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The amyotrophic lateral sclerosis (ALS) neurodegenerative disorder has been associated with multiple genetic lesions, including mutations in the gene for fused in sarcoma (FUS), a nuclear-localized RNA/DNA-binding protein. Neuronal expression of the pathological form of FUS proteins in Caenorhabditis elegans results in mislocalization and aggregation of FUS in the cytoplasm, and leads to impairment of motility. However, the mechanisms by which the mutant FUS disrupts neuronal health and function remain unclear. Here we investigated the impact of ALS-associated FUS on motor neuron health using correlative light and electron microscopy, electron tomography, and electrophysiology. We show that ectopic expression of wild-type or ALS-associated human FUS impairs synaptic vesicle docking at neuromuscular junctions. ALS-associated FUS led to the emergence of a population of large, electron-dense, and filament-filled endosomes. Electrophysiological recording revealed reduced transmission from motor neurons to muscles. Together, these results suggest a pathological effect of ALS-causing FUS at synaptic structure and function organization. This article has an associated First Person interview with the first author of the paper.

The prolamellar body (PLB) is a periodic bicontinuous membrane structure based on tubular tetrahedral units. PLBs are present in plant etioplasts and, upon illumination, directly transform into the lamellar thylakoid networks within chloroplasts. Efficient tubular-lamellar rearrangement and later formation of the photosynthetically active thylakoid membranes are crucial steps in the development of plant autotrophy. PLB membranes are mainly composed of galactolipids, carotenoids, and protochlorophyllide (Pchlide), the chlorophyll precursor, bound in a complex with NADPH and Pchlide oxidoreductase. Although the PLB structure has been studied for over 50 years, the direct role of particular membrane components in the formation of the PLB paracrystalline network remains elusive. Moreover, despite the numerous literature data regarding the PLB geometry, their reliable comparative analysis is complicated due to variable experimental conditions. Therefore, we performed comprehensive ultrastructural and low-temperature fluorescence analysis of wild type Arabidopsis thaliana (Arabidopsis) seedlings grown in different conditions typical for studies on etiolated seedlings. We established that the addition of sucrose to the growing media significantly affected the size and compactness of the PLB. The etiolation period was also an important factor influencing the PLB structural parameters and the ratio of free to complex-bound Pchlide. Thus, a reliable PLB structural and spectral analysis requires particular attention to the applied experimental conditions. We investigated the influence of the pigment and polyprenol components of the etioplast membranes on the formation of the PLB spatial structure. The PLB 3D structure in several Arabidopsis mutants (ccr1-1, lut5-1, szl1-1npq1-2, aba1-6, pif1, cpt7) with disturbed levels of particular pigments and polyprenols using electron tomography technique was studied. We found that the PLB nano-morphology was mainly affected in the pif1 and aba1-6 mutants. An increased level of Pchlide (pif1) resulted in the substantial shift of the structural balance between outer and inner PLB water channels and overall PLB compactness compared to wild type plants. The decrease in the relative content of β-branch xanthophylls in aba1-6 plants was manifested by local disturbances in the paracrystalline structure of the PLB network. Therefore, proper levels of particular etioplast pigments are essential for the formation of stable and regular PLB structure.

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.

Mechanosensory organelles (MOs) are specialized subcellular entities where force-sensitive channels and supporting structures (e.g., microtubule cytoskeleton) are organized in an orderly manner. The delicate structure of MOs needs to be resolved to understand the mechanisms by which they detect forces and how they are formed. Here, we describe a protocol that allows obtaining detailed information about the nanoscopic ultrastructure of fly MOs by using serial section electron tomography (SS-ET). To preserve fine structural details, the tissues are cryo-immobilized using a high-pressure freezer followed by freeze-substitution at low temperature and embedding in resin at room temperature. Then, sample sections are prepared and used to acquire the dual-axis tilt series images, which are further processed for tomographic reconstruction. Finally, tomograms of consecutive sections are combined into a single larger volume using microtubules as fiducial markers. Using this protocol, we managed to reconstruct the sensory organelles, which provide novel molecular insights as to how fly mechanosensory organelles work and are formed. Based on our experience, we think that, with minimal modifications, this protocol can be adapted to a wide range of applications using different cell and tissue samples. Key features • Resolving the high-resolution 3D ultrastructure of subcellular organelles using serial section electron tomography (SS-ET). • Compared with single-axis tilt series, dual-axis tilt series provides a much wider coverage of Fourier space, improving resolution and features in the reconstructed tomograms. • The use of high-pressure freezing and freeze-substitution maximally preserves the fine structural details., Competing Interests: Competing interestsThe authors declare that they have no competing interests., (©Copyright : © 2024 The Authors; This is an open access article under the CC BY-NC license.)

