Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

Because the ability to perform some form of chemical microanalysis has become an essential feature for any microscope, it is necessary to investigate what options are available in the new “ORION” helium ion microscope (HIM). The HIM has the ability to visualize local variations in specimen chemistry in both the ion induced secondary electron and the Rutherford backscattered imaging modes, but this provides only limited and qualitative information. Quantitative, elementally specific, microanalysis could be performed in the HIM using secondary electron spectroscopy, Rutherford backscattered ion spectroscopy, or secondary ion mass spectroscopy, but while each of these options has promise, none of them can presently guarantee either reliable element identification or quantitative analysis across the periodic table.

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2006

Electron microscopy (EM), cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) are essential techniques used for characterizing basic virus morphology and determining the three-dimensional structure of viruses. Enveloped viruses, which contain an outer lipoprotein coat, constitute the largest group of pathogenic viruses to humans. The purification of enveloped viruses from cell culture presents certain challenges. Specifically, the inclusion of host-membrane-derived vesicles, the complete destruction of the viruses, and the disruption of the internal architecture of individual virus particles. Here, we present a strategy for capturing enveloped viruses on affinity grids (AG) for use in both conventional EM and cryo-EM/ET applications. We examined the utility of AG for the selective capture of human immunodeficiency virus virus-like particles, influenza A, and measles virus. We applied nickel-nitrilotriacetic acid lipid layers in combination with molecular adaptors to selectively adhere the viruses to the AG surface. This further development of the AG method may prove essential for the gentle and selective purification of enveloped viruses directly onto EM grids for ultrastructural analyses.

Tibetan mural samples from the Jiazhaer mountain cave were studied using enzyme-linked immunosorbent assays (ELISA) and immunofluorescence microscopy (IFM). Samples containing protein binders were first identified using ELISA, and then IFM was used to determine the location of protein binders. Using these methods, we discovered gelatin and casein in samples from wall murals, distributed in both red and black pigments. We excluded the possibility of contamination by conducting further experiments where simulated samples were spiked with milk. We conclude that both gelatin and casein were used as binders in the pigments of the Tibetan Buddhist murals in the Jiazhaer (Transliteration from Tibetan) mountain cave. This is the first evidence of casein being used as a binder in Chinese mural pigments.

In recent years, an increasing number of studies utilizing in situ liquid and/or gaseous cell scanning/transmission electron microscopy (S/TEM) have been reported. Because of the difficulty in the preparation of suitable specimens, these environmental S/TEM studies have been generally limited to studies of nanoscale structured materials such as nanoparticles, nanowires, or sputtered thin films. In this paper, we present two methodologies which have been developed to facilitate the preparation of electron-transparent samples from conventional bulk metals and alloys for in situ liquid/gaseous cell S/TEM experiments. These methods take advantage of combining sequential electrochemical jet polishing followed by focused ion beam extraction techniques to create large electron-transparent areas for site-specific observation. As an example, we illustrate the application of this methodology for the preparation of in situ specimens from a cold-rolled Type 304 austenitic stainless steel sample, which was subsequently examined in both 1 atm of air as well as fully immersed in a H2O environment in the S/TEM followed by hyperspectral imaging. These preparation techniques can be successfully applied as a general procedure for a wide range of metals and alloys, and are suitable for a variety of in situ analytical S/TEM studies in both aqueous and gaseous environments.

As high-resolution biological transmission electron microscopy (TEM) has increased in popularity over recent years, the volume of data and number of projects underway has risen dramatically. A robust tool for effective data management is essential to efficiently process large data sets and extract maximum information from the available data. We present the Electron Microscopy Electronic Notebook (EMEN), a portable, object-oriented, web-based tool for TEM data archival and project management. EMEN has several unique features. First, the database is logically organized and annotated so multiple collaborators at different geographical locations can easily access and interpret the data without assistance. Second, the database was designed to provide flexibility to the user, so it can be used much as a lab notebook would be, while maintaining a structure suitable for data mining and direct interaction with data-processing software. Finally, as an object-oriented database, the database structure is dynamic and can be easily extended to incorporate information not defined in the original database specification.

