Characterization of biological macromolecules by combined mass mapping and electron energy-loss spectroscopy

The combination of scanning transmission electron microscopy (STEM) and parallel-detection energy-loss spectroscopy (EELS) was used to detect specific bound elements within macromolecules and macromolecular assemblies prepared by direct freezing. After cryotransferring and freeze-drying in situ, samples were re-cooled to liquid nitrogen temperature and low-dose (about 10³ e/nm²) digital dark-field images were obtained with single-electron sensitivity using a beam energy of approximately 100 keV and a probe current of approximately 5 pA. These maps provided a means of characterizing the molecular weights of the structures at low dose. The probe current was subsequently increased to about 5 nA in order to perform elemental analysis. The 320 copper atoms in a keyhole limpet haemocyanin molecule (mol.wt = 8 MDa) were detected with a sensitivity of ± 30 atoms in an acquisition time of 200 s. Phosphorus was detected in an approximately 10-nm length of single-stranded RNA contained in a tobacco mosaic virus particle (mol.wt = 130 kDa/nm) with a sensitivity of ± 25 atoms. Near single-atom sensitivity was achieved for the detection of iron in one haemoglobin molecule (mol.wt = 65 kDa, containing four Fe atoms). Such detection limits are only feasible if special processing methods are employed, as is demonstrated by the use of the second-difference acquisition technique and multiple least-squares fitting of reference spectra. Moreover, an extremely high electron dose (about 10¹⁰ e/nm²) is required resulting in mass loss that may be attributable to ‘knock-on’ radiation damage.     

Detecting single atoms of calcium and iron in biological structures by electron energy-loss spectrum-imaging

As techniques for electron energy‐loss spectroscopy (EELS) reach a higher degree of optimization, experimental detection limits for analysing biological structures are approaching values predicted by the physics of the electron scattering. Theory indicates that it should be possible to detect a single atom of certain elements like calcium and iron contained in a macromolecular assembly using a finely focused probe in the scanning transmission electron microscope (STEM). To test this prediction, EELS elemental maps have been recorded with the spectrum‐imaging technique in a VG Microscopes HB501 STEM coupled to a Gatan Enfina spectrometer, which is equipped with an efficient charge‐coupled device (CCD) array detector. By recording spectrum‐images of haemoglobin adsorbed onto a thin carbon film, it is shown that the four heme groups in a single molecule can be detected with a signal‐to‐noise ratio of ～10 : 1. Other measurements demonstrate that calcium adsorbed onto a thin carbon film can be imaged at single atom sensitivity with a signal‐to‐noise ratio of ～5 : 1. Despite radiation damage due to the necessarily high electron dose, it is anticipated that mapping single atoms of metals and other bound elements will find useful applications in characterizing large protein assemblies.     

Freeze-substitution and the preservation of diffusible ions

Freeze-substitution of biological material in pure acetone followed by low-temperature embedding in the Lowicryls K11M and HM23 yields stable preparations well suited for sectioning and subsequent morphological and microanalytical studies. Transmission electron microscopy of dry-cut sections shows that diffusible cellular thallium ions (Tl⁺) of Tl⁺-loaded muscle are localized at similar protein sites in freeze-substituted as in frozen-hydrated preparations. A comparison of X-ray micro-analytical data obtained from freeze-dried cryosections and sections of freeze-substituted normal (potassium-containing) muscle shows that K⁺ ion retention in the freeze-substituted sample is highly dependent on the freeze-substitution procedure used; so far, in the best case, about 67% of the cellular K⁺ is retained after freeze-substitution in pure acetone and low-temperature embedding. It is concluded that the retention of diffusible cellular ions is dependent on their interactions with cellular macromolecules during the preparative steps and that ion retention may be increased by further optimizing freeze-substitution and low-temperature embedding.     

Gentle STEM: ADF imaging and EELS at low primary energies

Aberration correction of the scanning transmission electron microscope (STEM) has made it possible to reach probe sizes close to 1 Å at 60 keV, an operating energy that avoids direct knock-on damage in materials consisting of light atoms such as B, C, N and O. Although greatly reduced, some radiation damage is still present at this energy, and this limits the maximum usable electron dose. Elemental analysis by electron energy loss spectroscopy (EELS) is then usefully supplemented by annular dark field (ADF) imaging, for which the signal is larger. Because of its strong Z dependence, ADF allows the chemical identification of individual atoms, both heavy and light, and it can also record the atomic motion of individual heavy atoms in considerable detail. We illustrate these points by ADF images and EELS of nanotubes containing nanopods filled with single atoms of Er, and by ADF images of graphene with impurity atoms.     

