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Three-dimensional Information (three-dimensional + information)
Selected AbstractsPole figure analysis of mineral nanoparticle orientation in individual trabecula of human vertebral boneJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-1 2003Daniel Jaschouz The spongious interior of human vertebral bone consists of interconnected trabecula with a thickness of about 0.2 mm. The texture of the bone material, a collagen-mineral nanocomposite, was studied within single trabecula by collecting two-dimensional small-angle X-ray scattering (SAXS) and X-ray diffraction (XRD) data exactly at the same specimen positions with an X-ray beam of 0.2 mm diameter. Three-dimensional information was reconstructed by combining measurements with different specimen orientations. The XRD data, and for the first time also the SAXS data, were subjected to a pole figure analysis. The method provides a quantitative description of the crystallographic orientation distribution as well as the morphological orientation distribution of the plate shaped nanoparticles, both with respect to the orientation of the investigated trabecula. As a main result it could be shown that a fibre-texture exists in the trabecula, and that the plate shaped nanoparticles are aligned with the lamellae within the trabecula. [source] Novel affinity tag system using structurally defined antibody-tag interaction: Application to single-step protein purificationPROTEIN SCIENCE, Issue 12 2008Terukazu Nogi Abstract Biologically important human proteins often require mammalian cell expression for structural studies, presenting technical and economical problems in the production/purification processes. We introduce a novel affinity peptide tagging system that uses a low affinity anti-peptide monoclonal antibody. Concatenation of the short recognition sequence enabled the successful engineering of an 18-residue affinity tag with ideal solution binding kinetics, providing a low-cost purification means when combined with nondenaturing elution by water-miscible organic solvents. Three-dimensional information provides a firm structural basis for the antibody,peptide interaction, opening opportunities for further improvements/modifications. [source] STED Microscopy to Monitor Agglomeration of Silica Particles Inside A549 Cells,ADVANCED ENGINEERING MATERIALS, Issue 5 2010Sabrina Schübbe The widespread use of engineered nanomaterials increases the exposure of the materials to humans. Therefore, it is necessary to know how these materials interact with cells. One approach is to trace particles by fluorescent labeling. The aim of the present work was to study the behavior of silica particles in A549 cells. For the first time, we applied stimulated emission depletion (STED) microscopy for this approach. Therefore, SiO2 particles conjugated with Atto647N were prepared by L -arginine-catalyzed hydrolysis of tetraethoxysilane. The Atto647N labeled SiO2 particles exhibit a mean size of 128,±,7,nm and a zeta-potential of ,11,mV in cell culture medium. STED microscopy enables subdiffraction resolution imaging of single Atto647N labeled SiO2 particles not only in pure solution but also in a cellular environment. To visualize Atto647N labeled SiO2 particles inside A549 cells, the membrane was labeled and image stacks, that give three-dimensional information, were taken after 5, 24, and 48 h exposure of particles to cells. During this incubation period, an increase in particle uptake was observed and STED micrographs allowed us to evaluate the agglomeration of Atto647N labeled SiO2 particles inside A549 cells. Our results show that STED microscopy is a powerful technique to study particles in a cellular environment. [source] New dimensions in endodontic imaging: Part 2.INTERNATIONAL ENDODONTIC JOURNAL, Issue 6 2009Cone beam computed tomography Abstract Cone beam computed tomography (CBCT) has been specifically designed to produce undistorted three-dimensional information of the maxillofacial skeleton, including the teeth and their surrounding tissues with a significantly lower effective radiation dose compared with conventional computed tomography (CT). Periapical disease may be detected sooner using CBCT compared with periapical views and the true size, extent, nature and position of periapical and resorptive lesions can be assessed. Root fractures, root canal anatomy and the nature of the alveolar bone topography around teeth may be assessed. The aim of this paper is to review current literature on the applications and limitations of CBCT in the management of endodontic problems. [source] Phlogopite and quartz lamellae in diamond-bearing diopside from marbles of the Kokchetav massif, Kazakhstan: exsolution or replacement reaction?JOURNAL OF METAMORPHIC GEOLOGY, Issue 9 