Quantitative electron energy loss spectroscopy in biology

Advances and Applications of Atomic-Resolution Scanning Transmission Electron Microscopy

Although scanning transmission electron microscopy (STEM) images of individual heavy atoms were reported 50 years ago, the applications of atomic-resolution STEM imaging became wide spread only after the practical realization of aberration correctors on field-emission STEM/TEM instruments to form sub-Ångstrom electron probes. The innovative designs and advances of electron optical systems, the fundamental understanding of electron–specimen interaction processes, and the advances in detector technology all played a major role in achieving the goal of atomic-resolution STEM imaging of practical materials. It is clear that tremendous advances in computer technology and electronics, image acquisition and processing algorithms, image simulations, and precision machining synergistically made atomic-resolution STEM imaging routinely accessible. It is anticipated that further hardware/software development is needed to achieve three-dimensional atomic-resolution STEM imaging with single-atom chemical sensitivity, even for electron-beam-sensitive materials. Artificial intelligence, machine learning, and big-data science are expected to significantly enhance the impact of STEM and associated techniques on many research fields such as materials science and engineering, quantum and nanoscale science, physics and chemistry, and biology and medicine. This review focuses on advances of STEM imaging from the invention of the field-emission electron gun to the realization of aberration-corrected and monochromated atomic-resolution STEM and its broad applications.

Direct transfer of electron microscopy samples to wetted carbon and graphene films via a support floatation block

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Design of a sample-support transfer block for negative stain and cryo-EM.

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Direct wetted transfer of 10 μL samples to carbon.

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Direct wetted transfer of 10 μL samples to graphene.

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Buffer exchange from 10 μL sample volumes in situ within the block.

Support films are commonly used during cryo-EM specimen preparation to both immobilise the sample and minimise the exposure of particles at the air-water interface. Here we report preparation protocols for carbon and graphene supported single particle electron microscopy samples using a novel 3D-printed sample transfer block to facilitate the direct, wetted, movement of both carbon and graphene supports from the substrate on which they were generated to small volumes (10 μL) of sample. These approaches are simple and inexpensive to implement, minimise hydrophobic contamination of the support films, and are widely applicable to single particle studies. Our approach also allows the direct exchange of the sample buffer on the support film in cases in which it is unsuitable for vitrification, e.g. for samples from centrifugal density gradients that help to preserve sample integrity.

Time-resolved cathodoluminescence of DNA triggered by picosecond electron bunches

Despite the tremendous importance of so-called ionizing radiations (X-rays, accelerated electrons and ions) in cancer treatment, most studies on their effects have focused on the ionization process itself, and neglect the excitation events the radiations can induce. Here, we show that the excited states of DNA exposed to accelerated electrons can be studied in the picosecond time domain using a recently developed cathodoluminescence system with high temporal resolution. Our study uses a table-top ultrafast, UV laser-triggered electron gun delivering picosecond electron bunches of keV energy. This scheme makes it possible to directly compare time-resolved cathodoluminescence with photoluminescence measurements. This comparison revealed qualitative differences, as well as quantitative similarities between excited states of DNA upon exposure to electrons or photons.

Using electron microscopes to look into the lung

In the nineteenth century, there was a dispute about the existence of a lung alveolar epithelium which remained unsolved until the invention of electron microscopy (EM) and its application to the lung. From the early 1960s, Ewald Weibel became the master of lung EM. He showed that the alveolar epithelium is covered with a lining layer containing surfactant. Weibel also explained the phenomenon of "non-nucleated plates" observed already in 1881 by Albert Kölliker. Weibel's most significant contribution was to the development of stereological methods. Therefore, quantitative characterization of lung structure revealing structure-function relationships became possible. Today, the spectrum of EM methods to study the fine structure of the lung has been extended significantly. Cryo-preparation techniques are available which are necessary for immunogold labeling of molecules. Energy-filtering techniques can be used for the detection of elements. There have also been major improvements in stereology, thus providing a very versatile toolbox for quantitative lung phenotype analyses. A new dimension was added by 3D EM techniques. Depending on the desired sample size and resolution, the spectrum ranges from array tomography via serial block face scanning EM and focused ion beam scanning EM to electron tomography. These 3D datasets provide new insights into lung ultrastructure. Biomedical EM is an ever-developing field. Its high resolution remains unparalleled. Moreover, EM has the unique advantage of providing an "open view" into cells and tissues within their full architectural context. Therefore, EM will remain an indispensable tool for a better understanding of the lung's functional design.

Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging (ESI)

The limits to optical resolution and the challenge of identifying specific protein populations in transmission electron microscopy have been obstacles in cell biology. Many phenomena cannot be explained by in vitro analysis in simplified systems and need additional structural information in situ, particularly in the range between 1 nm and 0.1 µm, in order to be fully understood. Here, electron spectroscopic imaging, a transmission electron microscopy technique that allows simultaneous mapping of the distribution of proteins and nucleic acids, and an expression tag, miniSOG, are combined to study the structure and organization of DNA double-strand break repair foci.

