Direct observation of unstained wet biological samples by scanning-electron generation X-ray microscopy

Analytical tools of nanometre-scale resolution are indispensable in the fields of biology, physics and chemistry. One suitable tool, the soft X-ray microscope, provides high spatial resolution of visible light for wet specimens. For biological specimens, X-rays of water-window wavelength between carbon (284 eV; 4.3 nm) and oxygen (540 eV; 2.3 nm) absorption edges provide high-contrast imaging of biological samples in water. Among types of X-ray microscope, the transmission X-ray microscope using a synchrotron radiation source with diffractive zone plates offers the highest spatial resolution, approaching 15-10 nm. However, even higher resolution is required to measure proteins and protein complexes in biological specimens; therefore, a new type of X-ray microscope with higher resolution that uses a simple light source is desirable. Here we report a novel scanning-electron generation X-ray microscope (SGXM) that demonstrates direct imaging of unstained wet biological specimens. We deposited wet yeasts in the space between two silicon nitride (Si₃N₄) films. A scanning electron beam of accelerating voltage 5 keV and current 1.6 nA irradiates the titanium (Ti)-coated Si₃N₄ film, and the soft X-ray signal from it is detected by an X-ray photodiode (PD) placed below the sample. The SGXM can theoretically achieve better than 5 nm resolution. Our method can be utilized easily for various wet biological samples of bacteria, viruses, and protein complexes.     

Measurement of the unstained biological sample by a novel scanning electron generation X-ray microscope based on SEM

We introduced a novel X-ray microscope system based on scanning electron microscopy using thin film, which enables the measurement of unstained biological samples without damage. An unstained yeast sample was adsorbed under a titanium (Ti)-coated silicon nitride (Si₃N₄) film 90 nm thick. The X-ray signal from the film was detected by an X-ray photodiode (PD) placed below the sample. With an electron beam at 2.6 kV acceleration and 6.75 nA current, the yeast image is obtained using the X-ray PD. The image is created by soft X-rays from the Ti layer. The Ti layer is effective in generating the characteristic 2.7-nm wavelength X-rays by the irradiation of electrons. Furthermore, we investigated the electron trajectory and the generation of the characteristic X-rays within the Ti-coated Si₃N₄ film by Monte Carlo simulation. Our system can be easily utilized to observe various unstained biological samples of cells, bacteria, and viruses.     

Laboratory cryo soft X-ray microscopy

Lens-based water-window X-ray microscopy allows two- and three-dimensional (2D and 3D) imaging of intact unstained cells in their near-native state with unprecedented contrast and resolution. Cryofixation is essential to avoid radiation damage to the sample. Present cryo X-ray microscopes rely on synchrotron radiation sources, thereby limiting the accessibility for a wider community of biologists. In the present paper we demonstrate water-window cryo X-ray microscopy with a laboratory-source-based arrangement. The microscope relies on a λ=2.48-nm liquid-jet high-brightness laser-plasma source, normal-incidence multilayer condenser optics, 30-nm zone-plate optics, and a cryo sample chamber. We demonstrate 2D imaging of test patterns, and intact unstained yeast, protozoan parasites and mammalian cells. Overview 3D information is obtained by stereo imaging while complete 3D microscopy is provided by full tomographic reconstruction. The laboratory microscope image quality approaches that of the synchrotron microscopes, but with longer exposure times. The experimental image quality is analyzed from a numerical wave-propagation model of the imaging system and a path to reach synchrotron-like exposure times in laboratory microscopy is outlined.     

Comparison of the decameric structure of peroxiredoxin-II by transmission electron microscopy and X-ray crystallography.

