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Transmission electron microscopy (TEM) has evolved into a powerful characterization tool that allows visualization of materials with finer resolution than any other type of microscope in existence. While numerous areas of the physical and biologically sciences and engineering benefit tremendously from TEM and its analytical features, the highest resolution can only be achieved if a sample fulfills certain requirements, including an optimal thickness as well as a sufficiently long e‐beam stability. At a fundamental level, the physical and chemical properties of organic polymers are generally problematic in conjunction with TEM, as they experience damage from the electron beam more readily than their hard materials counterparts. However, progress in polymer characterization using TEM has evolved considerably and the polymer community stands to benefit greatly from continued growth going forward. [ABSTRACT FROM AUTHOR]

Zn‐substituted iron oxide nanoparticles of ≈5 nm in diameter are synthetized by a microwave‐assisted thermal decomposition method. The addition of ethylene glycol results in a size increase to 22 nm. Cationic disorder has been observed by electron energy loss spectroscopy–scanning transmission electron microscopy. Using Mössbauer spectrometry combined with Rietveld analysis, the complete cationic and vacancies repartition in the lattice is determined, as well as the canting of magnetic moments. This allows the magnetic moment to be calculated, in good agreement with that measured. The alternating current magnetic susceptibility is modeled by the Néel–Brown and the Coffey models, showing some discrepancy between these two approaches which is discussed. The largest particles show a complex morphology involving an oriented attachment mechanism of smaller units. Their cationic disorder and internal porosity have been evidenced and quantified, and the work shows that despite these defects they behave rather as magnetically blocked nanoparticles. [ABSTRACT FROM AUTHOR]

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‐Al2O3 support in HAADF–STEM images of the θ‐Al2O3‐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–Al2O3 interface. The results demonstrate that 3D atomic‐scale analysis enables atomic structure‐based understanding and design of supported metal catalysts. [ABSTRACT FROM AUTHOR]

In this study we apply electron tomography to characterize 3D dislocation microstructures in two quartz mylonite specimens from the Moine and Main Central Thrusts, both of which accommodated displacements by dislocation creep in the presence of water. Both specimens show dislocation activity with dislocation densities of the order of 3–4 × 1012 m−2 and evidence of recovery from the presence of subgrain boundaries. 〈a〉 slip occurs predominantly on pyramidal and prismatic planes (〈a〉 basal glide is not active). [c] Glide is not significant. On the other hand, we observe a very high level of activation of 〈c + a〉 glide on the 101‾0 $\left\{10\overline{1}0\right\}$, 101‾1 $\left\{10\overline{1}1\right\}$, 112‾n $\left\{11\overline{2}n\right\}$ (n = 1,2) and even 213‾1 $\left\{21\overline{3}1\right\}$ planes. Approximately 60% of all dislocations show evidence of climb with a predominance of mixed climb, a deformation mechanism characterized by dislocations moving in a plane intermediate between the glide and the climb planes. This atypical mode of deformation demonstrates comparable glide and climb efficiency under natural deformation conditions. It promotes dislocation glide in planes not expected for the quartz structure, probably by inhibiting lattice friction. Our quantitative characterization of the microstructure enables us to assess the strain that dislocations can generate. We show that glide systems indicated by the observed dislocations are sufficient to accommodate any arbitrary 3D strain by themselves. Although historically dislocation glide has been regarded as being primarily responsible for producing strain, activation of climb can also directly contribute to the finite strain. On the basis of this characterization, we propose a numerical modeling approach for attempting to characterize the local stress state that gave rise to the observed microstructure. Plain Language Summary: In this study, we characterize dislocation microstructures generated in quartz deformed in natural shear zones by advanced transmission electron microscopy to better understand the geological deformation conditions and the response of quartz to applied stresses. We characterize the crystal defects responsible for deformation of the mineral and their three‐dimensional geometries. We highlight an original deformation mechanism activated at very low natural strain rates that involves simultaneous dislocation glide and climb outside of their crystallographic glide planes. Key Points: Deformation involves mostly 〈a〉 and 〈c + a〉 slip on pyramidal and prismatic planes; [c] glide is marginal, 〈a〉 basal is not activatedApproximately 60% of the dislocations move by mixed climb, that is, a combination of glide and climbUnder natural strain‐rates glide and climb velocities are comparable [ABSTRACT FROM AUTHOR]

