Three-dimensional transmission electron microscopy and its application to mitosis research

The application and development of electron microscopy for three-dimensional reconstruction in life science: a review

Imaging technologies have played a pivotal role in advancing biological research by enabling visualization of biological structures and processes. While traditional electron microscopy (EM) produces two-dimensional images, emerging techniques now allow high-resolution three-dimensional (3D) characterization of specimens in situ, meeting growing needs in molecular and cellular biology. Combining transmission electron microscopy (TEM) with serial sectioning inaugurated 3D imaging, attracting biologists seeking to explore cell ultrastructure and driving advancement of 3D EM reconstruction. By comprehensively and precisely rendering internal structure and distribution, 3D TEM reconstruction provides unparalleled ultrastructural insights into cells and molecules, holding tremendous value for elucidating structure-function relationships and broadly propelling structural biology. Here, we first introduce the principle of 3D reconstruction of cells and tissues by classical approaches in TEM and then discuss modern technologies utilizing TEM and on new SEM-based as well as cryo-electron microscope (cryo-EM) techniques. 3D reconstruction techniques from serial sections, electron tomography (ET), and the recent single-particle analysis (SPA) are examined; the focused ion beam scanning electron microscopy (FIB-SEM), the serial block-face scanning electron microscopy (SBF-SEM), and automatic tape-collecting lathe ultramicrotome (ATUM-SEM) for 3D reconstruction of large volumes are discussed. Finally, we review the challenges and development prospects of these technologies in life science. It aims to provide an informative reference for biological researchers.

Algorithm for Modern Electron Microscopic Examination of the Golgi Complex

The Golgi complex (GC) is an essential organelle of the eukaryotic exocytic pathway. It has a very complexed structure and thus localization of its resident proteins is not trivial. Fast development of microscopic methods generates a huge difficulty for Golgi researchers to select the best protocol to use. Modern methods of light microscopy, such as super-resolution light microscopy (SRLM) and electron microscopy (EM), open new possibilities in analysis of various biological structures at organelle, cell, and organ levels. Nowadays, new generation of EM methods became available for the study of the GC; these include three-dimensional EM (3DEM), correlative light-EM (CLEM), immune EM, and new estimators within stereology that allow realization of maximal goal of any morphological study, namely, to achieve a three-dimensional model of the sample with optimal level of resolution and quantitative determination of its chemical composition. Methods of 3DEM have partially overlapping capabilities. This requires a careful comparison of these methods, identification of their strengths and weaknesses, and formulation of recommendations for their application to cell or tissue samples. Here, we present an overview of 3DEM methods for the study of the GC and some basics for how the images are formed and how the image quality can be improved.

MCRS1 modulates the heterogeneity of microtubule minus-end morphologies in mitotic spindles

Faithful chromosome segregation requires the assembly of a bipolar spindle, consisting of two antiparallel microtubule (MT) arrays having most of their minus ends focused at the spindle poles and their plus ends overlapping in the spindle midzone. Spindle assembly, chromosome alignment, and segregation require highly dynamic MTs. The plus ends of MTs have been extensively investigated but their minus-end structure remains poorly characterized. Here, we used large-scale electron tomography to study the morphology of the MT minus ends in three dimensionally reconstructed metaphase spindles in HeLa cells. In contrast to the homogeneous open morphology of the MT plus ends at the kinetochores, we found that MT minus ends are heterogeneous, showing either open or closed morphologies. Silencing the minus end-specific stabilizer, MCRS1 increased the proportion of open MT minus ends. Altogether, these data suggest a correlation between the morphology and the dynamic state of the MT ends. Taking this heterogeneity of the MT minus-end morphologies into account, our work indicates an unsynchronized behavior of MTs at the spindle poles, thus laying the groundwork for further studies on the complexity of MT dynamics regulation.

