Single Crystal and Pentatwinned Gold Nanorods Result in Chiral Nanocrystals with Reverse Handedness

Handedness is an essential attribute of chiral nanocrystals, having a major influence on their properties. During chemical growth, the handedness of nanocrystals is usually tuned by selecting the corresponding enantiomer of chiral molecules involved in asymmetric growth, often known as chiral inducers. We report that, even using the same chiral inducer enantiomer, the handedness of chiral gold nanocrystals can be reversed by using Au nanorod seeds with either single crystalline or pentatwinned structure. This effect holds for chiral growth induced both by amino acids (e.g. cystine) and by chiral micelles (comprising cetyltrimethylammonium chloride and 1,1'-binaphthyl-2,2-diamine). Although it was challenging to discern the morphological handedness for L-cystine-directed particles, even using electron tomography, both cases showed circular dichroism bands of opposite sign, with nearly mirrored chiroptical signatures for chiral micelle-directed growth, along with quasi-helical wrinkles of inverted handedness. These results expand the chiral growth toolbox with an effect that might be exploited to yield a host of interesting morphologies with tunable optical properties.

Tomo Live: an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows

Data acquisition and processing for cryo-electron tomography can be a significant bottleneck for users. To simplify and streamline the cryo-ET workflow, Tomo Live, an on-the-fly solution that automates the alignment and reconstruction of tilt-series data, enabling real-time data-quality assessment, has been developed. Through the integration of Tomo Live into the data-acquisition workflow for cryo-ET, motion correction is performed directly after each of the acquired tilt angles. Immediately after the tilt-series acquisition has completed, an unattended tilt-series alignment and reconstruction into a 3D volume is performed. The results are displayed in real time in a dedicated remote web platform that runs on the microscope hardware. Through this web platform, users can review the acquired data (aligned stack and 3D volume) and several quality metrics that are obtained during the alignment and reconstruction process. These quality metrics can be used for fast feedback for subsequent acquisitions to save time. Parameters such as Alignment Accuracy, Deleted Tilts and Tilt Axis Correction Angle are visualized as graphs and can be used as filters to export only the best tomograms (raw data, reconstruction and intermediate data) for further processing. Here, the Tomo Live algorithms and workflow are described and representative results on several biological samples are presented. The Tomo Live workflow is accessible to both expert and non-expert users, making it a valuable tool for the continued advancement of structural biology, cell biology and histology.

Microtubule length correlates with spindle length in C. elegans meiosis

The accurate segregation of chromosomes during female meiosis relies on the precise assembly and function of the meiotic spindle, a dynamic structure primarily composed of microtubules. Despite the crucial role of microtubule dynamics in this process, the relationship between microtubule length and spindle size remains elusive. Leveraging Caenorhabditis elegans as a model system, we combined electron tomography and live imaging to investigate this correlation. Our analysis revealed significant changes in spindle length throughout meiosis, coupled with alterations in microtubule length. Surprisingly, while spindle size decreases during the initial stages of anaphase, the size of antiparallel microtubule overlap decreased as well. Detailed electron tomography shows a positive correlation between microtubule length and spindle size, indicating a role of microtubule length in determining spindle dimensions. Notably, microtubule numbers displayed no significant association with spindle length, highlighting the dominance of microtubule length regulation in spindle size determination. Depletion of the microtubule depolymerase KLP-7 led to elongated metaphase spindles with increased microtubule length, supporting the link between microtubule length and spindle size. These findings underscore the pivotal role of regulating microtubule dynamics, and thus microtubule length, in governing spindle rearrangements during meiotic division, shedding light on fundamental mechanisms dictating spindle architecture.

Understanding the Effect of Curvature on the Magnetization Reversal of Three-Dimensional Nanohelices

Comprehending the interaction between geometry and magnetism in three-dimensional (3D) nanostructures is important to understand the fundamental physics of domain wall (DW) formation and pinning. Here, we use focused-electron-beam-induced deposition to fabricate magnetic nanohelices with increasing helical curvature with height. Using electron tomography and Lorentz transmission electron microscopy, we reconstruct the 3D structure and magnetization of the nanohelices. The surface curvature, helical curvature, and torsion of the nanohelices are then quantified from the tomographic reconstructions. Furthermore, by using the experimental 3D reconstructions as inputs for micromagnetic simulations, we can reveal the influence of surface and helical curvature on the magnetic reversal mechanism. Hence, we can directly correlate the magnetic behavior of a 3D nanohelix to its experimental structure. These results demonstrate how the control of geometry in nanohelices can be utilized in the stabilization of DWs and control of the response of the nanostructure to applied magnetic fields.

Cardiac multiscale bioimaging: from nano- through micro- to mesoscales

Cardiac multiscale bioimaging is an emerging field that aims to provide a comprehensive understanding of the heart and its functions at various levels, from the molecular to the entire organ. It combines both physiologically and clinically relevant dimensions: from nano- and micrometer resolution imaging based on vibrational spectroscopy and high-resolution microscopy to assess molecular processes in cardiac cells and myocardial tissue, to mesoscale structural investigations to improve the understanding of cardiac (patho)physiology. Tailored super-resolution deep microscopy with advanced proteomic methods and hands-on experience are thus strategically combined to improve the quality of cardiovascular research and support future medical decision-making by gaining additional biomolecular information for translational and diagnostic applications.

Three-Dimensional Reconstruction of Interface Roughness and Alloy Disorder in Ge/GeSi Asymmetric Coupled Quantum Wells Using Electron Tomography

Interfaces play an essential role in the performance of ever-shrinking semiconductor devices, making comprehensive determination of their three-dimensional (3D) structural properties increasingly important. This becomes even more relevant in compositional interfaces, as is the case for Ge/GeSi heterostructures, where chemical intermixing is pronounced in addition to their morphology. We use the electron tomography method to reconstruct buried interfaces and layers of asymmetric coupled Ge/Ge0.8Si0.2 multiquantum wells, which are considered a potential building block in THz quantum cascade lasers. The three-dimensional reconstruction is based on a series of high-angle annular dark-field scanning transmission electron microscopy images. It allows chemically sensitive investigation of a relatively large interfacial area of about (80 × 80) nm2 with subnanometer resolution as well as the analysis of several interfaces within the multiquantum well stack. Representing the interfaces as iso-concentration surfaces in the tomogram and converting them to topographic height maps allows the determination of their morphological roughness as well as layer thicknesses, reflecting low variations in either case. Simulation of the reconstructed tomogram intensities using a sigmoidal function provides in-plane-resolved maps of the chemical interface widths showing a relatively large spatial variation. The more detailed analysis of the intermixed region using thin slices from the reconstruction and additional iso-concentration surfaces provides an accurate picture of the chemical disorder of the alloy at the interface. Our comprehensive three-dimensional image of Ge/Ge0.8Si0.2 interfaces reveals that in the case of morphologically very smooth interfaces─depending on the scale considered─the interface alloy disorder itself determines the overall characteristics, a result that is fundamental for highly miscible material systems.

