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

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 2005 in Honolulu, Hawaii, USA, July 31--August 4, 2005

Male, wild-type, FVB strain mice were fed a nutritionally complete liquid diet supplemented with 4% ethanol v/v over a time course of 1, 2, 4, 8, 12, and 14 weeks. Controls were offered an isocaloric liquid equivalent and pair fed with their ethanol counterparts. Changes in cardiac physiology were assessed at respective time points via echocardiography. Additionally, the use of histological techniques, mRNA analysis, apoptosis determination, and immunohistochemistry were employed to determine the functional and structural changes on the heart. Echocardiograph analysis revealed a compensatory phase that occurred early in the time course (1–8 weeks) and decompensation reverting toward heart failure at weeks 12 and 14. Throughout the study, an increase in cardiomyocyte hypertrophy, cardiac fibrosis, apoptosis, TGF-β, and the presence of α-SMA-positive cells were determined. A compensatory period in mice treated with ethanol occurred early followed by a transition to a dilated phenotype over time. A number of factors may be involved in this process including the activation of myofibroblasts and their fibrotic activities that is correlated with the presence of transforming growth factor beta.

The introduction of gases, such as water vapor, into an environmental scanning electron microscope is common practice to assist in the imaging of insulating or biological materials. However, this capability may also be exploited to introduce, or form, liquid phase precursors for electron-beam-induced deposition. In this work, the authors report the deposition of silver (Ag) and copper (Cu) structures using two different cell-less in situ deposition methods—the first involving the in situ hydration of solid precursors and the second involving the insertion of liquid droplets using a capillary style liquid injection system. Critically, the inclusion of surfactants is shown to drastically improve pattern replication without diminishing the purity of the metal deposits. Surfactants are estimated to reduce the droplet contact angle to below ~10°.

Tomography is a standard and invaluable technique that covers a large range of length scales. It gives access to the inner morphology of specimens and to the three-dimensional (3D) distribution of physical quantities such as elemental composition, crystalline phases, oxidation state, or strain. These data are necessary to determine the effective properties of investigated heterogeneous media. However, each tomographic technique relies on severe sampling conditions and physical principles that require the sample to be adequately shaped. For that purpose, a wide range of sample preparation techniques is used, including mechanical machining, polishing, sawing, ion milling, or chemical techniques. Here, we focus on the basics of tomography that justify such advanced sample preparation, before reviewing and illustrating the main techniques. Performances and limits are highlighted, and we identify the best preparation technique for a particular tomographic scale and application. The targeted tomography techniques include hard X-ray micro- and nanotomography, electron nanotomography, and atom probe tomography. The article mainly focuses on hard condensed matter, including porous materials, alloys, and microelectronics applications, but also includes, to a lesser extent, biological considerations.

With the purpose of enhancing the efficacy of microparticle-encapsulated therapeutic agents, in this study we evaluated the phagocytic ability of rat peritoneal exudate cells and the preferential location of poly(d,l-lactide-co-glycolic acid) (PLGA) microparticles inside these cells. The microparticles used were produced by a solvent evaporation method and were characterized by dynamic light scattering (DLS), transmission electron microscopy (TEM), and scanning electron microscopy (SEM). Size distribution analysis using DLS and SEM showed that the particles were spherical, with diameters falling between 0.5 and 1.5 μm. Results from cell adhesion by SEM assay, indicated that the PLGA microparticles are not toxic to cells and do not cause any distinct damage to them as confirmed by the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay. Among the large variety of cell populations found in the peritoneal exudates (neutrophils, eosinophils, monocytes, and macrophages), TEM showed that only the latter phagocytosed PLGA microparticles, in a time-dependent manner. The results obtained indicate that the microparticles studied show merits as possible carriers of drugs for intracellular delivery.

Adeno-associated virus (AAV) is a defective, nonpathogenic human parvovirus, which coinfects with a helper adenovirus or herpes virus. AAV's unique characteristics have made it an appealing vector system for gene delivery. AAV or recombinant AAV (rAAV) has been widely detected using negative stain transmission electron microscopy (TEM) but little has been detected using atomic force microscopy (AFM). In this article, we used AFM and TEM to observe the recombinant AAV-2 (rAAV-2) virus particles and applied statistical analysis to the AFM and TEM images. The results indicated that the rAAV-2 particle was a slightly elliptic particle close to round when it was detected by TEM (the mean length of major and minor axes of rAAV-2 particles was 24.77 ± 1.78 nm and 21.84 ± 1.57 nm, respectively), whereas when detected by AFM, the rAAV-2 particle was almost round. Even though the dimensions of the rAAV-2 particle exhibited a polymorphous distribution via off-line particle analysis of AFM, most of the rAAV-2 particles had a mean diameter of approximate 22.04 nm, which was similar to the results obtained by TEM. The results above suggested that AFM was important for accurately determining the average dimensions and distributions of virus particles.

