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Sample records for structural characterization magnetochemistry

  1. Magnetochemistry of the tetrahaloferrate (III) ions. 7. Crystal structure and magnetic ordering in (pyridinium){sub 3}Fe{sub 2}Br{sub 9}

    SciTech Connect

    Lowe, C.B.; Shaviv, R.; Carlin, R.L.

    1994-07-06

    A monoclinic crystal structure was found by X-ray diffraction for bis [pyridinium tetrabromferrate(III)]-pyridinium bromide. The double salt contains two slightly distorted [FeBr{sub 4}]{sup -} tetrahedra, three pyridinium rings, and an uncoordinated halide in each asymmetric unit, as is characteristic of the A{sub 3}Fe{sub 2}X{sub 9} series of compounds. Unit cell parameters, monoclinic space group P2{sub 1}, are a = 7.656(3) {angstrom}, b = 14.237(5) {angstrom}, c = 13.725(5) {angstrom}, {beta} = 93.42(3){degrees}, and V = 1493(1) {angstrom}{sup 3}, using Mo K{alpha} radiation {lambda} = 0.710 69 {angstrom}, {rho}{sub calc} = 2.38 g cm{sup -3}, and Z = 2. The tetrahedra are aligned with their 3-fold axes parallel to the crystallographic c axis. Bond lengths (Fe-Br) range from 2.271(9) {angstrom} to 2.379(9) {angstrom} for the two different slightly distorted tetrahedral units. Magnetic susceptibility studies show that the material orders three-dimensionally at 7.4 {+-} 0.2 K. The data are compared to a HTS expansion of 1/{sub {chi}} for the S = 5/2 three-dimensional Heisenberg model antiferromagnet for a sc lattice with g = 1.98 and J/k{sub B} = -0.43 K. The specific heat measurements indicate two odd-shaped {lambda} features, at 7.3 and 8 K.

  2. Heterobridged dinuclear, tetranuclear, dinuclear-based 1-d, and heptanuclear-based 1-D complexes of copper(II) derived from a dinucleating ligand: syntheses, structures, magnetochemistry, spectroscopy, and catecholase activity.

    PubMed

    Majumder, Samit; Sarkar, Sohini; Sasmal, Sujit; Sañudo, E Carolina; Mohanta, Sasankasekhar

    2011-08-15

    The work in this paper presents syntheses, characterization, crystal structures, variable-temperature/field magnetic properties, catecholase activity, and electrospray ionization mass spectroscopic (ESI-MS positive) study of five copper(II) complexes of composition [Cu(II)(2)L(μ(1,1)-NO(3))(H(2)O)(NO(3))](NO(3)) (1), [{Cu(II)(2)L(μ-OH)(H(2)O)}(μ-ClO(4))](n)(ClO(4))(n) (2), [{Cu(II)(2)L(NCS)(2)}(μ(1,3)-NCS)](n) (3), [{Cu(II)(2)L(μ(1,1)-N(3))(ClO(4))}(2)(μ(1,3)-N(3))(2)] (4), and [{Cu(II)(2)L(μ-OH)}{Cu(II)(2)L(μ(1,1)-N(3))}{Cu(II)(μ(1,1)-N(3))(4)(dmf)}{Cu(II)(2)(μ(1,1)-N(3))(2)(N(3))(4)}](n)·ndmf (5), derived from a new compartmental ligand 2,6-bis[N-(2-pyridylethyl)formidoyl]-4-ethylphenol, which is the 1:2 condensation product of 4-ethyl-2,6-diformylphenol and 2-(2-aminoethyl)pyridine. The title compounds are either of the following nuclearities/topologies: dinuclear (1), dinuclear-based one-dimensional (2 and 3), tetranuclear (4), and heptanuclear-based one-dimensional (5). The bridging moieties in 1-5 are as follows: μ-phenoxo-μ(1,1)-nitrate (1), μ-phenoxo-μ-hydroxo and μ-perchlorate (2), μ-phenoxo and μ(1,3)-thiocyanate (3), μ-phenoxo-μ(1,1)-azide and μ(1,3)-azide (4), μ-phenoxo-μ-hydroxo, μ-phenoxo-μ(1,1)-azide, and μ(1,1)-azide (5). All the five compounds exhibit overall antiferromagnetic interaction. The J values in 1-4 have been determined (-135 cm(-1) for 1, -298 cm(-1) for 2, -105 cm(-1) for 3, -119.5 cm(-1) for 4). The pairwise interactions in 5 have been evaluated qualitatively to result in S(T) = 3/2 spin ground state, which has been verified by magnetization experiment. Utilizing 3,5-di-tert-butyl catechol (3,5-DTBCH(2)) as the substrate, catecholase activity of all the five complexes have been checked. While 1 and 3 are inactive, complexes 2, 4, and 5 show catecholase activity with turn over numbers 39 h(-1) (for 2), 40 h(-1) (for 4), and 48 h(-1) (for 5) in dmf and 167 h(-1) (for 2) and 215 h(-1) (for 4) in acetonitrile

  3. Synthesis, structural characterization and thermal properties of a new copper(II) one-dimensional coordination polymer based on bridging N,N'-bis(2-hydroxybenzylidene)-2,2-dimethylpropane-1,3-diamine and dicyanamide ligands.

    PubMed

    Hopa, Cigdem; Cokay, Ismail

    2016-02-01

    The design and synthesis of polymeric coordination compounds of 3d transition metals are of great interest in the search for functional materials. The coordination chemistry of the copper(II) ion is of interest currently due to potential applications in the areas of molecular biology and magnetochemistry. A novel coordination polymer of Cu(II) with bridging N,N'-bis(2-hydroxyphenyl)-2,2-dimethylpropane-1,3-diamine (H2L-DM) and dicyanamide (dca) ligands, catena-poly[[[μ2-2,2-dimethyl-N,N'-bis(2-oxidobenzylidene)propane-1,3-diamine-1:2κ(6)O,N,N',O':O,O']dicopper(II)]-di-μ-dicyanamido-1:2'κ(2)N(1):N(5);2:1'κ(2)N(1):N(5)], [Cu2(C19H20N2O2)(C2N3)2]n, has been synthesized and characterized by CHN elemental analysis, IR spectroscopy, thermal analysis and X-ray single-crystal diffraction analysis. Structural studies show that the Cu(II) centres in the dimeric asymmetric unit adopt distorted square-pyramidal geometries, as confirmed by the Addison parameter (τ) values. The chelating characteristics of the L-DM(2-) ligand results in the formation of a Cu(II) dimer with a double phenolate bridge in the asymmetric unit. In the crystal, the dimeric units are further linked to adjacent dimeric units through μ1,5-dca bridges to produce one-dimensional polymeric chains. PMID:26846501

  4. Ultrasonic characterization of structural ceramics

    NASA Technical Reports Server (NTRS)

    Klima, S. J.; Baaklini, G. Y.

    1986-01-01

    Ultrasonic velocity and attenuation measurements were used to characterize density and microstructure in monolithic silicon nitride and silicon carbide. Research samples of these structural ceramics exhibited a wide range of density and microstructural variations. It was shown that bulk density variations correlate with and can be estimated by velocity measurements. Variations in microstructural features such as grain size or shape and pore morphology had a minor effect on velocity. However, these features had a pronounced effect on ultrasonic attenuation. The ultrasonic results are supplemented by low-energy radiography and scanning laser acoustic microscopy.

  5. Automated Characterization Of Vibrations Of A Structure

    NASA Technical Reports Server (NTRS)

    Bayard, David S.; Yam, Yeung; Mettler, Edward; Hadaegh, Fred Y.; Milman, Mark H.; Scheid, Robert E.

    1992-01-01

    Automated method of characterizing dynamical properties of large flexible structure yields estimates of modal parameters used by robust control system to stabilize structure and minimize undesired motions. Based on extraction of desired modal and control-design data from responses of structure to known vibrational excitations. Applicable to terrestrial structures where vibrations are important - aircraft, buildings, bridges, cranes, and drill strings.

  6. Structural characterization of multimetallic nanoparticles

    NASA Astrophysics Data System (ADS)

    Mukundan, Vineetha

    Bimetallic and trimetallic alloy nanoparticles have enhanced catalytic activities due to their unique structural properties. Using in situ time-resolved synchrotron based x-ray diffraction, we investigated the structural properties of nanoscale catalysts undergoing various heat treatments. Thermal treatment brings about changes in particle size, morphology, dispersion of metals on support, alloying, surface electronic properties, etc. First, the mechanisms of coalescence and grain growth in PtNiCo nanoparticles supported on planar silica on silicon were examined in detail in the temperature range 400-900°C. The sintering process in PtNiCo nanoparticles was found to be accompanied by lattice contraction and L10 chemical ordering. The mass transport involved in sintering is attributed to grain boundary diffusion and its corresponding activation energy is estimated from the data analysis. Nanoscale alloying and phase transformations in physical mixtures of Pd and Cu ultrafine nanoparticles were also investigated in real time with in situ synchrotron based x-ray diffraction complemented by ex situ high-resolution transmission electron microscopy. PdCu nanoparticles are interesting because they are found to be more efficient as catalysts in ethanol oxidation reaction (EOR) than monometallic Pd catalysts. The combination of metal support interaction and reactive/non-reactive environment was found to determine the thermal evolution and ultimate structure of this binary system. The composition of the as prepared Pd:Cu mixture in this study was 34% Pd and 66% Cu. At 300°C, the nanoparticles supported on silica and carbon black intermix to form a chemically ordered CsCl-type (B2) alloy phase. The B2 phase transforms into a disordered fcc alloy at higher temperature (>450°C). The alloy nanoparticles supported on silica and carbon black are homogeneous in volume, but evidence was found of Pd surface enrichment. In sharp contrast, when supported on alumina, the two metals

  7. Health Monitoring for Airframe Structural Characterization

    NASA Technical Reports Server (NTRS)

    Munns, Thomas E.; Kent, Renee M.; Bartolini, Antony; Gause, Charles B.; Borinski, Jason W.; Dietz, Jason; Elster, Jennifer L.; Boyd, Clark; Vicari, Larry; Ray, Asok; Cooper, E. G. (Technical Monitor)

    2002-01-01

    This study established requirements for structural health monitoring systems, identified and characterized a prototype structural sensor system, developed sensor interpretation algorithms, and demonstrated the sensor systems on operationally realistic test articles. Fiber-optic corrosion sensors (i.e., moisture and metal ion sensors) and low-cycle fatigue sensors (i.e., strain and acoustic emission sensors) were evaluated to validate their suitability for monitoring aging degradation; characterize the sensor performance in aircraft environments; and demonstrate placement processes and multiplexing schemes. In addition, a unique micromachined multimeasure and sensor concept was developed and demonstrated. The results show that structural degradation of aircraft materials could be effectively detected and characterized using available and emerging sensors. A key component of the structural health monitoring capability is the ability to interpret the information provided by sensor system in order to characterize the structural condition. Novel deterministic and stochastic fatigue damage development and growth models were developed for this program. These models enable real time characterization and assessment of structural fatigue damage.

  8. Experiments In Characterizing Vibrations Of A Structure

    NASA Technical Reports Server (NTRS)

    Yam, Yeung; Hadaegh, Fred Y.; Bayard, David S.

    1993-01-01

    Report discusses experiments conducted to test methods of identification of vibrational and coupled rotational/vibrational modes of flexible structure. Report one in series that chronicle development of integrated system of methods, sensors, actuators, analog and digital signal-processing equipment, and algorithms to suppress vibrations in large, flexible structure even when dynamics of structure partly unknown and/or changing. Two prior articles describing aspects of research, "Autonomous Frequency-Domain Indentification" (NPO-18099), and "Automated Characterization Of Vibrations Of A Structure" (NPO-18141).

  9. Structural characterization of unusually stable polycyclic ozonides

    NASA Astrophysics Data System (ADS)

    Cusati, R. C.; Pereira, U. A.; Barbosa, L. C. A.; Maltha, C. R. A.; Carneiro, José W. M.; Corrêa, R. S.; Doriguetto, A. C.

    2015-02-01

    The single crystal structure of seven tri- and tetracyclic ozonides derived from 8-oxabicycle[3.2.1]oct-6-en-3-ones have been characterized by X-ray diffraction method. Five ozonides (4, 5, 6, 7 and 8) crystallize in the monoclinic crystal system with P21/c space group. Compound 3 crystallize in the unusual centrosymmetric space group R 3 bar m, which represents ∼0.04% of the total number of structures know. The supramolecular structure of 3 forms infinite channels in a hexagram fashion, resulting in a honeycomb-like structure. Semi-empirical (PM6) and density functional theory methods (DFT) with the B3LYP functional and the 6-31G(d) basis set were used to optimize the geometries and compute structural parameters (bond lengths, angles and dihedral angles) that could be compared to the refined crystal structure. The theoretical results show good agreements with the experimental structure.

  10. Electrochemical characterization of InP structures

    NASA Technical Reports Server (NTRS)

    Faur, Maria; Faur, Mircea; Vargas-Aburto, Carlos; Wilt, David M.; Goradia, Manju

    1992-01-01

    Electrochemical (EC) techniques represent a simple and yet accurate method to characterize InP and related materials structures. With EC techniques, uncertainties in the measurements arising from factors such as surface effects, the composition and thickness of a front dead layer, the contacts, etc., can be significantly reduced when both a suitable electrolyte is used and the measuring conditions are carefully selected. In this work, the use of photoelectrochemical techniques with InP structures is reported. The work focuses on both the characterization and the optimization of structures grown by thermal diffusion and by epitaxial methods. Characterization of the structures is done by studying the variation in the density of surface states, number of defects, and net majority carrier concentration as a function of material removed. A step-by-step optimization process of n(sup +)p and p(sup+)n InP structures is also described. This involves the passivation and subsequent removal of damaged layers in order to extract the performance parameters of solar cells fabricated with these structures.

  11. Structural Characterization of Sm(III)(EDTMP).

    PubMed

    Yang, Y; Pushie, M J; Cooper, D M L; Doschak, M R

    2015-11-01

    Samarium-153 ethylenediamine-N,N,N',N'-tetrakis(methylenephosphonic acid) ((153)Sm-EDTMP, or samarium lexidronam), also known by its registered trademark name Quadramet, is an approved therapeutic radiopharmaceutical used in the palliative treatment of painful bone metastases. Typically, patients with prostate, breast, or lung cancer are most likely to go on to require bone pain palliation treatment due to bone metastases. Sm(EDTMP) is a bone-seeking drug which accumulates on rapidly growing bone, thereby delivering a highly region-specific dose of radiation, chiefly through β particle emission. Even with its widespread clinical use, the structure of Sm(EDTMP) has not yet been characterized at atomic resolution, despite attempts to crystallize the complex. Herein, we prepared a 1:1 complex of the cold (stable isotope) of Sm(EDTMP) under alkaline conditions and then isolated and characterized the complex using conventional spectroscopic techniques, as well as with extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional structure calculations, using natural abundance Sm. We present the atomic resolution structure of [Sm(III)(EDTMP)-8H](5-) for the first time, supported by the EXAFS data and complementary spectroscopic techniques, which demonstrate that the samarium coordination environment in solution is in agreement with the structure that has long been conjectured. PMID:26437889

  12. Synthesis and structural characterization of CZTS nanoparticles

    SciTech Connect

    Lydia, R.; Reddy, P. Sreedhara

    2013-06-03

    The CZTS nanoparticles were successfully synthesized by Chemical co-precipitation method with different pH values in the range of 6 to 8. The synthesized nanoparticles were characterized by X-ray diffraction, scanning electron microscopy and energy dispersive spectroscopy. XRD studies revealed that the CZTS nanoparticles exhibited Kesterite Structure with preferential orientation along the (112) direction. Sample at pH value of 7 reached the nearly stoichiometric ratio.

  13. Instrumentation for the Characterization of Inflatable Structures

    NASA Technical Reports Server (NTRS)

    Swanson, Gregory T.; Cassell, Alan M.; Johnson, R. Keith

    2012-01-01

    Current entry, descent, and landing technologies are not practical for heavy payloads due to mass and volume constraints dictated by limitations imposed by launch vehicle fairings. Therefore, new technologies are now being explored to provide a mass- and volume-efficient solution for heavy payload capabilities, including Inflatable Aerodynamic Decelerators (IAD) [1]. Consideration of IADs for space applications has prompted the development of instrumentation systems for integration with flexible structures to characterize system response to flight-like environment testing. This development opportunity faces many challenges specific to inflatable structures in extreme environments, including but not limited to physical flexibility, packaging, temperature, structural integration and data acquisition [2]. In the spring of 2012, two large scale Hypersonic Inflatable Aerodynamic Decelerators (HIAD) will be tested in the National Full-Scale Aerodynamics Complex s 40 by 80 wind tunnel at NASA Ames Research Center. The test series will characterize the performance of a 3.0 m and 6.0 m HIAD at various angles of attack and levels of inflation during flight-like loading. To analyze the performance of these inflatable test articles as they undergo aerodynamic loading, many instrumentation systems have been researched and developed. These systems will utilize new experimental sensing systems developed by the HIAD ground test campaign instrumentation team, in addition to traditional wind tunnel sensing techniques in an effort to improve test article characterization and model validation. During the 2012 test series the instrumentation systems will target inflatable aeroshell static and dynamic deformation, structural strap loading, surface pressure distribution, localized skin deflection, and torus inflation pressure. This paper will offer an overview of inflatable structure instrumentation, and provide detail into the design and implementation of the sensors systems that will

  14. Structural Characterization of LRRK2 Inhibitors.

    PubMed

    Gilsbach, Bernd K; Messias, Ana C; Ito, Genta; Sattler, Michael; Alessi, Dario R; Wittinghofer, Alfred; Kortholt, Arjan

    2015-05-14

    Kinase inhibition is considered to be an important therapeutic target for LRRK2 mediated Parkinson's disease (PD). Many LRRK2 kinase inhibitors have been reported but have yet to be optimized in order to qualify as drug candidates for the treatment of the disease. In order to start a structure-function analysis of such inhibitors, we mutated the active site of Dictyostelium Roco4 kinase to resemble LRRK2. Here, we show saturation transfer difference (STD) NMR and the first cocrystal structures of two potent in vitro inhibitors, LRRK2-IN-1 and compound 19, with mutated Roco4. Our data demonstrate that this system can serve as an excellent tool for the structural characterization and optimization of LRRK2 inhibitors using X-ray crystallography and NMR spectroscopy. PMID:25897865

  15. Nondestructive characterization of structural ceramic components

    SciTech Connect

    Ellingson, W.A.; Steckenrider, J.S.; Sivers, E.A.; Ling, J.R.

    1994-06-01

    Advanced structural ceramic components under development for heat-engine applications include both monolithic and continuous fiber composites (CFC). Nondestructive characterization (NDC) methods being developed differ for each material system. For monolithic materials, characterization during processing steps is important. For many CFC, only post process characterization is possible. Many different NDC systems have been designed and built A 3D x-ray micro computed tomographic (3DXCT) imaging system has been shown to be able to map density variations to better than 3% in pressure slip cast Si{sub 3}N{sub 4} monolithic materials. In addition, 3DXCT coupled to image processing has been shown to be able to map through-thickness fiber orientations in 2D lay-ups of 0{degrees}/45{degrees}, 0{degrees}/75{degrees}, 0{degrees}/90{degrees}, in SiC/SiC CVI CFC. Fourier optics based laser scatter systems have been shown to be able to detect surface and subsurface defects (as well as microstructural variations) in monolithic Si{sub 3}N{sub 4} bearing balls. Infrared methods using photothermal excitation have been shown to be able to detect and measure thermal diffusivity differences on SiC/SiC 2D laminated CFC which have been subjected to different thermal treatments including thermal shock and oxidizing environments. These NDC methods and their applications help provide information to allow reliable usage of ceramics in advanced heat engine applications.

  16. Diffractaic acid: Crystalline structure and physicochemical characterization

    NASA Astrophysics Data System (ADS)

    de Castro Fonseca, Jéssica; de Oliveira, Yara Santiago; Bezerra, Beatriz P.; Ellena, Javier; Honda, Neli Kika; Silva, Camilla V. N. S.; da Silva Santos, Noemia Pereira; Santos-Magalhães, Nereide Stela; Ayala, Alejandro Pedro

    2016-08-01

    Diffractaic acid (DA) is a secondary metabolite of lichens that belongs to the chemical class of depsides, and some relevant pharmacological properties are associated with this natural product, such as antioxidant, antiulcerogenic and gastroprotective effects. Considering the relevant biological activities and taking into account that the activities are intrinsically related to the structure, the main goal of this study was to elucidate the structure of diffractaic acid by single crystal X-ray diffraction as well to characterize its physicochemical properties by powder X-ray diffraction, thermal analysis and vibrational spectroscopy. It was observed that DA belongs to the monoclinic crystal system, crystallizing in the space group P21/c with the following cell parameters: a = 18.535(7) Å, b = 4.0439(18) Å, c = 23.964(6) Å, β = 91.55(3)°. The crystal packing is characterized by difractaic acid dimers, which are reflected in the vibrational spectrum. These observations were supported by quantum mechanical calculations.

  17. Thermomechanical characterization and modeling for TSV structures

    SciTech Connect

    Jiang, Tengfei; Zhao, Qiu; Im, Jay; Ho, Paul S.; Ryu, Suk-Kyu; Huang, Rui

    2014-06-19

    Continual scaling of devices and on-chip wiring has brought significant challenges for materials and processes beyond the 32-nm technology node in microelectronics. Recently, three-dimensional (3-D) integration with through-silicon vias (TSVs) has emerged as an effective solution to meet the future technology requirements. Among others, thermo-mechanical reliability is a key concern for the development of TSV structures used in die stacking as 3-D interconnects. This paper presents experimental measurements of the thermal stresses in TSV structures and analyses of interfacial reliability. The micro-Raman measurements were made to characterize the local distribution of the near-surface stresses in Si around TSVs. On the other hand, the precision wafer curvature technique was employed to measure the average stress and deformation in the TSV structures subject to thermal cycling. To understand the elastic and plastic behavior of TSVs, the microstructural evolution of the Cu vias was analyzed using focused ion beam (FIB) and electron backscattering diffraction (EBSD) techniques. Furthermore, the impact of thermal stresses on interfacial reliability of TSV structures was investigated by a shear-lag cohesive zone model that predicts the critical temperatures and critical via diameters.

  18. Closed benchmarks for network community structure characterization

    NASA Astrophysics Data System (ADS)

    Aldecoa, Rodrigo; Marín, Ignacio

    2012-02-01

    Characterizing the community structure of complex networks is a key challenge in many scientific fields. Very diverse algorithms and methods have been proposed to this end, many working reasonably well in specific situations. However, no consensus has emerged on which of these methods is the best to use in practice. In part, this is due to the fact that testing their performance requires the generation of a comprehensive, standard set of synthetic benchmarks, a goal not yet fully achieved. Here, we present a type of benchmark that we call “closed,” in which an initial network of known community structure is progressively converted into a second network whose communities are also known. This approach differs from all previously published ones, in which networks evolve toward randomness. The use of this type of benchmark allows us to monitor the transformation of the community structure of a network. Moreover, we can predict the optimal behavior of the variation of information, a measure of the quality of the partitions obtained, at any moment of the process. This enables us in many cases to determine the best partition among those suggested by different algorithms. Also, since any network can be used as a starting point, extensive studies and comparisons can be performed using a heterogeneous set of structures, including random ones. These properties make our benchmarks a general standard for comparing community detection algorithms.

  19. Structural characterization of rotor blades through photogrammetry

    NASA Astrophysics Data System (ADS)

    Bernardini, Giovanni; Serafini, Jacopo; Enei, Claudio; Mattioni, Luca; Ficuciello, Corrado; Vezzari, Valerio

    2016-06-01

    This paper deals with the use of photogrammetry for the experimental identification of structural and inertial properties of helicopter rotor blades4. The identification procedure is based upon theoretical/numerical algorithms for the evaluation of mass and flexural stiffness distributions which are an extension of those proposed in the past by Larsen, whereas the torsional properties (stiffness and shear center position) are determined through the Euler–Bernoulli beam theory. The identification algorithms require the knowledge of the blade displacement field produced by known steady loads. These data are experimentally obtained through photogrammetric detection technique, which allows the identification of 3D coordinates of labeled points (markers) on the structure through the correlation of 2D digital photos. Indeed, the displacement field is simply evaluated by comparing the markers positions on the loaded configuration with those on the reference one. The proposed identification procedure, numerically and experimentally validated in the past by the authors, has been here applied to the structural characterization of two main rotor blades, designed for ultra-light helicopters. Strain gauges measurements have been used to assess the accuracy of the identified properties through natural frequencies comparison as well as to evaluate the blades damping characteristics.

  20. Structural characterization of copolymer embedded magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Nedelcu, G. G.; Nastro, A.; Filippelli, L.; Cazacu, M.; Iacob, M.; Rossi, C. Oliviero; Popa, A.; Toloman, D.; Dobromir, M.; Iacomi, F.

    2015-10-01

    Small magnetic nanoparticles (Fe3O4) were synthesized by co-precipitation and coated by emulsion polymerization with poly(methyl methacrylate-co-acrylic acid) (PMMA-co-AAc) to create surface functional groups that can attach drug molecules and other biomolecules. The coated and uncoated magnetite nanoparticles were stored for two years in normal closed ships and than characterized by Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy, vibrating sample magnetometry, and electron paramagnetic resonance spectroscopy. The solid phase transformation of magnetite to maghemite, as well as an increase in particle size were evidenced for the uncoated nanoparticles. The coated nanoparticles preserved their magnetite structure and magnetic properties. The influences of monomers and surfactant layers on interactions between the magnetic nanoparticles evidenced that the thickness of the polymer has a significant effect on magnetic properties.

  1. Structural Characterization of Bimetallic Nanocrystal Electrocatalysts

    SciTech Connect

    Cullen, David A

    2016-01-01

    Late transition metal nanocrystals find applications in heterogeneous catalysis such as plasmon-enhanced catalysis and as electrode materials for fuel cells, a zero-emission and sustainable energy technology. Their commercial viability for automotive transportation has steadily increased in recent years, almost exclusively due to the discovery of more efficient bimetallic nanocatalysts for the oxygen reduction reaction (ORR) at the cathode. Despite improvements to catalyst design, achieving high activity while maintaining durability is essential to further enhance their performance for this and other important applications in catalysis. Electronic effects arising from the generation of metal-metal interfaces, from plasmonic metals, and from lattice distortions, can vastly improve sorption properties at catalytic surfaces, while increasing durability.[1] Multimetallic lattice-strained nanoparticles are thus an interesting opportunity for fundamental research.[2,3] A colloidal synthesis approach is demonstrated to produce AuPd alloy and Pd@Au core-shell nanoicosahedra as catalysts for electro-oxidations. The nanoparticles are characterized using aberration-corrected scanning transmission electron microscopy (ac-STEM) and large solid angle energy dispersive X-ray spectroscopy (EDS) on an FEI Talos 4-detector STEM/EDS system. Figure 1 shows bright-field (BF) and high-angle annular dark-field (HAADF) ac-STEM images of the alloy and core-shell nanoicosahedra together with EDS line-scans and elemental maps. These structures are unique in that the presence of twin boundaries, alloying, and core-shell morphology could create highly strained surfaces and interfaces. The shell thickness of the core-shell structures observed in HAADF-STEM images is tuned by adjusting the ratio between metal precursors (Figure 2a-f) to produce shells ranging from a few to several monolayers. Specific activity was measured in ethanol electro-oxidation to examine the effect of shell thickness on

  2. Structural Characterization of Crystalline Ice Nanoclusters

    NASA Technical Reports Server (NTRS)

    Blake, David

    2000-01-01

    Water ice nanoclusters are useful analogs for studying a variety of processes that occur within icy grains in the extraterrestrial environment. The surface of ice nanoclusters prepared in the laboratory is similar to the surface of interstellar ice grains. In cold molecular clouds, the silicate cores of interstellar grains are typically approx. 100 nm in diameter and have a coating of impure amorphous water ice. Depositional, thermal and radiolytic processes leave the surface and subsurface molecules in a disordered state. In this state, structural defects become mobile and reactions of trapped gases and small molecules can occur. The large surface area of nanocluster deposits relative to their bulk allows for routine observation of such surface-mediated processes. Furthermore, the disordered surface and subsurface layers in nanocluster deposits mimic the structure of amorphous ice rinds found on interstellar dust grains. Transmission Electron Microscopy (TEM has been used tn characterize the crystallinity, growth mechanism, and size distribution of nanoclusters formed from a mixture of water vapor with an inert carrier gas that has been rapidly cooled to 77K. E M imaging reveals a Gaussian size distribution around a modal diameter that increases from approx. 15 to 30 nm as the percentage of water vapor within the mixture increases from 0.5 to 2.007, respectively . TEM bright and dark field imaging also reveals the crystalline nature of the clusters. h4any of the clusters show a mosaic structure in which crystalline domains originate at the center Other images show mirror planes that are separated by approx. 10 nm. Electron diffraction patterns of these clusters show that the clusters are composed of cubic ice with only a small hexagonal component. Further, the crystalline domain size is approximately the same as the modal diameter suggesting that the clusters are single crystals.

