Showing papers on "Electron tomography published in 2023"
TL;DR: In this article, an open-source suite of ultrastructural quantifications, integrated into a single pipeline called the surface morphometrics pipeline, is proposed to quantify changes in membrane ultrastructure on a single-cell level using cryo-electron tomography (cryo-ET).
Abstract: Cellular cryo-electron tomography (cryo-ET) enables three-dimensional reconstructions of organelles in their native cellular environment at subnanometer resolution. However, quantifying ultrastructural features of pleomorphic organelles in three dimensions is challenging, as is defining the significance of observed changes induced by specific cellular perturbations. To address this challenge, we established a semiautomated workflow to segment organellar membranes and reconstruct their underlying surface geometry in cryo-ET. To complement this workflow, we developed an open-source suite of ultrastructural quantifications, integrated into a single pipeline called the surface morphometrics pipeline. This pipeline enables rapid modeling of complex membrane structures and allows detailed mapping of inter- and intramembrane spacing, curvedness, and orientation onto reconstructed membrane meshes, highlighting subtle organellar features that are challenging to detect in three dimensions and allowing for statistical comparison across many organelles. To demonstrate the advantages of this approach, we combine cryo-ET with cryo-fluorescence microscopy to correlate bulk mitochondrial network morphology (i.e., elongated versus fragmented) with membrane ultrastructure of individual mitochondria in the presence and absence of endoplasmic reticulum (ER) stress. Using our pipeline, we demonstrate ER stress promotes adaptive remodeling of ultrastructural features of mitochondria including spacing between the inner and outer membranes, local curvedness of the inner membrane, and spacing between mitochondrial cristae. We show that differences in membrane ultrastructure correlate to mitochondrial network morphologies, suggesting that these two remodeling events are coupled. Our pipeline offers opportunities for quantifying changes in membrane ultrastructure on a single-cell level using cryo-ET, opening new opportunities to define changes in ultrastructural features induced by diverse types of cellular perturbations.
6 citations
TL;DR: In this paper , the authors discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamella, tomography, data processing and correlative light and electron microscopy that have enabled these studies.
Abstract: Cryogenic electron microscopy and data processing enable the determination of structures of isolated macromolecules to near-atomic resolution. However, these data do not provide structural information in the cellular environment where macromolecules perform their native functions, and vital molecular interactions can be lost during the isolation process. Cryogenic focused ion beam (FIB) fabrication generates thin lamellae of cellular samples and tissues, enabling structural studies on the near-native cellular interior and its surroundings by cryogenic electron tomography (cryo-ET). Cellular cryo-ET benefits from the technological developments in electron microscopes, detectors and data processing, and more in situ structures are being obtained and at increasingly higher resolution. In this Review, we discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamellae, tomography, data processing and correlative light and electron microscopy that have enabled these studies. Finally, we explore the future of cryo-ET in terms of both methods development and biological application.
4 citations
TL;DR: In this article, the selective growth of AlOx in the pore-forming domains of block copolymers (BCPs) is harnessed to create an internal and stable contrast difference between the blocks.
Abstract: Block copolymers (BCPs) are promising materials for water purification. They enable the fabrication of integral asymmetric isoporous membranes with high permeability and good selectivity. Commonly, the characterization of such hierarchical structures is performed by conventional electron microscopy (EM) means, namely scanning and transmission electron microscopy (SEM and TEM, respectively). However, due to the inherent lack of contrast between BCP domains, external contrast agents are required to achieve informative, high-resolution imaging. In addition, such EM techniques are typically limited to a certain cross-section or surface morphology only. In this paper, we harness the selective growth of AlOx in the pore-forming domains of BCPs to create an internal and stable contrast difference between the blocks. This in turn allowed us to perform advanced three-dimensional characterization of the membranes with focused ion beam (FIB)-SEM and TEM tomography, providing an understanding of the 3D structure and properties such as 3D geometry of the pores, 3D tortuosity, and 3D permeability. This 3D characterization also provides better correlations between the membrane structure and its performance. Such knowledge can allow better design and fine-tuning of BCP membranes and other membranes for their applications.