Three-dimensional structure of kinetochore-fibers in human mitotic spindles

During cell division, kinetochore microtubules (KMTs) provide a physical linkage between the chromosomes and the rest of the spindle. KMTs in mammalian cells are organized into bundles, so-called kinetochore-fibers (k-fibers), but the ultrastructure of these fibers is currently not well characterized. Here, we show by large-scale electron tomography that each k-fiber in HeLa cells in metaphase is composed of approximately nine KMTs, only half of which reach the spindle pole. Our comprehensive reconstructions allowed us to analyze the three-dimensional (3D) morphology of k-fibers and their surrounding MTs in detail. We found that k-fibers exhibit remarkable variation in circumference and KMT density along their length, with the pole-proximal side showing a broadening. Extending our structural analysis then to other MTs in the spindle, we further observed that the association of KMTs with non-KMTs predominantly occurs in the spindle pole regions. Our 3D reconstructions have implications for KMT growth and k-fiber self-organization models as covered in a parallel publication applying complementary live-cell imaging in combination with biophysical modeling (Conway et al., 2022). Finally, we also introduce a new visualization tool allowing an interactive display of our 3D spindle data that will serve as a resource for further structural studies on mitosis in human cells.

2D and 3D immunogold localization on (epoxy) ultrathin sections with and without osmium tetroxide

For nearly 50 years immunogold labeling on ultrathin sections has been successfully used for protein localization in laboratories worldwide. In theory and in practice, this method has undergone continual improvement over time. In this study, we carefully analyzed circulating protocols for postembedding labeling to find out if they are still valid under modern laboratory conditions, and in addition, we tested unconventional protocols. For this, we investigated immunolabeling of Epon-embedded cells, immunolabeling of cells treated with osmium, and the binding behavior of differently sized gold particles. Here we show that (in contrast to widespread belief) immunolabeling of Epon-embedded cells and of cells treated with osmium tetroxide is actually working. Furthermore, we established a "speed protocol" for immunolabeling by reducing antibody incubation times. Finally, we present our results on three-dimensional immunogold labeling.

Electron tomography reveals aspects of spindle structure important for mechanical stability at metaphase

Metaphase spindles exert pole-directed forces on still-connected sister kinetochores. The spindle must counter these forces with extensive forces to prevent spindle collapse. In small spindles, kinetochore microtubules (KMTs) connect directly with the poles, and countering forces are supplied either by interdigitating MTs that form interpolar bundles or by astral MTs connected to the cell cortex. In bigger spindles, particularly those without structured poles, the origin of extensive forces is less obvious. We have used electron tomography of well-preserved metaphase cells to obtain structural evidence about interactions among different classes of MTs in metaphase spindles from Chlamydomonas rheinhardti and two strains of cultured mammalian cells. In all these spindles, KMTs approach close to and cross-bridge with the minus ends of non-KMTs, which form a framework that interdigitates near the spindle equator. Although this structure is not pole-connected, its organization suggests that it can support kinetochore tension. Analogous arrangements of MTs have been seen in even bigger spindles, such as metaphase spindles in Haemanthus endosperm and frog egg extracts. We present and discuss a hypothesis that rationalizes changes in spindle design with spindle size based on the negative exponential distribution of MT lengths in dynamically unstable populations of tubulin polymers.

Three dimensional reconstruction by electron microscopy in the life sciences: An introduction for cell and tissue biologists

Early applications of transmission electron microscopy (TEM) in the life sciences have contributed tremendously to our current understanding at the subcellular level. Initially limited to two-dimensional representations of three-dimensional (3D) objects, this approach has revolutionized the fields of cellular and structural biology-being instrumental for determining the fine morpho-functional characterization of most cellular structures. Electron microscopy has progressively evolved towards the development of tools that allow for the 3D characterization of different structures. This was done with the aid of a wide variety of techniques, which have become increasingly diverse and highly sophisticated. We start this review by examining the principles of 3D reconstruction of cells and tissues using classical approaches in TEM, and follow with a discussion of the modern approaches utilizing TEM as well as on new scanning electron microscopy-based techniques. 3D reconstruction techniques from serial sections and (cryo) electron-tomography are examined, and the recent applications of focused ion beam-scanning microscopes and serial-block-face techniques for the 3D reconstruction of large volumes are discussed. Alternative low-cost techniques and more accessible approaches using basic transmission or field emission scanning electron microscopes are also examined.