The Trimeric Autotransporter Adhesin EmaA and Infective Endocarditis

Infective endocarditis (IE), a disease of the endocardial surface of the heart, is usually of bacterial origin and disproportionally affects individuals with underlying structural heart disease. Although IE is typically associated with Gram-positive bacteria, a minority of cases are caused by a group of Gram-negative species referred to as the HACEK group. These species, classically associated with the oral cavity, consist of bacteria from the genera Haemophilus (excluding Haemophilus influenzae), Aggregatibacter, Cardiobacterium, Eikenella, and Kingella. Aggregatibacter actinomycetemcomitans, a bacterium of the Pasteurellaceae family, is classically associated with Aggressive Periodontitis and is also concomitant with the chronic form of the disease. Bacterial colonization of the oral cavity serves as a reservoir for infection at distal body sites via hematological spreading. A. actinomycetemcomitans adheres to and causes disease at multiple physiologic niches using a diverse array of bacterial cell surface structures, which include both fimbrial and nonfimbrial adhesins. The nonfimbrial adhesin EmaA (extracellular matrix binding protein adhesin A), which displays sequence heterogeneity dependent on the serotype of the bacterium, has been identified as a virulence determinant in the initiation of IE. In this chapter, we will discuss the known biochemical, molecular, and structural aspects of this protein, including its interactions with extracellular matrix components and how this multifunctional adhesin may contribute to the pathogenicity of A. actinomycetemcomitans.

Ultrastructure and Nanoporosity of Human Bone Shown with Correlative On-Axis Electron and Spectroscopic Tomographies

Mineralized collagen fibrils are the building block units of bone at the nanoscale. While it is known that collagen fibrils are mineralized both inside their gap zones (intra-fibrillar mineralization) and on their outer surfaces (extra-fibrillar mineralization), a clear visualization of this architecture in three dimensions (3D), combining structural and compositional information over large volumes, but without compromising the resolution, remains challenging. In this study, we demonstrate the use of on-axis Z-contrast electron tomography (ET) with correlative energy-dispersive X-ray spectroscopy (EDX) tomography to examine rod-shaped samples with diameters up to 700 nm prepared from individual osteonal lamellae in the human femur. Our work mainly focuses on two aspects: (i) low-contrast nanosized circular spaces ("holes") observed in sections of bone oriented perpendicular to the long axis of a long bone, and (ii) extra-fibrillar mineral, especially in terms of morphology and spatial relationship with respect to intra-fibrillar mineral and collagen fibrils. From our analyses, it emerges quite clearly that most "holes" are cross-sectional views of collagen fibrils. While this had been postulated before, our 3D reconstructions and reslicing along meaningful two-dimensional (2D) cross-sections provide a direct visual confirmation. Extra-fibrillar mineral appears to be composed of thin plates that are interconnected and span over several collagen fibrils, confirming that mineralization is cross-fibrillar, at least for the extra-fibrillar phase. EDX tomography shows mineral signatures (Ca and P) within the gap zones, but the signal appears weaker than that associated with the extra-fibrillar mineral, pointing toward the existence of dissimilarities between the two types of mineralization.

Evaluation of Electron Tomography Capabilities for Shale Imaging

Despite the advantageous resolution of electron tomography (ET), reconstruction of three-dimensional (3D) images from multiple two-dimensional (2D) projections presents several challenges, including small signal-to-noise ratios, and a limited projection range. This study evaluates the capabilities of ET for thin sections of shale, a complex nanoporous medium. A numerical phantom with 1.24 nm pixel size is constructed based on the tomographic reconstruction of a Barnett shale. A dataset of 2D projection images is numerically generated from the 3D phantom and studied over a range of conditions. First, common reconstruction techniques are used to reconstruct the shale structure. The reconstruction uncertainty is quantified by comparing overall values of storage and transport metrics, as well as the misclassification of pore voxels compared to the phantom. We then select the most robust reconstruction technique and we vary the acquisition conditions to quantify the effect of artifacts. We find a strong agreement for large pores over the different acquisition workflows, while a wider variability exists for nanometer-scale features. The limited projection range and reconstruction are identified as the main experimental bottlenecks, thereby suggesting that sample thinning, advanced holders, and advanced reconstruction algorithms offer opportunities for improvement.

Morphodynamics of non-canonical autophagic structures in Neurospora crassa

IMPORTANCE

Neurospora is a quintessential tip-growing organism, which is well known for packaging and longitudinal transport of tip-building blocks. Thus far, however, little attention has been paid to the co-essential process of reclamation, that is-taking apart of upstream, older structural elements, otherwise known as "autophagy". We are not yet prepared to set out the chemistry of that elaborate process, but its morphological start alone is worthy of attention. Carbon starvation triggers significant autophagic changes, beginning with prolific vacuolation along the plasma membrane, and eventual filling of 70% (or more) of cytoplasmic volume. Additionally, the Neurospora plasma membrane elaborates a variety of phagophores which themselves often look lytic. These have either dual enclosing membranes, like the familiar autophagosomes, can be doubled and have four wrapping membranes, or can be compounded with multiple membrane layers. These reclamation processes must be accommodated by the mechanism of tip growth.

Atomic-Scale 3D Structure of a Supported Pd Nanoparticle Revealed by Electron Tomography with Convolution Neural Network-Based Image Inpainting

Electron tomography based on scanning transmission electron microscopy (STEM) is used to analyze 3D structures of metal nanoparticles on the atomic scale. However, in the case of supported metal nanoparticle catalysts, the supporting material may interfere with the 3D reconstruction of metal nanoparticles. In this study, a deep learning-based image inpainting method is applied to high-angle annular dark field (HAADF)-STEM images of a supported metal nanoparticle to predict and remove the background image of the support. The inpainting method can separate an 11 nm Pd nanoparticle from the θ-Al2 O3 support in HAADF-STEM images of the θ-Al2 O3 -supported Pd catalyst. 3D reconstruction of the extracted images of the Pd nanoparticle reveals that the Pd nanoparticle adopts a deformed structure of the cuboctahedron model particle, resulting in high index surfaces, which account for the high catalytic activity for methane combustion. Using the xyz coordinate of each Pd atom, the local Pd-Pd bond distance and its variance in a real supported Pd nanoparticle are visualized, showing large strain and disorder at the Pd-Al2 O3 interface. The results demonstrate that 3D atomic-scale analysis enables atomic structure-based understanding and design of supported metal catalysts.

Three-dimensional reconstruction of interstitial extracellular vesicles in human liver as determined by electron tomography

Extracellular vesicles (EVs) are lipid bilayer nanoparticles involved in cell-cell communication that are released into the extracellular space by all cell types. The cargo of EVs includes proteins, lipids, nucleic acids, and metabolites reflecting their cell of origin. EVs have recently been isolated directly from solid tissues, and this may provide insights into how EVs mediate communication between cells in vivo. Even though EVs have been isolated from tissues, their point of origin when they are in the interstitial space has been uncertain. In this study, we performed three-dimensional (3D) reconstruction using transmission electron tomography of metastatic and normal liver tissues with a focus on the presence of EVs in the interstitium. After chemical fixation of the samples and subsequent embedding of tissue pieces in resin, ultrathin slices (300 nm) were cut and imaged on a 120 ekV transmission electron microscopy as a tilt series (a series of subsequent images tilted at different angles). These were then computationally illustrated in a 3D manner to reconstruct the imaged tissue volume. We identified the cells delimiting the interstitial space in both types of tissues, and small distinct spherical structures with a diameter of 30-200 nm were identified between the cells. These round structures appeared to be more abundant in metastatic tissue compared to normal tissue. We suggest that the observed spherical structures in the interstitium of the metastatic and non-metastatic liver represent EVs. This work thus provides the first 3D visualization of EVs in human tissue.

Tuning the Growth of Chiral Gold Nanoparticles Through Rational Design of a Chiral Molecular Inducer

The bottom-up production of chiral gold nanomaterials holds great potential for the advancement of biosensing and nano-optics, among other applications. Reproducible preparations of colloidal nanomaterials with chiral morphology have been reported, using cosurfactants or chiral inducers such as thiolated amino acids. However, the underlying growth mechanisms for these nanomaterials remain insufficiently understood. We introduce herein a purposely devised chiral inducer, a cysteine modified with a hydrophobic chain, as a versatile chiral inducer. The amphiphilic and chiral features of this molecule provide control over the chiral morphology and the chiroptical signature of the obtained nanoparticles by simply varying the concentration of chiral inducer. These results are supported by circular dichroism and electromagnetic modeling as well as electron tomography to analyze structural evolution at the facet scale. Our observations suggest complex roles for the factors involved in chiral synthesis: the chemical nature of the chiral inducers and the influence of cosurfactants.