2 citations
TL;DR: In this article , a multislice electron tomography (MSET) method based on four-dimensional STEM tilt series was proposed to reduce undesirable reconstruction artifacts from the nonlinear contrast.
Abstract: Electron tomography offers useful three-dimensional (3D) structural information, which cannot be observed by two-dimensional imaging. By combining annular dark-field scanning transmission electron microscopy (ADF STEM) with aberration correction, the resolution of electron tomography has reached atomic resolution. However, tomography based on ADF STEM inherently suffers from several issues, including a high electron-dose requirement, poor contrast for light elements, and artifacts from image-contrast nonlinearity. Here, we develop an alternative method called multislice electron tomography (MSET) based on four-dimensional STEM tilt series. Our simulations show that multislice-based 3D reconstruction can effectively reduce undesirable reconstruction artifacts from the nonlinear contrast, allowing precise determination of atomic structures with improved sensitivity for low-Z elements, at considerably low electron-dose conditions. We expect that the MSET method can be applied to a wide variety of materials, including radiation-sensitive samples and materials containing light elements whose 3D atomic structures have never been fully elucidated due to electron-dose limitations or nonlinear imaging contrast.
1 citations
TL;DR: In this paper , a review highlights notable computational software and discusses how they contribute to making automated structural pattern discovery a possibility, emphasizing the importance of features for user-friendliness and accessibility.
1 citations
TL;DR: In this article , the authors propose to use ion beam-assisted electron tomography (cryo-FIB-ET) to bridge structural and cell biology to discover new biology.
Abstract: Recent advances in cryo-electron microscopy have marked only the beginning of the potential of this technique. To bring structure into cell biology, the modality of cryo-electron tomography has fast developed into a bona fide in situ structural biology technique where structures are determined in their native environment, the cell. Nearly every step of the cryo-focused ion beam-assisted electron tomography (cryo-FIB-ET) workflow has been improved upon in the past decade, since the first windows were carved into cells, unveiling macromolecular networks in near-native conditions. By bridging structural and cell biology, cryo-FIB-ET is advancing our understanding of structure-function relationships in their native environment and becoming a tool for discovering new biology.
1 citations
TL;DR: In this paper , a dual-axis electron tomography was employed to visualize 3D macromolecular organization/biopolymeric nano-architecture of the secondary S2 layer of Norway spruce fiber wall.
Abstract: Abstract Lignocellulose biomass has a tremendous potential as renewable biomaterials for fostering the “bio-based society” and circular bioeconomy paradigm. It requires efficient use and breakdown of fiber cell walls containing mainly cellulose, hemicellulose and lignin biopolymers. Despite their great importance, there is an extensive debate on the true structure of fiber walls and knowledge on the macromolecular nano-organization is limited and remains elusive in 3D. We employed dual-axis electron tomography that allows visualization of previously unseen 3D macromolecular organization/biopolymeric nano-architecture of the secondary S2 layer of Norway spruce fiber wall. Unprecedented 3D nano-structural details with novel insights into cellulose microfibrils (~ 2 nm diameter), macrofibrils, nano-pore network and cell wall chemistry (volume %) across the S2 were explored and quantified including simulation of structure related permeability. Matrix polymer association with cellulose varied between microfibrils and macrofibrils with lignin directly associated with MFs. Simulated bio-nano-mechanical properties revealed stress distribution within the S2 and showed similar properties between the idealized 3D model and the native S2 (actual tomogram). Present work has great potential for significant advancements in lignocellulose research on nano-scale understanding of cell wall assembly/disassembly processes leading to more efficient industrial processes of functionalization, valorization and target modification technologies.
1 citations
12 May 2023
TL;DR: Transmission electron microscopy (TEM) and related techniques, such as scanning transmission electron microscope (STEM), tomography, holography, Lorentz microscopy, and so on, are preferred methods to understand the atomic-scale structure and chemistry of materials, especially for nanomaterials as mentioned in this paper .