  3. Structure and Characterization of Eriphia verrucosa Hemocyanin.

    PubMed

    Dolashki, A; Radkova, M; Todorovska, E; Ivanov, M; Stevanovic, S; Molin, L; Traldi, P; Voelter, W; Dolashka, P

    2015-12-01

    Arthropod hemocyanins (Hcs) are a family of large extracellular oxygen-transporting proteins with high molecular mass and hexameric or multi-hexameric molecular assembly. This study reports for the first time the isolation and characterization of the structure of an arthropod hemocyanin from crab Eriphia verrucosa (EvH) living in the Black Sea. Its oligomeric quaternary structure is based on different arrangements of a basic 6 × 75 kDa hexameric unit, and four of them (EvH1, EvH2, EvH3, and EvH4) were identified using ion-exchange chromatography. Subunit 3 (EvH3) shows high similarity scores (75.0, 87.5, 91.7, and 75.0 %, respectively) by comparison of the N-terminal sequence of subunit 1 from Cancer pagurus of the North Sea (Cp1), subunits 3 and 6 of Cancer magister (Cm3 and Cm6), and subunit 2 of Carcinus aestuarii (CaSS2), respectively. Moreover, a partial cDNA sequence (1309 bp) of E. verrucosa hemocyanin encoding a protein of 435 amino acids was isolated. The deduced amino acid sequence shows a high degree of similarity with subunits 3, 4, 5, and 6 of C. magister (81-84 %). Most of the hemocyanins are glycosylated, and three putative O-linkage sites were identified in the partial amino acid sequence of EvH at positions 444-446, 478-480, and 547-549, respectively. The higher stability of native Hc in comparison to its subunit EvH4 as determined by circular dichroism (CD) could be explained with the formation of a stabilizing quaternary structure. PMID:26256301

  4. Structural characterization of allomelanin from black oat.

    PubMed

    Varga, Mónika; Berkesi, Ottó; Darula, Zsuzsanna; May, Nóra Veronika; Palágyi, András

    2016-10-01

    The brown to black coloration found in plants is due to the melanins, which have been relatively poorly investigated among the plant pigments. The aim of this work was to study the dark pigment extracted from the black oat hull with respect to composition and structure. Ultraviolet-visible (UV-Vis) spectroscopy, electron paramagnetic resonance (EPR) spectroscopy, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and Fourier transform infrared (FT-IR) spectroscopy were applied for the characterization of the pigment. UV-Vis spectroscopy revealed that the extracted material displays a broadband, structureless absorption profile a common feature of melanins. MALDI-TOF MS measurements demonstrated that oat melanin is a homopolymer built up from p-coumaric acid and consists mainly of low molecular weight (527-1499 Da) oligomers of 3-9 monomer units. The tetramer oligomer proved to be dominant. The results of the FT-IR analysis indicated that oat melanin is a fully conjugated aromatic system containing tetrasubstituted aromatic rings linked by CC coupling. The in vitro preparation of melanin from p-coumaric acid by horseradish peroxidase was performed for comparison. The resulting polymer consisted of oligomers of 4-9 monomer units similarly to those in oat melanin. However, the building blocks proved to be connected to each other via COC linkages in contrast with the CC linkages in oat melanin. PMID:27427433

  5. Statistical characterization of phenolic-novolak structures

    NASA Technical Reports Server (NTRS)

    Parker, J. A.; Winkler, E. L.

    1971-01-01

    Three statistical methods of general validity are valuable for characterizing any polymer which results from chain polymerization of multifunctional branching monomers linked through bifunctional monomers.

  6. Structural Characterization of Nanoporous Pmssq Thin Films

    NASA Astrophysics Data System (ADS)

    Briber, R. M.; Yang, G. Y.; Huang, E.; Kim, H. C.; Rice, P. M.; Volksen, W.; Miller, R. D.; Shin, K.

    2002-03-01

    The semiconductor industry roadmap requires the next generation of interlayer dielectric materials to have a dielectric constant k below 2.0 and thermal stability to 500 ^oC. Porous Dielectrics are an attractive route to obtain such materials. One potential system is polymethylsilsesquioxane (PMSSQ) with nanometer sized pores templated by the incorporation of a thermally degradable polymer. Film were prepared by dissolving the matrix precursor materials (MSSQ oligomer mixture) and porogen (PMMA-co-DMAEMA) as a template for creating the pores in a common solvent (propylene glycol methyl ether) and spin casting onto a silicon single crystal substrate. The film is subjected to an initial heat treatment in nitrogen at 225^oC to cure the matrix (i.e. polymerize and cross-link) and then a second heat treatment to 375 450^oC to degrade the porogen to form the pores. The pore evolution and characterization are performed using small angle neutron scattering (SANS), transmission electron microscopy (TEM) and neutron reflectivity (NR). In-situ SANS experiments revealed that the pores evolution follows a process of phase separation and burnout of the porogen copolymer. TEM observation shows that pore size, morphology and spatial distribution depend on the concentration of porogen in the original hybrid material. Average pore size increases as a function of porogen concentration. Porous morphology changes from isolated pores at low porogen concentration (<10 wt. %) to fully interconnected pores at higher porogen concentration (>40 wt. %). Percolation threshold is located at 30 wt. % porogen content. Neutron reflectivity is used to study the pore structure and distribution normal to the film thickness.

  7. Structural and magnetic characterization of actinide materials

    SciTech Connect

    Cort, B.; Allen, T.H.; Lawson, A.C.

    1998-12-31

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at Los Alamos National Laboratory (LANL). The authors have successfully used neutron scattering techniques to investigate physicochemical properties of elements, compounds, and alloys of the light actinides. The focus of this work is to extend the fundamental research capability and to address questions of practical importance to stockpile integrity and long-term storage of nuclear material. Specific subject areas are developing neutron diffraction techniques for smaller actinide samples; modeling of inelastic scattering data for actinide metal hydrides; characterizing actinide oxide structures; and investigating aging effects in actinides. These studies utilize neutron scattering supported by equilibrium studies, kinetics, and x-ray diffraction. Major accomplishments include (1) development of encapsulation techniques for small actinide samples and neutron diffraction studies of AmD{sub 2.4} and PuO{sub 2.3}; (2) refinement of lattice dynamics model to elucidate hydrogen-hydrogen and hydrogen-metal interactions in rare-earth and actinide hydrides; (3) kinetic studies with PuO{sub 2} indicating that the recombination reaction is faster than radiolytic decomposition of adsorbed water but a chemical reaction produces H{sub 2}; (4) PVT studies of the reaction between PuO{sub 2} and water demonstrate that PuO{sub 2+x} and H{sub 2} form and that PuO{sub 2} is not the thermodynamically stable form of the oxide in air; and (5) model calculations of helium in growth in aged plutonium predicting bubble formation only at grain boundaries at room temperature. The work performed in this project has application to fundamental properties of actinides, aging, and long-term storage of plutonium.

  8. Structural characterization of soy protein nanoparticles from high shear microfluidization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soy protein nanoparticles were produced with a microfluidizer and characterized in terms of particle size, size distribution, morphology, rheological properties, and aggregate structure. Three stages of structure breakdown were observed when the soy protein dispersion was passed through the microflu...

  9. Structural characterization of human Uch37

    SciTech Connect

    Burgie, E. Sethe; Bingman, Craig A.; Soni, Ameet B.; Phillips, Jr., George N.

    2012-06-28

    Uch37 is a deubiquitylating enzyme (DUB) that is functionally linked with multiple protein complexes and signal transduction pathways. Uch37 associates with the 26S proteasome through Rpn13 where it serves to remove distal ubiquitin moeities from polyubiquitylated proteins. Uch37's proteasome associated activity was shown to liberate proteins from destruction. However, Uch37 may also specifically facilitate the destruction of inducible nitric oxide synthase and I{kappa}B-{alpha} at the proteasome. Wicks et al. established Uch37's potential to modulate the transforming growth factor-{beta}(TGF-{beta}) signaling cascade, through tis interaction with SMAD7. Yao et al. demonstrated that Uch37 also associates with the Ino80 chromatin-remodeling complex (Ino80 complex), which is involved in DNA repair and transcriptional regulation. Uch37's importance in metazoan development was underscored recently as Uch37 knockouts in mice result in prenatal lethality, where mutant embryos had severe defects in brain development. Protein ubiquitylation is an ATP-dependent post-translational modification that serves to signal a wide variety of cellular processes in eukaryotes. A protein cascade, generally comprising three enzymes, functions to activate, transport and specifically transfer ubiquitin to the targeted protein, culminating in an isopeptide linkage between the {epsilon}-amino group of a target protein's lysysl residue and the ubiquitin's terminal carboxylate. Monoubiquitination plays an important role in histone regulation, endocytosis, and viral budding. Further processing of the target protein may be accomplished by ubiquitylation of the protein on a different lysine, or through the formation of polyubiquitin chains, where the best-characterized outcome is destruction of the polyubiquitin-labeled protein in the proteasome. DUBs catalyze the removal of ubiquitin from proteins. This activity serves to reverse the effects of ubiquitination, permit ubiquitin recycling, or

  10. Characterization of Vapor Deposited Nano Structured Membranes

    SciTech Connect

    Jankowski, A; Cherepy, N; Ferreira, J; Hayes, J

    2004-03-25

    The vapor deposition methods of planar magnetron sputtering and electron-beam evaporation are used to synthesize materials with nano structured morphological features that have ultra-high surface areas with continuous open porosity at the nano scale. These nano structured membranes are used in a variety of fuel cells to provide electrode and catalytic functions. Specifically, stand alone and composite nickel electrodes for use in thin film solid-oxide, and molten carbonate fuel cells are formed by sputter deposition and electron bean evaporation, respectively. Also, a potentially high-performance catalyst material for the direct reformation of hydrocarbon fuels at low temperatures is deposited as a nano structure by the reactive sputtering of a copper-zinc alloy using a partial pressure of oxygen at an elevated substrate temperature.

  11. Characterization of structural connections for multicomponent systems

    NASA Technical Reports Server (NTRS)

    Lawrence, Charles; Huckelbridge, Arthur A.

    1988-01-01

    This study explores combining Component Mode Synthesis methods for coupling structural components with Parameter Identification procedures for improving the analytical modeling of the connections. Improvements in the connection stiffness and damping properties are computed in terms of physical parameters so that the physical characteristics of the connections can be better understood, in addition to providing improved input for the system model.

  12. Structural characterization of alpha-zein.

    PubMed

    Momany, Frank A; Sessa, David J; Lawton, John W; Selling, Gordon W; Hamaker, Sharon A H; Willett, Julious L

    2006-01-25

    A variety of published physical measurements, computational algorithms, and structural modeling methods have been used to create a molecular model of 19 kDa alpha-zein (Z19). Zetaeins are water-insoluble storage proteins found in corn protein bodies. Analyses of the protein sequence using probability algorithms, structural studies by circular dichroism, infrared spectroscopy, small-angle X-ray scattering (SAXS), light scattering, proton exchange, NMR, and optical rotatory dispersion experiments suggest that Z19 has approximately 35-60% helical character, made up of nine helical segments of about 20 amino acids with glutamine-rich "turns" or "loops". SAXS and light-scattering experiments suggest that in alcohol/water mixtures alpha-zein exists as an oblong structure with an axial ratio of approximately 6:1. Furthermore, ultracentifugation, birefringence, dielectric, and viscosity studies indicate that alpha-zein behaves as an asymmetric particle with an axial ratio of from 7:1 to 28:1. Published models of alpha-zein to date have not been consistent with the experimental data, and for this reason the structure was re-examined using molecular mechanics and dynamics simulations creating a new three-dimensional (3D) structure for Z19. From the amino acid sequence and probability algorithms this analysis suggested that alpha-zein has coiled-coil tendencies resulting in alpha-helices with about four residues per turn in the central helical sections with the nonpolar residue side chains forming a hydrophobic face inside a triple superhelix. The nine helical segments of the 19 kDa protein were modeled into three sets of three interacting coiled-coil helices with segments positioned end to end. The resulting structure lengthens with the addition of the N- and C-terminal sections, to give an axial ratio of approximately 6 or 7:1 in agreement with recent experiments. The natural carotenoid, lutein, is found to fit into the core of the triple-helical segments and help stabilize

  13. Large space structures control algorithm characterization

    NASA Technical Reports Server (NTRS)

    Fogel, E.

    1983-01-01

    Feedback control algorithms are developed for sensor/actuator pairs on large space systems. These algorithms have been sized in terms of (1) floating point operation (FLOP) demands; (2) storage for variables; and (3) input/output data flow. FLOP sizing (per control cycle) was done as a function of the number of control states and the number of sensor/actuator pairs. Storage for variables and I/O sizing was done for specific structure examples.

  14. Structural characterization of carangid fish myoglobins.

    PubMed

    Hasan, Muhammad Mehedi; Watabe, Shugo; Ochiai, Yoshihiro

    2012-10-01

    The primary structures of myoglobin (Mb) from the following five carangid species were determined: yellowtail Seriola quinqueradiata, greater amberjack Seriola dumerili, yellowtail kingfish Seriola lalandi, Japanese horse mackerel Trachurus japonicus, and silver trevally Pseudocaranx dentex. The sequences were of varying composition both in the coding and in the noncoding regions, but all contained the open reading frame of 444 nucleotides encoding 147 amino acids. Amino acid sequence identities of carangid Mbs were in the range of 81-99%. The similarity of the heme pocket and associated heme-binding residues of carangid Mbs were evidence of the conservative nature of Mbs. Similar to the other teleost Mbs, carangid Mbs did not contain a D helix and had mostly conserved A and E helices as well as E-F and G-H inter-helical segments. Hydropathy profiles of carangid Mbs showed species-specific variations where silver trevally Mb exhibited generally higher hydrophobicity. Phylogenetic analysis based on the primary structures was in agreement with conventional morphological taxonomy, establishing close proximity of carangid Mbs with those of cichlid and scombroid, the other members of the Perciformes order. PMID:22361749

  15. Characterizing the spatial structure of songbird cultures.

    PubMed

    Laiolo, Paola

    2008-10-01

    Recent advances have shown that human-driven habitat transformations can affect the cultural attributes of animal populations in addition to their genetic integrity and dynamics. Here I propose using the song of oscine birds for identifying the cultural spatial structure of bird populations and highlighting critical thresholds associated with habitat fragmentation. I studied song variation over a wide geographical scale in a small and endangered passerine, the Dupont's Lark Chersophilus duponti, focusing on (1) cultural population structure, to determine a statistical representation of spatial variation in song and identify cultural units, and (2) the minimum patch size needed for an individual to develop a stable repertoire. I found that overall song diversity depends on variation among populations (beta-cultural diversity). Abrupt thresholds occurred in the relationships between individual song dissimilarity and geographic distance, and between individual song diversity and patch area. Spatial autocorrelation analysis showed that populations located as little as 5 km apart may have independently evolved their song traditions. Song diversity stabilized in patches as small as 100 ha supporting as few as 8-20 males. Song repertoires of smaller patches were significantly poorer. Almost one-quarter of the study populations inhabited patches <100 ha, and their cultural traditions appear to have eroded. The analysis of spatial patterns in birdsong may be a useful tool for detecting subpopulations prone to extinction. PMID:18839771

  16. Structural Characterization of Methanol Substituted Lanthanum Halides

    PubMed Central

    Boyle, Timothy J.; Ottley, Leigh Anna M.; Alam, Todd M.; Rodriguez, Mark A.; Yang, Pin; Mcintyre, Sarah K.

    2010-01-01

    The first study into the alcohol solvation of lanthanum halide [LaX3] derivatives as a means to lower the processing temperature for the production of the LaBr3 scintillators was undertaken using methanol (MeOH). Initially the de-hydration of {[La(µ-Br)(H2O)7](Br)2}2 (1) was investigated through the simple room temperature dissolution of 1 in MeOH. The mixed solvate monomeric [La(H2O)7(MeOH)2](Br)3 (2) compound was isolated where the La metal center retains its original 9-coordination through the binding of two additional MeOH solvents but necessitates the transfer of the innersphere Br to the outersphere. In an attempt to in situ dry the reaction mixture of 1 in MeOH over CaH2, crystals of [Ca(MeOH)6](Br)2 (3) were isolated. Compound 1 dissolved in MeOH at reflux temperatures led to the isolation of an unusual arrangement identified as the salt derivative {[LaBr2.75•5.25(MeOH)]+0.25 [LaBr3.25•4.75(MeOH)]−0.25} (4). The fully substituted species was ultimately isolated through the dissolution of dried LaBr3 in MeOH forming the 8-coordinated [LaBr3(MeOH)5] (5) complex. It was determined that the concentration of the crystallization solution directed the structure isolated (4 concentrated; 5 dilute) The other LaX3 derivatives were isolated as [(MeOH)4(Cl)2La(µ-Cl)]2 (6) and [La(MeOH)9](I)3•MeOH (7). Beryllium Dome XRD analysis indicated that the bulk material for 5 appear to have multiple solvated species, 6 is consistent with the single crystal, and 7 was too broad to elucidate structural aspects. Multinuclear NMR (139La) indicated that these compounds do not retain their structure in MeOD. TGA/DTA data revealed that the de-solvation temperatures of the MeOH derivatives 4 – 6 were slightly higher in comparison to their hydrated counterparts. PMID:20514349

  17. Structural characterization of nanowires and nanowire arrays

    NASA Astrophysics Data System (ADS)

    Becker, Catherine Rose

    Nanowires, which have diameter less than a few hundred nanometers and high aspect ratios, may have the same properties as their corresponding bulk materials, or may exhibit unique properties due to their confined dimensions and increased surface to volume ratios. They are a popular field of technological investigation in applications that depend on the transport of charge carriers, because of expectations that microcircuit miniaturization will lead to the next boom in the electronics industry. In this work, the high spatial resolution afforded by transmission electron microscopy (TEM) is used to study nanowires formed by electrochemical deposition into porous alumina templates. The goal is to determine the effect of the synthesis and subsequent processing on the microstructure and crystallinity of the wires. A thorough understanding of the microstructural features of a material is vital for optimizing its performance in a desired application. Two material systems were studied in this work. The first is bismuth telluride (Bi 2Te3), which is used in thermoelectric applications. The second is metallic copper, the electrochemical deposition of which is of interest for interconnects in semiconductor devices. The first part of this work utilized TEM to obtain a thorough characterization of the microstructural features of individual Bi2Te3 nanowires following release from the templates. As deposited, the nanowires are fine grained and exhibit significant lattice strain. Annealing increases the grain size and dislocations are created to accommodate the lattice strain. The degree of these microstructural changes depends on the thermal treatment. However, no differences were seen in the nanowire microstructure as a function of the synthetic parameters. The second part of this work utilized a modified dark field TEM technique in order to obtain a spatially resolved, semi-quantitative understanding of the evolution of preferred orientation as a function of the electrochemical

  18. Fine-structural characterization of plant microbodies.

    PubMed

    Frederick, S E; Newcomb, E H; Vigil, E L; Wergin, W P

    1968-09-01

    Morphology and distribution of the relatively less well known organelles of plants have been studied with the electron microscope in tissues fixed in glutaraldehyde and postfixed in osmium tetroxide. An organelle comparable morphologically to the animal microbody and similar to the plant microbody isolated by MOLLENHAUER et al. (1966) has been encountered in a variety of plant species and tissues, and has been studied particularly in bean and radish roots, oat coleoptiles, and tobacco roots, stems and callus. The organelle has variable shape and is 0.5 to 1.5 μ in the greatest diameter. It has a single bounding membrane, a granular to fibrillar matrix of variable electron density, and an intimate association with one or two cisternae of rough endoplasmic reticulum (ER). Microbodies are easily the most common and generally distributed of the less well characterized organelles of plant cells. It seems very probable that they contain the enzymes characteristic of animal lysosomes (containing hydrolases) or animal microbodies (containing catalase and certain oxidases). Spherosomes are also possible sites of enzyme activity but are not as common or as widely distributed as microbodies. For this reason it appears likely that the particles designated as "plant lysosomes", "spherosomes", "peroxisomes", etc., in some of the cytochemical and biochemical studies on enzyme localization will prove to be microbodies.Variations in the morphology and ER associations of microbodies in tissues of bean and radish are described and discussed. "Crystal-containing bodies" (CCBs) are interpreted as a specialized type of microbody characteristic of metabolically less active cells. Stages in the formation of CCBs from microbodies of typical appearance are illustrated for Avena.The general occurrence of microbodies in meristematic and differentiating cells and their close association with the ER suggest that they may play active roles in cellular metabolism. The alterations in their

  19. Characterization of fluid transport in microscale structures

    SciTech Connect

    Paul, P.H.

    1998-01-01

    A new tool for imaging both scalar transport and velocity fields in liquid flows through microscale structures is described. The technique employs an ultraviolet laser pulse to write a pattern into the flow by uncaging a fluorescent dye. This is followed, at selected time delays, by flood illumination with a pulse of visible light which excites the uncaged dye. The resulting fluorescence image collected onto a sensitive CCD camera. The instrument is designed as an oil immersion microscope to minimize the beam steering effects. The caged fluorescent dye is seeded in trace quantities throughout the active fluid, thus images with high contrast and minimal distortion due to any molecular diffusion history can be obtained at any point within the microchannel by selectivity activating the dye in the immediate region of interest. The author reports images of pressure- and electrokinetically-driven steady flow within round cross section capillaries having micron scale inner diameters. The author also demonstrates the ability to recover the velocity profile from a time sequence of these scalar images by direct inversion of the conserved scalar advection-convection equation.

  20. Structural characterization of MAPLE deposited lipase biofilm

    NASA Astrophysics Data System (ADS)

    Aronne, Antonio; Ausanio, Giovanni; Bloisi, Francesco; Calabria, Raffaela; Califano, Valeria; Fanelli, Esther; Massoli, Patrizio; Vicari, Luciano R. M.

    2014-11-01

    Lipases (triacylglycerol ester hydrolases) are enzymes used in several industrial applications. Enzymes immobilization can be used to address key issues limiting widespread application at industrial level. Immobilization efficiency is related to the ability to preserve the native conformation of the enzyme. MAPLE (Matrix Assisted Pulsed Laser Evaporation) technique, a laser deposition procedure for treating organic/polymeric/biomaterials, was applied for the deposition of lipase enzyme in an ice matrix, using near infrared laser radiation. Microscopy analysis showed that the deposition occurred in micrometric and submicrometric clusters with a wide size distribution. AFM imaging showed that inter-cluster regions are uniformly covered with smaller aggregates of nanometric size. Fourier transform infrared spectroscopy was used for both recognizing the deposited material and analyzing its secondary structure. Results showed that the protein underwent reversible self-association during the deposition process. Actually, preliminary tests of MAPLE deposited lipase used for soybean oil transesterification with isopropyl alcohol followed by gas chromatography-mass spectrometry gave results consistent with undamaged deposition of lipase.

  1. Characterization of Nano-Structured Bainitic Steel

    NASA Astrophysics Data System (ADS)

    Beladi, Hossein; Timokhina, Ilana B.; Hodgson, Peter D.; Adachi, Yoshitaka

    A 0.79C-1.5Si-1.98Mn-0.98Cr-0.24Mo-1.06Al-1.58Co (wt%) steel was isothermally heat treated at 200°C for 10 days to produce a nano-structured bainitic steel. The microstructure consisted of nanobainitic ferrite laths with a high dislocation density and retained austenite films having extensive twins. The crystallographic analysis using TEM and EBSD revealed that the bainitic ferrite laths are close to the Nishiyama-Wassermann orientation relationship with their parent austenite. There was only one type of packet identified in a given transformed austenite grain. Each packet consisted of two different blocks having variants with the same habit plane, but different crystallographic orientations. Atom Probe Tomography (APT) revealed that the carbon content of nanobainitic ferrite laths was much higher than expected from the para-equilibrium level. This was explained due to the long heat treatment time, which led to the formation of fine Fe-C clusters on areas with high dislocation densities in bainitic ferrite laths.

  2. Carbon nano structures: Production and characterization

    NASA Astrophysics Data System (ADS)

    Beig Agha, Rosa

    L'objectif de ce memoire est de preparer et de caracteriser des nanostructures de carbone (CNS -- Carbon Nanostructures, en licence a l'Institut de recherche sur l'hydrogene, Quebec, Canada), un carbone avec un plus grand degre de graphitisation et une meilleure porosite. Le Chapitre 1 est une description generale des PEMFCs (PEMFC -- Polymer Electrolyte Membrane Fuel Cell) et plus particulierement des CNS comme support de catalyseurs, leur synthese et purification. Le Chapitre 2 decrit plus en details la methode de synthese et la purification des CNS, la theorie de formation des nanostructures et les differentes techniques de caracterisation que nous avons utilises telles que la diffraction aux rayons-X (XRD -- X-ray diffraction), la microscopie electronique a transmission (TEM -- transmission electron microscope ), la spectroscopie Raman, les isothermes d'adsorption d'azote a 77 K (analyse BET, t-plot, DFT), l'intrusion au mercure, et l'analyse thermogravimetrique (TGA -- thermogravimetric analysis). Le Chapitre 3 presente les resultats obtenus a chaque etape de la synthese des CNS et avec des echantillons produits a l'aide d'un broyeur de type SPEXRTM (SPEX/CertiPrep 8000D) et d'un broyeur de type planetaire (Fritsch Pulverisette 5). La difference essentielle entre ces deux types de broyeur est la facon avec laquelle les materiaux sont broyes. Le broyeur de type SPEX secoue le creuset contenant les materiaux et des billes d'acier selon 3 axes produisant ainsi des impacts de tres grande energie. Le broyeur planetaire quant a lui fait tourner et deplace le creuset contenant les materiaux et des billes d'acier selon 2 axes (plan). Les materiaux sont donc broyes differemment et l'objectif est de voir si les CNS produits ont les memes structures et proprietes. Lors de nos travaux nous avons ete confrontes a un probleme majeur. Nous n'arrivions pas a reproduire les CNS dont la methode de synthese a originellement ete developpee dans les laboratoires de l'Institut de

  3. Harnessing glycomics technologies: integrating structure with function for glycan characterization

    PubMed Central

    Robinson, Luke N.; Artpradit, Charlermchai; Raman, Rahul; Shriver, Zachary H.; Ruchirawat, Mathuros; Sasisekharan, Ram

    2013-01-01

    Glycans, or complex carbohydrates, are a ubiquitous class of biological molecules which impinge on a variety of physiological processes ranging from signal transduction to tissue development and microbial pathogenesis. In comparison to DNA and proteins, glycans present unique challenges to the study of their structure and function owing to their complex and heterogeneous structures and the dominant role played by multivalency in their sequence-specific biological interactions. Arising from these challenges, there is a need to integrate information from multiple complementary methods to decode structure-function relationships. Focusing on acidic glycans, we describe here key glycomics technologies for characterizing their structural attributes, including linkage, modifications, and topology, as well as for elucidating their role in biological processes. Two cases studies, one involving sialylated branched glycans and the other sulfated glycosaminoglycans, are used to highlight how integration of orthogonal information from diverse datasets enables rapid convergence of glycan characterization for development of robust structure-function relationships. PMID:22522536

  4. Thiosaccharine disulfide: Synthesis, crystal structure, spectroscopic characterization and theoretical study

    NASA Astrophysics Data System (ADS)

    Ferullo, Ricardo M.; Granados, Alejandro; Lanterna, Anabel; Güida, Jorge A.; Piro, Oscar E.; Castellano, Eduardo E.; Dennehy, Mariana

    2013-01-01

    The title compound, (thiosaccharine disulfide), bis[1,1'dioxide-2,3-dihidro-1,2-benzoisothiazol]disulfide, (tsac)2 has been synthesized and fully characterized by UV-Visible, IR, Raman, 1H and 13C NMR spectroscopy elemental analysis and structural X-ray crystallography. A DFT theoretical study has been performed and good agreement between experimental and theoretical values of structural parameters and vibration frequencies have been achieved.

  5. Photothermal characterization of solid two-layer spherical structures

    NASA Astrophysics Data System (ADS)

    Xie, Guangxi; Chen, Zhifeng; Wang, Chinhua; Mandelis, Andreas

    2010-03-01

    A theoretical model for evaluating 2-layer solid spherical samples that are heated by a modulated light is presented using the Green function method. The specific Green's function corresponding to the composite structure has been derived. The characteristics of the thermal-wave field with respect to the thermophysical properties of the material and the geometrical factors are presented. Experimental results obtained with laser infrared photothermal radiometry show the capability of the model for characterizing the spherical layered structures.

  6. Complexation of Actinides in Solution: Thermodynamic Measurementsand Structural Characterization

    SciTech Connect

    Rao, L.

    2007-02-01

    This paper presents a brief introduction of the studies of actinide complexation in solution at Lawrence Berkeley National Laboratory. An integrated approach of thermodynamic measurements and structural characterization is taken to obtain fundamental understanding of actinide complexation in solution that is of importance in predicting the behavior of actinides in separation processes and environmental transport.

  7. Fluorescence microscopy for the characterization of structural integrity

    NASA Technical Reports Server (NTRS)

    Street, Kenneth W.; Leonhardt, Todd A.

    1991-01-01

    The absorption characteristics of light and the optical technique of fluorescence microscopy for enhancing metallographic interpretation are presented. Characterization of thermally sprayed coatings by optical microscopy suffers because of the tendency for misidentification of the microstructure produced by metallographic preparation. Gray scale, in bright field microscopy, is frequently the only means of differentiating the actual structural details of porosity, cracking, and debonding of coatings. Fluorescence microscopy is a technique that helps to distinguish the artifacts of metallographic preparation (pullout, cracking, debonding) from the microstructure of the specimen by color contrasting structural differences. Alternative instrumentation and the use of other dye systems are also discussed. The combination of epoxy vacuum infiltration with fluorescence microscopy to verify microstructural defects is an effective means to characterize advanced materials and to assess structural integrity.