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/Ge 0.8 Si 0.2 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) nm 2 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/Ge 0.8 Si 0.2 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.

Malaria remains a major global threat, representing a severe public health problem worldwide. Annually, it is responsible for a high rate of morbidity and mortality in many tropical developing countries where the disease is endemic. The causative agent of malaria, Plasmodium spp., exhibits a complex life cycle, alternating between an invertebrate vector, which transmits the disease, and the vertebrate host. The disease pathology observed in the vertebrate host is attributed to the asexual development of Plasmodium spp. inside the erythrocyte. Once inside the red blood cell, malaria parasites cause extensive changes in the host cell, increasing membrane rigidity and altering its normal discoid shape. Additionally, during their intraerythrocytic development, malaria parasites incorporate and degrade up to 70 % of host cell hemoglobin. This mechanism is essential for parasite development and represents an important drug target. Blocking the steps related to hemoglobin endocytosis or degradation impairs parasite development and can lead to its death. The ultrastructural analysis of hemoglobin endocytosis on Plasmodium spp. has been broadly explored along the years. However, it is only recently that the proteins involved in this process have started to emerge. Here, we will review the most important features related to hemoglobin endocytosis and catabolism on malaria parasites. A special focus will be given to the recent analysis obtained through 3D visualization approaches and to the molecules involved in these mechanisms., (Copyright © 2024. Published by Elsevier Inc.)

Vacuoles in plant cells are the most prominent organelles that harbor distinctive features, including lytic function, storage of proteins and sugars, balance of cell volume, and defense responses. Despite their dominant size and functional versatility, the nature and biogenesis of vacuoles in plants per se remain elusive and several models have been proposed. Recently, we used the whole-cell 3D electron tomography (ET) technique to study vacuole formation and distribution at nanometer resolution and demonstrated that small vacuoles are derived from multivesicular body maturation and fusion. Good sample preparation is a critical step to get high-quality electron tomography images. In this chapter, we provide detailed sample preparation methods for high-resolution ET in Arabidopsis thaliana root cells, including high-pressure freezing, subsequent freeze-substitution fixation, embedding, and serial sectioning., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

High-pressure freezing/freeze substitution has been used to preserve biological samples for ultrastructure study instead of chemical fixation. For most plant samples, the water content is too high and cannot be properly preserved during cryofixation. Additionally, the cell wall is a barrier that prevents the substitution of water with the resin. In this chapter, we will discuss modified high-pressure freezing and subsequent processing protocols based on our routinely used methodology for examining Arabidopsis seeds in transmission electron microscopy and electron tomography., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Cells are dynamic machines that continuously change their architecture to adapt and respond to extracellular and intracellular stimuli. Deciphering dynamic processes with nanometer-scale resolution inside cells is critical for mechanistic understanding. Here, we present a protocol that enables the in situ study of dynamic changes in intracellular structures under close-to-native conditions at high spatiotemporal resolution. Importantly, the cells are grown, transported, and imaged in a chamber in which environmental conditions such as temperature and gas (e.g., carbon dioxide or oxygen) concentration can be controlled. We demonstrate this protocol to quantify ultrastructural changes that occur during the cell cycle of cultured mammalian cells. The environment control system opens up the possibility of applying this method to primary cells, tissues, and organoids by adjusting environmental conditions., (Copyright © 2024 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.)

Metamaterials, subwavelength nanostructured materials, can exhibit novel optical properties such as a negative index of refraction. Dielectric core–nanoparticle satellite clusters, termed "metamolecules," can have strong optical magnetic resonances in the visible wavelength range—a requirement to achieve negative refractive index materials. However, achieving the desired photonic properties is challenging due to limited control in forming the metamolecule structures. Here, polystyrene (PS) core–gold nanoparticle (AuNP) satellite metamolecules with highly ordered single layers (monolayers) of AuNPs are fabricated and single particle spectroscopy, electron tomography structural measurements, and electrodynamics simulations are conducted to study the photonic properties of metamolecules constituted of ≈100 AuNPs. The simulated and experimental spectra of the many metamolecules studied, including excitation with azimuthally and radially polarized light, are in excellent agreement. It is shown that the scattering properties of the metamolecules are dominated by the AuNPs near the "equator" of the cluster, and that backscattering is strongly suppressed when different multipolar modes (e.g., dipolar and quadrupolar) of electric or optical magnetic character have comparable intensity due to the π‐phase shift of their scattering. Both the optical excitation fields and the ordering of the nanoparticles within metamolecules affect their optical excitation and scattering properties, providing new insights into designing novel photonic metamaterials. [ABSTRACT FROM AUTHOR]