Chikungunya virus (CHIKV) is a mosquito-borne pathogen responsible for an acute musculoskeletal disease in humans. Replication of the viral RNA genome occurs in specialized membranous replication organelles (ROs) or spherules, which contain the viral replication complex. Initially generated by RNA synthesis-associated plasma membrane deformation, alphavirus ROs are generally rapidly endocytosed to produce type I cytopathic vacuoles (CPV-I), from which nascent RNAs are extruded for cytoplasmic translation. By contrast, CHIKV ROs are poorly internalized, raising the question of their fate and functionality at the late stage of infection. Here, using in situ cryogenic-electron microscopy approaches, we investigate the outcome of CHIKV ROs and associated replication machinery in infected human cells. We evidence the late persistence of CHIKV ROs at the plasma membrane with a crowned protein complex at the spherule neck similar to the recently resolved replication complex. The unexpectedly heterogeneous and large diameter of these compartments suggests a continuous, dynamic growth of these organelles beyond the replication of a single RNA genome. Ultrastructural analysis of surrounding cytoplasmic regions supports that outgrown CHIKV ROs remain dynamically active in viral RNA synthesis and export to the cell cytosol for protein translation. Interestingly, rare ROs with a homogeneous diameter are also marginally internalized in CPV-I near honeycomb-like arrangements of unknown function, which are absent in uninfected controls, thereby suggesting a temporal regulation of this internalization. Altogether, this study sheds new light on the dynamic pattern of CHIKV ROs and associated viral replication at the interface with cell membranes in infected cells. IMPORTANCE The Chikungunya virus (CHIKV) is a positive-stranded RNA virus that requires specialized membranous replication organelles (ROs) for its genome replication. Our knowledge of this viral cycle stage is still incomplete, notably regarding the fate and functional dynamics of CHIKV ROs in infected cells. Here, we show that CHIKV ROs are maintained at the plasma membrane beyond the first viral cycle, continuing to grow and be dynamically active both in viral RNA replication and in its export to the cell cytosol, where translation occurs in proximity to ROs. This contrasts with the homogeneous diameter of ROs during internalization in cytoplasmic vacuoles, which are often associated with honeycomb-like arrangements of unknown function, suggesting a regulated mechanism. This study sheds new light on the dynamics and fate of CHIKV ROs in human cells and, consequently, on our understanding of the Chikungunya viral cycle. [ABSTRACT FROM AUTHOR]

Abstract Huntington’s disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the coding sequence of huntingtin protein. Initially, it predominantly affects medium-sized spiny neurons (MSSNs) of the corpus striatum. No effective treatment is still available, thus urging the identification of potential therapeutic targets. While evidence of mitochondrial structural alterations in HD exists, previous studies mainly employed 2D approaches and were performed outside the strictly native brain context. In this study, we adopted a novel multiscale approach to conduct a comprehensive 3D in situ structural analysis of mitochondrial disturbances in a mouse model of HD. We investigated MSSNs within brain tissue under optimal structural conditions utilizing state-of-the-art 3D imaging technologies, specifically FIB/SEM for the complete imaging of neuronal somas and Electron Tomography for detailed morphological examination, and image processing-based quantitative analysis. Our findings suggest a disruption of the mitochondrial network towards fragmentation in HD. The network of interlaced, slim and long mitochondria observed in healthy conditions transforms into isolated, swollen and short entities, with internal cristae disorganization, cavities and abnormally large matrix granules.

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 and by chiral micelles. 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. [ABSTRACT FROM AUTHOR]

Huntington's disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the coding sequence of huntingtin protein. Initially, it predominantly affects medium-sized spiny neurons (MSSNs) of the corpus striatum. No effective treatment is still available, thus urging the identification of potential therapeutic targets. While evidence of mitochondrial structural alterations in HD exists, previous studies mainly employed 2D approaches and were performed outside the strictly native brain context. In this study, we adopted a novel multiscale approach to conduct a comprehensive 3D in situ structural analysis of mitochondrial disturbances in a mouse model of HD. We investigated MSSNs within brain tissue under optimal structural conditions utilizing state-of-the-art 3D imaging technologies, specifically FIB/SEM for the complete imaging of neuronal somas and Electron Tomography for detailed morphological examination, and image processing-based quantitative analysis. Our findings suggest a disruption of the mitochondrial network towards fragmentation in HD. The network of interlaced, slim and long mitochondria observed in healthy conditions transforms into isolated, swollen and short entities, with internal cristae disorganization, cavities and abnormally large matrix granules. [ABSTRACT FROM AUTHOR]