Giant mitochondria in human liver disease

This thematic review aims to provide an overview of the current state of knowledge about the occurrence of giant mitochondria or megamitochondria in liver parenchymal cells. Their presence and accumulation are considered to be a major pathological hallmark of the health and fate of liver parenchymal cells that leads to overall tissue deterioration and eventually results in organ failure. The first description on giant mitochondria dates back to the 1960s, coinciding with the availability of the first generation of electron microscopes in clinical diagnostic laboratories. Detailed accounts on their ultrastructure have mostly been described in patients suffering from alcoholic liver disease, chronic hepatitis, hepatocellular carcinoma and non-alcoholic fatty liver disease. Interestingly, from this extensive literature survey, it became apparent that giant mitochondria or megamitochondria present themselves with or without highly organised crystal-like intramitochondrial inclusions. The origin, formation and potential role of giant mitochondria remain to-date largely unanswered. Likewise, the biochemical composition of the well-organised crystal-like inclusions and their possible impact on mitochondrial function is unclear. Herein, concepts about the possible mechanism of their formation and three-dimensional architecture will be approached. We will furthermore discuss their importance in diagnostics, including future research outlooks and potential therapeutic interventions to cure liver disease where giant mitochondria are implemented.

Disruption of influenza virus packaging signals results in various misassembled genome complexes

IMPORTANCE

The influenza A virus genome consists of eight distinct viral RNAs (vRNAs) that are typically packaged into a single virion as an octameric complex. How this genome complex is assembled and incorporated into the virion is poorly understood, but previous research suggests a coordinative role for packaging signals present in all vRNAs. Here, we show that disruption of two packaging signals in a model H7N7 influenza A virus results in a mixture of virions with unusual vRNA content, including empty virions, virions with one to four vRNAs, and virions with octameric complexes composed of vRNA duplicates. Our results suggest that (i) the assembly of error-free octameric complexes proceeds through a series of defined vRNA sub-complexes and (ii) virions can bud without incorporating complete octameric complexes.

Autonomous Electron Tomography Reconstruction with Machine Learning

Modern electron tomography has progressed to higher resolution at lower doses by leveraging compressed sensing (CS) methods that minimize total variation (TV). However, these sparsity-emphasized reconstruction algorithms introduce tunable parameters that greatly influence the reconstruction quality. Here, Pareto front analysis shows that high-quality tomograms are reproducibly achieved when TV minimization is heavily weighted. However, in excess, CS tomography creates overly smoothed three-dimensional (3D) reconstructions. Adding momentum to the gradient descent during reconstruction reduces the risk of over-smoothing and better ensures that CS is well behaved. For simulated data, the tedious process of tomography parameter selection is efficiently solved using Bayesian optimization with Gaussian processes. In combination, Bayesian optimization with momentum-based CS greatly reduces the required compute time-an 80% reduction was observed for the 3D reconstruction of SrTiO3 nanocubes. Automated parameter selection is necessary for large-scale tomographic simulations that enable the 3D characterization of a wider range of inorganic and biological materials.

Prismatic Block Copolymer Hexosomes

Cubosomes and hexosomes are recent solution morphologies with an ordered porous structure and are observed for lipids and amphiphilic block copolymers (BCPs) with high hydrophobic fractions. Whereas lipid hexosomes typically exhibit a prismatic shape, BCP hexosomes have so far only been observed as closed microspheres where inner channels are not connected to the surrounding medium. Here, we describe the formation of flat, prismatic BCP hexosomes with pronounced faceting and a highly ordered lattice of hexagonally packed channels. We assemble polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP or SV) into the hexosome framework using polystyrene-block-poly(4-vinylpyridine)-block-poly(tert-butyl methacrylate) (PS-b-P4VP-b-PT or SVT) as a macromolecular surfactant in low-χ solvents. During solvent exchange, SV-rich domains form through liquid-liquid phase separation, followed by solidification and confined assembly within these domains. Since the final solvent (acetone) has a very low χ parameter toward PS and P4VP (equaling low interfacial tension), solidification of the hexosome occurs under confinement conditions that we term "supersoft". The low interfacial tension allows the stabilization of the hexagonal-prismatic shape, which originates from the hexagonal lattice of channels. Increasing the interfacial tension with polar cosolvents at some point dominates the particle shape, resulting in deformation of prismatic BCP hexosomes into spinning-top structures. The use of low-χ solvents for confined assembly of BCPs may allow the formation of unusual particle shapes simply by tuning the polymer-solvent interaction.

Transsynaptic Assemblies Link Domains of Presynaptic and Postsynaptic Intracellular Structures across the Synaptic Cleft

The chemical synapse is a complex machine separated into three parts: presynaptic, postsynaptic, and cleft. Super-resolution light microscopy has revealed alignment of presynaptic vesicle release machinery and postsynaptic neurotransmitter-receptors and scaffolding components in synapse spanning nanocolumns. Cryo-electron tomography confirmed that postsynaptic glutamate receptor-like structures align with presynaptic structures in proximity to synaptic vesicles into transsynaptic assemblies. In our electron tomographic renderings, nearly all transcleft structures visibly connect to intracellular structures through transmembrane structures to form transsynaptic assemblies, potentially providing a structural basis for transsynaptic alignment. Here, we describe the patterns of composition, distribution, and interactions of all assemblies spanning the synapse by producing three-dimensional renderings of all visibly connected structures in excitatory and inhibitory synapses in dissociated rat hippocampal neuronal cultures of both sexes prepared by high-pressure freezing and freeze-substitution. The majority of transcleft structures connect to material in both presynaptic and postsynaptic compartments. We found several instances of assemblies connecting to both synaptic vesicles and postsynaptic density scaffolding. Each excitatory synaptic vesicle within 30 nm of the active zone contacts one or more assembly. Further, intracellular structures were often shared between assemblies, entangling them to form larger complexes or association domains, often in small clusters of vesicles. Our findings suggest that transsynaptic assemblies physically connect the three compartments, allow for coordinated molecular organization, and may combine to form specialized functional association domains, resembling the light-level nanocolumns.SIGNIFICANCE STATEMENT A recent tomographic study uncovered that receptor-like cleft structures align across the synapse. These aligned structures were designated as transsynaptic assemblies and demonstrate the coordinated organization of synaptic transmission molecules between compartments. Our present tomographic study expands on the definition of transsynaptic assemblies by analyzing the three-dimensional distribution and connectivity of all cleft-spanning structures and their connected intracellular structures. While one-to-one component alignment occurs across the synapse, we find that many assemblies share components, leading to a complex entanglement of assemblies, typically around clusters of synaptic vesicles. Transsynaptic assemblies appear to form domains which may be the structural basis for alignment of molecular nanodomains into synapse spanning nanocolumns described by super-resolution light microscopy.

