Monte Carlo calculations of elastic and inelastic electron scattering in biological and plastic materials

A Versatile High-Vacuum Cryo-transfer System for Cryo-microscopy and Analytics

Cryogenic microscopy methods have gained increasing popularity, as they offer an unaltered view on the architecture of biological specimens. As a prerequisite, samples must be handled under cryogenic conditions below their recrystallization temperature, and contamination during sample transfer and handling must be prevented. We present a high-vacuum cryo-transfer system that streamlines the entire handling of frozen-hydrated samples from the vitrification process to low temperature imaging for scanning transmission electron microscopy and transmission electron microscopy. A template for cryo-electron microscopy and multimodal cryo-imaging approaches with numerous sample transfer steps is presented.

Backscattered electron SEM imaging of cells and determination of the information depth

Backscattered electron imaging of HT29 colon carcinoma cells in a scanning electron microscope was studied. Thin cell sections were placed on indium-tin-oxide-coated glass slides, which is a promising substrate material for correlative light and electron microscopy. The ultrastructure of HT29 colon carcinoma cells was imaged without poststaining by exploiting the high chemical sensitivity of backscattered electrons. Optimum primary electron energies for backscattered electron imaging were determined which depend on the section thickness. Charging effects in the vicinity of the SiO₂ nanoparticles contained in cell sections could be clarified by placing cell sections on different substrates. Moreover, a method is presented for information depth determination of backscattered electrons which is based on the imaging of subsurface nanoparticles embedded by the cells.

Image formation modeling in cryo-electron microscopy

Accurate modeling of image formation in cryo-electron microscopy is an important requirement for quantitative image interpretation and optimization of the data acquisition strategy. Here we present a forward model that accounts for the specimen's scattering properties, microscope optics, and detector response. The specimen interaction potential is calculated with the isolated atom superposition approximation (IASA) and extended with the influences of solvent's dielectric and ionic properties as well as the molecular electrostatic distribution. We account for an effective charge redistribution via the Poisson-Boltzmann approach and find that the IASA-based potential forms the dominant part of the interaction potential, as the contribution of the redistribution is less than 10%. The electron wave is propagated through the specimen by a multislice approach and the influence of the optics is included via the contrast transfer function. We incorporate the detective quantum efficiency of the camera due to the difference between signal and noise transfer characteristics, instead of using only the modulation transfer function. The full model was validated against experimental images of 20S proteasome, hemoglobin, and GroEL. The simulations adequately predict the effects of phase contrast, changes due to the integrated electron flux, thickness, inelastic scattering, detective quantum efficiency and acceleration voltage. We suggest that beam-induced specimen movements are relevant in the experiments whereas the influence of the solvent amorphousness can be neglected. All simulation parameters are based on physical principles and, when necessary, experimentally determined.

Quantifying the low-energy limit and spectral resolution in valence electron energy loss spectroscopy

While the development of monochromators for scanning transmission electron microscopes (STEM) has improved our ability to resolve spectral features in the 0-5 eV energy range of the electron energy loss spectrum, the overall benefits relative to unfiltered microscopes have been difficult to quantify. Simple curve fitting and reciprocal space models that extrapolate the expected behavior of the zero-loss peak are not enough to fully exploit the optimal spectral limit and can hinder the ease of interpreting the resulting spectra due to processing-induced artifacts. To address this issue, here we present a quantitative comparison of two processing methods for performing ZLP removal and for defining the low-energy spectral limit applied to three microscopes with different intrinsic emission and energy resolutions. Applying the processing techniques to spectroscopic data obtained from each instrument leads in each case to a marked improvement in the spectroscopic limit, regardless of the technique implemented or the microscope setup. The example application chosen to benchmark these processing techniques is the energy limit obtained from a silicon wedge sample as a function of thickness. Based on these results, we conclude on the possibility to resolve statistically significant spectral features to within a hundred meV of the native instrumental energy spread, opening up the future prospect of tracking phonon peaks as new and improved hardware becomes available.

