Freeze Substitution Research Articles

Filling the gap: adding super-resolution to array tomography for correlated ultrastructural and molecular identification of electrical synapses at the C. elegans connectome.

Correlating molecular labeling at the ultrastructural level with high confidence remains challenging. Array tomography (AT) allows for a combination of fluorescence and electron microscopy (EM) to visualize subcellular protein localization on serial EM sections. Here, we describe an application for AT that combines near-native tissue preservation via high-pressure freezing and freeze substitution with super-resolution light microscopy and high-resolution scanning electron microscopy (SEM) analysis on the same section. We established protocols that combine SEM with structured illumination microscopy (SIM) and direct stochastic optical reconstruction microscopy (dSTORM). We devised a method for easy, precise, and unbiased correlation of EM images and super-resolution imaging data using endogenous cellular landmarks and freely available image processing software. We demonstrate that these methods allow us to identify and label gap junctions in Caenorhabditis elegans with precision and confidence, and imaging of even smaller structures is feasible. With the emergence of connectomics, these methods will allow us to fill in the gap-acquiring the correlated ultrastructural and molecular identity of electrical synapses.

Technical Advances in Intracellular Detection Using Immuno-Gold Particles: Simple Cryofixation with Metal Contact Quick Freezing.

The preparation of biological specimens using cryofixation techniques ensures excellent visibility of intracellular structures and preserves the antigenic sites of subcellular molecules. Hence, cryofixation is an effective method of preparing samples for analyses using antibodies conjugated to gold nanoparticles that are designed to detect the localization of specific target molecules within cells. However, cryofixation cannot be utilized easily because it requires expensive equipment and skilled technologists, resulting in a high level of expense for researchers. Here, we describe a simple technical approach to cryofixation that uses metal contact quick freezing followed by a modified freeze substitution technique and immuno-gold labeling electron microscopy. Micrograph images of cells prepared using this modified cryofixation method demonstrated its superiority over chemical fixation for high contrast visualization of the morphologies of cellular components and preservation of antigenicity for immuno-gold labeling. This report provides valuable technical information related to the advancement of metal contact quick freezing techniques, which can be used to visualize biomedical events of interest in an easy, simple, and rapid manner.

Ultrastructure of embryonated eggs of the cestode Gyrocotyle urna (Gyrocotylidea) using cryo-methods

Ultrastructure of eggs of the cestode Gyrocotyle urna Grube and Wagener 1852 with fully formed shells and early embryonic stages is described for the first time. Multiple techniques used included cryo-methods of high-pressure freezing with freeze substitution combined with field emission scanning electron microscopy and transmission electron microscopy (TEM). After 20 days of in vitro maturation, eggs are composed, from the exterior to the interior, of a thick egg shell of vitelline origin, an early embryonic envelope, a ring of numerous large vitellocytes, and a group of differentiating blastomeres situated in the center, forming the early presumptive larva. The thick resistant egg shell is similar to that reported from other polylecithal neodermatan flatworms. The embryonic envelope is poorly formed at this stage and not yet divided into inner and outer envelopes as occurs in all neodermatans described to date. Vitellocytes are separate, not forming a syncytium, and are filled with diverse vitelline materials as well as lipid droplets and associated endomembrane components having ultrastructure consistent with macroautophagy systems seen among many animals in apoptotic or autophagic cells. These results largely corroborate the basic observations and interpretations of previous TEM studies on other neodermatans and provide insight into a powerful suite of cryo-techniques that can enhance our work with these challenging subjects.

Cryo-fixation and associated developments in transmission electron microscopy: a cool future for nematology

At present, the importance of sample preparation equipment for electron microscopy represents the driving force behind major breakthroughs in microscopy and cell biology. In this paper we present an introduction to the most commonly used cryo-fixation techniques, with special attention paid towards high-pressure freezing followed by freeze substitution. Techniques associated with cryo-fixation, such as immunolocalisation, cryo-sectioning, and correlative light and electron microscopy, are also highlighted. For studies that do not require high resolution, high quality results, or the immediate arrest of certain processes, conventional methods will provide answers to many questions. For some applications, such as immunocytochemistry, three-dimensional reconstruction of serial sections or electron tomography, improved preservation of the ultrastructure is required. This review of nematode cryo-fixation highlights that cryo-fixation not only results in a superior preservation of fine structural details, but also underlines the fact that some observations based on results solely obtained through conventional fixation approaches were either incorrect, or otherwise had severe limitations. Although the use of cryo-fixation has hitherto been largely restricted to model organisms, the advantages of cryo-fixation are sufficiently self-evident that we must conclude that the cryo-fixation method is highly likely to become the standard for nematode fixation in the near future.