  8. Structural characterization of adsorbed helical and beta-sheet peptides

    NASA Astrophysics Data System (ADS)

    Samuel, Newton Thangadurai

    Adsorbed peptides on surfaces have potential applications in the fields of biomaterials, tissue engineering, peptide microarrays and nanobiotechnology. The surface region, the "biomolecular interface" between a material and the biological environment, plays a crucial role in these applications. As a result, characterization of adsorbed peptide structure, especially with respect to identity, concentration, spatial distribution, conformation and orientation, is important. The present research employs NEXAFS (near-edge X-ray absorption fine structure spectroscopy) and SFG (sum frequency generation spectroscopy) to provide information about the adsorbed peptide structure. Soft X-ray NEXAFS is a synchrotron-based technique which typically utilizes polarized X-rays to interrogate surfaces under ultra-high vacuum conditions. SFG is a non-linear optical technique which utilizes a combination of a fixed visible and a tunable infrared laser beams to generate a surface-vibrational spectrum of surface species. SFG has the added advantage of being able to directly analyze the surface-structure at the solid-liquid interface. The main goals of the present research were twofold: characterize the structure of adsorbed peptides (1) ex situ using soft X-ray NEXAFS, and (2) in situ using non-linear laser spectroscopy (SFG). Achieving the former goal involved first developing a comprehensive characterization of the carbon, nitrogen and oxygen k-edge NEXAFS spectra for amino acids, and then using a series of helical and beta-sheet peptides to demonstrate the sensitivity of polarization-dependent NEXAFS to secondary structure of adsorbed peptides. Characterizing the structure of adsorbed peptides in situ using SFG involved developing a model system to probe the solid-liquid interface in situ; demonstrating the ability to probe the molecular interactions and adsorbed secondary structure; following the time-dependent ordering of the adsorbed peptides; and establishing the ability to obtain

  9. Solid state NMR strategy for characterizing native membrane protein structures.

    PubMed

    Murray, Dylan T; Das, Nabanita; Cross, Timothy A

    2013-09-17

    Unlike water soluble proteins, the structures of helical transmembrane proteins depend on a very complex environment. These proteins sit in the midst of dramatic electrical and chemical gradients and are often subject to variations in the lateral pressure profile, order parameters, dielectric constant, and other properties. Solid state NMR is a collection of tools that can characterize high resolution membrane protein structure in this environment. Indeed, prior work has shown that this complex environment significantly influences transmembrane protein structure. Therefore, it is important to characterize such structures under conditions that closely resemble its native environment. Researchers have used two approaches to gain protein structural restraints via solid state NMR spectroscopy. The more traditional approach uses magic angle sample spinning to generate isotropic chemical shifts, much like solution NMR. As with solution NMR, researchers can analyze the backbone chemical shifts to obtain torsional restraints. They can also examine nuclear spin interactions between nearby atoms to obtain distances between atomic sites. Unfortunately, for membrane proteins in lipid preparations, the spectral resolution is not adequate to obtain complete resonance assignments. Researchers have developed another approach for gaining structural restraints from membrane proteins: the use of uniformly oriented lipid bilayers, which provides a method for obtaining high resolution orientational restraints. When the bilayers are aligned with respect to the magnetic field of the NMR spectrometer, researchers can obtain orientational restraints in which atomic sites in the protein are restrained relative to the alignment axis. However, this approach does not allow researchers to determine the relative packing between helices. By combining the two approaches, we can take advantage of the information acquired from each technique to minimize the challenges and maximize the quality of the

  10. Thermodynamic and structural characterization of an antibody gel

    PubMed Central

    Esue, Osigwe; Xie, Anna X.; Kamerzell, Tim J.; Patapoff, Thomas W.

    2013-01-01

    Although extensively studied, protein–protein interactions remain highly elusive and are of increasing interest in drug development. We show the assembly of a monoclonal antibody, using multivalent carboxylate ions, into highly-ordered structures. While the presence and function of similar structures in vivo are not known, the results may present a possible unexplored area of antibody structure-function relationships. Using a variety of tools (e.g., mechanical rheology, electron microscopy, isothermal calorimetry, Fourier transform infrared spectroscopy), we characterized the physical, biochemical, and thermodynamic properties of these structures and found that citrate may interact directly with the amino acid residue histidine, after which the individual protein units assemble into a filamentous network gel exhibiting high elasticity and interfilament interactions. Citrate interacts exothermically with the monoclonal antibody with an association constant that is highly dependent on solution pH and temperature. Secondary structure analysis also reveals involvement of hydrophobic and aromatic residues. PMID:23425660

  11. New quinternary selenides: Syntheses, characterizations, and electronic structure calculations

    SciTech Connect

    Chung, Ming-Yan; Lee, Chi-Shen

    2013-06-01

    Five quinternary selenides, Sr₂.₆₃Y₀.₃₇Ge₀.₆₃Sb₂.₃₇Se₈ (I), Sr₂.₆₃La₀.₃₇Ge₀.₆₃Sb₂.₃₇Se₈ (II), Sr₂.₇₁La₀.₂₉Sn₀.₇₇Bi₂.₂₃Se₈ (III), Ba₂.₆₇ La₀.₃₃ Sn₀.₆₇Sb₂.₃₃Se₈ (IV), and Ba₂.₆₇ La₀.₃₃Sn₀.₆₇Bi₂.₃₃Se₈ (V), were synthesized by solid-state reaction in fused silica tubes. These compounds are isostructural and crystallize in the Sr₃GeSb₂Se₈ structural-type, which belongs to the orthorhombic space group Pnma (no. 62). Three structural units, 1[MSe₃], 1[M₄Se₁₀] (M=Tt, Pn) and M´ (M´=groups II and III element), comprise the entire one-dimensional structure, separated by M´. Measurements of electronic resistivity and diffused reflectance suggest that IV and V have semiconducting properties. Electronic structure calculations confirm the site preferences of Sr/La element discovered by crystal structure refinement. - Graphical abstract: Quinternary selenides Ae₂.₆₇M₀.₃₃Tt₀.₆₇Pn₂.₃₃Se₈ (Ae, M, Tt, Pn=Sr/Ba, Y/La, Ge/Sn, Sb/Bi) were synthesized and their site preferences were characterized by single-crystal X-ray diffraction and electronic structure calculation. Highlights: • Five new quinternary selenides were synthesized and characterized. • Structural units, 1[MSe₃] and 1[M₄Se₁₀] (M=Tt, Pn), construct the one-dimensional structure. • Calculations of electronic structure confirm site preference of Sr/La sites.

  12. RF and structural characterization of new SRF films

    SciTech Connect

    A.-M. Valente-Feliciano,H. L. Phillips,C. E. Reece,X. Zhao,D. Gu,R. Lukaszew,B. Xiao,K. Seo

    2009-09-01

    In the past years, energetic vacuum deposition methods have been developed in different laboratories to improve Nb/Cu technology for superconducting cavities. Jefferson Lab is pursuing energetic condensation deposition via Electron Cyclotron Resonance. As part of this study, the influence of the deposition energy on the material and RF properties of the Nb thin film is investigated. The film surface and structure analyses are conducted with various techniques like X-ray diffraction, Transmission Electron Microscopy, Auger Electron Spectroscopy and RHEED. The microwave properties of the films are characterized on 50 mm disk samples with a 7.5 GHz surface impedance characterization system. This paper presents surface impedance measurements in correlation with surface and material characterization for Nb films produced on copper substrates with different bias voltages and also highlights emerging opportunities for developing multilayer SRF films with a new deposition system.

  13. Characterization of Coherent Structures in the Cardiovascular System

    PubMed Central

    Shadden, Shawn C.; Taylor, Charles A.

    2013-01-01

    Recent advances in blood flow modeling have provided highly resolved, four-dimensional data of fluid mechanics in large vessels. The motivation for such modeling is often to better understand how flow conditions relate to health and disease, or to evaluate interventions that affect, or are affected by, blood flow mechanics. Vessel geometry and the pulsatile pumping of blood leads to complex flow, which is often difficult to characterize. This article discusses a computational method to better characterize blood flow kinematics. In particular, we compute Lagrangian coherent structures (LCS) to study flow in large vessels. We demonstrate that LCS can be used to characterize flow stagnation, flow separation, partitioning of fluid to downstream vasculature, and mechanisms governing stirring and mixing in vascular models. This perspective allows valuable under-standing of flow features in large vessels beyond methods traditionally considered. PMID:18437573

  14. Characterizing Protein Structure, Dynamics and Conformation in Lyophilized Solids

    PubMed Central

    Moorthy, Balakrishnan S.; Iyer, Lavanya K.; Topp, Elizabeth M.

    2015-01-01

    The long-term stability of protein therapeutics in the solid-state depends on the preservation of native structure during lyophilization and in the lyophilized powder. Proteins can reversibly or irreversibly unfold upon lyophilization, acquiring conformations susceptible to degradation during storage. Therefore, characterizing proteins in the dried state is crucial for the design of safe and efficacious formulations. This review summarizes the basic principles and applications of the analytical techniques that are commonly used to characterize protein structure, dynamics and conformation in lyophilized solids. The review also discusses the applications of recently developed mass spectrometry based methods (solid-state hydrogen deuterium exchange mass spectrometry (ssHDX-MS) and solid-state photolytic labeling mass spectrometry (ssPL-MS)) and their ability to study proteins in the solid-state at high resolution. PMID:26446463

  15. Preparation, structural, and calorimetric characterization of bicomponent metallic photonic crystals

    NASA Astrophysics Data System (ADS)

    Kozlov, M. E.; Murthy, N. S.; Udod, I.; Khayrullin, I. I.; Baughman, R. H.; Zakhidov, A. A.

    2007-03-01

    We report preparation and characterization of novel bicomponent metal-based photonic crystals having submicron three-dimensional (3D) periodicity. Fabricated photonic crystals include SiO2 sphere lattices infiltrated interstitially with metals, carbon inverse lattices filled with metal or metal alloy spheres, Sb inverse lattices, and Sb inverse lattices filled with Bi spheres. Starting from a face centered SiO2 lattice template, these materials were obtained by sequences of either templating and template extraction or templating, template extraction, and retemplating. Surprising high fidelity was obtained for all templating and template extraction steps. Scanning electron microscopy (SEM), small angle X-ray scattering (SAXS) and differential scanning calorimetry (DSC) were used to characterize the structure and the effects of the structure on calorimetric properties. To the best of our knowledge, SAXS data on metallic photonic crystals were collected for first time.

  16. Structural and electrical characterization of hybrid metal-polypyrrole nanowires

    NASA Astrophysics Data System (ADS)

    Gence, L.; Faniel, S.; Gustin, C.; Melinte, S.; Bayot, V.; Callegari, V.; Reynes, O.; Demoustier-Champagne, S.

    2007-09-01

    We present here the synthesis and structural characterization of hybrid Au-polypyrrole-Au and Pt-polypyrrole-Au nanowires together with a study of their electrical properties from room temperature down to very low temperature. A careful characterization of the metal-polymer interfaces by transmission electron microscopy revealed that the structure and mechanical strength of bottom and upper interfaces are very different. Variable temperature electrical transport measurements were performed on both multiple nanowires—contained within the polycarbonate template—and single nanowires. Our data show that the three-dimensional Mott variable-range-hopping model provides a complete framework for the understanding of transport in polypyrrole nanowires, including nonlinear current-voltage characteristics and magnetotransport at low temperatures.

  17. Structural characterization of bimetallic Pd-Cu vapor derived catalysts

    NASA Astrophysics Data System (ADS)

    Balerna, Antonella; Evangelisti, Claudio; Psaro, Rinaldo; Fusini, Graziano; Carpita, Adriano

    2016-05-01

    Pd-Cu bimetallic Solvated Metal Atoms (SMA) were synthesized by metal vapor synthesis technique and supported on PVPy resin. Since the catalytic activity, of the Pd-Cu system turned out to be quite high also compared to the corresponding monometallic system, a structural characterization, using electron microscopy techniques and X-ray Absorption Fine Structure spectroscopy, was performed. HRTEM analysis showed the presence of Pd particles distributed in a narrow range with a mean diameter of about 2.5 nm while the XAFS analysis, confirmed the presence of the Pd nanoparticles but revealed also some alloying with Cu atoms.

  18. Characterization of seismic hazard and structural response by energy flux

    USGS Publications Warehouse

    Afak, E.

    2000-01-01

    Seismic safety of structures depends on the structure's ability to absorb the seismic energy that is transmitted from ground to structure. One parameter that can be used to characterize seismic energy is the energy flux. Energy flux is defined as the amount of energy transmitted per unit time through a cross-section of a medium, and is equal to kinetic energy multiplied by the propagation velocity of seismic waves. The peak or the integral of energy flux can be used to characterize ground motions. By definition, energy flux automatically accounts for site amplification. Energy flux in a structure can be studied by formulating the problem as a wave propagation problem. For buildings founded on layered soil media and subjected to vertically incident plane shear waves, energy flux equations are derived by modeling the buildings as an extension of the layered soil medium, and considering each story as another layer. The propagation of energy flux in the layers is described in terms of the upgoing and downgoing energy flux in each layer, and the energy reflection and transmission coefficients at each interface. The formulation results in a pair of simple finite-difference equations for each layer, which can be solved recursively starting from the bedrock. The upgoing and downgoing energy flux in the layers allows calculation of the energy demand and energy dissipation in each layer. The methodology is applicable to linear, as well as nonlinear structures. ?? 2000 Published by Elsevier Science Ltd.

  19. Optical fiber sensors for materials and structures characterization

    NASA Technical Reports Server (NTRS)

    Lindner, D. K.; Claus, R. O.

    1991-01-01

    The final technical report on Optical Fiber Sensors for Materials and Structures Characterization, covering the period August 1990 through August 1991 is presented. Research programs in the following technical areas are described; sapphire optical fiber sensors; vibration analysis using two-mode elliptical core fibers and sensors; extrinsic Fabry-Perot interferometer development; and coatings for fluorescent-based sensor. Research progress in each of these areas was substantial, as evidenced by the technical publications which are included as appendices.

  20. Characterization of mirror-based modulation-averaging structures.

    PubMed

    Komljenovic, Tin; Babić, Dubravko; Sipus, Zvonimir

    2013-05-10

    Modulation-averaging reflectors have recently been proposed as a means for improving the link margin in self-seeded wavelength-division multiplexing in passive optical networks. In this work, we describe simple methods for determining key parameters of such structures and use them to predict their averaging efficiency. We characterize several reflectors built by arraying fiber-Bragg gratings along a segment of an optical fiber and show very good agreement between experiments and theoretical models. PMID:23669835

  1. In situ characterization of structural dynamics in swelling hydrogels.

    PubMed

    Guzman-Sepulveda, J R; Deng, J; Fang, J Y; Dogariu, A

    2016-07-01

    Characterizing the structural morphology and the local viscoelastic properties of soft complex systems raises significant challenges. Here we introduce a dynamic light scattering method capable of in situ, continuous monitoring of structural changes in evolving systems such as swelling gels. We show that the inherently non-stationary dynamics of embedded probes can be followed using partially coherent radiation, which effectively isolates only single scattering contributions even during the dramatic changes in the scattering regime. Using a simple and robust experimental setup, we demonstrate the ability to continuously monitor the structural dynamics of chitosan hydrogels formed by the Ag(+) ion-triggered gelation during their long-term swelling process. We demonstrate that both the local viscoelastic properties of the suspending medium and an effective cage size experienced by diffusing probe particles loaded into the hydrogel can be recovered and used to describe the structural dynamics of hydrogels with different levels of cross-linking. This characterization capability is critical for defining and controlling the hydrogel performance in different biomedical applications. PMID:27336408

  2. Characterization of electronic structure of periodically strained graphene

    SciTech Connect

    Aslani, Marjan; Garner, C. Michael Nishi, Yoshio; Kumar, Suhas; Nordlund, Dennis; Pianetta, Piero

    2015-11-02

    We induced periodic biaxial tensile strain in polycrystalline graphene by wrapping it over a substrate with repeating pillar-like structures with a periodicity of 600 nm. Using Raman spectroscopy, we determined to have introduced biaxial strains in graphene in the range of 0.4% to 0.7%. Its band structure was characterized using photoemission from valance bands, shifts in the secondary electron emission, and x-ray absorption from the carbon 1s levels to the unoccupied graphene conduction bands. It was observed that relative to unstrained graphene, strained graphene had a higher work function and higher density of states in the valence and conduction bands. We measured the conductivity of the strained and unstrained graphene in response to a gate voltage and correlated the changes in their behavior to the changes in the electronic structure. From these sets of data, we propose a simple band diagram representing graphene with periodic biaxial strain.

  3. Characterization of electronic structure of periodically strained graphene

    SciTech Connect

    Aslani, Marjan; Garner, C. Michael; Kumar, Suhas; Nordlund, Dennis; Pianetta, Piero; Nishi, Yoshio

    2015-11-03

    We induced periodic biaxial tensile strain in polycrystalline graphene by wrapping it over a substrate with repeating pillar-like structures with a periodicity of 600 nm. Using Raman spectroscopy, we determined to have introduced biaxial strains in graphene in the range of 0.4% to 0.7%. Its band structure was characterized using photoemission from valance bands, shifts in the secondary electron emission, and x-ray absorption from the carbon 1s levels to the unoccupied graphene conduction bands. It was observed that relative to unstrained graphene, strained graphene had a higher work function and higher density of states in the valence and conduction bands. Furthermore, we measured the conductivity of the strained and unstrained graphene in response to a gate voltage and correlated the changes in their behavior to the changes in the electronic structure. From these sets of data, we propose a simple band diagram representing graphene with periodic biaxial strain.

  4. Structural Characterization of Arabidopsis Leaf Arabinogalactan Polysaccharides1[W

    PubMed Central

    Tryfona, Theodora; Liang, Hui-Chung; Kotake, Toshihisa; Tsumuraya, Yoichi; Stephens, Elaine; Dupree, Paul

    2012-01-01

    Proteins decorated with arabinogalactan (AG) have important roles in cell wall structure and plant development, yet the structure and biosynthesis of this polysaccharide are poorly understood. To facilitate the analysis of biosynthetic mutants, water-extractable arabinogalactan proteins (AGPs) were isolated from the leaves of Arabidopsis (Arabidopsis thaliana) plants and the structure of the AG carbohydrate component was studied. Enzymes able to hydrolyze specifically AG were utilized to release AG oligosaccharides. The released oligosaccharides were characterized by high-energy matrix-assisted laser desorption ionization-collision-induced dissociation mass spectrometry and polysaccharide analysis by carbohydrate gel electrophoresis. The Arabidopsis AG is composed of a β-(1→3)-galactan backbone with β-(1→6)-d-galactan side chains. The β-(1→6)-galactan side chains vary in length from one to over 20 galactosyl residues, and they are partly substituted with single α-(1→3)-l-arabinofuranosyl residues. Additionally, a substantial proportion of the β-(1→6)-galactan side chain oligosaccharides are substituted at the nonreducing termini with single 4-O-methyl-glucuronosyl residues via β-(1→6)-linkages. The β-(1→6)-galactan side chains are occasionally substituted with α-l-fucosyl. In the fucose-deficient murus1 mutant, AGPs lack these fucose modifications. This work demonstrates that Arabidopsis mutants in AGP structure can be identified and characterized. The detailed structural elucidation of the AG polysaccharides from the leaves of Arabidopsis is essential for insights into the structure-function relationships of these molecules and will assist studies on their biosynthesis. PMID:22891237

  5. Structural characterizations of the chloroplast translocon protein Tic110

    PubMed Central

    Tsai, Jia-Yin; Chu, Chiung-Chih; Yeh, Yi-Hung; Chen, Lih-Jen; Li, Hsou-min; Hsiao, Chwan-Deng

    2013-01-01

    Tic110 is a major component of the chloroplast protein import translocon. Two functions with mutually exclusive structures have been proposed for Tic110: a protein-conducting channel with six transmembrane domains and a scaffold with two N-terminal transmembrane domains followed by a large soluble domain for binding transit peptides and other stromal translocon components. To investigate the structure of Tic110, Tic110 from Cyanidioschyzon merolae (CmTic110) was characterized. We constructed three fragments, CmTic110A, CmTic110B and CmTic110C, with increasing N-terminal truncations, to perform small-angle X-ray scattering (SAXS) and X-ray crystallography analyses and Dali structural comparison. Here we report the molecular envelope of CmTic110B and CmTic110C determined by SAXS, and the crystal structure of CmTic110C at 4.2 Å. Our data indicate that the C-terminal half of CmTic110 possesses a rod-shaped helix-repeat structure that is too flattened and elongated to be a channel. The structure is most similar to the HEAT-repeat motif that functions as scaffolds for protein–protein interactions. PMID:23711301

  6. EDITORIAL: (Nano)characterization of semiconductor materials and structures (Nano)characterization of semiconductor materials and structures

    NASA Astrophysics Data System (ADS)

    Bonanni, Alberta

    2011-06-01

    The latest impressive advancements in the epitaxial fabrication of semiconductors and in the refinement of characterization techniques have the potential to allow insight into the deep relation between materials' structural properties and their physical and chemical functionalities. Furthermore, while the comprehensive (nano)characterization of semiconductor materials and structures is becoming more and more necessary, a compendium of the currently available techniques is lacking. We are positive that an overview of the hurdles related to the specific methods, often leading to deceptive interpretations, will be most informative for the broad community working on semiconductors, and will help in shining some light onto a plethora of controversial reports found in the literature. From this perspective, with this special issue we address and highlight the challenges and misinterpretations related to complementary local (nanoscale) and more global experimental methods for the characterization of semiconductors. The six topical reviews and the three invited papers by leading experts in the specific fields collected in here are intended to provide the required broad overview on the possibilities of actual (nano)characterization methods, from the microscopy of single quantum structures, over the synchrotron-based absorption and diffraction of nano-objects, to the contentious detection of tiny magnetic signals by quantum interference and resonance techniques. We are grateful to all the authors for their valuable contributions. Moreover, I would like to thank the Editorial Board of the journal for supporting the realization of this special issue and for inviting me to serve as Guest Editor. We greatly appreciate the work of the reviewers, of the editorial staff of Semiconductor Science and Technology and of IOP Publishing. In particular, the efforts of Alice Malhador in coordinating this special issue are acknowledged.

  7. Characterization of the nanoscale structure of milk fat.

    PubMed

    Ramel, Pere Randy R; Peyronel, Fernanda; Marangoni, Alejandro G

    2016-07-15

    The nanoscale structure of milk fat (MF) crystal networks is extensively described for the first time through the characterization of milk fat-crystalline nanoplatelets (MF-CNPs). Removing oil by washing with cold isobutanol and breaking-down crystal aggregates by controlled homogenization allowed for the extraction and visualization of individual MF-CNPs that are mainly composed of high melting triacylglycerols (TAGs). By image analysis, the length and width of MF-CNPs were measured (600 nm × 200 nm-900 nm × 300 nm). Using small-angle X-ray scattering (SAXS), crystalline domain size, (i.e., thickness of MF-CNPs), was determined (27 nm (d001)). Through interpretation of ultra-small-angle X-ray scattering (USAXS) patterns of MF using Unified Fit and Guinier-Porod models, structural properties of MF-CNPs (smooth surfaces) and MF-CNP aggregations were characterized (RLCA aggregation of MF-CNPs to form larger structures that present diffused surfaces). Elucidation of MF-CNPs provides a new dimension of analysis for describing MF crystal networks and opens-up opportunities for modifying MF properties through nanoengineering. PMID:26948609

  8. Function discovery and structural characterization of a methylphosphonate esterase.

    PubMed

    Xiang, Dao Feng; Patskovsky, Yury; Nemmara, Venkatesh V; Toro, Rafael; Almo, Steven C; Raushel, Frank M

    2015-05-12

    Pmi1525, an enzyme of unknown function from Proteus mirabilis HI4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of Pmi1525 was determined with zinc and cacodylate bound in the active site (PDB id: 3RHG ). The structure was also determined with manganese and butyrate in the active site (PDB id: 4QSF ). Pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamily and cog1735. The substrate profile for Pmi1525 was determined via a strategy that marshaled the utilization of bioinformatics, structural characterization, and focused library screening. The protein was found to efficiently catalyze the hydrolysis of organophosphonate and carboxylate esters. The best substrates identified for Pmi1525 are ethyl 4-nitrophenylmethyl phosphonate (kcat and kcat/Km values of 580 s(-1) and 1.2 × 10(5) M(-1) s(-1), respectively) and 4-nitrophenyl butyrate (kcat and kcat/Km values of 140 s(-1) and 1.4 × 10(5) M(-1) s(-1), respectively). Pmi1525 is stereoselective for the hydrolysis of chiral methylphosphonate esters. The enzyme hydrolyzes the (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate 14 times faster than the corresponding (RP)-enantiomer. The catalytic properties of this enzyme make it an attractive template for the evolution of novel enzymes for the detection, destruction, and detoxification of organophosphonate nerve agents. PMID:25873441

  9. Function Discovery and Structural Characterization of a Methylphosphonate Esterase

    PubMed Central

    Xiang, Dao Feng; Patskovsky, Yury; Nemmara, Venkatesh V.; Toro, Rafael; Almo, Steven C.; Raushel, Frank M.

    2015-01-01

    Pmi1525, an enzyme of unknown function from Proteus Mirabilis HI4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of Pmi1525 was determined with zinc and cacodylate bound in the active site (PDB id: 3RHG). The structure was also determined with manganese and butyrate in the active site (PDB id: 4QSF). Pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamily and cog1735. The substrate profile for Pmi1525 was determined via a strategy that marshaled the utilization of bioinformatics, structural characterization and focused library screening. The protein was found to efficiently catalyze the hydrolysis of organophosphonate and carboxylate esters. The best substrates identified for Pmi1525 are ethyl 4-nitrophenylmethyl phosphonate (kcat and kcat/Km values of 580 s−1 and 1.2 × 105 M−1 s−1, respectively) and 4-nitrophenyl butyrate (kcat and kcat/Km values of 140 s−1 and 1.4 × 105 M−1 s−1, respectively). Pmi1525 is stereoselective for the hydrolysis of chiral methylphosphonate esters. The enzyme hydrolyzes the (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate 14 times faster than the corresponding (RP)-enantiomer. The catalytic properties of this enzyme make it an attractive template for the evolution of novel enzymes for the detection, destruction, and detoxification of organophosphonate nerve agents. PMID:25873441

  10. Nondestructive Structural Damage Detection in Flexible Space Structures Using Vibration Characterization

    NASA Technical Reports Server (NTRS)

    Ricles, James M.

    1991-01-01

    Spacecraft are susceptible to structural damage over their operating life from impact, environmental loads, and fatigue. Structural damage that is not detected and not corrected may potentially cause more damage and eventually catastrophic structural failure. NASA's current fleet of reusable spacecraft, namely the Space Shuttle, has been flown on several missions. In addition, configurations of future NASA space structures, e.g. Space Station Freedom, are larger and more complex than current structures, making them more susceptible to damage as well as being more difficult to inspect. Consequently, a reliable structural damage detection capability is essential to maintain the flight safety of these structures. Visual inspections alone can not locate impending material failure (fatigue cracks, yielding); it can only observe post-failure situations. An alternative approach is to develop an inspection and monitoring system based on vibration characterization that assesses the integrity of structural and mechanical components. A methodology for detecting structural damage is presented. This methodology is based on utilizing modal test data in conjunction with a correlated analytical model of the structure to: (1) identify the structural dynamic characteristics (resonant frequencies and mode shapes) from measurements of ambient motions and/or force excitation; (2) calculate modal residual force vectors to identify the location of structural damage; and (3) conduct a weighted sensitivity analysis in order to assess the extent of mass and stiffness variations, where structural damage is characterized by stiffness reductions. The approach is unique from other existing approaches in that varying system mass and stiffness, mass center locations, the perturbation of both the natural frequencies and mode shapes, and statistical confidence factors for structural parameters and experimental instrumentation are all accounted for directly.