Electron tomography for organelles, cells, and tissues

Electron tomography (ET) is an emerging electron microscopy (EM) technique for three-dimensional (3D) visualization of molecular arrangements and ultrastructural architectures in organelles, cells, and tissues at 2-10 nm resolution. The 3D tomogram is reconstructed from a series of 2D EM images taken from a single specimen at different projecting orientations. The specimen for ET must be specially prepared to meet the ET imaging requirements, i.e., ultrastructural preservation, specimen thickness, tolerance of electron dose and vacuum, and image contrast. In this chapter, the strategies of specimen preparation of organelles, cells, and tissues and the corresponding EM imaging requirements for ET will be described in detail. In addition, the general procedures tomographic reconstruction and tomogram interpretation will be described.

Extraction of three-dimensional information of biological membranous tissue with scanning confocal infrared laser microscope tomography

The "LEXT" confocal laser scanning microscope has been used for the three-dimensional (3D) imaging of the surface of specimens, especially in materials science fields, by the penetration of near-infrared (NIR) light without mechanical cutting, deposition, or other specimen pretreatment. Noninvasive investigation of various biological tissues such as human spinal dura mater, rat aorta, and cornea without the dehydration process was successfully carried out with the "LEXT," in order to access both surface and internal topographic images of the biological structures at a good status of the wet tissue such as in vivo, especially in measuring tissue thickness. The confocal NIR laser microscopy offers the viable means to visualize tissue architecture and its thickness in microdomain to integrate 3D images efficiently. We believe that the "LEXT" has a good application for biological researchers to study biomaterials, and it would be useful as a diagnostic tool in the near future.

Electron tomography of HEK293T cells using scanning electron microscope-based scanning transmission electron microscopy

Based on a scanning electron microscope operated at 30 kV with a homemade specimen holder and a multiangle solid-state detector behind the sample, low-kV scanning transmission electron microscopy (STEM) is presented with subsequent electron tomography for three-dimensional (3D) volume structure. Because of the low acceleration voltage, the stronger electron-atom scattering leads to a stronger contrast in the resulting image than standard TEM, especially for light elements. Furthermore, the low-kV STEM yields less radiation damage to the specimen, hence the structure can be preserved. In this work, two-dimensional STEM images of a 1-μm-thick cell section with projection angles between ±50° were collected, and the 3D volume structure was reconstructed using the simultaneous iterative reconstructive technique algorithm with the TomoJ plugin for ImageJ, which are both public domain software. Furthermore, the cross-sectional structure was obtained with the Volume Viewer plugin in ImageJ. Although the tilting angle is constrained and limits the resulting structural resolution, slicing the reconstructed volume generated the depth profile of the thick specimen with sufficient resolution to examine cellular uptake of Au nanoparticles, and the final position of these nanoparticles inside the cell was imaged.

Macromolecular structure modeling from 3D EM using VolRover 2.0

We review tools for structure identification and model-based refinement from three-dimensional electron microscopy implemented in our in-house software package, VOLROVER 2.0. For viral density maps with icosahedral symmetry, we segment the capsid, polymeric, and monomeric subunits using techniques based on automatic symmetry detection and multidomain fast marching. For large biomolecules without symmetry information, we again use our multidomain fast-marching method with manual or fit-based multiseeding to segment meaningful substructures. In either case, we subject the resulting segmented subunit to secondary structure detection when the EM resolution is sufficiently high, and rigid-body structure fitting when the corresponding X-ray structure is available. Secondary structure elements are identified by three techniques: our earlier volume-based and boundary-based skeletonization methods as well as a new method, currently in development, based on solving the grassfire flow equation. For rigid-body fitting, we adapt our earlier fast Fourier-based correlation scheme F2Dock. Our reported segmentation, secondary structure elements identification, and rigid-body fitting techniques, implemented in VOLROVER 2.0 are applied to the PSB 2011 cryo-EM modeling challenge data, and our results are briefly compared to similar results submitted from other research groups. The comparisons show that our techniques are equally capable of segmenting relatively accurate subunits from a viral or protein assembly, and that high segmentation quality leads in turn to higher-quality results of secondary structure elements identification and correlation-based rigid-body fitting. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 709-731, 2012.