The 3D determination of a nanomaterial's atomic structure is crucial for understanding their physical, chemical, and electronic properties. Electron tomography, as an important 3D imaging method, offers a powerful method to probe the 3D structure of materials from nanoscale to atomic scale. However, the grand challenge—the missing‐wedge‐induced information loss and artifacts—has greatly hindered them from obtaining 3D atomic structures with high contrast, high precision, and high fidelity. Herein, for the first time, by combining atomic electron tomography with an artificially intelligent "deepfake" neural network, this work demonstrates that the resolution of 3D imaging can be improved down to 0.71 Å, which is a record high resolution achieved by electron tomography. It is also shown that the lost information in reconstructed tomograms can be effectively recovered by only acquiring data from −50 to +50 ° (44% reduction of dosage compared with −90 to +90 ° full tilt series). In contrast to conventional methods, the deep‐learning model shows outstanding performance for both macroscopic objects and atomic features solving the long‐standing dosage and missing‐wedge problems in electron tomography. This work provides important guidance for the application of machine learning methods to tomographic imaging atomic‐scale features in nanomaterials. [ABSTRACT FROM AUTHOR]

Production of corrugated particles generally introduces several morphological heterogeneities, such as surface roughness and local variations in the corrugation pattern, which are known from model system studies to significantly alter the colloidal interaction energy. Thus, realistic particle morphologies need to be investigated and compared to simple model shapes to yield insights into how interactions are influenced by such morphological heterogeneities. We applied the surface element integration method to study the colloidal interactions of electron tomography-based, realistic, corrugated colloidal particles and their symmetric, concave polyhedral analogs by differentiating local surface features to vertices, ridges and ridge networks. We applied molecular modelling to assess the surface access of these features. Significant mixing of the interaction energy was found between the different surface features. Larger and smaller energy barrier heights and secondary minimum depths were observed compared to the concave polyhedral models with similar volume or surface area depending on the contacting surface feature. Analysis of surface area distributions suggests that the deviations originate from the altered effective contact distance as a result of surface roughness and other morphological heterogeneities. We also found that the surface access of nanoparticles is greatly impaired at the crevices between the surface corrugations. [ABSTRACT FROM AUTHOR]

Septins are a family of GTP-binding, membrane-interacting cytoskeletal proteins, highly conserved and essential in all eukaryotes (with the exception of plants). Septins play important roles in a number of cellular events that involve membrane remodeling and compartmentalization. One such event is cytokinesis, the last stage of cell division. While cytokinesis is ultimately achieved via the mechanical contraction of an actomyosin ring at the septum, determination of the location where cytokinesis will take place, and recruitment of factors involved in signaling events leading to septation requires the activity of septins. We are working towards dissecting the properties of septins from the budding yeast Saccharomyces cerevisiae, where they were first discovered as cell cycle mutants. In our studies we have employed several complementary electron microscopy techniques to describe the organization and structure of septins both in vitro and in situ.

C4 plants enhance photosynthesis efficiency by concentrating CO2 to the site of Rubisco action. Chloroplasts in C4 plants exhibit structural dimorphism because thylakoid architectures vary depending on energy requirements. Advances in electron microscopy imaging capacity and sample preparation technologies allowed characterization of thylakoid structures and their macromolecular arrangements with unprecedented precision mostly in C3 plants. The thylakoid is assembled during chloroplast biogenesis through collaboration between the plastid and nuclear genomes. Recently, the membrane dynamics involved in the assembly process has been investigated with 3D electron microscopy, and molecular factors required for thylakoid construction have been characterized. The two classes of chloroplasts in C4 plants arise from common precursors, but little is known about how a single type of chloroplasts grow, divide, and differentiate to mature into distinct chloroplasts. Here, we outline the thylakoid structure and its assembly processes in C3 plants to discuss ultrastructural analyses of dimorphic chloroplast biogenesis in C4 plant species. Future directions for electron microscopy research of C4 photosynthetic systems are also proposed.

Fusion of HIV-1 with the membrane of its target cell, an obligate first step in virus infectivity, is mediated by binding of the viral envelope (Env) spike protein to its receptors, CD4 and CCR5/CXCR4, on the cell surface. The process of viral fusion appears to be fast compared with viral egress and has not been visualized by EM. To capture fusion events, the process must be curtailed by trapping Env-receptor binding at an intermediate stage. We have used fusion inhibitors to trap HIV-1 virions attached to target cells by Envs in an extended pre-hairpin intermediate state. Electron tomography revealed HIV-1 virions bound to TZM-bl cells by 2–4 narrow spokes, with slightly more spokes present when evaluated with mutant virions that lacked the Env cytoplasmic tail. These results represent the first direct visualization of the hypothesized pre-hairpin intermediate of HIV-1 Env and improve our understanding of Env-mediated HIV-1 fusion and infection of host cells.