High-resolution investigation of nanoparticle interaction with a model pulmonary surfactant monolayer

The pulmonary surfactant film spanning the inner alveolar surface prevents alveolar collapse during the end-exhalation and reduces the work of breathing. Nanoparticles (NPs) present in the atmosphere or nanocarriers targeted through the pulmonary route for medical purposes challenge this biological barrier. During interaction with or passage of NPs through the alveolar surfactant, the biophysical functioning of the film may be altered. However, experimental evidence showing detailed biophysical interaction of NPs with the pulmonary surfactant film are scant. In this study, we have investigated the impact of a hydrophobic polyorganosiloxane (AmOrSil20) NPs on the integrity as well as on the structural organization of the model pulmonary surfactant film. Primarily, scanning force microscopic techniques and electron microscopy have been used to visualize the topology as well as to characterize the localization of nanoparticles within the compressed pulmonary surfactant film. We could show that the NPs partition in the fluid phase of the compressed film at lower surface pressure, and at higher surface pressure, such NPs interact extensively with the surface-associated structures. Major amounts of NPs are retained at the interface and are released slowly into the aqueous subphase during repeated compression/expansion cycles. Further, the process of vesicle insertion into the interfacial film was observed to slow down with increasing NP concentrations. The hydrophobic AmOrSil20 NPs up to a given concentration do not substantially affect the structural organization and functioning of pulmonary surfactant film; however, such NPs do show drastic impacts at higher concentrations.

Low-energy electron scattering in carbon-based materials analyzed by scanning transmission electron microscopy and its application to sample thickness determination

High-angle annular dark-field scanning transmission electron microscopy (HAADF STEM) at low energies (≤30 keV) was used to study quantitatively electron scattering in amorphous carbon and carbon-based materials. Experimental HAADF STEM intensities from samples with well-known composition and thickness are compared with results of Monte Carlo simulations and semiempirical equations describing multiple electron scattering. A well-defined relationship is found between the maximum HAADF STEM intensity and sample thickness which is exploited (a) to derive a quantitative description for the mean quadratic scattering angle and (b) to calculate the transmitted HAADF STEM intensity as a function of the relevant materials parameters and electron energy. The formalism can be also applied to determine TEM sample thicknesses by minimizing the contrast of the sample as a function of the electron energy.

Simulating STEM imaging of nanoparticles in micrometers-thick substrates

Scanning transmission electron microscope (STEM) images of three-dimensional (3D) samples were simulated. The samples consisted of a micrometer(s)-thick substrate and gold nanoparticles at various vertical positions. The atomic number (Z) contrast as obtained via the annular dark-field detector was generated. The simulations were carried out using the Monte Carlo method in the CASINO software (freeware). The software was adapted to include the STEM imaging modality, including the noise characteristics of the electron source, the conical shape of the beam, and 3D scanning. Simulated STEM images of nanoparticles on a carbon substrate revealed the influence of the electron dose on the visibility of the nanoparticles. The 3D datasets obtained by simulating focal series showed the effect of beam broadening on the spatial resolution and on the signal-to-noise ratio. Monte Carlo simulations of STEM imaging of nanoparticles on a thick water layer were compared with experimental data by programming the exact sample geometry. The simulated image corresponded to the experimental image, and the signal-to-noise levels were similar. The Monte Carlo simulation strategy described here can be used to calculate STEM images of objects of an arbitrary geometry and amorphous sample composition. This information can then be used, for example, to optimize the microscope settings for imaging sessions where a low electron dose is crucial for the design of equipment, or for the analysis of the composition of a certain specimen.

Monte Carlo electron-trajectory simulations in bright-field and dark-field STEM: implications for tomography of thick biological sections

A Monte Carlo electron-trajectory calculation has been implemented to assess the optimal detector configuration for scanning transmission electron microscopy (STEM) tomography of thick biological sections. By modeling specimens containing 2 and 3 at% osmium in a carbon matrix, it was found that for 1-microm-thick samples the bright-field (BF) and annular dark-field (ADF) signals give similar contrast and signal-to-noise ratio provided the ADF inner angle and BF outer angle are chosen optimally. Spatial resolution in STEM imaging of thick sections is compromised by multiple elastic scattering which results in a spread of scattering angles and thus a spread in lateral distances of the electrons leaving the bottom surface. However, the simulations reveal that a large fraction of these multiply scattered electrons are excluded from the BF detector, which results in higher spatial resolution in BF than in high-angle ADF images for objects situated towards the bottom of the sample. The calculations imply that STEM electron tomography of thick sections should be performed using a BF rather than an ADF detector. This advantage was verified by recording simultaneous BF and high-angle ADF STEM tomographic tilt series from a stained 600-nm-thick section of C. elegans. It was found that loss of spatial resolution occurred markedly at the bottom surface of the specimen in the ADF STEM but significantly less in the BF STEM tomographic reconstruction. Our results indicate that it might be feasible to use BF STEM tomography to determine the 3D structure of whole eukaryotic microorganisms prepared by freeze-substitution, embedding, and sectioning.