Abstract: Transmission electron microscope (TEM) and related techniques, scanning transmission electron microscope (STEM), tomography, holography, Lorentz microscopy, and so on, are preferred methods to understand the atomic-scale structure and chemistry of materials, especially for nanomaterials. This chapter is a brief reminder of some of the simple facts about the functioning of the TEM/STEM instruments. It provides a rapid review of TEM-based techniques that are available for in-situ measurements. Lorentz TEM is ideally suited to find structure and magnetic property relationship by determining the crystal and magnetic domain structures in correlation with their physical properties. During last few decades, a large number of TEM holders, as well as dedicated TEM for a specific application, have been developed to follow nanoscale changes in a material under different stimuli. The chapter also presents an overview on the key concepts discussed in this book.
01 Jan 2023
TL;DR: EMPIAR as discussed by the authors is a public resource for raw electron microscopy images related to EMDB, containing micrographs, particle sets and tilt-series, as well as other features from the EMBL-EBI archive.
Abstract: EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-series.
TL;DR: EMPIAR as mentioned in this paper is a public resource for raw electron microscopy images related to EMDB, containing micrographs, particle sets and tilt-series, as well as other features from the EMBL-EBI archive.
Abstract: EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-series.
TL;DR: In this article , the authors demonstrate the use of on-axis Z-contrast electron tomography (ET) with correlative energy-dispersive X-ray spectroscopy (EDX) tomography to examine rod-shaped samples with a diameter up to 700 nm prepared from individual osteonal lamellae in the human femur.
Abstract: Mineralized collagen fibrils are the building block units of bone at the nanoscale. While it is known that collagen fibrils are mineralized both inside their gap zones (intra-fibrillar mineralization) and on their outer surfaces (extra-fibrillar mineralization), a clear visualization of this architecture in three dimensions (3D), combining structural and compositional information over large volumes, but without compromising the resolution, remains challenging. In this study, we demonstrate the use of on-axis Z-contrast electron tomography (ET) with correlative energy-dispersive X-ray spectroscopy (EDX) tomography to examine rod-shaped samples with a diameter up to 700 nm prepared from individual osteonal lamellae in the human femur. Our work mainly focuses on two aspects: i) low-contrast nanosized circular spaces (“holes”) observed in sections of bone oriented perpendicular to the long axis of a long bone; and ii) extra-fibrillar mineral, especially in terms of morphology and spatial relationship with respect to intra-fibrillar mineral and collagen fibrils. From our analyses, it emerges quite clearly that most “holes” are cross-sectional views of collagen fibrils. While this had been postulated before, our 3D reconstructions and reslicing along meaningful two-dimensional (2D) cross-sections provide a direct visual confirmation. Extra-fibrillar mineral appears composed of thin plates that are interconnected and span over several collagen fibrils, confirming that mineralization is cross-fibrillar, at least for the extra-fibrillar phase. EDX tomography shows mineral signature (Ca and P) within the gap zones, but the signal appears weaker than that associated to the extra-fibrillar mineral, pointing towards the existence of dissimilarities between the two types of mineralization.
TL;DR: In this article , a rule-based imaging (RUBI) pipeline for low-cost, high throughput assessment of multiscale structure is presented, using structural landmarks identifiable via both light and electron microscopy.
11 Apr 2023
TL;DR: In this paper , the authors achieved sub-nanometer 3D resolution for a broad class of geometrically and compositionally complex materials using fused multi-modal electron tomography.
Abstract: Abstract Measuring the three-dimensional (3D) distribution of chemistry in nanoscale matter is a longstanding challenge for metrological science. The inelastic scattering events required for 3D chemical imaging are too rare, requiring high beam exposure that destroys the specimen before an experiment completes. Even larger doses are required to achieve high resolution. Thus, chemical mapping in 3D has been unachievable except at lower resolution with the most radiation-hard materials. Here, high-resolution 3D chemical imaging is achieved near or below one nanometer resolution in a Au-Fe 3 O 4 metamaterial, Co 3 O 4 - Mn 3 O 4 core-shell nanocrystals, and ZnS-Cu 0.64 S 0.36 nanomaterial using fused multi-modal electron tomography. Multi-modal data fusion enables high-resolution chemical tomography often with 99% less dose by linking information encoded within both elastic (HAADF) and inelastic (EDX / EELS) signals. Now sub-nanometer 3D resolution of chemistry is measurable for a broad class of geometrically and compositionally complex materials.
