bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tensegrity Architecture of an Agglutinated Foraminiferan Shell
Authors: Kinoshita Roy K , Rivas-Rivera Karla M , Bowser Samuel S 
Published: July 2020

Abstract
Shells of agglutinated foraminiferan protists are composed of mineral grains bound by secreted adhesives. As such, they are useful models for examining the evolution of “primitive” exoskeletons. Previous studies revealed the ultrastructure of shells in the giant Antarctic foraminiferan Astrammina rara and demonstrated that shucked specimens would reconstruct shells using glass beads. Here we further investigate shell architecture in this model species.
For micromechanical testing, an intact A. rara shell was placed between a fixed plate and a facing plate in series with a calibrated load cell. Displacement was effected by a high-precision drive, and 2-3 loading cycles were used to determine shell material properties. to assay tensile properties of the adhesive matrix, a network of pseudopodia and extracellular matrix fibers (i.e., the shell adhesive component) was obtained by incubating shucked cell bodies on 200-mesh gold grids. Pseudopodia were subsequently removed by detergent washes. Fibers in the resultant isolated matrix were severed with a Nd: YAG laser using an inverted DIC light microscope equipped with a 60× objective lens. Preliminary loading experiments using glass needles showed that Sepharose 2B beads were suitable strain gauges to assess compression within reconstructed shells (Fig. 1). in this assay, shucked cell bodies were incubated with a mixture of glass and Sepharose beads, and the reconstructed shells were examined by SEM.
Repeated loading and unloading demonstrated the elastic behavior of intact shells (Fig. 2). Adhesive matrix fibers snapped towards their attachment sites within 2 sec after cutting with a laser (Fig. 3), demonstrating that they are deployed under tension. SEM images of shells reconstructed with Sepharose show compressed particle profiles (Fig. 4).
Induction of Transfer Cell Formation in a Plant Infected by a Biotrophic Fungal Parasite
Authors: Mims Charles W , Richardson Elizabeth A 
Published: July 2020

Abstract
In this study a combination of scanning (SEM) and transmission electron microscopy (TEM) was used to examine leaf cells of the common weed Indian strawberry (Duchesnea indica) infected by the biotrophic rust fungus Frommeëla mexicana var. indicae. For SEM, free-hand sections of infected leaves cut with a razor blade were placed in a 5% (wt/vol) aqueous solutions of Ariel (Proctor and Gamble, Cincinnati, OH), a washing powder containing a bacterial protease. This treatment removed exposed host cell cytoplasm so as to reveal details of fungal haustoria and host cell wall responses to infection (Figs. 1, 2). Samples then were processed for study according to procedures described previously. For TEM, samples were prepared for study using high pressure freezing followed by freeze substitution. This fixation procedure has been used with excellent results to study hostpathogen interactions in rust-infected plants.
Frommeëla mexicana var. indicae produced specialized hyphal branches known as haustoria that extended through the walls of infected cells. Each haustorium possessed a long, slender neck region (Fig. 3) and an expanded body (Figs. 1, 4) that was separated from the host cell cytoplasm by the invaginated host cell plasma membrane. At maturity the neck region was surrounded by a extensive labyrinth cell wall in-growth or elaboration (Figs. 1-3) that appeared to be identical to wall elaborations that characterize plant transfer cells. Such cells are thought to be involved in intensive solute transfer over short distances. While transfer cells have been reported within cells of the haustoria of various plant parasitic higher plants and in plant giant cells induced by certain plant parasitic nematodes, this appears to be the first report of their formation in response to infection by a plant pathogenic fungus. Not only did these elaborations form in the immediate vicinity of haustoria, they also arose apart from haustoria in infected cells. However, such elaborations were not found in cells of uninfected leaves.
Napsin is Localized in the Lysosomal Compartments of Specialized Epithelial Cells in the Lungs and in the Kidney
Authors: Na C-L , Falconieri M W , Liu L , Melton K , Weaver T E 
Published: July 2020

