The formation of copper-rich precipitates of 17-4 precipitate hardened stainless steel has been investigated, after tempering at 350–570°C for 4 h, by atom probe tomography (APT). The results reveal that the clusters, enriched only with Cu, were observed after tempering at 420°C. Segregation of Ni, Mn to the Cu-rich clusters took place at 450°C, contributing to the increased hardening. After tempering at 510°C, Ni and Mn were rejected from Cu-rich precipitates and accumulated at the precipitate/matrix interfaces. Al and Si were present and uniformly distributed in the precipitates that were <1.5 nm in radius, but Ni, Mn, Al, and Si were enriched at the interfaces of larger precipitates/matrix. The proxigram profiles of the Cu-rich precipitates formed at 570°C indicated that Ni, Mn, Al, and Si segregated to the precipitate/matrix interfaces to form a Ni(Fe, Mn, Si, Al) shell, which significantly reduced the interfacial energy as the precipitates grew into an elongated shape. In addition, the number density of Cu-rich precipitates was increased with the temperature elevated from 350 up to 450°C and subsequently decreased at higher temperatures. Also, the composition of the matrix and the precipitates were measured and found to vary with temperature.

We evaluate the probe forming capability of a JEOL 2200FS transmission electron microscope equipped with a spherical aberration (Cs) probe corrector. The achievement of a real space sub-Angstrom (0.1 nm) probe for scanning transmission electron microscopy (STEM) imaging is demonstrated by acquisition and modeling of high-angle annular dark-field STEM images. We show that by optimizing the illumination system, large probe currents and large collection angles for electron energy loss spectroscopy (EELS) can be combined to yield EELS fine structure data spatially resolved to the atomic scale. We demonstrate the probe forming flexibility provided by the additional lenses in the probe corrector in several ways, including the formation of nanometer-sized parallel beams for nanoarea electron diffraction, and the formation of focused probes for convergent beam electron diffraction with a range of convergence angles. The different probes that can be formed using the probe corrected STEM opens up new applications for electron microscopy and diffraction.

There are two main projections used to transform, and reconstruct, field ion micrographs or atom probe tomography data into atomic coordinates at the specimen surface and, subsequently, in three dimensions. In this article, we present a perspective on the strength of the azimuthal equidistant projection in comparison with the more widely used and well-established point projection (or pseudo-stereographic projection), which underpins data reconstruction in most software packages currently in use across the community. After an overview of the reconstruction methodology, we demonstrate that the azimuthal equidistant is more robust with regards to errors on the parameters used to perform the reconstruction and is therefore more likely to yield more accurate tomographic reconstructions.

Defining the ultrastructure of endocytic sites and localization of endocytic proteins in Saccharomyces cerevisiae by immunoelectron microscopy is central in understanding the mechanisms of membrane deformation and scission during endocytosis. We show that an improved sample preparation protocol based on high-pressure freezing, freeze substitution, and low-temperature embedding allows us to maintain the cellular fine structure and to immunolabel green fluorescent protein–tagged endocytic proteins or actin in the same sections. Using this technique we analyzed the stepwise deformation of endocytic membranes and immunolocalized the endocytic proteins Abp1p, Sla1p, Rvs167p, and actin, and were able to draw a clear ultrastructural distinction between endocytic sites and eisosomes by immunolocalizing Pil1p. In addition to defining the geometry and the fine structure of budding yeast endocytic sites, we observed associated actin filaments forming a cage-like meshwork around the endocytic membrane.

The advent of aberration correction for transmission electron microscopy has transformed atomic resolution imaging into a nearly routine technique for structural analysis. Now an emerging frontier in electron microscopy is the development of in situ capabilities to observe reactions at atomic resolution in real time and within realistic environments. Here we present a new in situ gas cell holder that is designed for compatibility with a wide variety of sample type (i.e., dimpled 3-mm discs, standard mesh grids, various types of focused ion beam lamellae attached to half grids). Its capabilities include localized heating and precise control of the gas pressure and composition while simultaneously allowing atomic resolution imaging at ambient pressure. The results show that 0.25-nm lattice fringes are directly visible for nanoparticles imaged at ambient pressure with gas path lengths up to 20 μm. Additionally, we quantitatively demonstrate that while the attainable contrast and resolution decrease with increasing pressure and gas path length, resolutions better than 0.2 nm should be accessible at ambient pressure with gas path lengths less than the 15 μm utilized for these experiments.