Helical arrangement of filaments in microvillar actin bundles

Actin filament arrays in in vivo microvillar bundles of rat intestinal enterocyte were re-evaluated using electron tomography (ET). Conventional electron microscope observation of semi-thin cross sections (300nm thick) of high-pressure freeze fixed and resin embedded brush border has shown a whirling pattern in the center of the microvilli instead of hexagonally arranged dots, which strongly suggests that the bundle consists of a non-parallel array of filaments. A depth compensation method for the ET was developed to estimate the actual structure of the actin bundle. Specimen shrinkage by beam irradiation during image acquisition was estimated to be 63%, and we restored the original thickness in the reconstruction. The depth compensated tomogram displayed the individual actin filaments within the bundles and it indicated that the actin filaments do not lie exactly parallel to each other: instead, they are twisted in a clockwise coil with a pitch of ∼120°/μm. Furthermore, the lattice of actin filaments was occasionally re-arranged within the bundle. As the microvillar bundle mechanically interacts with the membrane and is thought to be compressed by the membrane's faint tensile force, we removed the shrouding membrane using detergents to eliminate the mechanical interaction. The bared bundles no longer showed the whirling pattern, suggesting that the bundle had released its coiled property. These findings indicate that the bundle has not rigid but elastic properties and a dynamic transformation in its structure caused by a change in the mechanical interaction between the membrane and the bundle.

Correlative microscopy: a powerful tool for exploring neurological cells and tissues

Imaging tools for exploring the neurological samples have seen a rapid transformation over the last decade. Approaches that allow clear and specific delineation of targeted tissues, individual neurons, and their cell-cell connections as well as subcellular constituents have been especially valuable. Considering the significant complexity and extent to which the nervous system interacts with every organ system in the body, one non-trivial challenge has been how to identify and target specific structures and pathologies by microscopy. To this end, correlative methods enable one to view the same exact structure of interest utilizing the capabilities of typically separate, but powerful, microscopy platforms. As such, correlative microscopy is well-positioned to address the three critical problems of identification, scale, and resolution inherent to neurological systems. Furthermore, the application of multiple imaging platforms to the study of singular biological events enables more detailed investigations of structure-function relationships to be conducted, greatly facilitating our understanding of relevant phenomenon. This comprehensive review provides an overview of methods for correlative microscopy, including histochemistry, transgenic markers, immunocytochemistry, photo-oxidation as well as various probes and tracers. An emphasis is placed on correlative light and electron microscopic strategies used to facilitate relocation of neurological structures. Correlative microscopy is an invaluable tool for neurological research, and we fully anticipate developments in automation of the process, and the increasing availability of genomic and transgenic tools will facilitate the adoption of correlative microscopy as the method of choice for many imaging experiments.

Expedited approaches to whole cell electron tomography and organelle mark-up in situ in high-pressure frozen pancreatic islets

We have developed a simplified, efficient approach for the 3D reconstruction and analysis of mammalian cells in toto by electron microscope tomography (ET), to provide quantitative information regarding 'global' cellular organization at approximately 15-20 nm resolution. Two insulin-secreting beta cells-deemed 'functionally equivalent' by virtue of their location at the periphery of the same pancreatic islet-were reconstructed in their entirety in 3D after fast-freezing/freeze-substitution/plastic embedment in situ within a glucose-stimulated islet of Langerhans isolated intact from mouse pancreata. These cellular reconstructions have afforded several unique insights into fundamental structure-function relationships among key organelles involved in the biosynthesis and release of the crucial metabolic hormone, insulin, that could not be provided by other methods. The Golgi ribbon, mitochondria and insulin secretory granules in each cell were segmented for comparative analysis. We propose that relative differences between the two cells in terms of the number, dimensions and spatial distribution (and for mitochondria, also the extent of branching) of these organelles per cubic micron of cellular volume reflects differences in the two cells' individual capacity (and/or readiness) to respond to secretagogue stimulation, reflected by an apparent inverse relationship between the number/size of insulin secretory granules versus the number/size of mitochondria and the Golgi ribbon. We discuss the advantages of this approach for quantitative cellular ET of mammalian cells, briefly discuss its application relevant to other complementary techniques, and summarize future strategies for overcoming some of its current limitations.