Abstract
Napsin is an aspartic proteinase which has two essential asparagine residues in the active peptide (Tatnell et al., 1997). Napsin may participate in the processing of pulmonary surfactant protein B (Weaver et al., 1992; Chuman et al., 1999). in addition, changes in napsin expression have been linked to primary adenocarcinoma as well as kidney dysfunction (Hirano et al., 2000; Schauer-Vukasinovic et al., 2000). Localization studies by light microscope immunocytochemistry and in situ hybridization detected napsin in the lungs as well as in the kidney (Tatnell et al., 1997; Chuman et al, 1999; Schauer- Vukasinovic et al., 1999). However, these studies did not resolve the ultrastructure localization of napsin. in this study, EM cryoimmunogold labeling was used to characterize the subcellular distribution of napsin in lung and kidney cells.
A truncated murine napsin propeptide construct (1212 b.p.) without the signal peptide sequence (47 b.p.) was cloned into pProEX™HTb plasmid vector for the generation of recombinant protein. Polyclonal antibodies were generated against purified recombinant protein. The specificity of polyclonal antibodies was determined by immunoprecipitation and Western blotting using isolated mouse alveolar type 2 epithelial cells and kidney homogenates. The napsin antibodies detected a single protein with Mr= 43 kD.
Localization of napsin by EM cryoimmunogold labeling was performed using protein A gold probes as previously described (Na et al, 2000). in the lungs, napsin was localized in both alveolar type 2 epithelial cells and in alveolar macrophages. in alveolar type 2 epithelial cells, napsin was detected in multivesicular bodies and in lamellar bodies; internalized BSA gold colocalized with napsin in the lysosomes of alveolar macrophages (Figure 1A and 1B), consistent with the observation that napsin is active at low pH (Schauer-Vukasinovic et al., 1999). Although Schauer-Vukasinovic et al. (1999) reported that napsin was expressed by some bronchiolar cells, we did not observe any significant napsin labeling in Clara cells or in ciliated epithelial cells.
Effects of Varying Salinity on Leaf Ultrastructure of Zannichellia Palustris
Authors: Barnabas AD , Jimmy R , Govender K , Przybylowicz WJ , Mesjasz-Przybylowicz J 
Published: July 2020

Abstract
Zanichellia palustris is a submerged halophyte which occurs in waters of low salinity (5%o to 10%o). It is not capable of surviving at high salinity. Reasons for its inability to tolerate hypersaline conditions is important to our understanding of its biology. in the present study, leaf ultrastructure of plants growing at normal salinity was compared with plants growing at high salinity so as to assess the effects of hypersalinity. Attention was focused on ultrstructural changes occurring in leaf blade epidermal cells.
Plants were grown in seawater at two salinities : 10%o (control) and 20%o (high salinity). Pieces of mature leaf blades from both treatments were harvested and prepared for Transmission Electron Microscopy (TEM) following standard procedures. in addition, the overall distribution and concentration of chlorine (Cl) in the leaves was ascertained since it is the most abundant anion in seawater and is important in considerations of salt tolerance in submerged halophytes. Cl was determined by means of a nuclear microprobe. Pieces of sectioned leaves were rapidly frozen, freeze dried and carbon coated. Elemental distribution maps of Cl were obtained using the true elemental imaging system (Dynamic Analysis). Two complementary techniques, Proton Induced X-Ray Emission (PLXE) and Proton Back Scattering (BS) were performed simultaneously using the GeoPIXE suite of programmes. Sample thickness and composition of major elements were obtained from the BS spectra.
The ultrastructural morphology of leaf blade epidermal cells, which possess transfer cell characteristics differed at each salinity. While the cytoplasm was well preserved in epidermal cells of plants at the control salinity : 10%o (Fig 1), considerable cytoplasmic damage occurred in epidermal cells of plants at high salinity, in the form of breakdown of membranes such as the plasmamembrane and tonoplast, and senescence of various organelles including chloroplasts and mitochondria (Fig. 2).
TEM Embedding Technique for Immunocytochemistry of Cultured Cells
Authors: Sands S , Meek W 
Published: July 2020