Resolution (global and local) is one of the most reported metrics of quality measurement in Single Particle Analysis (SPA). However, in electron tomography, the situation is different and its computation is not straightforward. Typically, resolution estimation is global and, therefore, reduces the assessment of a whole tomogram to a single number. However, it is known that tomogram quality is spatially variant. Still, up to our knowledge, a method to estimate local quality metrics in tomography is lacking. This work introduces MonoTomo, a method developed to estimate locally in a tomogram the highest reliable frequency component, expressed as a form of local resolution. The fundamentals lie in a local analysis of the density map via monogenic signals, which, in analogy to MonoRes, allows for local estimations. Results with experimental data show that the local resolution range that MonoTomo casts agrees with reported resolution values for experimental data sets, with the advantage of providing a local estimation. A range of applications of MonoTomo are suggested for further exploration.

Electron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images. This approach was marker-free, based on patch tracking and integrated in free software. Here, we present improvements to the method to make it more reliable, stable and accurate. In addition, we modified the image formation model underlying the alignment procedure to include different deformations occurring during acquisition. We propose a new way to correct these computed deformations to obtain reconstructions with reduced artifacts. The new approach has demonstrated to improve the quality of the final 3D reconstruction, giving access to better defined structures for different transmission electron tomography methods: resin embedded STEM-tomography and cryo-TEM tomography. The method is freely available in TomoJ software.

Abstract Background The insect-trapping leaves of Dionaea muscipula provide a model for studying the secretory pathway of an inducible plant secretory system. The leaf glands were induced with bovine serum albumin to secrete proteases that were characterized via zymogram activity gels over a 6-day period. The accompanying morphological changes of the endoplasmic reticulum (ER) and Golgi were analyzed using 3D electron tomography of glands preserved by high-pressure freezing/freeze substitution methods. Results Secretion of multiple cysteine and aspartic proteases occurred biphasically. The majority of the Golgi was organized in clusters consisting of 3–6 stacks surrounded by a cage-like system of ER cisternae. In these clusters, all Golgi stacks were oriented with their cis-most C1 cisterna facing an ER export site. The C1 Golgi cisternae varied in size and shape consistent with the hypothesis that they form de novo. Following induction, the number of ER-bound polysomes doubled, but no increase in COPII vesicles was observed. Golgi changes included a reduction in the number of cisternae per stack and a doubling of cisternal volume without increased surface area. Polysaccharide molecules that form the sticky slime cause swelling of the trans and trans Golgi network (TGN) cisternae. Peeling of the trans-most cisternae gives rise to free TGN cisternae. One day after gland stimulation, the free TGNs were frequently associated with loose groups of oriented actin-like filaments which were not seen in any other samples. Conclusions These findings suggest that the secretory apparatus of resting gland cells is “overbuilt” to enable the cells to rapidly up-regulate lytic enzyme production and secretion in response to prey trapping.

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.

Abstract Background The recent Zika virus (ZIKV) outbreak has linked ZIKV with microcephaly and other central nervous system pathologies in humans. Astrocytes are among the first cells to respond to ZIKV infection in the brain and are also targets for virus infection. In this study, we investigated the interaction between ZIKV and primary human brain cortical astrocytes (HBCA). Results HBCAs were highly sensitive to representatives of both Asian and African ZIKV lineages and produced high viral yields. The infection was associated with limited immune cytokine/chemokine response activation; the highest increase of expression, following infection, was seen in CXCL-10 (IP-10), interleukin-6, 8, 12, and CCL5 (RANTES). Ultrastructural changes in the ZIKV-infected HBCA were characterized by electron tomography (ET). ET reconstructions elucidated high-resolution 3D images of the proliferating and extensively rearranged endoplasmic reticulum (ER) containing viral particles and virus-induced vesicles, tightly juxtaposed to collapsed ER cisternae. Conclusions The results confirm that human astrocytes are sensitive to ZIKV infection and could be a source of proinflammatory cytokines in the ZIKV-infected brain tissue.