In this study, we analyzed the morphological structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human cells. We identified the two types of viral particles present within the vacuoles of infected cells. Using transmission electron microscopy, we observed that SARS-CoV-2 particles exhibited both low- and high-electron-density structures, which was further confirmed through three-dimensional reconstruction using electron tomography. The budding of these particles was exclusively observed within these vacuoles. Intriguingly, viral particles with low-electron-density structures were confined to vacuoles, whereas those with high-electron-density structures were found in vacuoles and on the cell membrane surface of infected cells. Notably, high-electron-density particles found within vacuoles exhibited the same morphology as those outside the infected cells. This observation suggests that the two types of viral particles identified in this study had different maturation status. Our findings provide valuable insights into the molecular details of SARS-CoV-2 particles, contributing to our understanding of the virus. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The analysis of nucleocytoplasmic transport of proteins and messenger RNA has been the focus of advanced microscopic approaches. Recently, it has been possible to identify and visualize individual pre-ribosomal particles on their way through the nuclear pore complex using both electron and light microscopy. In this review, we focused on the transport of pre-ribosomal particles in the nucleus on their way to and through the pores.

Raman spectroscopy enables label-free cardiac imaging revealing biochemical information on physiological changes induced by cardiac diseases: viability assessment of ischemic myocardium, cardiac cell analysis, and cardiac biomarker detection for early diagnosis. Super-resolution imaging extends optical imaging to the nanometer scale to allow studying the subcellular structures (like transverse tubules and macromolecular protein clusters) that play an important role in the nanodomain physiology and pathophysiology of cardiac cells. Large-specimen microscopy represents a fundamental tool for dissecting the complex and interconnected hierarchical organization of the heart: cellular organization can be probed across the organ opening the possibility of correlating the impact of pathologically induced structural remodeling and cardiac plasticity on heart functionality. 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. 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract The neuroprotective effects of umbelliferone (UMB) were visualized in three-dimensional (3D) images on vesicle density changes of organotypic hippocampal slice tissues (OHSCs) induced by scopolamine by high voltage electron microscopy. Observations revealed that the number of vesicles decreased in OHSCs induced by scopolamine, and UMB was found to inhibit scopolamine-induced reduction in vesicles, resulting in an increase in vesicle count. These 3D models provide valuable insight for understanding the increase of synapse vesicles in hippocampal tissues treated with UMB.

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. [ABSTRACT FROM AUTHOR]

The Z-disk of striated muscle defines the ends of the sarcomere, which repeats many times within the muscle fiber. Here we report application of cryoelectron tomography and subtomogram averaging to Z-disks isolated from the flight muscles of the large waterbug Lethocerus indicus. We use high salt solutions to remove the myosin containing filaments and use gelsolin to remove the actin filaments of the A- and I-bands leaving only the thin filaments within the Z-disk which were then frozen for cryoelectron microscopy. The Lethocerus Z-disk structure is similar in many ways to the previously studied Z-disk of the honeybee Apis mellifera. At the corners of the unit cell are positioned trimers of paired antiparallel F-actins defining a large solvent channel, whereas at the trigonal positions are positioned F-actin trimers converging slowly towards their (+) ends defining a small solvent channel through the Z-disk. These near parallel F-actins terminate at different Z-heights within the Z-disk. The two types of solvent channel in Lethocerus are similar in size compared to those of Apis which are very different in size. Two types of α-actinin crosslinks were observed between oppositely oriented actin filaments. In one of these, the α-actinin long axis is almost parallel to the F-actins it crosslinks. In the other, the α-actinins are at a small but distinctive angle with respect to the crosslinked actin filaments. The utility of isolated Z-disks for structure determination is discussed. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The optical range of localized surface plasmon resonance (LSPR) is extended into the infrared region, thanks to the development of highly doped semiconductor nanocrystals. Particularly, the near‐infrared (NIR) range holds a significant interest in managing solar radiation. However, practical applications necessitate the arrangement of particles, which is known to possibly impact their optical properties through LSPR coupling effects. How such coupling modifies the LSPR response in semiconductor hosts remains largely unexplored. In this study, a protocol for producing composite coatings composed of cesium‐doped tungsten bronze nanocrystals embedded in a silica matrix is presented. Achieving individual dispersion of nanocrystals is made possible through careful selection of a surface polyglycerol ligand exchange. This allows to tune the interparticle distance by adjusting the nanocrystal volume fraction in the composite. The findings demonstrate that LSPR coupling effects significantly influence the LSPR intensity of nanocrystals in the composite when the nanocrystal‐to‐nanocrystal distance matches their size. Beyond elucidating the LSPR coupling effect, this study provides insights into the potential use of Cs‐HTB nanocrystals for solar control applications. Through the optimization of morphology and film structure, remarkable selectivity is obtained in terms of maintaining good transparency in the visible range while achieving high absorption in the NIR. [ABSTRACT FROM AUTHOR]

