Parallel recording of electron energy loss spectra

Application of EELS and EFTEM to the life sciences enabled by the contributions of Ondrej Krivanek

The pioneering contributions of Ondrej Krivanek to the development of electron energy loss spectrometers, energy filters, and detectors for transmission and scanning transmission electron microscopes have provided researchers with indispensible tools across a wide range of disciplines in the physical sciences, ranging from condensed matter physics, to chemistry, mineralogy, materials science, and nanotechnology. In addition, the same instrumentation has extended its reach into the life sciences, and it is this aspect of Ondrej Krivanek's influential contributions that will be surveyed here, together with some personal recollections. Traditionally, electron microscopy has given a purely morphological view of the biological structures that compose cells and tissues. However, the availability of high-performance electron energy loss spectrometers and energy filters offers complementary information about the elemental and chemical composition at the subcellular scale. Such information has proven to be valuable for applications in cell and structural biology, microbiology, histology, pathology, and more generally in the biomedical sciences.

First realization of the piezoelectronic stress-based transduction device

We present the first realization of a monolithically integrated piezoelectronic transistor (PET), a new transduction-based computer switch which could potentially operate conventional computer logic at 1/50 the power requirements of current Si-based transistors (Chen 2014 Proc. IEEE ICICDT pp 1-4; Mamaluy et al 2014 Proc. IWCE pp 1-2). In PET operation, an input gate voltage expands a piezoelectric element (PE), transducing the input into a pressure pulse which compresses a piezoresistive element (PR). The PR resistance goes down, transducing the signal back to voltage and turning the switch 'on'. This transduction physics, in principle, allows fast, low-voltage operation. In this work, we address the processing challenges of integrating chemically incompatible PR and PE materials together within a surrounding cage against which the PR can be compressed. This proof-of-concept demonstration of a fully integrated, stand-alone PET device is a key step in the development path toward a fast, low-power very large scale integration technology.

Phosphorylation and subunit organization of axonal neurofilaments determined by scanning transmission electron microscopy

Phosphorylation plays a critical role in controlling the function of cytoskeletal assemblies but no direct method yet exists to measure the phosphorylation state of proteins at the level of individual molecules and assemblies. Herein, we apply scanning transmission electron microscopy in combination with electron energy loss spectroscopy to measure the distributions of mass and phosphorus in neurofilaments (NFs) isolated from the squid giant axon. We find that native squid NFs, in contrast to typical reconstituted intermediate filaments, are a relatively homogeneous population containing only eight coiled-coil dimers per cross section. The measured stoichiometry of approximately 1:1 for light/heavy peptides strongly suggests that squid NFs are composed of heterodimers. Furthermore, each heavy chain of the dimers carries at least 100 phosphate groups and is, therefore, near-maximally phosphorylated. These results also demonstrate that scanning transmission electron microscopy combined with electron energy loss spectroscopy at the nanometer scale is capable of characterizing the level and distribution of phosphorylation in individual mass-mapped protein assemblies.

A high-sensitivity CCD system for parallel electron energy-loss spectroscopy (CCD for EELS)

A cooled frame transfer CCD camera system was developed and tested as a parallel detector in an electron energy-loss spectrometer mounted on a transmission electron microscope. The use of a shutterless camera with a frame transfer CCD collected virtually 100% of the photon signal with a reasonably fast acquisition time. The system detective quantum efficiency was over 90% under normal experimental conditions. Because of the low channel to channel gain variations in the CCD, the signal-to-noise ratio and the detection limit were substantially better than that obtained with a silicon intensified target (SIT) camera, and direct fitting to the standard data was feasible. Quantitation at the phosphorus L edge generated from a phosphoprotein, phosvitin, showed that, under identical experimental conditions, direct fitting of spectra obtained with this CCD system gave better sensitivity than that given by the SIT camera system. Because of its larger pixel charge well, the CCD system can also operate at a much higher beam current, resulting in a significant reduction in the time required for elemental mapping at a given sensitivity.

