Automated electron microscope tomography using robust prediction of specimen movements

A new method was developed to acquire images automatically at a series of specimen tilts, as required for tomographic reconstruction. The method uses changes in specimen position at previous tilt angles to predict the position at the current tilt angle. Actual measurement of the position or focus is skipped if the statistical error of the prediction is low enough. This method allows a tilt series to be acquired rapidly when conditions are good but falls back toward the traditional approach of taking focusing and tracking images when necessary. The method has been implemented in a program, SerialEM, that provides an efficient environment for data acquisition. This program includes control of an energy filter as well as a low-dose imaging mode, in which tracking and focusing occur away from the area of interest. The program can automatically acquire a montage of overlapping frames, allowing tomography of areas larger than the field of the CCD camera. It also includes tools for navigating between specimen positions and finding regions of interest.

Electron microscopy of specimens in liquid

Imaging samples in liquids with electron microscopy can provide unique insights into biological systems, such as cells containing labelled proteins, and into processes of importance in materials science, such as nanoparticle synthesis and electrochemical deposition. Here we review recent progress in the use of electron microscopy in liquids and its applications. We examine the experimental challenges involved and the resolution that can be achieved with different forms of the technique. We conclude by assessing the potential role that electron microscopy of liquid samples can play in areas such as energy storage and bioimaging.

Dynamic microscopy of nanoscale cluster growth at the solid-liquid interface

Dynamic processes at the solid-liquid interface are of key importance across broad areas of science and technology. Electrochemical deposition of copper, for example, is used for metallization in integrated circuits, and a detailed understanding of nucleation, growth and coalescence is essential in optimizing the final microstructure. Our understanding of processes at the solid-vapour interface has advanced tremendously over the past decade due to the routine availability of real-time, high-resolution imaging techniques yielding data that can be compared quantitatively with theory. However, the difficulty of studying the solid-liquid interface leaves our understanding of processes there less complete. Here we analyse dynamic observations--recorded in situ using a novel transmission electron microscopy technique--of the nucleation and growth of nanoscale copper clusters during electrodeposition. We follow in real time the evolution of individual clusters, and compare their development with simulations incorporating the basic physics of electrodeposition during the early stages of growth. The experimental technique developed here is applicable to a broad range of dynamic phenomena at the solid-liquid interface.

Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli

We present a new reconstruction method that takes advantage of the fact that many biological macromolecular assemblies show a preferred orientation with respect to the plane of the specimen grid in the electron microscopic preparation. From one micrograph taken of such a specimen tilted by a large angle, a conical tilt series with random azimuthal angles can be extracted and used for a three-dimensional reconstruction. Our technique allows the determination of the molecular structure under low-dose conditions, which are not achievable with reconstruction methods that use conventional tilt series. The reconstruction method combines a number of existing image processing techniques with a newly developed weighted back-projection algorithm designed for three-dimensional reconstruction from projections taken with arbitrary projecting directions. The method is described as it was applied to the three-dimensional reconstruction of the structure of the 50S ribosomal subunit of Escherichia coli (E. coli).

Perspectives of molecular and cellular electron tomography

After a general introduction to three-dimensional electron microscopy and particularly to electron tomography (ET), the perspectives of applying ET to native (frozen-hydrated) cellular structures are discussed. In ET, a set of 2-D images of an object is recorded at different viewing directions and is then used for calculating a 3-D image. ET at a resolution of 2-5 nm would allow the 3-D organization of structural cellular components to be studied and would provide important information about spatial relationships and interactions. The question of whether it is a realistic long-term goal to visualize or--by sophisticated pattern recognition methods--identify macromolecules in cells frozen in toto or in frozen sections of cells is addressed. Because of the radiation sensitivity of biological specimens, a prerequisite of application of ET is the automation of the imaging process. Technical aspects of automated ET as realized in Martinsried and experiences are presented, and limitations of the technique are identified, both theoretically and experimentally. Possible improvements of instrumentation to overcome at least part of the limitations are discussed in some detail. Those means include increasing the accelerating voltage into the intermediate voltage range (300 to 500 kV), energy filtering, the use of a field emission gun, and a liquid-helium-cooled specimen stage. Two additional sections deal with ET of isolated macromolecules and of macromolecular structures in situ, and one section is devoted to possible methods for the detection of structures in volume data.

