The skeletal muscle extracellular matrix (ECM) supports muscle’s passive mechanical function and provides a unique environment for extracellular tissues such as nerves, blood vessels, and a cadre of mononuclear cells. Within muscle ECM, collagen is thought to be the primary load-bearing protein, yet its structure and organization with respect to muscle fibers, tendon, and mononuclear cells is unknown. Detailed examination of extracellular collagen morphology requires high-resolution electron microscopy performed over relatively long distances because multinucleated muscle cells are very long and extend from several millimeters to several centimeters. Unfortunately, there is no tool currently available for high resolution ECM analysis that extends over such distances relevant to muscle fibers. Serial block face scanning electron microscopy is reported here to examine skeletal muscle ECM ultrastructure over hundreds of microns. Ruthenium red staining was implemented to enhance contrast and utilization of variable pressure imaging reduced electron charging artifacts, allowing continuous imaging over a large ECM volume. This approach revealed previously unappreciated perimysial collagen structures that were reconstructed via both manual and semi-automated segmentation methods. Perimysial collagen structures in the ECM may provide a target for clinical therapies aimed at reducing skeletal muscle fibrosis and stiffness.

One of the few conclusions known about chromosome structure is that Mg2+ is required for the organization of chromosomes. Scanning electron microscopy is a powerful tool for studying chromosome morphology, but being nonconductive, chromosomes require metal/carbon coating that may conceal information about the detailed surface structure of the sample. Helium ion microscopy (HIM), which has recently been developed, does not require sample coating due to its charge compensation system. Here we investigated the structure of isolated human chromosomes under different Mg2+ concentrations by HIM. High-contrast and resolution images from uncoated samples obtained by HIM enabled investigation on the effects of Mg2+ on chromosome structure. Chromatin fiber information was obtained more clearly with uncoated than coated chromosomes. Our results suggest that both overall features and detailed structure of chromatin are significantly affected by different Mg2+ concentrations. Chromosomes were more condensed and a globular structure of chromatin with 30 nm diameter was visualized with 5 mM Mg2+ treatment, while 0 mM Mg2+ resulted in a less compact and more fibrous structure 11 nm in diameter. We conclude that HIM is a powerful tool for investigating chromosomes and other biological samples without requiring metal/carbon coating.

Operando transmission electron microscopy (TEM) of catalytic reactions requires that the gas composition inside the TEM be known during the in situ reaction. Two techniques for measuring gas composition inside the environmental TEM are described and compared here. First, electron energy-loss spectroscopy, both in the low-loss and core-loss regions of the spectrum was utilized. The data were quantified using a linear combination of reference spectra from individual gasses to fit a mixture spectrum. Mass spectrometry using a residual gas analyzer was also used to quantify the gas inside the environmental cell. Both electron energy-loss spectroscopy and residual gas analysis were applied simultaneously to a known 50/50 mixture of CO and CO2, so the results from the two techniques could be compared and evaluated. An operando TEM experiment was performed using a Ru catalyst supported on silica spheres and loaded into the TEM on a specially developed porous pellet TEM sample. Both techniques were used to monitor the conversion of CO to CO2 over the catalyst, while simultaneous atomic resolution imaging of the catalyst was performed.

Mycotoxins, such as aflatoxin (AF), fumonisin B1, zearalenone (ZEA), and deoxynivalenol (DON), are commonly found in many food commodities. Mycotoxins have been shown to increase DNA methylation levels in a human intestinal cell line. We previously showed that the developmental competence of oocytes was affected in mice that had been fed a mycotoxin-containing diet. In this study, we explored possible mechanisms of low mouse oocyte developmental competence after mycotoxin treatment in an epigenetic modification perspective. Mycotoxin-contaminated maize (DON at 3,875 μg/kg, ZEA at 1,897 μg/kg, and AF at 806 μg/kg) was included in diets at three different doses (mass percentage: 0, 15, and 30%) and fed to mice for 4 weeks. The fluorescence intensity analysis showed that the general DNA methylation levels increased in oocytes from high dose mycotoxin-fed mice. Mouse oocyte histone methylation was also altered. H3K9me3 and H4K20me3 level increased in oocytes from mycotoxin-fed mice, whereas H3K27me3 and H4K20me2 level decreased in oocytes from mycotoxin-fed mice. Thus, our results indicate that naturally occurring mycotoxins have effects on epigenetic modifications in mouse oocytes, which may be one of the reasons for reduced oocyte developmental competence.

