High-resolution (or “cross-correlation”) electron backscatter diffraction analysis (HR-EBSD) utilizes cross-correlation techniques to determine relative orientation and distortion of an experimental electron backscatter diffraction pattern with respect to a reference pattern. The integrity of absolute strain and tetragonality measurements of a standard Si/SiGe material have previously been analyzed using reference patterns produced by kinematical simulation. Although the results were promising, the noise levels were significantly higher for kinematically produced patterns, compared with real patterns taken from the Si region of the sample. This paper applies HR-EBSD techniques to analyze lattice distortion in an Si/SiGe sample, using recently developed dynamically simulated patterns. The results are compared with those from experimental and kinematically simulated patterns. Dynamical patterns provide significantly more precision than kinematical patterns. Dynamical patterns also provide better estimates of tetragonality at low levels of distortion relative to the reference pattern; kinematical patterns can perform better at large values of relative tetragonality due to the ability to rapidly generate patterns relating to a distorted lattice. A library of dynamically generated patterns with different lattice parameters might be used to achieve a similar advantage. The convergence of the cross-correlation approach is also assessed for the different reference pattern types.

A number of fluorescence microscopy techniques are described to study dynamics of fluorescently labeled proteins, lipids, nucleic acids, and whole organelles. However, for studies of plant plasma membrane (PM) proteins, the number of these techniques is still limited because of the high complexity of processes that determine the dynamics of PM proteins and the existence of cell wall. Here, we report on the usage of raster image correlation spectroscopy (RICS) for studies of integral PM proteins in suspension-cultured tobacco cells and show its potential in comparison with the more widely used fluorescence recovery after photobleaching method. For RICS, a set of microscopy images is obtained by single-photon confocal laser scanning microscopy (CLSM). Fluorescence fluctuations are subsequently correlated between individual pixels and the information on protein mobility are extracted using a model that considers processes generating the fluctuations such as diffusion and chemical binding reactions. As we show here using an example of two integral PM transporters of the plant hormone auxin, RICS uncovered their distinct short-distance lateral mobility within the PM that is dependent on cytoskeleton and sterol composition of the PM. RICS, which is routinely accessible on modern CLSM instruments, thus represents a valuable approach for studies of dynamics of PM proteins in plants.

Millipedes are ecologically important soil organisms and may also be an economically threatening species in rural and urban areas when population outbreaks occur. In order to control infestations commercial formulations of deltamethrin have been commonly applied, even though there are few studies about the effects of such insecticide on millipedes. This paper describes the effects of this insecticide on millipedes showing neurotoxic effects assessed by synapsin labeling and confocal microscopy. Deltamethrin concentrations related to the DL50 of the active ingredient and a field concentration were applied topically in the diplopod Gymnostreptus olivaceus to evaluate the behavior, mortality rate, and synapsin levels in the brain 12, 24, and 48h after contact with deltamethin. The insecticide caused mortality at the higher concentrations employed, in which no change was observed in neurotransmission in the survivors. In contrast, at field concentrations, deltamethrin did not cause any deaths, but triggered significant changes in synapsin levels. The results obtained form the synapsin labeling provide several interpretations suggesting that the isolated application of this tool must be associated with additional tools in order to evaluate biologically induced effects of deltamethrin in an accurate way. In addition, the feasibility of chemical control of millipedes with deltamethrin is questioned.

A reproducible way to transfer a single crystalline sample into a gas environmental cell holder for in situ transmission electron microscopic (TEM) analysis is shown in this study. As in situ holders have only single-tilt capability, it is necessary to prepare the sample precisely along a specific zone axis. This can be achieved by a very accurate focused ion beam lift-out preparation. We show a step-by-step procedure to prepare the sample and transfer it into the gas environmental cell. The sample material is a GaP/Ga(NAsP)/GaP multi-quantum well structure on Si. Scanning TEM observations prove that it is possible to achieve atomic resolution at very high temperatures in a nitrogen environment of 100,000 Pa.

Electron-excited X-ray microanalysis performed with scanning electron microscopy and energy-dispersive spectrometry (EDS) has been used to measure trace elemental constituents of complex multielement materials, where “trace” refers to constituents present at concentrations below 0.01 (mass fraction). High count spectra measured with silicon drift detector EDS were quantified using the standards/matrix correction protocol embedded in the NIST DTSA-II software engine. Robust quantitative analytical results for trace constituents were obtained from concentrations as low as 0.000500 (mass fraction), even in the presence of significant peak interferences from minor (concentration 0.01≤C≤0.1) and major (C>0.1) constituents. Limits of detection as low as 0.000200 were achieved in the absence of peak interference.