MASDET-A fast and user-friendly multiplatform software for mass determination by dark-field electron microscopy

Electron microscopy has been used to measure the mass of biological nanoparticles since the early 60s, and is the only way to obtain the mass of large structures or parameters such as the mass-per-length of filaments. The ability of this method to sort heterogeneous samples both in terms of mass and shape promises to make it a key tool for proteomics down to the single cell level. A new multiplatform software package, MASDET, that can be run under MATLAB or as a standalone program is described. Based on a user-friendly graphical interface MASDET streamlines mass evaluation and greatly increases the speed of required optimisation procedures. Importantly, the immediate application of Monte-Carlo simulations to describe multiple scattering is possible, allowing the mass analysis of thicker samples and the generation of mass thickness maps.

STEM Analysis of Caenorhabditis elegans muscle thick filaments: evidence for microdifferentiated substructures

In the thick filaments of body muscle in Caenorhabditis elegans, myosin A and myosin B isoforms and a subpopulation of paramyosin, a homologue of myosin heavy chain rods, are organized about a tubular core. As determined by scanning transmission electron microscopy, the thick filaments show a continuous decrease in mass-per-length (MPL) from their central zones to their polar regions. This is consistent with previously reported morphological studies and suggests that both their content and structural organization are microdifferentiated as a function of position. The cores are composed of a second distinct subpopulation of paramyosin in association with the alpha, beta, and gamma-filagenins. MPL measurements suggest that cores are formed from seven subfilaments containing four strands of paramyosin molecules, rather than the two originally proposed. The periodic locations of the filagenins within different regions and the presence of a central zone where myosin A is located, implies that the cores are also microdifferentiated with respect to molecular content and structure. This differentiation may result from a novel "induced strain" assembly mechanism based upon the interaction of the filagenins, paramyosin and myosin A. The cores may then serve as "differentiated templates" for the assembly of myosin B and paramyosin in the tapering, microdifferentiated polar regions of the thick filaments.

Structure and mass analysis by scanning transmission electron microscopy

In the scanning transmission electron microscope (STEM) an electron beam of a few angstroms diameter is raster scanned over a thin sample and the scattered electrons are sequentially measured for each sample element irradiated. The mass, the elemental composition and the structure of a protein can be simultaneously assessed if all detector systems of the STEM are used. Aspects affecting the accuracy of the mass measurement technique and the demands placed on the instrument's dark-field detector system are outlined. In addition, the influences of some sample preparation techniques are noted and the mass-loss induced at ambient temperatures by the incidence of 80kV electrons on various biological samples is reported. Finally, the importance of the STEM for the structural analysis of proteins is documented by examples.

Signal standardization of the secondary ion mass spectrometry (SIMS) microscope for quantification of halogens and calcium in biological applications

The secondary ion mass spectrometry (SIMS) microscope is able to map chemical elements in tissue sections. Although absolute quantification of an element remains difficult, a relative quantitative approach is possible for soft tissue by using carbon (12C) as an internal reference present at large homogeneous and constant concentration in specimen and embedding resin. In this study, this approach is used to standardize the signal of an SIMS microscope for the quantification of halogens (9F-, 35Cl- and 79Br-) and calcium (40Ca+). Standard preparation was determined based on homogeneity and stability criteria by molecular incorporation (halogens) or mixing (calcium) in methacrylate resin. Standard measurements were performed by depth analysis on areas of 8 microns (halogens) and 150 microns (calcium) in diameter for 10-30 min, under Cs+ (halogens) or Ox+ (calcium) bombardment. Results obtained from 100-120 measurements for each standard dilution show that the relationship between the signal intensity measured and the elemental concentration (micrograms/mg of wet tissue or mM) is linear in the range of biological concentrations. This quantitative approach was applied firstly to bromine of the 5-bromo-2'-deoxyuridine (BrdU) used as nuclear marker of rat hepatocytes in proliferation. The second model concerns depletion of calcium concentration in cortical compartment in Paramecium tetraurelia during exocytosis. Then signal standardization in SIMS microscopy allows us to correlate quantitative results with those obtained from other methods.

Monte Carlo simulations of electron scattering in bone

Relative changes in the mineralization level within bone can be studied using backscattered electron (BSE) imaging in a scanning electron microscope (SEM). We calculated the size and shape of the volume element studied, choosing conditions which are typical for practical experimental work with polymethylmethacrylate (PMMA)-embedded bone. Absolutely flat surfaces of embedded bone blocks cannot be generated, and a further aim was to examine the effect of the surface topography on the detected BSE signal level. For normal beam incidence, 20 kV, and modeling an annular detector by collecting BSE with take-off angles of between 45 degrees and 75 degrees to the flat sample surface, it was found that the collectable BSE signal intensity peaks for electrons which leave the specimen surface at a radial distance of approximately 1 micron from the beam impact point. The layered structure of the bone generates topographic relief on polishing. Modeling this by a sinusoidal profile of wavelength 5.0 and amplitude 0.5 micron and again for 20 kV, it was found that the signal derived from the troughs is reduced by 14.4% and that from the crests is increased by 17.2%. The two effects may add constructively to generate the frequently observed strong contrast correlating with the distribution of bone lamellae. No net change in mineral packing density would be expected from a change in collagen orientation, and the lamellar contrast observed in practice can be explained solely by the topographic contrast.