Measuring the changing thickness of a thin film, without a reference, using an atomic force microscope (AFM) is problematic. Here, we report a method for measuring film thickness based on in situ monitoring of surface roughness of films as their thickness changes. For example, in situ AFM roughness measurements have been performed on alloy film electrodes on rigid substrates as they react with lithium electrochemically. The addition (or removal) of lithium to (or from) the alloy causes the latter to expand (or contract) reversibly in the direction perpendicular to the substrate and, in principle, the change in the overall height of these materials is directly proportional to the change in roughness. If the substrate on which the film is deposited is not perfectly smooth, a correction to the direct proportionality is needed and this is also discussed.

Human epidermal growth factor receptor (HER2) is a tumor biomarker that when overexpressed and/or amplified is associated with a poor prognosis for women with breast cancer. This specific tumor subtype is eligible for a specific immunotherapy that increases survival period. However, in feline oncology, only a few studies have been performed on molecular characterization of feline (fHER2) in feline mammary carcinoma (FMC), and the available data are inconsistent. In this study, fHER2 protein levels and gene status in FMC were evaluated by immunohistochemistry and in situ hybridization. After being optimized, these techniques revealed that fHER2 is overexpressed in 33% of FMC cases, although fHER2 and fTOP2A gene amplification could not be observed. Our results support the possibility of using FMC as a natural model for comparative oncology. Additional data obtained may also improve the diagnostics, and consequently the treatment, of this type of tumor in veterinary medicine.

Lipid-containing nanostructures, in the form of solid lipid nanoparticles or iron oxide nanoparticles (NPs) coated with a lipid shell, were used as case studies for assessing and optimizing staining for transmission electron microscopy structural and compositional characterization. These systems are of paramount importance as drug delivery systems or as bio-compatible contrast agents. In particular, we have treated the systems with a negative (phospshotungstic acid) or with a positive (osmium tetroxide) staining agent. For iron-oxide NPs coated with the lipid shell, negative staining was more efficient with respect to the positive one. Nevertheless, in particular cases the combination of the two staining procedures provided more complete morphological and compositional characterization of the particles.

Recent evidence supports the notion that biological functions of extracellular matrix (ECM) are highly correlated to not only its composition but also its structure. This article integrates confocal microscopy imaging and image-processing techniques to analyze the microstructural properties of ECM. This report describes a two- and three-dimensional fiber middle-line tracing algorithm that may be used to quantify collagen fibril organization. We utilized computer simulation and statistical analysis to validate the developed algorithm. These algorithms were applied to confocal images of collagen gels made with reconstituted bovine collagen type I, to demonstrate the computation of orientations of individual fibers.

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005

Advances in DNA sequencing, based on fluorescent microscopy, have transformed many areas of biological research. However, only relatively short molecules can be sequenced by these technologies. Dramatic improvements in genomic research will require accurate sequencing of long (>10,000 base-pairs), intact DNA molecules. Our approach directly visualizes the sequence of DNA molecules using electron microscopy. This report represents the first identification of DNA base pairs within intact DNA molecules by electron microscopy. By enzymatically incorporating modified bases, which contain atoms of increased atomic number, direct visualization and identification of individually labeled bases within a synthetic 3,272 base-pair DNA molecule and a 7,249 base-pair viral genome have been accomplished. This proof of principle is made possible by the use of a dUTP nucleotide, substituted with a single mercury atom attached to the nitrogenous base. One of these contrast-enhanced, heavy-atom-labeled bases is paired with each adenosine base in the template molecule and then built into a double-stranded DNA molecule by a template-directed DNA polymerase enzyme. This modification is small enough to allow very long molecules with labels at each A-U position. Image contrast is further enhanced by using annular dark-field scanning transmission electron microscopy (ADF-STEM). Further refinements to identify additional base types and more precisely determine the location of identified bases would allow full sequencing of long, intact DNA molecules, significantly improving the pace of complex genomic discoveries.

