bluuebunny/crossref_metadata_2025_split huggingface dataset:
3-D Structure Analysis of Escherichia Coli Type 1 Pili
Authors: Hahn E , Wild P , Hermanns U , Sebbel P , Glockshuber R , Haener M , Taschner N , Müller S , Aebi U 
Published: July 2020

Abstract
Type 1 pili are outer membrane organelles formed by 80% of all E. coli strains. They are up to 2 μm long, rod-like appendages covering the bacterial body like spines on a hedgehog (Fig. 1). Type 1 pili expressed by uropathogenic E. coli strains mediate adhesion to specific receptors of the bladder epithelium. They allow colonization of the cell surface as a prelude to infection. Type 1 pili are composed of a rigid rod and a fibrillar tip (Fig. 2a). The minor subunit FimH mediates adhesion and is located at the fibrillar tip as demonstrated by immunolabeling (Fig. 2b). The pilus rod is built from a structural protein, the major subunit FimA. Brinton analyzed parameters describing the helix of the type 1 pilus rod based on paracrystalline arrays. Accordingly, the data predicted one helical repeat to be composed of 25 subunits in 8 turns with a helical pitch of either 2.32 or 2.4 nm.
Here, the 3-D helical structure of the pilus rod has been determined from isolated negatively stained type 1 pili imaged in the annular dark-field mode by scanning transmission electron microscopy (STEM) (Fig. 3a). The power spectra of unbent rods (Fig. 3b) exhibit the strongest layerline at a spacing of (2.42 ± 0.04 nm)−1 representing the pitch of the putative one-start genetic helix (Fig. 3c). The axial distance to its nearest layerline corresponds to the helical repeat (Fig. 3c). Averaging by a linear superposition, as employed for structural analysis of F18 fimbriae, another type of adhering E. coli appendages, confirmed the helical repeat to be 19.31 ± 0.34 nm. Mass-per-length (MPL) determination of unstained type 1 pili by STEM revealed one helical repeat to be composed of 26 ±1 15.8 kDA FimA molecules. All possible helical selection rules were tested by D(Z,k) filtering. Thereby, any data inconsistent with the employed helical selection rule are excluded (Fig. 3d). Hence, the helical selection rule yielding the most power recovery represents the closest selection rule describing the helix. We found l = 8n + 21m to be the optimum helical selection rule. Fig. 3e represents the filtered image. Accordingly, one helical repeat is made of 8 turns containing 27 FimA monomers occurring with an axial rise of 0.72 ± 0.01 nm. D(Z,k) filtering with the helical selection rule assumed by Brinton resulted in significant loss of structure. Hence, we conclude to have refined the previous indexation. The resulting 3-D structure of the type 1 pilus unveils a 6.8 nm wide right handed helical tube harboring an axial cavity (Fig. 4). The tube wall is formed by a coiled fiber comparable to the metal thread of a spring.
Ultrastructural Studies of Root Swelling in Mutants of Arabidopsis Thaliana
Authors: Naidoo Y , Baskin TI , Naidoo G 
Published: July 2020

Abstract
Growth is “anisotropic” when growth rates in different directions are not equal. Anisotropic elongation is controlled by cortical microtubules and cellulose microfibrils of the cell wall. Distorted anisotropic growth results when there are aberrations in either the cellulose network or microtubule cytoskeleton. in this ultrastructural study, the roots of wild type (control) and mutants of Arabidopsis thaliana (L.) Heynh, ecotype Columbia, were compared to determine the role of microtubule organisation, cellulose synthesis and cytokinesis on root expansion.
Three mutations, obtained by treating seeds of A. thaliana with ethane-methylsulfonate and backcrossing once to wild type after four selfed generations, were isolated and designated as rsw (radially swollen). These phenotypes are all temperature sensitive, growing and appearing as wild type at 19°C but expressing the mutant phenotype at or above 30°C. Segments of intact root tips from the three mutants and wild type were prepared and examined for TEM with a Jeol 1200EX. The overall appearance of rsw seedlings at 19°C is the same as wild type. At 30°C these phenotypes lead to extensive swelling of the root apex. Despite considerable alteration in the morphology of the root apex, the appearance of the root cap and root hairs seems essentially normal. When mutant roots expressing these phenotypes at 30°C are returned to 19°C, a wild type appearance of the root apex and elongation gradually returns.
The primary root of the wild type has a remarkably uniform cellular organisation with regularly arranged dense cytoplasmic cells (Fig. 1). At 19°C, rsw4, rsw6 and rsw7 were indistinguishable from wild type; however, at 30°C, the well-defined anatomy was distorted in all tissues by additional cell walls in unusual positions (Fig. 2).
Drought Induced Structural Changes in Developing Chloroplasts of Jalapeno Pepper (Capsicum annuum)
Authors: Fambrough Kristine , Ghoshroy Soumitra 
Published: July 2020