  11. Free energy contributions and structural characterization of stacking disordered ices.

    PubMed

    Hudait, Arpa; Qiu, Siwei; Lupi, Laura; Molinero, Valeria

    2016-04-14

    Crystallization of ice from deeply supercooled water and amorphous ices - a process of fundamental importance in the atmosphere, interstellar space, and cryobiology - results in stacking disordered ices with a wide range of metastabilities with respect to hexagonal ice. The structural origin of this high variability, however, has not yet been elucidated. Here we use molecular dynamics simulations with the mW water model to characterize the structure of ice freshly grown from supercooled water at temperatures from 210 to 270 K, the thermodynamics of stacking faults, line defects, and interfaces, and to elucidate the interplay between kinetics and thermodynamics in determining the structure of ice. In agreement with experiments, the ice grown in the simulations is stacking disordered with a random distribution of cubic and hexagonal layers, and a cubicity that decreases with growth temperature. The former implies that the cubicity of ice is determined by processes at the ice/liquid interface, without memory of the structure of buried ice layers. The latter indicates that the probability of building a cubic layer at the interface decreases upon approaching the melting point of ice, which we attribute to a more efficient structural equilibration of ice at the liquid interface as the driving force for growth wanes. The free energy cost for creating a pair of cubic layers in ice is 8.0 J mol(-1) in experiments, and 9.7 ± 1.9 J mol(-1) for the mW water model. This not only validates the simulations, but also indicates that dispersion in cubicity is not sufficient to explain the large energetic variability of stacking disordered ices. We compute the free energy cost of stacking disorder, line defects, and interfaces in ice and conclude that a characterization of the density of these defects is required to predict the degree of metastability and vapor pressure of atmospheric ices. PMID:26983558

  12. Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase

    PubMed Central

    Santini, Sébastien; Monchois, Vincent; Mouz, Nicolas; Sigoillot, Cécile; Rousselle, Tristan; Claverie, Jean-Michel; Abergel, Chantal

    2008-01-01

    Background In search of new antifungal targets of potential interest for pharmaceutical companies, we initiated a comparative genomics study to identify the most promising protein-coding genes in fungal genomes. One criterion was the protein sequence conservation between reference pathogenic genomes. A second criterion was that the corresponding gene in Saccharomyces cerevisiae should be essential. Since thiamine pyrophosphate is an essential product involved in a variety of metabolic pathways, proteins responsible for its production satisfied these two criteria. Results We report the enzymatic characterization and the crystallographic structure of the Candida albicans Thiamine pyrophosphokinase. The protein was co-crystallized with thiamine or thiamine-PNP. Conclusion The presence of an inorganic phosphate in the crystallographic structure opposite the known AMP binding site relative to the thiamine moiety suggests that a second AMP molecule could be accommodated in the C. albicans structure. Together with the crystallographic structures of the enzyme/substrate complexes this suggests the existence of a secondary, less specific, nucleotide binding site in the Candida albicans thiamine pyrophosphokinase which could transiently serve during the release or the binding of ATP. The structures also highlight a conserved Glutamine residue (Q138) which could interact with the ATP α-phosphate and act as gatekeeper. Finally, the TPK/Thiamine-PNP complex is consistent with a one step mechanism of pyrophosphorylation. PMID:18652651

  13. Rapid Characterization of Vegetation Structure with a Microsoft Kinect Sensor

    PubMed Central

    Azzari, George; Goulden, Michael L.; Rusu, Radu B.

    2013-01-01

    The importance of vegetation structure and biomass in controlling land-atmosphere exchange is widely recognized, but measurements of canopy structure are challenging, time consuming, and often rely on destructive methods. The Microsoft Kinect is an infrared sensor designed for video gaming that outputs synchronized color and depth images and that has the potential to allow rapid characterization of vegetation structure. We compared depth images from a Kinect sensor with manual measurements of plant structure and size for two species growing in a California grassland. The depth images agreed well with the horizontal and vertical measurements of plant size made manually. Similarly, the plant volumes calculated with a three-dimensional convex hulls approach was well related to plant biomass. The Kinect showed some limitations for ecological observation associated with a short measurement range and daytime light contamination. Nonetheless, the Kinect's light weight, fast acquisition time, low power requirement, and cost make it a promising tool for rapid field surveys of canopy structure, especially in small-statured vegetation. PMID:23435053

  14. Hierarchical structures of amorphous solids characterized by persistent homology

    PubMed Central

    Hiraoka, Yasuaki; Nakamura, Takenobu; Hirata, Akihiko; Escolar, Emerson G.; Matsue, Kaname; Nishiura, Yasumasa

    2016-01-01

    This article proposes a topological method that extracts hierarchical structures of various amorphous solids. The method is based on the persistence diagram (PD), a mathematical tool for capturing shapes of multiscale data. The input to the PDs is given by an atomic configuration and the output is expressed as 2D histograms. Then, specific distributions such as curves and islands in the PDs identify meaningful shape characteristics of the atomic configuration. Although the method can be applied to a wide variety of disordered systems, it is applied here to silica glass, the Lennard-Jones system, and Cu-Zr metallic glass as standard examples of continuous random network and random packing structures. In silica glass, the method classified the atomic rings as short-range and medium-range orders and unveiled hierarchical ring structures among them. These detailed geometric characterizations clarified a real space origin of the first sharp diffraction peak and also indicated that PDs contain information on elastic response. Even in the Lennard-Jones system and Cu-Zr metallic glass, the hierarchical structures in the atomic configurations were derived in a similar way using PDs, although the glass structures and properties substantially differ from silica glass. These results suggest that the PDs provide a unified method that extracts greater depth of geometric information in amorphous solids than conventional methods. PMID:27298351

  15. Characterizing Englacial and Subglacial Temperature Structure Using Airborne Radar Sounding

    NASA Astrophysics Data System (ADS)

    Schroeder, D. M.; Seroussi, H. L.

    2015-12-01

    The temperature structure of ice sheet and glaciers is a fundamental control on ice flow, rheology, and stability. However, it is difficult to observationally constrain temperature structures at the catchment to ice-sheet scale. The englacial attenuation of radar sounding data is strongly dependent on the temperature structure of the ice sheets. Therefore, echo strength profiles from airborne radar sounding observation do contain temperature information. However, direct interpretation of englacial attenuation rates from radar sounding profiles is often difficult or impossible due to the ambiguous contribution the geometric and material properties of the bed to echo strength variations. To overcome this challenge, we presents techniques that treat radar sounding echo strength and ice thickness profiles as continuous signals, taking advantage of along-profile ice thickness and echo strength variations to constrain the spatial pattern of englacial attenuation and basal reflectivity. We then apply these techniques to an airborne radar sounding survey in order to characterize the englacial and subglacial temperature structure of the Thwaites Glacier catchment in West Antarctic. We then interpreted this structure in context of local ice sheet velocity, advection, force balance, and bed conditions using the ISSM ice sheet model.

  16. Hierarchical structures of amorphous solids characterized by persistent homology.

    PubMed

    Hiraoka, Yasuaki; Nakamura, Takenobu; Hirata, Akihiko; Escolar, Emerson G; Matsue, Kaname; Nishiura, Yasumasa

    2016-06-28

    This article proposes a topological method that extracts hierarchical structures of various amorphous solids. The method is based on the persistence diagram (PD), a mathematical tool for capturing shapes of multiscale data. The input to the PDs is given by an atomic configuration and the output is expressed as 2D histograms. Then, specific distributions such as curves and islands in the PDs identify meaningful shape characteristics of the atomic configuration. Although the method can be applied to a wide variety of disordered systems, it is applied here to silica glass, the Lennard-Jones system, and Cu-Zr metallic glass as standard examples of continuous random network and random packing structures. In silica glass, the method classified the atomic rings as short-range and medium-range orders and unveiled hierarchical ring structures among them. These detailed geometric characterizations clarified a real space origin of the first sharp diffraction peak and also indicated that PDs contain information on elastic response. Even in the Lennard-Jones system and Cu-Zr metallic glass, the hierarchical structures in the atomic configurations were derived in a similar way using PDs, although the glass structures and properties substantially differ from silica glass. These results suggest that the PDs provide a unified method that extracts greater depth of geometric information in amorphous solids than conventional methods. PMID:27298351

  17. Rapid characterization of vegetation structure with a Microsoft Kinect sensor.

    PubMed

    Azzari, George; Goulden, Michael L; Rusu, Radu B

    2013-01-01

    The importance of vegetation structure and biomass in controlling land-atmosphere exchange is widely recognized, but measurements of canopy structure are challenging, time consuming, and often rely on destructive methods. The Microsoft Kinect is an infrared sensor designed for video gaming that outputs synchronized color and depth images and that has the potential to allow rapid characterization of vegetation structure. We compared depth images from a Kinect sensor with manual measurements of plant structure and size for two species growing in a California grassland. The depth images agreed well with the horizontal and vertical measurements of plant size made manually. Similarly, the plant volumes calculated with a three-dimensional convex hulls approach was well related to plant biomass. The Kinect showed some limitations for ecological observation associated with a short measurement range and daytime light contamination. Nonetheless, the Kinect's light weight, fast acquisition time, low power requirement, and cost make it a promising tool for rapid field surveys of canopy structure, especially in small-statured vegetation. PMID:23435053

  18. Structural characterization of impurified zinc oxide thin films

    SciTech Connect

    Trinca, L. M.; Galca, A. C. Stancu, V. Chirila, C. Pintilie, L.

    2014-11-05

    Europium doped zinc oxide (Eu:ZnO) thin films have been obtained by pulsed laser deposition (PLD). 002 textured thin films were achieved on glass and silicon substrates, while hetero-epilayers and homo-epilayers have been attained on single crystal SrTiO{sub 3} and ZnO, respectively. X-ray Diffraction (XRD) was employed to characterize the Eu:ZnO thin films. Extended XRD studies confirmed the different thin film structural properties as function of chosen substrates.

  19. Structural and Energetic Characterization of the Ankyrin Repeat Protein Family

    PubMed Central

    Parra, R. Gonzalo; Espada, Rocío; Verstraete, Nina; Ferreiro, Diego U.

    2015-01-01

    Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. Studying repeat protein families presents technical challenges due to the high sequence divergence among the repeating units. We developed and applied a systematic method to consistently identify and annotate the structural repetitions over the members of the complete Ankyrin Repeat Protein Family, with increased sensitivity over previous studies. We statistically characterized the number of repeats, the folding of the repeat-arrays, their structural variations, insertions and deletions. An energetic analysis of the local frustration patterns reveal the basic features underlying fold stability and its relation to the functional binding regions. We found a strong linear correlation between the conservation of the energetic features in the repeat arrays and their sequence variations, and discuss new insights into the organization and function of these ubiquitous proteins. PMID:26691182

  20. Structural and functional characterization of two alpha-synuclein strains

    NASA Astrophysics Data System (ADS)

    Bousset, Luc; Pieri, Laura; Ruiz-Arlandis, Gemma; Gath, Julia; Jensen, Poul Henning; Habenstein, Birgit; Madiona, Karine; Olieric, Vincent; Böckmann, Anja; Meier, Beat H.; Melki, Ronald

    2013-10-01

    α-synuclein aggregation is implicated in a variety of diseases including Parkinson’s disease, dementia with Lewy bodies, pure autonomic failure and multiple system atrophy. The association of protein aggregates made of a single protein with a variety of clinical phenotypes has been explained for prion diseases by the existence of different strains that propagate through the infection pathway. Here we structurally and functionally characterize two polymorphs of α-synuclein. We present evidence that the two forms indeed fulfil the molecular criteria to be identified as two strains of α-synuclein. Specifically, we show that the two strains have different structures, levels of toxicity, and in vitro and in vivo seeding and propagation properties. Such strain differences may account for differences in disease progression in different individuals/cell types and/or types of synucleinopathies.

  1. Synthesis and Structural Characterization of Orthorhombic Vanadium Oxide Nanorods

    NASA Astrophysics Data System (ADS)

    Garcia, L. M.; Chavira, E.; Santiago-Jacinto, P.; Rendon, L.; Marinero, E. E.; Tejada, A.; Fregoso-Israel, E.; Flores, C.

    2012-02-01

    Nanorod structures for Li storage are of interest for rechargeable battery applications. Vanadium pentoxide is a promising battery cathode material and in this work we report on the synthesis of V2O5 orthorhombic single crystal and polycrystalline nanorods by the sol-gel polymerizing acryl amide method via ethylenediamine tetra acetic acid EDTA assisted hydrothermal process. In order to determine the thermodynamic stability of nanostructured polymorphs vanadates, heat treatments were performed from 450 C to 500 ^oC with annealing times ranging from 48 to 72 h. The morphologies and structures of the nanorods were characterized by XRD, SEM and HRTEM. Thermo Gravimetric Analysis (TGA) was employed to monitor reaction mass losses during the course of the synthesis. Nanorod diameters ranging from 50 to 150 nm were observed. The lengths and diameter of the rods depended on the conditions of the preparation, such as concentration, and reaction time.

  2. Sparse Labeling of Proteins: Structural Characterization from Long Range Constraints

    PubMed Central

    Prestegard, James H.; Agard, David A.; Moremen, Kelley W.; Lavery, Laura A.; Morris, Laura C.; Pederson, Kari

    2014-01-01

    Structural characterization of biologically important proteins faces many challenges associated with degradation of resolution as molecular size increases and loss of resolution improving tools such as perdeuteration when non-bacterial hosts must be used for expression. In these cases, sparse isotopic labeling (single or small subsets of amino acids) combined with long range paramagnetic constraints and improved computational modeling offer an alternative. This perspective provides a brief overview of this approach and two discussions of potential applications; one involving a very large system (an Hsp90 homolog) in which perdeuteration is possible and methyl-TROSY sequences can potentially be used to improve resolution, and one involving ligand placement in a glycosylated protein where resolution is achieved by single amino acid labeling (the sialyltransferase, ST6Gal1). This is not intended as a comprehensive review, but as a discussion of future prospects that promise impact on important questions in the structural biology area. PMID:24656078

  3. Sparse labeling of proteins: Structural characterization from long range constraints

    NASA Astrophysics Data System (ADS)

    Prestegard, James H.; Agard, David A.; Moremen, Kelley W.; Lavery, Laura A.; Morris, Laura C.; Pederson, Kari

    2014-04-01

    Structural characterization of biologically important proteins faces many challenges associated with degradation of resolution as molecular size increases and loss of resolution improving tools such as perdeuteration when non-bacterial hosts must be used for expression. In these cases, sparse isotopic labeling (single or small subsets of amino acids) combined with long range paramagnetic constraints and improved computational modeling offer an alternative. This perspective provides a brief overview of this approach and two discussions of potential applications; one involving a very large system (an Hsp90 homolog) in which perdeuteration is possible and methyl-TROSY sequences can potentially be used to improve resolution, and one involving ligand placement in a glycosylated protein where resolution is achieved by single amino acid labeling (the sialyltransferase, ST6Gal1). This is not intended as a comprehensive review, but as a discussion of future prospects that promise impact on important questions in the structural biology area.

  4. Characterization of structure and thermophysical properties of three ESR slags

    NASA Astrophysics Data System (ADS)

    Plotkowski, A.; deBarbadillo, J.; Krane, Matthew J. M.

    2016-07-01

    The structure and properties of electroslag remelting (ESR) slags were characterized. Slags samples of three compositions were obtained from industrial remelting processes at Special Metals Corporation and from casting in a laboratory vacuum induction melter. The structure of the slag samples was observed using optical and electron microscopy, and phases were identified and their relative amounts quantified using X-ray diffraction. Laser flash thermal diffusivity, density, and differential scanning calorimetry measurements for specific heat were performed to determine the bulk thermal conductivity of the samples. Sample porosity was measured as a function of depth using a serial sectioning technique, and a onedimensional computational model was developed to estimate the thermal conductivity of the fully dense slags. These results are discussed in context with previous studies, and opportunities for future research are identified. AFRL Case Number: 88ABW-2015-1871.

  5. Integral structural-functional method for characterizing microbial populations

    NASA Astrophysics Data System (ADS)

    Yakushev, A. V.

    2015-04-01

    An original integral structural-functional method has been proposed for characterizing microbial communities. The novelty of the approach is the in situ study of microorganisms based on the growth kinetics of microbial associations in liquid nutrient broth media under selective conditions rather than on the level of taxa or large functional groups. The method involves the analysis of the integral growth model of a periodic culture. The kinetic parameters of such associations reflect their capacity of growing on different media, i.e., their physiological diversity, and the metabolic capacity of the microorganisms for growth on a nutrient medium. Therefore, the obtained parameters are determined by the features of the microbial ecological strategies. The inoculation of a dense medium from the original inoculate allows characterizing the taxonomic composition of the dominants in the soil community. The inoculation from the associations developed on selective media characterizes the composition of syntrophic groups, which fulfill a specific function in nature. This method is of greater information value than the classical methods of inoculation on selective media.

  6. Amyloid oligomer structure characterization from simulations: A general method

    SciTech Connect

    Nguyen, Phuong H.; Li, Mai Suan

    2014-03-07

    Amyloid oligomers and plaques are composed of multiple chemically identical proteins. Therefore, one of the first fundamental problems in the characterization of structures from simulations is the treatment of the degeneracy, i.e., the permutation of the molecules. Second, the intramolecular and intermolecular degrees of freedom of the various molecules must be taken into account. Currently, the well-known dihedral principal component analysis method only considers the intramolecular degrees of freedom, and other methods employing collective variables can only describe intermolecular degrees of freedom at the global level. With this in mind, we propose a general method that identifies all the structures accurately. The basis idea is that the intramolecular and intermolecular states are described in terms of combinations of single-molecule and double-molecule states, respectively, and the overall structures of oligomers are the product basis of the intramolecular and intermolecular states. This way, the degeneracy is automatically avoided. The method is illustrated on the conformational ensemble of the tetramer of the Alzheimer's peptide Aβ{sub 9−40}, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.

  7. Graphene Oxide: Synthesis, Characterization, Electronic Structure, and Applications

    NASA Astrophysics Data System (ADS)

    Stewart, Derek A.; Mkhoyan, K. Andre

    While graphite oxide was first identified in 1855 [1, 2], the recent discovery of stable graphene sheets has led to renewed interest in the chemical structure and potential applications of graphene oxide sheets. These structures have several physical properties that could aid in the large scale development of a graphene electronics industry. Depending on the degree of oxidization, graphene oxide layers can be either semiconducting or insulating and provide an important complement to metallic graphene layers. In addition, the electronic and optical properties of these films can be controlled by the selective removal or addition of oxygen. For example, selective oxidationof graphene sheets could lead to electronic circuit fabrication on the scale of a single atomic layer. Graphene oxide is also dispersible in water and other solvents and this provides a facile route for graphene deposition on a wide range of substrates for macroelectronics applications. Although graphite oxide has been known for roughly 150 years, key questions remain in regards to its chemical structure, electronic properties, and fabrication. Answering these issues has taken on special urgency with the development of graphene electronics. In this chapter, we will provide an overview of the field with special focus on synthesis, characterization, and first principles analysis of bonding and electronic structures. Finally, we will also address some of the most promising applications for graphene oxide in electronics and other industries.

  8. Characterization of the B/Si surface electronic structures

    SciTech Connect

    Cao, R.; Yang, X.; Pianetta, P.

    1992-11-01

    High resolution angle resolved core level and valence band photoelectron spectroscopy have been used to characterize the electronic structures of the B/Si(111)-({radical}3 x {radical}3) surfaces. The results have been compared with theoretic calculations and other group III metals and Si terminated Si(111) surfaces that share the same type of surface reconstruction. We have observed a structure evolution from B-T{sub 4} to B-S{sub 5} and finally to Si- T{sub 4} as deposited boron atoms diffuse into the substrate with increasing annealing temperature. The chemically shifted component appearing in the Si 2p core level spectrum is attributed to charge transfer from the top layer Si and Si adatoms to the sublayer B-S{sub 5} atoms. For the Si/Si(111)-({radical}3 {times} {radical}3) surface, a newly discovered chemically shifted component is associated with back bond formation between the Si adatoms and the underneath Si atoms. A new emission feature has been observed in the valence band spectra unique to the B/Si(111)-({radical}3 {times} {radical}3) surface with B-S{sub 5} configuration. Thin Ge layer growth on this structure has also been performed, and we found that no epitaxial growth could be achieved and the underneath structure was little disturbed.

  9. Cloning, expression, and preliminary structural characterization of RTN-1C

    SciTech Connect

    Fazi, Barbara; Melino, Sonia; Sano, Federica Di; Cicero, Daniel O.; Piacentini, Mauro . E-mail: mauro.piacentini@uniroma2.it; Paci, Maurizio

    2006-04-14

    Reticulons (RTNs) are endoplasmic reticulum-associated proteins widely distributed in plants, yeast, and animals. They are characterized by unique N-terminal parts and a common 200 amino acid C-terminal domain containing two long hydrophobic sequences. Despite their implication in many cellular processes, their molecular structure and function are still largely unknown. In this study, the reticulon family member RTN-1C has been expressed and purified in Escherichia coli and its molecular structure has been analysed by fluorescence and CD spectroscopy in different detergents in order to obtain a good solubility and a relative stability. The isotopically enriched protein has been also produced to perform structural studies by NMR spectroscopy. The preliminary results obtained showed that RTN-1C protein possesses helical transmembrane segments when a membrane-like environment is produced by detergents. Moreover, fluorescence experiments indicated the exposure of tryptophan side chains as predicted by structure prediction programs. We also produced the isotopically labelled protein and the procedure adopted allowed us to plan future NMR studies to investigate the biochemical behaviour of reticulon-1C and of its peptides spanning out from the membrane.

  10. Photogrammetric detection technique for rotor blades structural characterization

    NASA Astrophysics Data System (ADS)

    Enei, C.; Bernardini, G.; Serafini, J.; Mattioni, L.; Ficuciello, C.; Vezzari, V.

    2015-11-01

    This paper describes an innovative use of photogrammetric detection techniques to experimentally estimate structural/inertial properties of helicopter rotor blades. The identification algorithms for the evaluation of mass and flexural stiffness distributions are an extension of the ones proposed by Larsen, whereas the procedure for torsional properties determination (stiffness and shear center position) is based on the Euler-Prandtl beam theory. These algorithms rely on measurements performed through photogrammetric detection, which requires the collection of digital photos allowing the identification of 3D coordinates of labeled points (markers) on the structure through the correlation of 2D pictures. The displacements are evaluated by comparing the positions of markers in loaded and reference configuration. Being the applied loads known, the structural characteristics can be directly obtained from the measured displacements. The accuracy of the proposed identification algorithms has been firstly verified by comparison with numerical and experimental data, and then applied to the structural characterization of two main rotor blades, designed for ultra-light helicopter applications.

  11. Characterization of adhesive from oysters: A structural and compositional study

    NASA Astrophysics Data System (ADS)

    Alberts, Erik

    The inability for man-made adhesives to set in wet or humid environments is an ongoing challenging the design of biomedical and marine adhesive materials. However, we see that nature has already overcome this challenge. Mussels, barnacles, oysters and sandcastle worms all have unique mechanisms by which they attach themselves to surfaces. By understanding what evolution has already spent millions of years perfecting, we can design novel adhesive materials inspired by nature's elegant designs. The well-studied mussel is currently the standard for design of marine inspired biomimetic polymers. In the work presented here, we aim to provide new insights into the adhesive produced by the eastern oyster, Crassostrea virginica. Unlike the mussel, which produces thread-like plaques comprised of DOPA containing-protein, the oyster secretes an organic-inorganic hybrid adhesive as it settles and grows onto a surface. This form of adhesion renders the oyster to be permanently fixed in place. Over time, hundreds of thousands of oyster grow and agglomerate to form extensive reef structures. These reefs are not only essential to survival of the oyster, but are also vital to intertidal ecosystems. While the shell of the oyster has been extensively studied, curiously, only a few conflicting insights have been made into the nature of the adhesive and contact zone between shell and substrate, and even lesfs information has been ascertained on organic and inorganic composition. In this work, we provide microscopy and histochemical studies to characterize the structure and composition of the adhesive, using oyster in the adult and juvenile stages of life. Preliminary work on extracting and characterizing organic components through collaborative help with solid-state NMR (SSNMR) and proteomics are also detailed here. We aim to provide a full, comprehensive characterization of oyster adhesive so that in the future, we may apply what we learn to the design of new materials.

  12. Optical characterization of vitreous structure in health and disease

    NASA Astrophysics Data System (ADS)

    Sampathkumar, Ashwin; Khoshnevis, Matin; Ketterling, Jeffrey A.; Sebag, J.

    2015-03-01

    Patients with myopic vitreopathy (MV) and posterior vitreous detachment (PVD) see floaters, which often can degrade contrast sensitivity to a significant extent. The floaters are associated with irregularly shaped vitreous opacities. In contrast, asteroid hyalosis (AH), which is characterized by microscopic, spherical, white asteroid bodies (ABs) that move with vitreous displacement during eye movements, does not interfere significantly with vision. We hypothesize that the irregular surface of vitreous opacities associated with MV distinguish MV from AH and its smooth-surfaced ABs. A finite-element model was developed to characterize the light-scattering field of vitreous opacities in MV and AH. Vitreous opacities were modeled as spherical bodies and illuminated by a plane wave of light in the optical wavelength of 400-1000 nm. The model has provisions to add random perturbations to the spherical surfaces to vary light-scattering properties and mimic disturbances in vision from simple diffraction rings to more-complex patterns. Samples of ex vivo porcine vitreous (0.4-0.5 ml) were placed in a custom spectrophotometer and the static, light-scattering field of the sample was measured in the spectral range of 400-1000 nm with a resolution of 0.3 nm. Model solutions mimicking healthy vitreous and AH were experimentally validated using a laboratory optical apparatus. Model-based estimates of scattering cross-sections of calibrated gold nanoparticles were found to be in good agreement with experimental measurements. Simulation results potentially can complement experimental data to quantitatively characterize vitreous opacities and distinguish between structures that significantly impact vision, such as those due to myopic vitreopathy and aging, from those that have little impact, like ABs. Such techniques to determine the structural significance of vitreous opacification would be very useful in selecting patients for surgery as well as evaluating the efficacy of

  13. Structural and spectroscopic characterization of mixed planetary ices.

    PubMed

    Plattner, Nuria; Lee, Myung Won; Meuwly, Markus

    2010-01-01

    Mixed ices play a central role in characterizing the origin, evolution, stability and chemistry of planetary ice surfaces. Examples include the polar areas of Mars, the crust of the Jupiter moon Europa, or atmospheres of planets and their satellites, particularly in the outer solar system. Atomistic simulations using accurate representations of the interaction potentials have recently shown to be suitable to quantitatively describe both, the mid- and the far-infrared spectrum of mixed H2O/CO amorphous ices. In this work, molecular dynamics simulations are used to investigate structural and spectroscopic properties of mixed and crystalline ices containing H2O, CO and CO2. Particular findings include: (a) the sensitivity of the water bending mode to the local environment of the water molecules which, together with structural insights from MD simulations, provides a detailed picture for the relationship between spectroscopy and structure; and (b) the sensitivity of the low-frequency spectrum to the structure of the mixed CO2/H2O ice. Specifically, for mixed H2O/CO2 ices with low water contents isolated water molecules are found which give rise to a band shifted by only 12 cm(-1) from the gas-phase value whereas for increasing water concentration (for a 1 : 1 mixture) the band progressively shifts to higher frequency because water clusters can form. More generally it is found that changes in the ice structure due to the presence of CO2 are larger compared to changes induced by the presence of CO and that this difference is reflected in the shape of the water bending vibration. Thus, the water bending vibration appears to be a suitable diagnostic for structural and chemical aspects of mixed ices. PMID:21302549

  14. Pyroxene Spectroscopy: Remote Characterization of Composition, Structure and Thermal History

    NASA Astrophysics Data System (ADS)

    Klima, Rachel L.; Dyar, Darby; Glotch, Timothy; Lane, Melissa

    2014-11-01

    Pyroxene is one of the most commonly used minerals for remote analysis of mineralogy and composition of planetary bodies. This is in part due to the prevalence of pyroxene on the surfaces of objects in the inner solar system. Pyroxene also exhibits a distinctive spectrum that is highly sensitive to its specific composition, structure, and cation site occupancy. Cation ordering, which is partially a result of the cooling history of a pyroxene, affects the strengths of absorptions caused by Fe2+ in the M1 and M2 cation sites, which in turn affects the relative band 1 and band 2 areas. Terrestrial pyroxenes are generally quite well-ordered, as many have been exposed to and held for long times at temperatures warm enough to allow cations to exchange between the M1 and M2 sites. Extraterrestrial pyroxenes have been exposed to a vast array of cooling regimes, including flash heating and cooling in the protoplanetary disk, impact brecciation and melting, and more traditional igneous processes.To push pyroxene spectroscopy beyond simple mineral identification and develop it as a tool for characterizing the thermal history of a body, we have been working to characterize and document the crystal chemistry, structure, and site occupancies of a suite of 91 synthetic pyroxenes. This is accomplished by measuring single-crystal XRD, Attenuated Total Reflectance (ATR) and electron probe microanalysis (EMP), variable-temperature Mössbauer and Raman spectra. For each of the samples, visible-far IR spectra have also been collected. We will present the results of this integrated study, focusing on how the crystal structure, composition and site occupancy in pyroxenes is reflected in their visible-infrared spectra and how they can be used to evaluate the thermal history of asteroids and the Moon.

  15. Function Discovery and Structural Characterization of a Methylphosphonate Esterase

    SciTech Connect

    Xiang, Dao Feng; Patskovsky, Yury; Nemmara, Venkatesh V.; Toro, Rafael; Almo, Steven C.; Raushel, Frank M.

    2015-05-12

    Pmi1525, an enzyme of unknown function from Proteus mirabilis HI4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. The three-dimensional structure of Pmi1525 was determined with zinc and cacodylate bound in the active site (PDB id: 3RHG). We also determined the structure with manganese and butyrate in the active site (PDB id: 4QSF). Pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamily and cog1735. Moreover, the substrate profile for Pmi1525 was determined via a strategy that marshaled the utilization of bioinformatics, structural characterization, and focused library screening. The protein was found to efficiently catalyze the hydrolysis of organophosphonate and carboxylate esters. The best substrates identified for Pmi1525 are ethyl 4-nitrophenylmethyl phosphonate (kcat and kcat /Km values of 580 s–1 and 1.2 × 105 M–1 s–1, respectively) and 4-nitrophenyl butyrate (kcat and kcat /Km values of 140 s–1 and 1.4 × 105 M–1 s–1, respectively). Pmi1525 is stereoselective for the hydrolysis of chiral methylphosphonate esters. The enzyme hydrolyzes the (SP)-enantiomer of isobutyl 4-nitrophenyl methylphosphonate 14 times faster than the corresponding (RP)-enantiomer. The catalytic properties of this enzyme make it an attractive template for the evolution of novel enzymes for the detection, destruction, and detoxification of organophosphonate nerve agents.