Combining quantitative 2D and 3D image analysis in the serial block face SEM: application to secretory organelles of pancreatic islet cells

A combination of two-dimensional (2D) and three-dimensional (3D) analyses of tissue volume ultrastructure acquired by serial block face scanning electron microscopy can greatly shorten the time required to obtain quantitative information from big data sets that contain many billions of voxels. Thus, to analyse the number of organelles of a specific type, or the total volume enclosed by a population of organelles within a cell, it is possible to estimate the number density or volume fraction of that organelle using a stereological approach to analyse randomly selected 2D block face views through the cells, and to combine such estimates with precise measurement of 3D cell volumes by delineating the plasma membrane in successive block face images. The validity of such an approach can be easily tested since the entire 3D tissue volume is available in the serial block face scanning electron microscopy data set. We have applied this hybrid 3D/2D technique to determine the number of secretory granules in the endocrine α and β cells of mouse pancreatic islets of Langerhans, and have been able to estimate the total insulin content of a β cell.

Ultrastructural differences in pretangles between Alzheimer disease and corticobasal degeneration revealed by comparative light and electron microscopy

Pretangles are defined under the light microscope as diffuse and granular tau immunoreactivity in neurons in tissue from patients with Alzheimer disease (AD) or corticobasal degeneration (CBD) and are considered to be a premature stage before neurofibrillary tangle formation. However, the ultrastructure of pretangles remains to be described. To clarify the similarities and differences between pretangles from patients with AD and CBD (AD-pretangles and CBD-pretangles, respectively), we examined cortical pretangles in tissue from patients with each of diseases. For direct light and electron microscopic (LM/EM) correlation of the pretangles, we used quantum dot nanocrystals (QDs) with dual fluorescent and electron-dense properties. We first identified tau-labeled pretangles on fluorescence LM and subsequently examined the same neurons on EM. Energy dispersive X-ray spectrometry (EDX) color mapping identified selenium (Se) and cadmium (Cd) as elementary components of QDs and highlighted each QD particle clearly against gray-scale EM images. With these methods, we were successful for the first time in demonstrating accurately that LM-defined pretangles are tau-positive straight filaments sparsely distributed throughout neuronal cytoplasm and neurites in both AD and CBD at the EM level. Notably, AD-pretangles showed a strong tendency to form fibrillary tangles even at an early stage, whereas pretangles or Pick-like inclusions in tissue from patients with CBD did not even at an advanced stage. In conclusion, AD-pretangles and CBD-pretangles showed essential differences at the EM level.

Chemical mapping of DNA and counter-ion content inside phage by energy-filtered TEM

Double-stranded DNA in many bacterial viruses (phage) is strongly confined, which results in internal genome pressures of tens of atmospheres. This pressure is strongly dependent on local ion concentration and distribution within the viral capsid. Here, we have used electron energy loss spectroscopy (EELS), energy-filtered TEM (EFTEM) and X-ray energy dispersive spectroscopy to provide such chemical information from the capsid and the phage tail through which DNA is injected into the cell. To achieve this, we have developed a method to prepare thin monolayers of self-supporting virus/buffer films, suitable for EELS and EFTEM analysis. The method is based on entrapment of virus particles at air-liquid interfaces; thus, the commonly used method of staining by heavy metal salts can be avoided, eliminating the risk for chemical artifacts. We found that Mg(2 + ) concentration was approximately 2-4 times higher in the DNA-filled capsid than in the surrounding TM buffer (containing 10 mM Mg(2 + )). Furthermore, we also analyzed the DNA content inside the phage tail by mapping phosphorus and magnesium.

Development of Electron Energy Loss Spectroscopy in the Biological Sciences

The high sensitivity of electron energy loss spectroscopy (EELS) for detecting light elements at the nanoscale makes it a valuable technique for application to biological systems. In particular, EELS provides quantitative information about elemental distributions within subcellular compartments, specific atoms bound to individual macromolecular assemblies, and the composition of bionanoparticles. The EELS data can be acquired either in the fixed beam energy-filtered transmission electron microscope (EFTEM) or in the scanning transmission electron microscope (STEM), and recent progress in the development of both approaches has greatly expanded the range of applications for EELS analysis. Near single atom sensitivity is now achievable for certain elements bound to isolated macromolecules, and it becomes possible to obtain three-dimensional compositional distributions from sectioned cells through EFTEM tomography.

Limitations of beam damage in electron spectroscopic tomography of embedded cells