The ultrastructure of the kinetochore and kinetochore fiber in Drosophila somatic cells

Drosophila melanogaster is a widely used model organism for the molecular dissection of mitosis in animals. However, despite the popularity of this system, no studies have been published on the ultrastructure of Drosophila kinetochores and kinetochore fibers (K-fibers) in somatic cells. To amend this situation, we used correlative light (LM) and electron microscopy (EM) to study kinetochores in cultured Drosophila S2 cells during metaphase, and after colchicine treatment to depolymerize all microtubules (MTs). We find that the structure of attached kinetochores in S2 cells is indistinct, consisting of an amorphous inner zone associated with a more electron-dense peripheral surface layer that is approximately 40-50 nm thick. On average, each S2 kinetochore binds 11+/-2 MTs, in contrast to the 4-6 MTs per kinetochore reported for Drosophila spermatocytes. Importantly, nearly all of the kinetochore MT plus ends terminate in the peripheral surface layer, which we argue is analogous to the outer plate in vertebrate kinetochores. Our structural observations provide important data for assessing the results of RNAi studies of mitosis, as well as for the development of mathematical modelling and computer simulation studies in Drosophila and related organisms.

Electron tomography of membrane-bound cellular organelles

Electron microscope tomography produces three-dimensional reconstructions and has been used to image organelles both isolated and in situ, providing new insight into their structure and function. It is analogous to the various tomographies used in medical imaging. Compared with light microscopy, electron tomography offers an improvement in resolution of 30- to 80-fold and currently ranges from 3 to 8 nm, thus filling the gap between high-resolution structure determinations of isolated macromolecules and larger-scale studies on cells and tissues by light microscopy. Here, we provide an introduction to electron tomography and applications of the method in characterizing organelle architecture that also show its power for suggesting functional significance. Further improvements in labeling modalities, imaging tools, specimen preparation, and reconstruction algorithms promise to increase the quality and breadth of reconstructions by electron tomography and eventually to allow the mapping of the cellular proteomes onto detailed three-dimensional models of cellular structure.

Automated extraction of fine features of kinetochore microtubules and plus-ends from electron tomography volume

Kinetochore microtubules (KMTs) and the associated plus-ends have been areas of intense investigation in both cell biology and molecular medicine. Though electron tomography opens up new possibilities in understanding their function by imaging their high-resolution structures, the interpretation of the acquired data remains an obstacle because of the complex and cluttered cellular environment. As a result, practical segmentation of the electron tomography data has been dominated by manual operation, which is time consuming and subjective. In this paper, we propose a model-based automated approach to extracting KMTs and the associated plus-ends with a coarse-to-fine scale scheme consisting of volume preprocessing, microtubule segmentation and plus-end tracing. In volume preprocessing, we first apply an anisotropic invariant wavelet transform and a tube-enhancing filter to enhance the microtubules at coarse level for localization. This is followed with a surface-enhancing filter to accentuate the fine microtubule boundary features. The microtubule body is then segmented using a modified active shape model method. Starting from the segmented microtubule body, the plus-ends are extracted with a probabilistic tracing method improved with rectangular window based feature detection and the integration of multiple cues. Experimental results demonstrate that our automated method produces results comparable to manual segmentation but using only a fraction of the manual segmentation time.

Ewald sphere correction for single-particle electron microscopy

Most algorithms for three-dimensional (3D) reconstruction from electron micrographs assume that images correspond to projections of the 3D structure. This approximation limits the attainable resolution of the reconstruction when the dimensions of the structure exceed the depth of field of the microscope. We have developed two methods to calculate a reconstruction that corrects for the depth of field. Either method applied to synthetic data representing a large virus yields a higher resolution reconstruction than a method lacking this correction.

The de novo centriole assembly pathway in HeLa cells: cell cycle progression and centriole assembly/maturation

It has been reported that nontransformed mammalian cells become arrested during G1 in the absence of centrioles (Hinchcliffe, E., F. Miller, M. Cham, A. Khodjakov, and G. Sluder. 2001. Science. 291:1547-1550). Here, we show that removal of resident centrioles (by laser ablation or needle microsurgery) does not impede cell cycle progression in HeLa cells. HeLa cells born without centrosomes, later, assemble a variable number of centrioles de novo. Centriole assembly begins with the formation of small centrin aggregates that appear during the S phase. These, initially amorphous "precentrioles" become morphologically recognizable centrioles before mitosis. De novo-assembled centrioles mature (i.e., gain abilities to organize microtubules and replicate) in the next cell cycle. This maturation is not simply a time-dependent phenomenon, because de novo-formed centrioles do not mature if they are assembled in S phase-arrested cells. By selectively ablating only one centriole at a time, we find that the presence of a single centriole inhibits the assembly of additional centrioles, indicating that centrioles have an activity that suppresses the de novo pathway.