  16. ZnO Nanoporous Structure Growth, Optical and Structural Characterization by Aqueous Solution Route

    NASA Astrophysics Data System (ADS)

    Kashif, M.; Ali, Syed M. Usman; Foo, K. L.; Hashim, U.; Willander, Magnus

    2011-05-01

    In this study, we have demonstrated the structural and optical characterization of ZnO nanoporous structure grown on gold coated plastic substrate using low temperature aqueous chemical growth (ACG) technique and the annealing temperature was kept at 150° C. ZnO nanoporous structures were fabricated using hydrolysis process by reacting zinc acetate dehydrate with anhydrous ethanol. The crystalline morphology of ZnO nanoporous structures were investigated by using X-ray diffraction (XRD), surface morphology was observed by field emission scanning electron microscope (FESEM). The optical characteristics of ZnO nanoporous structures were investigated at room temperature, PL was observed using UV-Vis Spectrophotometer and the chemical composition is analyzed using Fourier Transform Infra-Red spectrometer (FTIR).

  17. Structural, Mechanistic, and Antigenic Characterization of the Human Astrovirus Capsid

    PubMed Central

    York, Royce L.; Yousefi, Payam A.; Bogdanoff, Walter; Haile, Sara; Tripathi, Sarvind

    2015-01-01

    ABSTRACT Human astroviruses (HAstVs) are nonenveloped, positive-sense, single-stranded RNA viruses that are a leading cause of viral gastroenteritis. HAstV particles display T=3 icosahedral symmetry formed by 180 copies of the capsid protein (CP), which undergoes proteolytic maturation to generate infectious HAstV particles. Little is known about the molecular features that govern HAstV particle assembly, maturation, infectivity, and immunogenicity. Here we report the crystal structures of the two main structural domains of the HAstV CP: the core domain at 2.60-Å resolution and the spike domain at 0.95-Å resolution. Fitting of these structures into the previously determined 25-Å-resolution electron cryomicroscopy density maps of HAstV allowed us to characterize the molecular features on the surfaces of immature and mature T=3 HAstV particles. The highly electropositive inner surface of HAstV supports a model in which interaction of the HAstV CP core with viral RNA is a driving force in T=3 HAstV particle formation. Additionally, mapping of conserved residues onto the HAstV CP core and spike domains in the context of the immature and mature HAstV particles revealed dramatic changes to the exposure of conserved residues during virus maturation. Indeed, we show that antibodies raised against mature HAstV have reactivity to both the HAstV CP core and spike domains, revealing for the first time that the CP core domain is antigenic. Together, these data provide new molecular insights into HAstV that have practical applications for the development of vaccines and antiviral therapies. IMPORTANCE Astroviruses are a leading cause of viral diarrhea in young children, immunocompromised individuals, and the elderly. Despite the prevalence of astroviruses, little is known at the molecular level about how the astrovirus particle assembles and is converted into an infectious, mature virus. In this paper, we describe the high-resolution structures of the two main astrovirus

  18. Structural and biochemical characterization of a halophilic archaeal alkaline phosphatase.

    PubMed

    Wende, Andy; Johansson, Patrik; Vollrath, Ronnald; Dyall-Smith, Mike; Oesterhelt, Dieter; Grininger, Martin

    2010-07-01

    Phosphate is an essential component of all cells that must be taken up from the environment. Prokaryotes commonly secrete alkaline phosphatases (APs) to recruit phosphate from organic compounds by hydrolysis. In this study, the AP from Halobacterium salinarum, an archaeon that lives in a saturated salt environment, has been functionally and structurally characterized. The core fold and the active-site architecture of the H. salinarum enzyme are similar to other AP structures. These generally form dimers composed of dominant beta-sheet structures sandwiched by alpha-helices and have well-accessible active sites. The surface of the enzyme is predicted to be highly negatively charged, like other proteins of extreme halophiles. In addition to the conserved core, most APs contain a crown domain that strongly varies within species. In the H. salinarum AP, the crown domain is made of an acyl-carrier-protein-like fold. Different from other APs, it is not involved in dimer formation. We compare the archaeal AP with its bacterial and eukaryotic counterparts, and we focus on the role of crown domains in enhancing protein stability, regulating enzyme function, and guiding phosphoesters into the active-site funnel. PMID:20438737

  19. Biochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase.

    PubMed

    Cook, William J; Senkovich, Olga; Hernandez, Agustin; Speed, Haley; Chattopadhyay, Debasish

    2015-03-01

    The protozoan parasite Cryptosporidium parvum causes waterborne diseases worldwide. There is no effective therapy for C. parvum infection. The parasite depends mainly on glycolysis for energy production. Lactate dehydrogenase is a major regulator of glycolysis. This paper describes the biochemical characterization of C. parvum lactate dehydrogenase and high resolution crystal structures of the apo-enzyme and four ternary complexes. The ternary complexes capture the enzyme bound to NAD/NADH or its 3-acetylpyridine analog in the cofactor binding pocket, while the substrate binding site is occupied by one of the following ligands: lactate, pyruvate or oxamate. The results reveal distinctive features of the parasitic enzyme. For example, C. parvum lactate dehydrogenase prefers the acetylpyridine analog of NADH as a cofactor. Moreover, it is slightly less sensitive to gossypol inhibition compared with mammalian lactate dehydrogenases and not inhibited by excess pyruvate. The active site loop and the antigenic loop in C. parvum lactate dehydrogenase are considerably different from those in the human counterpart. Structural features and enzymatic properties of C. parvum lactate dehydrogenase are similar to enzymes from related parasites. Structural comparison with malate dehydrogenase supports a common ancestry for the two genes. PMID:25542170

  20. A structural framework for anomalous change detection and characterization

    SciTech Connect

    Prasad, Lakshman; Theiler, James P

    2009-01-01

    We present a spatially adaptive scheme for automatically searching a pair of images of a scene for unusual and interesting changes. Our motivation is to bring into play structural aspects of image features alongside the spectral attributes used for anomalous change detection (ACD). We leverage a small but informative subset of pixels, namely edge pixels of the images, as anchor points of a Delaunay triangulation to jointly decompose the images into a set of triangular regions, called trixels, which are spectrally uniform. Such decomposition helps in image regularization by simple-function approximation on a feature-adaptive grid. Applying ACD to this trixel grid instead of pixels offers several advantages. It allows: (1) edge-preserving smoothing of images, (2) speed-up of spatial computations by significantly reducing the representation of the images, and (3) the easy recovery of structure of the detected anomalous changes by associating anomalous trixels with polygonal image features. The latter facility further enables the application of shape-theoretic criteria and algorithms to characterize the changes and recognize them as interesting or not. This incorporation of spatial information has the potential to filter out some spurious changes, such as due to parallax, shadows, and misregistration, by identifying and filtering out those that are structurally similar and spatially pervasive. Our framework supports the joint spatial and spectral analysis of images, potentially enabling the design of more robust ACD algorithms.

  1. Characterization of electronic structure of periodically strained graphene

    DOE PAGESBeta

    Aslani, Marjan; Garner, C. Michael; Kumar, Suhas; Nordlund, Dennis; Pianetta, Piero; Nishi, Yoshio

    2015-11-03

    We induced periodic biaxial tensile strain in polycrystalline graphene by wrapping it over a substrate with repeating pillar-like structures with a periodicity of 600 nm. Using Raman spectroscopy, we determined to have introduced biaxial strains in graphene in the range of 0.4% to 0.7%. Its band structure was characterized using photoemission from valance bands, shifts in the secondary electron emission, and x-ray absorption from the carbon 1s levels to the unoccupied graphene conduction bands. It was observed that relative to unstrained graphene, strained graphene had a higher work function and higher density of states in the valence and conduction bands.more » Furthermore, we measured the conductivity of the strained and unstrained graphene in response to a gate voltage and correlated the changes in their behavior to the changes in the electronic structure. From these sets of data, we propose a simple band diagram representing graphene with periodic biaxial strain.« less

  2. Statistical characterization of complex object structure by dynamic tomography

    NASA Astrophysics Data System (ADS)

    Tillack, Gerd-Rüdiger; Goebbels, Jürgen; Illerhaus, Bernhard; Artemiev, Valentin; Naumov, Alexander

    2002-05-01

    Considering modern materials like reinforced plastics or metal foams the mechanical properties of the component are not determined by every single structural element like a single fiber in a composite. Moreover the ensemble mean and correlation properties of all structural elements form the mechanical properties of the component. Accordingly a statistical description of material properties on a macroscopic scale allow to characterize its mechanical behavior or aging. State of the art tomographic techniques assign a measure of material properties to a volume element. The discretization, i.e., the volume or size of a single element, is limited mainly by the physical mechanisms and the equipment used for the data acquisition. In any case the result of reconstruction yields a statistical average within the considered volume element. To evaluate the integrity of the component the determined measures have to be correlated with the mechanical properties of the component. Special reconstruction algorithms are investigated that allow the statistical description of complex object structures including its dynamics. The algorithm is based on the Kalman filter using statistical prior. The prior includes knowledge about the covariance matrix as well as a prior assumption about the probability density distribution function. The resulting algorithm is recursive yielding a quasi-optimal solution at every reconstruction step. The applicability of the developed algorithm is discussed for the investigation of a specimen made from aluminum foam.

  3. Structural Characterization of a Monoclonal Antibody-Maytansinoid Immunoconjugate.

    PubMed

    Luo, Quanzhou; Chung, Hyo Helen; Borths, Christopher; Janson, Matthew; Wen, Jie; Joubert, Marisa K; Wypych, Jette

    2016-01-01

    Structural characterization was performed on an antibody-drug conjugate (ADC), composed of an IgG1 monoclonal antibody (mAb), mertansine drug (DM1), and a noncleavable linker. The DM1 molecules were conjugated through nonspecific modification of the mAb at solvent-exposed lysine residues. Due to the nature of the lysine conjugation process, the ADC molecules are heterogeneous, containing a range of species that differ with respect to the number of DM1 per antibody molecule. The DM1 distribution profile of the ADC was characterized by electrospray ionization mass spectrometry (ESI-MS) and capillary isoelectric focusing (cIEF), which showed that 0-8 DM1s were conjugated to an antibody molecule. By taking advantage of the high-quality MS/MS spectra and the accurate mass detection of diagnostic DM1 fragment ions generated from the higher-energy collisional dissociation (HCD) approach, we were able to identify 76 conjugation sites in the ADC, which covered approximately 83% of all the putative conjugation sites. The diagnostic DM1 fragment ions discovered in this study can be readily used for the characterization of other ADCs with maytansinoid derivatives as payload. Differential scanning calorimetric (DSC) analysis of the ADC indicated that the conjugation of DM1 destabilized the C(H)2 domain of the molecule, which is likely due to conjugation of DM1 on lysine residues in the C(H)2 domain. As a result, methionine at position 258 of the heavy chain, which is located in the C(H)2 domain of the antibody, is more susceptible to oxidation in thermally stressed ADC samples when compared to that of the naked antibody. PMID:26629796

  4. Isolation and structural characterization of chondroitin sulfate from bony fishes.

    PubMed

    Maccari, Francesca; Galeotti, Fabio; Volpi, Nicola

    2015-09-20

    Chondroitin sulfate (CS) was purified from the bones of common fishes, monkfish, cod, spiny dogfish, salmon and tuna, and characterized in an effort to find alternative sources and new peculiar structures of this complex biomacromolecule utilized in the pharmaceutical and nutraceutical industry. Quantitative analyses yielded a CS content ranging from 0.011% for cod up to 0.34% for monkfish. The disaccharide pattern showed the presence of nonsulfated disaccharide, monosulfated species ΔDi6s and ΔDi4s, and disulfated disaccharides in different percentages. The disulfated species ΔDi2,6dis was present in all CS extracts in a range of 1.3-10.5%. The presence of these disulfated disaccharides may be a useful marker for the marine origin of CS. The newly identified sources would certainly enable the production of CS with unique disaccharide composition and properties. PMID:26050899

  5. Facile chemical synthesis and structure characterization of copper molybdate nanoparticles

    NASA Astrophysics Data System (ADS)

    Rahimi-Nasrabadi, Mehdi; Pourmortazavi, Seied Mahdi; Khalilian-Shalamzari, Morteza

    2015-03-01

    Experimental parameters of a synthesis route were optimized by Taguchi robust design for the facile and controllable synthesis of copper molybdate nanoparticles. CuMoO4 nanoparticles were synthesized by chemical precipitation followed by hydrothermal process. Effects of different parameters of synthesis procedure, i.e. concentrations of both reagents, copper feeding flow rate and temperature of reactor on the particle size of prepared copper molybdate nanoparticles were investigated. The results of statistical optimization revealed that the size of copper molybdate particles is dependent on the procedure variables involving copper concentrations, flow rate and temperature of the reactor; while, molybdate concentration has a no considerable role in determining the size of CuMoO4 particles. Based on the results obtained by statistical optimization process, the nanoparticles of copper molybdate were prepared and then their structure and chemical composition were characterized by various techniques, i.e. SEM, TEM, XRD, EDX, FT-IR, UV-Vis and photoluminescence spectroscopy.

  6. Structural and functional characterization of enamel pigmentation in shrews.

    PubMed

    Dumont, M; Tütken, T; Kostka, A; Duarte, M J; Borodin, S

    2014-04-01

    Pigmented tooth enamel occurs in several vertebrate clades, ranging from mammals to fish. Although an iron compound is associated with this orange to red colored pigmentation, its chemical and structural organization within the enamel is unknown. To determine the nature of the iron compound, we investigated heavily pigmented teeth of the northern short-tailed shrew Blarina brevicauda using combined characterization techniques such as scanning and transmission electron microscopy and synchrotron X-ray diffraction. We found that the pigmentation of the enamel with an iron content of around 8wt% results from a close to amorphous magnetite phase deposited around the nm-sized enamel crystals. Furthermore, the influence of the pigmentation on the enamel hardness was determined by nanoindentation measurements. Finally, the biomechanical function and biological context are discussed in light of the obtained results. PMID:24556576

  7. Characterization of Thermal and Mechanical Impact on Aluminum Honeycomb Structures

    NASA Technical Reports Server (NTRS)

    Robinson, Christen M.

    2013-01-01

    This study supports NASA Kennedy Space Center's research in the area of intelligent thermal management systems and multifunctional thermal systems. This project addresses the evaluation of the mechanical and thermal properties of metallic cellular solid (MCS) materials; those that are lightweight; high strength, tunable, multifunctional and affordable. A portion of the work includes understanding the mechanical properties of honeycomb structured cellular solids upon impact testing under ambient, water-immersed, liquid nitrogen-cooled, and liquid nitrogen-immersed conditions. Additionally, this study will address characterization techniques of the aluminum honeycomb's ability to resist multiple high-rate loadings or impacts in varying environmental conditions, using various techniques for the quantitative and qualitative determination for commercial applicability.

  8. Fabrication, characterization, and optical properties of gold nanobowl submonolayer structures.

    PubMed

    Ye, Jian; Van Dorpe, Pol; Van Roy, Willem; Borghs, Gustaaf; Maes, Guido

    2009-02-01

    We report on a versatile method to fabricate hollow gold nanobowls and complex gold nanobowls (with a core) based on an ion milling and a vapor HF etching technique. Two different sized hollow gold nanobowls are fabricated by milling and etching submonolayers of gold nanoshells deposited on a substrate, and their sizes and morphologies are characterized by scanning electron microscopy (SEM) and atomic force microscopy (AFM). Optical properties of hollow gold nanobowls with different sizes are investigated experimentally and theoretically, showing highly tunable plasmon resonance ranging from the visible to the near-infrared region. Additionally, finite difference time domain (FDTD) calculations show an enhanced localized electromagnetic field around hollow gold nanobowl structures, which indicates a potential application in surface-enhanced Raman scattering (SERS) spectroscopy for biomolecular detection. Finally, we demonstrate the fabrication of complex gold nanobowls with a gold nanoparticle core which offers the capability to create plasmon hybridized nanostructures. PMID:19125593

  9. Fabrication, characterization, and application of microresonators and resonant structures

    NASA Astrophysics Data System (ADS)

    Cohoon, Gregory A.

    Optical resonators are structures that allow light to circulate and store energy for a duration of time. This work primarily looks at the fabrication, characterization, and application of whispering gallery mode microresonators and the analysis of organic photonic crystal-like structures and simulation of their resonant effects. Whispering gallery mode (WGM) microresonators are a class of cylindrically symmetric optical resonator which light circulates around the equator of the structure. These resonators are named after acoustic whispering galleries, where a whisper can be heard anywhere along the perimeter of a circular room. These optical structures are known for their ultra high Q-factor and their low mode volume. Q-factor describes the photon lifetime in the cavity and is responsible for the energy buildup within the cavity and sharp spectral characteristics of WGM resonators. The energy buildup is ideal for non-linear optics and the sharp spectral features are beneficial for sensing applications. Characterization of microbubble resonators is done by coupling light from a tunable laser source via tapered optical fiber into the cavity. The fabrication of quality tapered optical fiber on the order of 1--2 microm is critical to working on WGM resonators. The measurement of Q-factors up to 2x10 8 and mode spectra are possible with these resonators and experimental techniques. This work focuses on microdisk and microbubble WGM resonators. The microdisk resonators are fabricated by femtosecond laser micromachining. The micromachined resonators are fabricated by ablating rotating optical fiber to generate the disk shape and then heated to reflow the surface to improve optical quality. These resonators have a spares mode spectrum and display a Q factor as high a 2x106. The microbubble resonators are hollow microresonators fabricated by heating a pressurized capillary tube which forms a bubble in the area exposed to heat. These have a wall thickness of 2--5 microm and

  10. Structural characterization of macroscopic single-walled carbon nanotube materials

    NASA Astrophysics Data System (ADS)

    Zhou, Wei

    In this thesis, we studied the structural properties of macroscopic materials of single-walled carbon nanotubes (SWNTs) in the form of fibers, films and suspensions. We characterized the preferred orientations in partially aligned SWNT fibers and films, combining x-ray fiber diagram and polarized Raman scattering. Our texture model consists of an aligned fraction, characterized by the angular distribution width of tube axes, plus a completely unaligned fraction. For neat fibers extruded from SWNT/superacid suspensions through a small orifice, the distribution width and the aligned fraction both improve with decreasing orifice diameter. For magnetic field-aligned SWNT films deposited from surfactant suspensions, the aligning effects of deposition and external magnetic field force in the film plane are additive, the out-of-plane mosaic being narrower than the in-plane one. SWNTs dispersed in superacid or aqueous surfactant solutions are precursors for many applications. In oleum, SWNTs can be charged and protonated by H 2SO4 molecules. X-ray scattering indicates that H2SO 4 molecules align along nanotube axes to form cylindrical shells wrapped around nanotubes. This finding establishes the validity of a long-standing important but still debated physical chemistry concept, "structured solvent shells surrounding dissolved ions". Differential scanning calorimetry confirms that the partly ordered H2SO4 molecules are a new phase, with distinct freezing/melting behavior. X-ray scattering at low temperature further shows that crystallization of the bulk-like acid surrounding the structured shells is templated by the SWNTs. The specific orientation of the acid crystallites provides solid evidence for direct protonation of SWNT. We studied the morphologies of SWNT suspensions using small-angle neutron scattering. We observed rigid rod behavior from SWNTs dispersed in water using sodium dodecylbenzene sulfonate surfactant, suggesting that SWNTs exist mainly as individual tube

  11. Structural characterization of the interaction of human lactoferrin with calmodulin.

    PubMed

    Gifford, Jessica L; Ishida, Hiroaki; Vogel, Hans J

    2012-01-01

    Lactoferrin (Lf) is an 80 kDa, iron (Fe(3+))-binding immunoregulatory glycoprotein secreted into most exocrine fluids, found in high concentrations in colostrum and milk, and released from neutrophil secondary granules at sites of infection and inflammation. In a number of cell types, Lf is internalized through receptor-mediated endocytosis and targeted to the nucleus where it has been demonstrated to act as a transcriptional trans-activator. Here we characterize human Lf's interaction with calmodulin (CaM), a ubiquitous, 17 kDa regulatory calcium (Ca(2+))-binding protein localized in the cytoplasm and nucleus of activated cells. Due to the size of this intermolecular complex (∼100 kDa), TROSY-based NMR techniques were employed to structurally characterize Ca(2+)-CaM when bound to intact apo-Lf. Both CaM's backbone amides and the ε-methyl group of key methionine residues were used as probes in chemical shift perturbation and cross-saturation experiments to define the binding interface of apo-Lf on Ca(2+)-CaM. Unlike the collapsed conformation through which Ca(2+)-CaM binds the CaM-binding domains of its classical targets, Ca(2+)-CaM assumes an extended structure when bound to apo-Lf. Apo-Lf appears to interact predominantly with the C-terminal lobe of Ca(2+)-CaM, enabling the N-terminal lobe to potentially bind another target. Our use of intact apo-Lf has made possible the identification of a secondary interaction interface, removed from CaM's primary binding domain. Secondary interfaces play a key role in the target's response to CaM binding, highlighting the importance of studying intact complexes. This solution-based approach can be applied to study other regulatory calcium-binding EF-hand proteins in intact intermolecular complexes. PMID:23236421

  12. Characterization of natural photonic structures by means of optimization strategies

    NASA Astrophysics Data System (ADS)

    Macías, Demetrio; Vial, Alexandre; Luna, Ana; Skigin, Diana C.; Inchaussandague, Marina E.

    2015-03-01

    Natural photonic structures exhibit remarkable color effects such as metallic appearance and iridescence. A rigorous study of the electromagnetic response of such complex structures requires to accurately determine some of their relevant optical parameters, e.g. the dielectric constants of the materials involved. In a recent work, we have shown that heuristic optimization strategies are suitable tools for the retrieval of the complex refractive index of the materials comprising natural multilayer systems such as the Coleoptera's cuticle. Moreover, the numerical results obtained illustrate the great potential of this kind of algorithms not only for the study of natural photonic structures, but also for the design of biomimetic photonic devices for lightning, sensing or anti-counterfeiting applications. In a first stage, we assumed that the materials which comprise the layers are characterized by isotropic non-dispersive dielectric permittivities. However, it is well known that the cuticle of many Coleoptera exhibit anisotropy in their constituent materials, and also dispersion has been reported. In this contribution we improve our previous approach in order to have a more realistic and useful computational tool for the retrieval of the relevant parameters of biological structures. For this, we include, within the inversion algorithm, a dispersion model to describe the frequency-dependent dielectric permittivity of the layers' materials. Also, in order to guarantee the uniqueness of the solution and the convergence to the global optimum, we simultaneously include in the fitness function the information of several angles of incidence, as well as that of the p- and s-polarization states.

  13. Imaging and characterizing structure in Earth's deep interior

    NASA Astrophysics Data System (ADS)

    de Hoop, M. V.; van der Hilst, R. D.; Wang, P.; Tenorio, L.; Ma, P.

    2006-12-01

    We combine concepts from inverse scattering and statistics into an approach toward imaging and characterizing structure at and near interfaces in Earth's deep interior with large amounts of broad-band, three- component seismograms acquired by global seismograph networks. The retrieval of pertinent information requires few restrictive a priori assumptions about the structures of interest, which makes it complementary to forward modeling approaches. We discuss a generalized Radon transform admitting highly irregular source-receiver sampling to map broad-band seismogram windows -- comprising main arrivals with their coda and precursors -- into a set of multiple images of a target structure. The design of this transform is accomplished by a careful analysis of redundancy in the data. The `common image-point gathers' thus produced reveal multi-scale variations in acousto-elastic properties near interfaces and in boundary layers. Indeed, the image gathers admit a multi-resolution analysis of the discontinuities. Mixed-effects statistical modeling is used to turn these image gathers into quantitative singularity estimates and uncertainties. In this framework, random noise in the signal is separated into white and coherent components using the geometry of the imaging operators and a generalized cross-validation method, and uneven sampling and errors in the assumed background model are accounted for. As an example we present an application to imaging of the core mantle boundary. Finally, we address how beam forming through a phase-space transform can be integrated in the generalized Radon transform and applied, for example, to imaging of data from regional arrays. We elucidate the theory by synthetic data examples, and illustrate its performance by recently produced 3D images of D" revealing complex structure near the CMB with high levels of confidence.

  14. Structural Characterization of Myotoxic Ecarpholin S From Echis carinatus Venom

    SciTech Connect

    Zhou, X.; Tan, T; Valiyaveettil, S; Go, M; Kini, R; Velazquez-Campoy, A; Sivaraman, J

    2008-01-01

    Phospholipase A2 (PLA2), a common toxic component of snake venom, has been implicated in various pharmacological effects. Ecarpholin S, isolated from the venom of the snake Echis carinatus sochureki, is a phospholipase A2 (PLA2) belonging to the Ser49-PLA2 subgroup. It has been characterized as having low enzymatic but potent myotoxic activities. The crystal structures of native ecarpholin S and its complexes with lauric acid, and its inhibitor suramin, were elucidated. This is the first report of the structure of a member of the Ser49-PLA2 subgroup. We also examined interactions of ecarpholin S with phosphatidylglycerol and lauric acid, using surface plasmon resonance, and of suramin with isothermal titration calorimetry. Most Ca2+-dependent PLA2 enzymes have Asp in position 49, which plays a crucial role in Ca2+ binding. The three-dimensional structure of ecarpholin S reveals a unique conformation of the Ca2+-binding loop that is not favorable for Ca2+ coordination. Furthermore, the endogenously bound fatty acid (lauric acid) in the hydrophobic channel may also interrupt the catalytic cycle. These two observations may account for the low enzymatic activity of ecarpholin S, despite full retention of the catalytic machinery. These observations may also be applicable to other non-Asp49-PLA2 enzymes. The interaction of suramin in its complex with ecarpholin S is quite different from that reported for the Lys49-PLA2/suramin complex, where the interfacial recognition face (i-face), C-terminal region, and N-terminal region of ecarpholin S play important roles. This study provides significant structural and functional insights into the myotoxic activity of ecarpholin S and, in general, of non-Asp49-PLA2 enzymes.