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 λ. 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/λ) 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 μm² 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 2×10⁻⁴. Calcium concentrations in peripheral mitochondria of recently depolarized, and therefore stimulated and Ca loaded, frog sympathetic neurons were in reasonable agreement with previous data.     

The structure and continuous stoichiometry change of 1DTbBrx@SWCNTs

HRTEM and HAADF STEM of 1DTbBr_x@SWCNT meta‐nanotubes reveal three structural modifications of 1D nanocrystals within single wall carbon nanotube channels attributed to a different stoichiometry of the guest crystal. For SWCNTs with diameters D_m > 1.4 nm a most complete tetragonal unit cell is observed. When crystallization occurs inside SWCNT with D_m < 1.4 nm 1D TbBr_x crystal deforms a nanotube to elliptical shape in cross section. In this case the 1D crystal unit cell becomes monoclinic, with possible loss of a part of bromine atoms. Two modifications of a monoclinic unit cell appear. One of them is characterized by single or pair vacancies in the structure of the 1D crystal. Another structure is explained by peripheral and central bromine atoms loss. An appearance of such modifications can be stimulated by electron irradiation. The loss of bromine atoms is in agreement with chemical analysis data. Electronic properties of obtained meta‐nanotubes are investigated using optical absorption and Raman spectroscopy. It is shown that intercalation of terbium bromide into SWCNTs leads to acceptor doping of SWCNTs. According to local EDX analysis and elemental mapping this doping can arise from significant stoichiometry change in 1D nanocrystal indicating an average Tb:Br atomic ratio of 1:2.8 ± 0.1.     

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 × 10³ 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.     

Electron beam modifications of InP surfaces

InP surfaces have been modified by using the intense electron beam of a V.G. HB501 STEM and subsequently examined in the same instrument using the reflection microscopy geometry. The surface changes can be divided into two parts; first, a fairly local removal of material, and second, more widespread effects including faceting and the formation of an oxide layer which extends for several microns around the point of incidence of the electron beam.     

Advances in EELS spectroscopy by using new detector and new specimen preparation technologies

First results obtained with a Gatan UHV Enfina system, which was attached to a VG HB 501 UX dedicated STEM, are reported. The Enfina system is based on a CCD detector and offers, compared to the previously used photodiode array, a narrower point‐spread function, higher sensitivity, and faster read‐out capabilities. These improvements are demonstrated with electron energy‐loss measurements on various oxides, such as Al₂O₃, TiO₂ and SrTiO₃. It is shown that a better energy resolution is achieved and that acquisition of high‐energy absorption edges with a reasonable signal‐to‐noise ratio becomes possible. Furthermore, we report on the influence of the TEM specimen quality on the energy‐loss spectra. Thin amorphous layers at the specimen surfaces, which are induced by ion‐milling processes, can modify specific electron energy‐loss near‐edge structure features. We found that for the investigated ceramics the use of low‐energy ion‐milling systems is highly recommended, since the loss of energy‐loss near‐edge structure details by the presence of the amorphous layers is considerably reduced. This is especially true for very thin specimens.     

Towards single atom analysis of biological structures.

Mapping single atoms in biological structures is now becoming within the reach of analytical electron microscopy. Electron energy-loss spectroscopy (EELS) in the field-emission scanning transmission electron microscope (STEM) provides a particularly high sensitivity for detecting the biologically important element, phosphorus. Imaging can be performed at low dose with dark-field STEM prior to analysis at high dose, so that structures of macromolecular assemblies can be correlated with the numbers of specific atoms that they contain. Measurements confirm theoretical predictions that single atom detection requires a nanometer-sized probe. Although phosphorus atoms may have moved several nanometers from their original positions by beam-induced structural degradation at the high required dose of approximately 10(9) e/nm2, damaged molecules are nevertheless stable enough to be analyzed at 1 or 2 nm resolution. Such analyses can only be achieved by means of spectrum-imaging with correction for specimen drift. Optimal strategies for mapping small numbers of phosphorus atoms have been investigated using well-characterized specimens of DNA plasmids and tobacco mosaic virus.     

Bloch-wave-based STEM image simulation with layer-by-layer representation

In a dynamical STEM image simulation by the Bloch-wave method, Allen et al. formulated a framework for calculating the cross-section for any incoherent scattering process from the inelastic scattering coefficients: thermal diffuse scattering (TDS) for high-angle annular dark-field (HAADF) and back-scattered electron (BSE) STEM, and ionization for electron energy-loss spectroscopy (EELS) and energy-dispersive X-ray spectroscopy (EDX) STEM. Furthermore, their method employed a skilful approach for deriving the excitation amplitude and block diagonalization in the eigenvalue equation. In the present work, we extend their scheme to a layer-by-layer representation for application to inhomogeneous crystals that include precipitates, defects and atomic displacement. Calculations for a multi-layer sample of Si–Sb–Si were performed by multiplying Allen et al.'s block-diagonalized matrices. Electron intensities within the sample and EDX STEM images, as an example of the inelastic scattering, were calculated at various conditions. From the calculations, 3-dimensional STEM analysis was considered.     