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.

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

This work presents a systematic study that evaluates the feasibility and reliability of local band gap measurements of Cu(In,Ga)Se2 thin films by valence electron energy-loss spectroscopy (VEELS). The compositional gradients across the Cu(In,Ga)Se2 layer cause variations in the band gap energy, which are experimentally determined using a monochromated scanning transmission electron microscope (STEM). The results reveal the expected band gap variation across the Cu(In,Ga)Se2 layer and therefore confirm the feasibility of local band gap measurements of Cu(In,Ga)Se2 by VEELS. The precision and accuracy of the results are discussed based on the analysis of individual error sources, which leads to the conclusion that the precision of our measurements is most limited by the acquisition reproducibility, if the signal-to-noise ratio of the spectrum is high enough. Furthermore, we simulate the impact of radiation losses on the measured band gap value and propose a thickness-dependent correction. In future work, localized band gap variations will be measured on a more localized length scale to investigate, e.g., the influence of chemical inhomogeneities and dopant accumulations at grain boundaries.

This paper presents new developments on the provenance study of lapis lazuli started by our group in 2008: during the years a multi-technique approach has been exploited to obtain minero-petrographic characterization and creation of a database considering only rock samples of known provenance. Since the final aim of the study is to develop a method to analyze archeological findings and artworks made with lapis lazuli in a completely non-invasive way, ion beam analysis techniques were employed to trace the provenance of the raw material used for the production of artifacts. Continuing this goal and focusing the analysis on determination of more significant minero-chemical markers for the provenance study of trace elements in different minerals, the method was extended with the use of micro X-ray fluorescence (µ-XRF), to test the potential of the technique for this application. The analyzes were focused on diopside and pyrite in lapis lazuli samples of known provenance (Afghanistan, Tajikistan, and Siberia). In addition, µ-XRF data were compared with micro proton-induced X-ray emission (µ-PIXE) results to verify the agreement between the two databases and to compare the analytical performance of both techniques for this application.

Chemical nano-tomography of microbial cells in their natural, hydrated state provides direct evidence of metabolic and chemical processes. Cells of the nitrate-reducing Acidovorax sp. strain BoFeN1 were cultured in the presence of ferrous iron. Bacterial reduction of nitrate causes precipitation of Fe(III)-(oxyhydr)oxides in the periplasm and in direct vicinity of the cells. Nanoliter aliquots of cell-suspension were injected into custom-designed sample holders wherein polyimide membranes collapse around the cells by capillary forces. The immobilized, hydrated cells were analyzed by synchrotron-based scanning transmission X-ray microscopy in combination with angle-scan tomography. This approach provides three-dimensional (3D) maps of the chemical species in the sample by employing their intrinsic near-edge X-ray absorption properties. The cells were scanned through the focus of a monochromatic soft X-ray beam at different, chemically specific X-ray energies to acquire projection images of their corresponding X-ray absorbance. Based on these images, chemical composition maps were then calculated. Acquiring projections at different tilt angles allowed for 3D reconstruction of the chemical composition. Our approach allows for 3D chemical mapping of hydrated samples and thus provides direct evidence for the localization of metabolic and chemical processes in situ.

Three different bioactive materials suitable as dentine substitutes in tooth repair have been studied: glass-ionomer cement, particulate bioglass, and calcium-silicate cement. On 15 permanent human molars, Class V cavities were prepared and the bottom of each cavity was de-mineralized by an artificial caries gel. After the de-mineralization, the teeth were restored with: (1) Bioglass®45S5 and ChemFil® Superior; (2) Biodentine™ and ChemFil® Superior; and (3) ChemFil® Superior for a complete repair. The teeth were stored for 6 weeks in artificial saliva, then cut in half along the longitudinal axis: the first half was imaged in a scanning electron microscope (SEM) and the other half was embedded in resin and analyzed by SEM using energy-dispersive X-ray analysis. The glass-ionomer and the bioglass underwent ion exchange with the surrounding tooth tissue, confirming their bioactivity. However, the particle size of the bioglass meant that cavity adaptation was poor. It is concluded that smaller particle size bioglasses may give more acceptable results. In contrast, both the glass-ionomer and the calcium-silicate cements performed well as dentine substitutes. The glass-ionomer showed ion exchange properties, whereas the calcium silicate gave an excellent seal resulting from its micromechanical attachment.