Structural Analysis of Mitochondria in Cardiomyocytes: Insights into Bioenergetics and Membrane Remodeling

Mitochondria in mammalian cardiomyocytes display considerable structural heterogeneity, the significance of which is not currently understood. We use electron microscopic tomography to analyze a dataset of 68 mitochondrial subvolumes to look for correlations among mitochondrial size and shape, crista morphology and membrane density, and organelle location within rat cardiac myocytes. A tomographic analysis guided the definition of four classes of crista morphology: lamellar, tubular, mixed and transitional, the last associated with remodeling between lamellar and tubular cristae. Correlations include an apparent bias for mitochondria with lamellar cristae to be located in the regions between myofibrils and a two-fold larger crista membrane density in mitochondria with lamellar cristae relative to mitochondria with tubular cristae. The examination of individual cristae inside mitochondria reveals local variations in crista topology, such as extent of branching, alignment of fenestrations and progressive changes in membrane morphology and packing density. The findings suggest both a rationale for the interfibrillar location of lamellar mitochondria and a pathway for crista remodeling from lamellar to tubular morphology.

Realizing the Full Potential of Advanced Microscopy Approaches for Interrogating Plant-Microbe Interactions

Microscopy has served as a fundamental tool for insight and discovery in plant-microbe interactions for centuries. From classical light and electron microscopy to corresponding specialized methods for sample preparation and cellular contrasting agents, these approaches have become routine components in the toolkit of plant and microbiology scientists alike to visualize, probe and understand the nature of host-microbe relationships. Over the last three decades, three-dimensional perspectives led by the development of electron tomography, and especially, confocal techniques continue to provide remarkable clarity and spatial detail of tissue and cellular phenomena. Confocal and electron microscopy provide novel revelations that are now commonplace in medium and large institutions. However, many other cutting-edge technologies and sample preparation workflows are relatively unexploited yet offer tremendous potential for unprecedented advancement in our understanding of the inner workings of pathogenic, beneficial, and symbiotic plant-microbe interactions. Here, we highlight key applications, benefits, and challenges of contemporary advanced imaging platforms for plant-microbe systems with special emphasis on several recently developed approaches, such as light-sheet, single molecule, super-resolution, and adaptive optics microscopy, as well as ambient and cryo-volume electron microscopy, X-ray microscopy, and cryo-electron tomography. Furthermore, the potential for complementary sample preparation methodologies, such as optical clearing, expansion microscopy, and multiplex imaging, will be reviewed. Our ultimate goal is to stimulate awareness of these powerful cutting-edge technologies and facilitate their appropriate application and adoption to solve important and unresolved biological questions in the field. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Determination of 2D Particle Size Distributions in Plasmonic Nanoparticle Colloids via Analytical Ultracentrifugation: Application to Gold Bipyramids

Multidimensional particle properties determine the product properties in numerous advanced applications. Accurate and statistically meaningful measurements of complex particles and their multidimensional distributions are highly challenging but strongly needed. 2D particle size distributions of plasmonic nanoparticles of complex regular shape can be obtained from analytical ultracentrifugation experiments via the optical back coupling method. A workflow for the calculation of frictional properties of arbitrarily shaped nanoparticles was developed based on bead shell models and applied to gold bipyramids with a pentagonal cross-section. The obtained 2D particle length-diameter distributions and the reduced cumulative 1D length and diameter distributions were compared to transmission electron microscopy measurements. While we find very good agreement for most measurements, the obtained length and diameter distributions were shifted by a few nanometers for some samples. Transmission electron microscopy, energy-dispersive X-ray spectroscopy, electron tomography, and finite element modeling indicate that the shift originated from a slight mismatch between the assumed shape of the simulated perfect bipyramids and the real particle shape and composition due to the presence of silver in the particles. This study demonstrates the feasibility of the applied techniques for complex shape analysis of nanoparticle ensembles with unmatched particle count numbers.

Three-dimensional electron tomography and recent expansion of its applications in materials science

Electron tomography (ET) is a powerful tool for elucidating the properties and functionalities of materials. The innovative development of aberration-corrected electron microscopy in the early twenty-first century and the remarkable progress in the development of detectors, equipment, and devices related to ET have resulted in substantial improvements in resolution. However, not only advances in hardware but also remarkable developments in reconstruction algorithms and related three-dimensional (3D) analysis methods have contributed to the resolution improvements. ET has its own problems, including the missing wedge problem due to the limited tilt-angle range and the need to acquire numerous specimen-tilt images, the latter of which is time-consuming and can potentially damage the specimen. This review paper aims to (i) describe the established basic theories and definitions regarding 3D resolution of ET and practical 3D resolution measurement methods (ii) discuss various reconstruction algorithms that effectively overcome the aforementioned problems, and (iii) describe recent progress in the core of ET applications in materials science with respect to atomic ET, analytical ET, and in-situ ET. The aforementioned ET problems have been addressed with each method developed in each field of application. Notably, in terms of aim (ii), recently developed reconstruction algorithms can reduce the number of projection images (specimen tilt images) needed to attain a certain resolution without violating the Nyquist criterion. This approach is interpreted as a novel nonlinear sampling theorem.

Serotype-Specific Sugars Impact Structure but Not Functions of the Trimeric Autotransporter Adhesin EmaA of Aggregatibacter actinomycetemcomitans

The human oral pathobiont Aggregatibacter actinomycetemcomitans expresses multiple virulence factors, including the trimeric, extracellular matrix protein adhesin A (EmaA). The posttranslational modification of EmaA is proposed to be dependent on the sugars and enzymes associated with O-polysaccharide (O-PS) synthesis of the lipopolysaccharide (LPS). This modification is important for the structure and function of this adhesin. To determine if the composition of the sugars alters structure and/or function, the prototypic 202-kDa protein was expressed in a non-serotype b, emaA mutant strain. The transformed strain displayed EmaA adhesins similar in appearance to the prototypic adhesin as observed by two-dimensional (2D) electron microscopy of whole-mount negatively stained bacterial preparations. Biochemical analysis indicated that the protein monomers were posttranslationally modified. 3D electron tomographic reconstruction and structure analyses of the functional domain revealed three well-defined subdomains (SI, SII, and SIII) with a linker region between SII and SIII. Structural changes were observed in all three subdomains and the linker region of the adhesins synthesized compared with the known structure. These changes, however, did not affect the ability of the strain to bind collagen or form biofilms. The data suggest that changes in the composition of the glycan moiety alter the 3D structure of the molecule without negatively affecting the function(s) associated with this adhesin. IMPORTANCE The human oral pathogen A. actinomycetemcomitans is a causative agent of periodontal and several systemic diseases. EmaA is a trimeric autotransporter protein adhesin important for colonization by this pathobiont in vivo. This adhesin is modified with sugars associated with the O-polysaccharide (O-PS), and the modification is mediated using the enzymes involved in lipopolysaccharide (LPS) biosynthesis. The interaction with collagen is not mediated by the specific binding between the glycans and collagen but is attributed to changes in the final quaternary structure necessary to maintain an active adhesin. In this study, we have determined that the composition of the sugars utilized in the posttranslational modification of this adhesin is exchangeable without compromising functional activities.

Insights from the Infection Cycle of VSV-ΔG-Spike Virus

Fundamental key processes in viral infection cycles generally occur in distinct cellular sites where both viral and host factors accumulate and interact. These sites are usually termed viral replication organelles, or viral factories (VF). The generation of VF is accompanied by the synthesis of viral proteins and genomes and involves the reorganization of cellular structure. Recently, rVSV-ΔG-spike (VSV-S), a recombinant VSV expressing the SARS-CoV-2 spike protein, was developed as a vaccine candidate against SARS-CoV-2. By combining transmission electron microscopy (TEM) tomography studies and immuno-labeling techniques, we investigated the infection cycle of VSV-S in Vero E6 cells. RT-real-time-PCR results show that viral RNA synthesis occurs 3-4 h post infection (PI), and accumulates as the infection proceeds. By 10-24 h PI, TEM electron tomography results show that VSV-S generates VF in multi-lamellar bodies located in the cytoplasm. The VF consists of virus particles with various morphologies. We demonstrate that VSV-S infection is associated with accumulation of cytoplasmatic viral proteins co-localized with dsRNA (marker for RNA replication) but not with ER membranes. Newly formed virus particles released from the multi-lamellar bodies containing VF, concentrate in a vacuole membrane, and the infection ends with the budding of particles after the fusion of the vacuole membrane with the plasma membrane. In summary, the current study describes detailed 3D imaging of key processes during the VSV-S infection cycle.