A series of catalysts composed of Pt–Fe nanoparticles supported on mesoporous silica SBA-15 (ca. 7 nm pore diameter) have been prepared by ultrasound-assisted coimpregnation of the metal precursors and evaluated in the nonoxidative dehydrogenation of isobutane. Prereduced catalytic systems were characterized by STEM-HAADF + EDS mapping and XAS to determine the chemical environment of the highly dispersed platinum active sites on the iron host matrix. While the monometallic platinum (nanoparticles) supported on SBA-15 material presented a rapid catalyst deactivation under reaction conditions, coordinatively unsaturated Pt–Fe (Pt ≪ Fe) sites located in the mesopores of SBA-15 showed a high steady-state activity (43% conversion) and selectivity (96% to isobutylene) in the dehydrogenation of isobutane at 550 °C for several hours. Temperature-programmed reduction profiles determined not only the substantially higher reducibility of FeOx species with doping amounts of platinum in the as-prepared (calcined) catalysts but also the detrimental structural changes undergone after consecutive reaction–regeneration cycles. Finally, reactivation under controlled conditions allows to minimize irreversible catalyst deactivation after successive cycles. [ABSTRACT FROM AUTHOR]

The eight different genomic viral RNAs (vRNAs) of influenza A virus are typically packaged into virions as a (7 + 1) complex of seven viral ribonucleoproteins (vRNPs) around a central vRNP. Mutations in the packaging signals of these vRNAs are predicted to result in virions lacking specific vRNPs. However, whether these vRNPs are then replaced by vRNP-like host RNAs is an open question. Here, we report that mutations in two packaging signals of influenza A/SC35M virus, which cause the near-complete loss of four vRNAs from the total virion population, result in several distinct virion subpopulations with unusual vRNP content. Half of the virions analyzed are empty or contain incomplete genome complexes with one to four vRNPs. Unexpectedly, most other virions contain atypical (7 + 1) complexes consisting of multiple copies of the four efficiently packaged vRNAs, but no host RNAs. The reported set of misassembled genome complexes suggests that packaging signals coordinate a modular genome assembly process. 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. [ABSTRACT FROM AUTHOR]

AreTomo, an abbreviation for Alignment and Reconstruction for Electron Tomography, is a GPU accelerated software package that fully automates motion-corrected marker-free tomographic alignment and reconstruction in a single package. By correcting in-plane rotation, translation, and importantly, the local motion resulting from beam-induced motion from tilt to tilt, AreTomo can produce tomograms with sufficient accuracy to be directly used for subtomogram averaging. Another major application is the on-the-fly reconstruction of tomograms in parallel with tilt series collection to provide users with real-time feedback of sample quality allowing users to make any necessary adjustments of collection parameters. Here, the multiple alignment algorithms implemented in AreTomo are described and the local motions measured on a typical tilt series are analyzed. The residual local motion after correction for global motion was found in the range of ± 80 Å, indicating that the accurate correction of local motion is critical for high-resolution cryo-electron tomography (cryoET).

The neuroprotective effects of umbelliferone (UMB) were visualized in three-dimensional (3D) images on vesicle density changes of organotypic hippocampal slice tissues (OHSCs) induced by scopolamine by high voltage electron microscopy. Observations revealed that the number of vesicles decreased in OHSCs induced by scopolamine, and UMB was found to inhibit scopolamine-induced reduction in vesicles, resulting in an increase in vesicle count. These 3D models provide valuable insight for understanding the increase of synapse vesicles in hippocampal tissues treated with UMB. [ABSTRACT FROM AUTHOR]

Phase-separation is commonly observed in multimetallic nanomaterials, yet it is not well understood how immiscible elements distribute in a thermodynamically stable nanoparticle. Herein, we studied the phase-separation of Au and Rh in nanoparticles using electron microscopy and tomography techniques. The nanoparticles were thermally annealed to form thermodynamically stable structures. HAADF-STEM and EDS characterizations reveal that Au and Rh segregate into two domains while their miscibility is increased. Using aberration-corrected HAADF-STEM and atomic electron tomography, we show that the increased solubility of Au in Rh is achieved by forming Au clusters and single atoms inside the Rh domains and on the Rh surface. Furthermore, based on the three-dimensional reconstruction of a AuRh nanoparticle, we can visualize the uneven interface that is embedded in the nanoparticle. The results advance our understanding on the nanoscale thermodynamic behavior of metal mixtures, which is crucial for the optimization of multimetallic nanostructures for many applications.

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. [Graphic: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Abstract 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.