In this paper we investigate methods to characterize angular current density from atomically defined gas field ion sources. We show that the ion beam emitted from a single apex atom is described by a two-dimensional Gaussian profile. Owing to the Gaussian shape of the beam and the requirement to collect the majority of the ion current, fixed apertures have inhomogeneous illumination. Therefore, angular current density measurements through a fixed aperture record averaged angular current density. This makes comparison of data difficult as averaged angular current density depends on aperture size. For the same reasons, voltage normalization cannot be performed for fixed aperture measurements except for aperture sizes that are infinitely small. Consistent determination of angular current density and voltage normalization, however, can be achieved if the beam diameter as well as total ion current are known. In cases where beam profile cannot be directly imaged with a field ion microscope, the beam profile could be extracted from measurements taken at multiple acceleration voltages and/or with multiple aperture sizes.

Natural organic matter (NOM) generically refers to organic substances found in soils, waters, and sediments. It is the brown-to-black, heterogeneous organic material produced through the diagenetic alteration of plant tissue and microbial biomass via a myriad of biotic and abiotic reactions. Since NOM is the primary source of organic carbon in the earth’s surficial environment, understanding the processes by which NOM is produced is integral to understanding carbon sequestration, contaminant fate and transport, and other earth surface processes. NOM samples (HA0) consist of nonamphiphilic (HA1), lipid-like (L0 and L1), and strongly amphiphilic (HA2) components. Here we present the structure and morphology of self-assembled NOM components based on scanning electron microscopy (SEM), atomic force microscopy (AFM), and electrostatic force microscopy (EFM) characterizations. Effects of surface charge and hydrophobicity/hydrophilicity of the amphiphile on the interaction and resulting structures were investigated using SEM, AFM, and EFM. Data shows that the component’s amphiphilic nature plays a key role in the formation of NOM. SEM data show that aggregates form while AFM/EFM analysis verifies the existence of hydrophobic/hydrophilic moieties in different fractions of HA0. Subsequently, the amphiphilic nature of HA2 will have a substantial effect on interfacial interactions and subsequent self-assembly of HA0’s components.

Mechanical properties are vital for living cells, and various models have been developed to study the mechanical behavior of cells. However, there is debate regarding whether a cell behaves more similarly to a “cortical shell – liquid core” structure (membrane-like) or a homogeneous solid (cytoskeleton-like) when experiencing stress by mechanical forces. Unlike most experimental methods, which concern the small-strain deformation of a cell, we focused on the mechanical behavior of a cell undergoing small to large strain by conducting microinjection experiments on zebrafish embryo cells. The power law with order of 1.5 between the injection force and the injection distance indicates that the cell behaves as a homogenous solid at small-strain deformation. The linear relation between the rupture force and the microinjector radius suggests that the embryo behaves as membrane-like when subjected to large-strain deformation. We also discuss the possible reasons causing the debate by analyzing the mechanical properties of F-actin filaments.

In this work we study the interfaces between the Mott insulator LaMnO3 (LMO) and the band insulator SrTiO3 (STO) in epitaxially grown superlattices with different thickness ratios and different transport and magnetic behaviors. Using atomic resolution electron energy-loss spectral imaging, we analyze simultaneously the structural and chemical properties of these interfaces. We find changes in the oxygen octahedral tilts within the LaMnO3 layers when the thickness ratio between the manganite and the titanate layers is varied. Superlattices with thick LMO and ultrathin STO layers present unexpected octahedral tilts in the STO, along with a small amount of oxygen vacancies. On the other hand, thick STO layers exhibit undistorted octahedra while the LMO layers present reduced O octahedral distortions near the interfaces. These findings are discussed in view of the transport and magnetic differences found in previous studies.

The size of gold nanoparticles (AuNPs) can influence various aspects of their cellular uptake. Light microscopy is not capable of resolving most AuNPs, while electron microscopy (EM) is not practically capable of acquiring the necessary statistical data from many cells and the results may suffer from various artifacts. Here, we demonstrate the use of a fast EM method for obtaining high-resolution data from a much larger population of cells than is usually feasible with conventional EM. A549 (human lung carcinoma) cells were subjected to uptake protocols with 10, 15, or 30 nm diameter AuNPs with adsorbed serum proteins. After 20 min, 24 h, or 45 h, the cells were fixed and imaged in whole in a thin layer of liquid water with environmental scanning electron microscopy equipped with a scanning transmission electron microscopy detector. The fast preparation and imaging of 145 whole cells in liquid allowed collection of nanoscale data within an exceptionally small amount of time of ~80 h. Analysis of 1,041 AuNP-filled vesicles showed that the long-term AuNP storing lysosomes increased their average size by 80 nm when AuNPs with 30 nm diameter were uptaken, compared to lysosomes of cells incubated with AuNPs of 10 and 15 nm diameter.

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.