Bizarre alterations of the morphology of pineal synaptic bodies under constant light and an evaluation of suitable 3D-reconstruction software

Three dimensional (3D) reconstruction and modelling software was evaluated to find a procedure suitable for visualization of small subcellular structures in transmission electron microscope images. The method applied in this study demonstrates bizarre alterations of the structure of synaptic bodies (SBs) in pinealocytes of the guinea-pig pineal gland caused by constant illumination. It can, in general, be used for any 3D reconstruction from serial sections. Pineal glands of five guinea-pigs (two kept under a LD cycle of 12:12 h; three kept in constant light, for 4 months) were investigated. SBs consist of an electron-dense centre with attached vesicles. Under normal lighting conditions most SBs are flat plates (about 35 nm in thickness), which eventually may be bent. The proteins comprising the molecular basis of SBs, mainly RIBEYE A and B are polymerised in a regular manner in these plates. This is not the case in other SBs, which appear as spheres or irregular lumps. SBs lie in groups in which usually some of the plates are arranged in parallel arrays Constant illumination caused different changes in morphology: many of the SBs lie in 'paired fields', i.e. appear in groups attached to the cell membranes of two pinealocytes directly opposite to each other. Some of the SBs in such groups are strongly bent, showing blebs and irregular thickened areas, others seem to aggregate and show inclusions of cytoplasm. Further goblet-like, shield-like and other bizarre forms of SBs occurred and the relative number of spheroid and lump-like SBs increased. Protrusions on larger SBs suggest detachment or fusion of SB material to a greater extent than in the control animals. There is a reduction of areas in which the polymerisation of the SB proteins remains well ordered, i.e. where the typical thickness of 35 nm is maintained. It remains unclear why this polymerisation pattern is only partly affected by constant light.

Volumetric feature extraction and visualization of tomographic molecular imaging

Electron tomography is useful for studying large macromolecular complex within their cellular context. The associate problems include crowding and complexity. Data exploration and 3D visualization of complexes require rendering of tomograms as well as extraction of all features of interest. We present algorithms for fully automatic boundary segmentation and skeletonization, and demonstrate their applications in feature extraction and visualization of cell and molecular tomographic imaging. We also introduce an interactive volumetric exploration and visualization tool (Volume Rover), which encapsulates implementations of the above volumetric image processing algorithms, and additionally uses efficient multi-resolution interactive geometry and volume rendering techniques for interactive visualization.

Tomographic reconstruction of treponemal cytoplasmic filaments reveals novel bridging and anchoring components

An understanding of the involvement of bacterial cytoplasmic filaments in cell division requires the elucidation of the structural organization of those filamentous structures. Treponemal cytoplasmic filaments are composed of one protein, CfpA, and have been demonstrated to be involved in cell division. In this study, we used electron tomography to show that the filaments are part of a complex with a novel molecular organization that includes at least two distinct features decorating the filaments. One set of components appears to anchor the filaments to the cytoplasmic membrane. The other set of components appears to bridge the cytoplasmic filaments on the cytoplasmic side, and to be involved in the interfilament spacing within the cell. The filaments occupy between 3 and 18% of the inner surface of the cytoplasmic membrane. These results reveal a novel filamentous molecular organization of independent filaments linked by bridges and continuously anchored to the membrane.