ABSTRACTAutophagy is a major pathway for unspooling cytoplasmic constituents and recycling them. Here, we investigate autophagy in Neurospora crassa, a close ascomycete relative to the model yeast Saccharomyces cerevisiae. High-pressure-freeze and freeze-substitution techniques proved keys to preservation of the surprising autophagic structures observed in Neurospora by transmission electron microscopy and electron tomography. Depriving Neurospora of carbon triggers two parallel processes at the plasma membrane: formation of vacuoles, initially along the plasma membrane but stuffing 70%–80% of cytoplasmic volume after several hours. The vacuoles contain material left over from digested proteins, disrupted ribosomes or glycogen clumps, plus other discrete organelle-like objects. Also, they accumulate the canonical autophagy marker Atg8, appear to be lytic from the start, and probably grow from lysosomes. Formation of diverse phagophores and autophagosomes, multi-membrane organelles manufactured de novo by the plasma membrane—a feature so far unique to Neurospora. These autophagic structures can be observed attached either to the cell membrane, to the cell wall, or free in the cytoplasm, viz. as mature organelles after detachment from the cell membrane. Although phagophores are clearly observed in carbon-replete cells, their production increases with carbon starvation—and these, too, often appear lytic. ATG1, the canonical initiator of phagophore formation in yeast, is not required for the formation of phagophores in Neurospora. This work provides clear structural and functional evidence that Neurospora’s autophagic organelles differ from those observed by others in yeast.IMPORTANCENeurospora 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.

The development of new nanocomposites with added functionalities for Additive Manufacturing (AM) requires of a deep understanding of the 3D distribution of the selected nano-additives within the polymeric matrix, in order to optimize their performance. For this, electron tomography (ET) is an outstanding analysis technique that requires the material to withstand the electron exposure needed for the acquisition of several tens of images, becoming challenging for beam-sensitive materials. In this work, we analyse the parameters involved in the successful analysis by low dose ET of nanocomposites based in acrylic resins for stereolithography (SLA). Needle-shape electron-transparent specimens have been fabricated by focused ion beam (FIB), minimizing surface damage due to the high energy Ga+ ions. Microscope settings for tuning the electron dose applied during the ET analysis of these nanoneedles are discussed. A phenomenological study of the effect of increasing the electron dose in the scanning transmission electron microscopy (STEM) analysis of the material has been carried out, showing that ET can be effectively performed at low electron doses. Two case studies are presented, to illustrate the relevance of these analyses in the development of nanocomposites with added functionalities. Our results have revealed the crucial role of the dose rate and of inaccuracies in the calculation of critical electron doses for the design of ET experiments.

Myosin binding protein C (MyBP-C) is an accessory protein of the thick filament in vertebrate cardiac muscle arranged over 9 stripes of intervals of 430 Å in each half of the A-band in the region called the C-zone. Mutations in cardiac MyBP-C are a leading cause of hypertrophic cardiomyopathy the mechanism of which is unknown. It is a rod-shaped protein composed of 10 or 11 immunoglobulin- or fibronectin-like domains labelled C0 to C10 which binds to the thick filament via its C-terminal region. MyBP-C regulates contraction in a phosphorylation dependent fashion that may be through binding of its N-terminal domains with myosin or actin. Understanding the 3D organisation of MyBP-C in the sarcomere environment may provide new light on its function. We report here the fine structure of MyBP-C in relaxed rat cardiac muscle by cryo-electron tomography and subtomogram averaging of refrozen Tokuyasu cryosections. We find that on average MyBP-C connects via its distal end to actin across a disc perpendicular to the thick filament. The path of MyBP-C suggests that the central domains may interact with myosin heads. Surprisingly MyBP-C at Stripe 4 is different; it has weaker density than the other stripes which could result from a mainly axial or wavy path. Given that the same feature at Stripe 4 can also be found in several mammalian cardiac muscles and in some skeletal muscles, our finding may have broader implication and significance. In the D-zone, we show the first demonstration of myosin crowns arranged on a uniform 143 Å repeat. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Recent investigations analyzed in depth the biochemical and biophysical properties of the endothelial glycocalyx. In comparison, this complex cell-covering structure is largely understudied in alveolar epithelial cells. To better characterize the alveolar glycocalyx ultrastructure, unaffected versus injured human lung tissue explants and mouse lungs were analyzed by transmission electron microscopy. Lung tissue was treated with either heparinase (HEP), known to shed glycocalyx components, or pneumolysin (PLY), the exotoxin of Streptococcus pneumoniae not investigated for structural glycocalyx effects so far. Cationic colloidal thorium dioxide (cThO2) particles were used for glycocalyx glycosaminoglycan visualization. The level of cThO2 particles orthogonal to apical cell membranes (≙ stained glycosaminoglycan height) of alveolar epithelial type I (AEI) and type II (AEII) cells was stereologically measured. In addition, cThO2 particle density was studied by dual-axis electron tomography (≙ stained glycosaminoglycan density in three dimensions). For untreated samples, the average cThO2 particle level was ≈ 18 nm for human AEI, ≈ 17 nm for mouse AEI, ≈ 44 nm for human AEII and ≈ 35 nm for mouse AEII. Both treatments, HEP and PLY, resulted in a significant reduction of cThO2 particle levels on human and mouse AEI and AEII. Moreover, a HEP- and PLY-associated reduction in cThO2 particle density was observed. The present study provides quantitative data on the differential glycocalyx distribution on AEI and AEII based on cThO2 and demonstrates alveolar glycocalyx shedding in response to HEP or PLY resulting in a structural reduction in both glycosaminoglycan height and density. Future studies should elucidate the underlying alveolar epithelial cell type-specific distribution of glycocalyx subcomponents for better functional understanding. [ABSTRACT FROM AUTHOR]