The centrosome is the principal microtubule organization center in cells, giving rise to microtubule-based organelles (e.g., cilia, flagella). The aim was to study the osteocyte centrosome morphology at an ultrastructural level in relation to its mechanosensitive function. Osteocyte centrosomes and cilia in tibial cortical bone were explored by acetylated alpha-tubulin (AαTub) immunostaining under confocal microscopy. For the first time, fine ultrastructure and spatial orientation of the osteocyte centrosome were explored by transmission electron microscopy on serial ultrathin sections. AαTub-positive staining was observed in 94% of the osteocytes examined (222/236). The mother centriole formed a short primary cilium and was longer than the daughter centriole due to an intermediate zone between centriole and cilium. The proximal end of the mother centriole was connected with the surface of daughter centriole by striated rootlets. The mother centriole exhibited distal appendages that interacted with the cell membrane and formed a particular structure called “cilium membrane prolongation.” The primary cilium was mainly oriented perpendicular to the long axis of bone. Mother and daughter centrioles change their original mutual orientation during the osteocyte differentiation process. The short primary cilium is hypothesized as a novel type of fluid-sensing organelle in osteocytes.

Alnico alloys have long been used as strong permanent magnets because of their ferromagnetism and high coercivity. Understanding their structural details allows for better prediction of the resulting magnetic properties. However, quantitative three-dimensional characterization of the phase separation in these alloys is still challenged by the spatial quantification of nanoscale phases. Herein, we apply a dual tomography approach, where correlative scanning transmission electron microscopy (STEM) energy-dispersive X-ray spectroscopic (EDS) tomography and atom probe tomography (APT) are used to investigate the initial phase separation process of an alnico 8 alloy upon non-magnetic annealing. STEM-EDS tomography provides information on the morphology and volume fractions of Fe–Co-rich and Νi–Al-rich phases after spinodal decomposition in addition to quantitative information of the composition of a nanoscale volume. Subsequent analysis of a portion of the same specimen by APT offers quantitative chemical information of each phase at the sub-nanometer scale. Furthermore, APT reveals small, 2–4 nm Fe-rich α1 phases that are nucleated in the Ni-rich α2 matrix. From this information, we show that phase separation of the alnico 8 alloy consists of both spinodal decomposition and nucleation and growth processes. The complementary benefits and challenges associated with correlative STEM-EDS and APT are discussed.

Organophosphate pesticides (OPs) like malathion interfere with normal ovarian function resulting in an increased incidence of atresia and granulosa cell apoptosis that plays a consequential role in the loss of ovarian follicles or follicular atresia. The aim of present study was to assess malathion-induced (100 nM) reproductive stress, ultrastructural damage and changes in apoptosis frequency in ovarian granulosa cells of antral follicles. Transmission electron microscopy (TEM) was employed for ultrastructural characterization, oxidative stress was evaluated using thiobarbituric acid reactive substances (TBARS) assay to measure lipid peroxidation, and apoptosis was quantified via flow cytometry. By TEM, apoptosis was identified by the presence of an indented nuclear membrane with blebbing, pyknotic crescent-shaped fragmented nuclei, increased vacuolization, degenerating mitochondria, and lipid droplets. The results indicate a significant increase in malondialdehyde (MDA) level (nmols/g wet tissue) at a 100 nM dose of malathion i.e. 7.57±0.033*, 8.53±0.12*, and 12.87±0.78** at 4, 6, or 8 h, respectively, as compared with controls (6.07±0.033, p<0.01*, p<0.05**) showing a positive correlation between malathion-induced lipid peroxidation and percentage of granulosa cell apoptosis (r=1; p<0.01). The parallel use of these three methods enabled us to determine the role of malathion in inducing apoptosis as a consequence of cytogenetic damage and oxidative stress generated in granulosa cells of antral follicles.

