Helicobacter pylori is a human pathogen involved in gastritis and gastric cancer whose mode of transmission remains unknown. Association of H. pylori with humans is thought to date from remote antiquity and the bacterium has apparently evolved together with the human host. A few studies have shown the presence of H. pylori in aquatic environments, which might provide a route of transmission of the bacteria to humans. A recent study has also disclosed the association of the bacteria with Acantamoeba castellanii. Amoeba are known to harbor and promote the persistence of several human pathogens in the environment, representing a significant source of contamination in community and hospital acquired infections.

Redox reactions were studied at a single yttria-stabilized zirconia (YSZ)/Pt electrode interface, in parallel with pure YSZ with no catalyst electrode, by in situ analytical electron microscopy at elevated temperatures and in an oxygen atmosphere. In situ electron holography showed that the oxide underwent reduction at elevated temperatures in a vacuum and was consequently reoxidized upon exposure to an oxygen flux at the same temperature. In situ energy loss spectroscopy measurements were in agreement with in situ electron holography observations and indicated that the oxidation state of the host cation zirconium was altered in the reduced state of the YSZ to the metastable state Zr3+.

Atom probe tomography (APT) provides three-dimensional analytical imaging of materials with near-atomic resolution using pulsed field evaporation. The processes of field evaporation can cause atoms to be placed at positions in the APT reconstruction that can deviate slightly from their original site in the material. Here, we describe and model one such process—that of preferential retention of solute atoms in multicomponent systems. Based on relative field evaporation probabilities, we calculate the point spread function for the solute atom distribution in the “z,” or in-depth direction, and use this to extract more accurate solute concentration profiles.

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.

This article concerns application of cathodoluminescence (CL) spectroscopy to volcanic quartz and its utility in assessing variation in trace quantities of Ti within individual crystals. CL spectroscopy provides useful details of intragrain compositional variability and structure but generally limited quantitative information on element abundances. Microbeam analysis can provide such information but is time-consuming and costly, particularly if large numbers of analyses are required. To maximize advantages of both approaches, natural and synthetic quartz crystals were studied using high-resolution hyperspectral CL imaging (1.2–5.0 eV range) combined with analysis via laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). Spectral intensities can be deconvolved into three principal contributions (1.93, 2.19, and 2.72 eV), for which intensity of the latter peak was found to correlate directly with Ti concentration. Quantitative maps of Ti variation can be produced by calibration of the CL spectral data against relatively few analytical points. Such maps provide useful information concerning intragrain zoning or heterogeneity of Ti contents with the sensitivity of LA-ICPMS analysis and spatial resolution of electron microprobe analysis.

The physical and chemical characteristics of kaolinite (kaolin) may be variable, and minor amounts of other clay minerals, nonclay minerals, and other impurities may affect the properties of kaolinites. Thus specific technical properties of pharmaceutical grade kaolinites become very important because these clays are used in medical applications, e.g., as pharmaceutical excipients, and will be consumed by humans. Seven pharmaceutical grade kaolinite specimens were used in this study: K1004, KA105, 2242-01, K2-500, Acros, Acros-mono, and KX0007-1. In addition, two kaolinites from the Clay Minerals Society Source Clays, KGa-1b and KGa-2, were used for comparison purposes. The Acros-mono and 2242-01 kaolinites contained minor amounts of illite, which was demonstrated both compositionally and structurally by using inductively coupled plasma spectroscopy and powder X-ray diffraction. The KX0007-1 kaolinite powder was found to be heavily contaminated with quartz, cristobalite, and alunite. Crystal structure computations also showed excess Si in its tetrahedral site, and the mineral no longer has the typical kaolinite crystal structure. These widely-used industrial standards should be quantitatively characterized morphologically, compositionally, and structurally. Results of the mineralogical characteristics should be clearly labeled on the pharmaceutical grade kaolinites and reported to the relevant regulatory agencies.

We show that aberration-corrected scanning transmission electron microscopy operating at low accelerating voltages is able to analyze, simultaneously and with single atom resolution and sensitivity, the local atomic configuration, chemical identities, and optical response at point defect sites in monolayer graphene. Sequential fast-scan annular dark-field (ADF) imaging provides direct visualization of point defect diffusion within the graphene lattice, with all atoms clearly resolved and identified via quantitative image analysis. Summing multiple ADF frames of stationary defects produce images with minimized statistical noise and reduced distortions of atomic positions. Electron energy-loss spectrum imaging of single atoms allows the delocalization of inelastic scattering to be quantified, and full quantum mechanical calculations are able to describe the delocalization effect with good accuracy. These capabilities open new opportunities to probe the defect structure, defect dynamics, and local optical properties in 2D materials with single atom sensitivity.