Polymeric nanoparticles containing an oily core, named nanocapsules (NCs), have been widely studied in the life sciences field due to their therapeutic potentialities of drug targeting in the body accompanied also by its larger stability in the biological fluids compared to other colloidal carriers. Many studies have shown different applications of nanocapsules for therapeutic use concerning their properties [1] of loading poorly water-soluble drugs, protection drugs from inactivation in the gastro-intestinal tract [2], gastric mucosal toxicity protection [3,4], increased drug permeation through mucous epithelium [5,6] and prolongation of drugs in blood circulation for surface modified nanocapsules [7]. The characterization of the nanocapsules is frequently performed by mean size, surface charge of the particles (zeta potential), hydrophobicity, drug loading yield and release kinetic [8]. These features are of great importance for biodistribution profile and interactions with the cells of mononuclear phagocyte system of any injected particles by intravenous route [1]. However, few data on structural organization of the nanocapsules constituents are available in literature and several hypotheses only suggest the presence of an oil "capsular" structure surrounded by a polymeric envelope. Recently, atomic force microscope (AFM) has been used as a method for imaging the surfaces of colloidal systems, such as liposomes [9,10] and nanospheres [11], supplying high resolution information in nanoscaled dimension. In the present work, unloaded nanocapsules were deposited on mica in order to analyze by AFM the diameter, height, particles polydispersion, and topographic characteristics of nanocapsule surface.

Results for the X-ray emission efficiency (counts per C per sr) of K-lines for selected elements (C, Al, Si, Ti, Cu, Ge) and for the first time also for compounds and alloys (SiC, GaP, AlCu, TiAlC) are presented. An energy dispersive X-ray spectrometer (EDS) of known detection efficiency (counts per photon) has been used to record the spectra at a takeoff angle of 25° determined by the geometry of the secondary electron microscope's specimen chamber. Overall uncertainty in measurement could be reduced to 5 to 10% in dependence on the line intensity and energy. Measured emission efficiencies have been compared with calculated efficiencies based on models applied in standardless analysis. The widespread XPP and PROZA models give somewhat too low emission efficiencies. The best agreement between measured and calculated efficiencies could be achieved by replacing in the modular PROZA96 model the original expression for the ionization cross section by the formula given by Casnati et al. (1982) A discrepancy remains for carbon, probably due to the high overvoltage ratio.

A need exists to prolong the release of rapidly metabolized peptides of a low molecular weight, while delivering this peptide without environmental interference. Previous studies have used bovine serum albumin (BSA) as a model peptide to study release characteristics from alginate microcapsules. BSA is 66 kDa in size, while the peptide of interest here, connexin-43 carboxyl-terminus mimetic peptide (αCT1), is only 3.4 kDa. Such a change in size results in a much different set of release parameters. Our overall goal is a sustained release over a 24+ h period. Prolonged application of the peptide to a wound site to investigate therapeutic effects is ideal. As a result, a diffusion method using alginate microcapsules, along with the addition of poly-l-lysine and poly-l-ornithine, has been explored. We first aimed to establish and characterize our parameters through a set of parametric tests. Variations in polymer coating, change in pH, and changes in loading ratio have previously been shown to effect release using model compounds. Here we test specific changes in these parameters to show effects on the release of αCT1. Additionally, the microcapsules were attached to several biomaterials and surgical implants by ultraviolet cross-linking to study the effectiveness of attachment and delivery. Analysis and measurements using phase contrast microscopy, scanning electron microscopy, and atomic force microscopy were used to characterize changes in microcapsule morphology.

Fluorescent dyes like Rhodamine B (RB) have been used to identify the spatial distribution of adhesive restorative materials in the tooth/restoration interface. Potential effects of the addition of RB to dental adhesives were addressed in the past, but no further information is available on how to determine suitable concentrations of RB in these bonding agents for imaging in the confocal laser scanning microscope. This study provides systematical strategies for adding RB to viscous dental adhesive resins, focusing on the determination of the lowest range of dye concentrations necessary to achieve an acceptable image of the dentin/adhesive interface. It was demonstrated that optimized images of the resin distribution in dentin can be produced with 0.1–0.02 mg/mL of RB in the (tested) adhesives. Our approaches took into account aspects related to the dye concentration, photophysical parameters in different host media, specimen composition and morphology to develop a rational use of the fluorescent agent with the resin-based materials. Information gained from this work can help optimize labeling methods using dispersions of low-molecular-weight dyes in different monomer blend systems.

The development of Leydig cells in mammals has been widely described as a biphasic pattern with two temporally mature Leydig cell populations, fetal stage followed by the adult generation beginning at puberty. In the present study, mouse Leydig cells were examined for apoptosis during postnatal testis development using electron microscopy and in situ DNA fragmentation by terminal deoxynucleotidyl transferase staining (TdT). Both the morphological study and the DNA fragmentation analysis showed that cellular death by apoptosis did not occur in Leydig cells during the neonatal, prepubertal, puberty, and adult periods. From these results, we suggest that the remaining fetal Leydig cells in the neonatal testis are associated with the involution or degeneration processes. In contrast, in the prepubertal and puberty stages, fragmentation of apoptotic DNA was detected in germ cells present in some seminiferous tubules.