Elemental mapping in the energy filtering transmission electron microscope (EFTEM) can be extended into three dimensions (3D) by acquiring a series of two-dimensional (2D) core-edge images from a specimen oriented over a range of tilt angles, and then reconstructing the volume using tomographic methods. EFTEM has been applied to imaging the distribution of biological molecules in 2D, e.g. nucleic acid and protein, in sections of plastic-embedded cells, but no systematic study has been undertaken to assess the extent to which beam damage limits the available information in 3D. To address this question, 2D elemental maps of phosphorus and nitrogen were acquired from unstained sections of plastic-embedded isolated mouse thymocytes. The variation in elemental composition, residual specimen mass and changes in the specimen morphology were measured as a function of electron dose. Whereas 40% of the total specimen mass was lost at doses above 10(6) e(-)/nm(2), no significant loss of phosphorus or nitrogen was observed for doses as high as 10(8) e(-)/nm(2). The oxygen content decreased from 25 + or - 2 to 9 + or - 2 atomic percent at an electron dose of 10(4) e(-)/nm(2), which accounted for a major component of the total mass loss. The specimen thickness decreased by 50% after a dose of 10(8) e(-)/nm(2), and a lateral shrinkage of 9.5 + or - 2.0% occurred from 2 x 10(4) to 10(8) e(-)/nm(2). At doses above 10(7) e(-)/nm(2), damage could be observed in the bright field as well in the core edge images, which is attributed to further loss of oxygen and carbon atoms. Despite these artefacts, electron tomograms obtained from high-pressure frozen and freeze-substituted sections of C. elegans showed that it is feasible to obtain useful 3D phosphorus and nitrogen maps, and thus to reveal quantitative information about the subcellular distributions of nucleic acids and proteins.

Imaging and quantifying the morphology of an organic-inorganic nanoparticle at the sub-nanometre level

The development of hybrid organic-inorganic nanoparticles is of interest for applications such as drug delivery, DNA and protein recognition, and medical diagnostics. However, the characterization of such nanoparticles remains a significant challenge due to the heterogeneous nature of these particles. Here, we report the direct visualization and quantification of the organic and inorganic components of a lipid-coated silica particle that contains a smaller semiconductor quantum dot. High-angle annular dark-field scanning transmission electron microscopy combined with electron energy loss spectroscopy was used to determine the thickness and chemical signature of molecular coating layers, the element atomic ratios, and the exact positions of different elements in single nanoparticles. Moreover, the lipid ratio and lipid phase segregation were also quantified.

Towards native-state imaging in biological context in the electron microscope

Modern cell biology is reliant on light and fluorescence microscopy for analysis of cells, tissues and protein localisation. However, these powerful techniques are ultimately limited in resolution by the wavelength of light. Electron microscopes offer much greater resolution due to the shorter effective wavelength of electrons, allowing direct imaging of sub-cellular architecture. The harsh environment of the electron microscope chamber and the properties of the electron beam have led to complex chemical and mechanical preparation techniques, which distance biological samples from their native state and complicate data interpretation. Here we describe recent advances in sample preparation and instrumentation, which push the boundaries of high-resolution imaging. Cryopreparation, cryoelectron microscopy and environmental scanning electron microscopy strive to image samples in near native state. Advances in correlative microscopy and markers enable high-resolution localisation of proteins. Innovation in microscope design has pushed the boundaries of resolution to atomic scale, whilst automatic acquisition of high-resolution electron microscopy data through large volumes is finally able to place ultrastructure in biological context.

Quantitative EFTEM mapping of near physiological calcium concentrations in biological specimens

Although electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) provides high sensitivity for measuring the important element, calcium, in biological specimens, the technique has been difficult to apply routinely, because of long acquisition times required. Here we describe a refinement of the complementary analytical technique of energy-filtered transmission electron microscopy (EFTEM), which enables rapid imaging of large cellular regions and measurement of calcium concentrations approaching physiological levels. Extraction of precise quantitative information is possible by averaging large numbers of pixels that are contained in organelles of interest. We employ a modified two-window approach in which the behavior of the background signal in the EELS spectrum can be modeled as a function of specimen thickness t expressed in terms of the inelastic mean free path lambda. By acquiring pairs of images, one above and one below the Ca L(2,3) edge, together with zero-loss and unfiltered images, which are used to determine a relative thickness (t/lambda) map, it is possible to correct the Ca L(2,3) signal for plural scattering. We have evaluated the detection limits of this technique by considering several sources of systematic errors and applied this method to determine mitochondrial total calcium concentrations in freeze-dried cryosections of rapidly frozen stimulated neurons. By analyzing 0.1 microm2 areas of specimen regions that do not contain calcium, it was found that the standard deviation in the measurement of Ca concentrations was about 20 mmol/kg dry weight, corresponding to a Ca:C atomic fraction of approximately 2 x 10(-4). Calcium concentrations in peripheral mitochondria of recently depolarized, and therefore stimulated and Ca loaded, frog sympathetic neurons were in reasonable agreement with previous data.

Three-dimensional imaging of the highly bent architecture of Bdellovibrio bacteriovorus by using cryo-electron tomography

Bdellovibrio bacteriovorus cells are small deltaproteobacterial cells that feed on other gram-negative bacteria, including human pathogens. Using cryo-electron tomography, we demonstrated that B. bacteriovorus cells are capable of substantial flexibility and local deformation of the outer and inner membranes without loss of cell integrity. These shape changes can occur in less than 2 min, and analysis of the internal architecture of highly bent cells showed that the overall distribution of molecular machines and the nucleoid is similar to that in moderately bent cells. B. bacteriovorus cells appear to contain an extensive internal network of short and long filamentous structures. We propose that rearrangements of these structures, in combination with the unique properties of the cell envelope, may underlie the remarkable ability of B. bacteriovorus cells to find and enter bacterial prey.