Morphological and Optical Transitions during Micelle-Seeded Chiral Growth on Gold Nanorods

Chiral plasmonics is a rapidly developing field where breakthroughs and unsolved problems coexist. We have recently reported binary surfactant-assisted seeded growth of chiral gold nanorods (Au NRs) with high chiroptical activity. Such a seeded-growth process involves the use of a chiral cosurfactant that induces micellar helicity, in turn driving the transition from achiral to chiral Au NRs, from both the morphological and the optical points of view. We report herein a detailed study on both transitions, which reveals intermediate states that were hidden so far. The correlation between structure and optical response is carefully analyzed, including the (linear and CD) spectral evolution over time, electron tomography, the impact of NR dimensions on their optical response, the variation of the absorption-to-scattering ratio during the evolution from achiral to chiral Au NRs, and the near-field enhancement related to chiral plasmon modes. Our findings provide further understanding of the growth process of chiral Au NRs and the associated optical changes, which will facilitate further study and applications of chiral nanomaterials.

A high-throughput electron tomography workflow reveals over-elongated centrioles in relapsed/refractory multiple myeloma

Electron microscopy is the gold standard to characterize centrosomal ultrastructure. However, production of significant morphometrical data is highly limited by acquisition time. We therefore developed a generalizable, semi-automated high-throughput electron tomography strategy to study centrosome aberrations in sparse patient-derived cancer cells at nanoscale. As proof of principle, we present electron tomography data on 455 centrioles of CD138pos plasma cells from one patient with relapsed/refractory multiple myeloma and CD138neg bone marrow mononuclear cells from three healthy donors as a control. Plasma cells from the myeloma patient displayed 122 over-elongated centrioles (48.8%). Particularly mother centrioles also harbored gross structural abnormalities, including fragmentation and disturbed microtubule cylinder formation, while control centrioles were phenotypically unremarkable. These data demonstrate the feasibility of our scalable high-throughput electron tomography strategy to study structural centrosome aberrations in primary tumor cells. Moreover, our electron tomography workflow and data provide a resource for the characterization of cell organelles beyond centrosomes.

Isolation and structure of the fibril protein, a major component of the internal ribbon for Spiroplasma swimming

Spiroplasma, which are known pathogens and commensals of arthropods and plants, are helical-shaped bacteria that lack a peptidoglycan layer. Spiroplasma swim by alternating between left- and right-handed helicity. Of note, this system is not related to flagellar motility, which is widespread in bacteria. A helical ribbon running along the inner side of the helical cell should be responsible for cell helicity and comprises the bacterial actin homolog, MreB, and a protein specific to Spiroplasma, fibril. Here, we isolated the ribbon and its major component, fibril filament, for electron microscopy (EM) analysis. Single-particle analysis of the fibril filaments using the negative-staining EM revealed a three-dimensional chain structure composed of rings with a size of 11 nm wide and 6 nm long, connected by a backbone cylinder with an 8.7 nm interval with a twist along the filament axis. This structure was verified through EM tomography of quick-freeze deep-etch replica sample, with a focus on its handedness. The handedness and pitch of the helix for the isolated ribbon and fibril filament agreed with those of the cell in the resting state. Structures corresponding to the alternative state were not identified. These results suggest that the helical cell structure is supported by fibril filaments; however, the helical switch is caused by the force generated by the MreB proteins. The isolation and structural outline of the fibril filaments provide crucial information for an in-depth clarification of the unique swimming mechanism of Spiroplasma.

Ultrastructural analysis of wild-type and RIM1α knockout active zones in a large cortical synapse

Rab3A-interacting molecule (RIM) is crucial for fast Ca²⁺-triggered synaptic vesicle (SV) release in presynaptic active zones (AZs). We investigated hippocampal giant mossy fiber bouton (MFB) AZ architecture in 3D using electron tomography of rapid cryo-immobilized acute brain slices in RIM1α^-/- and wild-type mice. In RIM1α^-/-, AZs are larger with increased synaptic cleft widths and a 3-fold reduced number of tightly docked SVs (0-2 nm). The distance of tightly docked SVs to the AZ center is increased from 110 to 195 nm, and the width of their electron-dense material between outer SV membrane and AZ membrane is reduced. Furthermore, the SV pool in RIM1α^-/- is more heterogeneous. Thus, RIM1α, besides its role in tight SV docking, is crucial for synaptic architecture and vesicle pool organization in MFBs.

Precisely Picking Nanoparticles by a "Nano-Scalpel" for 360° Electron Tomography

Electron tomography (ET) has gained increasing attention for the 3D characterization of nanoparticles. However, the missing wedge problem due to a limited tilt angle range is still the main challenge for accurate reconstruction in most experimental TEM setups. Advanced algorithms could in-paint or compensate to some extent the missing wedge artifacts, but cannot recover the missing structural information completely. 360° ET provides an option to solve this problem by tilting a needle-shaped specimen over the full tilt range and thus filling the missing information. However, sample preparation especially for fine powders to perform full-range ET is still challenging, thus limiting its application. In this work, we propose a new universal sample preparation method that enables the transfer of selected individual nanoparticle or a few separated nanoparticles by cutting a piece of carbon film supporting the specimen particles and mounting them onto the full-range tomography holder tip with the help of an easily prepared sharp tungsten tip. This method is demonstrated by 360° ET of Pt@TiO2 hollow cage catalyst showing high quality reconstruction without missing wedge.

The distal central pair segment is structurally specialised and contributes to IFT turnaround and assembly of the tip capping structures in Chlamydomonas flagella

BACKGROUND INFORMATION

Cilia and flagella are dynamic organelles whose assembly and maintenance depend on an activetrafficking process known as the IntraFlagellar Transport (IFT), during which trains of IFT protein particles are moved by specific motors and carry flagellar precursors and turnover products along the axoneme. IFT consists of an anterograde (from base to tip) and a retrograde (from tip to base) phase. During IFT turnaround at the flagellar tip, anterograde trains release their cargoes and remodel to form the retrograde trains. Thus, turnaround is crucial for correct IFT. However, current knowledge of its mechanisms is limited.

RESULTS

We show here that in Chlamydomonas flagella the distal ∼200 nm central pair (CP) segment is structurally differentiated for the presence of a ladder-like structure (LLS). During IFT turnaround, the IFT172 subunit dissociates from the IFT- B protein complex and binds to the LLS-containing CP segment, while the IFT-B complex participates in the assembly of the CP capping structures. The IFT scaffolding function played by the LLS-containing CP segment relies on anchoring components other than the CP microtubules, since IFT turnaround occurs also in the CP-devoid pf18 mutant flagella.

CONCLUSIONS

During IFT turnaround in Chlamydomonas flagella, i) the LLS and the CP terminal plates act as anchoring platforms for IFT172 and the IFT-B complex, respectively, and ii) during its remodeling, the IFT-B complex contributes to the assembly of the CP capping structures.

SIGNIFICANCE

Our results indicate that in full length Chlamydomonas flagella IFT remodeling occurs by a specialized mechanism that involves flagellar tip structures and is distinct from the previously proposed model in which the capability to reverse motility would be intrinsic of IFT train and independent by any other flagellar structure.

