The present review is based on results of several years of investigation on the pathogenesis of plant wilt diseases using for one of the main aspects, several labeling techniques at the ultrastructural level: autoradiography with 3H-thymidine; gold-tagged lectins, enzymes, polyclonal, and monoclonal antibodies. Thus, opaque matter (OM), labeling for DNA with the appropriate markers, can be abundant in and associated with host tissue reactions and pronounced alterations (particularly in newly differentiated xylem). The presence of structures (called P-elements) in OM, paralleled by a similar occurrence in nuclei of both the host and pathogen cells, is considered as being also indicative of a cytoplasmic nature for this OM and most likely originating from fungal elements.

A simple parameterization is presented for the elastic electron scattering cross sections from single atoms into the annular dark-field (ADF) detector of a scanning transmission electron microscope (STEM). The dependence on atomic number, Z, and inner reciprocal radius of the annular detector, q0, of the cross section σ(Z,q0) is expressed by the empirical relation

where A(q0) is the cross section for hydrogen (Z = 1), and the detector is assumed to have a large outer reciprocal radius. Using electron elastic scattering factors determined from relativistic Hartree-Fock simulations of the atomic electron charge density, values of the exponent n(Z,q0) are tabulated as a function of Z and q0, for STEM probe sizes of 1.0 and 2.0 Å.

Comparison with recently published experimental data for single-atom scattering [Krivanek et al. (2010). Nature464, 571–574] suggests that experimentally measured exponent values are systematically lower than the values predicted for elastic scattering from low-Z atoms. It is proposed that this discrepancy arises from the inelastic scattering contribution to the ADF signal. A simple expression is proposed that corrects the exponent n(Z,q0) for inelastic scattering into the annular detector.

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

Arguably one of the most significant microscopy techniques of the past decade, electron backscatter diffraction (EBSD) has provided scientists and engineers with tremendous insight into the structure of crystalline materials. What started with basic observations of electron diffraction in the middle of the 20th century has grown into a mature technology that bridges the gap between the macro and micro length scales. EBSD has found a home in both the materials science and geological communities characterizing crystallographic texture and preferred orientations, residual strain, grain boundary character and networks, and identifying constituent phases. Advancements in computational power, camera technology, indexing algorithms, sample preparation, and dynamical simulations have made this possible.

The following seven papers in this section are from the 9th Region Workshop of the European Microbeam Analysis Society (EMAS) on Electron Probe Analysis of Materials Today—Practical Aspects that took place April 25–28, 2010 in Amsterdam, The Netherlands. The meeting was organized in collaboration with the Netherlands Institute for Cultural Heritage (ICN).

The benefits of using kinetic-energy information to aid ion discrimination in atom probe tomography (APT) are explored. Ion peak interferences in time-of-flight (TOF) mass spectra are categorized by difficulty of discrimination using TOF and kinetic-energy information. Several of these categories, which are intractable interferences when only TOF information is available, may be discriminated when kinetic-energy information also is available. Furthermore, many opportunities for removing noise from composition determinations and three-dimensional images are enabled. Modest kinetic-energy resolving powers (KRPs) of 10 or so should be sufficient to have a major impact on APT. With KRP of about 100, the energy deficits in voltage pulsing may be resolved to enable peak discrimination in straight-flight-path instruments. Real examples and simulated mass spectra are used to illustrate the benefits of kinetic-energy discrimination. Many of the conclusions are applicable generally in TOF spectroscopy. Current detectors do not provide the kinetic energy of incoming ions, but there are realistic prospects for building such detectors and these are discussed. A program to develop these detectors should be pursued.

The prospect of utilizing stem cells for clinical applications has generated an enormous amount of enthusiasm in the stem cell research community and has led to a wealth of new data that offer the possibility for practical applications into clinical translation. Recent advances in stem cell imaging has contributed greatly to the ultimate goal to identify and culture specific cell types for regeneration of tissue that had been affected by disease such as Parkinson's, Alzheimer's, heart disease, muscle diseases, and others.

