We used hybrid detectors (HyDs) to monitor the trajectories and interactions of promyelocytic leukemia (GFP-PML) nuclear bodies (NBs) and mCherry-53BP1-positive DNA lesions. 53BP1 protein accumulates in NBs that occur spontaneously in the genome or in γ-irradiation-induced foci. When we induced local DNA damage by ultraviolet irradiation, we also observed accumulation of 53BP1 proteins into discrete bodies, instead of the expected dispersed pattern. In comparison with photomultiplier tubes, which are used for standard analysis by confocal laser scanning microscopy, HyDs significantly eliminated photobleaching of GFP and mCherry fluorochromes during image acquisition. The low laser intensities used for HyD-based confocal analysis enabled us to observe NBs for the longer time periods, necessary for studies of the trajectories and interactions of PML and 53BP1 NBs. To further characterize protein interactions, we used resonance scanning and a novel bioinformatics approach to register and analyze the movements of individual PML and 53BP1 NBs. The combination of improved HyD-based confocal microscopy with a tailored bioinformatics approach enabled us to reveal damage-specific properties of PML and 53BP1 NBs.

Polistes paper wasps can be used to monitor trace metal contaminants, but the effects of pollution on the health of these insects are still unknown. We evaluated, in a south-eastern area of Spain, whether workers of Polistes dominula collected at urban and rural sites differ in health of midgut tissue and in fluctuating asymmetry, an estimate of developmental noise. We found that wasps collected at the urban sites had abundant lead (Pb)-containing spherites, which were less visible in wasps from the rural sites. Evident ultrastructural alterations in the epithelium of the midgut of the wasps collected at the urban sites included broken and disorganized microvilli, a high amount and density of heterochromatin in the nucleus of epithelial cells, cytoplasmic vacuolization and mitochondrial disruptions. Altogether, these findings suggest a negative effect on the transmembrane transport and a less efficient transcription. On the contrary, a healthy epithelium was observed in wasps from the rural sites. These differences may be preliminarily linked with levels of lead pollution, given that wasps from urban sites had double the Pb concentrations of wasps from rural sites. Level of fluctuating asymmetry was unrelated to wasp origin, thus suggesting no link between developmental noise and Pb-driven pollution.

Magnetron sputtered thin films of Cu, Nb, and Cu-Nb multilayers with 2.5 and 5 nm nominal layer thickness were deposited on Si and implanted with 4He+ and 3He+ ions. Secondary ion mass spectroscopy and nuclear reaction analysis, respectively, were used to measure the 4He+ and 3He+ concentration profile with depth inside the films. Cross-sectional transmission electron microscopy was used to characterize the helium bubbles. Analysis of the contrast from helium bubbles in defocused transmission electron microscope images showed a minimum bubble diameter of 1.25 nm. While pure Cu and Nb films showed bubble contrast over the entire range of helium implantation, the multilayers exhibited bubbles only above a critical He concentration that increased almost linearly with decreasing layer thickness. The work shows that large amounts of helium can be trapped at incoherent interfaces in the form of stable, nanometer-size bubbles.

This study evaluated the influence of fluoride mouth rinses and repolishing on the superficial morphology and color stability of nanofilled resin. About 150 specimens were prepared and polished using aluminum oxide discs for 15 s with a pressure of 2 kg. The experimental groups were divided according to the immersion medium (artificial saliva, 0.5% sodium fluoride, Fluordent Reach, Oral B, Fluorgard) and repolishing procedure (without and with). The specimens were continuously immersed for 1 week. Thereafter, half of each sample was repolished. A color reading was performed after 24 h of immersion in the artificial saliva baseline, after continuous immersion, and after repolishing. The superficial morphology was examined using scanning electron microscopy (SEM) in a qualitative way. Color change (∆E) data were submitted to a mixed analysis of variance using a Shapiro–Wilk test (p>0.05 for the different immersion media) and Sidak’s test (p<0.05 for the differences between groups). In the interaction between the repolishing and the immersion media, Fluorgard showed a statistical difference between the ∆E values with and without repolishing (p<0.0001). On the SEM observations, both Fluordent Reach and Fluorgard caused degradation of the superficial resinous matrix of the composite after continuous immersion. This matrix was removed after repolishing.