A detailed microstructural evaluation was executed on the crystallographic texture as well as the mechanisms for nucleation, phase transformation, and grain growth in a Al0.7CoCrFeNi high-entropy alloy. The microstructure and crystallographic orientations were characterized by electron backscatter diffraction, and the chemical composition variations by energy-dispersive X-ray spectroscopy. The cast Al0.7CoCrFeNi alloy started in the BCC phase and partially transformed into the FCC phase. It was found that the Pitsch orientation relationship (OR) dominates the nucleation mechanism of the FCC phase; however, deviations with respect to the Pitsch OR are observed and are attributed to the differently sized atoms forming an ordered B2 phase in the alloy causing lattice distortions. The dual phase BCC–FCC microstructure contains FCC Widmanstätten plates oriented parallel to the {110}BCC planes of the parent grain. It was found that the crystal orientation distribution after the BCC–FCC phase transformation is confined and is explained as a product of the governing mechanisms.

The days of being able to ascertain instrument performance by simply peering through the eye pieces at a specimen are gone. However, users and granting agencies need to be confident that data collected on these instruments is uniform and quantifiable both over time and between instruments. Ideally, a LASER should not fluctuate, illumination should be completely uniform, and colors should be perfectly aligned. To check the current performance of imaging equipment, we conducted a worldwide research study utilizing three image-based tests: long-/short-term illumination stability, co-registration of signals across various wavelengths, and field illumination uniformity. To differentiate between “acceptable” and “unacceptable” performance, the deviation in illumination power could not exceed 10% (long term) or 3% (short term), the difference in the center-of-mass of imaged multicolored beads could not exceed >1 pixel between different wavelengths, and field illumination values could not exceed 10% (horizontal) or 20% (diagonal) deviation. This study established the current state of microscope performance through simple, efficient, and robust tests, while defining relative standards to assist cores in maintaining their instruments in optimal operating conditions. We developed cross-platform performance standards that will improve the validity of quantitative measurements made using various light microscopes.

This article reports on the use of high pressure freezing followed by freeze substitution (HPF/FS) to study ultrastructural details of host–pathogen interactions in fungal diseases of plants. The specific host–pathogen systems discussed here include a powdery mildew infection of poinsettia and rust infections of daylily and Indian strawberry. The three pathogens considered here all attack the leaves of their hosts and produce specialized hyphal branches known as haustoria that invade individual host cells without killing them. We found that HPF/FS provided excellent preservation of both haustoria and host cells for all three host–pathogen systems. Preservation of fungal and host cell membranes was particularly good and greatly facilitated the detailed study of host–pathogen interfaces. In some instances, HPF/FS provided information that was not available in samples prepared for study using conventional chemical fixation. On the other hand, we did encounter various problems associated with the use of HPF/FS. Examples included freeze damage of samples, inconsistency of fixation in different samples, separation of plant cell cytoplasm from cell walls, breakage of cell walls and membranes, and splitting of thin sections. However, we believe that the outstanding preservation of ultrastructural details afforded by HPF/FS significantly outweighs these problems and we highly recommend the use of this fixation protocol for future studies of fungal host-plant interactions.

The oxidation state of iron oxide nanoparticles co-generated with soot during a combustion process was studied using electron energy-loss spectroscopy (EELS). Spatially resolved EELS spectra in the scanning transmission electron microscopy mode were collected to detect changes in the oxidation state between the cores and surfaces of the particles. Quantification of the intensity ratio of the white lines of the iron L-ionization edge was used to measure the iron oxidation state. Quantitative results obtained from Pearson's method, which can be directly compared with the literature data, indicated that the L3 /L2-intensity ratio for these particles changes from 5.5 ± 0.3 in the particles' cores to 4.4 ± 0.3 at their surfaces. This change can be directly related to the reduction of the iron oxidation state at the surface of the particles. Experimental results indicate that the cores of the particles are composed of γ-Fe2O3, which seems to be reduced to FeO at their surfaces. These results were also supported by the fine structure of the oxygen K-edge and by the significant chemical shift of the iron L-edge.

A microcompressor is a precision mechanical device that flattens and immobilizes living cells and small organisms for optical microscopy, allowing enhanced visualization of sub-cellular structures and organelles. We have developed an easily fabricated device, which can be equipped with microfluidics, permitting the addition of media or chemicals during observation. This device can be used on both upright and inverted microscopes. The apparatus permits micrometer precision flattening for nondestructive immobilization of specimens as small as a bacterium, while also accommodating larger specimens, such as Caenorhabditis elegans, for long-term observations. The compressor mount is removable and allows easy specimen addition and recovery for later observation. Several customized specimen beds can be incorporated into the base. To demonstrate the capabilities of the device, we have imaged numerous cellular events in several protozoan species, in yeast cells, and in Drosophila melanogaster embryos. We have been able to document previously unreported events, and also perform photobleaching experiments, in conjugating Tetrahymena thermophila.