Abstract
Vero cells (African green monkey kidney epithelium) contain very dense cytoplasm with numerous ribosomes and mitochondria. They also contain an impressive network of cytoskeletal proteins, especially vimentin intermediate filament. Vimentin is present in all cells of mesenchymal origin, but their localization in the cell is usually restricted to a perinuclear position. Vero cells exhibit large bundles of vimentin filaments in a network, coursing throughout the cell. Additionally, many vimentin filaments connect to each other in an intermediate filament focus, or vertex. We investigated these vimentin vertices using immunofluorescence, scanning and transmission electron microscopy.
The processing of cultured cells for transmission electron microscopy is a difficult task, especially when one desires to preserve in situ relationships. When sectioning epithelial cell lines, a single cell layer (approximately three micrometers) of tissue is available, so a few thick sections will remove all the cells in the block. A traditional method for TEM of cultured cells is to disrupt these cells from their substrate and then centrifuge these cells into a pellet which can be sectioned. While it may be easier to obtain thin sections of cultured cells employing this method, many characteristics of the cells cannot be adequately investigated, including cell-to-cell junctions, cell shape on a substrate, cell morphology associated with a substrate, position of organelles in a cell growing on a substrate, and morphology and relationship of mitotic cells.
Growing cells on Thermanox cover slips and embedding in LR White polymerized in gelatin capsules at 55°C affords an effective method of viewing and labeling cells in culture. When the resin has been polymerized, the Thermanox coverslip is carefully removed from the block by using a razor blade to pry it off. The cells remain in the LR White, exposing them to the surface of the block. in fact, the very first sections of the block contain cells. Although this prevents one from facing the block, the exposed surface is usually flat enough to obtain good thin sections.
Glutathione Distribution in Transformed Leukocytes Determined by Immunoelectron Microscopy
Authors: Ault Jeffrey G , Lawrence David A 
Published: July 2020

Abstract
Glutathione (GSH) is a tripeptide thiol found in virtually all mammalian cells. GSH is a cofactor in several enzymatic reactions and is important in intracellular cysteine storage. Probably the most interesting of its many functions is its role in protecting the cell against the detrimental effects of ionizing radiation, reactive oxygen compounds, free radicals, and toxic xenobiotics. GSH is the reduced form which can be oxidized to a disulfide form (GSSG) or to form mixed disulfides with proteins. The GSH oxidation-reduction cycle maintains a high GSH to GSSG ratio which provides a reservoir of reducing equivalents that can nullify reactive oxygen species and detoxify xenobiotics. The study of glutathione in the fields of cancer research and immunology has attracted much attention, especially with regard to changes with age.
In this study, we have determined the cellular distribution of glutathione using immunoelectron microscopy. A mouse monoclonal antibody (8.1-GSH) against the glutathione adduct with Nefhylmaleimide (NEM) was used.
A Novel Method of Data Collection for Automated Electron Tomography Based upon Pre-cal1bration of Image Shifts and Defocus Changes
Authors: Ziese Ulrike , Janssen Ries , Geerts Willie , van der Krift Theo , van Balen Auke , Ruijter Hans de , Jong Krijn de , Verkleij Arie , Koster Bram 
Published: July 2020

Abstract
Electron tomography is a three-dimensional (3D) imaging method with transmission electron microscopy (TEM) that provides high-resolution 3D images of structural arrangements. with electron tomography a series of images is acquired of a sample that is tilted over a large angular range (±70°) with small angular tilt increments. For the 3D-reconstruction, the images of the tilt series are aligned relative to each other and the 3D-reconstruction is computed. Electron tomography is the only technique that can provide 3D information with nm-scale resolution of individual and unique samples. Routine application of electron tomography will comprise a major step forward in the characterization of complex materials and cellular arrangements. When collecting tilt series for electron tomography image shifts and defocus changes have to be corrected for by the human operator. The repetitive correction of these changes is highly time consuming, error prone and very hard to carry out under low-dose imaging conditions.
Many practical problems are overcome when electron tomography data collection is performed in an automated fashion. Automation includes the (a) image acquisition on a (digital) CCD camera, which implies that (b) changes in image position and defocus can be detected by on-line image processing and (c) immediately be corrected for by computer control of the microscope, (d) Finally, tilt series are directly available in digital format for subsequent processing. Typically, carrying out such an experiment would take a day, and the actual data collection 2-4 hours. in spite of the enormous progress made in terms of data collection speed during the last few years, the current status of automated tomography still does not meet the requirements that would make it a routinely applicable tool. For a great number of biological assays and research projects, results obtained under different experimental conditions have to be compared, and series of experiments have to be carried out. Therefore, we propose a novel approach for recording a tilt series that significantly increases data collection speed, and widens the applicability of the technique.
Electron Spectroscopic Tomography for Materials Science
Authors: Möbus G , Inkson B J 
Published: July 2020