High-Pressure Freezing Electron Microscopy of Zebrafish Oocytes.

Oogenesis is an essential cellular and developmental process to prepare the oocyte for propagation of a species after fertilization. Oocytes of oviparous animals are enormous cells endowed with many, big cellular compartments, which are interconnected through active intracellular transport. The dynamic transport pathways and the big organelles of the oocyte provide the opportunity to study cellular trafficking with outstanding resolution. Hence, oocytes were classically used to investigate cellular compartments. Though many novel regulators of vesicle trafficking have been discovered in yeast, tissue culture cells and invertebrates, recent forward genetic screens in invertebrate and vertebrate oocytes isolated novel control proteins specific to multicellular organisms. Zebrafish is a widely used vertebrate model to study cellular and developmental processes in an entire animal. The transparency of zebrafish embryos allows following cellular events during early development with in vivo imaging. Unfortunately, the active endocytosis of the oocyte also represents a drawback for imaging. The massive amounts of yolk globules prevent the penetration of light-beams and currently make in vivo microscopy a challenge. As a consequence, electron microscopy (EM) still provides the highest resolution to analyze the ultra-structural details of compartments and organelles and the mechanisms controlling many cellular pathways of the oocyte. Among different fixation approaches for EM, High Pressure Freezing (HPF) in combination with freeze substitution significantly improves the samples preservation closest to their natural status. Here, we describe the HPF with freeze substitution embedding method for analyzing cellular processes in zebrafish oocytes using electron microscopy.

The ability to survive intracellular freezing in nematodes is related to the pattern and distribution of ice formed.

A few species of nematodes can survive extensive intracellular freezing throughout all their tissues, an event that is usually thought to be fatal to cells. How are they able to survive in this remarkable way? The pattern and distribution of ice formed, after freezing at -10°C, can be observed using freeze substitution and transmission electron microscopy, which preserves the former position of ice as white spaces. We compared the pattern and distribution of ice formed in a nematode that survives intracellular freezing well (Panagrolaimus sp. DAW1), one that survives poorly (Panagrellus redivivus) and one with intermediate levels of survival (Plectus murrayi). We also examined Panagrolaimus sp. in which the survival of freezing had been compromised by starvation. Levels of survival were as expected and the use of vital dyes indicated cellular damage in those that survived poorly (starved Panagrolaimus sp. and P. murrayi). In fed Panagrolaimus sp. the intracellular ice spaces were small and uniform, whereas in P. redivivus and starved Panagrolaimus sp. there were some large spaces that may be causing cellular damage. The pattern and distribution of ice formed was different in P. murrayi, with a greater number of individuals having no ice or only small intracellular ice spaces. Control of the size of the ice formed is thus important for the survival of intracellular freezing in nematodes.

Induction of Embryogenesis in Brassica Napus Microspores Produces a Callosic Subintinal Layer and Abnormal Cell Walls with Altered Levels of Callose and Cellulose.

The induction of microspore embryogenesis produces dramatic changes in different aspects of the cell physiology and structure. Changes at the cell wall level are among the most intriguing and poorly understood. In this work, we used high pressure freezing and freeze substitution, immunolocalization, confocal, and electron microscopy to analyze the structure and composition of the first cell walls formed during conventional Brassica napus microspore embryogenesis, and in cultures treated to alter the intracellular Ca2+ levels. Our results revealed that one of the first signs of embryogenic commitment is the formation of a callose-rich, cellulose-deficient layer beneath the intine (the subintinal layer), and of irregular, incomplete cell walls. In these events, Ca2+ may have a role. We propose that abnormal cell walls are due to a massive callose synthesis and deposition of excreted cytoplasmic material, and the parallel inhibition of cellulose synthesis. These features were absent in pollen-like structures and in microspore-derived embryos, few days after the end of the heat shock, where abnormal cell walls were no longer produced. Together, our results provide an explanation to a series of relevant aspects of microspore embryogenesis including the role of Ca2+ and the occurrence of abnormal cell walls. In addition, our discovery may be the explanation to why nuclear fusions take place during microspore embryogenesis.