We demonstrate that the second-Stokes output from a diamond Raman laser, pumped by a femtosecond Ti:Sapphire laser, can be used to efficiently excite red-emitting dyes by two-photon excitation at 1,080 nm and beyond. We image HeLa cells expressing red fluorescent protein, as well as dyes such as Texas Red and Mitotracker Red. We demonstrate the potential for simultaneous two-color, two-photon imaging with this laser by using the residual pump beam for excitation of a green-emitting dye. We demonstrate this for the combination of Alexa Fluor 488 and Alexa Fluor 568. Because the Raman laser extends the wavelength range of the Ti:Sapphire laser, resulting in a laser system tunable to 680–1,200 nm, it can be used for two-photon excitation of a large variety and combination of dyes.

The effect of heavy metal in fish has been the focus of extensive research for many years. However, the combined effect of heavy metals and nanomaterials is still a new subject that needs to be studied. The aim of this study was to examine histopathologic alterations in the gills of Nile tilapia (Oreochromis niloticus) to determine possible effects of lead (Pb), carbon nanotubes, and Pb+carbon nanotubes on their histological integrity, and if this biological system can be used as a tool for evaluating water quality in monitoring programs. For this, tilapia were exposed to Pb, carbon nanotubes and Pb+carbon nanotubes for 4 days. The main alterations observed were epithelial structure, hyperplasia and displacement of epithelial cells, and alterations of the structure and occurrence of aneurysms in the secondary lamella. The most severe alterations were related to the Pb+carbon nanotubes. We conclude that the oxidized multi-walled carbon nanotubes enhanced the acute lead toxicity in Nile tilapias. This work draws attention to the implications of carbon nanomaterials released in the aquatic environment and their interaction with classical pollutants.

Characterization of collagen fiber angle distribution throughout the blood vessel wall provides insight into the mechanical behavior of healthy and diseased arteries and their capacity to remodel. Atherosclerotic plaque contributes to the overall mechanical behavior, yet little is known experimentally about how collagen fiber orientation is influenced by atherogenesis. We hypothesized that atherosclerotic lesion development, and the factors contributing to lesion development, leads to a shift in collagen fiber angles within the aorta. Second-harmonic generation microscopy was used to visualize the three-dimensional organization of collagen throughout the aortic wall and to examine structural differences in mice maintained on high-fat Western diet versus age-matched chow diet mice in a model of atherosclerosis. Image analysis was performed on thoracic and abdominal sections of the aorta from each mouse to determine fiber orientation, with the circumferential (0°) and blood flow directions (axial ±90°) as the two reference points. All measurements were used in a multiple regression analysis to determine the factors having a significant influence on mean collagen fiber angle. We found that mean absolute angle of collagen fibers is 43° lower in Western diet mice compared with chow diet mice. Mice on a chow diet have a mean collagen fiber angle of ±63°, whereas mice on a Western diet have a more circumferential fiber orientation (~20°). This apparent shift in absolute angle coincides with the development of extensive aortic atherosclerosis, suggesting that atherosclerotic factors contribute to collagen fiber angle orientation.

The resolution of high-resolution transmission electron microscopes (TEM) has been improved down to subangstrom levels by correcting the spherical aberration (Cs) of the objective lens, and the information limit is thus determined mainly by partial temporal coherence. As a traditional Young’s fringe test does not reveal the true information limit for an ultra-high-resolution electron microscope, new methods to evaluate temporal coherence have been proposed based on a tilted-beam diffractogram. However, the diffractogram analysis cannot be applied when the nonlinear contribution becomes significant. Therefore, we have proposed a method based on the three-dimensional (3D) Fourier transform (FT) of through-focus TEM images, and evaluated the performance of some Cs-corrected TEMs at lower voltages. In this report, we generalize the 3D FT analysis and derive the 3D transmission cross-coefficient. The profound difference of the 3D FT analysis from the diffractogram analysis is its capability to extract linear image information from the image intensity, and further to evaluate two linear image contributions separately on the Ewald sphere envelopes. Therefore, contrary to the diffractogram analysis the 3D FT analysis can work with a strong scattering object. This is the necessary condition if we want to directly observe the linear image transfer down to a few tens of picometer.

