Radiation dose optimized lateral expansion of the field of view in synchrotron radiation X-ray tomographic microscopy

Volumetric data at micrometer level resolution can be acquired within a few minutes using synchrotron-radiation-based tomographic microscopy. The field of view along the rotation axis of the sample can easily be increased by stacking several tomograms, allowing the investigation of long and thin objects at high resolution. On the contrary, an extension of the field of view in the perpendicular direction is non-trivial. This paper presents an acquisition protocol which increases the field of view of the tomographic dataset perpendicular to its rotation axis. The acquisition protocol can be tuned as a function of the reconstruction quality and scanning time. Since the scanning time is proportional to the radiation dose imparted to the sample, this method can be used to increase the field of view of tomographic microscopy instruments while optimizing the radiation dose for radiation-sensitive samples and keeping the quality of the tomographic dataset on the required level. This approach, dubbed wide-field synchrotron radiation tomographic microscopy, can increase the lateral field of view up to five times. The method has been successfully applied for the three-dimensional imaging of entire rat lung acini with a diameter of 4.1 mm at a voxel size of 1.48 microm.

Evaluation and quantification of spectral information in tissue by confocal microscopy

A confocal imaging and image processing scheme is introduced to visualize and evaluate the spatial distribution of spectral information in tissue. The image data are recorded using a confocal laser-scanning microscope equipped with a detection unit that provides high spectral resolution. The processing scheme is based on spectral data, is less error-prone than intensity-based visualization and evaluation methods, and provides quantitative information on the composition of the sample. The method is tested and validated in the context of the development of dermal drug delivery systems, introducing a quantitative uptake indicator to compare the performances of different delivery systems is introduced. A drug penetration study was performed in vitro. The results show that the method is able to detect, visualize and measure spectral information in tissue. In the penetration study, uptake efficiencies of different experiment setups could be discriminated and quantitatively described. The developed uptake indicator is a step towards a quantitative assessment and, in a more general view apart from pharmaceutical research, provides valuable information on tissue composition. It can potentially be used for clinical in vitro and in vivo applications.

NANOSCALE ELECTROCHEMISTRY BY IN-SITU TRANSMISSION ELECTRON MICROSCOPY

Nanoscale research in energy storage has recently focused on investigating the properties of nanostructures in order to increase energy density, power rate, and capacity. To better understand the intrinsic properties of nanomaterials, a new and advanced in situ system was designed that allows atomic scale observation of materials under external fields. A special holder equipped with a scanning tunneling microscopy (STM) probe inside a transmission electron microscopy (TEM) system was used to perform the in situ studies on mechanical, electrical, and electrochemical properties of nanomaterials. The nanostructures of titanium dioxide (TiO2) nanotubes are characterized by electron imaging, diffraction, and chemical analysis techniques inside TEM. TiO2 nanotube is one of the candidates as anode materials for lithium ion batteries. It is necessary to study their morphological, mechanical, electrical, and electrochemical properties at atomic level. The synthesis of TiO2 nanotubes showed that the aspect ratio of TiO2 could be controlled by processing parameters, such as anodization time and voltage. Ammonium hydroxide (NH4OH) treated TiO2 nanotubes showed unexpected instability. Observation revealed the nanotubes were disintegrated into nanoparticles and the tubular morphology was vanished after annealing. The nitrogen compounds incorporated in surface defects weaken the nanotube and result in the collapse of nanotube into nanoparticles during phase transformation. Next, the electrical and mechanical properties of TiO2 nanotubes were studied by in situ TEM system. Phase transformation of anatase TiO2 nanotubes into rutile nanoparticles was studied by in situ Joule heating. The results showed that single anatase TiO2 nanotubes broke into ultrafine small anatase nanoparticles. On further increasing the bias, the nanoclusters of anatase particles became prone to a solid state reaction and were grown into stable large rutile nanoparticles. The relationship between mechanical and electrical properties of TiO2 nanotubes was also investigated. Initially, both anatase and amorphous TiO2 nanotubes were characterized by using I-V test to demonstrate the semiconductor properties. The observation of mechanical bending on TiO2 nanotubes revealed that the conductivity would increase when bending deformation happened. The defects on the nanotubes created by deformation helped electron transportation to increase the conductivity. Lastly, the electrochemical properties of amorphous TiO2 nanotubes were characterized by in situ TEM system. The direct chemical and imaging evidence of lithium-induced atomic ordering in amorphous TiO2 nanotubes was studied. The results indicated that the lithiation started with the valance reduction of Ti4+ to Ti3+ leading to a LixTiO2 intercalation compound. The continued intercalation of Li ions in TiO2 nanotubes triggered an amorphous to crystalline phase transformation. The crystals were formed as nano islands and identified to be Li2Ti2O4 with cubic structure (a = 8.375 Å). This phase transformation is associated with local inhomogeneities in Li distribution. Based on these observations, a new reaction mechanism is proposed to explain the first cycle lithiation behavior in amorphous TiO2 nanotubes.