C3-P-06Structome analysis of freeze-substituted virulentMycobacterium tuberculosisbased on direct enumeration of the serial ultrathin sections with TEM

Serial ultrathin sections of virulent Mycobacterium tuberculosis H37Rv (ATCC 27294) were examined by transmission electron microscope and “structome” analysis (i.e., the quantitative three-dimensional structural analysis of a whole cell through direct enumeration and measurement at the electron microscopic level) was performed [ 1 ]. Five M. tuberculosis cells were cut into 24, 36, 69, 55, and 63 serial ultrathin cross sections, respectively. On average, the cells were 2.71 ± 1.05 μm in length, and the average diameter of the cell was 0.345 ± 0.029 μm. The outer membrane and plasma membrane surface areas were 3.04 ± 1.33 μm 2 and 2.67 ± 1.19 μm 2 , respectively. The cell and cytoplasm volumes were 0.293 ± 0.113 fl (= μm 3 ) and 0.210 ± 0.091 fl, respectively. The average total ribosome number per cell was 1,672 ± 568, and the ribosome density was 716.5 ± 171.4/0.1 fl. This is the first report of a structome analysis of M. tuberculosis cells prepared as serial ultrathin sections following cryofixation and rapid freeze substitution. These data are based on the direct measurement and enumeration of exquisitely preserved single-cell structures in transmission electron microscopy images rather than calculations or assumptions from indirect biochemical or molecular biological data, and may explain the slow growth of M. tuberculosis and enhance understanding of the structural properties related to the expression of antigenicity, acid-fastness, and the mechanism of drug resistance, particularly in regard to the ratio of target to drug concentrations.

In situ structure of FtsZ mini-rings in Arabidopsis chloroplasts

AbstractChloroplasts are essential plant organelles that divide by binary fission through a coordinated ring-shaped division machinery located both on the outside and inside of the chloroplast. The first step in chloroplast division is the assembly of an internal division ring (Z-ring) that is composed of the key filamentous chloroplast division proteins FtsZ1 and FtsZ2. How the individual FtsZ filaments assemble into higher-order structures to form the dividing Z-ring is not well understood and the most detailed insights have so far been gleaned from prokaryotic FtsZ. Here, we present in situ data of chloroplast FtsZ making use of a smaller ring-like FtsZ assembly termed mini-rings that form under well-defined conditions. Structured illumination microscopy (SIM) permitted their mean diameter to be determined as 208 nm and also showed that 68 % of these rings are terminally attached to linear FtsZ filaments. A correlative microscopy-compatible specimen preparation based on freeze substitution after high-pressure freezing is presented addressing the challenges such as autofluorescence and specific fluorescence attenuation. Transmission electron microscopy (TEM) and scanning TEM (STEM) imaging of thin sections exhibited ring-like densities that matched in size with the SIM data, and TEM tomography revealed insights into the molecular architecture of mini-rings demonstrating the following key features: (1) overall, a roughly bipartite split into a more ordered/curved and less ordered/curved half is readily discernible; (2) the density distribution in individual strands matches with the X-ray data, suggesting they constitute FtsZ protofilaments; (3) in the less ordered half of the ring, the protofilaments are able to assemble into higher-order structures such as double helices and supercoiled structures. Taken together, the data suggest that the state of existence of mini-rings could be described as metastable and their possible involvement in filament storage and Z-ring assembly is discussed.