Multimode Electron Tomography Sheds Light on Synthesis, Structure, and Properties of Complex Metal-Based Nanoparticles

Electron tomography has become a cornerstone technique for the visualization of nanoparticle morphology in three dimensions. However, to obtain in-depth information about a nanoparticle beyond surface faceting and morphology, different electron microscopy signals must be combined. The most notable examples of these combined signals include annular dark-field scanning transmission electron microscopy (ADF-STEM) with different collection angles and the combination of ADF-STEM with energy-dispersive X-ray or electron energy loss spectroscopies. Here, the experimental and computational development of various multimode tomography techniques in connection to the fundamental materials science challenges that multimode tomography has been instrumental to overcoming are summarized. Although the techniques can be applied to a wide variety of compositions, the study is restricted to metal and metal oxide nanoparticles for the sake of simplicity. Current challenges and future directions of multimode tomography are additionally discussed.

A new method for obtaining the magnetic shape anisotropy directly from electron tomography images

A new methodology to obtain magnetic information on magnetic nanoparticle (MNP) systems via electron tomography techniques is reported in this work. The new methodology is implemented in an under-development software package called Magn3t, written in Python and C++. A novel image-filtering technique that reduces the highly undesired diffraction effects in the tomography tilt-series has been also developed in order to increase the reliability of the correlations between morphology and magnetism. Using the Magn3t software, the magnetic shape anisotropy magnitude and direction of magnetite nanoparticles has been extracted for the first time directly from transmission electron tomography.

The Bacterial Flagellar Motor: Insights Into Torque Generation, Rotational Switching, and Mechanosensing

The flagellar motor is a bidirectional rotary nanomachine used by many bacteria to sense and move through environments of varying complexity. The bidirectional rotation of the motor is governed by interactions between the inner membrane-associated stator units and the C-ring in the cytoplasm. In this review, we take a structural biology perspective to discuss the distinct conformations of the stator complex and the C-ring that regulate bacterial motility by switching rotational direction between the clockwise (CW) and counterclockwise (CCW) senses. We further contextualize recent in situ structural insights into the modulation of the stator units by accessory proteins, such as FliL, to generate full torque. The dynamic structural remodeling of the C-ring and stator complexes as well as their association with signaling and accessory molecules provide a mechanistic basis for how bacteria adjust motility to sense, move through, and survive in specific niches both outside and within host cells and tissues.

Electron Tomography Reveals Porosity Degradation Spatially on Individual Pt-Based Nanocatalysts

Probing porosity evolution is essential to understand the degradation mechanism of electrocatalytic activity. However, spatially dependent degradation pathways for porous catalysts remain elusive. Here, we reveal the multiple degradation behaviors of individual PtCu₃ nanocatalysts spatially by three-dimensional (3D) electron tomography. We demonstrate that the surface area-volume ratio (SVR) of cycled porous particles decreases linearly rather than reciprocally with particle size. Additionally, an improved SVR (about 3-fold enhancement) results in increased oxygen reduction reaction (ORR) efficiency at the early stage. However, in the subsequent cycles, the degradation of catalytic activity is due to the excessive growth of pores, the reduction of reaction sites, and the chemical segregation of Cu atoms. The spatial porosity evolution model of nanocatalysts is applicable for a wide range of catalytic reactions, providing a critical insight into the degradation of catalyst activity.

Bimodal endocytic probe for three-dimensional correlative light and electron microscopy

We present a bimodal endocytic tracer, fluorescent BSA-gold (fBSA-Au), as a fiducial marker for 2D and 3D correlative light and electron microscopy (CLEM) applications. fBSA-Au consists of colloidal gold (Au) particles stabilized with fluorescent BSA. The conjugate is efficiently endocytosed and distributed throughout the 3D endolysosomal network of cells and has an excellent visibility in both fluorescence microscopy (FM) and electron microscopy (EM). We demonstrate that fBSA-Au facilitates rapid registration in several 2D and 3D CLEM applications using Tokuyasu cryosections, resin-embedded material, and cryoelectron microscopy (cryo-EM). Endocytosed fBSA-Au benefits from a homogeneous 3D distribution throughout the endosomal system within the cell, does not obscure any cellular ultrastructure, and enables accurate (50-150 nm) correlation of fluorescence to EM data. The broad applicability and visibility in both modalities makes fBSA-Au an excellent endocytic fiducial marker for 2D and 3D (cryo)CLEM applications.

Exploring the Preparation Dependence of Crystalline 2D-Extended Ultrathin C8-BTBT-C8 Films

Crystalline organic semiconducting thin films from the benchmark molecule C8-BTBT-C8 were obtained using physical vapor deposition and various solution-based methods. Utilizing atomic force microscopy and X-ray spectromicroscopy, we illustrate the influence of the underlying growth mechanism and determine the highly preparation-dependent orientation of the thiophene backbone. We observe a continuous trend for crystalline C8-BTBT-C8 thin film domains to extend into the square millimeter-range under near-equilibrium growth conditions. For such well-defined systems, electron diffraction tomography allows us to precisely determine the unit cell directly after film deposition and to reveal an 8° molecular tilt angle with respect to the surface normal. This finding is in almost perfect accordance with the values derived from near-edge X-ray absorption fine structure linear dichroism. Within this work, we shine a light on both the successes and challenges connected to the realization of potent, thiophene-based semiconducting films, paving the way toward square centimeter-sized ultrathin organic crystals and their application in organic circuitry.

Mitochondrial Population in Mouse Eosinophils: Ultrastructural Dynamics in Cell Differentiation and Inflammatory Diseases

Mitochondria are multifunctional organelles of which ultrastructure is tightly linked to cell physiology. Accumulating evidence shows that mitochondrial remodeling has an impact on immune responses, but our current understanding of the mitochondrial architecture, interactions, and morphological changes in immune cells, mainly in eosinophils, is still poorly known. Here, we applied transmission electron microscopy (TEM), single-cell imaging analysis, and electron tomography, a technique that provides three-dimensional (3D) views at high resolution, to investigate mitochondrial dynamics in mouse eosinophils developing in cultures as well as in the context of inflammatory diseases characterized by recruitment and activation of these cells (mouse models of asthma, H1N1 influenza A virus (IAV) infection, and schistosomiasis mansoni). First, quantitative analyses showed that the mitochondrial area decrease 70% during eosinophil development (from undifferentiated precursor cells to mature eosinophils). Mitophagy, a consistent process revealed by TEM in immature but not in mature eosinophils, is likely operating in mitochondrial clearance during eosinophilopoiesis. Events of mitochondria interaction (inter-organelle membrane contacts) were also detected and quantitated within developing eosinophils and included mitochondria-endoplasmic reticulum, mitochondria-mitochondria, and mitochondria-secretory granules, all of them significantly higher in numbers in immature compared to mature cells. Moreover, single-mitochondrion analyses revealed that as the eosinophil matures, mitochondria cristae significantly increase in number and reshape to lamellar morphology. Eosinophils did not change (asthma) or reduced (IAV and Schistosoma infections) their mitochondrial mass in response to inflammatory diseases. However, asthma and schistosomiasis, but not IAV infection, induced amplification of both cristae numbers and volume in individual mitochondria. Mitochondrial cristae remodeling occurred in all inflammatory conditions with the proportions of mitochondria containing only lamellar or tubular, or mixed cristae (an ultrastructural aspect seen just in tissue eosinophils) depending on the tissue/disease microenvironment. The ability of mitochondria to interact with granules, mainly mobilized ones, was remarkably captured by TEM in eosinophils participating in all inflammatory diseases. Altogether, we demonstrate that the processes of eosinophilopoiesis and inflammation-induced activation interfere with the mitochondrial dynamics within mouse eosinophils leading to cristae remodeling and inter-organelle contacts. The understanding of how mitochondrial dynamics contribute to eosinophil immune functions is an open interesting field to be explored.

