Images of paraffin monolayer crystals with perfect contrast: minimization of beam-induced specimen motion

Quantitative analysis of electron microscope images of organic and biological two-dimensional crystals has previously shown that the absolute contrast reached only a fraction of that expected theoretically from the electron diffraction amplitudes. The accepted explanation for this is that irradiation of the specimen causes beam-induced charging or movement, which in turn causes blurring of the image due to image or specimen movement. In this paper, we used three different approaches to try to overcome this image-blurring problem in monolayer crystals of paraffin. Our first approach was to use an extreme form of spotscan imaging, in which a single image was assembled on film by the successive illumination of up to 50,000 spots, each of a diameter of around 7 nm. The second approach was to use the Medipix II detector with its zero-noise readout to assemble a time-sliced series of images of the same area in which each frame from a movie with up to 400 frames had an exposure of only 500 electrons. In the third approach, we simply used a much thicker carbon support film to increase the physical strength and conductivity of the support. Surprisingly, the first two methods involving dose fractionation in space or time produced only partial improvements in contrast whereas the third approach produced many virtually perfect images, where the absolute contrast predicted from the electron diffraction amplitudes was observed in the images. We conclude that it is possible to obtain consistently almost perfect images of beam-sensitive specimens if they are attached to an appropriately strong and conductive support; however great care is needed in practice and the problem remains of how to best image ice-embedded biological structures in the absence of a strong, conductive support film.     

Adhesion of microbes using 3-aminopropyl triethoxy silane and specimen stabilisation techniques for analytical transmission electron microscopy

A variety of adhesive support-films were tested for their ability to adhere various biological specimens for transmission electron microscopy. Support films primed with 3-amino-propyl triethoxy silane (APTES), poly- l -lysine, carbon and ultraviolet-B (UV-B)-irradiated carbon were tested for their ability to adhere a variety of biological specimens including axenic cultures of Bacillus subtilis and Escherichia coli and wild-type magnetotactic bacteria. The effects of UV-B irradiation on the support film in the presence of air and electrostatic charge on primer deposition were tested and the stability of adhered specimens on various surfaces was also compared. APTES-primed UV-B-irradiated Pioloform^TM was consistently the best adhesive, especially for large cells, and when adhered specimens were UV-B irradiated they became remarkably stable under an electron beam. This assisted the acquisition of in situ phase-contrast lattice images from a variety of biominerals in magnetotactic bacteria, in particular metastable greigite magnetosomes. Washing tests indicated that specimens adhering to APTES-primed UV-B-irradiated Pioloform^TM were covalently coupled. The electron beam stability was hypothesised to be the result of mechanical strengthening of the specimen and support film and the reduced electrical resistance in the specimen and support film due to their polymerization and covalent coupling.     

Estimating contrast transfer function and associated parameters by constrained non-linear optimization

The three-dimensional reconstruction of macromolecules from two-dimensional single-particle electron images requires determination and correction of the contrast transfer function (CTF) and envelope function. A computational algorithm based on constrained non-linear optimization is developed to estimate the essential parameters in the CTF and envelope function model simultaneously and automatically. The application of this estimation method is demonstrated with focal series images of amorphous carbon film as well as images of ice-embedded icosahedral virus particles suspended across holes.     

Electron holographic observation for biological specimens: electron holography of bio-specimens

Electron holography has been applied to the observation of biological filaments. The technique has some advantages over conventional imaging for observing weak-phase objects such as small unstained biological structures. To avoid artificial structural transformation of the sample owing to the interaction with the supporting film, a holey carbon film was used to support the filaments. A tobacco mosaic virus bridged over a hole was observed as a cylindrical shape; the contrast distribution across the filament represents its actual shape, which is difficult to obtain with conventional transmission electron microscopy. A number of technical limitations which at present prevent high-resolution structure analysis of biological macromolecules by electron holography are discussed in this report.     

SEM examination of human erythrocytes in uncoated bloodstains on stone: use of conventional as environmental-like SEM in a soft biological tissue (and hard inorganic material)

Although nowadays the so-called environmental scanning electron microscopes (ESEMs) allow the observation of the samples without metal or carbon coating, many conventional scanning electron microscopes (SEMs) are still in use. On the other hand, the presence of erythrocytes (red blood cells, RBCs) in a smear is considered a blood confirmation. Such a presence has been previously reported even in Lower Stone Age implements. In previous works, I have reported several studies dealing with cytomorphology of RBCs in bloodstains using scanning electron microscopy with standard specimen preparation procedures, i.e. via coating the samples before SEM analysis. In order to explore the potential of conventional SEM as environmental-like SEM in haemotaphonomical studies, two alkaline (limestone) and two acid (flint) rock fragments were smeared with human blood from a male and a female. The bloodstains obtained in this way were then air dried indoors and stored into a non-hermetic plastic box. Afterwards, the smears and their rock substrates were examined directly without coating, via secondary electrons, using a JEOL JSM-6400 scanning electron microscope. Satisfactory results reveal the capability of a conventional SEM to work in secondary-electron mode as an environmental-like SEM on these kinds of biological and inorganic materials, and probably in many other biological and non-biological samples.     