Two cultural heritage objects studied with scanning electron microscopy–energy dispersive spectroscopy (EDS) are presented in this article: (1) archeological iron present in a soil sample and (2) a chip from a purple-colored area of an undisclosed 17th century painting. Novel PARC software was used to interpret the data in terms of quantitative distribution of mineral and organo-mineral phases as well as their chemical composition. The study serves to demonstrate the power of PARC rather than solving specific archeological issues. The observations on archeological iron potentially can assist in (1) studing the source of iron-metal and the style of forging, (2) learning about alteration processes of artifacts in the particular soil from which the sample originated, and (3) determining the nature of the fractures in the Fe-oxide envelope (desiccation of the sample after excavation, or as primary feature caused by volume change from oxidation). In the paint chip, 11 consecutive layers can be distinguished using the PARC software. In general, each layer consists of a carrier supporting inorganic fragments. In the basal layer the fragments are dominant; in the superimposed layers the carrier usually is. Both organic and inorganic carriers appear to be present. Organic carriers can contain typically inorganic constituents (e.g., Pb, Al), beyond the chemical spatial resolution of EDS (i.e., <1 μm).

Fiber alignment plays a critical role in the structure and function of cells and tissues. While fiber alignment quantification is important to experimental analysis and several different methods for quantifying fiber alignment exist, many studies focus on qualitative rather than quantitative analysis perhaps due to the complexity of current fiber alignment methods. Speed and sensitivity were compared in edge detection and fast Fourier transform (FFT) for measuring actin fiber alignment in cells exposed to shear stress. While edge detection using matrix multiplication was consistently more sensitive than FFT, image processing time was significantly longer. However, when MATLAB functions were used to implement edge detection, MATLAB's efficient element-by-element calculations and fast filtering techniques reduced computation cost 100 times compared to the matrix multiplication edge detection method. The new computation time was comparable to the FFT method, and MATLAB edge detection produced well-distributed fiber angle distributions that statistically distinguished aligned and unaligned fibers in half as many sample images. When the FFT sensitivity was improved by dividing images into smaller subsections, processing time grew larger than the time required for MATLAB edge detection. Implementation of edge detection in MATLAB is simpler, faster, and more sensitive than FFT for fiber alignment quantification.

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

The grain size statistics, commonly derived from the grain map of a material sample, are important microstructure characteristics that greatly influence its properties. The grain map for nanomaterials is usually obtained manually by visual inspection of the transmission electron microscope (TEM) micrographs because automated methods do not perform satisfactorily. While the visual inspection method provides reliable results, it is a labor intensive process and is often prone to human errors. In this article, an automated grain mapping method is developed using TEM diffraction patterns. The presented method uses wide angle convergent beam diffraction in the TEM. The automated technique was applied on a platinum thin film sample to obtain the grain map and subsequently derive grain size statistics from it. The grain size statistics obtained with the automated method were found in good agreement with the visual inspection method.

Since the automation of the electron backscatter diffraction (EBSD) technique, EBSD systems have become commonplace in microscopy facilities within materials science and geology research laboratories around the world. The acceptance of the technique is primarily due to the capability of EBSD to aid the research scientist in understanding the crystallographic aspects of microstructure. There has been considerable interest in using EBSD to quantify strain at the submicron scale. To apply EBSD to the characterization of strain, it is important to understand what is practically possible and the underlying assumptions and limitations. This work reviews the current state of technology in terms of strain analysis using EBSD. First, the effects of both elastic and plastic strain on individual EBSD patterns will be considered. Second, the use of EBSD maps for characterizing plastic strain will be explored. Both the potential of the technique and its limitations will be discussed along with the sensitivity of various calculation and mapping parameters.

Pluripotent cells are unique because of their ability to differentiate into the cell lineages forming the entire organism. True pluripotent stem cells with germ line contribution have been reported for mice and rats. Human pluripotent cells share numerous features of pluripotentiality, but confirmation of their in vivo capacity for germ line contribution is impossible due to ethical and legal restrictions. Progress toward derivation of embryonic stem cells from domestic species has been made, but the derived cells were not able to produce germ line chimeras and thus are termed embryonic stem-like cells. However, domestic animals, in particular the domestic pig (Sus scrofa), are excellent large animals models, in which the clinical potential of stem cell therapies can be studied. Reprogramming technologies for somatic cells, including somatic cell nuclear transfer, cell fusion, in vitro culture in the presence of cell extracts, in vitro conversion of adult unipotent spermatogonial stem cells into germ line derived pluripotent stem cells, and transduction with reprogramming factors have been developed with the goal of obtaining pluripotent, germ line competent stem cells from domestic animals. This review summarizes the present state of the art in the derivation and maintenance of pluripotent stem cells in domestic animals.