Quantification and thickness correction of EFTEM phosphorus maps

We describe a method for correcting plural inelastic scattering effects in elemental maps that are acquired in the energy filtering transmission electron microscope (EFTEM) using just two energy windows, one above and one below a core edge in the electron energy loss spectrum (EELS). The technique is demonstrated for mapping low concentrations of phosphorus in biological samples. First, the single-scattering EELS distributions are obtained from specimens of pure carbon and plastic embedding material. Then, spectra are calculated for different specimen thicknesses t, expressed in units of the inelastic mean free path lambda. In this way, standard curves are generated for the ratio k0 of post-edge to pre-edge intensities at the phosphorus L2,3 excitation energy, as a function of relative specimen thickness t/lambda. Thickness effects in a two-window phosphorus map are corrected by successive acquisition of zero-loss and unfiltered images, from which it is possible to determine a t/lambda image and hence a background k0-ratio image. Knowledge of the thickness-dependent k0-ratio at each pixel thus enables a more accurate determination of the phosphorus distribution in the specimen. Systematic and statistical errors are calculated as a function of specimen thickness, and elemental maps are quantified in terms of the number of phosphorus atoms per pixel. Further analysis of the k0-curve shows that the EFTEM can be used to obtain reliable two-window phosphorus maps from specimens that are considerably thicker than previously possible.

Morphological and chemical studies of pathological human and mice brain at the subcellular level: Correlation between light, electron, and nanosims microscopies

Neurodegenerative diseases induce morphological and chemical alterations in well-characterized regions of the brain. Understanding their pathological processes requires the use of methods that assess both morphological and chemical alterations in the tissues. In the past, microprobe approaches such as scanning electron microscopy combined with an X-ray spectrometer, Proton induced X-ray emission, secondary ion mass spectrometry (SIMS), and laser microprobe mass analysis have been used for the study of pathological human brain with limited success. At the present, new SIMS instruments have been developed, such as the NanoSIMS-50 ion microprobe, that allow the simultaneous identification of five elements with high sensitivity, at subcellular spatial resolution (about 50-100 nm with the Cs(+) source and about 150-200 nm with O(-) source). Working in scanning mode, 2D distribution of five elements (elemental maps) can be obtained, thus providing their exact colocalization. The analysis can be performed on semithin or ultrathin embedded sections. The possibility of using transmission electron microscopy and SIMS on the same ultrathin sections allows the correlation between structural and analytical observations at subcellular and ultrastructural level to be established. Our observations on pathological brain areas allow us to establish that the NanoSIMS-50 ion microprobe is a highly useful instrument for the imaging of the morphological and chemical alterations that take place in these brain areas. In the human brain our results put forward the subcellular distribution of iron-ferritin-hemosiderin in the hippocampus of Alzheimer disease patients. In the thalamus of transgenic mice, our results have shown the presence of Ca-Fe mineralized amyloid deposits.

Organization of interphase chromatin

The organization of interphase chromatin spans many topics, ranging in scale from the molecular level to the whole nucleus, and its study requires a concomitant range of experimental approaches. In this review, we examine these approaches, the results they have generated, and the interfaces between them. The greatest challenge appears to be the integration of information on whole nuclei obtained by light microscopy with data on nucleosome-nucleosome interactions and chromatin higher-order structures, obtained in vitro using biophysical characterization, atomic force microscopy, and electron microscopy. We consider strategies that may assist in the integration process, and we review emerging technologies that promise to reduce the "resolution gap."

Lessons from tomographic studies of the mammalian Golgi

Basic structure studies of the biosynthetic machinery of the cell by electron microscopy (EM) have underpinned much of our fundamental knowledge in the areas of molecular cell biology and membrane traffic. Driven by our collective desire to understand how changes in the complex and dynamic structure of this enigmatic organelle relate to its pivotal roles in the cell, the comparatively high-resolution glimpses of the Golgi and other compartments of the secretory pathway offered to us through EM have helped to inspire the development and application of some of our most informative, complimentary (molecular, biochemical and genetic) approaches. Even so, no one has yet even come close to relating the basic molecular mechanisms of transport, through and from the Golgi, to its ultrastructure, to everybody's satisfaction. Over the past decade, EM tomography has afforded new insights into structure-function relationships of the Golgi and provoked a re-evaluation of older paradigms. By providing a set of tools for structurally dissecting cells at high-resolution in three-dimensions (3D), EM tomography has emerged as a method for studying molecular cell biology in situ. As we move rapidly toward the establishment of molecular atlases of organelles through advances in proteomics and genomics, tomographic studies of the Golgi offer the tantalizing possibility that one day, we will be able to map the spatio-temporal coordinates of Golgi-related proteins and lipids accurately in the context of 4D cellular space.