Molecular structure determination is important for understanding functionalities and dynamics of macromolecules, such as proteins and nucleic acids. Cryo-electron tomography (ET) is a technique that can be used to determine the structures of individual macromolecules, thus providing the snapshots of their native conformations. Such 3-D reconstructions encounter several types of imperfections due to missing, corrupted, and low-contrast data. In this paper, we demonstrate that extending the reconstruction space, which increases the dimensionality of the linear system being solved during reconstruction, facilitates the separation of signal and noise. A considerable amount of the noise associated with collected projection data arises independently from the geometric constraint of image formation, whereas the solution to the reconstruction problem must satisfy such geometric constraints. Increasing the dimensionality thereby allows for a redistribution of such noise within the extended reconstruction space, while the geometrically constrained approximate solution stays in an effectively lower dimensional subspace. Employing various tomographic reconstruction methods with a regularization capability we performed extensive simulation and testing and observed that enhanced dimensionality significantly improves the accuracy of the reconstruction. Our results were validated with reconstructions of colloidal silica nanoparticles as well as P. falciparum erythrocyte membrane protein 1. Although the proposed method is used in the context of Cryo-ET, the method is general and can be extended to a variety of other tomographic modalities.

Abstract Background In order to improve the reliability of the electron tomography (ET) technique, which reveals three-dimensional information of nanostructured materials from a series of tilted two-dimensional images, it is essential that the mechanical tilt angle be accurately measured by the transmission electron microscopy (TEM) goniometer. Findings In this study, a calibration specimen was fabricated by nanohole patterning using a focused ion beam in order to determine mechanical tilt angles. The TEM goniometer tilt-angle accuracies were directly confirmed by measuring the changing areas of the projected nanosized hole. New calibration equations were developed and applied for the accurate determination of tilt angle. Conclusion We expect that the calibration specimen will effectively determine and correct the mechanical tilt angles in TEM goniometers leading to improvements in the ET technique.

The primary cilium has recently become the focus of intensive investigations into understanding the physical structure and processes of eukaryotic cells. This paper describes two tilt-series image datasets, acquired by transmission electron microscopy, of in situ chick-embryo sternal-cartilage primary cilia. These data have been released under an open-access licence, and are well suited to tomographic reconstruction and modelling of the cilium.

In this work, we propose an experimental approach allowing for the identification and the subsequent quantification of nanoparticles crystallographic facets, based on 3D data obtained using Transmission Electron Microscopy (TEM). The particle shape and faceting can be determined using Electron Tomography (ET) combined with High‐Resolution TEM (HR‐TEM). The quantitative analysis of faceting is carried out on the particles 3D models using a geometrical approach that automatically detects planar regions on particle boundaries. In order to check the reliability of our approach, we analyzed palladium particles confined inside or located at the outer surface of a mesoporous silica shell (Pd@SiO2) after an annealing treatment at 250 °C under hydrogen for 12 hours. From the materials perspective, the aim of the current work is to investigate the encapsulation effect of silica (SiO2) shells on the change in morphology and faceting of palladium nanoparticles during such annealing treatment. [ABSTRACT FROM AUTHOR]

Microscopic studies of chloroplasts can be traced back to the year 1678 when Antonie van Leeuwenhoek reported to the Royal Society in London that he saw green globules in grass leaf cells with his single-lens microscope. Since then, microscopic studies have continued to contribute critical insights into the complex architecture of chloroplast membranes and how their structure relates to function. This review is organized into three chronological sections: During the classic light microscope period (1678–1940), the development of improved microscopes led to the identification of green grana, a colorless stroma, and a membrane envelope. More recent (1990–2020) chloroplast dynamic studies have benefited from laser confocal and 3D-structured illumination microscopy. The development of the transmission electron microscope (1940–2000) and thin sectioning techniques demonstrated that grana consist of stacks of closely appressed grana thylakoids interconnected by non-appressed stroma thylakoids. When the stroma thylakoids were shown to spiral around the grana stacks as multiple right-handed helices, it was confirmed that the membranes of a chloroplast are all interconnected. Freeze-fracture and freeze-etch methods verified the helical nature of the stroma thylakoids, while also providing precise information on how the electron transport chain and ATP synthase complexes are non-randomly distributed between grana and stroma membrane regions. The last section (2000–2020) focuses on the most recent discoveries made possible by atomic force microscopy of hydrated membranes, and electron tomography and cryo-electron tomography of cryofixed thylakoids. These investigations have provided novel insights into thylakoid architecture and plastoglobules (summarized in a new thylakoid model), while also producing molecular-scale views of grana and stroma thylakoids in which individual functional complexes can be identified. [ABSTRACT FROM AUTHOR]