2D crystallization: from art to science

The techniques as well as the principles of the 2D crystallization of membrane and water-soluble proteins for electron crystallography are reviewed. First, the biophysics of the interactions between proteins, lipids and detergents is surveyed. Second, crystallization of membrane proteins in situ and by reconstitution methods is discussed, and the various factors involved are addressed. Third, we elaborate on the 2D crystallization of water-soluble proteins, both in solution and at interfaces, such as lipid monolayers, mica, carbon film or mercury surfaces. Finally, techniques and instrumentations that are required for 2D crystallization are described.

Imaging extracellular vesicles: current and emerging methods

Extracellular vesicles (EVs) are lipid bilayer-enclosed nanoparticles released by cells. They range from 30 nm to several micrometers in diameter, and ferry biological cargos such as proteins, lipids, RNAs and DNAs for local and distant intercellular communications. EVs have since been found to play a role in development, as well as in diseases including cancers. To elucidate the roles of EVs, researchers have established different methods to visualize and study their spatiotemporal properties. However, since EV are nanometer-sized, imaging them demands a full understanding of each labeling strategy to ensure accurate monitoring. This review covers current and emerging strategies for EV imaging for prospective studies.

4D ultrafast electron diffraction, crystallography, and microscopy

In this review, we highlight the progress made in the development of 4D ultrafast electron diffraction (UED), crystallography (UEC), and microscopy (UEM) with a focus on concepts, methodologies, and prototypical applications. The joint atomic-scale resolutions in space and time, and sensitivity reached, make it possible to determine complex transient structures and assemblies in different phases. These applications include studies of isolated chemical reactions (molecular beams), interfaces, surfaces and nanocrystals, self-assembly, and 2D crystalline fatty-acid bilayers. In 4D UEM, we are now able, using timed, single-electron packets, to image nano-to-micro scale structures of materials and biological cells. Future applications of these methods are foreseen across areas of physics, chemistry, and biology.

Electron microscope visualization of chromatin and other DNA-protein complexes

In this review we have tried to cover the direct mounting techniques currently in use and, through micrographs kindly supplied by our colleagues, to illustrate uses of the different methods. For the novice, it is important to select one technique, taking time to become acquainted with its use in visualizing simple test samples before applying it to examine more complex structures. We have tried to emphasize the importance of controlling the fixation for two reasons. First, confidence in the fixation step allows one to correlate structures observed by EM with structures present in solution. Second, fixation of otherwise labile samples allows one to apply powerful purification techniques.

Microlithography by using neutral metastable atoms and self-assembled monolayers

Lithography can be performed with beams of neutral atoms in metastable excited states to pattern self-assembled monolayers (SAMs) of alkanethiolates on gold. An estimated exposure of a SAM of dodecanethiolate (DDT) to 15 to 20 metastable argon atoms per DDT molecule damaged the SAM sufficiently to allow penetration of an aqueous solution of ferricyanide to the surface of the gold. This solution etched the gold and transformed the patterns in the SAMs into structures of gold; these structures had edge resolution of less than 100 nanometers. Regions of SAMs as large as 2 square centimeters were patterned by exposure to a beam of metastable argon atoms. These observations suggest that this system may be useful in new forms of micro- and nanolithography.

Transmission electron microscopy with Zernike phase plate

The possibility of implementing a Zernike phase plate in a transmission electron microscope is investigated both theoretically and experimentally. The phase-retarding plate in the form of thin film with a hole in the center is positioned in the back-focal plane of the objective lens. The experiments show that the phase plate functions as predicted, producing a cosine-type phase contrast transfer function. Images of negatively stained horse spleen ferritin were highly improved in the contrast and the image-modulation, compared to those acquired without the phase plate. Charging and related difficulties were encountered during the phase plate experiments. In order to make the technique user-friendly a number of improvements have to be made, and are discussed in terms of the current level of technology and instrumentation.