The distribution of light elements in biological cells measured by electron probe X-ray microanalysis of cryosections

The intracellular distribution of the elements carbon, nitrogen, and oxygen was measured in cultured rat hepatocytes by energy dispersive electron probe X-ray microanalysis of 100-nm-thick freeze-dried cryosections. Electron irradiation with a dose up to 106 e/nm2 caused no or merely negligible mass loss in mitochondria and in cytoplasm. Cell nuclei lost carbon, nitrogen, and-to a clearly higher extent-oxygen with increasing electron irradiation. Therefore, electron doses less than 3 x 105 e/nm2 were used to measure the subcellular compartmentation of carbon, nitrogen, and oxygen in cytoplasm, mitochondria, and nuclei of the cells. The subcellular distribution of carbon, nitrogen, and oxygen reflects the intracellular compartmentation of various biomolecules. Cells exposed to inorganic mercury before cryofixation showed an increase of oxygen in nuclei and cytoplasm. Concomitantly the phosphorus/nitrogen ratio decreased in mitochondria. The data suggest mercury-induced production of ribonucleic acid (RNA) and decrease of adenosine triphosphate (ATP). Although biomolecules cannot be identified by X-ray microanalysis, measurements of the whole element spectrum including the light elements carbon, nitrogen, and oxygen can be useful to study specific biomolecular activity in cellular compartments depending on the functional state of the cell.

Three-dimensional distributions of elements in biological samples by energy-filtered electron tomography

By combining electron tomography with energy-filtered electron microscopy, we have shown the feasibility of determining the three-dimensional distributions of phosphorus in biological specimens. Thin sections of the nematode, Caenorhabditis elegans were prepared by high-pressure freezing, freeze-substitution and plastic embedding. Images were recorded at energy losses above and below the phosphorus L2,3 edge using a post-column imaging filter operating at a beam energy of 120 keV. The unstained specimens exhibited minimal contrast in bright-field images. After it was determined that the specimen was sufficiently thin to allow two-window ratio imaging of phosphorus, pairs of pre-edge and post-edge images were acquired in series over a tilt range of +/-55 degrees at 5 degrees increments for two orthogonal tilt axes. The projected phosphorus distributions were aligned using the pre-edge images that contained inelastic contrast from colloidal gold particles deposited on the specimen surface. A reconstruction and surface rendering of the phosphorus distribution clearly revealed features 15-20 nm in diameter, which were identified as ribosomes distributed along the stacked membranes of endoplasmic reticulum and in the cytoplasm. The sensitivity of the technique was estimated at < 35 phosphorus atoms per voxel based on the known total ribosomal phosphorus content of approximately 7000 atoms. Although a high electron dose of approximately 10(7)e/nm2 was required to record two-axis tilt series, specimens were sufficiently stable to allow image alignment and tomographic reconstruction.

Subcellular localization of boron in cultured melanoma cells by electron energy-loss spectroscopy of freeze-dried cryosections

Boron neutron capture therapy (BNCT) is based on the ability of the non-radioactive isotope 10B to capture thermal neutrons and to disintegrate instantaneously. This reaction opens a way to selectively destroy tumour cells after specific uptake of 10B. In this paper, a method based on electron energy-loss spectroscopy is presented for detecting and quantifying boron in freeze-dried cryosections of human melanoma cells. A practical detection limit of around 6 mmol kg-1 in 0.1- micro m2 areas is estimated using specimens prepared from standard boron solutions. Preliminary results of boron mapping in the spectrum-imaging acquisition mode reveal boron penetration and probably spot-like accumulation within melanoma cells when exposed to culture medium containing sodium borocaptate.

A critical assessment of boron target compounds for boron neutron capture therapy

Boron neutron capture therapy (BNCT) has undergone dramatic developments since its inception by Locher in 1936 and the development of nuclear energy during World War II. The ensuing Cold War spawned the entirely new field of polyhedral borane chemistry, rapid advances in nuclear reactor technology and a corresponding increase in the number to reactors potentially available for BNCT. This effort has been largely oriented toward the eradication of glioblastoma multiforme (GBM) and melanoma with reduced interest in other types of malignancies. The design and synthesis of boron-10 target compounds needed for BNCT was not channeled to those types of compounds specifically required for GBM or melanoma. Consequently, a number of potentially useful boron agents are known which have not been biologically evaluated beyond a cursory examination and only three boron-10 enriched target species are approved for human use following their Investigational New Drug classification by the US Food and Drug Administration; BSH, BPA and GB-10. All ongoing clinical trials with GBM and melanoma are necessarily conducted with one of these three species and most often with BPA. The further development of BNCT is presently stalled by the absence of strong support for advanced compound evaluation and compound discovery driven by recent advances in biology and chemistry. A rigorous demonstration of BNCT efficacy surpassing that of currently available protocols has yet to be achieved. This article discusses the past history of compound development, contemporary problems such as compound classification and those problems which impede future advances. The latter include means for biological evaluation of new (and existing) boron target candidates at all stages of their development and the large-scale synthesis of boron target species for clinical trials and beyond. The future of BNCT is bright if latitude is given to the choice of clinical disease to be treated and if a recognized study demonstrating improved efficacy is completed. Eventually, BNCT in some form will be commercialized.