Particle Morphology of Medusavirus Inside and Outside the Cells Reveals a New Maturation Process of Giant Viruses

Medusavirus, a giant virus, is phylogenetically closer to eukaryotes than the other giant viruses and has been recently classified as an independent species. However, details of its morphology and maturation process in host cells remain unclear. Here, we investigated the particle morphology of medusavirus inside and outside infected cells using conventional transmission electron microscopy (C-TEM) and cryo-electron microscopy (cryo-EM). The C-TEM of amoebae infected with the medusavirus showed four types of particles, i.e., pseudo-DNA-empty (p-Empty), DNA-empty (Empty), semi-DNA-full (s-Full), and DNA-full (Full). Time-dependent changes in the four types of particles and their intracellular localization suggested a new maturation process for the medusavirus. Viral capsids and viral DNAs are produced independently in the cytoplasm and nucleus, respectively, and only the empty particles located near the host nucleus can incorporate the viral DNA into the capsid. Therefore, all four types of particles were found outside the cells. The cryo-EM of these particles showed that the intact virus structure, covered with three different types of spikes, was preserved among all particle types, although with minor size-related differences. The internal membrane exhibited a structural array similar to that of the capsid, interacted closely with the capsid, and displayed open membrane structures in the Empty and p-Empty particles. The results suggest that these open structures in the internal membrane are used for an exchange of scaffold proteins and viral DNA during the maturation process. This new model of the maturation process of medusavirus provides insight into the structural and behavioral diversity of giant viruses.

IMPORTANCE Giant viruses exhibit diverse morphologies and maturation processes. In this study, medusavirus showed four types of particle morphologies, both inside and outside the infected cells, when propagated in amoeba culture. Time-course analysis and intracellular localization of the medusavirus in the infected cells suggested a new maturation process via the four types of particles. Like the previously reported pandoravirus, the viral DNA of medusavirus is replicated in the host’s nucleus. However, viral capsids are produced independently in the host cytoplasm, and only empty capsids near the nucleus can take up viral DNA. As a result, many immature particles were released from the host cell along with the mature particles. The capsid structure is well conserved among the four types of particles, except for the open membrane structures in the empty particles, suggesting that they are used to exchange scaffold proteins for viral DNAs. These findings indicate that medusavirus has a unique maturation process.

FliL ring enhances the function of periplasmic flagella

SignificanceHow flagella sense complex environments and control bacterial motility remain fascinating questions. Here, we deploy cryo-electron tomography to determine in situ structures of the flagellar motor in wild-type and mutant cells of Borrelia burgdorferi, revealing that three flagellar proteins (FliL, MotA, and MotB) form a unique supramolecular complex in situ. Importantly, FliL not only enhances motor function by forming a ring around the stator complex MotA/MotB in its extended, active conformation but also facilitates assembly of the stator complex around the motor. Our in situ data provide insights into how cooperative remodeling of the FliL-stator supramolecular complex helps regulate the collective ion flux and establishes the optimal function of the flagellar motor to guide bacterial motility in various environments.

Thermal Evolution of C-Fe-Bi Nanocomposite System: From Nanoparticle Formation to Heterogeneous Graphitization Stage

Carbon xerogel nanocomposites with integrated Bi and Fe particles (C–Bi–Fe) represent an interesting model of carbon nanostructures decorated with multifunctional nanoparticles (NPs) with applicability for electrochemical sensors and catalysts. The present study addresses the fundamental aspects of the catalyzed growth of nano-graphites in C–Bi–Fe systems, relevant in charge transport and thermo-chemical processes. The thermal evolution of a C–Bi–Fe xerogel is investigated using different pyrolysis treatments. At lower temperatures (~750°C), hybrid bismuth iron oxide (BFO) NPs are frequently observed, while graphitization manifests under more specific conditions such as higher temperatures (~1,050°C) and reduction yields. An in situ heating TEM experiment reveals graphitization activity between 800 and 900°C. NP motion is directly correlated with textural changes of the carbon support due to the catalyzed growth of graphitic nanoshells and nanofibers as confirmed by HR-TEM and electron tomography (ET) for the graphitized sample. An exponential growth model for the catalyst dynamics enables the approximation of activation energies as 0.68 and 0.29–0.34 eV during reduction and graphitization stages. The results suggest some similarities with the tip growth mechanism, while oxygen interference and the limited catalyst–feed gas interactions are considered as the main constraints to enhanced growth.

Fiber-Like Organization as a Basic Principle for Euchromatin Higher-Order Structure

A detailed understanding of the principles of the structural organization of genetic material is of great importance for elucidating the mechanisms of differential regulation of genes in development. Modern ideas about the spatial organization of the genome are based on a microscopic analysis of chromatin structure and molecular data on DNA–DNA contact analysis using Chromatin conformation capture (3C) technology, ranging from the “polymer melt” model to a hierarchical folding concept. Heterogeneity of chromatin structure depending on its functional state and cell cycle progression brings another layer of complexity to the interpretation of structural data and requires selective labeling of various transcriptional states under nondestructive conditions. Here, we use a modified approach for replication timing-based metabolic labeling of transcriptionally active chromatin for ultrastructural analysis. The method allows pre-embedding labeling of optimally structurally preserved chromatin, thus making it compatible with various 3D-TEM techniques including electron tomography. By using variable pulse duration, we demonstrate that euchromatic genomic regions adopt a fiber-like higher-order structure of about 200 nm in diameter (chromonema), thus providing support for a hierarchical folding model of chromatin organization as well as the idea of transcription and replication occurring on a highly structured chromatin template.

Simultaneous Successive Twinning Captured by Atomic Electron Tomography

Shape-controlled synthesis of multiply twinned nanostructures is heavily emphasized in nanoscience, in large part due to the desire to control the size, shape, and terminating facets of metal nanoparticles for applications in catalysis. Direct control of the size and shape of solution-grown nanoparticles relies on an understanding of how synthetic parameters alter nanoparticle structures during synthesis. However, while outcome populations can be effectively studied with standard electron microscopy methods, transient structures that appear during some synthetic routes are difficult to study using conventional high resolution imaging methods due to the high complexity of the 3D nanostructures. Here, we have studied the prevalence of transient structures during growth of multiply twinned particles and employed atomic electron tomography to reveal the atomic-scale three-dimensional structure of a Pd nanoparticle undergoing a shape transition. By identifying over 20 000 atoms within the structure and classifying them according to their local crystallographic environment, we observe a multiply twinned structure consistent with a simultaneous successive twinning from a decahedral to icosahedral structure.

Optogenetics and electron tomography for structure-function analysis of cochlear ribbon synapses

Ribbon synapses of cochlear inner hair cells (IHCs) are specialized to indefatigably transmit sound information at high rates. To understand the underlying mechanisms, structure-function analysis of the active zone (AZ) of these synapses is essential. Previous electron microscopy studies of synaptic vesicle (SV) dynamics at the IHC AZ used potassium stimulation, which limited the temporal resolution to minutes. Here, we established optogenetic IHC stimulation followed by quick freezing within milliseconds and electron tomography to study the ultrastructure of functional synapse states with good temporal resolution in mice. We characterized optogenetic IHC stimulation by patch-clamp recordings from IHCs and postsynaptic boutons revealing robust IHC depolarization and neurotransmitter release. Ultrastructurally, the number of docked SVs increased upon short (17-25 ms) and long (48-76 ms) light stimulation paradigms. We did not observe enlarged SVs or other morphological correlates of homotypic fusion events. Our results indicate a rapid recruitment of SVs to the docked state upon stimulation and suggest that univesicular release prevails as the quantal mechanism of exocytosis at IHC ribbon synapses.

