An energy filter for biological electron microscopy

Electron energy loss analysis and imaging in biology

The major advances in our understanding of subcellular morphology have come about largely due to the imaging capabilities of the electron microscope. Image detail with spatial resolutions of 2 to 3 nm is common, and in special cases resolutions better than 1 nm have been achieved on individual macromolecules. However, the desire to add a knowledge of chemistry to structural analysis invariably has led to a compromise in which spatial resolution has had to be sacrificed. At worst, e.g., in biochemical analysis, morphology is entirely destroyed. Light optical histochemical techniques, though often very specific, need only preserve structure to within about 500 nm, light optical resolution. Electron microscopic cytochemical techniques are somewhat better but are limited in specificity by chemical approaches that must incorporate heavy atoms or deposit massive precipitates at or near the primary site of analysis. This site is therefore localized relatively poorly or is covered up completely.

Microanalysis in the EM 902: Tests on a new TEM for ESI and EELS

One important goal in biological and medical research as well as in material sciences is the microanalysis of specimens, i. e. the determination of the spatial distribution and concentration of relevant atomic elements, such as Ca, P, S, N, O, Al, Fe, Ti or Mg ideally over every point in the image in relation to the underlying matrix. Microanalysis has generally been carried out in a probe forming or scanning system by spot analysis using EDX or EELS. Elemental mapping is however more efficacious in a spectrometer that filters entire images in parallel. For energy loss electrons several such systems have been built experimentally (1-7), but inspite of results which have indicated a sensitivity of detection as good as 2 x 10-21 g and a spatial resolution in analysis of about 0.5 nm, applications in biology and material sciences (2,7 - 9) no commercial EM with an integrated imaging spectrometer is available today.

Application of electron spectroscopic imaging to frozen hydrated specimens

Techniques and equipment for examination of biological specimens by TEM in the frozen hydrated state are rapidly improving. A major advantage of these methods is the capability of examining delicate cellular components in their native state. This advantage can be realized only by taking care to avoid artefacts of sample preparation that have confused interpretation of EM images in the past. Thus it is preferred to examine the frozen hydrated samples without fixation or staining. In this case, the contrast in the image depends entirely on the difference in electron density between water and the constituents of the sample, generally protein, carbohydrate, nucleic acids, and to a lesser degree, lipid. These electron density differences are quite small, and the image contrast is correspondingly low.

High-Resolution Macromolecular Structure Determination by MicroED, a cryo-EM Method

Microelectron diffraction (MicroED) is a new cryo-electron microscopy (cryo-EM) method capable of determining macromolecular structures at atomic resolution from vanishingly small 3D crystals. MicroED promises to solve atomic resolution structures from even the tiniest of crystals, less than a few hundred nanometers thick. MicroED complements frontier advances in crystallography and represents part of the rebirth of cryo-EM that is making macromolecular structure determination more accessible for all. Here we review the concept and practice of MicroED, for both the electron microscopist and crystallographer. Where other reviews have addressed specific details of the technique (Hattne et al., 2015; Shi et al., 2016; Shi, Nannenga, Iadanza, & Gonen, 2013), we aim to provide context and highlight important features that should be considered when performing a MicroED experiment.

Low energy loss electron microscopy of chromophores

A novel prism-mirror-prism imaging electron spectrometer with 1 eV energy resolution for a transmission electron microscope permits imaging with spectral energies corresponding to light-optical colour absorptions. The instrument selects the molecular orbital excitations of natural chromophores or of specific dyes normally used in biological light microscopy for delineation and chemical identification, but images them with electron microscopic detail. Heavy atom contrast agents customarily used in electron microscopy are not required. The first results exploit the intrinsic red colour of hematin molecules to demonstrate the potential of the technique and address its spatial resolution. Glycosaminoglycans in cartilage stained with Alcian blue are selectively depicted in situ by means of the electron-induced molecular absorption of this chromophore. Thus, with the use of specific colours the direct or indirect analysis of local chemistry by electron microscopy is possible, and can be carried out with a depiction of spatial detail as small as 16 A, or at least 100-fold finer than observed by light microscopy.

Microwave fixation and localization of calcium in synaptic terminals using x-ray microanalysis and electron energy loss spectroscopy imaging

The distribution of calcium ions is demonstrated in synaptic terminals by means of a two-step chemical precipitation of calcium ions in the rat brain. K-oxalate/K-antimonate chemical replacement with simultaneous computerized microwave irradiation was used. This precipitate in nerve cell structures was investigated by computerized electron probe x-ray microanalysis (EDX) and electron energy loss spectroscopic (EELS) imaging. The values obtained by EDX agreed with those of the standard sample and theoretical values of Ca-antimonate. Typical EELS spectra of Ca:L, O:K, and Sb:M were obtained from nerve terminals in the same tissue block as that used for EDX analysis. Excellent net Ca:L and Sb:M EELS digital images were obtained after their background images were subtracted. Calcium ions were distributed in the nerve terminals, synaptic vesicles, mitochondria, and synaptic membranes.