Abstract
Chloroplasts, present in leaves of higher plants have an extensive, folded network of photosynthetic membranes. These membranes have closely appressed (grana) and non-appressed (stroma) regions and they are responsible for the conversion of solar energy into biochemically useful forms. Light plays an important role for the development of mature chloroplasts from proplastids. However, when seeds germinate in the dark, the proplastids do not form mature chloroplasts and instead they form etioplasts. The etioplasts contain a compact, highly regular lattice of inner membranes called prolamellar body. Exposure of dark grown seedlings to light induces formation of fully mature chloroplasts from etioplasts. Plant growth and development is dependent on various environmental factors and drought has profound effect on plant metabolism. Leaves depend on adequate water for both turgor pressure and photosynthesis. Turgor pressure enables nutrients in the form of carbon and minerals to be transported from soil to leaves where they are needed for synthesis of organic compounds. in this study we evaluated the influence of drought on the ultrastructure of developing chloroplasts in pepper plants.
Jalapeno pepper plants were grown from seeds in the dark and drought was induced to experimental group of plants after they developed the first pair of primary leaves. The dark grown control plants received water throughout the drought induction period. At the end of tenth day of drought, plants in both control and experimental groups were exposed to light for up to 48 hours and leaf samples from both groups were obtained at various time intervals after exposure to light. The samples were fixed, dehydrated and embedded for transmission electron microscopy. Ultrathin sections were made, observed under a Hitachi H7000 TEM and data were collected for ultrastructural study. The mature chloroplast and etioplast structures were compared between experimental and control group of plants.
Investigating the Tissue Specific Expression Patterns of Murine Semaphorins 3C, 4D, 4G, 6A and 7A in Primary Lymphoid Tissues
Authors: Chalasani Sreedevi , Matthes David 
Published: July 2020

Abstract
Semaphorins are primarily known for the important role they play in the guidance of growth cones during neuronal development. There is evidence, however, that semaphorins are expressed outside the nervous system as well, suggesting a wider scope for semaphorin function. The overall objective of our study is to identify the functions of semaphorins outside central nervous system especially in T cell development. Some of the 20 semaphorins have been shown to have extra-neural functions that include (for different semaphorins) bone differentiation, promotion of B-cell survival and aggregation, and activation of T-cells. Apart from central nervous system statement of most semaphorins, one semaphorin (CD 100) has transcripts in T cells, B cells, neutrophils, monocytes and granulocytes. EST analysis suggests that other semaphorins are expressed in lymphoid tissues such as thymus, spleen, tonsil, and the interfollicular areas and germinal centers of lymph nodes.
Semaphorins have been related to several cell survival mechanisms, immunosuppression and promotion of cell death resistance. in preliminary studies our lab found that viral semaphorins inhibit the migration of human T cells and human SEMA3A can inhibit migration of human neutrophils.
Three-Dimensional Cellular Organization of Gap Junction Connexins Revealed by Specific Labeling and Electron Tomography
Authors: Sosinsky G , Hand G , Gaietta G , Deerinck T , Martone M , Adams S , Stelljes A , Jordan K , W. Laird D , Tsien R , Ellisman M 
Published: July 2020