Ultrastructure of Grapefruit Secretory Cavities and Immunocytochemical Localization of (+)-Limonene Synthase

Premise of research. The genus Citrus includes species that are among the most important tree fruit crops. Although fruit juice is the primary product, monoterpenoid essential oil obtained from the peel is an important value-added commodity. Peel monoterpenes are synthesized by subepidermal secretory cavities that consist of glandular cells surrounding an extracellular oil storage space. Several previous studies have focused on early secretory cavity development, ending with the initiation of secretion. In order to better understand the process of monoterpene formation, transport, and storage, it is important to obtain detailed information concerning plant oil glands during all phases of development.Methodology. TEM was performed on secretory cavities isolated from the exocarp of grapefruit (Citrus × paradisi Macfad. ‘Duncan’) preserved by microwave-assisted fixation or high-pressure freezing and freeze substitution. Immunocytochemistry was employed to localize (+)-limonene synthase. Tomography was used t...

Analysis of chromatin fibers in Hela cells with electron tomography.

The presence and folding pattern of chromatin in eukaryotic cells remain elusive and controversial. In this study, we prepared ultra-thin sections of Hela cells with three different fixation and sectioning methods, i.e., chemical fixation, high pressure freezing with freeze substitution, and cryo-ultramicrotomy with SEM-FIB (focused ion beam), and analyzed in vivo architecture of chromatin fibers in Hela nuclei with electron tomography technology. The results suggest that the chromatin fibers in eukaryotic Hela cells are likely organized in an architecture with a diameter of about 30 nm.

Optimized and Improved Immunogold Labeling on Ultrathin Sections of Nervous Tissue Following High Pressure Freezing, Freeze Substitution and Low Temperature Embedding

Optimized and Improved Immunogold Labeling on Ultrathin Sections of Nervous Tissue Following High Pressure Freezing, Freeze Substitution and Low Temperature Embedding

K+ accumulation in the cytoplasm and nucleus of the salt gland cells of Limonium bicolor accompanies increased rates of salt secretion under NaCl treatment using NanoSIMS

Recretohalophytes with specialized salt-secreting structures (salt glands) can secrete excess salts from plant, while discriminating between Na+ and K+. K+/Na+ ratio plays an important role in plant salt tolerance, but the distribution and role of K+ in the salt gland cells is poorly understood. In this article, the in situ subcellular localization of K and Na in the salt gland of the recretohalophyte Limonium bicolor Kuntze is described. Samples were prepared by high-pressure freezing (HPF), freeze substitution (FS) and analyzed using NanoSIMS. The salt gland of L. bicolor consists of sixteen cells. Higher signal strength of Na+ was located in the apoplast of salt gland cells. Compared with control, 200mM NaCl treatment led to higher signal strength of K+ and Na+ in both cytoplasm and nucleus of salt gland cells although K+/Na+ ratio in both cytoplasm and nucleus were slightly reduced by NaCl. Moreover, the rate of Na+ secretion per salt gland of L. bicolor treated with 200mM NaCl was five times that of controls. These results suggest that K+ accumulation both in the cytoplasm and nucleus of salt gland cells under salinity may play an important role in salt secretion, although the exact mechanism is unknown.

Electron microscopic tomography reveals discrete transcleft elements at excitatory and inhibitory synapses.

Electron microscopy has revealed an abundance of material in the clefts of synapses in the mammalian brain, and the biochemical and functional characteristics of proteins occupying synaptic clefts are well documented. However, the detailed spatial organization of the proteins in the synaptic clefts remains unclear. Electron microscope tomography provides a way to delineate and map the proteins spanning the synaptic cleft because freeze substitution preserves molecular details with sufficient contrast to visualize individual cleft proteins. Segmentation and rendering of electron dense material connected across the cleft reveals discrete structural elements that are readily classified into five types at excitatory synapses and four types at inhibitory synapses. Some transcleft elements resemble shapes and sizes of known proteins and could represent single dimers traversing the cleft. Some of the types of cleft elements at inhibitory synapses roughly matched the structure and proportional frequency of cleft elements at excitatory synapses, but the patterns of deployments in the cleft are quite different. Transcleft elements at excitatory synapses were often evenly dispersed in clefts of uniform (18 nm) width but some types show preference for the center or edges of the cleft. Transcleft elements at inhibitory synapses typically were confined to a peripheral region of the cleft where it narrowed to only 6 nm wide. Transcleft elements in both excitatory and inhibitory synapses typically avoid places where synaptic vesicles attach to the presynaptic membrane. These results illustrate that elements spanning synaptic clefts at excitatory and inhibitory synapses consist of distinct structures arranged by type in a specific but different manner at excitatory and inhibitory synapses.