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.

Concentration evaluation of chromatin in unstained resin-embedded sections by means of low-dose ratio-contrast imaging in STEM

Quantitative STEM with the imaging mode of ratio-contrast was investigated in order to evaluate the local concentration of DNA in situ for different kinds of DNA plasms in terms of intracellular packing densities (p.d.). The ability of ratio imaging to suppress thickness variations provided the basis to use unstained sections from cryofixed and freeze-substituted material. The DNA p.d. within the nucleoid of E. coli was determined to be about 100 mg ml-1. Quantitative data concerning the p.d. of DNA in condensed eukaryotic chromatin assuming equal amounts of DNA and protein were evaluated for the first time: approximately 400 mg ml-1 chromatin which corresponds to 200 mg ml-1 DNA. The p.d. of DNA in chromosomes from the dinoflagellate Amphidinium carterae, a eukaryote devoid of histones and with only small relative amounts of histone-like protein, was also found to be of the order of 200 mg ml-1. The highest p.d. of DNA was measured for the head of the bacteriophage T4 with more than 800 mg ml-1, in fair agreement with previous calculations. The results provide further support for a condensation mode of low protein chromatins that involves a liquid-crystalline organization of the DNA filaments.

Quantitative analysis of electron energy-loss spectra from ultrathin-sectioned biological material. I. Optimization of the background-fit with the use of Bio-standards

A computer program for quantitative spectral analysis is proposed for the elemental analysis of biological material by electron energy-loss spectroscopy in a conventional transmission electron microscope, the Zeiss EM902. Bio-standards are used to test the performance of this program. The application of a simplex optimization method for curve-fitting is proposed to separate the ionization edge from the background. Making use of Ce-, Ca- and Fe-bio-standards, this method is compared with Egerton's well-known two-area method.

Filtered dark-field and pure Z-contrast: two novel imaging modes in a Scanning Transmission Electron Microscope

For the investigation of biological objects with a Scanning Transmission Electron Microscope (STEM) the dark-field imaging mode is the one used most often. We will show, regarding calculations that we have done which took into account the finite angle of the illumination and multiple scattering processes, that the collected amount of inelastically scattered electrons with an annular dark-field detector is higher then normally expected. According to the above calculations, we designed a new detection system to enable us to acquire three different images (inelastic, filtered dark-field and filtered bright-field) simultaneously.

Resolution as a function of accelerating voltage in electron microscopy of semithick biological specimens

In the past, biological sections ranging in thickness from 0.10- to 0.50-micron have usually been examined with high-voltage (greater than 500 kV) electron microscopes (HVEM). Now investigators are increasingly using intermediate voltage (200-500 kV) electron microscopes (IVEM), which are more readily available and demand less maintenance. In a study of "typical" plastic-embedded, stained sections of mouse liver ranging from 0.10 to 1.0 micron thick, we determined the resolution obtainable at 100, 200, and 1000 kV. At all three accelerating voltages the resolution (2.7 nm) for 0.10-micron sections was limited only by the sections stain granularity. For 0.25-micron thickness the resolutions were 5.8, 3.1, and 3.1 nm at 100, 200, and 1000 kV, respectively. The maximum usable thickness at 200 kV with resolution sufficient to resolve membranes clearly was between 0.75 and 1.0 micron, depending on the magnification. Resolution at 100 kV was adequate for screening sections up to 1.0-micron thick for preparation defects prior to examination with an IVEM or HVEM.

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-micron thick sections can be used for X-ray microanalysis of frozen-hydrated biological samples.

Isolation and reassembly of bacteriophage T4 core proteins

The products of genes 22, 67 and 68, and the internal proteins IPI, IPII and IPIII, as components of the scaffolding core of the bacteriophage T4 prohead, have been isolated and purified by hydroxylapatite column chromatography. Under conditions promoting reassembly in vitro, the proteins associated into elongated particles of practically constant width but variable length that we have called polycores. Preliminary optical diffraction experiments indicate that polycores may have an ordered structure, possibly helical, as has been suggested for the polyhead core. The coassembly of core proteins and the purified shell protein gp23 results in the formation of core-containing polyheads. Occasionally, prolate core-like particles have been observed but their reproducible formation has not been attained. Attempts to investigate the role of the minor prohead component gp20 in core assembly have been made through the cloning of the corresponding gene in an expression vector and subsequent purification of the protein.