Light elements quantification in stimulated cells cryosections studied by electron probe microanalysis

The quantification of intracellular light elements such as carbon, nitrogen and oxygen may be useful in understanding the biological mechanisms, for example the generation of nitric oxide which is involved in apoptosis and inflammatory reaction. Electron energy loss spectroscopy (EELS) coupled with scanning transmission electron microscopy is a useful method to detect light elements in thin cryosections. Recent developments of X-ray detectors with ultra-thin protection windows allows the detection of such elements by energy dispersive X-ray spectroscopy. In the present study, we have demonstrated using both methods that the stimulation of BV-2 murine microglial cell line by gamma-interferon and lipopolysaccharide leads to the increase of intracellular oxygen concentration and no change in the intracellular nitrogen concentration. This indicates the use of exogeneous molecular oxygen in response to the stimulation. But the increase of oxygen concentration detected could not be only due to NO expression because the NO production was 1000 times less than the oxygen concentration increase observed.

An approach to an objective background subtraction for elemental mapping with core-edges down to 50 eV: description, evaluation and application

To image the distribution of a specific element in a specimen with an energy filtering TEM, the element-unspecific background under the core-edge has to be subtracted. The most commonly used procedure is the three-window power-law method leading to considerable systematic errors for low-energy core-edges. Here a new method is described which can be considered as a generalized difference method. Characteristic examples for element detection in biological specimens using this method are shown. The background under the core-edge can be described by one or two pre-edge windows as a polynome of third order. This function can be deduced from specimen areas that are not known to contain the element or from a second specimen used as a standard. Control experiments showed that background subtraction for on-overlapping core-edges in the low-loss region (50-200 eV) needs two pre-edge images, whereas at higher-energy losses (> 300 eV) only one pre-edge image is necessary. With the method described, objective elemental mapping becomes possible even for edges at 50-100 eV. This was proven for the M2,3-edge of iron at 60 eV. The detection of phosphorous was possible with a signal-to-noise ratio five times higher than when using the three-window method. Preliminary data showed that it should be possible to detect calcium with only one image before the edge.

Adhesion-related glycocalyx study: quantitative approach with imaging-spectrum in the energy filtering transmission electron microscope (EFTEM)

Large polysaccharide molecules composing the glycocalyx have been shown to prevent cell adhesion. However, this process was not observed microscopically. Terbium labeling, combined with a new quantitative imaging method based on electron energy loss spectroscopy, allowed specific glycocalyx staining with excellent contrast. Image analysis enabled us to compare glycocalyx structure in free membrane areas and contacts between monocytic cells and bound erythrocytes. Apparent glycocalyx thickness, in contact areas, was half of the sum of glycocalyx thicknesses in free areas without label density increase. Ultrastructural immunogold localization of CD43 molecules, a major component of glycocalyx, was also demonstrated to be excluded from contact areas during adhesion. Thus, both approaches strongly suggest that some glycocalyx elements must exit from contact to allow binding of adhesion molecules.

In situ compositional analysis of acidocalcisomes in Trypanosoma cruzi

We measured the elemental content of different compartments in Trypanosoma cruzi epimastigotes using quick freezing, ultracryomicrotomy, and electron probe microanalysis. Vacuoles identified by high electron density contained (in units of mmol/kg dry weight +/- S.E.) large amounts of phosphorus (1390 +/- 13), magnesium (646 +/- 19), calcium (171 +/- 5), sodium (161 +/- 18), and zinc (148 +/- 6). No other compartment had appreciable calcium or zinc content. Iron (128 +/- 16 mmol/kg) was detected only in vacuoles distinct from the electron-dense vacuoles and other organelles. Incubation of cells for 70 min in culture medium in the presence of ionomycin plus nigericin led to a very significant 3- or 2-fold increase in potassium in the electron-dense vacuoles and the iron-rich vacuoles, respectively, with no significant change in the other elements investigated. This indicated the acidic nature of the vacuoles and demonstrated that the electron-dense vacuoles correspond to what were described previously as acidocalcisomes, i.e. acidic compartments rich in Ca2+. The acidocalcisomes were investigated by separation of epimastigote fractions on Percoll gradients in combination with Triton WR-1339 treatment. This detergent caused a rapid vacuolation; these vacuoles were shown by electron microscopy to be largely transparent, with a diffuse matrix. Percoll gradient fractionation demonstrated decreases in the density of various organelle markers in detergent-treated cells compared with controls. Large decreases in the density of the acidocalcisome and the mitochondrion were seen, as well as smaller decreases in the density of the other markers. Conventional electron microscopy of epimastigotes loaded with gold-labeled transferrin indicated that the endosomal system was separate from vacuoles that probably corresponded to the calcium-containing organelles detected by electron probe microanalysis. The combined results provide evidence that acidocalcisomes are organelles different from lysosomes or other organelles previously described in these parasites.