Tin-containing fluoride solutions as anti-erosive agents in enamel: an in vitro tin-uptake, tissue-loss, and scanning electron micrograph study

Tin-containing fluoride solutions can reduce erosive tissue loss, but the effects of the reaction between tin and enamel are still not clear. During a 10-d period, enamel specimens were cyclically demineralized (0.05 M citric acid, pH 2.3, 6 x 5 min d(-1)) and remineralized (between the demineralization cycles and overnight). In the negative-control group, no further treatment was performed. Three groups were treated (2 x 2 min d(-1)) with tin-containing fluoride solutions (400, 1,400 or 2,100 ppm Sn2+, all 1,500 ppm F-, pH 4.5). Three additional groups were treated with test solutions twice daily, but without demineralization. Tissue loss was determined profilometrically. Energy-dispersive X-ray spectroscopy was used to measure the tin content on and within three layers (10 mum each) beneath the surface. In addition, scanning electron microscopy was conducted. All test preparations significantly reduced tissue loss. Deposition of tin on surfaces was higher without erosion than with erosion, but no incorporation of tin into enamel was found without demineralization. Under erosive conditions, both highly concentrated solutions led to the incorporation of tin up to a depth of 20 mum; the less-concentrated solution led to small amounts of tin in the outer 10 mum. The efficacy of tin-containing solutions seems to depend mainly on the incorporation of tin into enamel.

Electrochemical current-sensing atomic force microscopy in conductive solutions

Insulated atomic force microscopy probes carrying gold conductive tips were fabricated and employed as bifunctional force and current sensors in electrolyte solutions under electrochemical potential control. The application of the probes for current-sensing imaging, force and current–distance spectroscopy as well as scanning electrochemical microscopy experiments was demonstrated.

Scanning electron microscope study of the developing microvasculature in the postnatal rat lung.

During postnatal growth the parenchymal septa of rat lung undergo an impressive restructuring. While immature septa are thick and contain two capillary layers, mature septa are slender and contain a single microvascular network. Using the Mercox casting technique and scanning electron microscopy, we investigated the mode and the timing of the transformation of the pulmonary capillary bed. During the third postnatal week the parenchymal septa rapidly mature to match adult morphology. Even in adult lungs, however, remnants of the immature status are present: A capillary bilayer is regularly found at the base and the tip of the septa. Our observations support the concept that reduction of intervening tissue, partial fusion of the two capillary networks, and preferential growth lead to the mature vascular arrangement. The fact that true mature interalveolar septa show a denser capillary network than alveolar walls abutting onto pleura, bronchi, or larger vessels is consonant with the fusion theory. Towards the nonparenchyma, the capillary network surrounding every airspace had no counterpart to fuse with. From quantitative data it can be calculated that owing to lung growth, mesh size should increase more than four times between birth and adult age. The adult lung network, however, is denser than the one in young animals. This means that new meshes must be added during growth. We propose that small holes observed in sheet-like regions of the microvasculature enlarge to form new capillary meshes. With this mechanism of in-itself or intussusceptional growth, sprouting of individual capillary segments to increase network size is no longer needed.