Low-dose thickness measurement of glucose-embedded protein crystals by electron energy loss spectroscopy and STEM dark-field imaging

Electron energy loss spectroscopy and dark-field imaging in a scanning transmission electron microscope were used to determine the thickness of glucose-embedded crotoxin complex crystals. The results demonstrate the feasibility of identifying protein crystals with a thickness of half a unit cell (12.8 nm) under low-dose and low-temperature conditions. The accuracy of this method is limited by the amount of surface coating of the crystal's embedding glucose used for preserving the high-resolution structure of the protein. The histogram of the crystal thickness distribution and the spread of the anticipated crystal thickness allow us to make an estimate of the uncertainty in the glucose layer thickness. This approach can be incorporated as part of the experimental procedure in the three-dimensional data collection for structure determination of protein crystals with variable thicknesses. The measurement can be done on areas approximately 200 nm in diameter so that crystals of suitable thickness can be pre-selected before the high-resolution data is recorded. Accurate determination of the crystal thickness will optimize the data collection efficiency by avoiding the collection and subsequent analysis of unmatchable data for the three-dimensional reconstruction.

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.

Measurement of low calcium concentrations in cryosectioned cells by parallel-EELS mapping

Electron energy loss spectroscopy (EELS) in the scanning transmission electron microscope provides a high sensitivity for microanalysis of certain important biological elements such as calcium whose physiological concentrations in cells are rather low. Application of parallel-EELS mapping to the analysis of freeze-dried cryosections of rapidly frozen tissue provides a means of detecting small amounts of calcium in structures with diameter approximately 50 nm. Detector pattern noise due to channel gain variations can be reduced by acquiring difference spectra at each pixel. By segmenting nitrogen maps that reflect the structure through the protein distribution it is possible to sum spectra from specific compartments. These are then processed by fitting reference spectra for the Ca L23-edge and the carbon background. It has been found that useful data can be collected at 100 keV beam energy from freeze-dried cryosections of cerebellar cortex cut to nominal thickness of 100 nm. The analysis results in a sensitivity of +/- 0.4 mmol Ca/kg dry weight with a total acquisition time of 400 s, a significant improvement over that achievable with energy-dispersive X-ray spectroscopy.

Optimization of quantitative electron energy loss spectroscopy in the low loss region: phosphorus L-edge

The purpose of this study was to optimize quantitative electron energy loss spectroscopy (EELS) of elements that have characteristic edges in the low energy loss region and are components of organic matrices. The optimum parameters for phosphorus L2,3-edge (at 135 eV) detection were determined by numerical analysis of computer-generated, Poisson-noisy spectra and by experimental measurements (at 80 keV) of films of the phosphoprotein, phosvitin. When the first, second and third valence electron/plasmon scatterings are included in the multiple least-squares (MLS) fit, the background subtraction of (first-difference) spectra is significantly more accurate than that obtained with the "inverse power law" method, even for a specimen thickness of only 0.25 lambda. Taking into account the effects of plural scattering, the optimal thickness for P quantitation is approximately 0.3 lambda. Signal-to-noise (S/N) ratio decreases rapidly with thickness, and at 1.0 lambda, it is only about 60% of the optimum S/N. The combined effects of the statistical uncertainty of measurements and of the systematic error due to gain variations of the parallel detector were evaluated, and the relative sensitivities of the no-difference (raw spectrum), first-difference and second-difference methods were compared. For channel-to-channel gain variations greater than 0.1% and up to 0.8%, the first-difference method results in the lowest uncertainty of P measurements. In the absence of gain variations, direct fitting provides the greatest sensitivity (least uncertainty), whereas at larger gain variations it may be necessary to use the second-difference method. The optimum energy shift for collecting a first-difference spectrum, approximately 15 eV, did not show any great variation between 5 and 25 eV, and is, in general, specimen dependent. Quantitation with EELS showed excellent correlation with simultaneous electron probe X-ray microanalysis, but, for the detection of P in a 0.25 lambda thick specimen, EELS was approximately five to six times more sensitive than X-ray. The minimal detectable P concentration, with 0.5 nA beam current for 100 s in a 0.25 lambda thick specimen, was 8.4 mmol/kg (0.01 at%) at the 99% confidence level, equivalent to 34 phosphorus atoms for a 15 nm probe. This value is close to the theoretical prediction of 7.5 mmol/kg, and can be improved only by further reducing the gain variation and directly fitting the non-difference spectrum. Appropriate reduction of the gain variations to less than 0.1% would result in a further, approximately two-fold, improvement in the parallel EELS detection system.(ABSTRACT TRUNCATED AT 400 WORDS)

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 10(3) 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 10(10) e/nm2) is required resulting in mass loss that may be attributable to 'knock-on' radiation damage.