As a major improvement in three-dimensional (3D) atom probe, the range of applicable material classes has recently been broadened by the establishment of laser-assisted atom probes (LA-3DAP). Meanwhile, measurements of materials of low conductivity, such as dielectrics, ceramics, and semiconductors, have widely been demonstrated. However, besides different evaporation probabilities, heterogeneous dielectric properties are expected to give rise to additional artifacts in the 3D volume reconstruction on which the method is based. In this article, these conceivable artifacts are discussed based on a numeric simulation of the field evaporation. Sample tips of layer- or precipitate-type geometry are considered. It is demonstrated that dielectric materials tend to behave similarly to metals of reduced critical evaporation field.

To analyze nanocrystalline structures quantitatively in 3D, a novel method is presented based on electron diffraction. It allows determination of the average size and morphology of the coherently scattering domains (CSD) in a straightforward way without the need to prepare multiple sections. The method is applicable to all kinds of bulk nanocrystalline materials. As an example, the average size of the CSD in nanocrystalline FeAl made by severe plastic deformation is determined in 3D. Assuming ellipsoidal CSD, it is deduced that the CSD have a width of 19 ± 2 nm, a length of 18 ± 1 nm, and a height of 10 ± 1 nm.

The pattern center of an electron backscatter diffraction (EBSD) image indicates the relative position of the image with reference to the interaction volume of the sample. As interest grows in high-resolution EBSD techniques, accurate knowledge of this position is essential for precise interpretation of the EBSD features. In a typical EBSD framework, Kikuchi bands are recorded on a phosphor screen. If the flat phosphor were instead shaped as a sphere, with its center at the specimen's electron interaction volume, then the incident backscattered electrons would form Kikuchi bands on that sphere with parallel band edges centered on great circles. In this article, the authors present a method of pattern center (PC) refinement that maps bands from the planar phosphor onto a virtual spherical screen and measures the deviation of bands from a great circle and from possessing parallel edges. Potential sources of noise and error, as well as methods for reducing these, are discussed. Finally, results are presented on the application of the PC algorithm to two types of simulated EBSD patterns and two experimental setups, and the resolution of the method is discussed.

The biomechanical response of tissues serves as a valuable marker in the prediction of disease and in understanding the related behavior of the body under various disease and age states. Alterations in the macroscopic biomechanical response of diseased tissues are well documented; however, a thorough understanding of the microstructural events that lead to these changes is poorly understood. In this article we introduce a novel microbiaxial optomechanical device that allows two-photon imaging techniques to be coupled with macromechanical stimulation in hydrated planar tissue specimens. This allows that the mechanical response of the microstructure can be quantified and related to the macroscopic response of the same tissue sample. This occurs without the need to fix tissue in strain states that could introduce a change in the microstructural configuration. We demonstrate the passive realignment of fibrous proteins under various types of loading, which demonstrates the ability of tissue microstructure to reinforce itself in periods of high stress. In addition, the collagen and elastin response of tissue during viscoelastic behavior is reported showing interstitial fluid movement and fiber realignment potentially responsible for the temporal behavior. We also demonstrate that nonhomogeneities in fiber strain exist over biaxial regions of assumed homogeneity.

At the beginning of the last century, reproductive biologists have discussed whether in mammalian species the fetal oocytes persist or are replaced by neo-oogenesis during adulthood. Currently the prevailing view is that neo-oogenesis is functional in lower vertebrates but not in mammalian species. However, contrary to the evolutionary rules, this suggests that females of lower vertebrates have a better opportunity to provide healthy offspring compared to mammals with oocytes subjected to environmental threats for up to several decades. During the last 15 years, a new effort has been made to determine whether the oocyte pool in adult mammals is renewed as well. Most recently, Ji Wu and colleagues reported a production of offspring from female germline stem cells derived from neonatal and adult mouse ovaries. This indicates that both neonatal and adult mouse ovaries carry stem cells capable of producing functional oocytes. However, it is unclear whether neo-oogenesis from ovarian somatic stem cells is physiologically involved in follicular renewal and why menopause occurs. Here we review observations that indicate an involvement of immunoregulation in physiological neo-oogenesis and follicular renewal from ovarian stem cells during the prime reproductive period and propose why menopause occurs in spite of persisting ovarian stem cells.