Radial mass density functions of vitrified helical specimens determined by scanning transmission electron microscopy: their potential use as substitutes for equatorial data.

Using STEM dark field images, we have determined linear mass densities and radial density profiles of vitrified helical particles. The samples studied are: TMV, RNA-free helical polymers of TMV coat protein (TMV-P), Salmonella typhimurium bacterial flagellar filaments and Escherichia coli pili. The difference between the profiles obtained for TMV and TMV-P shows a maximum at a radius of about 4 nm, corresponding to the RNA in TMV. Of the peaks that are resolved in X-ray diffraction analysis we can resolve the ones for TMV at radii of approximately 4.2 and approximately 6.7 nm and a shoulder at approximately 7.8 nm. Density peaks in bacterial flagellar filaments appear at radii of approximately 4.2, approximately 6.5, approximately 8.5, and approximately 10.5 nm. Accurate mass data can be obtained if the filaments are embedded in ice layers of uniform thickness; their diameters need to be similar to that of the mass standard (TMV) when these data are measured in a comparative manner. Ice layers are often not uniform, and thickness variations are well revealed in STEM dark field. The signal-to-noise ratio and contrast for the transverse projections are lower than those measured for freeze-dried specimens: half an order and one order of magnitude, respectively. The thinnest uniformly thick ice layer still containing a single layer of particles is approximately 10-15 nm thicker than the particles. Radial mass density functions that are directly determined in STEM may have a potential use as substitutes for the unreliable equatorial data in helical reconstructions of TEM bright field images of vitrified specimens.     

Electron cryo-microscopy of biological specimens on conductive titanium-silicon metal glass films

Thin films of the metal glass Ti88Si12 were produced by evaporation and characterized by AFM and conductivity measurements. Thin Ti88Si12 support films for electron microscopy were prepared by coating standard EM grids with evaporated films floated off mica, and characterized by electron imaging and electron diffraction. At room temperature, the specific resistance of a thin TiSi film was 10(6) times lower than that of an amorphous carbon film. At 77K, the specific resistance of TiSi films decreased, whereas that of carbon became immeasurably high. The effective scattering cross-section of TiSi and amorphous carbon for 120 kV electrons is roughly equal, but TiSi films for routine use can be approximately 10 times thinner due to their high mechanical strength, so that they would contribute less background noise to the image. Electron diffraction of purple membrane on a TiSi substrate confirmed that the support film was amorphous, and indicated that the high-resolution order of the biological sample was preserved. Electron micrographs of TiSi films tilted by 45 degrees relative to the electron beam recorded at approximately 4 K indicated that the incidence of beam-induced movements was reduced by 50% compared to amorphous carbon film under the same conditions. The success rate of recording high-resolution images of purple membranes on TiSi films was close to 100%. We conclude that TiSi support films are ideal for high-resolution electron cryo-microscopy (cryo-EM) of biological specimens, as they reduce beam-induced movement significantly, due to their high electrical conductivity at low temperature and their favorable mechanical properties.     

Optimal strategies for imaging thick biological specimens: exit wavefront reconstruction and energy-filtered imaging

In transmission electron microscopy (TEM) of thick biological specimens, the relationship between the recorded image intensities and the projected specimen mass density is distorted by incoherent electron–specimen interactions and aberrations of the objective lens. It is highly desirable to develop a strategy for maximizing and extracting the coherent image component, thereby allowing the projected specimen mass density to be directly related to image intensities. For this purpose, we previously used exit wavefront reconstruction to understand the nature of image formation for thick biological specimens in conventional TEM. Because electron energy-loss filtered imaging allows the contributions of inelastically scattered electrons to be removed, it is potentially advantageous for imaging thick, biological samples. In this paper, exit wavefront reconstruction is used to quantitatively analyse the imaging properties of an energy-filtered microscope and to assess its utility for thick-section microscopy. We found that for imaging thick biological specimens (> 0.5 μm) at 200 keV, only elastically scattered electrons contribute to the coherent image component. Surprisingly little coherent transfer was seen when using energy-filtering at the most probable energy loss (in this case at the first plasmon energy-loss peak). Furthermore, the use of zero-loss filtering in combination with exit wavefront reconstruction is considerably more effective at removing the effects of multiple elastic and inelastic scattering and microscope objective lens aberrations than either technique by itself. Optimization of the zero-loss signal requires operation at intermediate to high primary voltages (> 200 keV). These results have important implications for the accurate recording of images of thick biological specimens as, for instance, in electron microscope tomography.     