(Table T1) Scanning electron microscope (SEM) analyses of IODP Site 321-U1338

The late Miocene to early Pliocene carbonate-rich sediments recovered at Integrated Ocean Drilling Program (IODP) Site U1338 during the Expedition 320/321 Pacific Equatorial Age Transect (PEAT) program contain abundant calcareous nanno- and microfossils. Geochemical proxies from benthic and planktonic foraminiferal and coccolithophore calcite could be very useful at this location; however, good preservation of the calcite is crucial for the proxies to be robust. Here, we evaluate the preservation of specific benthic and planktonic foraminifer species and coccolithophores in fine fraction sediment at Site U1338 using backscattered electron (topography mode) scanning electron microscopy (BSE-TOPO SEM). Both investigated foraminiferal species, Cibicidoides mundulus and Globigerinoides sacculifer, have undergone some alteration. The C. mundulus show minor evidence for dissolution, and only some specimens show evidence of overgrowth. The Gs. sacculifer show definite signs of alteration and exhibit variable preservation, ranging from fair to poor; some specimens show minor overgrowth and internal recrystallization but retain original features such as pores, spine pits, and internal test-wall growth structure, whereas in other specimens the recrystallization and overgrowth disguise many of the original features. Secondary electron and BSE-TOPO SEM images show that coccolith calcite preservation is moderate or moderate to poor. Slight to moderate etching has removed central heterococcolith features, and a small amount of secondary overgrowth is also visible. Energy dispersive spectroscopy analyses indicate that the main sedimentary components of the fine fraction sediment are biogenic CaCO3 and SiO2, with some marine barite. Based on the investigations in this data report, geochemical analyses on benthic foraminifers are unlikely to be affected by preservation, although geochemical analyses on the planktonic foraminifers should be treated cautiously because of the fair to poor and highly variable preservation.

ESPINA: a tool for the automated segmentation and counting of synapses in large stacks of electron microscopy images

The synapses in the cerebral cortex can be classified into two main types, Gray’s type I and type II, which correspond to asymmetric (mostly glutamatergic excitatory) and symmetric (inhibitory GABAergic) synapses, respectively. Hence, the quantification and identification of their different types and the proportions in which they are found, is extraordinarily important in terms of brain function. The ideal approach to calculate the number of synapses per unit volume is to analyze 3D samples reconstructed from serial sections. However, obtaining serial sections by transmission electron microscopy is an extremely time consuming and technically demanding task. Using focused ion beam/scanning electron microscope microscopy, we recently showed that virtually all synapses can be accurately identified as asymmetric or symmetric synapses when they are visualized, reconstructed, and quantified from large 3D tissue samples obtained in an automated manner. Nevertheless, the analysis, segmentation, and quantification of synapses is still a labor intensive procedure. Thus, novel solutions are currently necessary to deal with the large volume of data that is being generated by automated 3D electron microscopy. Accordingly, we have developed ESPINA, a software tool that performs the automated segmentation and counting of synapses in a reconstructed 3D volume of the cerebral cortex, and that greatly facilitates and accelerates these processes.

Three-dimensional spatial distribution of synapses in the neocortex: A dual-beam electron microscopy study

In the cerebral cortex, most synapses are found in the neuropil, but relatively little is known about their 3-dimensional organization. Using an automated dual-beam electron microscope that combines focused ion beam milling and scanning electron microscopy, we have been able to obtain 10 three-dimensional samples with an average volume of 180 µm(3) from the neuropil of layer III of the young rat somatosensory cortex (hindlimb representation). We have used specific software tools to fully reconstruct 1695 synaptic junctions present in these samples and to accurately quantify the number of synapses per unit volume. These tools also allowed us to determine synapse position and to analyze their spatial distribution using spatial statistical methods. Our results indicate that the distribution of synaptic junctions in the neuropil is nearly random, only constrained by the fact that synapses cannot overlap in space. A theoretical model based on random sequential absorption, which closely reproduces the actual distribution of synapses, is also presented.

