Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Three-dimensional X-ray observation of atmospheric biological samples by linear-array scanning-electron generation X-ray microscope system.

ABSTRACT: Recently, we developed a soft X-ray microscope called the scanning-electron generation X-ray microscope (SGXM), which consists of a simple X-ray detection system that detects X-rays emitted from the interaction between a scanning electron beam (EB) and the thin film of the sample mount. We present herein a three-dimensional (3D) X-ray detection system that is based on the SGXM technology and designed for studying atmospheric biological samples. This 3D X-ray detection system contains a linear X-ray photodiode (PD) array. The specimens are placed under a CuZn-coated Si?N? thin film, which is attached to an atmospheric sample holder. Multiple tilt X-ray images of the samples are detected simultaneously by the linear array of X-ray PDs, and the 3D structure is calculated by a new 3D reconstruction method that uses a simulated-annealing algorithm. The resulting 3D models clearly reveal the inner structure of the bacterium. In addition, the proposed method can easily be used for diverse samples in a broad range of scientific fields.

SUBMITTER: Ogura T

PROVIDER: S-EPMC3121776 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Nanoscale observation of PM2.5 incorporated into mammalian cells using scanning electron-assisted dielectric microscope.

Project description:PM2.5 has been correlated with risk factors for various diseases and infections. It promotes tissue injury by direct effects of particle components. However, effects of PM2.5 on cells have not been fully investigated. Recently, we developed a novel imaging technology, scanning electron-assisted dielectric-impedance microscopy (SE-ADM), which enables observation of various biological specimens in aqueous solution. In this study, we successfully observed PM2.5 incorporated into living mammalian cells in culture media. Our system directly revealed the process of PM2.5 aggregation in the cells at a nanometre resolution. Further, we found that the PM2.5 aggregates in the intact cells were surrounded by intracellular membrane-like structures of low-density in the SE-ADM images. Moreover, the PM2.5 aggregates were shown by confocal Raman microscopy to be located inside the cells rather than on the cell surface. We expect our method to be applicable to the observation of various nanoparticles inside cells in culture media.

| S-EPMC7794539 | biostudies-literature

Scanning electron microscope studies of human metaphase chromosomes.

Project description:Scanning electron microscopy (SEM) is used to evaluate potential chromosome preparations and staining methods for application in high-resolution three-dimensional X-ray imaging. Our starting point is optical fluorescence microscopy, the standard method for chromosomes, which only gives structural detail at the 200?nm scale. In principle, with suitable sample preparation protocols, including contrast enhancing staining, the surface structure of the chromosomes can be viewed at the 1?nm level by SEM. Here, we evaluate a heavy metal nucleic-acid-specific stain, which gives strong contrast in the backscattered electron signal. This study uses SEM to examine chromosomes prepared in different ways to establish a sample preparation protocol for X-rays. Secondary electron and backscattered electron signals are compared to evaluate the effectiveness of platinum-based stains used to enhance the contrast.

| S-EPMC3900039 | biostudies-literature

Three-dimensional ultrastructural analysis of cells in the periodontal ligament using focused ion beam/scanning electron microscope tomography.

Project description:The accurate comprehension of normal tissue provides essential data to analyse abnormalities such as disease and regenerative processes. In addition, understanding the proper structure of the target tissue and its microenvironment may facilitate successful novel treatment strategies. Many studies have examined the nature and structure of periodontal ligaments (PDLs); however, the three-dimensional (3D) structure of cells in normal PDLs remains poorly understood. In this study, we used focused ion beam/scanning electron microscope tomography to investigate the whole 3D ultrastructure of PDL cells along with quantitatively analysing their structural properties and ascertaining their orientation to the direction of the collagen fibre. PDL cells were shown to be in contact with each other, forming a widespread mesh-like network between the cementum and the alveolar bone. The volume of the cells in the horizontal fibre area was significantly larger than in other areas, whereas the anisotropy of these cells was lower than in other areas. Furthermore, the orientation of cells to the PDL fibres was not parallel to the PDL fibres in each area. As similar evaluations are recognized as being challenging using conventional two-dimensional methods, these novel 3D findings may contribute necessary knowledge for the comprehensive understanding and analysis of PDLs.

| S-EPMC5171660 | biostudies-literature

Comparing Scanning Electron Microscope and Transmission Electron Microscope Grain Mapping Techniques Applied to Well-Defined and Highly Irregular Nanoparticles.

Project description:Investigating how grain structure affects the functional properties of nanoparticles requires a robust method for nanoscale grain mapping. In this study, we directly compare the grain mapping ability of transmission Kikuchi diffraction (TKD) in a scanning electron microscope to automated crystal orientation mapping (ACOM) in a transmission electron microscope across multiple nanoparticle materials. Analysis of well-defined Au, ZnO, and ZnSe nanoparticles showed that the grain orientations and GB geometries obtained by TKD are accurate and match those obtained by ACOM. For more complex polycrystalline Cu nanostructures, TKD provided an interpretable grain map whereas ACOM, with or without precession electron diffraction, yielded speckled, uninterpretable maps with orientation errors. Acquisition times for TKD were generally shorter than those for ACOM. Our results validate the use of TKD for characterizing grain orientation and grain boundary distributions in nanoparticles, providing a framework for the broader exploration of how microstructure influences nanoparticle properties.

| S-EPMC7033971 | biostudies-literature

Longitudinal and transverse electron paramagnetic resonance in a scanning tunneling microscope

