Cryo-EM sample preparation for high-resolution structure studies

High-resolution structures of biomolecules can be obtained using single-particle cryo-electron microscopy (SPA cryo-EM), and the rapidly growing number of structures solved by this method is encouraging more researchers to utilize this technique. As with other structural biology methods, sample preparation for an SPA cryo-EM data collection requires some expertise and an understanding of the strengths and limitations of the technique in order to make sensible decisions in the sample-preparation process. In this article, common strategies and pitfalls are described and practical advice is given to increase the chances of success when starting an SPA cryo-EM project.

Formalin-fixed stool improves the performance of the Kato-Katz method

Background and Aim

Parasitic infections are a public health problem worldwide, including in Thailand. An epidemiological survey for helminthiasis based on stool examination uses the Kato-Katz method as recommended by the World Health Organization. Limitations of this method include the need for fresh stool, time requirement, and lack of quality control. The aim of this study was to enhance the efficiency of the Kato-Katz technique using formalin and glycerol solutions and to implement specimen preparation in fieldwork.

Materials and Methods

For the Kato-Katz method, stool samples were divided into formalin-fixed and unfixed groups at various time points and processes. Fresh echinostome eggs were added to each stool group. Incubation with glycerol increased the clearing process. Each group was observed and photographed using a light microscope. Parasite eggs were imaged and compared using the standard Kato-Katz method.

Results

Visualization of echinostome eggs from formalin-fixed stool slides was significantly better than that from unfixed stool slides (p < 0.01). Stool samples fixed for 7 days retained normal echinostome eggs morphology. Incubation with glycerol for 1 h resulted in increased Kato-Katz performance by digesting the stool content and enhancing egg observation. Moreover, the results of the Kato-Katz method using fixed and fixed stool plus glycerol for natural helminth infection showed good quality of Opisthorchis viverrini and Taenia egg visualization and normal morphology with a clear background of slides.

Conclusion

Formalin-fixed stool could be more suitable than fresh stool for the Kato-Katz method.

Scalable substrate development for aqueous sample preparation for atom probe tomography

Reliable and consistent preparation of atom probe tomography (APT) specimens from aqueous and hydrated biological specimens remains a significant challenge. One particularly difficult process step is the use of a focused ion beam (FIB) instrument for preparing the required needle-shaped specimen, typically involving a 'lift-out' procedure of a small sample of material. Here, two alternative substrate designs are introduced that enable using FIB only for sharpening, along with example APT datasets. The first design is a laser-cut FIB-style half-grid close to those used for transmission electron microscopy (TEM) that can be used in a grid holder compatible with APT pucks. The second design is a larger, standalone self-supporting substrate called a 'crown', with several specimen positions, which self-aligns in APT pucks, prepared by electrical discharge machining (EDM). Both designs are made nanoporous, to provide strength to the liquid-substrate interface, using chemical and vacuum dealloying. Alpha brass, a simple, widely available, lower-cost alternative to previously proposed substrates, was selected for this work. The resulting designs and APT data are presented and suggestions are provided to help drive wider community adoption.

The effect of specimen preparation on the nanostructure of SLES aqueous solutions observed by cryo-TEM

Sodium lauryl ether sulphate (SLES) is a detergent widely used in cosmetics and personal-care industries; hence, it is of particular interest to study the self-assembled nanostructure it forms at different conditions. Cryogenic transmission electron microscopy (cryo-TEM) is the most suitable technique for the direct-imaging of such systems. However, since SLES is sensitive to flow and shear, specimen preparation artefacts may misrepresent the native state of the solution. In this paper, we present different cryo-TEM specimen preparation methods, and show how they affect the nanostructure of the system. In fact, for this system, we were able to record the native state of the solution only after sufficient time of on-the-grid relaxation (OGR) after blotting. Here, we also intend to point out the importance of considering the nature of the solution when preparing cryo-TEM specimens.