The decameric human erythrocyte protein torin is identical to the thiol-specific antioxidant protein-II (TSA-II), also termed peroxiredoxin-II (Prx-II). Single particle analysis from electron micrographs of Prx-II molecules homogeneously orientated across holes in the presence of a thin film of ammonium molybdate and trehalose has facilitated the production of a >/=20 A 3-D reconstruction by angular reconstitution that emphasises the D5 symmetry of the ring-like decamer. The X-ray structure for Prx-II was fitted into the transmission electron microscopic reconstruction by molecular replacement. The surface-rendered transmission electron microscopy (TEM) reconstruction correlates well with the solvent-excluded surface of the X-ray structure of the Prx-II molecule. This provides confirmation that transmission electron microscopy of negatively stained specimens, despite limited resolution, has the potential to reveal a valid representation of surface features of protein molecules. 2-D crystallisation of the Prx-II protein on mica as part of a TEM study resulted in the formation of a p2 crystal form with parallel linear arrays of stacked rings. This latter 2-D form correlates well with that observed from the 2.7 A X-ray structure of Prx-II solved from a new orthorhombic 3-D crystal form.     

X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells,tissues, and organs

Capturing complete internal anatomies of plant organs and tissues within their relevant morphological context remains a key challenge in plant science. While plant growth and development are inherently multiscale, conventional light, fluorescence, and electron microscopy platforms are typically limited to imaging of plant microstructure from small flat samples that lack a direct spatial context to, and represent only a small portion of, the relevant plant macrostructures. We demonstrate technical advances with a lab-based X-ray microscope (XRM) that bridge the imaging gap by providing multiscale high-resolution three-dimensional (3D) volumes of intact plant samples from the cell to the whole plant level. Serial imaging of a single sample is shown to provide sub-micron 3D volumes co-registered with lower magnification scans for explicit contextual reference. High-quality 3D volume data from our enhanced methods facilitate sophisticated and effective computational segmentation. Advances in sample preparation make multimodal correlative imaging workflows possible, where a single resin-embedded plant sample is scanned via XRM to generate a 3D cell-level map, and then used to identify and zoom in on sub-cellular regions of interest for high-resolution scanning electron microscopy. In total, we present the methodologies for use of XRM in the multiscale and multimodal analysis of 3D plant features using numerous economically and scientifically important plant systems.

Lab-based X-ray microscopy allows high-resolution 3D imaging of intact plant samples over a wide range of sample types and sizes, filling the imaging gap between light and electron microscopy.     

X-ray mosaic nanotomography of large microorganisms

Full-field X-ray microscopy is a valuable tool for 3D observation of biological systems. In the soft X-ray domain organelles can be visualized in individual cells while hard X-ray microscopes excel in imaging of larger complex biological tissue. The field of view of these instruments is typically 10(3) times the spatial resolution. We exploit the assets of the hard X-ray sub-micrometer imaging and extend the standard approach by widening the effective field of view to match the size of the sample. We show that global tomography of biological systems exceeding several times the field of view is feasible also at the nanoscale with moderate radiation dose. We address the performance issues and limitations of the TOMCAT full-field microscope and more generally for Zernike phase contrast imaging. Two biologically relevant systems were investigated. The first being the largest known bacteria (Thiomargarita namibiensis), the second is a small myriapod species (Pauropoda sp.). Both examples illustrate the capacity of the unique, structured condenser based broad-band full-field microscope to access the 3D structural details of biological systems at the nanoscale while avoiding complicated sample preparation, or even keeping the sample environment close to the natural state.     

Silver Nanoparticles Textured Oxide Thin Films for Surface Plasmon Enhanced Photovoltaic Properties

In this report, Ag nanoparticles were fabricated using the single-step glancing angle deposition (SS-GLAD) technique upon In₂O₃/TiO₂ thin film. Afterward, a detailed analysis was done for the two samples such as In₂O₃/TiO₂ thin film and In₂O₃/TiO₂ thin film/Ag nanoparticles, to inspect the field emission scanning electron microscopy (FESEM), energy-dispersive X-ray analysis (EDAX), X-ray diffraction (XRD), ultraviolet (UV) spectroscopy, and electrical properties. The reduction in bandgap energy for the samples of In₂O₃/TiO₂ thin film/Ag nanoparticles (~4.16 eV) in comparison with the In₂O₃/TiO₂ thin film (~4.28 eV) was due to trapped e–h recombination at the oxygen vacancies and electron transmission of Ag to the conduction band of the In₂O₃/TiO₂ thin films. Moreover, under irradiation of photons Ag nanoparticles generated inorganic Ag–O compound attributable to the localized surface plasmon resonance (LSPR). Also, a?~90% high transmittance,?~60% and?~25% low reflectance in UV and visible region, fill factor (FF) of 53%, as well as power conversion efficiency (PCE) of 15.12% was observed for In₂O₃/TiO₂ thin film/Ag nanoparticles than the In₂O₃/TiO₂ thin film. Therefore, the use of Ag nanoparticles textured In₂O₃/TiO₂ thin film–based device is a promising approach for the forthcoming photovoltaic applications.