Analysis of directly frozen macromolecules and tissues in the field-emission STEM

A VG Microscopes HB501 field-emission high-resolution scanning transmission electron microscope (STEM) was used to image and analyse rapidly frozen, isolated macromolecules and small organelles in tissue cryosections. Dark-field images were obtained from frozen-hydrated microtubules demonstrating that sufficient contrast is available to reveal structural information. The samples were subsequently freeze-dried in the STEM and low-dose (approximately 10(3) e/nm2) dark-field mass maps were recorded with single electron sensitivity. Elemental analysis of individual macromolecules was achievable at high dose using parallel-detection electron energy-loss spectroscopy, albeit with some structural degradation. Detection of copper (320 atoms) in di-decameric haemocyanin molecules was easily within the limits of sensitivity. Elemental analysis of hydrated cryosections is limited by radiation damage to a resolution of approximately 1 micron2. For freeze-dried sections, however, the high probe current and stable cold stage of the HB501 STEM allow energy-dispersive X-ray (EDX) microanalysis of low elemental concentrations in highly localized subcellular volumes. EDX spectra from cryosections of cerebellar cortex show that a 100-s analysis time is sufficient to quantify the calcium content of 400-nm2 regions within Purkinje cell dendrites with an uncertainty of +/- 2 mmol/kg dry weight, equivalent to +/- 12 atoms.

Quantitative electron energy loss spectroscopy in biology

The potential for applying electron energy loss spectroscopy (EELS) in biology is assessed. Some recent developments in instrumentation, spectrometer design, parallel detection and elemental mapping are discussed. Quantitation is demonstrated by means of the spectrum from DNA which gives an elemental ratio for N:P close to the expected value. A range of biologically important elements that can be usefully analyzed by EELS is tabulated and some possible applications for each are indicated. Detection limits and the effects of radiation damage are illustrated by spectra from the protein, insulin, and from the fluorinated amino-acid, histidine. Calcium detectability under optimum conditions may be as low as 1 mmol/kg dry weight. The application of EELS to analysis of cryosectioned adrenomedullary (chromaffin) cells is described in order to help determine the composition of the secretory granule. Water content can be determined from the amount of inelastic scattering as measured by the low-loss spectrum. The nitrogen/phosphorus ratio can be measured to provide information about the relative concentrations of ATP, chromogranin, and catecholamines. Quantitative EELS elemental maps are obtained in the STEM mode from chromaffin cells in order to measure the distribution of light elements.

High spatial resolution spectroscopy in the elemental microanalysis and imaging of biological systems

The application of analytical electron microscopy to the high spatial resolution study of biological systems is reviewed. Specimen preparation, quantitative analysis, capabilities and limitations are all discussed, principally in the context of energy-dispersive X-ray analysis. Results are presented using both current techniques and the developing quantitative image analysis. Finally the role of new instrumental approaches, including electron energy loss spectrometry, is discussed.

Electron energy loss analysis of near-trace-element concentrations of calcium

The quantitation of near-trace-element concentrations of calcium (25 ppm atomic fraction) with electron energy loss spectroscopy (EELS) is demonstrated. The data collection, with an energy-stabilized parallel recording spectrometer, subsequent signal processing, and quantitation procedures are described. The quantitative results obtained with EELS, in the biologically relevant range of 1 to 100 mmol/kg, are directly compared with simultaneously collected and previously validated energy-dispersive X-ray spectroscopy (EPMA). The experimentally determined sensitivity of EELS for Ca detection is five-fold better than for EPMA, and the theoretically attainable sensitivity of EELS is ten-fold better than for EPMA. However, the attainment of this sensitivity with EELS is technically more difficult and limited by specimen thickness. The sensitivity of EELS experimentally demonstrated in this study permits the detection of three calcium atoms in a 10 nm diameter spot of an organic matrix, with a field-emission-gun-equipped scanning transmission electron microscope.