Atom probe specimen preparation methods for nanoparticles

Revealing the position of materials with chemical selectivity at atomic scale within functional nanoparticles is essential to understand and control their performance and cutting-edge atom probe tomography is a powerful tool to undertake this task. In this paper, we demonstrate three effective methods to prepare the needle-shaped specimens required for atom probe tomography measurements from nanoparticles of different sizes and provide examples of how atom probe can be used to provide data that is critical to their functionality. Samples measured include lithium-ion batteries (LIBs) cathode nanoparticles (300 - 500 nm), nickel-doped silicon dioxide (Ni@SiO2) catalytic nanoparticles (100 - 200 nm) and tin-doped copper (Sn@Cu) catalytic nanoparticles (<100 nm). The methods presented can be used to address the ongoing challenge of specimen preparation from particle samples for atom probe measurement, and they provide high quality data. These methods will broaden the application of atom probe tomography and will provide alternative option for researchers to assess the performance/structure of their functional nanomaterials.

The Influence of Blade Type and Feeding Force during Resin Bonded Dentin Specimen Preparation on the Microtensile Bond Strength Test

This paper presents the effect of blade type and feeding force during resin-bonded dentin specimen preparation on the microtensile bond strength (μTBS) test. Forty resin-bonded flat middle dentin specimens were divided into four groups. The specimens of each group were sectioned according to type of blade and feeding force as follows: fine grit/20 N, fine grit/40 N, medium grit/20 N, and medium grit/40 N to obtain resin-dentin sticks with a cross-sectional area of 1.0 mm². Four sticks from the center of each tooth were subjected to the μTBS test. Five remaining sticks of each group were selected for surface topography observation under a scanning electron microscope (SEM). As a result, the bond strength of the medium-grit group was higher than that of the fine-grit group (p < 0.001), whereas the feeding force had no influence on bond strength values (p = 0.648). From the SEM, sticks prepared with the fine-grit blade showed a smoother surface integrity and fewer defects on the specimen edges in comparison with the sticks prepared with the medium-grit blade. The grit type of the blade is one of the considerable factors that may affect the bond strength and the surface integrity of resin-dentin specimens for microtensile testing.

Serial Block-Face Scanning Electron Microscopy (SBF-SEM) of Biological Tissue Samples

Serial block-face scanning electron microscopy (SBF-SEM) allows for the collection of hundreds to thousands of serially-registered ultrastructural images, offering an unprecedented three-dimensional view of tissue microanatomy. While SBF-SEM has seen an exponential increase in use in recent years, technical aspects such as proper tissue preparation and imaging parameters are paramount for the success of this imaging modality. This imaging system benefits from the automated nature of the device, allowing one to leave the microscope unattended during the imaging process, with the automated collection of hundreds of images possible in a single day. However, without appropriate tissue preparation cellular ultrastructure can be altered in such a way that incorrect or misleading conclusions might be drawn. Additionally, images are generated by scanning the block-face of a resin-embedded biological sample and this often presents challenges and considerations that must be addressed. The accumulation of electrons within the block during imaging, known as "tissue charging," can lead to a loss of contrast and an inability to appreciate cellular structure. Moreover, while increasing electron beam intensity/voltage or decreasing beam-scanning speed can increase image resolution, this can also have the unfortunate side effect of damaging the resin block and distorting subsequent images in the imaging series. Here we present a routine protocol for the preparation of biological tissue samples that preserves cellular ultrastructure and diminishes tissue charging. We also provide imaging considerations for the rapid acquisition of high-quality serial-images with minimal damage to the tissue block.

Through-grid wicking enables high-speed cryoEM specimen preparation

Blotting times for conventional cryoEM specimen preparation complicate time-resolved studies and lead to some specimens adopting preferred orientations or denaturing at the air-water interface. Here, it is shown that solution sprayed onto one side of a holey cryoEM grid can be wicked through the grid by a glass-fiber filter held against the opposite side, often called the `back', of the grid, producing a film suitable for vitrification. This process can be completed in tens of milliseconds. Ultrasonic specimen application and through-grid wicking were combined in a high-speed specimen-preparation device that was named `Back-it-up' or BIU. The high liquid-absorption capacity of the glass fiber compared with self-wicking grids makes the method relatively insensitive to the amount of sample applied. Consequently, through-grid wicking produces large areas of ice that are suitable for cryoEM for both soluble and detergent-solubilized protein complexes. The speed of the device increases the number of views for a specimen that suffers from preferred orientations.