2009L. F. DOBRZHINETSKAYA Abstract Exsolution lamellae of pyroxene in garnet (grt), coesite in titanite and omphacite from UHPM terranes are widely accepted as products of decompression. However, interpretation of oriented lamellae of phyllosilicates, framework silicates and oxides as a product of decompression of pyroxene is very often under debate. Results are presented here of FIB-TEM, FEG-EMP and synchrotron-assisted infrared (IR) spectroscopy studies of phlogopite (Phlog) and phlogopite + quartz (Qtz) lamellae in diamond-bearing clinopyroxene (Cpx) from ultra-high pressure (UHP) marble. These techniques allowed collection of three-dimensional information from the grain boundaries of both the single (phlogopite), two-phase lamellae (phlogopite + quartz), and fluid inclusions inside of diamond included in K-rich Cpx and understanding their relationships and mechanisms of formation. The Cpx grains contain in their cores lamellae-I, which are represented by topotactically oriented extremely thin lamellae of phlogopite (that generally are two units cell wide but locally can be seen to be somewhat broader) and microdiamond. The core composition is: (Ca0.94K0.04Na0.02) (Al0.06Fe0.08Mg0.88) (Si1.98Al0.02)O6.00. Fluid inclusions rich in K and Si are recognized in the core of the Cpx, having no visible connections to the lamellae-I. Lamellar-II inclusions consist of micron-size single laths of phlogopite and lens-like quartz or slightly elongated phlogopite + quartz intergrowths; all are situated in the rim zone of the Cpx. The composition of the rim is (Ca0.95Fe0.03Na0.02) (Al0.05Fe0.05Mg0.90)Si2O6, and the rim contains more Ca, Mg then the core, with no K there. Such chemical tests support our microstructural observations and conclusion that the phlogopite lamellae-I are exsolved from the K-rich Cpx-precursor during decompression. It is assumed that Cpx-precursor was also enriched in H2O, because diamond included in the core of this Cpx contains fluid inclusions. The synchrotron IR spectra of such diamond record the presence of OH, stretching and H2O bending motion regions. Lamellar-II inclusions are interpreted as forming partly because of modification of the lamellae-I in the presence of fluid enriched in K, Fe and Si during deformation of the host diopside; the latter is probably related to the shallower stage of exhumation of the UHP marble. This study emphasizes that in each case to understand the mechanism of lamellar inclusion formation more detailed studies are needed combining both compositional, structural and three-dimensional textural features of lamellar inclusions and their host. [source] Generation and Evaluation of a Homology Model of PfGSK-3ARCHIV DER PHARMAZIE, Issue 6 2009Sebastian Kruggel Abstract Plasmodial GSK-3 is a potential new target for malaria therapy. For a structure-based design project, the three-dimensional information of the designated target is needed. Unfortunately, experimental structure data for plasmodial GSK-3 is not yet available. Homology building can be used to generate such three-dimensional structure data using structure information of a homologous protein. GSK-3 possesses a very flexible ATP-binding site, a fact reflected in the variety of X-ray structures of the human GSK-3, which are deposited in the protein data base and are crystallized with different ligands. We used ten different HsGSK-3, templates for the model building of plasmodial GSK-3 and generated 200 models for each template with different modeling protocols. The quality of the models was evaluated with different tools. The results of these evaluations were used to calculate a rank-by-rank consensus score. The top models of this were used to compile an ensemble of PfGSK-3 models that reflect the flexibility of the ATP-binding site and that will be used for the structure-based design of potential ATP-binding site inhibitors of PfGSK-3. [source] Three-Dimensional Protein,Ligand Interaction Scaling of Two-Dimensional FingerprintsCHEMICAL BIOLOGY & DRUG DESIGN, Issue 5 2009Lu Tan We introduce a computational scaling methodology that utilizes protein,ligand interaction information extracted from complex crystal structures to enrich similarity searching using structural fingerprints with compound class-specific information. Scaling factors are derived to emphasize fingerprint bit positions that result from interacting fragments of bound ligands and correspond to frequently occurring structural features. Through interaction-based scaling, this information is transferred to standard fingerprints of multiple reference compounds. In systematic search calculations, fingerprints scaled on the basis of three-dimensional information are found to produce higher recall rates of active compounds than alternative types of scaled and non-scaled fingerprints. [source] | ||||||||||