This study examines histometrical changes induced by sodium arsenite (SA), as an environmental pollutant, and investigates the protective effect of α-tocopherol on ovaries of SA-treated rats during the prenatal stage until sexual maturity. Rats were classified into groups: control, SA (8 ppm/day), α-tocopherol (100 ppm/day), and SA+α-tocopherol. Treatment was performed from pregnancy until maturation when the rats and ovaries were weighed. The Cavalieri method was used to estimate volume of the ovaries, cortex, medulla, and corpus luteum. The mean diameter of oocytes, granulosa cells, and nuclei were measured and volume was estimated using the Nucleator method. The number of oocytes and thickness of the zona pellucida (ZP) were determined using an optical dissector and orthogonal intercept method, respectively. SA reduced the body and ovary weight, the number of secondary, antral and Graafian oocytes, volume of the ovaries, cortex, medulla and corpus luteum, mean diameter and volume of oocytes in primordial and primary follicles, mean diameter and volume of oocyte nuclei in all types of follicles, and mean thickness of the ZP in secondary and antral follicles. Also, the mean diameter and volume of granulosa cells and their nuclei in antral and Graafian follicles decreased significantly. Vacuolization and vascular congestion in the corpus luteum and an increase in the number of atretic oocytes were seen in the SA group. Most of these parameters were unchanged from the control level in the SA+α-tocopherol group. It was concluded that α-tocopherol supplementation reduced the toxic effects of SA exposure on ovarian tissue in rats.

We demonstrate the combined use of large area depth-profiling dislocation imaging and quantitative composition and strain measurement for a strained Si/SiGe/Si sample based on nondestructive techniques of electron beam-induced current (EBIC) and X-ray diffraction reciprocal space mapping (XRD RSM). Depth and improved spatial resolution is achieved for dislocation imaging in EBIC by using different electron beam energies at a low temperature of ~7 K. Images recorded clearly show dislocations distributed in three regions of the sample: deep dislocation networks concentrated in the “strained” SiGe region, shallow misfit dislocations at the top Si/SiGe interface, and threading dislocations connecting the two regions. Dislocation densities at the top of the sample can be measured directly from the EBIC results. XRD RSM reveals separated peaks, allowing a quantitative measurement of composition and strain corresponding to different layers of different composition ratios. High-resolution scanning transmission electron microscopy cross-section analysis clearly shows the individual composition layers and the dislocation lines in the layers, which supports the EBIC and XRD RSM results.

We propose a practical method of producing a single mode electron vortex beam suitable for use in a scanning transmission electron microscope (STEM). The method involves using a holographic “fork” aperture to produce a row of beams of different orbital angular momenta, as is now well established, magnifying the row so that neighboring beams are separated by about 1 µm, selecting the desired beam with a narrow slit, and demagnifying the selected beam down to 1–2 Å in size. We show that the method can be implemented by adding two condenser lenses plus a selection slit to a straight-column cold-field emission STEM. It can also be carried out in an existing instrument, the monochromated Nion high-energy-resolution monochromated electron energy-loss spectroscopy-STEM, by using its monochromator in a novel way. We estimate that atom-sized vortex beams with ≥20 pA of current should be attainable at 100–200 keV in either instrument.

Antibiotic resistance is a major risk to human health, and to provide valuable insights into mechanisms of resistance, innovative methods are needed to examine the cellular responses to antibiotic treatment. Focused ion beam tomography is proposed to image and assess the detailed three-dimensional (3D) ultrastructure of single bacterial cells. By iteratively removing slices of thickness in the order of 10 nm, high magnification 2D images can be acquired by scanning electron microscopy at single-digit nanometer resolution. In this study, Klebsiella pneumoniae was treated with polymyxin B, and 3D models of both cell envelope and cytoplasm regions containing the nucleoid and ribosomes were reconstructed. The 3D volume containing the nucleoid and ribosomes was significantly smaller, and the cell length along the longitudinal axis was extended by 40% in the treated cells, implying stress responses to the drug treatment. More than a 200% increase in protrusions per unit surface area on the cell envelope was observed in the curvature analysis after treatment. Experiments by conventional transmission electron microscopy and atomic force microscopy were also performed, followed by comparison and discussions. In conclusion, the proposed 3D imaging method and associated analysis provide a unique tool for the assessment of antibiotic effects on multidrug-resistant bacteria at nanometer resolution.

The directional dark-field signal obtained with X-ray grating interferometry yields direction-dependent information about the X-ray scattering taking place inside the examined sample. It allows examination of its morphology without the requirement of resolving the micrometer size structures directly causing the scattering. The local morphology in turn gives rise to macroscopic mechanical properties of the investigated specimen. In this study, we investigate the relation between the biomechanical elasticity (Young’s modulus) and the measured directional dark-field parameters of a well-defined sample made of wood. In our proof-of-principle experiment, we found a correlation between Young’s modulus, the average dark-field signal, and the average dark-field anisotropy. Hence, we are able to show that directional dark-field imaging is a new method to predict mechanical sample properties. As grating interferometry provides absorption, phase-contrast, and dark-field data at the same time, this technique appears promising to combine imaging and mechanical testing in a single testing stage. Therefore, we believe that directional dark-field imaging will have a large impact in the materials science world.