Cryo-electron microscopy of helical particles TMV and T4 polyheads

Vitrified Tobacco Mosaic Virus (TMV) and T4 polyhead suspensions have been studied by cryo-electron microscopy. The order of TMV particles is preserved to distances better than 0.3 nm when vitrified. In spite of the high beam sensitivity of unstained biological material, the resolution of images extends to 1.15 nm. Radial density distributions calculated from images of TMV and the helical aggregate of TMV protein (TMVP) show that the RNA is likely visualized in the virus. However, due to the imaging conditions of unstained vitrified specimens, the position of the RNA is erroneous. While TMV and TMVP do not show any departure from cylindrical symmetry, T4 polyheads are sensitive to the thickness of the ice layer in which they are embedded. To avoid flattening, T4 polyheads have to be embedded in an ice layer thicker than their diameter.     

Combining Ar ion milling with FIB lift-out techniques to prepare high quality site-specific TEM samples

Focused ion beam (FIB) techniques can prepare site‐specific transmission electron microscopy (TEM) cross‐section samples very quickly but they suffer from beam damage by the high energy Ga⁺ ion beam. An amorphous layer about 20–30 nm thick on each side of the TEM lamella and the supporting carbon film makes FIB‐prepared samples inferior to the traditional Ar⁺ thinned samples for some investigations such as high resolution transmission electron microscopy (HRTEM) and electron energy loss spectroscopy (EELS). We have developed techniques to combine broad argon ion milling with focused ion beam lift‐out methods to prepare high‐quality site‐specific TEM cross‐section samples. Site‐specific TEM cross‐sections were prepared by FIB and lifted out using a Narishige micromanipulator onto a half copper‐grid coated with carbon film. Pt deposition by FIB was used to bond the lamellae to the Cu grid, then the coating carbon film was removed and the sample on the bare Cu grid was polished by the usual broad beam Ar⁺ milling. By doing so, the thickness of the surface amorphous layers is reduced substantially and the sample quality for TEM observation is as good as the traditional Ar⁺ milled samples.     

Comparison of different preparation methods of biological samples for FIB milling and SEM investigation

When a new approach in microscopy is introduced, broad interest is attracted only when the sample preparation procedure is elaborated and the results compared with the outcome of the existing methods. In the work presented here we tested different preparation procedures for focused ion beam (FIB) milling and scanning electron microscopy (SEM) of biological samples. The digestive gland epithelium of a terrestrial crustacean was prepared in a parallel for FIB/SEM and transmission electron microscope (TEM). All samples were aldehyde-fixed but followed by different further preparation steps. The results demonstrate that the FIB/SEM samples prepared for conventional scanning electron microscopy (dried) is suited for characterization of those intracellular morphological features, which have membranous/lamellar appearance and structures with composition of different density as the rest of the cell. The FIB/SEM of dried samples did not allow unambiguous recognition of cellular organelles. However, cellular organelles can be recognized by FIB/SEM when samples are embedded in plastic as for TEM and imaged by backscattered electrons. The best results in terms of topographical contrast on FIB milled dried samples were obtained when samples were aldehyde-fixed and conductively stained with the OTOTO method (osmium tetroxide/thiocarbohydrazide/osmium tetroxide/thiocarbohydrazide/osmium tetroxide). In the work presented here we provide evidence that FIB/SEM enables both, detailed recognition of cell ultrastructure, when samples are plastic embedded as for TEM or investigation of sample surface morphology and subcellular composition, when samples are dried as for conventional SEM.     