How to obtain a thickness-independent image in a STEM

"Z" contrast is independent of thickness only for extremely thin specimens (3 nm of carbon). Following Egerton [Ultramicroscopy 10 (1983) 293], we propose a new method of imaging which is really independent of thickness and which provides absolute values. It consists of a mixing of the unscattered, the annular darkfield and the inelastic signal. Two-dimensional histograms are used to determine the relative efficiency factors of the different images. Thus, in addition to the obtaining of lambda i/lambda e images, the method allows the calculations of the ratios of the detection factors, of the primary beam intensity image and the production of image free of beam fluctuations. An example of such a treatment is given for a biological specimen with knife-marks.

Contrast and resolution of scanning transmission electron microscope imaging modes

Image blurring due to delocalization of inelastic events was studied for scanning transmission electron microscopy (STEM) of unstained thin sections. The delocalization probability was obtained from the angular distribution of inelastic scattering, which was calculated from experimental electron loss spectra of organic samples. This probability was implemented in a Monte Carlo program to simulate the effects of multiple scattering and delocalization for STEM images collected by either the annular detector or the spectrometer, and images generated by a combination of these two signals. Depending on the illumination, the detector geometry and the energy-loss range selected for imaging the annular detector image is blurred by a non-negligible fraction of inelastically scattered electrons. Simultaneous acquisition of an inelastic image using a spectrometer allows the blurring to be reduced by calculation of either the ratio or the difference of the two darkfield signals. While inherent nonlinearities reduce the interpretability of ratio-contrast images, difference-contrast improves the visibility of details submerged in a diffuse background without introducing artifacts.

Polymorphism of reconstituted human epidermal keratin filaments: determination of their mass-per-length and width by scanning transmission electron microscopy (STEM)

We have determined the mass-per-length (MPL) and the width of unstained freeze-dried reconstituted human epidermal keratin filaments by scanning transmission electron microscopy (STEM). Filaments were reassembled from keratins extracted from four different sources: cultured human epidermal cells (CHEC), human callus (CAL), and the living layers (LL) and stratum corneum (SC) of normal human epidermis. MPL histograms of all four keratin filament types could be fitted by a superposition of two or three Gaussians, with their respective major peaks located between 17 and 20 kDa/nm. We interpreted the multiple MPL peaks to represent different polymorphic forms of the reconstituted filaments. The number of subunits per filament cross section calculated from MPL peak positions, average subunit molecular weight, and an axial repeat of the subunits within the filament of 46.5 nm revealed an average difference between polymorphic variants of 7.5 +/- 0.9 subunits. These data suggest that reconstituted human epidermal keratin filaments are made of two to four 8-stranded "protofibrils" (i.e., made of two laterally aggregated 4-stranded protofilaments), in agreement with earlier observations. The average widths of unstained freeze-dried keratin filaments were larger than those of negatively stained filaments: 12.6 nm (9.6 nm) for CHEC, 12.3 nm (9.7 nm) for CAL, 11.6 nm (8.3 nm) for LL, and 11.3 nm (7.9 nm) for SC keratin filaments, with the values in brackets corresponding to negatively stained samples. Assuming the MPL to be proportional to the square of the filament width, there is a good correlation between the MPL and width measurements both for filaments within a given type as well as among those reconstituted from different types of keratin extracts.

Unconventional modes for STEM imaging of biological structures

In this paper recent developments are discussed in instrumentation and methodology associated with scanning transmission electron microscopes (STEM), which are of great potential interest for solving structural and chemical problems in biological specimens. After describing the main features of the instrument, an attempt is made to define which type of signal acquisition and processing is best suited to obtain a given type of information. Starting with a definition of cross sections of interest, a discussion follows of methods using angular selection, energy selection of the transmitted beam, and several ways of signal mixing. More specific attention is devoted to two main modes of processing signals: ratio contrast, which emphasizes slight changes in scattering factors, rather independent of thickness variations; and elemental mapping, which provides semi-quantitative information on the distribution of low Z elements of great significance in biological specimens. Data relevant to typical biological objects are presented and discussed; they allow for the definition of the capabilities and limitations of these methods. These unconventional imaging modes define a new attitude for improving the efficiency of this modern generation of electron microscopes.

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.