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 10⁶ e^?/nm², no significant loss of phosphorus or nitrogen was observed for doses as high as 10⁸ e^?/nm². The oxygen content decreased from 25 ± 2 to 9 ± 2 atomic percent at an electron dose of 10⁴ e^?/nm², which accounted for a major component of the total mass loss. The specimen thickness decreased by 50% after a dose of 10⁸ e^?/nm², and a lateral shrinkage of 9.5 ± 2.0% occurred from 2 × 10⁴ to 10⁸ e^?/nm². At doses above 10⁷ e^?/nm², 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.     

X-ray microanalysis of freeze-dried and frozen-hydrated cryosections

The elemental composition and the ultrastructure of biological cells were studied by scanning transmission electron microscopy (STEM) combined with energy dispersive X-ray microanalysis. The preparation technique involves cryofixation, cryoultramicrotomy, cryotransfer, and freeze-drying of samples. Freeze-dried cryosections 100-nm thick appeared to be appropriate for measuring the distribution of diffusible elements and water in different compartments of the cells. The lateral analytical resolution was less than 50 nm, depending on ice crystal damage and section thickness. The detection limit was in the range of 10 mmol/kg dry weight for all elements with an atomic number higher than 12; for sodium and magnesium the detection limits were about 30 and 20 mmol/kg dry weight, respectively. The darkfield intensity in STEM is linearly related to the mass thickness. Thus, it becomes possible to measure the water content in intracellular compartments by using the darkfield signal of the dry mass remaining after freeze-drying. By combining the X-ray microanalytical data expressed as dry weight concentrations with the measurements of the water content, physiologically more meaningful wet weight concentrations of elements were determined. In comparison to freeze-dried cryosections frozen-hydrated sections showed poor contrast and were very sensitive against radiation damage, resulting in mass loss. The high electron exposure required for recording X-ray spectra made reproducible microanalysis of ultrathin (about 100-nm thick) frozen-hydrated sections impossible. The mass loss could be reduced by carbon coating; however, the improvement achieved thus far is still insufficient for applications in X-ray microanalysis. Therefore, at present only bulk specimens or at least 1-μm thick sections can be used for X-ray microanalysis of frozen-hydrated biological samples.     

Elemental concentrations in air-exposed and vacuum-stored cryosections of rat liver cells

Elemental concentrations in different compartments of cryosections of isolated rat liver cells cryotransferred and freeze-dried were compared with those obtained after storage under vacuum for 12 or 60 h and after exposure to room air for 2 min. Poorer image contrast and segregation artefacts are frequently found in air-exposed sections, together with a slight but significant decrease of the K concentration in the cytoplasm and an increase of the S concentration in the liver cell nuclei and the extracellular medium. Extreme distortions of both ultrastructure and elemental distributions are observed if the sections are even slightly colder than the surrounding atmosphere. While storage of frozen-dried cryosections under vacuum for less than 12 h does not lead to alterations in the sections, gross changes are found both in morphology and elemental distribution in sections stored under vacuum for about 60 h. Long-time vacuum storage of frozen-dried cryosections is, therefore, not recommended.     

Direct space structure solution from precession electron diffraction data: Resolving heavy and light scatterers in Pb13Mn9O25

The crystal structure of a novel compound Pb₁₃Mn₉O₂₅ has been determined through a direct space structure solution with a Monte-Carlo-based global optimization using precession electron diffraction data (a=14.177(3) Å, c=3.9320(7) Å, SG P4/m, R_F=0.239) and compositional information obtained from energy dispersive X-ray analysis and electron energy loss spectroscopy. This allowed to obtain a reliable structural model even despite the simultaneous presence of both heavy (Pb) and light (O) scattering elements and to validate the accuracy of the electron diffraction-based structure refinement. This provides an important benchmark for further studies of complex structural problems with electron diffraction techniques. Pb₁₃Mn₉O₂₅ has an anion- and cation-deficient perovskite-based structure with the A-positions filled by the Pb atoms and 9/13 of the B positions filled by the Mn atoms in an ordered manner. MnO₆ octahedra and MnO₅ tetragonal pyramids form a network by sharing common corners. Tunnels are formed in the network due to an ordered arrangement of vacancies at the B-sublattice. These tunnels provide sufficient space for localization of the lone 6s² electron pairs of the Pb²⁺ cations, suggested as the driving force for the structural difference between Pb₁₃Mn₉O₂₅ and the manganites of alkali-earth elements with similar compositions.     