Imaging in five dimensions: time-dependent membrane potentials in individual mitochondria

Because of its importance in the chemiosmotic theory, mitochondrial membrane potential has been the object of many investigations. Significantly, however, quantitative data on how energy transduction might be regulated or perturbed by the physiological state of the cell has only been gathered via indirect studies on isolated mitochondrial suspensions; quantitative studies on individual mitochondria in situ have not been possible because of their small size, their intrinsic motility, and the absence of appropriate analytical reagents. In this article, we combine techniques for rapid, high resolution, quantitative three-dimensional imaging microscopy and mathematical modeling to determine accurate distributions of a potentiometric fluorescent probe between the cytosol and individual mitochondria inside a living cell. Analysis of this distribution via the Nernst equation permits assignment of potentials to each of the imaged mitochondrial membranes. The mitochondrial membrane potentials are distributed over a narrow range centered at -150 mV within the neurites of differentiated neuroblastoma cells. We find that the membrane potential of a single mitochondrion is generally remarkably stable over times of 40-80 s, but significant fluctuations can occasionally be seen. The motility of individual mitochondria is not directly correlated to membrane potential, but mitochondria do become immobile after prolonged treatment with respiratory inhibitors or uncouplers. Thus, three spatial dimensions, a key physiological parameter, and their changes over time are all quantitated for objects at the resolution limit of light microscopy. The methods described may be readily extended to permit investigations of how mitochondrial function is integrated with other processes in the intact cell.

Plasmon resonant particles for biological detection

Several recent advances in the optical observation, fabrication, and bioconjugation of nanometer-sized gold or silver colloids have produced a robust new class of label. These plasmon resonant particle (PRP) conjugates have several important advantages: they are ultra-bright, so the light scattered from the individual particles can be viewed using a simple optical microscope system with a white light illumination source; they do not photo-bleach; PRPs can be prepared that preferentially scatter light of a chosen color; and it is possible to prepare bioconjugated PRPs that are stable in solution. These properties, and the automation of PRP identification, discrimination, and counting, have enabled the development of ultrasensitive, multicolor, and multiplex applications in the life science field.

Pregnancy outcome following transfer of human blastocysts vitrified on electron microscopy grids after induced collapse of the blastocoele

BACKGROUND

The purpose of this study was to examine the effects on blastocyst survival and subsequent pregnancy rate of 'artificial shrinkage' (i.e. induced collapse of the blastocoele) before vitrification of human blastocysts.

METHODS

After embryo transfer in IVF cycles, surplus embryos that developed to the expanded blastocyst stage were cryopreserved. Before vitrification on electron microscopy (EM) grids, artificial shrinkage was induced in expanded blastocysts using a 29-gauge needle. After thawing, transfers were performed on 25 couples. Post-thaw survival rates and clinical outcome after the transfer of vitrified blastocysts were examined.

RESULTS

Of 90 expanded blastocysts vitrified from 25 patients, 81 survived (90.0%) and 40 of them were hatched (49.4%) at the time of transfer. The implantation rate was 29.0% (20/69), and the pregnancy rate was 48.0% (12/25). Nine patients delivered 15 infants, two pregnancies are ongoing and one ended in miscarriage.

CONCLUSIONS

The results suggest that artificial shrinkage is a useful technique for vitrification of expanded blastocysts on EM grids.

Automated microscopy for electron tomography

Instrumentation and methodology for the automatic collection of tomographic tilt series data for the three-dimensional reconstruction of single particles is described. The system consists of a Philips EM 430 TEM, with a Gatan 673 cooled slow-scan CCD camera and a Philips C400 microscope computer control unit attached. The procedure for data collection includes direct digital recording of the images on the CCD camera and the automatic measurement and correction of (a) image shifts resulting from tilting the specimen, (b) variation of defocus and (c) the eucentric height position of the specimen. Experiments are described illustrating the possibilities and limitations of automatic data collection. Data collection at a magnification of 30k shows that the exposure time of the specimen to the beam is reduced by a factor of 10-100 compared to manual operation of the TEM.