The morphological changes of phosphonate polypeptoid electrolyte membranes, poly-N-(2-ethyl)hexylglycine-block-poly-N-phosphonomethylglycine (pNehm-b-pNpmn), in hydrated and dry states were characterized by cryogenic transmission electron microscopy (cryo-TEM) and cryogenic electron tomography (cryo-ET). The analysis of 3D tomograms revealed that the pNeh9-b-pNpm9 thin films absorbed a large amount of water, resulting in the formation of membranes that were nearly flat and giant multicompartment vesicles dispersed in the water phase. A simple lamellar phase appeared when the films were dried. In contrast, pNeh18-b-pNpm18 thin films absorbed little water and formed small highly curved unilamellar and multilamellar vesicles. Water was located mainly outside the closely-packed vesicles. When water was removed by drying, the walls of adjacent vesicles collapsed to form honeycomb-like capsules. The changes in domain size reflected changes in chain conformations. The pNpm9 blocks were saturated by water and fully extended, while pNpm18 blocks were neither saturated by water nor fully extended. In addition, the thicknesses of hydrophobic blocks in the hydrated films of both pNeh9-b-pNpm9 and pNeh18-b-pNpm18 were smaller than those in the dry films, reflecting an increase of the average distance between the neighboring junctions of polypeptoid molecules.

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.

Complex 3D architectures of nanoscale building blocks can be created by self‐assembly, but characterization of the atomic to mesoscale structure of such materials is limited by the difficulty of visualizing atoms across multiple length scales. Here, scanning transmission electron microscopy (STEM) and full‐tilt tomographic reconstruction are used to image a single‐crystalline region of a 3D epitaxially‐fused PbSe quantum dot (QD) superlattice containing 633 QDs at a spatial resolution of 2.16 Å. The combined real‐space and reciprocal‐space analysis enables 3D mesoscale correlations of atomic lattice and superlattice order across hundreds of nanocrystals in 3D for the first time. Inhomogeneity in QD positional and orientational order reveals that the QD surface layers template the superlattice and that orientational entropy is higher in the interior layers than the surface layers. The measurement and analysis techniques presented here are applicable to a broad range of 3D nanostructured materials. [ABSTRACT FROM AUTHOR]

Nanoscale gadolinium oxide (Gd2O3) is a promising nanomaterial with unique physicochemical properties that finds various applications ranging from biomedicine to catalysis. The preparation of highly porous Gd2O3 nanofoam greatly increases its surface area thereby boosting its potential for functional use in applications such as water purification processes and in catalytic applications. By using the combustion synthesis method, a strong exothermic redox reaction between gadolinium nitrate hexahydrate and glycine causes the formation of crystalline nanoporous Gd2O3. In this study, the synthesis of Gd2O3 nanofoam is achieved with combustion synthesis at large scale (grams). Its nanoscale porosity is investigated by nitrogen physisorption and its nanoscale 3D structure by electron tomography, and the formation process is investigated as well by means of in situ heating inside the transmission electron microscope. The bulk nanofoam product is highly crystalline and porous with a surface area of 67 m2 g−1 as measured by physisorption, in good agreement with the electron tomographic 3D reconstructions showing an intricate interconnected pore network with pore sizes varying from 2 to 3 nm to tens of nanometers. In situ heating experiments point to many possibilities for tuning the porosity of the Gd2O3 nanofoam by varying the experimental synthesis conditions. [ABSTRACT FROM AUTHOR]

Commonly used methods to assess crystallinity, micro-/mesoporosity, Brønsted acid site density and distribution (in micro- vs. mesopores), and catalytic activity suggest nearly invariant structure and function for aluminosilicate zeolite MFI two-dimensional nanosheets before and after superheated steam treatment. Yet, pronounced reaction rate decrease for benzyl alcohol alkylation with mesitylene, a reaction that cannot take place in the zeolite micropores, is observed. Transmission electron microscopy images reveal pronounced changes in nanosheet thickness, aspect ratio and roughness indicating that nanosheet coarsening and the associated changes in the external (mesoporous) surface structure are responsible for the changes in the external surface catalytic activity. Superheated steam treatment of hierarchical zeolites can be used to alter nanosheet morphology and regulate external surface catalytic activity while preserving micro- and mesoporosity, and micropore reaction rates.