High-resolution calcium mapping of the endoplasmic reticulum-Golgi-exocytic membrane system. Electron energy loss imaging analysis of quick frozen-freeze dried PC12 cells

The calcium pools segregated within the endoplasmic reticulum, Golgi complex, exocytic, and other organelles are believed to participate in the regulation of a variety of cell functions. Until now, however, the precise intracellular distribution of the element had not been established. Here, we report about the first high-resolution calcium mapping obtained in neurosecretory PC12 cells by the imaging mode of the electron energy loss spectroscopy technique. The preparation procedure used included quick freezing of cell monolayers, followed by freeze-drying, fixation with OSO4 vapors, resin embedding, and cutting of very thin sections. Conventional electron microscopy and high-resolution immunocytochemistry revealed a high degree of structural preservation, a condition in which inorganic elements are expected to maintain their native distribution. Within these cells, calcium signals of nucleus, cytosol, and most mitochondria remained below detection, whereas in other organelles specific patterns were identified. In the endoplasmic reticulum, the distribution was heterogeneous with strongly positive cisternae (more often the nuclear envelope and stacks of parallel elements that are frequent in quick frozen preparations) lying in the proximity of or even in direct continuity with other, apparently negative cisternae. The Golgi complexes were labeled strongly and uniformly in all cisternae and part of their vesicles, with no appreciable differences along the cis-trans axis. Weaker or negative signals were recorded from the trans-Golgi network elements and from scattered vesicles, whereas in contrast secretion granules were strongly positive for calcium. These results are discussed in relation to the existing knowledge about the mechanisms of calcium transport in the variations organelles, and about the processes and functions regulated by organelle lumenal calcium in eukaryotic cells.

High resolution ultrastructural mapping of total calcium: electron spectroscopic imaging/electron energy loss spectroscopy analysis of a physically/chemically processed nerve-muscle preparation

We report on a procedure for tissue preparation that combines thoroughly controlled physical and chemical treatments: quick-freezing and freeze-drying followed by fixation with OsO4 vapors and embedding by direct resin infiltration. Specimens of frog cutaneous pectoris muscle thus prepared were analyzed for total calcium using electron spectroscopic imaging/electron energy loss spectroscopy (ESI/EELS) approach. The preservation of the ultrastructure was excellent, with positive K/Na ratios revealed in the fibers by x-ray microanalysis. Clear, high-resolution EELS/ESI calcium signals were recorded from the lumen of terminal cisternae of the sarcoplasmic reticulum but not from longitudinal cisternae, as expected from previous studies carried out with different techniques. In many mitochondria, calcium was below detection whereas in others it was appreciable although at variable level. Within the motor nerve terminals, synaptic vesicles as well as some cisternae of the smooth endoplasmic reticulum yielded positive signals at variance with mitochondria, that were most often below detection. Taken as a whole, the present study reveals the potential of our experimental approach to map with high spatial resolution the total calcium within individual intracellular organelles identified by their established ultrastructure, but only where the element is present at high levels.

Thickness measurement of hydrated and dehydrated cryosections by EELS

Electron energy-loss spectroscopy (EELS) provides a useful method for determining the thickness of frozen-hydrated and dehydrated cryosections in terms of the inelastic mean free path. Cryosection thickness is an important parameter because plural inelastic scattering limits the sensitivity of elemental microanalysis based on core-loss EELS, and because overlapping structures can affect interpretation of microanalytical data as well as the quality of electron images. The purpose of this work was to establish the minimum practical thickness for cutting cryosections and to explain the measured values for hydrated and dehydrated specimens. Hydrated sections were typically found to be between 1.5-2.5 times thicker than expected from the nominal microtome setting; this difference can be largely explained by compression during cutting. Comparison of micrographs from hydrated and dehydrated cryosections of rapidly-frozen, vitrified liver revealed a lateral shrinkage of approximately 20% on drying. The measured compression and shrinkage factors are consistent with dark-field scanning transmission electron microscopy (STEM) mass measurements on freeze-dried sections. Freeze-dried cryosections, cut to a nominal thickness of 90 nm and supported on thin Formvar/carbon films, had a relative thickness t/lambda i in the range of 0.5 for cytoplasm to 0.9 for mitochondria when analyzed at 100 keV beam energy. Mass loss of approximately 30% occurring at high electron dose enabled useful core-loss spectra to be recorded even from high-mass compartments such as mitochondria without excessive plural scattering.

Quantitative water mapping of cryosectioned cells by electron energy-loss spectroscopy

A direct technique based on electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) has been developed to map subcellular distributions of water in frozen-hydrated biological cryosections. Previously, methods for water determination have been indirect in that they have required the cryosections to be dehydrated first. The new approach makes use of spectrum-imaging, where EELS data are collected in parallel at each pixel. Several operations are required to process the spectra including: subtraction of the detector dark current, deconvolution by the detector point-spread function, removal of plural inelastic scattering and correction for the support film. The resulting single scattering distributions are fitted to standard reference spectra at each pixel, and water content can be determined from the fitting coefficients. Although the darkfield or brightfield image from a hydrated cryosection shows minimal structure, the processed EELS image reveals strong contrast due to variations in water content. Reference spectra have been recorded from the major biomolecules (protein, lipid, carbohydrate, nucleic acid) as well as from vitrified water and crystalline ice. It has been found that quantitative results can be obtained for the majority of subcellular compartments by fitting only water and protein reference spectra, and the accuracy of the method for these compartments has been estimated as +/- 3.5%. With the present instrumentation the maximum allowed dose of 2 x 10(3) e/nm2 limits the useful spatial resolution to around 80 nm for +/- 5% precision at a single pixel. By averaging pixel intensities a value of 56.8% with a precision of +/- 2.0% has been determined for the water content of liver mitochondria. The water mapping technique may prove useful for applications to cell physiology and pathophysiology.