Abstract 450: Tumor Necrosis Factor Disrupts Endothelial Surface Glycocalyx Imaged by High-pressure Freezing, Freeze Substitution TEM

Objective: The endothelial surface glycocalyx (GCX) is a hydrated mesh formed from a wide variety of endothelial cell membrane-associated macromolecules including glycoproteins bearing sialic acid and proteoglycans. It is thought to be damaged in diseases associated with elevated levels of tumor necrosis factor α (TNF-α) since surface proteoglycan and sialic acid amount decreased after TNF treatment. We imaged in vitro GCX in response to TNF-α using rapid freezing/freeze substitution (RF/FS) transmission electron microscopy (TEM) so that the GCX can be stably preserved in its hydrated configuration. Methods and Results: Human glomerular ECs (HGenC) were seeded onto fibronectin- coated PET membrane of the 96-multiwell inserts and allowed to grow to confluence for 4 days. Before experimentation, cells were then treated with TNF (20 ng/ml) or control medium for 24 h. The PET membrane with the cells attached were removed from the Transwell insert by carefully cutting around the membrane edges with a scalpel, and transferred to aluminum planchettes (Ted Pella). The membranes were then subjected to RF/FS-TEM. RF/FS-TEM revealed impressively thick HGenC GCX of ≈13 μm under control condition. In cells treated with TNF, the GCX completely disappeared. Immunoconfocal studies confirmed that in vitro GCX was damaged by TNF. Conclusions: New observations by RF/FS-TEM reveal substantial GCX layers on cultured human glomerular EC, which are completely abolished by TNF-α.

Presynaptic architecture of the larval zebrafish neuromuscular junction.

This article shows the ultrastructural architecture of larval zebrafish (Danio rerio) neuromuscular junctions in three dimensions. We compare classical electron microscopy fixation techniques with high-pressure freezing followed by freeze substitution (HPF/FS) in combination with electron tomography. Furthermore, we compare the structure of neuromuscular junctions in 4- and 8-dpf zebrafish larvae with HPF/FS because this allows for close-to-native ultrastructural preservation. We discovered that synaptic vesicles of 4-dpf zebrafish larvae are larger than those of 8-dpf larvae. Furthermore, we describe two types of dense-core vesicles and quantify a filamentous network of small filaments interconnecting synaptic vesicles as well as tethers connecting synaptic vesicles to the presynaptic cell membrane. In the center of active zones, we found elaborate electron-dense projections physically connecting vesicles of the synaptic vesicle pool to the presynaptic membrane. Overall this study establishes the basis for systematic comparisons of synaptic architecture at high resolution in three dimensions of an intact vertebrate in a close-to-native state. Furthermore, we provide quantitative information that builds the basis for diverse systems biology approaches in neuroscience, from comparative anatomy to cellular simulations.

Correlative in-resin super-resolution and electron microscopy using standard fluorescent proteins.

We introduce a method for correlative in-resin super-resolution fluorescence and electron microscopy (EM) of biological structures in mammalian culture cells. Cryo-fixed resin embedded samples offer superior structural preservation, performing in-resin super-resolution, however, remains a challenge. We identified key aspects of the sample preparation procedure of high pressure freezing, freeze substitution and resin embedding that are critical for preserving fluorescence and photo-switching of standard fluorescent proteins, such as mGFP, mVenus and mRuby2. This enabled us to combine single molecule localization microscopy with transmission electron microscopy imaging of standard fluorescent proteins in cryo-fixed resin embedded cells. We achieved a structural resolution of 40–50 nm (~17 nm average single molecule localization accuracy) in the fluorescence images without the use of chemical fixation or special fluorophores. Using this approach enabled the correlation of fluorescently labeled structures to the ultrastructure in the same cell at the nanometer level and superior structural preservation.