Abstract
Gap junction channels serve important functions for the homeostasis of organ systems. These membrane channels serve as low-resistance pathways for the diffusion of small molecular species such as ions, metabolites and second messengers between two neighboring cells (1). Recent intense investigations have been pursuing the effects that defects in gap junction proteins, the connexins, have in hereditary diseases. Mutations in the primary sequence of several connexins have been shown to be responsible for several hereditary human diseases including X-linked Charcot-Marie- Tooth demyelinating neuropathies, nonsyndromic sensorineural deafness, erythrokeratodermia and congenital cataractogenesis (c.f. (2, 3) for recent reviews). Many of the published mutations are being investigated thoroughly to determine at what stage and why the protein fails to make functional channels. Steps involved in connexin trafficking and assembly are: translation of the protein; transport from the endoplasmic reticulum to the Golgi apparatus; oligomerization of the subunits into a hexamer (called a connexon); transport of the connexon to non-junctional areas of the plasma membrane; correct docking with a partner connexon from an apposing cell to form a functional intercellular channel; and incorporation into aggregates (gap junction plaques).
Tomography of Carbon Black for Surface Area Measurement
Authors: Hunt E M , Herd CR 
Published: July 2020

Abstract
Currently, the morphology of carbon black is described by distributive morphological properties that are measured using two dimensional TEM projections of the carbon black aggregates. The area, perimeter and several Feret diameters of 2000 such aggregate projections are measured with an automated system and used to calculate a number of parameters including the mean primary particle diameter and the surface area of the carbon black in m2/g. Several assumptions must be made in order to carry out these calculations, the first being that the aggregates are either isotropic or randomly oriented. True random orientation is impossible due to the flat surface on which the carbon black is deposited. For relatively compact spherical, ellipsoidal and linear aggregates this assumption works fairly well. However, the more highly structured a carbon black aggregate is, the worse this assumption becomes. Studies of these types of aggregates have shown that the two dimensional projected area and perimeter can decrease up to 25% as the viewing angle is increased from 0° to 45°. The use of electron tomography to determine surface area will eliminate this problem. in addition, the use of tomographically reconstructed carbon black aggregates for the determination of surface area is a more direct measurement technique, although limitations to its accuracy do exist.
Novel Molecular Specializations of the Pinceau in Rat Cerebellum as Revealed by Correlated Confocal Microscopy and Electron Tomography
Authors: Bobik Marketta , Capani F , Martone M E , Ellisman M 
Published: July 2020

Abstract
The pinceau is a cerebellar structure formed by GABA-ergic descending basket cell axonal terminals converging on the initial axonal segment of Purkinje cell. Although it exerts a powerful inhibitory influence on the output of the cerebellar cortex, the exact ultrastructural organization and function of this structure are not understood. The unique morphology of the pinceau lies in several elements: lack of synaptic contacts between basket cell terminals and the initial axonal segment, the absence of postsynaptic densities, and heavy ensheathment of the initial segment with glial processes, making astrocytes the only intervening cellular element between the two types of axonal structures. Several plasticity related proteins in this area have been previously characterized by immunocytochemistry. Those include nitric oxide synthase, PSD95, GABA transporters, and several voltage gated potassium channel subunits. We are using a combination of confocal and electron microscopy, correlated photooxidation, EM and tomography to reveal the ultrastructural distribution of novel proteins and their relationships to morphological compartments in the pinceau.
We describe here Kv3.2, a recently discovered member of the Shaw-like subfamily of potassium channels, and the correlated distribution of other proteins described below. Pre-embedding immunolabeling, electron microscopy and tomography showed that Kv3.2 was selectively localized to basket cell axons.
Electron Tomography of Insect Flight Muscle in Isometric Contraction and Rigor States
Authors: Taylor Kenneth A 
Published: July 2020

Abstract
Electron microscopy is a technology fully capable of bridging the light microscopic world with the world of protein structure at atomic resolution. There are numerous examples of cases where cryoelectron microscopy has been used to fit an atomic structure into a structure that has been difficult to crystallize for high resolution structure analysis. More difficult is the fitting of atomic structures into more conventionally prepared tissue like that used in freeze substitution.
We have been using electron tomography to obtain 3-D images of insect flight muscle in various states, including those produced in an active isometric contraction as well as in rigor. These tomograms were obtained using non-uniform tilt angles, cross correlation alignment, area matching and Whittaker-Shannon interpolation of the 3-D transform. The fitting of atomic structures into raw tomograms is a difficult proposition because of the relatively highly noisy feature of the images. Better results are obtained when averages are produced. We have used two method for producing averages. One of these, the so-called column average is used when the muscle filaments are relatively straight with good axial order, or can be straightened in 3-D but their lateral ordering is poor. Column averaging improved considerably reduced the noise in tomograms of contracting muscle enabling the four major crossbridge conformation to be observed (Fig. 1).
Ultrastructure of Bone Mineralization and Osseointegration with Hydroxyapatite-Coated Bone Implants in Vivo
Authors: W. Hobbs Linn , Porter AE , Benezra VI , Blunn GW , Coathup MJ , Spector M 
Published: July 2020