Study of the solid electrolyte interphase of Li-O2 battery electrolyte by analytical transmission electron microscopy

Investigation of solid electrolyte interphases (SEIs) on negative electrode surfaces is essential to improve the stable charge-discharge performance of rechargeable lithium-air batteries (Li-O2 batteries). In this study, a direct investigation of SEI films is conducted using analytical transmission electron microscopy (TEM). A thin Cu specimen is prefabricated for TEM observation and is utilised as a model substrate for SEI formation. The electrochemical cell constructed using dissolved oxygen in the electrolyte exhibits a greater electrochemical overpotential during the Li-metal deposition process than that constructed with a pristine electrolyte. This suggests that different electrochemical passivation features occur in each different electrochemical cell. TEM observation confirms that the surface film formed by O2 dissolute electrolyte is a polycrystalline Li2O film with a thickness of ~5 nm, whereas the film formed by the pristine electrolyte is organic-based, amorphous-like and 20-50 nm thick. The dissolved oxygen molecules are more easily reduced than the components of the electrolyte, leading to the formation of Li2O as a stable passivation SEI film, which is expected to exhibit good charge-discharge features during the operation of the Li-O2 battery.

Shake-it-off: a simple ultrasonic cryo-EM specimen-preparation device

A method is presented for high-speed low-volume cryo-EM specimen preparation with a device constructed from readily available components.

Although microscopes and image-analysis software for electron cryomicroscopy (cryo-EM) have improved dramatically in recent years, specimen-preparation methods have lagged behind. Most strategies still rely on blotting microscope grids with paper to produce a thin film of solution suitable for vitrification. This approach loses more than 99.9% of the applied sample and requires several seconds, leading to problematic air–water interface interactions for macromolecules in the resulting thin film of solution and complicating time-resolved studies. Recently developed self-wicking EM grids allow the use of small volumes of sample, with nanowires on the grid bars removing excess solution to produce a thin film within tens of milliseconds from sample application to freezing. Here, a simple cryo-EM specimen-preparation device that uses components from an ultrasonic humidifier to transfer protein solution onto a self-wicking EM grid is presented. The device is controlled by a Raspberry Pi single-board computer and all components are either widely available or can be manufactured by online services, allowing the device to be constructed in laboratories that specialize in cryo-EM rather than instrument design. The simple open-source design permits the straightforward customization of the instrument for specialized experiments.

Focused Ion Beam Preparation of Specimens for Micro-Electro-Mechanical System-based Transmission Electron Microscopy Heating Experiments

Micro-electro-mechanical systems (MEMS)-based heating holders offer exceptional control of temperature and heating/cooling rates for transmission electron microscopy experiments. The use of such devices is relatively straightforward for nano-particulate samples, but the preparation of specimens from bulk samples by focused ion beam (FIB) milling presents significant challenges. These include: poor mechanical integrity and site selectivity of the specimen, ion beam damage to the specimen and/or MEMS device during thinning, and difficulties in transferring the specimen onto the MEMS device. Here, we describe a novel FIB protocol for the preparation and transfer of specimens from bulk samples, which involves a specimen geometry that provides mechanical support to the electron-transparent region, while maximizing the area of that region and the contact area with the heater plate on the MEMS chip. The method utilizes an inclined stage block that minimizes exposure of the chip to the ion beam during milling. This block also allows for accurate and gentle placement of the FIB-cut specimen onto the chip by using simultaneous electron and ion beam imaging during transfer. Preliminary data from Si and Ag on Si samples are presented to demonstrate the quality of the specimens that can be obtained and their stability during in situ heating experiments.

Comparison of multiple techniques for endobronchial ultrasound-transbronchial needle aspiration specimen preparation in a single institution experience

BACKGROUND

The optimal method for specimen preparation of endobronchial ultrasound-transbronchial needle aspiration (EBUS-TBNA) is still controversial. This study aims to compare several techniques available for EBUS-TBNA specimen acquisition and processing, in order to identify the best performing technique.

