beam vibrational spectroscopy to probe different bonds in biological samples with no significant radiation damage.

Calcium carbonate nucleation driven by ion binding in a biomimetic matrix revealed by in situ electron microscopy

The characteristic shapes, structures and properties of biominerals arise from their interplay with a macromolecular matrix. The developing mineral interacts with acidic macromolecules, which are either dissolved in the crystallization medium or associated with insoluble matrix polymers, that affect growth habits and phase selection or completely inhibit precipitation in solution. Yet little is known about the role of matrix-immobilized acidic macromolecules in directing mineralization. Here, by using in situ liquid-phase electron microscopy to visualize the nucleation and growth of CaCO3 in a matrix of polystyrene sulphonate (PSS), we show that the binding of calcium ions to form Ca-PSS globules is a key step in the formation of metastable amorphous calcium carbonate (ACC), an important precursor phase in many biomineralization systems. Our findings demonstrate that ion binding can play a significant role in directing nucleation, independently of any control over the free-energy barrier to nucleation.

Seeing tobacco mosaic virus through direct electron detectors

With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require comparative characterization, we have used tobacco mosaic virus (TMV) as a test specimen to study the quality of 3D image reconstructions from data recorded on the two direct electron detector cameras, K2 Summit and Falcon II. Using DED movie frames, we explored related image-processing aspects and compared the performance of micrograph-based and segment-based motion correction approaches. In addition, we investigated the effect of dose deposition on the atomic-resolution structure of TMV and show that radiation damage affects negative carboxyl chains first in a side-chain specific manner. Finally, using 450,000 asymmetric units and limiting the effects of radiation damage, we determined a high-resolution cryo-EM map at 3.35 Å resolution. Here, we provide a comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2 Å in resolution using cryo-EM.

Chemical and structural stability of lithium-ion battery electrode materials under electron beam

The investigation of chemical and structural dynamics in battery materials is essential to elucidation of structure-property relationships for rational design of advanced battery materials. Spatially resolved techniques, such as scanning/transmission electron microscopy (S/TEM), are widely applied to address this challenge. However, battery materials are susceptible to electron beam damage, complicating the data interpretation. In this study, we demonstrate that, under electron beam irradiation, the surface and bulk of battery materials undergo chemical and structural evolution equivalent to that observed during charge-discharge cycling. In a lithiated NiO nanosheet, a Li₂CO₃-containing surface reaction layer (SRL) was gradually decomposed during electron energy loss spectroscopy (EELS) acquisition. For cycled LiNi_0.4Mn_0.4Co_0.18Ti_0.02O₂ particles, repeated electron beam irradiation induced a phase transition from an layered structure to an rock-salt structure, which is attributed to the stoichiometric lithium and oxygen removal from 3a and 6c sites, respectively. Nevertheless, it is still feasible to preserve pristine chemical environments by minimizing electron beam damage, for example, using fast electron imaging and spectroscopy. Finally, the present study provides examples of electron beam damage on lithium-ion battery materials and suggests that special attention is necessary to prevent misinterpretation of experimental results.

Image formation modeling in cryo-electron microscopy

Accurate modeling of image formation in cryo-electron microscopy is an important requirement for quantitative image interpretation and optimization of the data acquisition strategy. Here we present a forward model that accounts for the specimen's scattering properties, microscope optics, and detector response. The specimen interaction potential is calculated with the isolated atom superposition approximation (IASA) and extended with the influences of solvent's dielectric and ionic properties as well as the molecular electrostatic distribution. We account for an effective charge redistribution via the Poisson-Boltzmann approach and find that the IASA-based potential forms the dominant part of the interaction potential, as the contribution of the redistribution is less than 10%. The electron wave is propagated through the specimen by a multislice approach and the influence of the optics is included via the contrast transfer function. We incorporate the detective quantum efficiency of the camera due to the difference between signal and noise transfer characteristics, instead of using only the modulation transfer function. The full model was validated against experimental images of 20S proteasome, hemoglobin, and GroEL. The simulations adequately predict the effects of phase contrast, changes due to the integrated electron flux, thickness, inelastic scattering, detective quantum efficiency and acceleration voltage. We suggest that beam-induced specimen movements are relevant in the experiments whereas the influence of the solvent amorphousness can be neglected. All simulation parameters are based on physical principles and, when necessary, experimentally determined.

Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images

The typical dose used to record cryo-electron microscopy images from vitrified biological specimens is so high that radiation-induced structural alterations are bound to occur during data acquisition. Integration of all scattered electrons into one image can lead to significant blurring, particularly if the data are collected from an unsupported thin layer of ice suspended over the holes of a support film. Here, the dose has been fractioned and exposure series have been acquired in order to study beam-induced specimen movements under low dose conditions, prior to bubbling. Gold particles were added to the protein sample as fiducial markers. These were automatically localized and tracked throughout the exposure series and showed correlated motions within small patches, with larger amplitudes of motion vectors at the start of a series compared with the end of each series. A non-rigid scheme was used to register all images within each exposure series, using natural neighbor interpolation with the gold particles as anchor points. The procedure increases the contrast and resolution of the examined macromolecules.

Radiation damage to biological macromolecules: some answers and more questions

Research into radiation damage in macromolecular crystallography has matured over the last few years, resulting in a better understanding of both the processes and timescales involved. In turn this is now allowing practical recommendations for the optimization of crystal dose lifetime to be suggested. Some long-standing questions have been answered by recent investigations, and from these answers new challenges arise and areas of investigation can be proposed. Six papers published in this volume give an indication of some of the current directions of this field and also that of single-particle cryo-microscopy, and the brief summary below places them into the overall framework of ongoing research into macromolecular crystallography radiation damage.

Large multimeric assemblies of nucleosome assembly protein and histones revealed by small-angle X-ray scattering and electron microscopy

The nucleosome assembly protein (NAP) family represents a key group of histone chaperones that are essential for cell viability. Several x-ray structures of NAP1 dimers are available; however, there are currently no structures of this ubiquitous chaperone in complex with histones. We have characterized NAP1 from Xenopus laevis and reveal that it forms discrete multimers with histones H2A/H2B and H3/H4 at a stoichiometry of one NAP dimer to one histone fold dimer. These complexes have been characterized by size exclusion chromatography, analytical ultracentrifugation, multiangle laser light scattering, and small-angle x-ray scattering to reveal their oligomeric assembly states in solution. By employing single-particle cryo-electron microscopy, we visualized these complexes for the first time and show that they form heterogeneous ring-like structures, potentially acting as large scaffolds for histone assembly and exchange.