Four-dimensional ultrafast electron microscopy

Electron microscopy is arguably the most powerful tool for spatial imaging of structures. As such, 2D and 3D microscopies provide static structures with subnanometer and increasingly with angstrom-scale spatial resolution. Here we report the development of 4D ultrafast electron microscopy, whose capability imparts another dimension to imaging in general and to dynamics in particular. We demonstrate its versatility by recording images and diffraction patterns of crystalline and amorphous materials and images of biological cells. The electron packets, which were generated with femtosecond laser pulses, have a de Broglie wavelength of 0.0335 angstroms at 120 keV and have as low as one electron per pulse. With such few particles, doses of few electrons per square ångstrom, and ultrafast temporal duration, the long sought after but hitherto unrealized quest for ultrafast electron microscopy has been realized. Ultrafast electron microscopy should have an impact on all areas of microscopy, including biological imaging.

Application of digital image analysis and flow cytometry to enumerate marine viruses stained with SYBR gold

A novel nucleic acid stain, SYBR Gold, was used to stain marine viral particles in various types of samples. Viral particles stained with SYBR Gold yielded bright and stable fluorescent signals that could be detected by a cooled charge-coupled device camera or by flow cytometry. The fluorescent signal strength of SYBR Gold-stained viruses was about twice that of SYBR Green I-stained viruses. Digital images of SYBR Gold-stained viral particles were processed to enumerate the concentration of viral particles by using digital image analysis software. Estimates of viral concentration based on digitized images were 1.3 times higher than those based on direct counting by epifluorescence microscopy. Direct epifluorescence counts of SYBR Gold-stained viral particles were in turn about 1.34 times higher than those estimated by the transmission electron microscope method. Bacteriophage lysates stained with SYBR Gold formed a distinct population in flow cytometric signatures. Flow cytometric analysis revealed at least four viral subpopulations for a Lake Erie sample and two subpopulations for a Georgia coastal sample. Flow cytometry-based viral counts for various types of samples averaged 1.1 times higher than direct epifluorescence microscopic counts. The potential application of digital image analysis and flow cytometry for rapid and accurate measurement of viral abundance in aquatic environments is discussed.

Individual nucleus accumbens-projection neurons receive both basolateral amygdala and ventral subicular afferents in rats

The nucleus accumbens is regarded as the limbic-motor interface, in view of its limbic afferent and somatomotor and autonomic efferent connections. Within the accumbens, there appear to be specific areas in which limbic afferent fibres, derived from the hippocampus and the amygdala, overlap. These afferent inputs have been suggested to converge monosynaptically on cells within the accumbens and are hypothesized to play a role in paradigms such as conditioned place preference. Convergence between inputs from basolateral amygdala and hippocampus can be demonstrated with electrophysiological recording methods, but these do not conclusively preclude polysynaptic mechanisms. We examined the synaptic input to the projection neurons of the accumbens, the medium-sized densely spiny neurons. We labelled the projection neurons with a small injection of biotinylated dextran amine into the accumbens, and the afferents from the basolateral amygdala and ventral subiculum of the hippocampus with injections of biotinylated dextran amine and Phaseolus vulgaris-leucoagglutinin respectively, and revealed the anterogradely labelled fibres with different chromogens. The labelled accumbens-projection neurons were studied with correlated light and electron microscopy for identified monosynaptic inputs. With this technique we have demonstrated anatomically that monosynaptic convergence between the ventral subicular region of the hippocampus and the basolateral region of the amygdala occurs at the level of the proximal as well as distal dendrites. Finally, we suggest that these anatomical arrangements may represent the framework for the integrative role that has been assigned to the accumbens.

Structure of wet specimens in electron microscopy. Improved environmental chambers make it possible to examine wet specimens easily