     

Energy Dispersive X-ray Tomography for 3D Elemental Mapping of Individual Nanoparticles

Energy dispersive X-ray spectroscopy within the scanning transmission electron microscope (STEM) provides accurate elemental analysis with high spatial resolution, and is even capable of providing atomically resolved elemental maps. In this technique, a highly focused electron beam is incident upon a thin sample and the energy of emitted X-rays is measured in order to determine the atomic species of material within the beam path. This elementally sensitive spectroscopy technique can be extended to three dimensional tomographic imaging by acquiring multiple spectrum images with the sample tilted along an axis perpendicular to the electron beam direction.Elemental distributions within single nanoparticles are often important for determining their optical, catalytic and magnetic properties. Techniques such as X-ray tomography and slice and view energy dispersive X-ray mapping in the scanning electron microscope provide elementally sensitive three dimensional imaging but are typically limited to spatial resolutions of > 20 nm. Atom probe tomography provides near atomic resolution but preparing nanoparticle samples for atom probe analysis is often challenging. Thus, elementally sensitive techniques applied within the scanning transmission electron microscope are uniquely placed to study elemental distributions within nanoparticles of dimensions 10-100 nm.Here, energy dispersive X-ray (EDX) spectroscopy within the STEM is applied to investigate the distribution of elements in single AgAu nanoparticles. The surface segregation of both Ag and Au, at different nanoparticle compositions, has been observed.     

Atomic Layer Deposition of Functional Layers for on Chip 3D Li‐Ion All Solid State Microbattery

Nowadays, millimeter scale power sources are key devices for providing autonomy to smart, connected, and miniaturized sensors. However, until now, planar solid state microbatteries do not yet exhibit a sufficient surface energy density. In that context, architectured 3D microbatteries appear therefore to be a good solution to improve the material mass loading while keeping small the footprint area. Beside the design itself of the 3D microbaterry, one important technological barrier to address is the conformal deposition of thin films (lithiated or not) on 3D structures. For that purpose, atomic layer deposition (ALD) technology is a powerful technique that enables conformal coatings of thin film on complex substrate. An original, robust, and highly efficient 3D scaffold is proposed to significantly improve the geometrical surface of miniaturized 3D microbattery. Four functional layers composing the 3D lithium ion microbattery stacking has been successfully deposited on simple and double microtubes 3D templates. In depth synchrotron X‐ray nanotomography and high angle annular dark field transmission electron microscope analyses are used to study the interface between each layer. For the first time, using ALD, anatase TiO₂ negative electrode is coated on 3D tubes with Li₃PO₄ lithium phosphate as electrolyte, opening the way to all solid‐state 3D microbatteries. The surface capacity is significantly increased by the proposed topology (high area enlargement factor – “thick” 3D layer), from 3.5 μA h cm^?2 for a planar layer up to 0.37 mA h cm^?2 for a 3D thin film (105 times higher).     

5 K extended X-ray absorption fine structure and 40 K 10-s resolved extended X-ray absorption fine structure studies of photolyzed carboxymyoglobin