Changes in microstructure of Zr, Ti, and Ti-6%Al-%V resulting from ion-beam sputtering used to prepare samples for transmission electron microscopy have been correlated with hydrogen absorption. Zr was particularly sensitive to this phenomenon, resulting in extensive hydride formation in thin foil samples. Hydrogen enrichment extending to several micrometers in depth could also be produced in bulk samples in a few hours of sputtering. The performance of various sputtering units in different configurations has been examined. It is concluded that hydride formation appears to be caused primarily by the presence of hydrocarbons, for example, from the backstreaming of diffusion pump oil, in the residual vacuum background of the sputtering chamber.

Human cadaveric skin allografts are used in the treatment of burns and can be preserved in glycerol at high concentrations. Previously, glycerol has been attributed some antimicrobial effect. In an experimental set-up, we aimed at investigating this effect of prolonged incubation of bacteria in 85% glycerol. Staphylococcus epidermidis, Staphylococcus aureus, Pseudomonas aeruginosa, and Bacillus subtilis were incubated in 85% glycerol. The influence of duration of incubation and temperature on ultrastructure and viability were investigated. Unstressed cultures served as controls. Survival was studied after 24–36 h and 10 days incubation in 85% glycerol at 4°C and 36°C with transmission electron microscopy (TEM) and flow cytometry using viability stains indicating membrane damage (SYTO9, propidium iodide) or esterase activity (carboxyfluorescein diacetate). TEM clearly demonstrated variability in morphological changes of bacteria suggesting different mechanisms of damage. Viability stains supported these findings with faster declining viable cell populations in 85% glycerol at 36°C compared with 4°C. Both methods demonstrated that Gram-negative species were more susceptible than Gram-positive species. In conclusion, 85% glycerol may have some additional antimicrobial effect. Temperature is an important factor herein and Gram-negatives are most susceptible. The latter finding probably reflects the difference in cell wall composition between Gram-positive and Gram-negative bacteria.

Many cellular processes are organized in a compartmentalized and dynamic fashion to ensure effective adaptation to physiological changes. Thus, in response to stress and disease, cells initiate protective mechanisms to restore homeostasis. Among these mechanisms are the arrest of translation and remodeling of ribonucleoprotein complexes into granular compartments in the cytoplasm, known as stress granules (SGs). To date, the analysis of SGs has relied on the manual demarcation and measurement of the compartment, making quantitative studies time-consuming, while preventing the efficient use of high-throughput technology. We developed the first fully automated, computer-based procedures that measure the association of fluorescent molecules with granular compartments. Our methods quantify automatically multiple granule parameters and generate data at the level of single cells or individual SGs. These techniques detect simultaneously in an automated fashion proteins and RNAs located in SGs. The effectiveness of our protocols is demonstrated by studies that reveal several of the unique biological and structural characteristics of SGs. In particular, we show that the type of stress determines granule size and composition, as illustrated by the concentration of poly(A)-RNA and a specific SG marker protein. Furthermore, we took advantage of the computer-based and automated methods to design assays suitable for high-throughput screening.

Protocols for conducting in situ transmission electron microscopy (TEM) reactions using an environmental TEM with dry gases have been well established. However, many important reactions that are relevant to catalysis or high-temperature oxidation occur at atmospheric pressure and are influenced by the presence of water vapor. These experiments necessitate using a closed-cell gas reaction TEM holder. We have developed protocols for introducing and controlling water vapor concentrations in experimental gases from 2% at a full atmosphere to 100% at ~17 Torr, while measuring the gas composition using a residual gas analyzer (RGA) on the return side of the in situ gas reactor holder. Initially, as a model system, cube-shaped MgO crystals were used to help develop the protocols for handling the water vapor injection process and confirming that we could successfully inject water vapor into the gas cell. The interaction of water vapor with MgO triggered surface morphological and chemical changes as a result of the formation of Mg(OH)2, later validated with mass spectra obtained with our RGA system with and without water vapor. Integrating an RGA with an in situ scanning/TEM closed-cell gas reaction system can thus provide critical measurements correlating gas composition with dynamic surface restructuring of materials during reactions.