Abstract
The need to optimize adhesion between the femoral stem and surrounding tissue has led to the development of plasma-sprayed HA (PSHA) coatings as attachment facilitators for hip prostheses. The mechanisms underlying this facilitation are incompletely understood, and the long-term efficacy of HA coatings in maintaining bonding to bone remains largely unexplored. in this study, two in vivo models—canine and human—were employed for study by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) to elucidate the sequence of early bone mineralization and the longer term fate of HA coatings. High-resolution SEM and TEM of whole bone and anorganic bone were employed to establish the structure of mature bone for comparison.
Whole and Anorganic Bone.Anorganic bone derived from bovine trabecular bone was examined in low-voltage field-emission SEM(LV-FESEM) and high-resolution TEM to establish the morphology of the mineral component of bone [1,2]. Trabeculae were seen to comprise oriented fiber bundles (Fig. 1), each fiber comprising an array of oriented apatite platelets (Fig. 2) arranged like a sheared stack of dominoes with approximately the 64-nm stagger of collagen hole zones.
ESEM Study of Dental Adhesive Polymerization
Authors: Dusevich VM , Eick JD 
Published: July 2020

Abstract
Dental adhesives are bonded to a wet surface of live tissue, dentin. There are two important stages of surface preparation for adhesive application: 1) Etching the tooth structure creating a layer of collagen network free from mineral, and 2) Applying a primer, in this case a water solution of hydrophilic monomer of 2-hydroxyethylmethacrylate (ScotchBond Multipurpose®, 3M). During the priming stage, the resin monomer should penetrate the fibril network and coat collagen fibrils. Subsequent adhesive resin penetration into the collagen network (hybrid layer) is not uniform, influenced by the presence of residual water and degree of resin polymerization. Dependence of bond strength of dental adhesives on time or intensity of light activation is well known, but no direct microscopic observations of the dynamics of polymerization were performed. This was due to the fact that during specimen dehydration for conventional SEM the polymerization process is still proceeding and residual monomer could be washed out.
Molecular-Scale Studies of Proteins at Model Biomaterial Surfaces by Atomic Force Microscopy
Authors: Siedlecki Christopher A 
Published: July 2020

Abstract
A widely accepted tenet of biomaterials research is that the initial step following contact of a synthetic material with blood is the rapid adsorption of plasma proteins. The composition of this adsorbed protein layer is dependent on a variety of factors, including the surface properties of the implant material and the nature of the adsorbing proteins, and the composition and function of this protein layer is important in the subsequent biological response and ultimately the success or failure of the implanted material. While a great amount of effort has gone into developing structure/function responses for implanted biomaterials, there is still much about the molecular level interactions to be determined. We utilized atomic force microscopy (AFM) to investigate the molecular-level interactions of proteins with model biomaterial substrates. The AFM is unique in that it offers the opportunity to characterize interfacial environments, determine material properties, measure protein/surface interaction forces, and visualize the tertiary structure of adsorbed proteins.
Micro-Patterning of Polymers for High Resolution Microscopy Analysis
Authors: Inglis William , Davies Martyn C , Roberts Clive J , Tendler Saul JB , Williams Philip M 
Published: July 2020