Elemental imaging and resolution in energy-filtered conventional electron microscopy

Energy-filtered transmission electron microscopy (EFEM) was used to image the distributions of uranium and carbon in uranyl acetate stained catalase crystals. The spatial resolution obtained from inelastic C K-edge and U O4,5-edge images, determined from the highest-order reflection in the computed diffraction pattern, was 3.4 nm for both carbon and uranium. The resolution limit imposed by the delocalization of inelastic scattering was estimated from cross-section measurements to be 0.6 nm for U and 0.2 nm for C. Considering both delocalization and the effects of microscope aberrations, for an objective lens chromatic aberration coefficient of 2.8 mm and 10 eV energy window, the calculated resolutions are 2.0 nm for C and 1.2 nm for U. The effects of plural inelastic and elastic-inelastic scattering were sufficiently large to show crystalline structure in unprocessed pre-edge inelastic images. Previously suggested methods for eliminating these artifacts were applied to obtain the compositional information in the catalase EFEM images.

Optimized acquisition parameters and statistical detection limit in quantitative EELS

Optimizing the acquisition parameters for EELS recording has to be accomplished simultaneously from the physical and the statistical points of view; the statistical aspect of the question is covered here. Approximate probability density functions of the variables of interest are derived, which provide a global measure of signal-to-noise ratio taking into account every step of the EELS edge area estimation process. Qualitative and quantitative advice is given regarding the critical choice of the estimation and integration energy regions. The notion of visual contrast is presented; it permits the introduction of the concept of statistical detection limit. It is found that for typical experimental conditions, when other factors are equal, the required analysis time for the sample varies approximately as the inverse square of the concentration.

Imaging of biological structures with the scanning transmission electron microscope

The scanning transmission electron microscope (STEM) is discussed in view of biological applications. Theoretical considerations are given, but the emphasis is directed to practical examples from a range of biological projects. The STEM is most efficiently used in elastic and inelastic dark-field modes providing information on the scattering power of the irradiated sample. Thus, the STEM is an ideal tool for quantitative measurements such as mass-mapping or element-mapping at high resolution. Limitations of such methods due to multiple scattering and quantum noise are briefly reviewed.

Electron probe and electron energy loss analysis in biology

Methods, applications and limitations of quantitative electron probe analysis, X-ray mapping, electron energy loss analysis and energy filtered imaging are described, with emphasis on the analysis of thin (less than 200nm) cryosections. Energy dispersion electron probe analysis can measure reliably 5 to 10mM/Kg of biologically prevalent elements in 50nm diameter areas of 100 to 150 nm thick cryo sections during 100-300 sec counts. The minimal detectable mass (MDM) with a conventional thermionic electron source is approximately 10(-19)g Fe (100 sec count) and can be reduced to 10(-20)g through the use of a field emission gun (FEG). A spatial resolution of 8.7nm is demonstrated in two-dimensional Fourier transforms of Mo X-ray maps of stained catalase crystals. Significant biological results of quantitative electron probe analysis include the measurement of total Ca released from the Mg and K taken up by the sarcoplasmic reticulum during muscle contraction, and the demonstration that mitochondria do not contribute to the physiological regulation of cytoplasmic free Ca levels in cardiac, vascular smooth and striated muscle. Electron energy loss analysis (EELS) promises a significant improvement in sensitivity for the measurement of Ca; based on statistical errors of the measurement, 250 microM/Kg Ca should be measureable with EELS in 250 sec. through the Ca L-edge loss. The use of a doubly corrected magnetic sector spectrometer as a transmission electron microscope imaging filter outside the microscope vacuum is illustrated, and the resolution of the iron core (7.5nm) and surrounding organic shell of single ferritin molecules is demonstrated in, respectively, iron M and carbon K loss images.

Energy-filtered transmission electron microscopy of ferritin

The focusing properties of a magnetic-sector spectrometer are shown to be suitable for forming high-spatial-resolution, energy-filtered transmission electron microscope images. Filtered images of ferritin molecules by using electrons scattered from the characteristic iron M2,3 and carbon K absorption edges clearly distinguish the 75-A iron core and 120-A protein shell. The minimum detectable mass is estimated to be 0.84 X 10(-20) g for Fe for an electron dose of 18 C/cm2 and 99% confidence.