Immune progenitor cells differentiate in bone marrow (BM) and then migrate to tissues. HIV-1 infects multiple BM cell types, but virus dissemination within BM has been poorly understood. We used light microscopy and electron tomography to elucidate mechanisms of HIV-1 dissemination within BM of HIV-1-infected BM/liver/thymus (BLT) mice. Tissue clearing combined with confocal and light sheet fluorescence microscopy revealed distinct populations of HIV-1 p24-producing cells in BM early after infection, and quantification of these populations identified macrophages as the principal subset of virus-producing cells in BM over time. Electron tomography demonstrated three modes of HIV-1 dissemination in BM: (i) semi-synchronous budding from T-cell and macrophage membranes, (ii) mature virus association with virus-producing T-cell uropods contacting putative target cells, and (iii) macrophages engulfing HIV-1-producing T-cells and producing virus within enclosed intracellular compartments that fused to invaginations with access to the extracellular space. These results illustrate mechanisms by which the specialized environment of the BM can promote virus spread locally and to distant lymphoid tissues.

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.

Using a nanostructured platform (a controlled‐shape nano‐oxide) and conventional wet impregnation techniques, powder‐type materials have been prepared in which atomically thin surface layers are deposited under very mild conditions. More importantly, an advanced methodology, combining energy dispersive X‐ray spectroscopy‐scanning transmission electron tomography (STEM‐EDX ET) and deep learning denoising techniques, has been developed for the 3D compositional characterization of these unique nanosystems. The complex case of LaOx‐coated CeO2 nanocubes is illustrated. For these, aberration corrected 2D STEM‐EDX evidence that ceria nanocubes become covered with a 2–4 atom‐thick layer of a La, Ce‐mixed oxide with spatially varying composition. However, STEM‐EDX ET reveals that this layer distributes unevenly, patching most of the available nanocube surface. The large flexibility and spread availability of the involved synthetic techniques enables, using the tools here developed, a wide exploration of the wealth of questions and applications of these intriguing, atomically thin, surface oxide phases. [ABSTRACT FROM AUTHOR]

Herein, a multistep synthesis method was implemented to prepare nanoscale core@shell spherical heterostructures for H2 optical detection. The resulting nanoheterostructures are built with gold cores and silica shells further coated by a thin layer of spherical palladium nanoparticles. Samples with various thicknesses of silica and densities of palladium nanoparticles were synthesized and characterized by transmission electron microscopy. In particular, the three-dimensional core@shell configuration was confirmed by electron tomography. The optical properties of the obtained nanostructures were first analyzed by optical absorbance measurements, and their potential use for H2 detection was evaluated by simulations based on the discrete dipole approximation method. Thus, the optical response of the studied nanostructures is investigated theoretically when the Pd layer is hydrogenated, showing the great sensitivity achievable with these nanostructures. [ABSTRACT FROM AUTHOR]

A 4-dimensional modality of a scanning transmission electron microscope (4D-STEM) acquires diffraction images formed by a coherent and focused electron beam scanning the specimen. Newly developed ultrafast detectors offer a possibility to acquire high throughput diffraction patterns at each pixel of the scan, enabling rapid tilt series acquisition for 4D-STEM tomography. Here we present a solution to the problem of synchronizing the electron probe scan with the diffraction image acquisition, and demonstrate on a fast hybrid-pixel detector camera (ARINA, DECTRIS). Image-guided tracking and autofocus corrections are handled by the freely-available microscope-control software SerialEM, in conjunction with a high angle annular dark field (HAADF) image acquired simultaneously. The open source SavvyScan system offers a versatile set of scanning patterns, operated by commercially available multi-channel acquisition and signal generator computer cards (Spectrum Instrumentation GmbH). Images are recorded only within a sub-region of the total field, so as to avoid spurious data collection during flyback and/or acceleration periods in the scan. Hence, the trigger of the fast camera follows selected pulses from the scan generator clock gated according to the chosen scan pattern. Software and protocol are provided for gating the trigger pulses via a microcontroller (ST Microelectronics ARM Cortex). We demonstrate the system on a standard replica grating and by diffraction imaging of a ferritin specimen.