The Effects of the F-Actin Inhibitor Latrunculin A on the Pathogenic Yeast Cryptococcus neoformans

Background: This basic research aimed to investigate the effects of the actin inhibitor latrunculin A (LA) on the human pathogen Cryptococcus neoformans, by freeze-substitution (FS) and electron microscopy (EM), to determine whether the actin cytoskeleton can become a new antifungal target for inhibition of cell division. Methods: Cells treated with LA for 20 h in yeast-extract peptone dextrose medium were investigated by phase-contrast and fluorescent microscopy, FS and transmission EM, counted in a Bürker chamber and the absorbance was then measured. Results: The disappearance of actin patches, actin cables and actin rings demonstrated the response of the cells of C. neoformans to the presence of the actin inhibitor LA. The removal of actin cables and patches arrested proliferation and led to the production of cells that had ultrastructural disorder, irregular morphology of the mitochondria and thick aberrant cell walls. Budding cells lysed in the buds and septa. Conclusion: LA exerts fungistatic, fungicidal and fungilytic effects on the human pathogenic yeast C. neoformans.

Structome analysis of virulent Mycobacterium tuberculosis, which survives with only 700 ribosomes per 0.1 fl of cytoplasm.

We previously reported the exquisite preservation of the ultrastructures of virulent Mycobacterium tuberculosis cells processed through cryofixation and rapid freeze substitution. Here, we report the “structome” analysis (i.e., the quantitative three-dimensional structural analysis of a whole cell at the electron microscopic level) of virulent M. tuberculosis using serial ultrathin sections prepared after cryofixation and rapid freeze substitution and analyzed by transmission electron microscopy. Five M. tuberculosis cells, which were contained in the serial ultrathin cross sections encompassing from one end to the other, were cut into 24, 36, 69, 55, and 63 serial ultrathin sections, respectively. On average, the cells were 2.71 ± 1.05 μm in length, and the average diameter of the cell was 0.345 ± 0.029 μm. The outer membrane and plasma membrane surface areas were 3.04 ± 1.33 μm2 and 2.67 ± 1.19 μm2, respectively. The cell, outer membrane, periplasm, plasma membrane, and cytoplasm volumes were 0.293 ± 0.113 fl (= μm3), 0.006 ± 0.003 fl, 0.060 ± 0.021 fl, 0.019 ± 0.008 fl, and 0.210 ± 0.091 fl, respectively. The average total ribosome number was 1,672 ± 568, and the ribosome density was 716.5 ± 171.4/0.1 fl. This is the first report of a structome analysis of M. tuberculosis cells prepared as serial ultrathin sections following cryofixation and rapid freeze substitution and examined by transmission electron microscopy. These data are based on the direct measurement and enumeration of exquisitely preserved single-cell structures in transmission electron microscopy images rather than calculations or assumptions from indirect biochemical or molecular biological data. In addition, these data may explain the slow growth of M. tuberculosis and enhance understanding of the structural properties related to the expression of antigenicity, acid-fastness, and the mechanism of drug resistance, particularly in regard to the ratio of target to drug concentrations.

High-Pressure Freeze and Freeze Substitution Electron Microscopy in C. elegans.

While traditional chemical fixation methods for C. elegans electron microscopy (EM) have provided invaluable anatomical and structural information, the development of high-pressure freeze (HPF) and freeze substitution (FS) protocols offers advantages for high-resolution imaging. Specimens prepared using HPF methodology exhibit fewer distortion artifacts due to fixation and dehydration, have improved antigenicity, and result in a more physiologically accurate structural representation of the worm. In the HPF technique, freely moving worms are frozen at high-pressure (2100 bar) and low temperature (-180 °C) within milliseconds. These conditions prevent the formation of ice crystals that can damage cellular structures. Samples then undergo FS, during which worms are slowly brought to room temperature while substituting amorphous ice with organic solvents to preserve tissue in its near native state and provide contrast for imaging. FS can be performed in an automatic freeze substitution (AFS) machine or in makeshift, temperature controlled chambers. Fixed worms can be embedded in plastic resin and further processed for a variety of imaging techniques. Samples then viewed using scanning (SEM) or transmission electron microscopy (TEM) will show enhanced preservation of organelles, cell morphology, and antigenicity for immunocytochemistry.