Genetically encoded Förster resonance energy transfer (FRET)-based biosensors have been used to report relative concentrations of ions and small molecules, as well as changes in protein conformation, posttranslational modifications, and protein–protein interactions. Changes in FRET are typically quantified through ratiometric analysis of fluorescence intensities. Here we describe methods to evaluate ratiometric imaging data acquired through confocal microscopy of a FRET-based inorganic phosphate biosensor in different cells and subcellular compartments of Arabidopsis thaliana. Linear regression was applied to donor, acceptor, and FRET-derived acceptor fluorescence intensities obtained from images of multiple plants to estimate FRET ratios and associated location-specific spectral correction factors with high precision. FRET/donor ratios provided a combination of high dynamic range and precision for this biosensor when applied to the cytosol of both root and leaf cells, but lower precision when this ratiometric method was applied to chloroplasts. We attribute this effect to quenching of donor fluorescence because high precision was achieved with FRET/acceptor ratios and thus is the preferred ratiometric method for this organelle. A ligand-insensitive biosensor was also used to distinguish nonspecific changes in FRET ratios. These studies provide a useful guide for conducting quantitative ratiometric studies in live plants that is applicable to any FRET-based biosensor.

Cardiovascular disease remains the leading cause of mortality worldwide. Here we suggest a novel approach for tracking atherosclerosis progression based on the use of atomic force microscopy (AFM). Using AFM, we studied cross-sections of coronary arteries with the following types of lesions: Type II—thickened intima; Type III—thickened intima with a lipid streak; Type IV—fibrotic layer over a lipid core; Type Va—unstable fibrotic layer over a lipid core; Type Vc—very thick fibrotic layer. AFM imaging revealed that the fibrotic layer of an atherosclerotic plaque is represented by a basket-weave network of collagen fibers and a subscale network of fibrils that become looser with atherosclerosis progression. In an unstable plaque (Type Va), packing of the collagen fibers and fibrils becomes even less uniform than that at the previous stages, while a stable fibrotic plaque (Vc) has significantly tighter packing. Such alterations of the collagen network morphology apparently, led to deterioration of the Type Va plaque mechanical properties, that, in turn, resulted in its instability and propensity to rupture. Thus, AFM may serve as a useful tool for tracking atherosclerosis progression in the arterial wall tissue.

The aim of the present study was to compare dynamics of the bone healing process after different types of osteotomies. In total, 24 Wistar rats were subjected to different types of osteotomy performed with standard steel bur, piezosurgery, contact, and non-contact Erbium:yttrium-aluminum-garnet (Er:YAG) laser ablation. The animals were randomly divided into four groups, to be euthanized immediately after the procedure, or at 1, 2, or 3 weeks after surgery. The obtained bone samples were analyzed by scanning electron microscopy (SEM). Immediately after surgery, there were significant differences in the appearance of the bone defects, with presence of bone fragments and debris after standard steel bur preparation, compared with the clean smooth walls and relatively sharp edges in all other groups. The initial bone formation in defects prepared by piezosurgery was observed to be the most rapid. After 3 weeks, all bone defects were completely restored; although, differences in the healing pattern were noted, with a modest initial delay in healing after laser preparation. The first stage of the bone healing process was delayed when contact and non-contact Er:YAG laser modes were used and accelerated by piezosurgery; however, the results after 3 weeks demonstrated similar restitution of defects in all tested groups.

Acquiring an atomic-resolution compositional map of crystalline specimens has become routine practice, thus opening possibilities for extracting subatomic information from such maps. A key challenge for achieving subatomic precision is the improvement of signal-to-noise ratio (SNR) of compositional maps. Here, we report a simple and reliable solution for achieving high-SNR energy-dispersive X-ray (EDX) spectroscopy spectrum images for individual atomic columns. The method is based on standard cross-correlation aided by averaging of single-column EDX maps with modifications in the reference image. It produces EDX maps with minimal specimen drift, beam drift, and scan distortions. Step-by-step procedures to determine a self-consistent reference map with a discussion on the reliability, stability, and limitations of the method are presented here.

Three-dimensional (3D) nondestructive microstructural characterization was performed using full-field transmission X-ray microscopy on an Sn-rich alloy, at a spatial resolution of 60 nm. This study highlights the use of synchrotron radiation along with Fresnel zone plate optics to perform absorption contrast tomography for analyzing nanoscale features of fine second phase particles distributed in the tin matrix, which are representative of the bulk microstructure. The 3D reconstruction was also used to quantify microstructural details of the analyzed volume.