The composition of GaAs measured by laser-assisted atom probe tomography may be inaccurate depending on the experimental conditions. In this work, we assess the role of the DC field and the impinging laser energy on such compositional bias. The DC field is found to have a major influence, while the laser energy has a weaker one within the range of parameters explored. The atomic fraction of Ga may vary from 0.55 at low-field conditions to 0.35 at high field. These results have been interpreted in terms of preferential evaporation of Ga at high field. The deficit of As is most likely explained by the formation of neutral As complexes either by direct ejection from the tip surface or upon the dissociation of large clusters. The study of multiple detection events supports this interpretation.

The damage and ion distribution induced in Si by an inductively coupled plasma Xe focused ion beam was investigated by atom probe tomography. By using predefined patterns it was possible to prepare the atom probe tips with a sub 50 nm end radius in the ion beam microscope. The atom probe reconstruction shows good agreement with simulated implantation profiles and interplanar distances extracted from spatial distribution maps. The elemental profiles of O and C indicate co-implantation during the milling process. The presence of small disc-shaped Xe clusters are also found in the three-dimensional reconstruction. These are attributed to the presence of Xe nanocrystals or bubbles that open during the evaporation process. The expected accumulated dose points to a loss of >95% of the Xe during analysis, which escapes undetected.

A systematic distortion in high-angle annular dark-field scanning transmission electron microscope (HAADF-STEM) images, which may be caused by residual electrical interference, has been evaluated. Strain mapping, using the geometric phase methodology, has been applied to images acquired in an aberration-corrected STEM. This allows this distortion to be removed and so quantitative analysis of HAADF-STEM images was enabled. The distortion is quantified by applying this technique to structurally perfect and strain-free material. As an example, the correction is used to analyse an InAs/GaAs dot-in-quantum well heterostructure grown by molecular beam epitaxy. The result is a quantitative measure of internal strain on an atomic scale. The measured internal strain field of the heterostructure can be interpreted as being due to variations of indium concentration in the quantum dot.

Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009

The immune system is highly evolved and can respond to infection throughout the body. Pathogen-specific immune cells are usually generated in secondary lymphoid tissues (e.g., spleen, lymph nodes) and then migrate to sites of infection where their functionality is shaped by the local milieu. Because immune cells are so heavily influenced by the infected tissue in which they reside, it is important that their interactions and dynamics be studied in vivo. Two-photon microscopy is a powerful approach to study host-immune interactions in living tissues, and recent technical advances in the field have enabled researchers to capture movies of immune cells and infectious agents operating in real time. These studies have shed light on pathogen entry and spread through intact tissues as well as the mechanisms by which innate and adaptive immune cells participate in thwarting infections. This review focuses on how two-photon microscopy can be used to study tissue-specific immune responses in vivo, and how this approach has advanced our understanding of host-immune interactions following infection.

Extended abstract of a paper presented at Microscopy and Microanalysis 2008 in Albuquerque, New Mexico, USA, August 3 – August 7, 2008

Microscopy has played a critical role in first identifying and then defining the role of lysosomes in formation of atherosclerotic foam cells. We review the evidence implicating lysosomal lipid accumulation as a factor in the pathogenesis of atherosclerosis with reference to the role of microscopy. In addition, we explore mechanisms by which lysosomal lipid engorgement occurs. Low density lipoproteins which have become modified are the major source of lipid for foam cell formation. These altered lipoproteins are taken into the cell via receptor-mediated endocytosis and delivered to lysosomes. Under normal conditions, lipids from these lipoproteins are metabolized and do not accumulate in lysosomes. In the atherosclerotic foam cell, this normal metabolism is inhibited so that cholesterol and cholesteryl esters accumulate in lysosomes. Studies of cultured cells incubated with modified lipoproteins suggests this abnormal metabolism occurs in two steps. Initially, hydrolysis of lipoprotein cholesteryl esters occurs normally, but the resultant free cholesterol cannot exit the lysosome. Further lysosomal cholesterol accumulation inhibits hydrolysis, producing a mixture of cholesterol and cholesteryl esters within swollen lysosomes. Various lipoprotein modifications can produce this lysosomal engorgement in vitro and it remains to be seen which modifications are most important in vivo.