  15. Characterization of structural relaxation in inorganic glasses using length dilatometry

    NASA Astrophysics Data System (ADS)

    Koontz, Erick

    The processes that govern how a glass relaxes towards its thermodynamic quasi-equilibrium state are major factors in understanding glass behavior near the glass transition region, as characterized by the glass transition temperature (Tg). Intrinsic glass properties such as specific volume, enthalpy, entropy, density, etc. are used to map the behavior of the glass network below in and near the transition region. The question of whether a true thermodynamic second order phase transition takes place in the glass transition region is another pending question. Linking viscosity behavior to entropy, or viewing the glass configuration as an energy landscape are just a couple of the most prevalent methods used for attempting to understand the glass transition. The structural relaxation behavior of inorganic glasses is important for more than scientific reasons, many commercial glass processing operations including glass melting and certain forms of optical fabrication include significant time spent in the glass transition region. For this reason knowledge of structural relaxation processes can, at a minimum, provide information for annealing duration of melt-quenched glasses. The development of a predictive model for annealing time prescription has the potential to save glass manufacturers significant time and money as well as increasing volume throughput. In optical hot forming processes such as precision glass molding, molded optical components can significantly change in shape upon cooling through the glass transition. This change in shape is not scientifically predictable as of yet though manufacturers typically use empirical rules developed in house. The classification of glass behavior in the glass transition region would allow molds to be accurately designed and save money for the producers. The work discussed in this dissertation is comprised of the development of a dilatometric measurement and characterization method of structural relaxation. The measurement and

  16. Characterizing 3D Vegetation Structure from Space: Mission Requirements

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G.; Bergen, Kathleen; Blair, James B.; Dubayah, Ralph; Houghton, Richard; Hurtt, George; Kellndorfer, Josef; Lefsky, Michael; Ranson, Jon; Saatchi, Sasan; Shugart, H. H.; Wickland, Diane

    2012-01-01

    Human and natural forces are rapidly modifying the global distribution and structure of terrestrial ecosystems on which all of life depends, altering the global carbon cycle, affecting our climate now and for the foreseeable future, causing steep reductions in species diversity, and endangering Earth s sustainability. To understand changes and trends in terrestrial ecosystems and their functioning as carbon sources and sinks, and to characterize the impact of their changes on climate, habitat and biodiversity, new space assets are urgently needed to produce high spatial resolution global maps of the three-dimensional (3D) structure of vegetation, its biomass above ground, the carbon stored within and the implications for atmospheric green house gas concentrations and climate. These needs were articulated in a 2007 National Research Council (NRC) report (NRC, 2007) recommending a new satellite mission, DESDynI, carrying an L-band Polarized Synthetic Aperture Radar (Pol-SAR) and a multi-beam lidar (Light RAnging And Detection) operating at 1064 nm. The objectives of this paper are to articulate the importance of these new, multi-year, 3D vegetation structure and biomass measurements, to briefly review the feasibility of radar and lidar remote sensing technology to meet these requirements, to define the data products and measurement requirements, and to consider implications of mission durations. The paper addresses these objectives by synthesizing research results and other input from a broad community of terrestrial ecology, carbon cycle, and remote sensing scientists and working groups. We conclude that: (1) current global biomass and 3-D vegetation structure information is unsuitable for both science and management and policy. The only existing global datasets of biomass are approximations based on combining land cover type and representative carbon values, instead of measurements of actual biomass. Current measurement attempts based on radar and multispectral

  17. Development of an in-situ soil structure characterization methodology

    NASA Astrophysics Data System (ADS)

    Debos, Endre; Kriston, Sandor

    2015-04-01

    The agricultural cultivation has several direct and indirect effects on the soil properties, among which the soil structure degradation is the best known and most detectable one. Soil structure degradation leads to several water and nutrient management problems, which reduce the efficiency of agricultural production. There are several innovative technological approaches aiming to reduce these negative impacts on the soil structure. The tests, validation and optimization of these methods require an adequate technology to measure the impacts on the complex soil system. This study aims to develop an in-situ soil structure and root development testing methodology, which can be used in field experiments and which allows one to follow the real time changes in the soil structure - evolution / degradation and its quantitative characterization. The method is adapted from remote sensing image processing technology. A specifically transformed A/4 size scanner is placed into the soil into a safe depth that cannot be reached by the agrotechnical treatments. Only the scanner USB cable comes to the surface to allow the image acquisition without any soil disturbance. Several images from the same place can be taken throughout the vegetation season to follow the soil consolidation and structure development after the last tillage treatment for the seedbed preparation. The scanned image of the soil profile is classified using supervised image classification, namely the maximum likelihood classification algorithm. The resulting image has two principal classes, soil matrix and pore space and other complementary classes to cover the occurring thematic classes, like roots, stones. The calculated data is calibrated with filed sampled porosity data. As the scanner is buried under the soil with no changes in light conditions, the image processing can be automated for better temporal comparison. Besides the total porosity each pore size fractions and their distributions can be calculated for

  18. Characterization of iron-phosphate-silicate chemical garden structures.

    PubMed

    Barge, Laura M; Doloboff, Ivria J; White, Lauren M; Stucky, Galen D; Russell, Michael J; Kanik, Isik

    2012-02-28

    Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life. PMID:22035594

  19. Characterization of large structural genetic mosaicism in human autosomes.

    PubMed

    Machiela, Mitchell J; Zhou, Weiyin; Sampson, Joshua N; Dean, Michael C; Jacobs, Kevin B; Black, Amanda; Brinton, Louise A; Chang, I-Shou; Chen, Chu; Chen, Constance; Chen, Kexin; Cook, Linda S; Crous Bou, Marta; De Vivo, Immaculata; Doherty, Jennifer; Friedenreich, Christine M; Gaudet, Mia M; Haiman, Christopher A; Hankinson, Susan E; Hartge, Patricia; Henderson, Brian E; Hong, Yun-Chul; Hosgood, H Dean; Hsiung, Chao A; Hu, Wei; Hunter, David J; Jessop, Lea; Kim, Hee Nam; Kim, Yeul Hong; Kim, Young Tae; Klein, Robert; Kraft, Peter; Lan, Qing; Lin, Dongxin; Liu, Jianjun; Le Marchand, Loic; Liang, Xiaolin; Lissowska, Jolanta; Lu, Lingeng; Magliocco, Anthony M; Matsuo, Keitaro; Olson, Sara H; Orlow, Irene; Park, Jae Yong; Pooler, Loreall; Prescott, Jennifer; Rastogi, Radhai; Risch, Harvey A; Schumacher, Fredrick; Seow, Adeline; Setiawan, Veronica Wendy; Shen, Hongbing; Sheng, Xin; Shin, Min-Ho; Shu, Xiao-Ou; VanDen Berg, David; Wang, Jiu-Cun; Wentzensen, Nicolas; Wong, Maria Pik; Wu, Chen; Wu, Tangchun; Wu, Yi-Long; Xia, Lucy; Yang, Hannah P; Yang, Pan-Chyr; Zheng, Wei; Zhou, Baosen; Abnet, Christian C; Albanes, Demetrius; Aldrich, Melinda C; Amos, Christopher; Amundadottir, Laufey T; Berndt, Sonja I; Blot, William J; Bock, Cathryn H; Bracci, Paige M; Burdett, Laurie; Buring, Julie E; Butler, Mary A; Carreón, Tania; Chatterjee, Nilanjan; Chung, Charles C; Cook, Michael B; Cullen, Michael; Davis, Faith G; Ding, Ti; Duell, Eric J; Epstein, Caroline G; Fan, Jin-Hu; Figueroa, Jonine D; Fraumeni, Joseph F; Freedman, Neal D; Fuchs, Charles S; Gao, Yu-Tang; Gapstur, Susan M; Patiño-Garcia, Ana; Garcia-Closas, Montserrat; Gaziano, J Michael; Giles, Graham G; Gillanders, Elizabeth M; Giovannucci, Edward L; Goldin, Lynn; Goldstein, Alisa M; Greene, Mark H; Hallmans, Goran; Harris, Curtis C; Henriksson, Roger; Holly, Elizabeth A; Hoover, Robert N; Hu, Nan; Hutchinson, Amy; Jenab, Mazda; Johansen, Christoffer; Khaw, Kay-Tee; Koh, Woon-Puay; Kolonel, Laurence N; Kooperberg, Charles; Krogh, Vittorio; Kurtz, Robert C; LaCroix, Andrea; Landgren, Annelie; Landi, Maria Teresa; Li, Donghui; Liao, Linda M; Malats, Nuria; McGlynn, Katherine A; McNeill, Lorna H; McWilliams, Robert R; Melin, Beatrice S; Mirabello, Lisa; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M; Prokunina-Olsson, Ludmila; Purdue, Mark; Qiao, You-Lin; Rabe, Kari G; Rajaraman, Preetha; Real, Francisco X; Riboli, Elio; Rodríguez-Santiago, Benjamín; Rothman, Nathaniel; Ruder, Avima M; Savage, Sharon A; Schwartz, Ann G; Schwartz, Kendra L; Sesso, Howard D; Severi, Gianluca; Silverman, Debra T; Spitz, Margaret R; Stevens, Victoria L; Stolzenberg-Solomon, Rachael; Stram, Daniel; Tang, Ze-Zhong; Taylor, Philip R; Teras, Lauren R; Tobias, Geoffrey S; Viswanathan, Kala; Wacholder, Sholom; Wang, Zhaoming; Weinstein, Stephanie J; Wheeler, William; White, Emily; Wiencke, John K; Wolpin, Brian M; Wu, Xifeng; Wunder, Jay S; Yu, Kai; Zanetti, Krista A; Zeleniuch-Jacquotte, Anne; Ziegler, Regina G; de Andrade, Mariza; Barnes, Kathleen C; Beaty, Terri H; Bierut, Laura J; Desch, Karl C; Doheny, Kimberly F; Feenstra, Bjarke; Ginsburg, David; Heit, John A; Kang, Jae H; Laurie, Cecilia A; Li, Jun Z; Lowe, William L; Marazita, Mary L; Melbye, Mads; Mirel, Daniel B; Murray, Jeffrey C; Nelson, Sarah C; Pasquale, Louis R; Rice, Kenneth; Wiggs, Janey L; Wise, Anastasia; Tucker, Margaret; Pérez-Jurado, Luis A; Laurie, Cathy C; Caporaso, Neil E; Yeager, Meredith; Chanock, Stephen J

    2015-03-01

    Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 × 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population. PMID:25748358

  20. Characterization and crystal structure of D-mannitol hemihydrate.

    PubMed

    Nunes, Cletus; Suryanarayanan, Raj; Botez, Cristian E; Stephens, Peter W

    2004-11-01

    The objectives of this study were (i) to isolate and characterize mannitol hydrate, and (ii) to solve its crystal structure from high-resolution synchrotron X-ray powder diffraction data. Mannitol hydrate was prepared by freeze-drying aqueous mannitol solutions (5% w/v) under controlled conditions. X-ray powder diffractometry, differential scanning calorimetry, and thermogravimetric analyses indicated that mannitol exists as a hemihydrate (C(6)H(14)O(6) . 0.5H(2)O). Synchrotron data were collected on the X3B1 beamline at the National Synchrotron Light Source. The simulated annealing program PSSP was used to solve the structure, which was subsequently refined by Rietveld analysis using the program package GSAS. The compound crystallizes in space group P1, with a = 9.8963 A, b = 10.5424 A, c = 4.7860 A, alpha = 102.589 degrees , beta = 86.092 degrees , and gamma = 116.079 degrees . The unit cell contains two dissimilar D-mannitol molecules and one water molecule, forming a hydrogen bonding pattern significantly different from that seen in the anhydrous polymorphs. PMID:15368529

  1. Production and Structural Characterization of Lactobacillus helveticus Derived Biosurfactant

    PubMed Central

    Sharma, Deepansh; Saharan, Baljeet Singh; Chauhan, Nikhil; Bansal, Anshul; Procha, Suresh

    2014-01-01

    A probiotic strain of lactobacilli was isolated from traditional soft Churpi cheese of Yak milk and found positive for biosurfactant production. Lactobacilli reduced the surface tension of phosphate buffer saline (PBS) from 72.0 to 39.5 mNm−1 pH 7.2 and its critical micelle concentration (CMC) was found to be 2.5 mg mL−1. Low cost production of Lactobacilli derived biosurfactant was carried out at lab scale fermenter which yields 0.8 mg mL−1 biosurfactant. The biosurfactant was found least phytotoxic and cytotoxic as compared to the rhamnolipid and sodium dodecyl sulphate (SDS) at different concentration. Structural attributes of biosurfactant were determined by FTIR, NMR (1H and 13C), UPLC-MS, and fatty acid analysis by GCMS which confirmed the presence of glycolipid type of biosurfactant closely similar to xylolipids. Biosurfactant is mainly constituted by lipid and sugar fractions. The present study outcomes provide valuable information on structural characterization of the biosurfactant produced by L. helveticus MRTL91. These findings are encouraging for the application of Lactobacilli derived biosurfactant as nontoxic surface active agents in the emerging field of biomedical applications. PMID:25506070

  2. Polyelectrolyte/magnetite nanoparticle multilayers: preparation and structure characterization.

    PubMed

    Grigoriev, D; Gorin, D; Sukhorukov, G B; Yashchenok, A; Maltseva, E; Möhwald, H

    2007-11-20

    Polyelectrolyte composite planar films containing a different number of iron oxide (Fe3O4) nanoparticle layers have been prepared using the layer-by-layer adsorption technique. The nanocomposite assemblies were characterized by ellipsometry, UV-vis spectroscopy, and AFM. Linear growth of the multilayer thickness with the increase of the layer number, N, up to 12 reflects an extensive character of this parameter in this range. A more complicated behavior of the refractive index is caused by changes in the multilayer structure, especially for the thicker nanocomposites. A quantitative analysis of the nanocomposite structure is provided comparing a classical and a modified effective medium approach taking into account the influence of light absorption by the Fe3O4 nanoparticles on the complex refractive index of the nanocomposite and contributions of all components to film thickness. Dominant influence of co-adsorbed water on their properties was found to be another interesting peculiarity of the nanocomposite film. This effect, as well as possible film property modulation by light, is discussed. PMID:17958452

  3. Production and structural characterization of Lactobacillus helveticus derived biosurfactant.

    PubMed

    Sharma, Deepansh; Saharan, Baljeet Singh; Chauhan, Nikhil; Bansal, Anshul; Procha, Suresh

    2014-01-01

    A probiotic strain of lactobacilli was isolated from traditional soft Churpi cheese of Yak milk and found positive for biosurfactant production. Lactobacilli reduced the surface tension of phosphate buffer saline (PBS) from 72.0 to 39.5 mNm(-1) pH 7.2 and its critical micelle concentration (CMC) was found to be 2.5 mg mL(-1). Low cost production of Lactobacilli derived biosurfactant was carried out at lab scale fermenter which yields 0.8 mg mL(-1) biosurfactant. The biosurfactant was found least phytotoxic and cytotoxic as compared to the rhamnolipid and sodium dodecyl sulphate (SDS) at different concentration. Structural attributes of biosurfactant were determined by FTIR, NMR ((1)H and (13)C), UPLC-MS, and fatty acid analysis by GCMS which confirmed the presence of glycolipid type of biosurfactant closely similar to xylolipids. Biosurfactant is mainly constituted by lipid and sugar fractions. The present study outcomes provide valuable information on structural characterization of the biosurfactant produced by L. helveticus MRTL91. These findings are encouraging for the application of Lactobacilli derived biosurfactant as nontoxic surface active agents in the emerging field of biomedical applications. PMID:25506070

  4. Characterizing monoclonal antibody structure by carboxyl group footprinting

    PubMed Central

    Kaur, Parminder; Tomechko, Sara E; Kiselar, Janna; Shi, Wuxian; Deperalta, Galahad; Wecksler, Aaron T; Gokulrangan, Giridharan; Ling, Victor; Chance, Mark R

    2015-01-01

    Structural characterization of proteins and their antigen complexes is essential to the development of new biologic-based medicines. Amino acid-specific covalent labeling (CL) is well suited to probe such structures, especially for cases that are difficult to examine by alternative means due to size, complexity, or instability. We present here a detailed account of carboxyl group labeling (with glycine ethyl ester (GEE) tagging) applied to a glycosylated monoclonal antibody therapeutic (mAb). The experiments were optimized to preserve the structural integrity of the mAb, and experimental conditions were varied and replicated to establish the reproducibility of the technique. Homology-based models were generated and used to compare the solvent accessibility of the labeled residues, which include aspartic acid (D), glutamic acid (E), and the C-terminus (i.e., the target probes), with the experimental data in order to understand the accuracy of the approach. Data from the mAb were compared to reactivity measures of several model peptides to explain observed variations in reactivity. Attenuation of reactivity in otherwise solvent accessible probes is documented as arising from the effects of positive charge or bond formation between adjacent amine and carboxyl groups, the latter accompanied by observed water loss. A comparison of results with previously published data by Deperalta et al using hydroxyl radical footprinting showed that 55% (32/58) of target residues were GEE labeled in this study whereas the previous study reported 21% of the targets were labeled. Although the number of target residues in GEE labeling is fewer, the two approaches provide complementary information. The results highlight advantages of this approach, such as the ease of use at the bench top, the linearity of the dose response plots at high levels of labeling, reproducibility of replicate experiments (<2% variation in modification extent), the similar reactivity of the three target probes

  5. Characterization of Polyimide Foams for Ultra-Lightweight Space Structures

    NASA Technical Reports Server (NTRS)

    Meador, Michael (Technical Monitor); Hillman, Keithan; Veazie, David R.

    2003-01-01

    Ultra-lightweight materials have played a significant role in nearly every area of human activity ranging from magnetic tapes and artificial organs to atmospheric balloons and space inflatables. The application range of ultra-lightweight materials in past decades has expanded dramatically due to their unsurpassed efficiency in terms of low weight and high compliance properties. A new generation of ultra-lightweight materials involving advanced polymeric materials, such as TEEK (TM) polyimide foams, is beginning to emerge to produce novel performance from ultra-lightweight systems for space applications. As a result, they require that special conditions be fulfilled to ensure adequate structural performance, shape retention, and thermal stability. It is therefore important and essential to develop methodologies for predicting the complex properties of ultra-lightweight foams. To support NASA programs such as the Reusable Launch Vehicle (RLV), Clark Atlanta University, along with SORDAL, Inc., has initiated projects for commercial process development of polyimide foams for the proposed cryogenic tank integrated structure (see figure 1). Fabrication and characterization of high temperature, advanced aerospace-grade polyimide foams and filled foam sandwich composites for specified lifetimes in NASA space applications, as well as quantifying the lifetime of components, are immensely attractive goals. In order to improve the development, durability, safety, and life cycle performance of ultra-lightweight polymeric foams, test methods for the properties are constant concerns in terms of timeliness, reliability, and cost. A major challenge is to identify the mechanisms of failures (i.e., core failure, interfacial debonding, and crack development) that are reflected in the measured properties. The long-term goal of the this research is to develop the tools and capabilities necessary to successfully engineer ultra-lightweight polymeric foams. The desire is to reduce density

  6. Structural Characterization of the Fla2 Flagellum of Rhodobacter sphaeroides

    PubMed Central

    de la Mora, Javier; Uchida, Kaoru; del Campo, Ana Martínez; Camarena, Laura; Aizawa, Shin-Ichi

    2015-01-01

    ABSTRACT Rhodobacter sphaeroides is a free-living alphaproteobacterium that contains two clusters of functional flagellar genes in its genome: one acquired by horizontal gene transfer (fla1) and one that is endogenous (fla2). We have shown that the Fla2 system is normally quiescent and under certain conditions produces polar flagella, while the Fla1 system is always active and produces a single flagellum at a nonpolar position. In this work we purified and characterized the structure and analyzed the composition of the Fla2 flagellum. The number of polar filaments per cell is 4.6 on average. By comparison with the Fla1 flagellum, the prominent features of the ultra structure of the Fla2 HBB are the absence of an H ring, thick and long hooks, and a smoother zone at the hook-filament junction. The Fla2 helical filaments have a pitch of 2.64 μm and a diameter of 1.4 μm, which are smaller than those of the Fla1 filaments. Fla2 filaments undergo polymorphic transitions in vitro and showed two polymorphs: curly (right-handed) and coiled. However, in vivo in free-swimming cells, we observed only a bundle of filaments, which should probably be left-handed. Together, our results indicate that Fla2 cell produces multiple right-handed polar flagella, which are not conventional but exceptional. IMPORTANCE R. sphaeroides possesses two functional sets of flagellar genes. The fla1 genes are normally expressed in the laboratory and were acquired by horizontal transfer. The fla2 genes are endogenous and are expressed in a Fla1− mutant grown phototrophically and in the absence of organic acids. The Fla1 system produces a single lateral or subpolar flagellum, and the Fla2 system produces multiple polar flagella. The two kinds of flagella are never expressed simultaneously, and both are used for swimming in liquid media. The two sets of genes are certainly ready for responding to specific environmental conditions. The characterization of the Fla2 system will help us to understand

  7. Characterization of structural relaxation in inorganic glasses using length dilatometry

    NASA Astrophysics Data System (ADS)

    Koontz, Erick

    The processes that govern how a glass relaxes towards its thermodynamic quasi-equilibrium state are major factors in understanding glass behavior near the glass transition region, as characterized by the glass transition temperature (Tg). Intrinsic glass properties such as specific volume, enthalpy, entropy, density, etc. are used to map the behavior of the glass network below in and near the transition region. The question of whether a true thermodynamic second order phase transition takes place in the glass transition region is another pending question. Linking viscosity behavior to entropy, or viewing the glass configuration as an energy landscape are just a couple of the most prevalent methods used for attempting to understand the glass transition. The structural relaxation behavior of inorganic glasses is important for more than scientific reasons, many commercial glass processing operations including glass melting and certain forms of optical fabrication include significant time spent in the glass transition region. For this reason knowledge of structural relaxation processes can, at a minimum, provide information for annealing duration of melt-quenched glasses. The development of a predictive model for annealing time prescription has the potential to save glass manufacturers significant time and money as well as increasing volume throughput. In optical hot forming processes such as precision glass molding, molded optical components can significantly change in shape upon cooling through the glass transition. This change in shape is not scientifically predictable as of yet though manufacturers typically use empirical rules developed in house. The classification of glass behavior in the glass transition region would allow molds to be accurately designed and save money for the producers. The work discussed in this dissertation is comprised of the development of a dilatometric measurement and characterization method of structural relaxation. The measurement and

  8. Structural and functional characterization of the trifunctional antibody catumaxomab.

    PubMed

    Chelius, Dirk; Ruf, Peter; Gruber, Patrick; Plöscher, Matthias; Liedtke, Reinhard; Gansberger, Eva; Hess, Juergen; Wasiliu, Michael; Lindhofer, Horst

    2010-01-01

    The Triomab family of trifunctional, bispecific antibodies that maintain an IgG-like shape are novel tumor targeting agents. These chimeras consist of two half antibodies, each with one light and one heavy chain, that originate from parental mouse IgG2a and rat IgG2b isotypes. This combination allows cost-effective biopharmaceutical manufacturing at an industrial scale since this specific mouse/rat isotype combination favors matching of corresponding antibody halves during production by means of quadroma technology. Whereas every Triomab family member is composed of an anti-CD3 rat IgG2b half antibody for T cell recognition, the antigen binding site presented by the mouse IgG2a isotype is exchangeable. Several Triomab antibodies have been generated that bind to tumor-associated antigens, e.g., EpCAM (catumaxomab), HER2/neu (ertumaxomab), CD20 (FBTA05), gangliosides GD2/GD3 (Ektomun), on appropriate tumor target cells associated with carcinomas, lymphomas or melanomas. Catumaxomab (Removab) was launched in Europe for treatment of malignant ascites in April 2009. Here, we report the structural and functional characterization of this product. Mass spectrometry revealed an intact mass of 150511 Dalton (Da) and 23717 Da, 24716 Da, 51957 Da and 52019 Da of the reduced and alkylated rat light chain, mouse light chain, rat heavy chain, mouse heavy chain chains, respectively. The observed masses were in agreement with the expected masses based on the amino acid sequence obtained from cDNA sequencing. The glycosylation profile was similar to other human IgG consisting of biantennary oligosaccharides with different numbers of terminal galactose. CD spectroscopy showed mainly beta-sheets secondary structure that is typical for IgG antibodies. Binding measurement revealed the unique trifunctional features of catumaxomab. Other analytical tools were used to evaluate characteristics of catumaxomab preparations, including the presence of isoforms and aggregates. PMID:20418662

  9. Characterization of Large Structural Genetic Mosaicism in Human Autosomes

    PubMed Central

    Machiela, Mitchell J.; Zhou, Weiyin; Sampson, Joshua N.; Dean, Michael C.; Jacobs, Kevin B.; Black, Amanda; Brinton, Louise A.; Chang, I-Shou; Chen, Chu; Chen, Constance; Chen, Kexin; Cook, Linda S.; Crous Bou, Marta; De Vivo, Immaculata; Doherty, Jennifer; Friedenreich, Christine M.; Gaudet, Mia M.; Haiman, Christopher A.; Hankinson, Susan E.; Hartge, Patricia; Henderson, Brian E.; Hong, Yun-Chul; Hosgood, H. Dean; Hsiung, Chao A.; Hu, Wei; Hunter, David J.; Jessop, Lea; Kim, Hee Nam; Kim, Yeul Hong; Kim, Young Tae; Klein, Robert; Kraft, Peter; Lan, Qing; Lin, Dongxin; Liu, Jianjun; Le Marchand, Loic; Liang, Xiaolin; Lissowska, Jolanta; Lu, Lingeng; Magliocco, Anthony M.; Matsuo, Keitaro; Olson, Sara H.; Orlow, Irene; Park, Jae Yong; Pooler, Loreall; Prescott, Jennifer; Rastogi, Radhai; Risch, Harvey A.; Schumacher, Fredrick; Seow, Adeline; Setiawan, Veronica Wendy; Shen, Hongbing; Sheng, Xin; Shin, Min-Ho; Shu, Xiao-Ou; VanDen Berg, David; Wang, Jiu-Cun; Wentzensen, Nicolas; Wong, Maria Pik; Wu, Chen; Wu, Tangchun; Wu, Yi-Long; Xia, Lucy; Yang, Hannah P.; Yang, Pan-Chyr; Zheng, Wei; Zhou, Baosen; Abnet, Christian C.; Albanes, Demetrius; Aldrich, Melinda C.; Amos, Christopher; Amundadottir, Laufey T.; Berndt, Sonja I.; Blot, William J.; Bock, Cathryn H.; Bracci, Paige M.; Burdett, Laurie; Buring, Julie E.; Butler, Mary A.; Carreón, Tania; Chatterjee, Nilanjan; Chung, Charles C.; Cook, Michael B.; Cullen, Michael; Davis, Faith G.; Ding, Ti; Duell, Eric J.; Epstein, Caroline G.; Fan, Jin-Hu; Figueroa, Jonine D.; Fraumeni, Joseph F.; Freedman, Neal D.; Fuchs, Charles S.; Gao, Yu-Tang; Gapstur, Susan M.; Patiño-Garcia, Ana; Garcia-Closas, Montserrat; Gaziano, J. Michael; Giles, Graham G.; Gillanders, Elizabeth M.; Giovannucci, Edward L.; Goldin, Lynn; Goldstein, Alisa M.; Greene, Mark H.; Hallmans, Goran; Harris, Curtis C.; Henriksson, Roger; Holly, Elizabeth A.; Hoover, Robert N.; Hu, Nan; Hutchinson, Amy; Jenab, Mazda; Johansen, Christoffer; Khaw, Kay-Tee; Koh, Woon-Puay; Kolonel, Laurence N.; Kooperberg, Charles; Krogh, Vittorio; Kurtz, Robert C.; LaCroix, Andrea; Landgren, Annelie; Landi, Maria Teresa; Li, Donghui; Liao, Linda M.; Malats, Nuria; McGlynn, Katherine A.; McNeill, Lorna H.; McWilliams, Robert R.; Melin, Beatrice S.; Mirabello, Lisa; Peplonska, Beata; Peters, Ulrike; Petersen, Gloria M.; Prokunina-Olsson, Ludmila; Purdue, Mark; Qiao, You-Lin; Rabe, Kari G.; Rajaraman, Preetha; Real, Francisco X.; Riboli, Elio; Rodríguez-Santiago, Benjamín; Rothman, Nathaniel; Ruder, Avima M.; Savage, Sharon A.; Schwartz, Ann G.; Schwartz, Kendra L.; Sesso, Howard D.; Severi, Gianluca; Silverman, Debra T.; Spitz, Margaret R.; Stevens, Victoria L.; Stolzenberg-Solomon, Rachael; Stram, Daniel; Tang, Ze-Zhong; Taylor, Philip R.; Teras, Lauren R.; Tobias, Geoffrey S.; Viswanathan, Kala; Wacholder, Sholom; Wang, Zhaoming; Weinstein, Stephanie J.; Wheeler, William; White, Emily; Wiencke, John K.; Wolpin, Brian M.; Wu, Xifeng; Wunder, Jay S.; Yu, Kai; Zanetti, Krista A.; Zeleniuch-Jacquotte, Anne; Ziegler, Regina G.; de Andrade, Mariza; Barnes, Kathleen C.; Beaty, Terri H.; Bierut, Laura J.; Desch, Karl C.; Doheny, Kimberly F.; Feenstra, Bjarke; Ginsburg, David; Heit, John A.; Kang, Jae H.; Laurie, Cecilia A.; Li, Jun Z.; Lowe, William L.; Marazita, Mary L.; Melbye, Mads; Mirel, Daniel B.; Murray, Jeffrey C.; Nelson, Sarah C.; Pasquale, Louis R.; Rice, Kenneth; Wiggs, Janey L.; Wise, Anastasia; Tucker, Margaret; Pérez-Jurado, Luis A.; Laurie, Cathy C.; Caporaso, Neil E.; Yeager, Meredith; Chanock, Stephen J.

    2015-01-01

    Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 × 10−31) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population. PMID:25748358

  10. Growth and characterization of nanocrystalline zirconium nitride-inconel structures

    NASA Astrophysics Data System (ADS)

    Aouadi, S. M.; Maeruf, T.; Sodergren, M.; Mihut, D. M.; Rohde, S. L.; Xu, J.; Mishra, S. R.

    2005-07-01

    This paper reports on the investigation of the physical, chemical, optical, mechanical, and tribological properties of reactively sputtered zirconium nitride-inconel composite nanocrystalline mixture films. These films were co-sputtered from a Zr and an inconel targets onto Si (111) substrates at room temperature using a fixed power to the Zr target (PZr) and a fixed flow of nitrogen and argon. Two sets of samples were produced by (1) varying the power to the inconel target (Pinc) and using a fixed bias voltage Vb and (2) by varying Vb and keeping Pinc fixed. The elemental composition was deduced from x-ray photoelectron spectroscopy, and was found to be influenced by Pinc and Vb. X-ray diffraction revealed the presence of nanocrystals of ZrN with a pattern typical of the NaCl structure. The grain size was found to decrease with the increase in ``inconel'' content in the film. The optical constants were measured using spectroscopic ellipsometry and were subsequently simulated using a Drude-Lorentz model. A correlation between film structure-composition and optical constants was established. The hardness and elastic modulus of each sample were measured by nanoindentation. The hardest films were produced using a Vb=-130 V bias voltage and Pinc=4 W. Microwear measurements were carried out using positive constant normal loads and the wear tracks were imaged and processed. The measured values for the friction coefficients, residual depth of tip indentations, wear volumes, and surface roughness were reported. The lowest recorded wear volume using a load of 4 mN was 10-3 μm. Finally, the coatings were worn against ball-bearing steel using a ball-on-disk tribotester. Characterization of the wear tracks were performed by profilometry. A low wear coefficient of 1.7×10-7 mm3/s was obtained for a load of 5 N.

  11. Structural characterization of semicrystalline polymer morphologies by imaging-SANS

    NASA Astrophysics Data System (ADS)

    Radulescu, A.; Fetters, L. J.; Richter, D.