Tomographic evidence for continuous turnover of Golgi cisternae in Pichia pastoris

The budding yeast Pichia pastoris contains ordered Golgi stacks next to discrete transitional endoplasmic reticulum (tER) sites, making this organism ideal for structure-function studies of the secretory pathway. Here, we have used P. pastoris to test various models for Golgi trafficking. The experimental approach was to analyze P. pastoris tER-Golgi units by using cryofixed and freeze-substituted cells for electron microscope tomography, immunoelectron microscopy, and serial thin section analysis of entire cells. We find that tER sites and the adjacent Golgi stacks are enclosed in a ribosome-excluding "matrix." Each stack contains three to four cisternae, which can be classified as cis, medial, trans, or trans-Golgi network (TGN). No membrane continuities between compartments were detected. This work provides three major new insights. First, two types of transport vesicles accumulate at the tER-Golgi interface. Morphological analysis indicates that the center of the tER-Golgi interface contains COPII vesicles, whereas the periphery contains COPI vesicles. Second, fenestrae are absent from cis cisternae, but are present in medial through TGN cisternae. The number and distribution of the fenestrae suggest that they form at the edges of the medial cisternae and then migrate inward. Third, intact TGN cisternae apparently peel off from the Golgi stacks and persist for some time in the cytosol, and these "free-floating" TGN cisternae produce clathrin-coated vesicles. These observations are most readily explained by assuming that Golgi cisternae form at the cis face of the stack, progressively mature, and ultimately dissociate from the trans face of the stack.

Use of frozen-hydrated axonemes to assess imaging parameters and resolution limits in cryoelectron tomography

Using a 400-kV cryoelectron microscope, we have obtained tomographic reconstructions of frozen-hydrated sea urchin axonemes with 8-10-nm resolution, as assessed by detection of characteristic components including doublet microtubules, radial spokes, central sheath projections, and outer dynein arms. We did not detect the inner dynein arms or the microtubule lattice. The 1/(8 nm) and 1/(16 nm) layer lines are consistently present in power spectra of both projection images and tomographic reconstructions. Strength and detection of the layer lines are dependent upon total electron dose and defocus. Both layer lines are surprisingly resistant to electron doses of up to 11000 electrons/nm(2). We present a summary of resolution considerations in cryoelectron tomography and conclude that the fundamental limitation is the total electron dose required for statistical significance. The electron dose can be fractionated among the numerous angular views in a tomographic data set, but there is an unavoidable fourth-power dependence of total dose on target resolution. Since higher-resolution features are more beam-sensitive, this dose requirement places an ultimate limit on the resolution of individual tomographic reconstructions. Instrumental and computational strategies to circumvent this limitation are discussed.

Membrane architecture of mitochondria in neurons of the central nervous system

Electron tomography was used to help redefine the membrane architecture of mitochondria in neurons of the brain. Investigations were conducted on unexplored questions of structural homogeneity between mitochondria in the four intensely studied regions of the brain and in the functionally distinct neuronal sub-compartments. These mitochondria have the majority of cristae composed of both tubular and lamellar segments with the tubes arranged more peripherally and the lamellae more centrally located. Cristae that are entirely tubular were not commonly seen and those that are entirely lamellar were rare. It was determined that cristae connect through narrow, sometimes very long tubular regions to the peripheral surface of the inner membrane. A structurally distinct type of contact site was revealed in brain mitochondria, which we named the bridge contact site. These bridges may play a role in the structural integrity of the outer and inner membrane systems. It was found that the membrane architecture in the various brain regions and neuronal compartments was strikingly uniform, including consistently tubular crista junctions. The functional consequences of this junctional architecture are discussed in relation to the segregation of proteins between the inner boundary membrane and the cristae membranes, and in relation to the model of microcompartmentation of macromolecules inside cristae.

Automatic alignment of transmission electron microscope tilt series without fiducial markers

Accurate image alignment is needed for computing three-dimensional reconstructions from transmission electron microscope tilt series. So far, the best results have been obtained by using colloidal gold beads as fiducial markers. If their use has not been possible for some reason, the only option has been the automatic cross-correlation-based registration methods. However, the latter methods are inaccurate and, as we will show, inappropriate for the whole problem. Conversely, we propose a novel method that uses the actual 3D motion model but works without any fiducial markers in the images. The method is based on matching and tracking some interest points of the intensity surface by first solving the underlying geometrical constraint of consecutive images in the tilt series. The results show that our method is near the gold marker alignment in the level of accuracy and hence opens the way for new opportunities in the analysis of electron tomography reconstructions, especially when markers cannot be used.

Electron tomographic and other approaches for imaging molecular machines

Two new methods, single-particle cryo-electron microscopy reconstruction and electron tomography, are increasingly used to visualize molecular machines in vitro and in the cellular context, respectively. Current efforts focus on the development of methods capable of visualizing molecular signatures in the cell, and first progress in this direction has now been made.