Structures of small subunit ribosomal RNAs in situ from Escherichia coli and Thermomyces lanuginosus

Small ribosomal subunits from the prokaryote Escherichia coli and the eukaryote Thermomyces lanuginosus were imaged electron spectroscopically, and single particle analysis used to yield three-dimensional reconstructions of the net phosphorus distribution representing the nucleic acid (RNA) backbone. This direct approach showed both ribosomal RNAs to have a three domain structure and other characteristic morphological features. The eukaryotic small ribosomal subunit had a prominent bill present in the head domain, while the prokaryotic subunit had a small vestigial bill. Both ribosomal subunits contained a thick 'collar' central domain which correlates to the site of the evolutionarily conserved ribosomal RNA core, and the location of the majority of ribosomal RNA bases that have been implicated in translation. The reconstruction of the prokaryotic subunit had a prominent protrusion extending from the collar, forming a channel approximately 1.5 nm wide and potentially representing a 'bridge' to the large subunit in the intact monosome. The basal domain of the prokaryotic ribosomal subunit was protein free. In this region of the eukaryotic subunit, there were two basal lobes composed of ribosomal RNA, consistent with previous hypotheses that this is a site for the 'non-conserved core' ribosomal RNA.

Iron distribution in thalassemic bone by energy-loss spectroscopy and electron spectroscopic imaging

Iron overload occurs frequently in thalassemia as a consequence of regular blood transfusions, and iron has been found to accumulate in bone, but skeletal toxicity of iron is not clearly established. In this study, bone biopsies of thalassemic patients were investigated by light (n = 6) and electron microscopy (n = 8) in order to analyze iron distribution and possible iron-associated cellular lesions. Sections (5 microns thick) were used for histomorphometry and iron histochemistry. Ultrathin sections were examined with an energy filtering transmission electron microscope. Iron was identified by electron energy loss spectroscopy (EELS), and iron distribution was visualized by electron spectroscopic imaging (ESI) associated with computer-assisted treatment (two-window method). This study shows that EELS allows the detection of 4500-9000 iron atoms, and that computer-assisted image processing is essential to eliminate background and to obtain the net distribution of an element by ESI. This study shows also that stainable iron was present along trabecular surfaces, mineralizing surfaces, and on cement lines in the biopsies of all patients. Moreover, iron was detected by EELS in small granules (diffusely distributed or condensed in large clusters), in osteoid tissue, and in the cytoplasm of bone cells, but not in the mineralized matrix. The shape and size (9-13 nm) of these granules were similar to those reported for ferritin. As for iron toxicity, all patients had osteoid volume and thickness and osteoblast surface in the normal range. Stainable iron surfaces did not correlate with osteoblast surfaces, plasma ferritin concentrations, or the duration of transfusion therapy.(ABSTRACT TRUNCATED AT 250 WORDS)

Electron spectroscopic study (ESI, EELS) of Nanoplast-embedded mammalian lung

The potential of Nanoplast melamine resin embedding for the study of mammalian lung parenchyma was examined by means of electron spectroscopic imaging (ESI) and electron energy-loss spectroscopy (EELS). Samples were either fixed with glutaraldehyde-paraformaldehyde or glutaraldehyde-tannic acid, or were directly transferred to the embedding medium without prior fixation. Organic dehydrants, as well as fixatives containing heavy metals and stains, were omitted. A very high level of ultrastructural detail of chromatin, ribosomes, mitochondria and plasma membranes was achieved by ESI from the Nanoplast-embedded samples. The most prominent gain in ultrastructural detail was achieved when moving from an energy loss just below the L2,3 edge of phosphorus at 132 eV to an energy loss just beyond this edge. This reflects the prominent P L2,3 edge observed by EELS of Nanoplast-embedded samples in comparison with conventionally processed samples. Thus, taking into account possible sectioning artefacts, excellent heterochromatin images which rely on the phosphorus distribution can be obtained from Nanoplast-embedded samples by computer-assisted analysis of electron spectroscopic images. In this respect glutaraldehyde-paraformaldehyde fixation is preferable to glutaraldehyde-tannic acid fixation because the presence of silicon, revealed by EELS, in tannic-acid-fixed samples may introduce artefacts in phosphorus distribution images obtained by the three-window method because of the close proximity of the L2,3 edges of silicon and phosphorus.

The use of parallel EEL spectral imaging and elemental mapping in the rapid assessment of anti-cancer drug localization

Both electron spectroscopic imaging (ESI) and electron energy-loss spectroscopy (EELS) have great potential for use in several areas of cancer research. In biologically targeted radiotherapy, cytotoxic drug therapy and boron neutron capture therapy the effectiveness of many drugs is often critically dependent upon the intracellular localization of the agent employed. We describe the use of parallel EEL spectral imaging to assess the penetration and location of the iodine-containing drug meta-iodobenzyl guanidine, of potential value in targeted radiotherapy, and for the rapid detection of boron within borate-adsorbed polystyrene beads, of potential value in boron neutron capture therapy. We also describe elemental mapping of boron following low-temperature embedding. These results show how the techniques could be applied to many forms of cancer research by discussing the validity and limitations of the techniques experimentally. We also provide an outline of other areas in this field which could benefit from the future application of ESI and EELS.