A previous extended X-ray absorption fine structure (EXAFS) study of photolyzed carboxymyoglobin (MbCO) [Chance, B., Fischetti, R., & Powers, L. (1983) Biochemistry 22, 3820-3829; Powers, L., Sessler, J. L., Woolery, G. L., & Chance, B. (1984) Biochemistry 23, 5519-5523] has provoked much discussion on the heme structure of the photoproduct (MbCO). The EXAFS interpretation that the Fe-CO distance increases by no more than 0.05 A following photodissociation has been regarded as inconsistent with optical, infrared, and magnetic susceptibility studies [Fiamingo, F. G., & Alben, J. O. (1985) Biochemistry 24, 7964-7970; Sassaroli, M., & Rousseau, D. L. (1986) J. Biol. Chem. 261, 16292-16294]. The present experiment was performed with well-characterized dry film samples in which MbCO molecules were embedded in a poly(vinyl alcohol) matrix [Teng, T. Y., & Huang, H. W. (1986) Biochim. Biophys. Acta 874, 13-18]. The sample had a high protein concentration (12 mM) to yield adequate EXAFS signals but was very thin (40 micron) so that complete photolysis could be easily achieved by a single flash from a xenon lamp. Although the electronic state of MbCO resembles that of deoxymyoglobin (deoxy-Mb), direct comparison of EXAFS spectra indicates that structurally MbCO is much closer to MbCO than to deoxy-Mb.(ABSTRACT TRUNCATED AT 250 WORDS)     

Hemoglobin and myoglobin embedded in dry poly(vinyl alcohol) film for X-ray absorption studies

Solid hemoprotein samples are prepared by embedding proteins in thin poly(vinyl alcohol) films. These film samples have several unique qualities: in the solid poly(vinyl alcohol) matrix, hemoproteins have the same properties as in frozen buffer solution (proven by optical absorption, ligand recombination kinetics and EXAFS); they are very stable, easy to store and resistant to radiation; damage; protein concentration can be as high as 15 mM; light transparency is as good as liquid solution samples; and they can be made as thin as 20 microns, so that 100% photolysis across a film, even with a high protein concentration, is easily achievable. The film samples are ideal for X-ray studies of optically illuminated hemoproteins.     

Cryo X-ray microscope with flat sample geometry for correlative fluorescence and nanoscale tomographic imaging

X-ray imaging offers a new 3-D view into cells. With its ability to penetrate whole hydrated cells it is ideally suited for pairing fluorescence light microscopy and nanoscale X-ray tomography. In this paper, we describe the X-ray optical set-up and the design of the cryo full-field transmission X-ray microscope (TXM) at the electron storage ring BESSY II. Compared to previous TXM set-ups with zone plate condenser monochromator, the new X-ray optical layout employs an undulator source, a spherical grating monochromator and an elliptically shaped glass capillary mirror as condenser. This set-up improves the spectral resolution by an order of magnitude. Furthermore, the partially coherent object illumination improves the contrast transfer of the microscope compared to incoherent conditions. With the new TXM, cells grown on flat support grids can be tilted perpendicular to the optical axis without any geometrical restrictions by the previously required pinhole for the zone plate monochromator close to the sample plane. We also developed an incorporated fluorescence light microscope which permits to record fluorescence, bright field and DIC images of cryogenic cells inside the TXM. For TXM tomography, imaging with multi-keV X-rays is a straightforward approach to increase the depth of focus. Under these conditions phase contrast imaging is necessary. For soft X-rays with shrinking depth of focus towards 10nm spatial resolution, thin optical sections through a thick specimen might be obtained by deconvolution X-ray microscopy. As alternative 3-D X-ray imaging techniques, the confocal cryo-STXM and the dual beam cryo-FIB/STXM with photoelectron detection are proposed.     

Optimal Interfacial Engineering with Different Length of Alkylammonium Halide for Efficient and Stable Perovskite Solar Cells

Recently, two‐dimensional (2D) structure on three‐dimensional (3D) perovskites (graded 2D/3D) has been reported to be effective in significantly improving both efficiency and stability. However, the electrical properties of the 2D structure as a passivation layer on the 3D perovskite thin film and resistance to the penetration of moisture may vary depending on the length of the alkyl chain. In addition, the surface defects of the 2D itself on the 3D layer may also be affected by the correlation between the 2D structure and the hole conductive material. Therefore, systematic interfacial study with the alkyl chain length of long‐chained alkylammonium iodide forming a 2D structure is necessary. Herein, the 2D interfacial layers formed are compared with butylammonium iodide (BAI), octylammonium iodide (OAI), and dodecylammonium iodide (DAI) iodide on a 3D (FAPbI₃)_0.95(MAPbBr₃)_0.05 perovskite thin film in terms of the PCE and humidity stability. As the length of the alkyl chain increased from BA to OA to DA, the electron‐blocking ability and humidity resistance increase significantly, but the difference between OA and DA is not large. The PSC post‐treated with OAI has slightly higher PCE than those treated with BAI and DAI, achieving a certified stabilized efficiency of 22.9%.     