Visualization of Cavitated Vessels in Winter and Refilled Vessels in Spring in Diffuse-Porous Trees by Cryo-Scanning Electron Microscopy1

Xylem cavitation in winter and recovery from cavitation in the spring were visualized in two species of diffuse-porous trees, Betula platyphylla var. japonica Hara and Salix sachalinensis Fr. Schm., by cryo-scanning electron microscopy after freeze-fixation of living twigs. Water in the vessel lumina of the outer three annual rings of twigs of B. platyphylla var. japonica and of S. sachalinensis gradually disappeared during the period from January to March, an indication that cavitation occurs gradually in these species during the winter. In April, when no leaves had yet expanded, the lumina of most of the vessels of both species were filled with water. Many vessel lumina in twigs of both species were filled with water during the period from the subsequent growth season to the beginning of the next winter. These observations indicate that recovery in spring occurs before the onset of transpiration and that water transport through twigs occurs during the subsequent growing season. We found, moreover, that vessels repeat an annual cycle of winter cavitation and spring recovery from cavitation for several years until irreversible cavitation occurs.

Multiphoton fluorescence excitation: new spectral windows for biological nonlinear microscopy.

Intrinsic, three-dimensionally resolved, microscopic imaging of dynamical structures and biochemical processes in living preparations has been realized by nonlinear laser scanning fluorescence microscopy. The search for useful two-photon and three-photon excitation spectra, motivated by the emergence of nonlinear microscopy as a powerful biophysical instrument, has now discovered a virtual artist's palette of chemical indicators, fluorescent markers, and native biological fluorophores, including NADH, flavins, and green fluorescent proteins, that are applicable to living biological preparations. More than 25 two-photon excitation spectra of ultraviolet and visible absorbing molecules reveal useful cross sections, some conveniently blue-shifted, for near-infrared absorption. Measurements of three-photon fluorophore excitation spectra now define alternative windows at relatively benign wavelengths to excite deeper ultraviolet fluorophores. The inherent optical sectioning capability of nonlinear excitation provides three-dimensional resolution for imaging and avoids out-of-focus background and photodamage. Here, the measured nonlinear excitation spectra and their photophysical characteristics that empower nonlinear laser microscopy for biological imaging are described.

Structure and conformational changes of DNA topoisomerase II visualized by electron microscopy.

Type II DNA topoisomerases, which create a transient gate in duplex DNA and transfer a second duplex DNA through this gate, are essential for topological transformations of DNA in prokaryotic and eukaryotic cells and are of interest not only from a mechanistic perspective but also because they are targets of agents for anticancer and antimicrobial chemotherapy. Here we describe the structure of the molecule of human topoisomerase II [DNA topoisomerase (ATP-hydrolyzing), EC 5.99.1.3] as seen by scanning transmission electron microscopy. A globular approximately 90-angstrom diameter core is connected by linkers to two approximately 50-angstrom domains, which were shown by comparison with genetically truncated Saccharomyces cerevisiae topoisomerase II to contain the N-terminal region of the approximately 170-kDa subunits and that are seen in different orientations. When the ATP-binding site is occupied by a nonhydrolyzable ATP analog, a quite different structure is seen that results from a major conformational change and consists of two domains approximately 90 angstrom and approximately 60 angstrom in diameter connected by a linker, and in which the N-terminal domains have interacted. About two-thirds of the molecules show an approximately 25 A tunnel in the apical part of the large domain, and the remainder contain an internal cavity approximately 30 A wide in the large domain close to the linker region. We propose that structural rearrangements lead to this displacement of an internal tunnel. The tunnel is likely to represent the channel through which one DNA duplex, after capture in the clamp formed by the N-terminal domains, is transferred across the interface between the enzyme's subunits. These images are consistent with biochemical observations and provide a structural basis for understanding the reaction of topoisomerase II.

The international bibliography of electron microscopy.

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