TL;DR: In this paper , an Individual Particle Cryogenic Transmission Electron Tomography (IPET) technique was used to obtain detailed 3D morphology of monodispersed mesoporous silica nanoparticles with diameters below 50 nm.
Abstract: Sintered agglomerate of synthetic mesoporous silica nanoparticles (MSNs) is an architected geomaterial that provides confinement-mediated flow and transport properties of fluids needed for environmental research such as geological subsurface energy storage or carbon capture. The design of those properties can be guided by numerical simulations but is hindered by the lack of method to characterize the permeable pores within MSNs due to pore size. This work uses the advances of an Individual Particle cryogenic transmission Electron Tomography (IPET) technique to obtain detailed 3D morphology of monodispersed MSNs with diameters below 50 nm. The 3D reconstructed density-maps show the diameters of those MSNs vary from 35–46 nm, containing connected intraparticle pores in diameter of 2–20 nm with a mean of 9.2 ± 3 nm, which is comparable to the mean interparticle pore diameters in sintered agglomerate. The characterization of the pore shape and dimensions provides key information for estimating the flow and transport properties of fluids within the sintered agglomerate of those MSNs and for modeling the atomic MSN structures needed for pore-fluid simulations.
TL;DR: In this paper , the authors demonstrate the quantitative 3D mapping of the charge density and long-range electric field associated with an electrically biased carbon fiber nanotip with a spatial resolution of approximately 5 nm using electron holographic tomography in the transmission electron microscope combined with model-based iterative reconstruction.
Abstract: The operation of nanoscale electronic devices is related intimately to the three-dimensional (3D) charge density distributions within them. Here, we demonstrate the quantitative 3D mapping of the charge density and long-range electric field associated with an electrically biased carbon fiber nanotip with a spatial resolution of approximately 5 nm using electron holographic tomography in the transmission electron microscope combined with model-based iterative reconstruction. The approach presented here can be applied to a wide range of other nanoscale materials and devices.
TL;DR: EMPIAR as discussed by the authors is a public resource for raw electron microscopy images related to EMDB, containing micrographs, particle sets and tilt-series, as well as other features from the EMBL-EBI archive.
Abstract: EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-series.
TL;DR: A review of the existing and emergent techniques for observing catalysts using S/TEM is presented in this article , where challenges and opportunities highlighted aim to inspire and accelerate the use of electron microscopy to further investigate the complex interplay of catalytic systems.
Abstract: Catalysts are the primary facilitator in many dynamic processes. Therefore, a thorough understanding of these processes has vast implications for a myriad of energy systems. The scanning/transmission electron microscope (S/TEM) is a powerful tool not only for atomic-scale characterization but also in situ catalytic experimentation. Techniques such as liquid and gas phase electron microscopy allow the observation of catalysts in an environment conducive to catalytic reactions. Correlated algorithms can greatly improve microscopy data processing and expand multidimensional data handling. Furthermore, new techniques including 4D-STEM, atomic electron tomography, cryogenic electron microscopy, and monochromated electron energy loss spectroscopy (EELS) push the boundaries of our comprehension of catalyst behavior. In this review, we discuss the existing and emergent techniques for observing catalysts using S/TEM. Challenges and opportunities highlighted aim to inspire and accelerate the use of electron microscopy to further investigate the complex interplay of catalytic systems.
TL;DR: In this article , the structure of the tripartite attachment complex (TAC) of trypanosomes was investigated and the authors found that the majority of the TAC consists of a string of spectrin-like repeats.