Project description:Longitudinal and transverse magnetic field gradients drive single-atom EPR in an STM owing to piezoelectric excitations. Electron paramagnetic resonance (EPR) spectroscopy is widely used to characterize paramagnetic complexes. Recently, EPR combined with scanning tunneling microscopy (STM) achieved single-spin sensitivity with sub-angstrom spatial resolution. The excitation mechanism of EPR in STM, however, is broadly debated, raising concerns about widespread application of this technique. We present an extensive experimental study and modeling of EPR-STM of Fe and hydrogenated Ti atoms on a MgO surface. Our results support a piezoelectric coupling mechanism, in which the EPR species oscillate adiabatically in the inhomogeneous magnetic field of the STM tip. An analysis based on Bloch equations combined with atomic-multiplet calculations identifies different EPR driving forces. Specifically, transverse magnetic field gradients drive the spin-1/2 hydrogenated Ti, whereas longitudinal magnetic field gradients drive the spin-2 Fe. Also, our results highlight the potential of piezoelectric coupling to induce electric dipole moments, thereby broadening the scope of EPR-STM to nonpolar species and nonlinear excitation schemes.

| S-EPMC7527223 | biostudies-literature

The scanning electron microscope in microbiology and diagnosis of infectious disease.

Project description:Despite being an excellent tool for investigating ultrastructure, scanning electron microscopy (SEM) is less frequently used than transmission electron microscopy for microbes such as viruses or bacteria. Here we describe rapid methods that allow SEM imaging of fully hydrated, unfixed microbes without using conventional sample preparation methods. We demonstrate improved ultrastructural preservation, with greatly reduced dehydration and shrinkage, for specimens including bacteria and viruses such as Ebola virus using infiltration with ionic liquid on conducting filter substrates for SEM.

| S-EPMC4876401 | biostudies-literature

Manipulation of nanoparticles of different shapes inside a scanning electron microscope.

Project description:In this work polyhedron-like gold and sphere-like silver nanoparticles (NPs) were manipulated on an oxidized Si substrate to study the dependence of the static friction and the contact area on the particle geometry. Measurements were performed inside a scanning electron microscope (SEM) that was equipped with a high-precision XYZ-nanomanipulator. To register the occurring forces a quartz tuning fork (QTF) with a glued sharp probe was used. Contact areas and static friction forces were calculated by using different models and compared with the experimentally measured force. The effect of NP morphology on the nanoscale friction is discussed.

| S-EPMC3943919 | biostudies-literature

Direct-Write Printing of Josephson Junctions in a Scanning Electron Microscope.

Project description:Josephson junctions are the building blocks of superconducting electronics, with well-established applications in precision metrology and quantum computing. Fabricating a Josephson junction has been a resource-intensive and multistep procedure, involving lithography and wet-processing, which are not compatible with many applications. Here, we introduce a fully additive direct-write approach, where a scanning electron microscope can print substrate-conformal Josephson devices in a matter of minutes, requiring no additional processing. The junctions are made entirely by electron-beam-induced deposition (EBID) of tungsten carbide. We utilize EBID-tunable material properties to write, in one go, full proximity junctions with superconducting electrodes and metallic weak links and tailor their Josephson coupling. The Josephson behavior of these junctions is established and characterized by their microwave-induced Shapiro response and field-dependent transport. Our efforts provide a versatile and nondestructive alternative to conventional nanofabrication and can be expanded to print three-dimensional superconducting sensor arrays and quantum networks.

| S-EPMC7844821 | biostudies-literature

Scanning Magnetic Microscope Using a Gradiometric Configuration for Characterization of Rock Samples.

Project description:Scanning magnetic microscopy is a tool that has been used to map magnetic fields with good spatial resolution and field sensitivity. This technology has great advantages over other instruments; for example, its operation does not require cryogenic technology, which reduces its operational cost and complexity. Here, we presented a spatial domain technique based on an equivalent layer approach for processing the data set produced by magnetic microscopy. This approach estimated a magnetic moment distribution over a fictitious layer composed by a set of dipoles located below the observation plane. For this purpose, we formulated a linear inverse problem for calculating the magnetic vector and its amplitude. Vector field maps are valuable tools for the magnetic interpretation of samples with a high spatial variability of magnetization. These maps could provide comprehensive information regarding the spatial distribution of magnetic carriers. In addition, this approach might be useful for characterizing isolated areas over samples or investigating the spatial magnetization distribution of bulk samples at the micro and millimeter scales. This technique could be useful for many applications that require samples that need to be mapped without a magnetic field at room temperature, including rock magnetism.

| S-EPMC6947304 | biostudies-literature

Three-dimensional ultrastructural and histomorphological analysis of the periodontal ligament with occlusal hypofunction via focused ion beam/scanning electron microscope tomography.

Project description:The periodontal ligament (PDL) maintains the environment and function of the periodontium. The PDL has been remodelled in accordance with changes in mechanical loading. Three-dimensional (3D) structural data provide essential information regarding PDL function and dysfunction. However, changes in mechanical loading associated with structural changes in the PDL are poorly understood at the mesoscale. This study aimed to investigate 3D ultrastructural and histomorphometric changes in PDL cells and fibres associated with unloading condition (occlusal hypofunction), using focused ion beam/scanning electron microscope tomography, and to quantitatively analyse the structural properties of PDL cells and fibres. PDL cells formed cellular networks upon morphological changes induced via changes in mechanical loading condition. Drastic changes were observed in a horizontal array of cells, with a sparse and disorganised area of collagen bundles. Furthermore, collagen bundles tended to be thinner than those in the control group. FIB/SEM tomography enables easier acquisition of serial ultrastructural images and quantitative 3D data. This method is powerful for revealing 3D architecture in complex tissues. Our results may help elucidate architectural changes in the PDL microenvironment during changes in mechanical loading condition and regeneration, and advance a wide variety of treatments in dentistry.

| S-EPMC6606634 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data