Contrast in the electron spectroscopic imaging mode of a TEM. IV. Thick specimens imaged by the most-probable energy loss

When the zero-loss transmission falls below 10(-3) for biological sections of mass-thickness greater than 70 micrograms/cm2, the energy window in the electron spectroscopic imaging (ESI) mode of an energy-filtering electron microscope (EFEM) can be shifted to the most-probable energy loss of the electron energy-loss spectrum. This enables mass-thicknesses up to 150 micrograms/cm2 or thicknesses of 1.5 microns to be examined. Electron energy-loss spectra of thick carbon films calculated by a Fourier method agree with experimental spectra. Measurements of the electron energy-loss spectroscopy and ESI image intensities with an additional platinum film confirm a scattering model for the calculation of the image intensity. This model considers the angular broadening at the most-probable energy loss by introducing an effective illumination aperture of the order of the full-width at half-maximum of the angular distribution.

Experimental ionization cross-sections of phosphorus and calcium by electron spectroscopic imaging

The absolute partial electron scattering cross-section for the phosphorus L2,3-shell ionization was measured by electron spectroscopic imaging using poliovirus as a primary standard. The equivalent calcium cross-section was obtained in relation to phosphorus using the stoichiometric ratio for these two elements in hydroxyapatite, Ca10(PO4)6(OH)2. At 80 keV, the partial cross-section of phosphorus was 2.26 x 10(-20) and 2.68 x 10(-20) cm2/atom for poliovirus and hydroxyapatite, respectively, at 150 eV loss for a 15-eV energy window and an acceptance angle of 15 mrad. Under the same conditions the calcium cross-section was 0.49 x 10(-20) cm2/atom at 360 eV loss. The experimental values are slightly higher than the theoretical cross-sections calculated either by hydrogenic or Hartree-Slater approaches.

Energy filtered STEM imaging of thick biological sections

Energy filtered imaging of thick biological specimens was analysed using a dedicated STEM fitted with an energy loss spectrometer and interfaced with a sophisticated data collection setup. All images were digital, thus permitting a quantitative analysis of the data. We also present a mathematical explanation of the data, which is useful in predicting the quality of thick specimen images formed with energy filtered electrons. It is known that increasing specimen thickness leads to a decrease of the zero energy loss intensity and an increase in higher (multiply scattered) energy loss electrons. We show that contrast decreases gradually with increased energy loss but, most important, the signal to noise ratio is maximal at an energy loss position slightly below the intensity maximum. This is the optimal position for imaging thick specimens. Moreover our studies confirm that the following parameters have similar effects on the energy loss spectra: (1) increased thickness (t); (2) higher average Z number elements (or lower mean free path); and (3) lower primary voltage (V0).

Electron spectroscopic imaging: parallel energy filtering and microanalysis in the fixed-beam electron microscope

A new imaging modality in electron microscopy uses energy filtration to produce micrographs with elastically scattered electrons or with electrons that have lost a specific, often characteristic amount of energy in interacting with the specimen. No deleterious effects on microscope performance are encountered. Instead, microanalysis of specimens is made possible with a spatial resolution of 3 to 5 A and a sensitivity of detection of 2 X 10(-21) g corresponding to about 50 atoms of phosphorus. Elements detected range from hydrogen (Z = 1) to uranium (Z = 92). Examples of elemental mapping show membrane structure, DNA within nucleosomes, and RNA within ribosomal particles.

Minimization of dose as a criterion for the selection of imaging modes in electron microscopy of amorphous specimens

A fundamental limitation in electron microscopy of organic specimens is radiation damage by the electron beam. To minimize damage it is necessary to have maximum information collection for a given dose. Various modes of operation of conventional and scanning transmission microscopes are compared with respect to their ability to detect small changes in specimen thickness or density with a given signal to noise ratio. Incoherent imaging is assumed, and this is expected to apply to amorphous specimens under a variety of microscope conditions. For either very thin or very thick specimens, the scanning transmission microscope is found to require nearly 10 times less dose than a conventional microscope for the same signal to noise ratio in the image. For specimens of intermediate thickness, scanning and conventional transmission electron microscopes are roughly equivalent.

A method for the improvement of the visibility of transmission electron microscope images

A method is presented of improving the visibility of transmission electron microscope images in any situation in which a high resolution in only one chosen direction is of interest. The technique is based on the use of slot shaped objective apertures. Such apertures are of reduced area relative to a circular aperture giving the same all round resolution. The background intensity due to inelastically scattered electrons is thus reduced. The aperture device developed is described, while the value of the method is demonstrated by its application to the observation of dislocations. Further possible applications are indicated.