Abstract Nanoscale gadolinium oxide (Gd2O3) is a promising nanomaterial with unique physicochemical properties that finds various applications ranging from biomedicine to catalysis. The preparation of highly porous Gd2O3 nanofoam greatly increases its surface area thereby boosting its potential for functional use in applications such as water purification processes and in catalytic applications. By using the combustion synthesis method, a strong exothermic redox reaction between gadolinium nitrate hexahydrate and glycine causes the formation of crystalline nanoporous Gd2O3. In this study, the synthesis of Gd2O3 nanofoam is achieved with combustion synthesis at large scale (grams). Its nanoscale porosity is investigated by nitrogen physisorption and its nanoscale 3D structure by electron tomography, and the formation process is investigated as well by means of in situ heating inside the transmission electron microscope. The bulk nanofoam product is highly crystalline and porous with a surface area of 67 m2 g−1 as measured by physisorption, in good agreement with the electron tomographic 3D reconstructions showing an intricate interconnected pore network with pore sizes varying from 2 to 3 nm to tens of nanometers. In situ heating experiments point to many possibilities for tuning the porosity of the Gd2O3 nanofoam by varying the experimental synthesis conditions.

The catalytic activity of low-dimensional electrocatalysts is highly dependent on their local atomic structures, particularly those less-coordinated sites found at edges and corners; therefore, a direct probe of the electrocatalytic current at specified local sites with true nanoscopic resolution has become critically important. Despite the growing availability of operando imaging tools, to date it has not been possible to measure the electrocatalytic activities from individual material edges and directly correlate those with the local structural defects. Herein, we show the possibility of using feedback and generation/collection modes of operation of the scanning electrochemical microscope (SECM) to independently image the topography and local electrocatalytic activity with 15-nm spatial resolution. We employed this operando microscopy technique to map out the oxygen evolution activity of a semi-2D nickel oxide nanosheet. The improved resolution and sensitivity enables us to distinguish the higher activities of the materials' edges from that of the fully coordinated surfaces in operando The combination of spatially resolved electrochemical information with state-of-the-art electron tomography, that unravels the 3D complexity of the edges, and ab initio calculations allows us to reveal the intricate coordination dependent activity along individual edges of the semi-2D material that is not achievable by other methods. The comparison of the simulated line scans to the experimental data suggests that the catalytic current density at the nanosheet edge is ∼200 times higher than that at the NiO basal plane.

Outer Hair Cells (OHCs) in the mammalian cochlea display a unique type of voltage-induced mechanical movement termed electromotility, which amplifies auditory signals and contributes to the sensitivity and frequency selectivity of mammalian hearing. Electromotility occurs in the OHC lateral wall, but it is not fully understood how the supramolecular architecture of the lateral wall enables this unique form of cellular motility. Employing electron tomography of high-pressure frozen and freeze-substituted OHCs, we visualized the 3D structure and organization of the membrane and cytoskeletal components of the OHC lateral wall. The subsurface cisterna (SSC) is a highly prominent feature, and we report that the SSC membranes and lumen possess hexagonally ordered arrays of particles. We also find the SSC is tightly connected to adjacent actin filaments by short filamentous protein connections. Pillar proteins that join the plasma membrane to the cytoskeleton appear as variable structures considerably thinner than actin filaments and significantly more flexible than actin-SSC links. The structurally rich organization and rigidity of the SSC coupled with apparently weaker mechanical connections between the plasma membrane (PM) and cytoskeleton reveal that the membrane-cytoskeletal architecture of the OHC lateral wall is more complex than previously appreciated. These observations are important for our understanding of OHC mechanics and need to be considered in computational models of OHC electromotility that incorporate subcellular features.

Using a nanostructured platform (a controlled‐shape nano‐oxide) and conventional wet impregnation techniques, powder‐type materials have been prepared in which atomically thin surface layers are deposited under very mild conditions. More importantly, an advanced methodology, combining energy dispersive X‐ray spectroscopy‐scanning transmission electron tomography (STEM‐EDX ET) and deep learning denoising techniques, has been developed for the 3D compositional characterization of these unique nanosystems. The complex case of LaOx‐coated CeO2 nanocubes is illustrated. For these, aberration corrected 2D STEM‐EDX evidence that ceria nanocubes become covered with a 2–4 atom‐thick layer of a La, Ce‐mixed oxide with spatially varying composition. However, STEM‐EDX ET reveals that this layer distributes unevenly, patching most of the available nanocube surface. The large flexibility and spread availability of the involved synthetic techniques enables, using the tools here developed, a wide exploration of the wealth of questions and applications of these intriguing, atomically thin, surface oxide phases.

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]