Abstract
Tomographic 3D-reconstructions from tilt series of projections differ in two major aspects when moving from biochemistry (e.g.) to materials science applications: (I) Crystalline inorganic materials fail the weak phase image formation approximation and suffer from dynamic and nonlinear contrast contributions (which depend for both CTEM and HREM on atomic lattice plane orientation). (II) exposure tolerance increases by two orders of magnitude. We therefore propose energy filtered tomography with inelastic electrons (electron spectroscopic imaging, ESI) as a new method for 3D-reconstruction of free or buried subsurface nanostructures or nanoparticles. Energy filters are not used here to improve SNR by removing inelastic background, but to provide the necessary projection relationship between a 3D concentration distribution and the (processed) image intensity. Ideally, a 4-dimensional data space is recorded for a single tilt axis tomography experiment, D=D(δE, Θ,x,y), (with 5E as energy loss, Θ as tilt, and (x,y) as image coordinates). The material has to withstand exposures of T = t × Ntilt × Nloss (t = 5...20sec per image, Ntilt &gt;12 directions, Nloss = 5....20 energy loss values).
Using Electron Tomography to Determine How Kinetochores Bind and Alter the Conformations of Microtubule Plus Ends
Authors: McEwen BF , Barnard RM , Hsieh C-E , J. Frank  
Published: July 2020

Abstract
Chromosome alignment during mitosis and meiosis is mediated through the interaction between kinetochores and spindle microtubules (Mts). Kinetochores are fibrous mat-like structures, located at the primary constriction of chromosomes, that bind spindle Mts, generate poleward chromosome motion, and delay progression through mitosis until chromosome alignment is complete. Mts are polar polymers that function as tracks for the movement of a variety of cellular organelles and vesicles. Chromosome alignment requires a unique form of Mt-based motion because kinetochores capture and bind the plus ends of a bundle of Mts, rather than moving along the lateral surface of a single Mt. As a result, the direction of chromosome motion must be coordinated with the growth and shrinkage of Mts. Furthermore, the kinetochore maintains continuous attachment to growing and shrinking Mts and simultaneously permits the addition and dissociation of tubulin subunits within its confines
Automation of Tilt Series Acquisition in Transmission Electron Microscopy for Applications in Biology and Materials Science
Authors: Daberkow Ingo , Feja Bernhard , Sparlinek Peter , Tietz Hans R 
Published: July 2020

Abstract
During the last decade, computation of a three-dimensional image from a tilt series (3D reconstruction) has become a well established method, of which a variety of implementations are available. The term “electron tomography” is now generally used for this type of data acquisition and 3D reconstruction. An overview over the techniques involved is given in.
With the introduction of micro-processor-controlled TEMs and cooled slow-scan CCD cameras and with the progress in performance of high-speed computers, automation of complex imaging procedures became mainly a task of developing appropriate software, using the control facilities of the microscope. in this way, automated electron tomography was realized in 1990 at the Max- Planck-Institute for Biochemistry in Martinsried, and at about the same time at the University of California in San Francisco (UCSF). New techniques for automatic focusing and alignment, developed somewhat earlier, have been integrated in these automated tomography procedures. in the following we discuss the requirements of automatic data acquisition and the present implementation for several TEMs.
Bringing Together High- and Low-Resolution Data: Electron Tomography of Budding Enveloped Alpha Virus
Authors: Cheng RH , Hultenby K , Haag L , Forsell K , Garoff H , Hsieh C-E , Marko M 
Published: July 2020