Abstract
Micro-patterned surfaces are of interest in biology and chemistry due to the ability to confine functional sample materials to specific areas. If patterns are visible, either through optical microscopy, or topographically, with scanning probe microscopy, investigating samples in a manner that is cheap and accessible to most laboratories is possible. Examples include micropatterning cells in tissue engineering, and protein micro-array analysis. We have created a micro-patterned surface with tailored optical and topographic properties. These were investigated using the microscopy techniques, confocal microscopy (CM), atomic force microscopy (AFM) and near field scanning optical microscopy (NSOM). AFM and CM were used to investigate different aspects of the micro-pattern. to confirm the properties of the micro-pattern, we show the advantages of NSOM in investigating surfaces with both optical and topographic properties simultaneously. Micro-patterns were fabricated using a soft lithography technique, micro-contact printing, where reagents are ‘stamped’ upon substrates using an elastomeric moulding of a micro-template.
Microbial Reduction of Chromium(VI): In-Situ Environmental Cell Transmission Electron Microscopy Study Using Electron Energy Loss Spectroscopy
Authors: Daulton Tyrone L , Little Brenda J , Lowe Kristine , Jones-Meehan Joanne 
Published: July 2020

Abstract
The geochemistry and toxicity of chromium is controlled by its valence state. Chromium is a redox active 3d transition metal with a wide range (− to +6) of possible oxidation states; however only Cr(III) and Cr(VI) are stable. Hexavalent Cr(VI) can be readily reduced to the trivalent state by Fe2+, S2−, organic compounds, wetland plants, and several species of microorganisms. The associated mechanisms of Cr(VI) reduction are technologically and biologically important because they convert a toxic, mobile element into a less toxic, immobile form.
Reduction of Cr(VI) by the bacterium, Shewanella oneidensis (previously classified Shewanella putrefaciens strain MR-1), was studied by absorption spectrophotometry and in-situ, environmental cell (EC) - transmission electron microscopy (TEM) coupled with electron energy loss spectroscopy (EELS). Shewanella oneidensis (S. oneidensis), a gram-negative, facultative bacterium is capable of respiring aerobically and anaerobically using a variety of compounds, including O2, Fe(III), Mn(IV), NO2 −, NO3 −, SO2, SO3 2−, thiosulfate (S2O3 2−), trimethyamine oxide, fumarate, U(VI), and Cr(VI) as terminal electron acceptors.
Holistic Mapping in an Electron Microprobe
Authors: M. MacRae Colin , Wilson NC , Otsuki M 
Published: July 2020

Abstract
When an electron beam interacts with a solid target a number of interactions occur which produce electrons, x-rays and light. Typically in an electron microprobe analyser (EPMA) both the electron and x-ray signals are collected for analysis and imaging. However, if the EPMA is equipped with an optical spectrometer then all three signals can be collected. Commonly, the optical or CathodoLuminescence (CL) spectrometer is a monochromator type and can only collect a single frequency or small range of frequencies at a time. Simultaneous collection of the complete visible spectrum is not possible. The collection optics associated with the spectrometer often must be moved into place to start collection, this then obscures the other detectors and prevents simultaneous collection. At CSIRO Minerals an optical spectrometer has been integrated into a JEOL 8900R EPMA and allows simultaneous collect of all light, x-rays and electron signals. This form of mapping, termed Holistic Mapping, has significant advantages over traditional mapping in that it removes the need to have a priori knowledge about what the important frequencies are that will provide the solution to the problem at hand.
Characterization of Process Induced Contamination and Residues on Semiconductor Components Via FTIR and Raman Microanalysis
Authors: Gotts H 
Published: July 2020

Abstract
FTIR and Raman microanalysis may be used as a powerful combination to determine the identity, and hence infer the source, of contaminant particles which diminish yields of semiconductor components and devices. The complimentarity of these techniques arises from the underlying spectroscopic selection rules.
Vibrational spectroscopic techniques are commonly used to characterize the molecular structure of bulk organic materials. These bulk materials typically represent purified fractions of components which may be further investigated with various classical instrumental techniques such as Differential Scanning Calorimetry (DSC), Nuclear Magnetic Resonance (NMR) spectroscopy, UV-Vis spectroscopy. However, these classical technique may have limited value for the interrogation of small impure particles or materials of limited quantity(ng.).
Elemental techniques such as Scanning Electron Microscopy coupled to Energy Dispersive Spectroscopy are enhanced by the specificity of FTIR Microprobe Spectroscopy and Raman Microprobe Spectroscopy which are now used in process laboratories to characterize and identify particulate and thin film residues with the intent of device yield enhancement.