    2012-02-01

    Control and optimization of polymer properties require the global knowledge of the constitutive microstructures of polymer morphologies in various conditions. The microstructural features can be typically explored over a wide length scale by combining pinhole-, focusing- and ultra-small-angle neutron scattering (SANS) techniques. Though it proved to be a successful approach, this involves major efforts related to the use of various scattering instruments and large amount of samples and the need to ensure the same crystallization kinetics for the samples investigated at various facilities, in different sample cell geometries and at different time intervals. With the installation and commissioning of the MgF2 neutron lenses at the KWS-2 SANS diffractometer installed at the Heinz Maier-Leibnitz neutron source (FRMII reactor) in Garching, a wide Q-range, between 10-4Å-1 and 0.5Å-1, can be covered at a single instrument. This enables investigation of polymer microstructures over a length scale from lnm up to 1μm, while the overall polymer morphology can be further examined up to 100μm by optical microscopy (including crossed polarizers). The study of different semi-crystalline polypropylene-based polymers in solution is discussed and the new imaging-SANS approach allowing for an unambiguous and complete structural characterization of polymer morphologies is presented.

  12. Crystal structure controlled synthesis and characterization of copper sulfide nanoparticles

    NASA Astrophysics Data System (ADS)

    Senthilkumar, M.; Babu, S. Moorthy

    2016-05-01

    Phase pure, controlled crystal structure of digenite (Cu9S5) copper sulfide nanoparticles were synthesized by hot injection method at the temperature of 180°C. The mixture of Oleylamine, 1-Octadecene and 1-Dodecanethiol were taken as solvent as well as capping agents. The effect of the mixture of solvents on the phase formation and morphology of the synthesized nanoparticles were analysed. The nanocrystals were characterized using X-Ray diffraction (XRD) which confirms the presence of single phase rhombohedral digenite Cu9S5 NPs, Morphological analysis clearly depicts the formation of hexagonal faceted Cu9S5 NPs, Energy dispersive X-ray absorption spectroscopy (EDS) reveals the stoichiometric ratio of 1.8:1 for synthesized NPs. From the UV-Vis absorption spectroscopy the bandgap value of Cu1.8S is found to be 1.71 eV. The presence of capping agents along the surface of the Cu9S5 NPs was confirmed from FTIR analysis.

  13. Identification and Structural Characterization of a Legionella Phosphoinositide Phosphatase*

    PubMed Central

    Toulabi, Leila; Wu, Xiaochun; Cheng, Yanshu; Mao, Yuxin

    2013-01-01

    Bacterial pathogen Legionella pneumophila is the causative agent of Legionnaires' disease, which is associated with intracellular replication of the bacteria in macrophages of human innate immune system. Recent studies indicate that pathogenic bacteria can subvert host cell phosphoinositide (PI) metabolism by translocated virulence effectors. However, in which manner Legionella actively exploits PI lipids to benefit its infection is not well characterized. Here we report that L. pneumophila encodes an effector protein, named SidP, that functions as a PI-3-phosphatase specifically hydrolyzing PI(3)P and PI(3,5)P2 in vitro. This activity of SidP rescues the growth phenotype of a yeast strain defective in PI(3)P phosphatase activity. Crystal structure of SidP orthologue from Legionella longbeachae reveals that this unique PI-3-phosphatase is composed of three distinct domains: a large catalytic domain, an appendage domain that is inserted into the N-terminal portion of the catalytic domain, and a C-terminal α-helical domain. SidP has a small catalytic pocket that presumably provides substrate specificity by limiting the accessibility of bulky PIs with multiple phosphate groups. Together, our identification of a unique family of Legionella PI phosphatases highlights a common scheme of exploiting host PI lipids in many intracellular bacterial pathogen infections. PMID:23843460

  14. Synthesis, single crystal structure and characterization of pentanitromonoformylhexaazaisowurtzitane.

    PubMed

    Chen, Huaxiong; Chen, Shusen; Li, Lijie; Jiao, Qingze; Wei, Tianyu; Jin, Shaohua

    2010-03-15

    Pentanitromonoformylhexaazaisowurtzitane (PNMFIW) was synthesized by the nitrolysis of tetraacetyldiformylhexaazaisowurtzitane (TADFIW) in mixed nitric and sulfuric acids and structurally characterized by element analysis, FT-IR, MS and (1)H NMR. Single crystals of PNMFIW were grown from aqueous solution employing the technique of controlled evaporation. PNMFIW belongs to the orthorhombic system having four molecules in the unit cell, with space group P2(1)2(1)2(1) and the lattice parameters a=8.8000(18)A, b=12.534(2)A, and c=12.829(3)A. The calculated density reaches 1.977 g/cm(3) at 93 K, while the experimental density is 1.946 g/cm(3) at 20 degrees C. The calculated detonation velocity and pressure of PNMFIW according to the experimental density are 9195.76 m/s and 39.68G Pa, respectively. PNMFIW is insensitive compared with epsilon-HNIW through drop hammer impact sensitivity test. PMID:19913358

  15. Structural Characterization of Hydroxyl Radical Adducts in Aqueous Media

    NASA Astrophysics Data System (ADS)

    Janik, Ireneusz; Tripathi, G. N. R.

    2015-06-01

    The oxidation by the hydroxyl (OH) radical is one of the most widely studied reactions because of its central role in chemistry, biology, organic synthesis, and photocatalysis in aqueous environments, wastewater treatment, and numerous other chemical processes. Although the redox potential of OH is very high, direct electron transfer (ET) is rarely observed. If it happens, it mostly proceeds through the formation of elusive OH adduct intermediate which facilitates ET and formation of hydroxide anion. Using time resolved resonance Raman technique we structurally characterized variety of OH adducts to sulfur containing organic compounds, halide ions as well as some metal cations. The bond between oxygen of OH radical and the atom of oxidized molecule differs depending on the nature of solute that OH radical reacts with. For most of sulfur containing organics, as well as halide and pseudo-halide ions, our observation suggested that this bond has two-center three-electron character. For several metal aqua ions studied, the nature of the bond depends on type of the cation being oxidized. Discussion on spectral parameters of all studied hydroxyl radical adducts as well as the role solvent plays in their stabilization will be presented.

  16. Characterizing unknown systematics in large scale structure surveys

    SciTech Connect

    Agarwal, Nishant; Ho, Shirley; Myers, Adam D.; Seo, Hee-Jong; Ross, Ashley J.; Bahcall, Neta; Brinkmann, Jonathan; Eisenstein, Daniel J.; Muna, Demitri; Palanque-Delabrouille, Nathalie; Yèche, Christophe; Petitjean, Patrick; Schneider, Donald P.; Streblyanska, Alina; Weaver, Benjamin A.

    2014-04-01

    Photometric large scale structure (LSS) surveys probe the largest volumes in the Universe, but are inevitably limited by systematic uncertainties. Imperfect photometric calibration leads to biases in our measurements of the density fields of LSS tracers such as galaxies and quasars, and as a result in cosmological parameter estimation. Earlier studies have proposed using cross-correlations between different redshift slices or cross-correlations between different surveys to reduce the effects of such systematics. In this paper we develop a method to characterize unknown systematics. We demonstrate that while we do not have sufficient information to correct for unknown systematics in the data, we can obtain an estimate of their magnitude. We define a parameter to estimate contamination from unknown systematics using cross-correlations between different redshift slices and propose discarding bins in the angular power spectrum that lie outside a certain contamination tolerance level. We show that this method improves estimates of the bias using simulated data and further apply it to photometric luminous red galaxies in the Sloan Digital Sky Survey as a case study.

  17. Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution

    SciTech Connect

    Franca, Eduardo D.; Lins, Roberto D.; Freitas, Luiz C.; Straatsma, t. P.

    2008-11-08

    Molecular dynamics simulations have been used to characterize the structure of chitin and chitosan fibers in aqueous solutions. Chitin fibers, whether isolated or in the form of a β-chitin nanoparticle, adopt the so-called 2-fold helix with Φ and φ values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)•••O5(n+1) responsible for the 2-fold helical motif is stabilized by hydrogen bonds with water molecules in a well-defined orientation. On the other hand, chitosan can adopt five distinct helical motifs and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin. Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)•••O5(n+1) hydrogen bond, which is affect by the water exchange around the O3-HO3 hydroxyl group.

  18. Structure and characterization of RNase H3 from Aquifex aeolicus.

    PubMed

    Jongruja, Nujarin; You, Dong-Ju; Angkawidjaja, Clement; Kanaya, Eiko; Koga, Yuichi; Kanaya, Shigenori

    2012-08-01

    The crystal structure of ribonuclease H3 from Aquifex aeolicus (Aae-RNase H3) was determined at 2.0 Å resolution. Aae-RNase H3 consists of an N-terminal TATA box-binding protein (TBP)-like domain (N-domain) and a C-terminal RNase H domain (C-domain). The structure of the C-domain highly resembles that of Bacillus stearothermophilus RNase H3 (Bst-RNase H3), except that it contains three disulfide bonds, and the fourth conserved glutamate residue of the Asp-Glu-Asp-Glu active site motif (Glu198) is located far from the active site. These disulfide bonds were shown to contribute to hyper-stabilization of the protein. Non-conserved Glu194 was identified as the fourth active site residue. The structure of the N-domain without the C-domain also highly resembles that of Bst-RNase H3. However, the arrangement of the N-domain relative to the C-domain greatly varies for these proteins because of the difference in the linker size between the domains. The linker of Bst-RNase H3 is relatively long and flexible, while that of Aae-RNase H3 is short and assumes a helix formation. Biochemical characterizations of Aae-RNase H3 and its derivatives without the N- or C-domain or with a mutation in the N-domain indicate that the N-domain of Aae-RNase H3 is important for substrate binding, and uses the flat surface of the β-sheet for substrate binding. However, this surface is located far from the active site and on the opposite side to the active site. We propose that the N-domain of Aae-RNase H3 is required for initial contact with the substrate. The resulting complex may be rearranged such that only the C-domain forms a complex with the substrate. PMID:22686566

  19. Pore- and micro-structural characterization of a novel structural binder based on iron carbonation

    SciTech Connect

    Das, Sumanta; Stone, David; Convey, Diana; Neithalath, Narayanan

    2014-12-15

    The pore- and micro-structural features of a novel binding material based on the carbonation of waste metallic iron powder are reported in this paper. The binder contains metallic iron powder as the major ingredient, followed by additives containing silica and alumina to facilitate favorable reaction product formation. Compressive strengths sufficient for a majority of concrete applications are attained. The material pore structure is investigated primarily through mercury intrusion porosimetry whereas electron microscopy is used for microstructural characterization. Reduction in the overall porosity and the average pore size with an increase in carbonation duration from 1 day to 4 days is noticed. The pore structure features are used in predictive models for gas and moisture transport (water vapor diffusivity and moisture permeability) through the porous medium which dictates its long-term durability when used in structural applications. Comparisons of the pore structure with those of a Portland cement paste are also provided. The morphology of the reaction products in the iron-based binder, and the distribution of constituent elements in the microstructure are also reported. - Highlights: • Carbonation of iron produces a dense microstructure. • Pore volume in iron carbonate lower, critical size higher than those in OPC pastes • Reaction product contains iron, carbon, silicon, aluminum and calcium. • Power-law for porosity-moisture permeability relationship was established.

  20. Structural characterization and electronic structure of laser treated TiN thin film

    SciTech Connect

    Soni, Sheetal; Nair, K. G. M.; Phase, D. M.; Gupta, Ratnesh

    2012-06-05

    TiN thin films prepared by laser treatment using Kr-F excimer laser in the controlled atmosphere. The depth distribution and composition of nitrogen and contaminated oxygen have been determined by non-Rutherford proton backscattering using 1.7 MeV Tendetron accelerator. The electronic structure of TiN thin film have been characterized by resonant photoelectron spectroscopy using indus-I synchrotron radiation. Specifically, complex resonance profile that shows the enhancement at 45 eV which is consistent with the resonant photoemission of Ti 3d states involved in the Titanium nitride and oxide.

  1. Underground structure characterization using motor vehicles as passive seismic sources

    NASA Astrophysics Data System (ADS)

    Kuzma, H. A.; Liu, Y.; Zhao, Y.; Rector, J.; Vaidya, S.

    2009-12-01

    The ability to detect and characterize underground voids will be critical to the success of On-Site Inspections (OSI) as mandated by the nuclear Comprehensive Test Ban Treaty (CTBT). OSIs may be conducted in order to successfully locate the Ground Zero of underground tests as well as infrastructure related to testing. Recently, our team has shown the potential of a new technique to detect underground objects using the amplitude of seismic surface waves generated by motor vehicles. In an experiment conducted in June, 2009 we were able to detect an abandoned railroad tunnel by recognizing a clear pattern in the surface waves scattered by the tunnel, using a signal generated by driving a car on a dirt road across the tunnel. Synthetic experiments conducted using physically realistic wave-equation models further suggest that the technique can be readily applied to detecting underground features: it may be possible to image structures of importance to OSI simply by laying out an array of geophones (or using an array already in place for passive listening for event aftershocks) and driving vehicles around the site. We present evidence from a set of field experiments and from synthetic modeling and inversion studies to illustrate adaptations of the technique for OSI. Signature of an abandoned underground railroad tunnel at Donner Summit, CA. To produce this image, a line of geophones was placed along a dirt road perpendicular to the tunnel (black box) and a single car was driven along the road. A normalized mean power-spectrum is displayed on a log scale as a function of meters from the center of the tunnel. The top of the tunnel was 18m below ground surface. The tunnel anomaly is made up of a shadow (light) directly above the tunnel and amplitude build-up (dark) on either side of the tunnel. The size of the anomaly (6 orders of magnitude) suggests that the method can be extended to find deep structures at greater distances from the source and receivers.

  2. Group 12 metal zwitterionic thiolate compounds: preparation and structural characterization.

    PubMed

    Tang, Xiao-Yan; Yuan, Rong-Xin; Chen, Jin-Xiang; Zhao, Wei; Zheng, Ai-Xia; Yu, Miao; Li, Hong-Xi; Ren, Zhi-Gang; Lang, Jian-Ping

    2012-05-28

    Reactions of TabHPF(6) (Tab = 4-(trimethylammonio)benzenethiolate) with three equiv. of M(OAc)(2)·2H(2)O (M = Zn, Cd) gave rise to two tetranuclear adamantane-like compounds, [M(4)(μ-Tab)(6)(Tab)(4)](PF(6))(8)·S (·S: M = Zn, S = DMF·4H(2)O; ·S: M = Cd, S = DMF·5H(2)O). The similar reactions of MCl(2) (M = Zn, Cd, Hg) with four equiv. of TabHPF(6) in the presence of Et(3)N afforded three mononuclear compounds [M(Tab)(4)](PF(6))(2)·S (·S: M = Zn, S = 2(H(2)O)(0.5); ·S: M = Cd, S = 2(H(2)O)(0.5); ·S: M = Hg, S = 2DMF). Treatment of the precursor complex or with equimolar MCl(2) and two equiv. of TabHPF(6) and Et(3)N produced one dinuclear compounds [M(μ-Tab)(Tab)(2)](2)(PF(6))(4)·2DMF·2H(2)O (·2DMF·2H(2)O: M = Zn; ·2DMF·2H(2)O: M = Hg) while analogous reactions of with CdCl(2)·2H(2)O gave rise to [Cd(μ-Tab)(2)(Tab)](2)(PF(6))(4)·2DMF (·2DMF). These compounds were characterized by elemental analysis, IR spectra, UV-Vis spectra, (1)H NMR and single-crystal X-ray crystallography. In or , four M(2+) ions and six S atoms of Tab ligands constitute an adamantane-like [M(4)(μ-S)(6)] cage in which each M(2+) ion is tetrahedrally coordinated by one terminal S and three bridged S atoms from four different Tab ligands. In , each M(2+) center of the [M(Tab)(4)](2+) dication is tetrahedrally coordinated by four S atoms of Tab ligand. Two [M(Tab)(2)](2+) dications in or are further bridged by a pair of Tab ligands to form a dimeric [M(μ-Tab)(Tab)(2)](2)(4+) structure. Each dimeric [(Tab)Cd(μ-Tab)(2)Cd(Tab)](4+) unit in is linked to its two neighboring units via two couples of bridging Tab ligands, thereby generating a unique 1D cationic chain. These results may provide useful information on interpreting structural data of MTs containing group 12 metals. PMID:22546878

  3. Structural and Biochemical Characterization of Peroxiredoxin Qβ from Xylella fastidiosa

    PubMed Central

    Horta, Bruno Brasil; de Oliveira, Marcos Antonio; Discola, Karen Fulan; Cussiol, José Renato Rosa; Netto, Luis Eduardo Soares

    2010-01-01

    The phytopathogenic bacterium Xylella fastidiosa is the etiological agent of various plant diseases. To survive under oxidative stress imposed by the host, microorganisms express antioxidant proteins, including cysteine-based peroxidases named peroxiredoxins. This work is a comprehensive analysis of the catalysis performed by PrxQ from X. fastidiosa (XfPrxQ) that belongs to a peroxiredoxin class still poorly characterized and previously considered as moderately reactive toward hydroperoxides. Contrary to these assumptions, our competitive kinetics studies have shown that the second-order rate constants of the peroxidase reactions of XfPrxQ with hydrogen peroxide and peroxynitrite are in the order of 107 and 106 m−1 s−1, respectively, which are as fast as the most efficient peroxidases. The XfPrxQ disulfides were only slightly reducible by dithiothreitol; therefore, the identification of a thioredoxin system as the probable biological reductant of XfPrxQ was a relevant finding. We also showed by site-specific mutagenesis and mass spectrometry that an intramolecular disulfide bond between Cys-47 and Cys-83 is generated during the catalytic cycle. Furthermore, we elucidated the crystal structure of XfPrxQ C47S in which Ser-47 and Cys-83 lie ∼12.3 Å apart. Therefore, significant conformational changes are required for disulfide bond formation. In fact, circular dichroism data indicated that there was a significant redox-dependent unfolding of α-helices, which is probably triggered by the peroxidatic cysteine oxidation. Finally, we proposed a model that takes data from this work as well data as from the literature into account. PMID:20335172

  4. Synthesis, structure, and spectroscopic characterization of three uranyl phosphates with unique structural units

    NASA Astrophysics Data System (ADS)

    Wylie, Ernest M.; Dawes, Colleen M.; Burns, Peter C.

    2012-12-01

    Single crystals of Zn4(OH)2[(UO2)(PO4)2(OH)2(H2O)] (UZnP), Cs[(UO2)(HPO4)NO3] (UCsP), and In3[(UO2)2(PO4)4OH(H2O)6].2H2O (UInP) were obtained from hydrothermal reactions and have been structurally and chemically characterized. UZnP crystallizes in space group Pbcn, a=8.8817(7), b=6.6109(5), c=19.569(1) Å; UCsP crystallizes in P-1, a=7.015(2), b=7.441(1), c=9.393(2) Å, α=72.974(2), β=74.261(2), γ=79.498(2); and UInP crystallizes in P-1, a=7.9856(5), b=9.159(1), c=9.2398(6) Å α=101.289(1), β=114.642(1), γ=99.203(2). The U6+ cations are present as (UO2)2+ uranyl ions coordinated by five O atoms to give pentagonal bipyramids. The structural unit in UZnP is a finite cluster containing a uranyl pentagonal bipyramid that shares corners with two phosphate tetrahedra. The structural unit in UCsP is composed of uranyl pentagonal bipyramids with one chelating nitrate group that are linked into chains by three bridging hydrogen phosphate tetrahedra. In UInP, the structural unit contains pairs of edge-sharing uranyl pentagonal bipyramids with two chelating phosphate tetrahedra that are linked into chains through two bridging phosphate tetrahedra. Indium octahedra link these uranyl phosphate chains into a 3-dimensional framework. All three compounds exhibit unique structural units that deviate from the typical layered structures observed in uranyl phosphate solid-state chemistry.

  5. Thermoelectric and structural characterizations of individual electrodeposited bismuth telluride nanowires

    NASA Astrophysics Data System (ADS)

    Mavrokefalos, Anastassios; Moore, Arden L.; Pettes, Michael T.; Shi, Li; Wang, Wei; Li, Xiaoguang

    2009-05-01

    The thermoelectric properties and crystal structure of individual electrodeposited bismuth telluride nanowires (NWs) were characterized using a microfabricated measurement device and transmission electron microscopy. Annealing in hydrogen was used to obtain electrical contact between the NW and the supporting Pt electrodes. By fitting the measured Seebeck coefficient with a two-band model, the NW samples were determined to be highly n-type doped. Higher thermal conductivity and electrical conductivity were observed in a 52 nm diameter monocrystalline NW than a 55 nm diameter polycrystalline NW. The electron mobility of the monocrystalline NW was found to be about 19% lower than that of bulk crystal at a similar carrier concentration and about 2.5 times higher than that of the polycrystalline NW. The specularity parameter for electron scattering by the NW surface was determined to be about 0.7 and partially specular and partially diffuse, leading to a reduction in the electron mean-free path from 61 nm in the bulk to about 40 nm in the 52 nm NW. Because of the already short phonon mean-free path of about 3 nm in bulk bismuth telluride, diffuse phonon-surface scattering is expected to reduce the lattice thermal conductivity of the 52-55 nm diameter NWs by only about 20%, which is smaller than the uncertainty in the extracted lattice thermal conductivity based on the measured total thermal conductivity and calculated electron thermal conductivity. Although the lattice thermal conductivity of the polycrystalline NW is likely lower than the bulk values, the lower thermal conductivity observed in this polycrystalline sample is mainly caused by the lower electron concentration and mobility. For both samples, the thermoelectric figure of merit (ZT) increases with temperature and is about 0.1 at a temperature of 400 K. The low ZT compared to that of bulk crystals is mainly caused by a high doping level, suggesting the need for better control of the chemical composition in

  6. Reflection spectra and magnetochemistry of iron oxides and natural surfaces

    NASA Technical Reports Server (NTRS)

    Wasilewski, P.

    1978-01-01

    The magnetic properties and spectral characteristics of iron oxides are distinctive. Diagnostic features in reflectance spectra (0.5 to 2.4 micron) for alpha Fe2O3, gamma Fe2O3, and FeOOH include location of Fe3(+) absorption features, intensity ratios at various wavelengths, and the curve shape between 1.2 micron and 2.4 micron. The reflection spectrum of natural rock surfaces are seldom those of the bulk rock because of weathering effects. Coatings are found to be dominated by iron oxides and clay. A simple macroscopic model of rock spectra (based on concepts of stains and coatings) is considered adequate for interpretation of LANDSAT data. The magnetic properties of materials associated with specific spectral types and systematic changes in both spectra and magnetic properties are considered.

  7. Growth, structure, and optical characterization of diluted magnetic semiconductor nanowires

    NASA Astrophysics Data System (ADS)

    Cooley, Benjamin Joseph

    ˜ 10 nm, with ˜ 15--20 nm being fairly common. Structural characterization done by transmission electron microscopy (TEM) shows that the long nanowires are largely single crystal, though often with many stacking faults, and tend to form in the wurtzite crystal structure with c-axis growth direction. Elemental analysis performed on individual nanowires using X-ray energy dispersive spectroscopy shows that Mn can be incorporated into Zn1-xMn xSe nanowires in high concentrations, up to x ˜ 0.6. Magneto-photoluminescence (magneto-PL) measurements of as-grown samples reveal substantial Zeeman shifts in the nearband edge luminescence, but only partial polarization, indicating the luminescence is originating in a nanostructured environment. Surprisingly, however, nearly all of the PL signal comes from the nanostructured undergrowth rather than the long nanowires, as shown from magneto-PL measurements of samples which were sonicated to remove the long nanowires. The next set of experiments covers ZnSe and (Zn,Mn)Se nanowires grown using a two-stage process. The substrates are prepared in a similar manner as the in the previous samples. The first stage of growth is carried out at lower than normal substrate temperature, which results in highly tapered nanoneedles with narrow tips (˜ 10 nm). The second stage of growth is performed under normal nanowire growth conditions, yielding narrow nanowires growing from the tips of the nanoneedles. These nanowires have far fewer defects than nanowires grown in a single stage process. Magneto-PL measurements carried out in a micro-PL system show many localized emitters and near band edge emission that shifts in a magnetic field. Sonicated samples gave similar results, indicating that the undergrowth is still responsible for much of the luminescence, even though there is much less undergrowth than in the single stage nanowires. Measurements of dispersed samples suggests that some of the luminescence may be coming from nanowires, but

  8. Characterizing 3D RNA structure by single molecule FRET.

    PubMed

    Stephenson, James D; Kenyon, Julia C; Symmons, Martyn F; Lever, Andrew M L

    2016-07-01

    The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model. PMID:26853327

  9. Fabrication and Characterization of Woodpile Structures for Direct Laser Acceleration

    SciTech Connect

    McGuinness, C.; Peralta, E.; Soong, K.; Colby, E.; England, R. J.; Ng, J.; Noble, R. J.; Spencer, J.; Walz, D.; Cowan, B.; Byer, R. L.

    2010-11-04

    Eight and nine layer three dimensional photonic crystals with a defect designed specifically for accelerator applications have been fabricated. The structures were fabricated using a combination of nanofabrication techniques, including low pressure chemical vapor deposition, optical lithography, and chemical mechanical polishing. Limits imposed by the optical lithography set the minimum feature size to 400 nm, corresponding to a structure with a bandgap centered at 4.26 {mu}m. Reflection spectroscopy reveal a peak in reflectivity about the predicted region, and good agreement with simulation is shown. The eight and nine layer structures will be aligned and bonded together to form the complete seventeen layer woodpile accelerator structure.

  10. Fabrication and Characterization of Woodpile Structures for Direct Laser Acceleration

    SciTech Connect

    McGuinness, C.; Colby, E.; England, R.J.; Ng, J.; Noble, R.J.; Peralta, E.; Soong, K.; Spencer, J.; Walz, D.; Byer, R.L.

    2010-08-26

    An eight and nine layer three dimensional photonic crystal with a defect designed specifically for accelerator applications has been fabricated. The structures were fabricated using a combination of nanofabrication techniques, including low pressure chemical vapor deposition, optical lithography, and chemical mechanical polishing. Limits imposed by the optical lithography set the minimum feature size to 400 nm, corresponding to a structure with a bandgap centered at 4.26 {micro}m. Reflection spectroscopy reveal a peak in reflectivity about the predicted region, and good agreement with simulation is shown. The eight and nine layer structures will be aligned and bonded together to form the complete seventeen layer woodpile accelerator structure.

  11. AFM characterization of the shape of surface structures with localization factor.

    PubMed

    Bonyár, Attila

    2016-08-01

    Although with the use of scanning probe microscopy (SPM) methods the topographical imaging of surfaces is now widely available, the characterization of surface structures, especially their shape, and the processes which change these features is not trivial with the existing surface describing parameters. In this work the application of a parameter called localization factor is demonstrated for the quantitative characterization of surface structures and for processes which alter the shape of these structures. The theory and optimal operation range of this parameter are discussed with three application examples: microstructure characterization of gold thin films, characterization of the changes in the grain structure of these films during thermal annealing, and finally, characterization of the oxidation processes on a polished tin surface. PMID:27174696

  12. Synthesis, characterization, hydrolase and catecholase activity of a dinuclear iron(III) complex: Catalytic promiscuity.

    PubMed

    Camargo, Tiago P; Maia, Fernanda F; Chaves, Cláudia; de Souza, Bernardo; Bortoluzzi, Adailton J; Castilho, Nathalia; Bortolotto, Tiago; Terenzi, Hernán; Castellano, Eduardo E; Haase, Wolfgang; Tomkowicz, Zbigniew; Peralta, Rosely A; Neves, Ademir

    2015-05-01

    Herein, we report the synthesis and characterization of the new di-iron(III) complex [(bbpmp)(H2O)(Cl)Fe(III)(μ-Ophenoxo)Fe(III)(H2O)Cl)]Cl (1), with the symmetrical ligand 2,6-bis{[(2-hydroxybenzyl)(pyridin-2-yl)methylamino]methyl}-4-methylphenol (H3bbpmp). Complexes 2 with the unsymmetrical ligand H2bpbpmp - {2-[[(2-hydroxybenzyl)(2-pyridylmethyl)]aminomethyl]-6-bis(pyridylmethyl) aminomethyl}-4-methylphenol and 3 with the ligand L(1)=4,11-dimethyl-1,8-bis{2-[N-(di-2-pyridylmethyl)amino]ethyl}cyclam were included for comparison purposes. Complex 1 was characterized through elemental analysis, X-ray crystallography, magnetochemistry, electronic spectroscopy, electrochemistry, mass spectrometry and potentiometric titration. The magnetic data show a very weak antiferromagnetic coupling between the two iron centers of the dinuclear complex 1 (J=-0.29cm(-1)). Due to the presence of labile coordination sites in both iron centers the hydrolysis of both the diester model substrate 2,4-BDNPP and DNA was studied in detail. Complex 1 was also able to catalyze the oxidation of the substrate 3,5-di-tert-butylcatechol (3,5-DTBC) to give the corresponding quinone, and thus it can be considered as a catalytically promiscuous system. PMID:25792035

  13. Structure characterization of protein fractions from lotus ( Nelumbo nucifera) seed

    NASA Astrophysics Data System (ADS)

    Zeng, Hong-Yan; Cai, Lian-Hui; Cai, Xi-Ling; Wang, Ya-Ju; Li, Yu-Qin

    2011-08-01

    Protein fractionation of lotus seed was carried out and the structures of the protein fractions were studied. Fourier transform infrared spectroscopy (FTIR) as well as ultraviolet visible spectroscopy (UV-vis) was used to investigate changes in molecular structures of the protein fractions. FTIR and UV-vis spectra showed the protein fractions had different protein molecular structures. FTIR spectra showed β-sheets and β-turns as the major secondary structures in the individual protein fractions, while the amounts of α-helix and random coil structures among the different fractions did not significantly change. The amounts of β-sheet structures of albumin and globulin were significantly higher than ones of prolamin and glutelin, implying albumin and globulin had high stabilities because of the high content in β-sheet structures. The observed similarity in the amounts of α-helix, random coil, β-sheet and β-turn structures shared by albumin and globulin indicated that their interior conformations were similar.