METHODS

We retrospectively reviewed the data of 199 consecutive patients [male, 73%; median age, 64 years (IQR: 52-74 years)] undergoing EBUS-TBNA at our institution from 2012 through 2014 for diagnosis of hilar-mediastinal lymph node enlargement suspect of neoplastic (n=139) or granulomatous (n=60) disease. All procedures were performed by two experienced bronchoscopists, under conscious sedation and local anaesthesia, using 21/22-Gauge (G) needle, without rapid on-site evaluation (ROSE). Five specimen-processing techniques were used: cytology slides in 42 cases (21%); cell-block in 25 (13%); core-tissue in 60 (30%); combination of cytology slides and core-tissue in 51 (26%); combination of cytology slides and cell-block in 21 (10%). To assess the diagnostic accuracy of each tissue-processing technique we compared the EBUS-TBNA results to those obtained with surgical lymphadenectomy, or 1-year follow-up in non-operated patients.

RESULTS

Diagnostic yield, accuracy and area under the curve (AUC) were as follows. Cytology slides: 81%, 80%, 0.90; cell-block: 48%, 33%, 0.67; core-tissue: 87%, 99%, 0.96; cytology slides + core-tissue: 80%, 100%, 1.00; cytology slides + cell-block: 86%, 100%, 1.00. Cytology slides and core-tissue method showed non-significantly different diagnostic yield (P=0.435) and AUC (P=0.152).

CONCLUSIONS

In our single-institution experience, cytology slides and core-tissue preparations demonstrated high and similar diagnostic performance. Cytology slides combination with core-tissue or cell-block showed the highest performance, however these combination methods were more resource-consuming.

Modern Focused-Ion-Beam-Based Site-Specific Specimen Preparation for Atom Probe Tomography

Approximately 30 years after the first use of focused ion beam (FIB) instruments to prepare atom probe tomography specimens, this technique has grown to be used by hundreds of researchers around the world. This past decade has seen tremendous advances in atom probe applications, enabled by the continued development of FIB-based specimen preparation methodologies. In this work, we provide a short review of the origin of the FIB method and the standard methods used today for lift-out and sharpening, using the annular milling method as applied to atom probe tomography specimens. Key steps for enabling correlative analysis with transmission electron-beam backscatter diffraction, transmission electron microscopy, and atom probe tomography are presented, and strategies for preparing specimens for modern microelectronic device structures are reviewed and discussed in detail. Examples are used for discussion of the steps for each of these methods. We conclude with examples of the challenges presented by complex topologies such as nanowires, nanoparticles, and organic materials.

Preserving elemental content in adherent mammalian cells for analysis by synchrotron-based x-ray fluorescence microscopy

Trace metals play important roles in biological function, and x-ray fluorescence microscopy (XFM) provides a way to quantitatively image their distribution within cells. The faithfulness of these measurements is dependent on proper sample preparation. Using mouse embryonic fibroblast NIH/3T3 cells as an example, we compare various approaches to the preparation of adherent mammalian cells for XFM imaging under ambient temperature. Direct side-by-side comparison shows that plunge-freezing-based cryoimmobilization provides more faithful preservation than conventional chemical fixation for most biologically important elements including P, S, Cl, K, Fe, Cu, Zn and possibly Ca in adherent mammalian cells. Although cells rinsed with fresh media had a great deal of extracellular background signal for Cl and Ca, this approach maintained cells at the best possible physiological status before rapid freezing and it does not interfere with XFM analysis of other elements. If chemical fixation has to be chosen, the combination of 3% paraformaldehyde and 1.5 % glutaraldehyde preserves S, Fe, Cu and Zn better than either fixative alone. When chemically fixed cells were subjected to a variety of dehydration processes, air drying was proved to be more suitable than other drying methods such as graded ethanol dehydration and freeze drying. This first detailed comparison for x-ray fluorescence microscopy shows how detailed quantitative conclusions can be affected by the choice of cell preparation method.