Application of scanning transmission electron microscopy to the study of biological structure

The scanning transmission electron microscope provides structural and chemical information of a specimen at atomic-scale resolution and complements conventional transmission electron microscopy techniques. Mass measurements can now be performed routinely on a wide range of molecular and supramolecular structures using elastically scattered electrons. Recent progress in the acquisition and analysis of electron energy-loss spectroscopy data indicates that the scanning transmission electron microscope is an efficient tool for mapping the chemical composition of biological samples.

Water distributions of hydrated biological specimens by valence electron energy loss spectroscopy

A technique has been developed for measuring the water distribution in thin frozen hydrated biological specimens by means of electron energy loss spectroscopy (EELS). The method depends on the quantification of subtle changes in the valence electron excitation spectrum as a function of composition. It involves determining the single-scattering intensities, calculating oscillator strengths and applying a multiple-least-squares fitting procedure to reference spectra for water and the organic constituents. The direct EELS approach has an important advantage over other indirect methods that are based on X-ray generation or elastic scattering measurements since these are applied to freeze-dried specimens where differential shrinkage between compartments may produce errors. Precision and accuracy of the EELS method have been tested on cryosectioned solution of bovine serum albumin; data have also been obtained from cryosections of rapidly frozen erythrocytes. Results suggest that a precision of better than +/- 5% (s.d.) is attainable from a single measurement and the accuracy may be as high as +/- 2% if repeated measurements are made. The lateral spatial resolution of the water determinations is limited by radiation damage to approximately 100 nm which is of the same order as the specimen thickness.

Radiation damage of fluorinated organic compounds measured by parallel electron energy loss spectroscopy

The sensitivity of fluorinated organic compounds to radiation damage in the electron microscope was measured by electron energy loss spectroscopy (EELS). Five classes of molecules were investigated with fluorine atoms situated on: (1) an aliphatic chain, (2) an aromatic ring, (3) a trifluoromethyl group on an aromatic ring, (4) a trifluoromethyl group on a heterocyclic ring, and (5) a trifluoromethyl group next to a carbonyl group. The damage dose for fluorine loss was found to depend strongly on the position of the fluorine atoms and on specimen temperature. For poly-substituted fluorine on an aliphatic chain, approximately half of the fluorine was retained at doses in excess of 10(7) e/nm2. At room temperature molecules containing trifluoromethyl groups on aromatic or heterocyclic rings were much more sensitive to fluorine loss than compounds having fluorine substituted directly on the rings. This behavior is consistent with the relatively low chemical stability of the trifluoromethyl group in these structures. The rapid loss of fluorine at low electron doses (approximately 10(4) e/nm2) in the trifluoromethyl aromatic compounds was reduced several orders of magnitude by cooling the specimen to liquid-nitrogen temperatures. An understanding of how specific types of fluorinated compounds suffer damage under the electron beam will be important in their potential application as biochemical or pharmacological probes.

Use of the uranaffin reaction in the identification of neuroendocrine granules

This overview emphasizes the utility of the uranaffin reaction in the diagnosis of tumors derived from neuroendocrine cells. The history, cell organelle specificity, tissue specificity, pH requirements, and detailed procedure of the uranaffin reaction is provided. Uranaffin-positive granules are also identified within the NS granules of the stem cell paraneuron (archiparaneuron) of coelenterates, and a hypothetical evolutionary scheme depicting the possible origins of the key biochemical features of the advanced mammalian NS granule is included. The role of nucleotides, a major component of true NS granules, is discussed. A possible intragranular function of ATP as a regulator of osmotic pressure and the extracellular physiologic effects of secreted intragranular nucleotides are discussed in some detail.

Real-time quantitative elemental analysis and mapping: microchemical imaging in cell physiology

Recent advances in widely available microcomputers have made the acquisition and processing of digital quantitative X-ray maps of one to several cells readily feasible. Here we describe a system which uses a graphics-based microcomputer to acquire spectrally filtered X-ray elemental image maps that are fitted to standards, to display the image in real time, and to correct the post-acquisition image map with regard to specimen drift. Both high-resolution quantitative energy-dispersive X-ray images of freeze-dried cyrosections and low-dose quantitative bright-field images of frozen-hydrated sections can be acquired to obtain element and water content from the same intracellular regions. The software programs developed, together with the associated hardware, also allow static probe acquisition of data from selected cell regions with spectral processing and quantification performed on-line in real time. In addition, the unified design of the software program provides for off-line processing and analysing by several investigators at microcomputers remote from the microscope. The overall experimental strategy employs computer-aided imaging, combined with static probes, as an essential interactive tool of investigation for biological analysis. This type of microchemical microscopy facilitates studies in cell physiology and pathophysiology which focus on mechanisms of ionic (elemental) compartmentation, i.e. structure-function correlation at cellular and subcellular levels; it allows investigation of intracellular concentration gradients, of the heterogeneity of cell responses to stimuli, of certain fast physiological events in vivo at ultrastructural resolution, and of events occurring with low incidence or involving cell-to-cell interactions.