Among the many aspects of laser ablation, development of conical structures induced by excimer laser radiation on polyimide surfaces has been thoroughly investigated. Because the mechanisms that produce these surface textures are not fully understood, two theories, photochemical bond breaking and thermal reaction, have been introduced. Here we present the first study of ultraviolet laser ablation behavior of thin films made from fluorinated poly(naphthyl-imide)s containing oxadiazole rings and the investigation of the mechanism of cone-like structure formation at two laser fluences, 57 and 240 mJ/cm2. The morphology of thin films before and after laser ablation was studied by using various spectroscopy techniques such as Fourier transform infrared spectroscopy, time-resolved emission and X-ray photoelectron spectroscopy, atomic force microscopy, and contact angle measurements. All of the data suggest impurities shielded at low fluence radiation (57 mJ/cm2) and a radiation hardening process at high value fluence (240 mJ/cm2), which are proposed as the main mechanisms for laser ablation of our polyimide films, and we bring evidence to support them.

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.

The synaptic ribbon is a unique presynaptic structure with an intricate morphology in photoreceptors. Because of the resolution limit in conventional fluorescence microscopy, investigating ribbon protein locations has been challenging, especially in the early development stages of model animals. Here, we used stimulated emission depletion microscopy, a super-resolution imaging technique, to look at retina sections in 4 days post-fertilization (dpf) zebrafish. We observed that in photoreceptor cells, RIBEYE and RIM2 are expressed along the synaptic ribbon, with RIM2 consistently located inside of the horseshoe-shaped synaptic ribbon structure with RIBEYE located on the outside. The L-type calcium channel subunit, CACNA1F, exhibited small spot-like staining beneath the RIM2 and RIBEYE structures. Using morpholino antisense oligonucleotides to knock down RIBEYE expression, we observed fewer and shorter ribbons in the photoreceptor outer plexiform layers of 4 dpf fish retina as well as a reduction in RIM2 expression. The clustering of CACNA1F in these blind fish was no longer observed, but instead showed a diffuse expression in the photoreceptor terminal.

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.

Despite recent advances in hematopoietic tissue research, effects of aging on hematopoietic erythroid precursor (EP) cells are unclear. In this article we present results suggesting that chromatin textural entropy of EP cells in mouse spleen increases with age, while chromatin homogeneity decreases. The experiment was conducted on a total of 32 male Swiss white mice. Spleen tissue was acquired from four age groups: 10 days, 1 month, 4 months, and 7 months old mice. A total of 640 randomly selected, nonoverlapping EP cell nuclei (20 per animal) were analyzed using the gray level co-occurrence matrix method. There was statistically highly significant difference between the age groups, both in chromatin entropy (ANOVA, F = 12.99, p < 0.0001) and in homogeneity (ANOVA, F = 7.05, p < 0.001). When the individual groups were compared (ANOVA post hoc test), statistical difference was detected in all group pairs, except between the animals 4 months and 7 months old, either in chromatin entropy or homogeneity. The detected increase of chromatin disorder in mouse juvenile period/early adulthood suggests that cell intrinsic factors such as epigenetic dysregulation and DNA damage accumulation may have an important role in EP cell aging.

The possibility of scanning electron microscope (SEM) observation and energy dispersive X-ray (EDX) spectrometry analysis in microscale regions of insulating samples using diluted ionic liquid was investigated. It is possible to obtain clear secondary electron images of insulating samples such as a rock and mineral at 5,000 times magnification by dropping 10 μL of 1 wt% of 1-ethyl-3-methylimidazolium acetate (EMI-CH3COO) diluted with ethanol onto the samples. We also obtained EDX spectra of the samples in microscale regions (∼5 μm2) without overlapping EDX spectra of other minerals with different composition. It might be possible to perform quantitative analysis of the samples if a method that does not need standard samples is applied or an X-ray detector sensitive for light elements was attached. The method of dropping 1 wt% EMI-CH3COO diluted with ethanol onto insulating samples is useful for SEM observation, EDX analysis in microscale regions, and the preservation of scarce rock and mineral samples because ionic liquid can be easily removed with acetone.

Heterotermic vertebrates are hosts of a variety of iridoviruses, many with recognized economical importance for aquaculture and with a role in the decline of amphibian populations, and others with no known disease associations. These include members of the Lymphocystisvirus, Magalocystisvirus and Ranavirus genera.