Double-layer coating for high-resolution low-temperature scanning electron microscopy

Specimen damage caused by mass loss due to electron beam irradiation is a major limitation in low-temperature scanning electron microscopy of bulk specimens. At high primary magnifications (e.g. 100 000x) a hydrated sample is usually severely damaged after one slow scan (about 3000 e^— nm^—2). The consequences of this beam damage are significantly reduced by coating the frozen-hydrated sample with a 5–10-nm-thick carbon layer. Since this layer covers up surface details, the sample is first unidirectionally shadowed with a thin heavy metal layer (e.g. 2 nm of platinum) that is in close contact with the biological surface (double layer coating). This heavy metal layer can be visualized in field-emission scanning electron microscopy with the material-dependent backscattered electron signal. The method allows for routine observation of large frozen-hydrated samples. By use of an in-lens field-emission SEM and a sensitive backscattered electron detector, structural information comparable to that obtained with the transmission electron microscopy freeze-fracture replica technique can be achieved.     

Interfacial energies and surface-tension forces involved in the preparation of thin,flat crystals of biological macromolecules for high-resolution electron microscopy

It is generally agreed that surface-tension forces and the direct interaction between the specimen and either the air-water interface or the water-substrate interface can influence significantly the preparation of biological materials for electron microscopy. Even so, there is relatively little systematic information available that would make it possible to control surface-tension forces and interfacial energies in a quantitative fashion. The main objective in undertaking the present work has been to understand somewhat better the factors that influence the degree of specimen flatness of large, monolayer crystals of biological macromolecules. However, the data obtained in our work should be useful in understanding the preparation of specimens of biological macromolecules in general. Data collection by electron diffraction and electron microscopy at high resolution and high tilt angles requires thin crystals of biological macromolecules that are flat to at least 1°, and perhaps less than 0·2°, over areas as large as 1 μm² or more. In addition to determining empirically by electron diffraction experiments whether sufficiently flat specimens can be prepared on various types of modified or unmodified carbon support films, we have begun to use other techniques to characterize both the surfaces involved and the interaction of our specimen with these surfaces. In the specific case of large, monolayer crystals of bacteriorhodopsin prepared as glucose-embedded specimens on hydrophobic carbon films, it was concluded that the initial interfacial interaction involves adsorption of the specimen to the air-water interface rather than adsorption of the specimen to the substrate. Surface-tension forces at the air-water interface and an apparently repulsive interaction between the specimen and the hydrophobic carbon seem to be major factors influencing the specimen flatness in this case. In the more general case it seems likely that interfacial interactions with either the substrate or the air-water interface can be variously manipulated in the search to find desirable conditions of specimen preparation.     

Reduction of charging in protein electron cryomicroscopy

Charging causes a loss of resolution in electron cryomicroscopy with biological specimens prepared without a continuous carbon support film. Thin conductive films were deposited onto catalase crystals prepared across holes using ion-beam sputtering and thermal evaporation and evaluated for the effectiveness of charge reduction. Deposits applied by ion-beam sputtering reduced charging but concurrently resulted in structural damage. Coatings applied by thermal evaporation also reduced charging, and preserved the specimen structure beyond 5 Å resolution as judged from electron diffraction patterns and images of glucose-embedded catalase crystals tilted to 45° in the microscope. This study demonstrates for the first time the feasibility of obtaining high-resolution data from unstained, unsupported protein crystals with a conductive surface coating.     

Fabrication of a Cr thin-film AEM characterization standard

The need for an analytical electron microscope (AEM) characterization standard capable of determining the consistency and relative quality of analytical performance has become increasingly evident as advances in the instrumentation are made. In this paper the fabrication of a Cr thin-film AEM standard by conventional thermal evaporation techniques is described. A 100-nm-thick Cr film on a 20-nm C-support film provided by the National Institute of Standards and Technology (NIST) served as a model against which the present film was evaluated. Improvements over the NIST film in terms of diffraction pattern clarity and simplification of parallel electron energy-loss spectrometry (PEELS) analysis were achieved by removal of the C-support film and the creation of a self-supported Cr (SS-Cr) film. Qualitative grain-size comparisons between the NIST model and the SS-Cr films made by scanning transmission electron microscopy found the SS-Cr films to have a slightly larger grain size. Thickness measurements were verified by X-ray energy dispersive spectrometry, PEELS and field-emission gun scanning electron microscopy. SS-Cr film standard specimens are available for use by the AEM community, by contacting the authors directly.     

Unconventional immuno double labelling by energy filtered transmission electron microscopy

A new method of immuno double labelling of biological specimens with a very high spatial resolution is presented. The advantage over conventional techniques is the possibility of using two very small labels leading to higher labelling efficiency, better penetration into the specimen and reduced steric hindrance between labels at closely spaced sites. The two labels are distinguished by their electron energy loss spectra using principal component analysis and then identified by comparison with an external standard using discriminant function analysis. The method is tested on samples of insect flight muscle labelled with 8 nm colloidal gold and silver and the statistical reliability of the classification is assessed. Extensions of the method are suggested and its potential for biological research is discussed.     