The rhythmic electrical activity of the heart's natural pacemaker, the sinoatrial node (SAN), determines cardiac beating rate (BR). SAN electrical activity is tightly controlled by multiple factors, including tissue stretch, which may contribute to adaptation of BR to changes in venous return. In most animals, including human, there is a robust increase in BR when the SAN is stretched. However, the chronotropic response to sustained stretch differs in mouse SAN, where it causes variable responses, including decreased BR. The reasons for this species difference are unclear. They are thought to relate to dissimilarities in SAN electrophysiology (particularly action potential morphology) between mouse and other species and to how these interact with subcellular stretch-activated mechanisms. Furthermore, species-related differences in structural and mechanical properties of the SAN may influence the chronotropic response to SAN stretch. Here we assess (i) how the BR response to sustained stretch of rabbit and mouse isolated SAN relates to tissue stiffness, (ii) whether structural differences could account for observed differences in BR responsiveness to stretch, and (iii) whether pharmacological modification of mouse SAN electrophysiology alters stretch-induced chronotropy. We found disparities in the relationship between SAN stiffness and the magnitude of the chronotropic response to stretch between rabbit and mouse along with differences in SAN collagen structure, alignment, and changes with stretch. We further observed that pharmacological modification to prolong mouse SAN action potential plateau duration rectified the direction of BR changes during sustained stretch, resulting in a positive chronotropic response akin to that of other species. Overall, our results suggest that structural, mechanical, and background electrophysiological properties of the SAN influence the chronotropic response to stretch. Improved insight into the biophysical determinants of stretch effects on SAN pacemaking is essential for a comprehensive understanding of SAN regulation with important implications for studies of SAN physiology and its dysfunction, such as in the aging and fibrotic heart. [ABSTRACT FROM AUTHOR]

C4 plants enhance photosynthesis efficiency by concentrating CO2 to the site of Rubisco action. Chloroplasts in C4 plants exhibit structural dimorphism because thylakoid architectures vary depending on energy requirements. Advances in electron microscopy imaging capacity and sample preparation technologies allowed characterization of thylakoid structures and their macromolecular arrangements with unprecedented precision mostly in C3 plants. The thylakoid is assembled during chloroplast biogenesis through collaboration between the plastid and nuclear genomes. Recently, the membrane dynamics involved in the assembly process has been investigated with 3D electron microscopy, and molecular factors required for thylakoid construction have been characterized. The two classes of chloroplasts in C4 plants arise from common precursors, but little is known about how a single type of chloroplasts grow, divide, and differentiate to mature into distinct chloroplasts. Here, we outline the thylakoid structure and its assembly processes in C3 plants to discuss ultrastructural analyses of dimorphic chloroplast biogenesis in C4 plant species. Future directions for electron microscopy research of C4 photosynthetic systems are also proposed. [ABSTRACT FROM AUTHOR]

Cellular membranes differ in their molecular organisation, shape, and dynamics. Knowing how these properties of membrane architecture relate to the presence and function of specific membrane components is fundamental for understanding membrane-associated cellular processes. Correlative light and electron microscopy (CLEM) is ideally poised to address such problems. Fluorescence microscopy allows identification of cellular membranes through labelled components and can provide temporal information, while electron microscopy allows visualisation of the structure of the same membranes at high resolution. In recent years, various CLEM protocols have been applied to gain insights into cellular membrane architecture. Here, we review conceptually novel approaches by which CLEM has provided insights on membrane reshaping, subcellular localisation of components, host–pathogen interactions, and has answered longstanding mechanistic questions. New CLEM approaches allow addressing diverse questions on cellular membrane architecture. CLEM can add temporal and compositional information to membrane shape and topology, and can facilitate identification of rare structures or events. The large diversity of CLEM protocols permits precisely tailoring the experimental set-up to specific biological questions. The conceptual advances enabled by CLEM emphasise the importance of architecture for membrane-associated cellular functions. [ABSTRACT FROM AUTHOR]

Electron tomography (ET) has been demonstrated to be a powerful tool in addressing challenging problems, such as understanding 3D interactions among various microstructures. Advancing ET to broader applications requires novel instrumentation design to break the bottlenecks both in theory and in practice. In this work, we built a compact four-degree-of-freedom (three-directional positionings plus self-rotation) nano-manipulator dedicated to ET applications, which is called X-Nano transmission electron microscope (TEM) holder. All the movements of the four degrees of freedom are precisely driven by built-in piezoelectric actuators, minimizing the artefacts due to vibration and drifting of the TEM stage. Full 360° rotation is realized with an accuracy of 0.05° in the whole range, which solves the missing wedge problem. Meanwhile, the specimen can move to the rotation axis with an integrated 3D nano-manipulator, greatly reducing the effort in tracking sample locations during tilting. Meanwhile, in-situ stimulation function can be seamlessly integrated into the X-Nano TEM holder so that dynamic information can be uncovered. We expect that more delicate researches, such as those about 3D microstructural evolution, can be carried out extensively by means of this holder in the near future. [ABSTRACT FROM AUTHOR]

Transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) enable the visualization of three-dimensional (3D) microstructures ranging from atomic to micrometer scales using 3D reconstruction techniques based on computed tomography algorithms. This 3D microscopy method is called electron tomography (ET) and has been utilized in the fields of materials science and engineering for more than two decades. Although atomic resolution is one of the current topics in ET research, the development and deployment of intermediate-resolution (non-atomic-resolution) ET imaging methods have garnered considerable attention from researchers. This research trend is probably not irrelevant due to the fact that the spatial resolution and functionality of 3D imaging methods of scanning electron microscopy (SEM) and X-ray microscopy have come to overlap with those of ET. In other words, there may be multiple ways to carry out 3D visualization using different microscopy methods for nanometer-scale objects in materials. From the above standpoint, this review paper aims to (i) describe the current status and issues of intermediate-resolution ET with regard to enhancing the effectiveness of TEM/STEM imaging and (ii) discuss promising applications of state-of-the-art intermediate-resolution ET for materials research with a particular focus on diffraction contrast ET for crystalline microstructures (superlattice domains and dislocations) including a demonstration of in situ dislocation tomography. [ABSTRACT FROM AUTHOR]

An antireflective coating presenting a continuous refractive index gradient is theoretically better than its discrete counterpart because it can give rise to a perfect broadband transparency. This kind of surface treatment can be obtained with nanostructures like moth-eye. Despite the light scattering behavior must be accounted as it can lead to a significant transmittance drop, no methods are actually available to anticipate scattering losses in such nanostructured antireflective coatings. To overcome this current limitation, we present here an original way to simulate the scattering losses in these systems and routes to optimize the transparency. This method, which was validated by a comparative study of coatings presenting refractive indices with either discrete or continuous gradient, shows that a discrete antireflective coating bilayer made by oblique angle deposition allows reaching ultra-high mean transmittance of 98.97% over the broadband [400–1800] nm. Such simple surface treatment outperforms moth-eye architectures thanks to both interference effect and small dimensions nanostructures that minimize the scattering losses as confirmed by finite-difference time domain simulations performed on reconstructed volumes obtained from electron tomography experiments. Image, graphical abstract [ABSTRACT FROM AUTHOR]

Summary: Electron tomography methods using the conventional transmission electron microscope have been widely used to investigate the three‐dimensional distribution patterns of various cellular structures including microtubules in neurites. Because the penetrating power of electrons depends on the section thickness and accelerating voltage, conventional TEM, having acceleration voltages up to 200 kV, is limited to sample thicknesses of 0.2 µm or less. In this paper, we show that the ultra‐high voltage electron microscope (UHVEM), employing acceleration voltages of higher than 1000 kV (1 MV), allowed distinct reconstruction of the three‐dimensional array of microtubules in a 0.7‐µm‐thick neurite section. The detailed structure of microtubules was more clearly reconstructed from a 0.7‐µm‐thick section at an accelerating voltage of 1 MV compared with a 1.0 µm section at 2 MV. Furthermore, the entire distribution of each microtubule in a neurite could be reconstructed from serial‐section UHVEM tomography. Application of optimised UHVEM tomography will provide new insights, bridging the gap between the structure and function of widely‐distributed cellular organelles such as microtubules for neurite outgrowth. Lay Description: An optimal 3D visualisation of microtubule cytoskeleton using ultra‐high voltage electron microscopy tomography The ultra‐high voltage electron microscope (UHVEM) is able to visualise a micrometre‐thick specimen at nanoscale spatial resolution because of the high‐energy electron beam penetrating such a specimen. In this study, we determined the optimal conditions necessary for microtubule cytoskeleton imaging within 0.7‐µm‐thick section using a combination with UHVEM and electron tomography method. Our approach provides excellent 3D information about the complex arrangement of the individual microtubule filaments that make up the microtubule network. [ABSTRACT FROM AUTHOR]