Abstract: In contrast to many eukaryotic organisms, trypanosomes only contain a single mitochondrion per cell. Within that singular mitochondrion, the protist carries a single mitochondrial genome that consists of a complex DNA network, the kinetoplast DNA (kDNA). Segregation of the replicated kDNA is coordinated by the basal body of the cell’s single flagellum. The tripartite attachment complex (TAC) forms a physical connection between the proximal end of the basal body and the kDNA. This allows anchoring of the kDNA throughout the cell cycle and couples kDNA segregation with the separation of the basal bodies prior to cell division. Over the past years, several components of the TAC have been identified. To shed light on the structure of the cytoplasmic part of the TAC (known as the exclusion zone), we performed cryo-electron tomography on whole cells. This allowed us to acquire three-dimensional high-resolution images of the exclusion zone in situ. We observed that the exclusion zone filaments offer great mechanical flexibility for basal body movement. We measured the dimensions of the individual structural elements of the area, as well as the overall orientation and positioning of the basal bodies towards the mitochondrial kDNA pocket. Using a combination of experimental data and modelling, we generated a structural model of the exclusion zone protein p197. Our findings suggest that the majority of p197 consists of a string of spectrin-like repeats. We propose that these structural units provide the architecture of a molecular spring and that they are required in the TAC to withstand the mechanical forces generated through basal body repositioning events during kDNA segregation and motility of the organism.
TL;DR: In this paper , a method for direct measurement of all five parameters of the grain boundary in a transmission electron microscopy specimen of various morphologies is presented. But this method is only applicable to atom probe specimens, where only a single-tilt axis is generally available, allowing the crystallographic description to be matched to the detailed chemical data available in the atom probe tomography.
Abstract:
Grain boundaries are critical in determining the properties of materials, including mechanical stability, conductivity, and corrosion resistance. The specific properties of materials depend not only on the misorientation of the crystals, the three most commonly characterized parameters, but also on the angle of the grain boundary plane between the two crystals, the final two parameters in the five-parameter macroscopic description of the grain boundary. The method presented here allows for the direct measurement of all five parameters of the grain boundary in a transmission electron microscopy specimen of various morphologies. This is especially applicable to atom probe specimens, where only a single-tilt axis is generally available, allowing the crystallographic description to be matched to the detailed chemical data available in the atom probe tomography. This method provides a platform for efficient grain boundary analysis in unique samples, saving operator time and allowing for ease of acquisition and interpretation in comparison with traditional electron diffraction methods.
TL;DR: In this article , a novel in situ three-dimensional electron microscopy technique for thermally activated solid-state reaction processes in nanoparticles (NPs) was successfully visualized and analyzed in four-dimensional space-time.
Abstract: The nanoscale characterization of thermally activated solid reactions plays a pivotal role in products manufactured by nanotechnology. Recently, in situ observation in transmission electron microscopy combined with electron tomography, namely four-dimensional observation for heat treatment of nanomaterials, has attracted great interest. However, because most nanomaterials are highly reactive, i.e., oxidation during transfer and electron beam irradiation would likely cause fatal artefacts; it is challenging to perform the artifact-free four-dimensional observation. Herein, we demonstrate our development of a novel in situ three-dimensional electron microscopy technique for thermally activated solid-state reaction processes in nanoparticles (NPs). The sintering behaviour of Cu NPs was successfully visualized and analyzed in four-dimensional space-time. An advanced image processing protocol and a newly designed state-of-the-art MEMS-based heating holder enable the implementation of considerably low electron dose imaging and prevent air exposure, which is of central importance in this type of observation. The total amount of electron dose for a single set of tilt-series images was reduced to 250 e- nm-2, which is the lowest level for inorganic materials electron tomography experiments. This study evaluated the sintering behaviour of Cu NPs in terms of variations in neck growth and particle distance. A negative correlation between the two parameters is shown, except for the particle pair bound by neighbouring NPs. The nanoscale characteristic sintering behavior of neck growth was also captured in this study.
TL;DR: In this article , the authors used a combination of atom probe tomography (APT), TEM, focused ion beam (FIB), ion mill thinning and scanning electron microscopy (SEM) to investigate the sequestration and transformation of silver (Ag) and arsenic (As) ions in soil organic matter (OM) at the nanoscale.