The projection of a negatively-stained filamentous object down its central axis as revealed by image reconstruction from tilt series

Helical reconstructions of negatively stained biological objects contain distortions arising from filament flattening and the non-cylindrical profile of the stain envelope. Current methods of estimating flattening do not make full use of the information available in electron micrographs. We have applied the more rigorous approach of reconstructing the density profile from tilt series using digital image processing techniques. Tilt series were collected for tobacco mosaic viruses (TMV) and seven independent reconstructions were calculated using equatorial data out as far as ～1/9·3 nm^—1. They indicated that the filaments were flattened with an axial ratio of about 2·4:1, which was probably closer to 3:1 in the original specimen, because the limited resolution caused flattening to be underestimated. The stain envelope around TMV and some indication of the underlying carbon substrate were also observed. This information could enable correction factors for flattening to be developed, which could be useful when calculating helical reconstructions or indexing helical diffraction patterns. This method could also be extended to non-equatorial layer planes, which would provide three-dimensional information on a wide range of macromolecules that possess a one-dimensional repeat.     

Static-charging mitigation and contamination avoidance by selective carbon coating of TEM samples

Prior to transmission electron microscopy (TEM) analyses, insulating specimens need to become coated with a charge-draining layer. Rather than coating the entire TEM foil with a thin film of homogeneous thickness, selective coating is proposed. Using a novel preparation tool, peripheral parts of the sample are coated with a relatively thick (4-8 nm) carbon film while the central, electron-transparent part of the sample is hidden behind a shape-adopted mask and thus not directly exposed to carbon deposition. Beneath the mask, an ultrathin (3-7 A) carbon film is formed that is (i) thick enough to drain charges evolving upon electron irradiation in the electron microscope and (ii) thin enough to avoid typical contamination effects caused by superficial carbon diffusion. Consequently, image quality is becoming enhanced in high-resolution imaging and sensitivity is significantly increased in all nano-beam related techniques including elemental analytics, convergent-beam and nano-beam electron diffraction, and spectral imaging.     

Glucose alone does not completely hydrate bacteriorhodopsin in glucose-embedded purple membrane

Glucose embedding is a simple and highly effective method for preparing biological macromolecules for high-resolution electron microscopy. The investigation of conditions that can trap the M-state intermediate in the bacteriorhodopsin (bR) photocycle has revealed, however, that when glucose-embedded bR is prepared at ambient humidity, it does not fully retain the capability to execute a proper photocycle. However, ‘native’ photocycle properties are returned after glucose-embedded samples are equilibrated at 81% relative humidity. Equilibration at relative humidities significantly higher than 81% causes glucose to dissolve in its own water of hydration, resulting in samples that may be too thick to be suitable for electron microscopy. The results obtained with bR indicate that caution should be taken with other biological specimens, and it cannot be assumed that glucose-embedded biological macromolecules retain completely their native, hydrated structure, even when high-resolution electron diffraction patterns are obtained. Equilibration of such samples at high humidity may generally be a worthwhile precaution when using the glucose-embedding technique.     

Electron microscopic visualization of complementary labeled DNA with platinum‐containing guanine derivative

The object of the present report is to provide a method for a visualization of DNA in TEM by complementary labeling of cytosine with guanine derivative, which contains platinum as contrast‐enhanced heavy element. The stretched single‐chain DNA was obtained by modifying double‐stranded DNA. The labeling method comprises the following steps: (i) stretching and adsorption of DNA on the support film of an electron microscope grid (the hydrophobic carbon film holding negative charged DNA); (ii) complementary labeling of the cytosine bases from the stretched single‐stranded DNA pieces on the support film with platinum containing guanine derivative to form base‐specific hydrogen bond; and (iii) producing a magnified image of the base‐specific labeled DNA. Stretched single‐stranded DNA on a support film is obtained by a rapid elongation of DNA pieces on the surface between air and aqueous buffer solution. The attached platinum‐containing guanine derivative serves as a high‐dense marker and it can be discriminated from the surrounding background of support carbon film and visualized by use of conventional TEM observation at 100 kV accelerated voltage. This method allows examination of specific nucleic macromolecules through atom‐by‐atom analysis and it is promising way toward future DNA‐sequencing or molecular diagnostics of nucleic acids by electron microscopic observation. Microsc. Res. Tech. 79:280–284, 2016. © 2016 Wiley Periodicals, Inc.