A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0

We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D experimental images. In addition, analogous to Bayesian polishing and contrast transfer function (CTF) refinement in single-particle analysis, we describe the approaches that exploit the increased signal-to-noise ratio in the averaged structure to optimise tilt-series alignments, beam-induced motions of the particles throughout the tilt-series acquisition, defoci of the individual particles, as well as higher-order optical aberrations of the microscope. Implementation of our approaches in the open-source software package RELION aims to facilitate their general use, particularly for those researchers who are already familiar with its single-particle analysis tools. We illustrate for three applications that our approaches allow structure determination from cryo-ET data to resolutions sufficient for de novo atomic modelling.

New Phenotype and Mineralization of Biogenic Iron Oxide in Magnetotactic Bacteria

Many magnetotactic bacteria (MTB) biomineralize magnetite crystals that nucleate and grow inside intracellular membranous vesicles originating from invaginations of the cytoplasmic membrane. The crystals together with their surrounding membranes are referred to as magnetosomes. Magnetosome magnetite crystals nucleate and grow using iron transported inside the vesicle by specific proteins. Here, we tackle the question of the organization of magnetosomes, which are always described as constituted by linear chains of nanocrystals. In addition, it is commonly accepted that the iron oxide nanocrystals are in the magnetite-based phase. We show, in the case of a wild species of coccus-type bacterium, that there is a double organization of the magnetosomes, relatively perpendicular to each other, and that the nanocrystals are in fact maghemite. These findings were obtained, respectively, by using electron tomography of whole mounts of cells directly from the environment and high-resolution transmission electron microscopy and diffraction. Structure simulations were performed with the MacTempas software. This study opens new perspectives on the diversity of phenotypes within MTBs and allows to envisage other mechanisms of nucleation and formation of biogenic iron oxide crystals.

Structure of cell-cell adhesion mediated by the Down syndrome cell adhesion molecule

The Down syndrome cell adhesion molecule (DSCAM) belongs to the immunoglobulin superfamily (IgSF) and plays important roles in neural development. It has a large ectodomain, including 10 Ig-like domains and 6 fibronectin III (FnIII) domains. Previous data have shown that DSCAM can mediate cell adhesion by forming homophilic dimers between cells and contributes to self-avoidance of neurites or neuronal tiling, which is important for neural network formation. However, the organization and assembly of DSCAM at cell adhesion interfaces has not been fully understood. Here we combine electron microscopy and other biophysical methods to characterize the structure of the DSCAM-mediated cell adhesion and generate three-dimensional views of the adhesion interfaces of DSCAM by electron tomography. The results show that mouse DSCAM forms a regular pattern at the adhesion interfaces. The Ig-like domains contribute to both trans homophilic interactions and cis assembly of the pattern, and the FnIII domains are crucial for the cis pattern formation as well as the interaction with the cell membrane. By contrast, no obvious assembly pattern is observed at the adhesion interfaces mediated by mouse DSCAML1 or Drosophila DSCAMs, suggesting the different structural roles and mechanisms of DSCAMs in mediating cell adhesion and neural network formation.

Major Factors Influencing the Size Distribution Analysis of Cellulose Nanocrystals Imaged in Transmission Electron Microscopy

Size distributions of cellulose nanocrystals (CNCs), extracted from softwood pulp via strong sulfuric acid hydrolysis, exhibit large variability when analyzed from transmission electron microscopy (TEM) images. In this article, the causes of this variability are studied and discussed. In order to obtain results comparable with those reported, a reference material of CNCs (CNCD-1) was used to evaluate size distribution. CNC TEM specimens were prepared as-stained and dried with a rapid-flushing staining method or hydrated and embedded in vitreous ice with the plunge-freezing method. Several sets of bright-field TEM (BF-TEM), annular dark-field scanning TEM (ADF-STEM) and cryogenic-TEM (cryo-TEM) images were acquired for size distribution analysis to study the contributing factors. The rapid-flushing staining method was found to be the most effective for contrast enhancement of CNCs, not only revealing the helical structure of single CNCs but also resolving the laterally jointed CNCs. During TEM specimen preparation, CNCs were fractionated on TEM grids driven by the coffee-ring effect, as observed from contrast variation of CNCs with a stain-depth gradient. From the edge to the center of the TEM grids, the width of CNCs increases, while the aspect ratio (length to width) decreases. This fractionated dispersion of CNCs suggests that images taken near the center of a droplet would give a larger mean width. In addition to particle fractionation driven by the coffee-ring effect, the arrangement and orientation of CNC particles on the substrate significantly affect the size measurement when CNC aggregation cannot be resolved in images. The coexistence of asymmetric cross-section CNC particles introduces a large variation in size measurement, as TEM images of CNCs are mixed projections of the width and height of particles. As a demonstration of how this contributes to inflated size measurement, twisted CNC particles, rectangular cross-section particles and end-to-end jointed CNCs were revealed in reconstructed three-dimensional (3D) micrographs by electron tomography (ET).

Targeted Chemical Modifications Identify Key Features of Carbohydrate Assemblies and Generate Tailored Carbohydrate Materials

The molecular level description of carbohydrate assemblies is hampered by their structural complexity and the lack of suitable analytical methods. Here, we employed systematic chemical modifications to identify key non-covalent interactions that triggered the supramolecular assembly of a disaccharide model. While some modifications disrupted the supramolecular organization, others were tolerated, delivering important information on the aggregation process. The screening identified new geometries, including nanotubes, and twisted ribbons that were characterized with electron tomography and electron diffraction (ED) methods. This work demonstrates that the combination of synthetic chemistry and ED methods is a powerful tool to draw correlations between the molecular structure and the nanoscale architecture of carbohydrate assemblies.

Multiscale characterization of pathological bone tissue

Bone is a complex natural material with a complex hierarchical multiscale organization, crucial to perform its functions. Ultrastructural analysis of bone is crucial for our understanding of cell to cell communication, the healthy or pathological composition of bone tissue, and its three‐dimensional (3D) organization. A variety of techniques has been used to analyze bone tissue. This article describes a combined approach of optical, scanning electron, and transmission electron microscopy for the ultrastructural analysis of bone from the nanoscale to the macroscale, as illustrated by two pathological bone tissues. By following a top‐down approach to investigate the multiscale organization of pathological bones, quantitative estimates were made in terms of calcium content, nearest neighbor distances of osteocytes, canaliculi diameter, ordering, and D‐spacing of the collagen fibrils, and the orientation of intrafibrillar minerals which enable us to observe the fine structural details. We identify and discuss a series of two‐dimensional (2D) and 3D imaging techniques that can be used to characterize bone tissue. By doing so we demonstrate that, while 2D imaging techniques provide comparable information from pathological bone tissues, significantly different structural details are observed upon analyzing the pathological bone tissues in 3D. Finally, particular attention is paid to sample preparation for and quantitative processing of data from electron microscopic analysis.

Visualizing Trace Pollutants in Solids at Nanoscale via Electron Tomography

Visualizing trace pollutants such as toxic metals and viruses in environmental solids such as soils, sediments, aerosols, and suspended particles in water has long been the holy grail for scientists and engineers. In this Perspective, progress on the state-of-the-art electron tomography is highlighted as an increasingly indispensable tool for visualizing contaminant distribution and transformation in three-dimension (3D), including environmental pollutants at the water-minerals interfaces, toxicology assessment, environmental behavior of viruses in heterogeneous environmental media, etc. Adding a third dimension to the pollutant characterization will surely enrich our understanding on the complex and emerging environmental issues facing the global society, and provide vital support to the ongoing research and development of life-saving mitigation technologies from air filtration, to drinking water purification, to virus disinfection.