A new substance to relax polychaete worms (Annelida) prior to morphological study

A variety of chemical substances have been used to relax and/or immobilize polychaete worms, and other invertebrates, prior to specimen preparation for morphological examination. To solve difficulties encountered during the study of nereidid polychaetes (Annelida: Phyllodocida), an experiment was designed and carried out to investigate a new relaxing agent to immobilize nereidid specimens and stimulate pharynx eversion. The new substance, Dentol® (Khoraman laboratory, Iran), a dental anesthetic and antiseptic medicine containing 10% Carvacrol as the effective ingredient, was used for the first time and compared with other substances that have been used traditionally in polychaete studies. Crosstab analysis showed significant differences between different treatment groups, with Dentol® providing much better results for all considered criteria.

Application of polystyrene disk substrates in cellular cultivation methods: generalized specimen preparation protocol for scanning electron microscopy

Sample preparation for scanning electron microscopy (SEM) may vary by cellular type, composition and method of cultivation. It has been proposed here that a generalized method of sample preparation may be applied for the visualization of bacteria, fungi, and human cellular tissue without modification of protocol between cell types. The following protocol was developed to incorporate polystyrene disk substrates in the simplification of sample preparation for SEM and reduce the possibility of processing artefacts. The proposed method of preparation may be applied to samples grown in either liquid or solid cultural medium regardless of cell type. With the proposed protocol, centrifugation, isolation and critical point drying are not required, therefore increasing specimen integrity. The incorporation of polystyrene disks showed positive cellular adhesion and applications in SEM for bacterial, fungal and human neuronal tissue. In addition, the simplicity of the proposed protocol is highly adaptable and may be further incorporated to visually analyse the effects of antifungals, antibiotics and disease pathogenesis through pathogen-host interactions. The proposed method of specimen preparation was incorporated in either liquid or solid state growth mediums during the cultivation of the selected cellular samples and revealed great promise in the preservation and visualization under the scanning electron microscope.

Influence of Specimen Preparation and Test Methods on the Flexural Strength Results of Monolithic Zirconia Materials

The aim of this work was to evaluate the influence of specimen preparation and test method on the flexural strength results of monolithic zirconia. Different monolithic zirconia materials (Ceramill Zolid (Amann Girrbach, Koblach, Austria), Zenostar ZrTranslucent (Wieland Dental, Pforzheim, Germany), and DD Bio zx² (Dental Direkt, Spenge, Germany)) were tested with three different methods: 3-point, 4-point, and biaxial flexural strength. Additionally, different specimen preparation methods were applied: either dry polishing before sintering or wet polishing after sintering. Each subgroup included 40 specimens. The surface roughness was assessed using scanning electron microscopy (SEM) and a profilometer whereas monoclinic phase transformation was investigated with X-ray diffraction. The data were analyzed using a three-way Analysis of Variance (ANOVA) with respect to the three factors: zirconia, specimen preparation, and test method. One-way ANOVA was conducted for the test method and zirconia factors within the combination of two other factors. A 2-parameter Weibull distribution assumption was applied to analyze the reliability under different testing conditions. In general, values measured using the 4-point test method presented the lowest flexural strength values. The flexural strength findings can be grouped in the following order: 4-point < 3-point < biaxial. Specimens prepared after sintering showed significantly higher flexural strength values than prepared before sintering. The Weibull moduli ranged from 5.1 to 16.5. Specimens polished before sintering showed higher surface roughness values than specimens polished after sintering. In contrast, no strong impact of the polishing procedures on the monoclinic surface layer was observed. No impact of zirconia material on flexural strength was found. The test method and the preparation method significantly influenced the flexural strength values.

An improved preparation method for cross-sectional TEM specimens of films deposited on metallic substrates

Cross-sectional TEM analysis is one of the most important techniques to characterize microstructures of films. However, the complex process, low efficiency, and low success rate of specimen preparation limit its application. This paper analyzed the main causes of low success rate and proposed an improved method for specimen preparation of films deposited on metallic substrates. This method consisting of twin-jet electropolishing and one-sided rocking ion milling is high in efficiency and success rate.