Rapid freezing,cryosectioning, and x-ray microanalysis on cardiac muscle preparations in defined functional states

Electrically stimulated heart muscle preparations can be quickly frozen in undercooled propane at defined times of the mechanically controlled contraction cycle. The apparatus for triggered freezing of the muscle strips in undercooled propane is described in detail. Freeze substitution of some strips after freezing shows the degree of ice crystal formation without the potential interference of artifacts introduced later by cryosectioning and freeze drying. Ultrathin longitudinal and transversal cryosections are cut with a LKB cryoultramicrotome at temperatures of −130 to −140°C, freeze-dried at 10⁻⁶ Torr vacuum and carbon-coated before analysis. The freeze-dried cryosections are analyzed in a Siemens Elmiskop 102 electron microscope equipped with a Kevex energy dispersive system, and the elemental concentrations (in mMol/kg d.w.) of Na, Mg, P, S, Cl, K, and Ca are determined in subcellular compartments of muscle frozen in different functional states. The methodology of quantitation, i.e, determination of elemental net peak and continuum, correction of continuum, preparation of standards, and deconvolution of overlapping peaks are described. The minimum detectable elemental concentration using the reported methods is in the range of a few mMol/kg d.w. This also applies to Ca, which can be accumulated in heart muscle in readily detectable amounts in intracellularly located stores as well as structures connected with the cell membrane. The present report shows that cryotechniques and x-ray microanalysis can be successfully applied to heart physiology.     

Quantitative analysis of image contrast in phase contrast STEM for low dose imaging

This work quantitatively evaluates the contrast in phase contrast images of thin vermiculite crystals recorded by TEM and aberration-corrected bright-field STEM. Specimen movement induced by electron irradiation remains a major problem limiting the phase contrast in TEM images of radiation-sensitive specimens. While spot scanning improves the contrast, it does not eliminate the problem. One possibility is to utilise aberration-corrected scanning transmission electron microscopy (STEM) with an Ångstrom-sized probe to illuminate the sample, and thus further reduce irradiation-induced specimen movement. Vermiculite is relatively radiation insensitive in TEM to electron fluences below 100,000 e⁻/Ų and this is likely to be similar for STEM although different damage mechanisms could occur. We compare the performance of a TEM with a thermally assisted field emission electron gun (FEG) and charge coupled device (CCD) image capture to the performance of STEMs with spherical aberration correction, cold field emission electron sources and photomultiplier tube image capture at a range of electron fluences and similar illumination areas. We show that the absolute contrast of the phase contrast images obtained by aberration-corrected STEM is better than that obtained by TEM. Although the STEM contrast is higher, the efficiency of collection of electrons in bright field STEM is still much less than that in bright field TEM (where for thin samples virtually all the electrons contribute to the image), and the SNR of equivalent STEM images is three times lower. This is better than expected, probably due to the absence of a frequency dependent modulation transfer function in the STEM detection system. With optimisation of the STEM bright field collection angles, the efficiency may approach that of bright field TEM, and if reductions in beam-induced specimen movement are found, STEM could surpass the overall performance of TEM.     

High-Angle annular dark-field imaging on a tem/stem system

The technique of high-angle annular dark-field (HAADF) imaging, which is highly sensitive to atomic-number contrast, can be performed on TEM/STEM systems using the standard annular dark-field detector. For optimum HAADF imaging, the TEM/STEM must have a high maximum diffraction angle, small minimum camera length, and a descanning facility. The sensitivity of the technique is demonstrated to be about 10⁵ to 10⁶ times higher than energy-dispersive X-ray spectroscopy. Examples are shown from semiconductor, catalysis, ceramics, and particle analysis applications.     

The cryopuncher: A pneumatic cryofixation device for X-ray microanalysis of tissue specimens

A cryopunching device is described which allows cryofixation of tissue specimens by quick contact with a precooled copper surface during excision. The advantage of the cryopuncher for analytical electron microscopy of cells and tissues in defined functional states is illustrated by electron probe X-ray microanalysis of freeze-dried cryosections from rat liver and dogfish kidney. In comparison with results obtained from specimens plunged into liquid propane, cryopunching in situ results in similar preservation of morphology and remarkably improved intracellular K/Na ratio.     

Simulation of annular dark field stem images using a modified multislice method

The multislice method of image simulation has been extensively applied to conventional transmission electron micrographs (CTEM), but not yet to scanning transmission electron micrographs (STEM). In this paper the multislice method is adapted for application to the STEM and several examples relevant to the VG-HB501 STEM are presented. Annular dark field images of a (111) crystal silicon substrate supporting a single heavy atom are calculated.