The emergence of electron tomography as an important tool for investigating cellular ultrastructure

Electron tomography has emerged as the leading method for the study of three-dimensional (3D) ultrastructure in the 5-20-nm resolution range. It is ideally suited for studying cell organelles, subcellular assemblies and, in some cases, whole cells. Tomography occupies a place in 3D biological electron microscopy between the work now being done at near-atomic resolution on isolated macromolecules or 2D protein arrays and traditional serial-section reconstructions of whole cells and tissue specimens. Tomography complements serial-section reconstruction by providing higher resolution in the depth dimension, whereas serial-section reconstruction is better able to trace continuity over long distances throughout the depth of a cell. The two techniques can be combined with good results for favorable specimens. Tomography also complements 3D macromolecular studies by offering sufficient resolution to locate the macromolecular complexes in their cellular context. The technology has matured to the point at which application of electron tomography to specimens in plastic sections is routine, and new developments to overcome limitations due to beam exposure and specimen geometry promise to further improve its capabilities. In this review we give a brief description of the methodology and a summary of the new insights gained in a few representative applications.(J Histochem Cytochem 49:553-563, 2001)

Electron tomography of mitochondria after the arrest of protein import associated with Tom19 depletion

In a mutant form of Neurospora crassa, in which sheltered RIP (repeat induced point mutation) was used to deplete Tom19, protein transport through the TOM/TIM pathway is arrested by the addition of p-fluorophenylalanine (FPA). Using intermediate-voltage electron tomography, we have generated three-dimensional reconstructions of 28 FPA-treated mitochondria at four time points (0-32 h) after the addition of FPA. We determined that the cristae surface area and volume were lost in a roughly linear manner. A decrease in mitochondrial volume was not observed until after 16 h of FPA treatment. The inner boundary membrane did not appear to shrink or contract away from the outer membrane. Interestingly, the close apposition of these membranes remained over the entire periphery, even after all of the cristae had disappeared. The different dynamics of the shrinkage of cristae membrane and inner boundary membrane has implications for compartmentalization of electron transport proteins. Two structurally distinct types of contact sites were observed, consistent with recently published work. We determined that the cristae in the untreated (control) mitochondria are all lamellar. The cristae of FPA-treated mitochondria retain the lamellar morphology as they reduce in size and do not adopt tubular shapes. Importantly, the crista junctions exhibit tubular as well as slot-like connections to the inner boundary membrane, persisting until the cristae disappear, indicating that their stability is not dependent on continuous protein import through the complex containing Tom19.

A new look at kinetochore structure in vertebrate somatic cells using high-pressure freezing and freeze substitution

Three decades of structural analysis have produced the view that the kinetochore in vertebrate cells is a disk-shaped structure composed of three distinct structural domains. The most prominent of these consists of a conspicuous electron opaque outer plate that is separated by a light-staining electron-translucent middle plate from an inner plate associated with the surface of the pericentric heterochromatin. Spindle microtubules terminate in the outer plate and, in their absence, a conspicuous corona of fine filaments radiates from the cytoplasmic surface of this plate. Here we report for the first time the ultrastructure of kinetochores in untreated and Colcemid-treated vertebrate somatic (PtK1) cells prepared for optimal structural preservation using high-pressure freezing and freeze substitution. In serial thin sections, and electron tomographic reconstructions, the kinetochore appears as a 50-75 nm thick mat of light-staining fibrous material that is directly connected with the more electron-opaque surface of the centromeric heterochromatin. This mat corresponds to the outer plate in conventional preparations, and is surrounded on its cytoplasmic surface by a conspicuous 100-150 nm wide zone that excludes ribosomes and other cytoplasmic components. High magnification views of this zone reveal that it contains a loose network of light-staining, thin (<9 nm diameter) fibers that are analogous to the corona fibers in conventional preparations. Unlike the chromosome arms, which appear uniformly electron opaque, the chromatin in the primary constriction appears mottled. Since the middle plate is not visible in these kinetochore preparations this feature is likely an artifact produced by extraction and coagulation during conventional fixation and/or dehydration procedures.