Abstract: This study investigates the sequestration and transformation of silver (Ag) and arsenic (As) ions in soil organic matter (OM) at the nanoscale using the combination of atom probe tomography (APT), transmission electron microscopy (TEM), focused ion beam (FIB), ion mill thinning and scanning electron microscopy (SEM). Silver-arsenic contaminated organic-rich soils were collected along the shore of Cobalt Lake, a former mining and milling site of the famous Ag deposits at Cobalt, Ontario, Canada. SEM examinations show that particulate organic matter (OM grains) contains mineral inclusions composed of mainly Fe, S, and Si with minor As and traces of Ag. Four OM grains with detectable concentrations of Ag (by SEM-EDS) were further characterized with either a combination of TEM and APT or TEM alone. These examinations show that As is predominantly sequestered by OM through either co-precipitation with Fe-(hydr)oxide inclusions or adsorption on Fe-(hydr)oxides and their subsequent transformation into scorodite (FeAsO4·2H2O)/amorphous Fe-arsenate (AFA). Silver nanoparticles (NPs) with diameters in the range of ∼5-20 nm occur in the organic matrix as well as on the surface of Fe-rich inclusions (Fe-hydroxides, Fe-arsenates, Fe-sulfides), whereas Ag sulfide NPs were only observed on the surfaces of the Fe-rich inclusions. Rims of Ag-sulfides on Ag NPs (TEM data), accumulation of S atoms within and around Ag NPs (APT data), and the occurrence of dendritic as well as euhedral acanthite NPs with diameters in the range of ∼100-400 nm (TEM data) indicate that the sulfidation of the Ag NPs occurred via a mineral-replacement reaction (rims) or a complete dissolution of the Ag NPs, the subsequent precipitation of acanthite NPs and their aggregation (dendrites) and Ostwald ripening (euhedral crystals). These results show the importance of OM and, specifically the mineral inclusions in the sequestration of Ag and As to less bioavailable forms such as acanthite and scorodite, respectively.
TL;DR: In this article , a multi-color super-resolution radial fluctuation light microscopy under cryogenic conditions (cryo-SRRF) was proposed for the visualization of organelles and their interactions with other features in the native cell.
01 Jan 2023
TL;DR: In this paper , the authors overview the application of electron tomography in biology and discuss future challenge, including future application to biology and the future challenges of applying it to microscopy.
Abstract: Electron tomography in biology is a technique to reconstruct the three-dimensional structure of macro-molecular, sub-cellular or cellular objects by transmission electron microscopy (TEM). In this technique, micrographs of the sample are recorded from various orientations by tilting the specimen, which are then computationally merged into a 3D structure. Combined with recent developments of cryo-electron microscopy, cryo-electron tomography (cryo-ET) have allowed us to visualize detailed 3D structures of biological macromolecules in vivo at sub-atomic resolution, filling the gap between X-ray crystallography or NMR and light microscopy. In this section, we overview this technique and application to biology and discuss future challenge.
14 Oct 2022
TL;DR: A series of protocols designed to obtain high-quality cryo-electron tomography data of biomolecular condensates reconstituted in vitro are described, designed to investigate the three-dimensional architecture of such pleomorphic interaction networks at nanometer resolution.
01 Jan 2023
24 Apr 2023
TL;DR: In this article , the authors achieved sub-nanometer 3D resolution for a broad class of geometrically and compositionally complex materials using fused multi-modal electron tomography.
Abstract: Measuring the three-dimensional (3D) distribution of chemistry in nanoscale matter is a longstanding challenge for metrological science. The inelastic scattering events required for 3D chemical imaging are too rare, requiring high beam exposure that destroys the specimen before an experiment completes. Even larger doses are required to achieve high resolution. Thus, chemical mapping in 3D has been unachievable except at lower resolution with the most radiation-hard materials. Here, high-resolution 3D chemical imaging is achieved near or below one nanometer resolution in a Au-Fe$_3$O$_4$ metamaterial, Co$_3$O$_4$ - Mn$_3$O$_4$ core-shell nanocrystals, and ZnS-Cu$_{0.64}$S$_{0.36}$ nanomaterial using fused multi-modal electron tomography. Multi-modal data fusion enables high-resolution chemical tomography often with 99\% less dose by linking information encoded within both elastic (HAADF) and inelastic (EDX / EELS) signals. Now sub-nanometer 3D resolution of chemistry is measurable for a broad class of geometrically and compositionally complex materials.