Abstract
The multi-layered architecture of alphaviruses is built up with the registration of nucleocapsid (NC) proteins and envelope spike proteins across a lipid bilayer. At the surface of the NC, capsid proteins are organized as 42 capsomers such that the three tails from each spike complex bind three capsomers. Alphaviruses have been extensively studied using cryo-EM and X-ray crystallography at near-atomic resolution (see review by Sedzik et al.). This work involves averaging images of many isolated virions, and makes use of the symmetry of the particle. The study of assembly and budding of virus particles at the cell surface, however, requires structural determination of individual virions in situ. Electron tomography offers a means for such studies.
Small features are obscured in typical thin-section (ca. 50nm) TEM micrographs due to the projection in 2D of all the structures throughout the section thickness. However, slices thinner than lnm can easily be obtained from tomographic reconstructions. Thus, small structures such as capsomers can be seen, even in thick (&gt;100nm) specimens (Fig. 1b).
CTF Correction in Electron Tomography of Insect Flight Muscle
Authors: Winkler Hanspeter , Taylor Kenneth A 
Published: July 2020

Abstract
In order to extend the resolution available in electron tomograms, we have been experimenting with various deconvolution procedures that will ultimately enable correction of the focus gradient thereby allowing the resolution to be extended to beyond the first zero in the contrast transfer function (CTF). This effort requires first a determination of the amount of amplitude and phase contrast in the typical specimen used by us.
For the determination of the percentage of amplitude contrast a focus series of 19 images was taken at a magnification of 13500 on a CM300. The micrographs were digitized on a PDS scanner, the pixel size was 0.888 nm. After correction of translational shifts, rotations, and defocus dependent magnification differences the image restoration was carried out according to [1,2]. From the resulting complex wave function an averaged amplitude contrast amount of 18% was obtained for the stained specimen. The phase contrast part and amplitude contrast part are shown in Figs, 1b, and 1c, respectively, and can be compared with the micrograph taken at 960 nm underfocus (Fig. 1a).
Porous Vycor Glass as a Model System for Biodevices: An AFM Study of Properties of Water in Confined Geometries
Authors: Quist Arjan P , Lal Ratnesh 
Published: July 2020

Abstract
Structural and dynamic studies of the adsorption behavior of small molecules within and on the surface of porous systems are of great interest for designing biocompatible and sustainable biodevices. Porous vycor glass is an ideal system for such studies because of its well characterized hydrophilic network of cylindrical pores. Moreover, the pore sizes in vycor are directly comparable to pore sizes of systems like macromolecules and biological membranes. Molecular dynamics simulations of vycor-water interactions as well as some structural data from neutron scattering and diffraction experiments are available. Close to the pore surface the number of water-water hydrogen bonds is reduced, and compensated by vycor-water hydrogen bonds. Insight into the behavior of water molecules in those confined geometries could provide necessary and relevant information for designing biodevices for tissue generation, as well as about contamination- and inflammation affinities of implant materials.
Here we present an Atomic Force Microscopy (AFM) study of vycor at different levels of surface hydration.
A Tissue Engineering Model for Tractional Organization of Cells and Matrices
Authors: Bhatnagar Rajendra S , Nicoll Steven B , Qian Jing Jing , Smith Nancy 
Published: July 2020

Abstract
Tissues are characterized by highly distinctive microarchitecture and overall form that are critical to tissue specific function. with increasing interest in tissue engineering to create surrogates for human tissues and organs, innovative techniques have been developed to generate scaffolds that display form, and microarchitecture mimicking physiological structures. While this artifice may generate pre-programmed shapes, it fails to take advantage of the inherent ability of cells to organize themselves and their surroundings. The generation of mechanical forces by the cellular cytoskeleton plays a critical role in the organization of matrix and of cellular colonies. The anchorage of the cytoskeleton to a substrate is essential for cellular tractional processes. in tissues, cells are anchored in a stationary, 3-D network of collagen in a highly characteristic spatial arrangement. This spatial order arises from vectorial deposition of matrix and its subsequent tractional organization by cells. The junction of the cell binding domain of collagen with specific integrin receptors, and the cells’ cytoskeleton comprises the apparatus for the interconversion of mechanical and biochemical energy.