Cilia serve as cellular antennae that translate sensory information into physiological responses. In the sperm flagellum, a single chemoattractant molecule can trigger a Ca2+ rise that controls motility. The mechanisms underlying such ultra‐sensitivity are ill‐defined. Here, we determine by mass spectrometry the copy number of nineteen chemosensory signaling proteins in sperm flagella from the sea urchin Arbacia punctulata. Proteins are up to 1,000‐fold more abundant than the free cellular messengers cAMP, cGMP, H+, and Ca2+. Opto‐chemical techniques show that high protein concentrations kinetically compartmentalize the flagellum: Within milliseconds, cGMP is relayed from the receptor guanylate cyclase to a cGMP‐gated channel that serves as a perfect chemo‐electrical transducer. cGMP is rapidly hydrolyzed, possibly via "substrate channeling" from the channel to the phosphodiesterase PDE5. The channel/PDE5 tandem encodes cGMP turnover rates rather than concentrations. The rate‐detection mechanism allows continuous stimulus sampling over a wide dynamic range. The textbook notion of signal amplification—few enzyme molecules process many messenger molecules—does not hold for sperm flagella. Instead, high protein concentrations ascertain messenger detection. Similar mechanisms may occur in other small compartments like primary cilia or dendritic spines. Synopsis: Cellular sensory compartments serve highly specialised functions by means of a unique repertoire of signalling proteins. Here, quantitative protein profiling combined with structural analyses in sea urchin sperm flagella reveal reversed enzyme‐messenger ratios in chemosensory signalling, which ensure high‐sensitivity, low‐noise messenger detection. Absolute quantification of 11 chemosensory signaling proteins is applied to purified flagella of Arbacia punctulata.Determination of flagellar volume by cryo‐electron tomography allows for calculation of protein concentrations.Signaling proteins are orders of magnitude more abundant than free messengers.Opto‐chemical techniques show kinetic compartmentalisation of the flagellum at the cGMP‐gated channel/PDE5 tandem. [ABSTRACT FROM AUTHOR]

The last 20 years have seen incredible advances in electron microscopy (EM). Cryoelectron microscopy can now resolve protein structures to a previously unimaginable resolution but the advances in cellular EM are just as significant. I will take this opportunity to briefly summarize some of the new developments in cellular EM. [ABSTRACT FROM AUTHOR]

• Both UBTF isoforms are distributed and organized differently within nucleolar FC. • Results are included into a model of 3D organization of active transcribing r-gene. • Similar distribution of both isoforms is observed when rRNA synthesis is inhibited. • Roles for both variants are suggested in the organization of active/inactive r-genes. Upstream binding transcription factor (UBTF) is a co-regulator of RNA polymerase I by constituting an initiation complex on rRNA genes. UBTF plays a role in rDNA bending and its maintenance in "open" state. It exists as two splicing variants, UBTF1 and UBTF2, which cannot be discerned with antibodies raised against UBTF. We investigated the ultrastructural localization of each variant in cells synthesizing GFP-tagged UBTF1 or UBTF2 by using anti-GFP antibodies and pre-embedding nanogold strategy. Detailed 3D distribution of UBTF1 and 2 was also studied by electron tomography. In control cells, the two isoforms are very abundant within fibrillar centers, but their repartition strongly differs. Electron tomography shows that UBTF1 is disposed as fibrils that are folded in coils whereas UBTF2 is localized homogenously, preferentially at their cortical area. As UBTF is a useful marker to trace rDNA genes, we used these data to improve our previous model of 3D organization of active transcribing rDNA gene within fibrillar centers. Finally, when rRNA synthesis is inhibited during actinomycin D treatment or entry in mitosis, UBTF1 and UBTF2 show a similar distribution along extended 3D loop-like structures. Altogether these data suggest new roles for UBTF1 and UBTF2 isoforms in the organization of active and inactive rDNA genes. [ABSTRACT FROM AUTHOR]

Plant photosynthetic (thylakoid) membranes are organized into complex networks that are differentiated into 2 distinct morphological and functional domains called grana and stroma lamellae. How the 2 domains join to form a continuous lamellar system has been the subject of numerous studies since the mid-1950s. Using different electron tomography techniques, we found that the grana and stroma lamellae are connected by an array of pitch-balanced right- and left-handed helical membrane surfaces of different radii and pitch. Consistent with theoretical predictions, this arrangement is shown to minimize the surface and bending energies of the membranes. Related configurations were proposed to be present in the rough endoplasmic reticulum and in dense nuclear matter phases theorized to exist in neutron star crusts, where the right- and left-handed helical elements differ only in their handedness. Pitch-balanced helical elements of alternating handedness may thus constitute a fundamental geometry for the efficient packing of connected layers or sheets. [ABSTRACT FROM AUTHOR]

The spot auto-focusing (AF) method with a unique high-definition auto-correlation function (HD-ACF) proposed in the previous paper is improved and is now applicable to general specimens at a wide range of magnifications. According to the definition where the AF is defocused to obtain the highest resolution, the proposed method achieves the sharpest HD-ACF profile in the AF spot image. The relationship where the sharpest HD-ACF profile gives the highest resolution is theoretically explained, and practical AF examples for different specimens and magnifications are experimentally demonstrated. Specimens include a yeast cell thin section at 10-k magnification, a standard grating replica used as a ruler at 50-k, a crystal lattice of graphitized carbon at 400-k and a 60°-tilted thin section (yeast cell) at 10-k. Different procedures are prepared to actively identify the defocus position that gives the sharpest HD-ACF profile. Every AF result demonstrates the highest-resolution image. [ABSTRACT FROM AUTHOR]