Analysis of oxazepam in urine using solid-phase extraction and high-performance liquid chromatography with fluorescence detection by post-column derivatization

A reversed-phase high-performance liquid chromatographic method for oxazepam in human urine samples has been developed. The sample preparation consists of an enzymatic hydrolysis with β-glucuronidase, followed by a solid-phase extraction process using Bond-Elut C₂ cartridges. The mobile phase used was a methanol—water (60:40, v/v) mixture at a flow-rate of 0.50 ml/min. The column was a 3.5 cm × 4.6 mm I.D. C₁₈ reversed-phase column. The detection system was based on a fluorescence post-column derivatization of oxazepam in mixtures of methanol and acetic acid. A linear range from 0.01 to 1 μg/ml of urine and a limit of detection of 4 ng/ml of urine were attained. Within-day recoveries and reproducibilities from urine samples spiked with 0.2 and 0.02 μg/ml oxazepam were 97.9 and 95.0 and 2.1 and 9.4%, respectively.     

Visualizing Proteins and Macromolecular Complexes by Negative Stain EM: from Grid Preparation to Image Acquisition

Single particle electron microscopy (EM), of both negative stained or frozen hydrated biological samples, has become a versatile tool in structural biology ¹. In recent years, this method has achieved great success in studying structures of proteins and macromolecular complexes ^{2, 3}. Compared with electron cryomicroscopy (cryoEM), in which frozen hydrated protein samples are embedded in a thin layer of vitreous ice ⁴, negative staining is a simpler sample preparation method in which protein samples are embedded in a thin layer of dried heavy metal salt to increase specimen contrast ⁵. The enhanced contrast of negative stain EM allows examination of relatively small biological samples. In addition to determining three-dimensional (3D) structure of purified proteins or protein complexes ⁶, this method can be used for much broader purposes. For example, negative stain EM can be easily used to visualize purified protein samples, obtaining information such as homogeneity/heterogeneity of the sample, formation of protein complexes or large assemblies, or simply to evaluate the quality of a protein preparation.In this video article, we present a complete protocol for using an EM to observe negatively stained protein sample, from preparing carbon coated grids for negative stain EM to acquiring images of negatively stained sample in an electron microscope operated at 120kV accelerating voltage. These protocols have been used in our laboratory routinely and can be easily followed by novice users.     

Investigations on the cuticle of the polychaete elytra using energy dispersive X-ray analysis

Energy dispersive X-ray analysis of elements with Z>11 in a SEM (scanning electron microscope) was used to investigate the elytra ofLagisca extenuata, Lepidonotus clava, andHarmothoe areolata from Naples (Italy) and Banyuls (France). High concentrations of halogens and a few other elements were found in certain papillae in samples from both locations. Additional TEM-examinations and X-ray analysis of thin sections revealed that the halogen concentration is inversely related to the collagen content of the matrix. The halogens are presumably bound to tyrosines, which occur in these structures. In addition, accumulation of Mn²⁺ and possibly Fe³⁺ in the papillae might depend on environmental conditions. The results show that valuable information about the chemical composition of biological structures can be obtained by energy dispersive X-ray analysis. Moreover, the results indicate that this method may be useful for environmental investigations.This work is part of a doctoral thesis, written at the Zoological Institute of the University at Hamburg.     