This paper presents a statistical method to analyze instabilities that can be introduced during imaging in scanning electron microscopy (SEM). The method is based on the correlation of digital images and it can be used at different length scales. It consists of the evaluation of three different approaches with four parameters in total. The methodology is exemplified with a specific case of internal stress measurements where ion milling and SEM imaging are combined with digital image correlation. It is concluded that before these measurements it is important to test the SEM column to ensure the minimization and randomization of the imaging instabilities. The method has been applied onto three different field emission gun SEMs (Philips XL30, Tescan Lyra, FEI Helios 650) that represent three successive generations of SEMs. Important to note that the imaging instability can be quantified and its source can be identified.

Confocal fluorescence microscopy is a broadly used imaging technique that enhances the signal-to-noise ratio by removing out of focal plane fluorescence. Confocal microscopes come with a variety of modifications depending on the particular experimental goals. Microscopes, illumination pathways, and light collection were originally focused upon obtaining the highest resolution image possible, typically on fixed tissue. More recently, live-cell confocal imaging has gained importance. Since measured signals are often rapid or transient, thus requiring higher sampling rates, specializations are included to enhance spatial and temporal resolution while maintaining tissue viability. Thus, a balance between image quality, temporal resolution, and tissue viability is needed. A subtype of confocal imaging, termed swept field confocal (SFC) microscopy, can image live cells at high rates while maintaining confocality. SFC systems can use a pinhole array to obtain high spatial resolution, similar to spinning disc systems. In addition, SFC imaging can achieve faster rates by using a slit to sweep the light across the entire image plane, thus requiring a single scan to generate an image. Coupled to a high-speed charge-coupled device camera and a laser illumination source, images can be obtained at greater than 1,000 frames per second while maintaining confocality.

Different approaches using microscopy image analysis procedures were employed for characterization of activated sludge systems. The approaches varied mainly on the type of visualization and acquisition method used for collection of data. In this context, this study focused on the comparison of the two most common acquisition methods: bright field and phase-contrast microscopy. Images were acquired from seven different wastewater treatment plants for a combined period of two years. Advantages and disadvantages of each acquisition technique and the results are discussed. Bright field microscopy proved to be more simple and inexpensive and provided the best overall results.

Extended abstract of a paper presented at Microscopy and Microanalysis 2007 in Ft. Lauderdale, Florida, USA, August 5 – August 9, 2007

Using an in situ load frame within a scanning electron microscope, a microstructural section on the surface of an annealed tantalum (Ta) polycrystalline specimen was mapped at successive tensile strain intervals, up to ~20% strain, using electron backscatter diffraction. A grain identification and correlation technique was developed for characterizing the evolving microstructure during loading. Presenting the correlated results builds on the reference orientation deviation (ROD) map concept where individual orientation measurements within a grain are compared with a reference orientation associated with that grain. In this case, individual orientation measurements in a deformed grain are measured relative to a reference orientation derived from the undeformed (initial) configuration rather than the current deformed configuration as has been done for previous ROD schemes. Using this technique helps reveal the evolution of crystallographic orientation gradients and development of deformation-induced substructure within grains. Although overall crystallographic texture evolved slowly during deformation, orientation spread within grains developed quickly. In some locations, misorientation relative to the original orientation of a grain exceeded 20° by 15% strain. The largest orientation changes often appeared near grain boundaries suggesting that these regions were preferred locations for the initial development of subgrains.