Evaluating the Use of Synthetic Replicas for SEM Identification of Bloodstains (with Emphasis on Archaeological and Ethnographic Artifacts)

Some archaeological or ethnographic specimens are unavailable for direct examination using a scanning electron microscope (SEM) due to methodological obstacles or legal issues. In order to assess the feasibility of using SEM synthetic replicas for the identification of bloodstains (BSs) via morphology of red blood cells (RBCs), three fragments of different natural raw material (inorganic, stone; plant, wood; animal, shell) were smeared with peripheral human blood. Afterwards, molds and casts of the bloodstained areas were made using vinyl polysiloxane (VPS) silicone impression and polyurethane (PU) resin casting material, respectively. Then, the original samples and the resulting casts were coated with gold and examined in secondary-electron mode using a high-vacuum SEM. Results suggest that PU resin casts obtained from VPS silicone molds can preserve RBC morphology in BSs, and consequently that synthetic replicas are feasible for SEM identification of BSs on cultural heritage specimens made of natural raw materials. Although the focus of this study was on BSs, the method reported in this paper may be applicable to organic residues other than blood, as well as to the surface of other specimens when, for any reason, the original is unavailable for an SEM.

Cryogenic-temperature electron microscopy direct imaging of carbon nanotubes and graphene solutions in superacids

Cryogenic electron microscopy (cryo-EM) is a powerful tool for imaging liquid and semiliquid systems. While cryogenic transmission electron microscopy (cryo-TEM) is a standard technique in many fields, cryogenic scanning electron microscopy (cryo-SEM) is still not that widely used and is far less developed. The vast majority of systems under investigation by cryo-EM involve either water or organic components. In this paper, we introduce the use of novel cryo-TEM and cryo-SEM specimen preparation and imaging methodologies, suitable for highly acidic and very reactive systems. Both preserve the native nanostructure in the system, while not harming the expensive equipment or the user. We present examples of direct imaging of single-walled, multiwalled carbon nanotubes and graphene, dissolved in chlorosulfonic acid and oleum. Moreover, we demonstrate the ability of these new cryo-TEM and cryo-SEM methodologies to follow phase transitions in carbon nanotube (CNT)/superacid systems, starting from dilute solutions up to the concentrated nematic liquid-crystalline CNT phases, used as the 'dope' for all-carbon-fibre spinning. Originally developed for direct imaging of CNTs and graphene dissolution and self-assembly in superacids, these methodologies can be implemented for a variety of highly acidic systems, paving a way for a new field of nonaqueous cryogenic electron microscopy.

Use of permanent marker to deposit a protection layer against FIB damage in TEM specimen preparation

Permanent marker deposition (PMD), which creates permanent writing on an object with a permanent marker, was investigated as a method to deposit a protection layer against focused ion beam damage. PMD is a simple, fast and cheap process. Further, PMD is excellent in filling in narrow and deep trenches, enabling damage-free observation of high aspect ratio structures with atomic resolution in transmission electron microscopy (TEM). The microstructure, composition, gap filling ability and planarization of the PMD layer were studied using dual beam focused ion beam, transmission electron microscopy, energy dispersive X-ray spectroscopy and electron energy loss spectroscopy. It was found that a PMD layer is basically an amorphous carbon structure, and that such a layer should be at least 65 nm thick to protect a surface against 30 keV focused ion beam damage. We suggest that such a PMD layer can be an excellent protection layer to maintain a pristine sample structure against focused ion beam damage during transmission electron microscopy specimen preparation.

An improved cryogen for plunge freezing

The use of an alkane mixture that remains liquid at 77 K to freeze specimens has advantages over the use of a pure alkane that is solid at 77 K. It was found that a mixture of methane and ethane did not give a cooling rate adequate to produce vitreous ice, but a mixture of propane and ethane did result in vitreous ice. Furthermore, the latter mixture produced less damage to specimens mounted on a very thin, fragile holey carbon substrate.