X-ray fluorescence analysis using synchrotron radiation at the photon factory

X-ray fluorescence experiments at the Photon Factory in Japan are described. An energy-dispersive X-ray fluorescence system was combined with various excitation modes, i.e., a continuum and a monochromatic excitation, which consist of a crystal monochromator or a wide band pass monochromator. These excitation modes provide a wide range of band width and photon flux of excitation beams. Minimum detection limits obtained for a thin sample were less than 0.1 ppm and 0.1 pg when there was no line interference. Advantages of using monochromatic excitation are discussed, with emphasis on the possibility of chemical state analysis. Grazing incidence X-ray fluorescence is a technique very appropriate to synchrotron radiation characteristics. Near-surface analysis and trace analysis of solution samples placed on a total reflection support were made. Future plans are discussed, including microbeam analysis, tomography, X-ray excited optical fluorescence, and applications of insertion devices (undulator and wiggler).     

Highly sensitive and selective electrochemiluminescence determination of cholesterol utilizing a functional electrode with a core–shell nanostructure

A highly sensitive and selective method for the determination of cholesterol is required to evaluate trace amounts of cholesterol in test samples. In this work, selected gold nanoparticles (AuNPs) and 5‐amino‐2‐mercapto‐1,3,4‐thiadiazole (AMT) were used and a thin film of three‐dimensional gold–AMT core–shell nanoparticles (p‐AMT–AuNPs) was prepared using an electrochemical method. Cholesterol oxidase was then bonded to the film surface to give a functional electrode. Based on catalysis by the electrode functionalized for cholesterol and a luminol–H₂O₂ electrochemiluminescence (ECL) system, a highly sensitive and selective ECL method was developed for the determination of cholesterol. Under optimized conditions, ECL intensity showed a good linear relationship with cholesterol over the concentration range 0.05–11.0 µg/ml, with a correlation coefficient of 0.999 and a limit of detection of 0.02 µg/ml. The proposed method was used to determine cholesterol in dairy products with a relative standard deviation of < 1.8% and recovery rates of 98.1–104%. Copyright © 2015 John Wiley & Sons, Ltd.     

A rapid method for determination of Proteus vulgaris with a piezoelectric quartz crystal sensor coated with a thin liquid film

A rapid method for microorganism detection using a piezoelectric quartz crystal sensor (PQC) coated with a thin liquid culture medium film was developed and applied to detect the cell number of Proteus vulgaris. This method employed the viscosity and density response of PQC and utilized the coagulation of gelatine medium solution in which the microorganisms had grown to determine the microorganism indirectly. Three time points (TT₁, DT, TT₂) were obtained from the coagulation curve and were found to be in good linear relationship with the logarithm of the initial number of P. vulgaris in the range 1·3 × 10²−1·3 × 10⁵ cells/ml. The detection was rapid and accurate because the coagulation of the thin liquid culture medium film was quick and the time points in the response curve were sharp and so were easy to determine accurately. The detection time was less than 4 h and only a micro sample was needed. A 5 h preincubation was needed before detection. Some experimental conditions are discussed in detail.     

X-ray absorption and phase contrast imaging to study the interplay between plant roots and soil structure

Plant performance is, at least partly, linked to the location of roots with respect to soil structure features and the micro-environment surrounding roots. Measurements of root distributions from intact samples, using optical microscopy and field tracings have been partially successful but are imprecise and labour-intensive. Theoretically, X-ray computed micro-tomography represents an ideal solution for non-invasive imaging of plant roots and soil structure. However, before it becomes fast enough and affordable or easily accessible, there is still a need for a diagnostic tool to investigate root/soil interplay. Here, a method for detection of undisturbed plant roots and their immediate physical environment is presented. X-ray absorption and phase contrast imaging are combined to produce projection images of soil sections from which root distributions and soil structure can be analyzed. The clarity of roots on the X-ray film is sufficient to allow manual tracing on an acetate sheet fixed over the film. In its current version, the method suffers limitations mainly related to (i) the degree of subjectivity associated with manual tracing and (ii) the difficulty of separating live and dead roots. The method represents a simple and relatively inexpensive way to detect and quantify roots from intact samples and has scope for further improvements. In this paper, the main steps of the method, sampling, image acquisition and image processing are documented. The potential use of the method in an agronomic perspective is illustrated using surface and sub-surface soil samples from a controlled wheat trial. Quantitative characterization of root attributes, e.g. radius, length density, branching intensity and the complex interplay between roots and soil structure, is presented and discussed. This revised version was published online in June 2006 with corrections to the Cover Date.