Cryptosporidium parvum (Apicomplexa, formerly Sporozoa) is the causative agent of cryptosporidiosis, an enteric disease of substantial medical and veterinary importance. C. parvum shows a number of unique features that differ from the rest of the class of coccidea in which it is currently grouped taxonomically. Differences occur in the overall structure of the transmission form and the invasive stages of the parasite, its intracellular location, the presence of recently described additional extracellular stages, the host range and target cell tropism, the ability to autoinfection, the nonresponsiveness to anticoccidial drugs, the immune response of the host, and immunochemical and genetic characteristics. These differences have an important impact on the infectivity, the epidemiology, the therapy, and the taxonomy of the parasite. The present article describes the structural analysis of the parasite using light and electron microscopy with an emphasis on structural details unique to C. parvum.

The adsorption of humic acid (HA) onto highly ordered pyrolytic graphite (HOPG) surfaces at different concentrations has been studied by atomic force microscopy. When HA concentration was increased from 10 to 1,000 mg/L, HA can sequentially form spherical particles, layered structures, and connected blocks on HOPG surfaces. The findings of the layer structures and small amount of fine chains have been verified and discussed. When HA was acidified by addition of acetic acid, it changed into small rigid particles. These results indicated that HA can be considered as supramolecular associations of self-assembling heterogeneous and relatively small molecules, and a small amount of polymers. The present results are important for understanding HA molecular structures and their adsorption characteristic on carbonaceous surfaces.

The results of a three-dimensional atom probe (3DAP) analysis, on a subnanometer scale, of a ceramic/metal heterophase interface, MgO/Cu, are presented. Segregation of Ag, from the Cu (Ag) matrix, at MgO/Cu interfaces is investigated and the Gibbsian interfacial excess of silver is determined; the range is 2.33 × 1018 to 5.81 × 1018 m−2. Also, silver segregation at the same MgO/Cu interfaces is analyzed employing a new approach that utilizes a proximity histogram or proxigram.

Ndc80 (called Hec1 in human), the core component of the Ndc80 complex, is involved in regulation of both kinetochore-microtubule interactions and the spindle assembly checkpoint in mitosis; however, its role in meiosis remains unclear. Here, we report Ndc80 expression, localization, and possible functions in mouse oocyte meiosis. Ndc80 mRNA levels gradually increased during meiosis. Immunofluorescent staining showed that Ndc80 was restricted to the germinal vesicle and associated with spindle microtubules from the Pro-MI to MII stages. Ndc80 was localized on microtubules and asters in the cytoplasm after taxol treatment, while Ndc80 staining was diffuse after disruption of microtubules by nocodazole treatment, confirming its microtubule localization. Disruption of Ndc80 function by either siRNA injection or antibody injection resulted in severe chromosome misalignment, spindle disruption, and precocious polar body extrusion. Our data show a unique localization pattern of Ndc80 in mouse oocytes and suggest that Ndc80 may be required for chromosome alignment and spindle organization, and may regulate spindle checkpoint activity during mouse oocyte meiosis.

Transmission electron microscope samples of two types of metal matrix composites were prepared using both traditional thinning methods and the more novel focused ion beam miller. Electropolishing methods were able to produce, very rapidly, thin foils where the matrix was electron transparent, but the ceramic reinforcement particles remained unthinned. Thus, it was not possible in these foils to study either the matrix-reinforcement interface or the microstructure of the reinforcement particles themselves. In contrast, both phases in the composites prepared using the focused ion beam miller thinned uniformly. The interfaces in these materials were clearly visible and the ceramic reinforcement was electron transparent. However, microstructural artifacts associated with ion beam damage were also observed. The extent of these artifacts and methods of minimizing their effect were dependent on both the materials and the milling conditions used.