Several recent technological advances have increased the practicality and usefulness of the technique of electron microscopy of wet objects. (i) There have been gains in the effective penetration of high-voltage microscopes, scanning transmission microscopes, and high-voltage scanning microscopes. The extra effective penetration gives more scope for obtaining good images through film windows, gas, and liquid layers. (ii) Improved methods of obtaining contrast are available (especially dark field and inelastic filtering) that often make it possible to obtain sufficient contrast with wet unstained objects. (iii) Improved environmental chamber design makes it possible to insert and examine wet specimens as easily as dry specimens. The ultimate achievable resolution for wet objects in an environmental chamber will gradually become clear experimentally. Resolution is mainly a function of gas path, liquid and wet specimen thickness, specimen stage stability, acceleration voltage, and image mode (fixed or scanning beam) (13). Much depends on the development of the technique for controlling the thickness of extraneous water film around wet objects or the technique for depositing wet objects onto dry, hydrophobic support films. Although some loss of resolution due to water or gas scattering will always occur, an effective gain is anticipated in preserving the shape of individual molecules and preventing the partial collapse that usually occurs on drying or negative staining. The most basic question for biological electron microscopy is probably whether any living functions of cells can be observed so that the capabilities of the phase contrast and interference light microscopes can be extended. Investigators are now rapidly approaching a final answer to this question. The two limiting factors are (i) maintaining cell motility in spread cells immersed in thin layers of media and (ii) reducing beam radiation damage to an acceptable level. The use of sensitive emulsions and image intensifiers can bring the observation dose below that required to stop cell motility. Use of a timed, pulsed deflector system enables sufficiently short exposures to be obtained to eliminate blurring due to Brownian motion. Environmental chambers have enhanced the possibilities of electron diffraction analysis of minute crystals and ordered biological structures. High-resolution electron diffraction patterns (especially kinematic) of protein crystals can only be obtained in a wet environment. Hence, it may now be possible to obtain undistorted images of protein molecules. Moreover, by subjecting diffraction patterns to image-iterative techniques (56), it will be possible to phase the electron diffraction patterns to give a calculated image with a higher resolution than that which can be produced by electron microscope objective lenses. Environmental chambers offer exciting prospects for the determination of water structure and water and ice nucleation (atmospheric science). Nucleation data near the molecular level have been badly needed for some time. The application of environmental chambers in industrial chemistry, for example, in studies of polymerization, catalysis, and corrosion, are awaiting exploration. They offer an unusual approach to measurements of reaction kinetics through images that should be both sensitive and rapid.

Formulation of amphotericin B as nanosuspension for oral administration

Amphotherin B was formulated in a nanosuspension as a new oral drug delivery system for the treatment of experimental visceral leishmaniasis. Amphotericin B (AmB) nanosuspensions were produced by high pressure homogenisation obtaining particles with a PCS diameter of 528 nm. Environmental stability was determined in artificial gastrointestinal fluids at different pH and electrolyte concentrations. In vivo efficacy was determined in a mouse model of visceral leishmaniasis. Following oral administration (5 mg kg(-1)), micronised amphotericin B did not show any curative effect. However, administrations of amphotericin B nanosuspension, reduced liver parasite load by 28.6% compared to untreated controls.

Golgi twins in late mitosis revealed by genetically encoded tags for live cell imaging and correlated electron microscopy

Combinations of molecular tags visible in light and electron microscopes become particularly advantageous in the analysis of dynamic cellular components like the Golgi apparatus. This organelle disassembles at the onset of mitosis and, after a sequence of poorly understood events, reassembles after cytokinesis. The precise location of Golgi membranes and resident proteins during mitosis remains unclear, partly due to limitations of molecular markers and the resolution of light microscopy. We generated a fusion consisting of the first 117 residues of alpha-mannosidase II tagged with a fluorescent protein and a tetracysteine motif. The mannosidase component guarantees docking into the Golgi membrane, with the tags exposed in the lumen. The fluorescent protein is optically visible without further treatment, whereas the tetracysteine tag can be reduced acutely with a membrane-permeant phosphine, labeled with ReAsH, monitored in the light microscope, and used to trigger the photoconversion of diaminobenzidine, allowing 4D optical recording on live cells and correlated ultrastructural analysis by electron microscopy. These methods reveal that Golgi reassembly is preceded by the formation of four colinear clusters at telophase, two per daughter cell. Within each daughter, the smaller cluster near the midbody gradually migrates to rejoin the major cluster on the far side of the nucleus and asymmetrically reconstitutes a single Golgi apparatus, first in one daughter cell and then in the other. Our studies provide previously undescribed insights into Golgi disassociation and reassembly during mitosis and offer a powerful approach to follow recombinant protein distribution in 4D imaging and correlated high-resolution analysis.