Multislice simulations in the transmission electron microscope (TEM) were used to examine changes in annular-dark-field scanning TEM (ADF-STEM) images, conventional bright-field TEM (BF-CTEM) images, and selected-area electron diffraction (SAED) patterns as atomically thin hexagonal boron nitride (h-BN) samples are tilted up to 500 mrad off of the [0001] zone axis. For monolayer h-BN the contrast of ADF-STEM images and SAED patterns does not change with tilt in this range, while the contrast of BF-CTEM images does change; h-BN multilayer contrast varies strongly with tilt for ADF-STEM imaging, BF-CTEM imaging, and SAED. These results indicate that tilt series analysis in ADF-STEM image mode or SAED mode should permit identification of h-BN monolayers from raw TEM data as well as from quantitative post-processing.

The effects of plasma lipid overload on pancreatic islet function and on mineral imbalance are issues under debate. However, the outcomes may be biased by the different metabolisms of different species. This prospective study evaluated whether a high fat diet intake changed the distribution of physiologically relevant elements within pancreatic endocrine and exocrine tissues of Sprague Dawley rats and New Zealand White rabbits. Nuclear microscopy techniques provided images of the specimen density and structure as well as the elemental distributions and quantification of P, S, Cl, K, Ca, Fe, and Zn using unstained cryosections of pancreas. Our results indicate that pancreatic islets in normal rats and rabbits had lower tissue density and higher Ca, Fe, and Zn content compared to exocrine tissue, and that rabbit islets exhibit the highest Zn content (3,300 μg/g in rabbits versus 510 μg/g in rats). Fat diet intake resulted in large deposits of fat in the pancreas, which modified the density contrast of tissues and also resulted in a twofold decrease of Ca and Zn concentrations in islets of both rats and rabbits. This result indicates that a fat diet leads to a reduction in essential trace element concentrations in pancreas, which in turn may hamper endocrine function.

Microstructural evolution in a CeO2-Gd2O3 system at atomic and nanoscale levels with increasing Gd concentration has been comprehensively investigated by transmission electron microscopy. When the Gd concentration was increased from 10 to 80 at.%, the phase transformation from ceria with fluorite structure to solid solution with C-type structure was not a sudden change but an evolution in the sequence of clusters, domains, and precipitates with C-type structure in the fluorite-structured matrix. Moreover, the ordering of aggregated Gd cations and oxygen vacancies in these microstructural inhomogeneities developed continuously with increasing Gd concentration. This microstructural evolution can be further described based on the development of defect clusters containing Gd cations and oxygen vacancies.

Amoebae graze on bacteria from the environment. In some cases, bacteria acquire resistance to the destructive action of amoebae and survive inside the host. The resistance of microorganisms to amoebae is often accompanied by resistance to the physiologically related human macrophage and displays increased pathogenic potential to humans. The association of bacteria with amoebae, that are ubiquitous in the environment, protects the bacteria from common disinfection measures. This leads to the creation of reservoirs of pathogenic microorganisms that are difficult to eradicate. This process occurs widely in the environment, but is of special concern in hospitals, where many established and emerging pathogens involved in nosocomial disease, such as Legionella pneumophila, are increasingly being identified in association with amoebae. One particularly important amoeba-associated microorganism (AAM) is the newly recognized giant mimivirus, a member of the Nucleo-Cytoplasmic Large Deoxyribovirus (NCLDV) group. The virus has been isolated from hospital sources in France and, together with other members of the NCLDV group, is known from metagenomic studies to be widespread in the Oceans, representing one of the main groups of marine viruses. Our project aims to detect amoeba and potentially pathogenic AAMs with particular relevance to the NCLDVs in the environment and in hospital facilities. In the present work we have developed methods for detection, isolation and in vitro culture of amoebae from several environmental sources including hospital dust, sea water and estuarine sediments.

Electron backscatter diffraction (EBSD) is a powerful technique for surface microstructure analysis. EBSD analysis of cubic yttria-stabilized zirconia (YSZ) is demonstrated. The statistics related to EBSD indexing reliability shows that the probability of accurate grain orientation detection increased significantly when the electron beam energy was increased from 10 to 30 kV. As a result of better sampling with increased interaction volume, a disparity between local and average grain misorientation angle also exhibited the dependence of the electron beam energy to determine the accuracy of grain orientation. To study EBSD indexing reliability as a function of surface roughness and overlayer formation, rapid EBSD measurement tests were performed on (a) YSZ surfaces ion-polished at ion beam energies of 65 nA at 30 kV and 1 nA at 30 kV and (b) carbon-coated versus uncoated YSZ surfaces. The EBSD results at both 10 and 30 kV electron beam energies indicate that EBSD indexing reliability is negatively affected by higher ion beam milling current and amorphous overlayer formation.

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.