  14. Characterization of photodeposited selenium planar structures by scanning force microscopy

    NASA Astrophysics Data System (ADS)

    Peled, A.; Baranauskas, V.; Rodrigues, C.; Art-Weisman, D.; Grantman, L.; Friesem, A. A.

    1995-06-01

    This article describes the results of a surface morphology study of photodeposited thin film devices of Selenium by scanning force microscopy (SFM). First, the structures of the photodeposited films were investigated at device level dimensions of the order of visible wavelength. Specifically, ultrathin sinusoidal holographic gratings with spatial periods in the range 480-514 nm were visually identified from SFM nanograph images. Second, grain level structural investigation was performed using image processing techniques such as filtering and one- and two-dimensional Fourier transforms analysis. The variation of the surface grain structure was sampled across the Gaussian profiles of the laser photodeposited patterns. It was found that the random amorphous clustering at the perimeter of the deposited structures becomes progressively grainy towards the center, creating protrusions above the surface with trigonal Selenium (t-Se) crystalline features. Third, performing image enhancement analysis at high magnification—the nanometer level structure was investigated for amorphous Selenium (a-Se) and the laser thermally induced structural transformations of the a-Se films. It was found that the atomic solid-state structure of a-Se films, previously deduced only by indirect methods, consists mainly of a random mixture of Sex branched chains containing also a small concentration of imperfect ring structures characteristic of the α- and β-monoclinic phases. The triclinic crystalline phase (t-Se) was identified in the center of the laser overheated regions of the film Gaussian profile. The results enable us to conclude about the debate in the literature regarding the crystalline and amorphous structure of Selenium thin films.

  15. Structural characterization of mRNA-tRNA translocation intermediates

    PubMed Central

    Agirrezabala, Xabier; Liao, Hstau Y.; Schreiner, Eduard; Fu, Jie; Ortiz-Meoz, Rodrigo F.; Schulten, Klaus; Green, Rachel; Frank, Joachim

    2012-01-01

    Cryo-EM analysis of a wild-type Escherichia coli pretranslocational sample has revealed the presence of previously unseen intermediate substates of the bacterial ribosome during the first phase of translocation, characterized by intermediate intersubunit rotations, L1 stalk positions, and tRNA configurations. Furthermore, we describe the domain rearrangements in quantitative terms, which has allowed us to characterize the processivity and coordination of the conformational reorganization of the ribosome, along with the associated changes in tRNA ribosome-binding configuration. The results are consistent with the view of the ribosome as a molecular machine employing Brownian motion to reach a functionally productive state via a series of substates with incremental changes in conformation. PMID:22467828

  16. Structural characterization of mRNA-tRNA translocation intermediates.

    PubMed

    Agirrezabala, Xabier; Liao, Hstau Y; Schreiner, Eduard; Fu, Jie; Ortiz-Meoz, Rodrigo F; Schulten, Klaus; Green, Rachel; Frank, Joachim

    2012-04-17

    Cryo-EM analysis of a wild-type Escherichia coli pretranslocational sample has revealed the presence of previously unseen intermediate substates of the bacterial ribosome during the first phase of translocation, characterized by intermediate intersubunit rotations, L1 stalk positions, and tRNA configurations. Furthermore, we describe the domain rearrangements in quantitative terms, which has allowed us to characterize the processivity and coordination of the conformational reorganization of the ribosome, along with the associated changes in tRNA ribosome-binding configuration. The results are consistent with the view of the ribosome as a molecular machine employing Brownian motion to reach a functionally productive state via a series of substates with incremental changes in conformation. PMID:22467828

  17. Structural characterization of ice polymorphs from self-avoiding walks

    NASA Astrophysics Data System (ADS)

    Herrero, Carlos P.

    2014-08-01

    Topological properties of crystalline ice structures are studied by means of self-avoiding walks on their H-bond networks. The number of self-avoiding walks, Cn, for eight ice polymorphs has been obtained by direct enumeration up to walk length n=27. This has allowed us to determine the ‘connective constant' or effective coordination number μ of these structures as the limit of the ratio Cn/Cn-1 for large n. This structure-dependent parameter μ is related with other topological characteristics of ice polymorphs, such as the mean and minimum ring size, or the topological density of network sites. A correlation between the connective constant and the configurational entropy of hydrogen-disordered ice structures is discussed.

  18. Structural Characterization of Layered Morphologies in Precise Copolymers

    NASA Astrophysics Data System (ADS)

    Trigg, Edward; Gaines, Taylor; Wagener, Kenneth; Winey, Karen

    2015-03-01

    Layered morphologies have been observed in precise polyethylene-based copolymers that contain acid, charged, or polar functional groups precisely spaced along a linear alkane chain. Sufficiently long alkane segments form structures resembling orthorhombic polyethylene crystals, while the functional groups form 2-D layers that disrupt the alkane crystal structure to varying degrees. Here, layered morphologies in precise copolymers containing acrylic acid, phosphonic acid, imidazolium bromide, and sulfone groups are studied via X-ray scattering. Specifically, the composition profiles of the layered structures are obtained by Fourier synthesis, and the coherence length is investigated using peak width analysis. This analysis indicates that the layers of functional groups are frequently bordered by two crystallites, which suggests different dynamics relative to layers bordered by one crystalline and one amorphous microdomain. Detailed understanding of the structure of the layered morphologies will allow for a systematic investigation of proton and ion conductivity mechanisms, which are expected to occur through the high-dielectric layers.

  19. Synthesis and structural characterization of polyaniline/cobalt chloride composites

    NASA Astrophysics Data System (ADS)

    Asha, Goyal, Sneh Lata; Kishore, Nawal

    2016-05-01

    Polyaniline (PANI) and PANI /cobalt chloride composites were synthesized by in situ chemical oxidative polymerization of aniline with CoCl2.6H2O using ammonium peroxidisulphate as an oxidant. These composites were characterized by X-ray diffraction (XRD) and Scanning electron microscopy (SEM). The XRD study reveals that both PANI and composites are amorphous. The XRD and SEM results confirm the presence of cobalt chloride in the composites.

  20. Characterization of flow-induced structures in carbon nanotube suspensions

    NASA Astrophysics Data System (ADS)

    Khalkhal, Fatemeh

    Carbon nanotubes (CNTs) are fibre-like nano-particles with many different applications. Due to their high specific surface area, high electric current density, thermal stability and excellent mechanical properties, they are used to reinforce physical properties of polymer matrices. The macroscopic properties of suspensions are inherited from their properties at micron and sub-micron scales. The suspensions structure can be easily influenced by many parameters such as the extent of external shear forces, the suspension concentration, temperature, the particles specifications, etc. This makes the study of the suspension structure a very challenging task and has been the subject of interest to many researchers. In this thesis, the structure of a model carbon nanotube suspension dispersed in an epoxy is studied by employing a set of rheological methods, scaling and fractal theories and a structural thixotropic model. The effect of flow history on linear viscoelastic properties of suspensions and the evolution of structure upon cessation of shear flow has been studied over a wide range of pre-shearing rates, concentration and temperature. The results of these analyses are as follows. The effect of flow history is more pronounced on the suspensions structure in dilute and semi-dilute concentration regimes. By pre-shearing at low rates, more inter-particle entanglements were induced, which resulted in reduction of rheological percolation thresholds. After cessation of shear flow, for dilute and semi-dilute suspensions, the formed metastable structures were distinguishable by different storage moduli, which were inversely related to the rate of pre-shearing. However, for the concentrated suspensions, the formed metastable structures had an approximately equal storage modulus regardless of the rate of the applied pre-shearing. It was shown that the rate of formation of these metastable structures was enhanced by increasing concentration. Furthermore, the rate of structure

  1. Structural characterization of human cholesterol 7α-hydroxylase

    PubMed Central

    Tempel, Wolfram; Grabovec, Irina; MacKenzie, Farrell; Dichenko, Yaroslav V.; Usanov, Sergey A.; Gilep, Andrei A.; Park, Hee-Won; Strushkevich, Natallia

    2014-01-01

    Hepatic conversion to bile acids is a major elimination route for cholesterol in mammals. CYP7A1 catalyzes the first and rate-limiting step in classic bile acid biosynthesis, converting cholesterol to 7α-hydroxycholesterol. To identify the structural determinants that govern the stereospecific hydroxylation of cholesterol, we solved the crystal structure of CYP7A1 in the ligand-free state. The structure-based mutation T104L in the B′ helix, corresponding to the nonpolar residue of CYP7B1, was used to obtain crystals of complexes with cholest-4-en-3-one and with cholesterol oxidation product 7-ketocholesterol (7KCh). The structures reveal a motif of residues that promote cholest-4-en-3-one binding parallel to the heme, thus positioning the C7 atom for hydroxylation. Additional regions of the binding cavity (most distant from the access channel) are involved to accommodate the elongated conformation of the aliphatic side chain. Structural complex with 7KCh shows an active site rigidity and provides an explanation for its inhibitory effect. Based on our previously published data, we proposed a model of cholesterol abstraction from the membrane by CYP7A1 for metabolism. CYP7A1 structural data provide a molecular basis for understanding of the diversity of 7α-hydroxylases, on the one hand, and cholesterol-metabolizing enzymes adapted for their specific activity, on the other hand. PMID:24927729

  2. Characterization of the structures of poly(urea-urethane) microcapsules.

    PubMed

    Matsunami, Yuki; Ichikawa, Kimio

    2002-08-21

    A series of poly(urea-urethane) microcapsules containing phthalate derivatives as a core material were prepared by an interfacial polymerization process in order to investigate the structural formation mechanism. Scanning electron microscopy (SEM) analysis for the cross sections of microcapsules revealed the systematic formations of porous structures followed by the formation of core/shell structures. Critical values of the core oil content for the formation of porous and core/shell structures were obtained from SEM results and the critical values were found to be proportional to the solubility parameters of core materials. Dynamic mechanical measurements indicated an amorphous structure of wall membrane and the glass transition temperature was found to decrease with increasing the core oil content suggesting a plasticizing effect. The surface amount of the core oils absorbed in the wall membrane was estimated using time of flight secondary ion spectroscopy analysis and found to increase with increasing the oil content before reaching constant. This tendency was interpreted in terms of the structural formation of the microcapsules. The results obtained in the present investigation were reasonably understood on the basis of swelling theory of wall membrane and the Flory-Huggins interaction parameters of the systems were discussed. PMID:12176237

  3. Structural characterization of human cholesterol 7α-hydroxylase.

    PubMed

    Tempel, Wolfram; Grabovec, Irina; MacKenzie, Farrell; Dichenko, Yaroslav V; Usanov, Sergey A; Gilep, Andrei A; Park, Hee-Won; Strushkevich, Natallia

    2014-09-01

    Hepatic conversion to bile acids is a major elimination route for cholesterol in mammals. CYP7A1 catalyzes the first and rate-limiting step in classic bile acid biosynthesis, converting cholesterol to 7α-hydroxycholesterol. To identify the structural determinants that govern the stereospecific hydroxylation of cholesterol, we solved the crystal structure of CYP7A1 in the ligand-free state. The structure-based mutation T104L in the B' helix, corresponding to the nonpolar residue of CYP7B1, was used to obtain crystals of complexes with cholest-4-en-3-one and with cholesterol oxidation product 7-ketocholesterol (7KCh). The structures reveal a motif of residues that promote cholest-4-en-3-one binding parallel to the heme, thus positioning the C7 atom for hydroxylation. Additional regions of the binding cavity (most distant from the access channel) are involved to accommodate the elongated conformation of the aliphatic side chain. Structural complex with 7KCh shows an active site rigidity and provides an explanation for its inhibitory effect. Based on our previously published data, we proposed a model of cholesterol abstraction from the membrane by CYP7A1 for metabolism. CYP7A1 structural data provide a molecular basis for understanding of the diversity of 7α-hydroxylases, on the one hand, and cholesterol-metabolizing enzymes adapted for their specific activity, on the other hand. PMID:24927729

  4. Synthesis and characterization of a new structure of gas hydrate

    SciTech Connect

    Tulk, Christopher A; Chakoumakos, Bryan C; Ehm, Lars; Klug, Dennis D; Parise, John B; Yang, Ling; Martin, Dave; Ripmeester, John; Moudrakovski, Igor; Ratcliffe, Chris

    2009-01-01

    Atoms and molecules 0.4 0.9 nm in diameter can be incorporated in the cages formed by hydrogen-bonded water molecules making up the crystalline solid clathrate hydrates. There are three structural families of these hydrates , known as sI, sII and sH, and the structure usually depends on the largest guest molecule in the hydrate. Species such as Ar, Kr, Xe and methane form sI or sII hydrate, sH is unique in that it requires both small and large cage guests for stability. All three structures, containing methane, other hydrocarbons, H2S and CO2, O2 and N2 have been found in the geosphere, with sI methane hydrate by far the most abundant. At high pressures (P > 0.7 kbar) small guests (Ar, Kr, Xe, methane) are also known to form sH hydrate with multiple occupancy of the largest cage in the hydrate. The high-pressure methane hydrate of sH has been proposed as playing a role in the outer solar system, including formation models for Titan , and yet another high pressure phase of methane has been reported , although its structure remains unknown. In this study, we report a new and unique hydrate structure that is derived from the high pressure sH hydrate of xenon. After quench recovery at ambient pressure and 77 K it shows considerable stability at low temperatures (T < 160 K) and is compositionally similar to the sI Xe clathrate starting material. This evidence of structural complexity in compositionally similar clathrate compounds indicates that thermodynamic pressure temperature conditions may not be the only important factor in structure determination, but also the reaction path may have an important effect.

  5. Characterization of crystalline structures in Opuntia ficus-indica.

    PubMed

    Contreras-Padilla, Margarita; Rivera-Muñoz, Eric M; Gutiérrez-Cortez, Elsa; del López, Alicia Real; Rodríguez-García, Mario Enrique

    2015-01-01

    This research studies the crystalline compounds present in nopal (Opuntia ficus-indica) cladodes. The identification of the crystalline structures was performed using X-ray diffraction, scanning electron microscopy, mass spectrometry, and Fourier transform infrared spectroscopy. The crystalline structures identified were calcium carbonate (calcite) [CaCO3], calcium-magnesium bicarbonate [CaMg(CO3)2], magnesium oxide [MgO], calcium oxalate monohydrate [Ca(C2O4)•(H2O)], potassium peroxydiphosphate [K4P2O8] and potassium chloride [KCl]. The SEM images indicate that calcite crystals grow to dipyramidal, octahedral-like, prismatic, and flower-like structures; meanwhile, calcium-magnesium bicarbonate structures show rhombohedral exfoliation and calcium oxalate monohydrate is present in a drusenoid morphology. These calcium carbonate compounds have a great importance for humans because their bioavailability. This is the first report about the identification and structural analysis of calcium carbonate and calcium-magnesium bicarbonate in nopal cladodes, as well as the presence of magnesium oxide, potassium peroxydiphosphate and potassium chloride in these plants. The significance of the study of the inorganic components of these cactus plants is related with the increasing interest in the potential use of Opuntia as a raw material of products for the food, pharmaceutical, and cosmetic industries. PMID:25465849

  6. The Structural Characterization of Tumor Fusion Genes and Proteins.

    PubMed

    Wang, Dandan; Li, Daixi; Qin, Guangrong; Zhang, Wen; Ouyang, Jian; Zhang, Menghuan; Xie, Lu

    2015-01-01

    Chromosomal translocation, which generates fusion proteins in blood tumor or solid tumor, is considered as one of the major causes leading to cancer. Recent studies suggested that the disordered fragments in a fusion protein might contribute to its carcinogenicity. Here, we investigated the sequence feature near the breakpoints in the fusion partner genes, the structure features of breakpoints in fusion proteins, and the posttranslational modification preference in the fusion proteins. Results show that the breakpoints in the fusion partner genes have both sequence preference and structural preference. At the sequence level, nucleotide combination AG is preferred before the breakpoint and GG is preferred at the breakpoint. At the structural level, the breakpoints in the fusion proteins prefer to be located in the disordered regions. Further analysis suggests the phosphorylation sites at serine, threonine, and the methylation sites at arginine are enriched in disordered regions of the fusion proteins. Using EML4-ALK as an example, we further explained how the fusion protein leads to the protein disorder and contributes to its carcinogenicity. The sequence and structural features of the fusion proteins may help the scientific community to predict novel breakpoints in fusion genes and better understand the structure and function of fusion proteins. PMID:26347798

  7. The Structural Characterization of Tumor Fusion Genes and Proteins

    PubMed Central

    Wang, Dandan; Li, Daixi; Qin, Guangrong; Zhang, Wen; Ouyang, Jian; Zhang, Menghuan; Xie, Lu

    2015-01-01

    Chromosomal translocation, which generates fusion proteins in blood tumor or solid tumor, is considered as one of the major causes leading to cancer. Recent studies suggested that the disordered fragments in a fusion protein might contribute to its carcinogenicity. Here, we investigated the sequence feature near the breakpoints in the fusion partner genes, the structure features of breakpoints in fusion proteins, and the posttranslational modification preference in the fusion proteins. Results show that the breakpoints in the fusion partner genes have both sequence preference and structural preference. At the sequence level, nucleotide combination AG is preferred before the breakpoint and GG is preferred at the breakpoint. At the structural level, the breakpoints in the fusion proteins prefer to be located in the disordered regions. Further analysis suggests the phosphorylation sites at serine, threonine, and the methylation sites at arginine are enriched in disordered regions of the fusion proteins. Using EML4-ALK as an example, we further explained how the fusion protein leads to the protein disorder and contributes to its carcinogenicity. The sequence and structural features of the fusion proteins may help the scientific community to predict novel breakpoints in fusion genes and better understand the structure and function of fusion proteins. PMID:26347798

  8. Processing-structure characterization of rheocast IN-100 superalloy

    NASA Technical Reports Server (NTRS)

    Cheng, Jung-Jen Allen; Apelian, Diran; Doherty, Roger D.

    1986-01-01

    The rheocasting solidification process was applied in the production of IN-100 nickel base superalloy, and the effects of processing variables, such as stirring speed, isothermal stirring time, and volume fraction solid during isothermal stirring, on the resultant rheocast structure were investigated. Ingots that were furnace cooled at the same rate but without stirring were compared with the rheocast ingots. Rheocasting yielded fine-grained structures, where the extent of microsegregation, the variation in macrostructure, and the solidification-induced porosity and ingot cracking were found to be reduced in comparison to the unstirred ingots. The grain size and nonuniformity were reduced by increasing the stirring speed, isothermal stirring time, or the volume fraction solid during stirring; decreased microsegregation was achieved by an increase in the volume fraction solid. The structures of grain boundaries lent support to the grain boundary mechanism proposed by Vogel et al. (1977) for rheocasting.

  9. Raman scattering characterization of space solar cell structures

    NASA Technical Reports Server (NTRS)

    Mintairov, Alexander M.; Khvostikov, V. P.; Paleeva, E. V.; Sorokina, S. V.

    1995-01-01

    A contactless method for the determination of the free-carrier density and the composition distribution across the thickness of 3-5 multi-layer solar cell structures, using the Raman scattering method, is developed. The method includes a step analysis of Raman spectra from optical phonons and phonon-plasmon modes of different layers. The method provides simultaneous measurements of the element composition and the thickness of the structure's layers together with the free-carrier density. The results of measurements of the free-carrier density composition distributions of the liquid phase epitaxy grown AlGaAs/GaAs and GaSb solar cell structures are presented and discussed.

  10. Progress in the structural and functional characterization of kinetochores.

    PubMed

    Pesenti, Marion E; Weir, John R; Musacchio, Andrea

    2016-04-01

    Kinetochores are macromolecular complexes built on a specialized chromatin domain called the centromere. Kinetochores provide a site of attachment for spindle microtubules during mitosis. They also control a cell cycle checkpoint, the spindle assembly checkpoint, which coordinates mitotic exit with the completion of chromosome alignment on the mitotic spindle. Correct kinetochore operation is therefore indispensable for accurate chromosome segregation. With multiple copies of at least 30 structural core subunits and a myriad of regulatory subunits, kinetochores are among the largest known macromolecular machines. Biochemical reconstitution and structural analysis, together with functional studies, are bringing to light the organizational principles of these complex and fascinating structures. We summarize recent work and identify a few challenges for future work. PMID:27039078

  11. Structural characterization of coatomer in its cytosolic state.

    PubMed

    Wang, Shengliu; Zhai, Yujia; Pang, Xiaoyun; Niu, Tongxin; Ding, Yue-He; Dong, Meng-Qiu; Hsu, Victor W; Sun, Zhe; Sun, Fei

    2016-08-01

    Studies on coat protein I (COPI) have contributed to a basic understanding of how coat proteins generate vesicles to initiate intracellular transport. The core component of the COPI complex is coatomer, which is a multimeric complex that needs to be recruited from the cytosol to membrane in order to function in membrane bending and cargo sorting. Previous structural studies on the clathrin adaptors have found that membrane recruitment induces a large conformational change in promoting their role in cargo sorting. Here, pursuing negative-stain electron microscopy coupled with single-particle analyses, and also performing CXMS (chemical cross-linking coupled with mass spectrometry) for validation, we have reconstructed the structure of coatomer in its soluble form. When compared to the previously elucidated structure of coatomer in its membrane-bound form we do not observe a large conformational change. Thus, the result uncovers a key difference between how COPI versus clathrin coats are regulated by membrane recruitment. PMID:27472951

  12. Preparation, characterization, and sequential transformation of dicarbide cluster compounds with permetalated ethyne, ethene, and ethane structures

    SciTech Connect

    Akita, Munetaka; Sugimoto, Shuichiro; Tanaka, Masako; Moro-oka, Yoshihiko

    1992-09-09

    The preparation, characterization and sequential transformation of dicarbide cluster compounds with permetalated ethyne, ethene and ethane structures is discussed. The group reporting has developed a preparative method for ethynediyldimetal complexes via deprotonation. 10 refs., 3 figs.

  13. Dynamic characterization of thin-film inflatable structures

    NASA Astrophysics Data System (ADS)

    Slade, Kara Nicole

    Inflatable structures constructed from thin polyimide films form a key part of several technology development programs for solar thermal propulsion for satellites, as well as for other applications both in space and on earth. This project investigates the mechanical properties of several of these structures, focusing primarily on their dynamic behavior. The primary focus is the Shooting Star Experiment prototype developed by NASA, but a simpler cylindrical structure is also considered in order to provide an analytically tractable situation for the evaluation of testing and modeling techniques. The cylindrical strut is tested statically to determine its load-deflection characteristics both in linear and nonlinear regimes. The phenomenon of wrinkling is observed under large deflection conditions, particularly at lower pressure. Then, modal testing is used to determine the dynamic properties of the strut for comparison to numerical models. Modal testing is also conducted on Pathfinder 3, a prototype inflatable solar concentrator for the Shooting Star Experiment, both in vacuum and ambient atmospheric conditions. The orbital terminator crossing test is used to determine the dynamic susceptibility of the Pathfinder 3 structure to thermal shock, and it is found to undergo only quasistatic deformations. Finite element models of the cylinder and the Pathfinder 3 concentrator are then constructed using MSC NASTRAN. The inflatable cylinder may be modeled as a beam if only global bending is considered. This restriction leads to the development of a frequency-dependent modulus of elasticity in bending for the structure, developed from engineering beam theory. Both frequency-dependent beam models and shell models are constructed and evaluated for their efficacy. The results from the modeling of the strut are then applied to the inflatable concentrator, where it is found that the shell model captures more of the dynamic subtleties of the system than the beam model, but that both

  14. Microstructural Characterization of Hierarchical Structured Surfaces by Atomic Force Microscopy

    NASA Astrophysics Data System (ADS)

    Ponomareva, A. A.; Moshnikov, V. A.; Suchaneck, G.

    2013-12-01

    In this work, we evaluate the hierarchical surface topography of reactively sputtered nanocrystalline Pb(Zr,Ti)O3 and TiO2 thin films as well as plasma-treated antireflective PET films by means of determining the fractal dimension and power spectral density (PSD) of surface topography recorded by atomic force microscopy (AFM). Local fractal dimension was obtained using the triangulation method. The PSDs of all samples were fitted to the k-correlation model (also called ABC model) valid for a self-affine surface topography. Fractal analysis of AFM images was shown to be an appropriate and easy to use tool for the characterization of hierarchical nanostructures.

  15. Characterization of the structure and tectonic of South America

    NASA Technical Reports Server (NTRS)

    Keller, G. R.; Lidiak, E. G. (Principal Investigator)

    1981-01-01

    Geologic studies of the South American plate were undertaken. The Guayana shield is reasonably well studied, and although data are sparce, the central Brazilian shield appears similar. Both the Amazon and Parnaiba basins seem to be related to an aulocogen structure. The collection of crustal structure information and the generation of measurement of surface wave dispersion in the shield areascontinues. Long period seismograms are digitized and analyzed. Exisiting crusted and upper mantle studies were indexed. Both MAGSAT scaler and vector magnetic anomaly data were used with regional gravity anomaly data to investigate the regional tectonic features of the South American plate.

  16. Characterization of damped structural connections for multi-component systems

    NASA Technical Reports Server (NTRS)

    Lawrence, Charles; Huckelbridge, Arthur A.

    1989-01-01

    The inability to model connections adequately has historically limited the ability to predict overall system dynamic response. Connections between structural components are often mechanically complex and difficult to accurataely model analytically. Improved analytical models for connections are needed to improve system dynamic predictions. This study explores combining Component Mode Synthesis methods for coupling structural components with Parameter Identification procedures for improving the analytical modeling of the connections. Improvements in the connection stiffness and damping properties are computed in terms of physical parameters so the physical characteristics of the connections can be better understood, in addition to providing improved input for the system model.

  17. Characterization of damped structural connections for multi-component systems

    NASA Technical Reports Server (NTRS)

    Lawrence, Charles; Huckelbridge, Arthur A.

    1988-01-01

    The inability to model connections adequately has historically limited the ability to predict overall system dynamic response. Connections between structural components are often mechanically complex and difficult to accurately model analytically. Improved analytical models for connections are needed to improve system dynamic predictions. This study explores combining Component Mode Synthesis methods for coupling structural components with Parameter Identification procedures for improving the analytical modeling of the connections. Improvements in the connection stiffness and damping properties are computed in terms of physical parameters so the physical characteristics of the connections can be better understood, in addition to providing improved input for the system model.

  18. Fabrication and characterization of nanometric SiOx/SiOy multilayer structures obtained by LPCVD

    SciTech Connect

    Román-López, S.; Aceves-Mijares, M.; Pedraza-Chávez, J.; Carrillo-López, J.

    2014-05-15

    This work presents the fabrication of nanometric multilayer structures and their characterization by Atomic Force Microscopy, Photoluminescence and Fourier Transform Infra Red spectroscopy. The structures were deposited by Low Pressure Chemical Vapor Deposition (LPCVD). Three types of multilayer structure were fabricated. After the deposition some samples were annealed in N{sub 2} ambient for three hours. It was found that the structures keep the characteristics of each layer.

  19. Fabrication and characterization of nanometric SiOx/SiOy multilayer structures obtained by LPCVD

    NASA Astrophysics Data System (ADS)

    Román-López, S.; Aceves-Mijares, M.; Carrillo-López, J.; Pedraza-Chávez, J.

    2014-05-01

    This work presents the fabrication of nanometric multilayer structures and their characterization by Atomic Force Microscopy, Photoluminescence and Fourier Transform Infra Red spectroscopy. The structures were deposited by Low Pressure Chemical Vapor Deposition (LPCVD). Three types of multilayer structure were fabricated. After the deposition some samples were annealed in N2 ambient for three hours. It was found that the structures keep the characteristics of each layer.

  20. Structural and functional characterization of elastases from horse neutrophils.

    PubMed Central

    Dubin, A; Potempa, J; Travis, J

    1994-01-01

    In order better to understand the pathophysiology of the equine form of emphysema, two elastinolytic enzymes from horse neutrophils, referred to as proteinases 2A and 2B, have been extensively characterized and compared with the human neutrophil proteinases, proteinase-3 and elastase. Specificity studies using both the oxidized insulin B-chain and synthetic peptides revealed that cleavage of peptide bonds with P1 alanine or valine residues was preferred. Further characterization of the two horse elastases by N-terminal sequence and reactive-site analyses indicated that proteinases 2A and 2B have considerable sequence similarity to each other, to proteinase-3 from human neutrophils (proteinase 2A), to human neutrophil elastase (proteinase 2B) and to a lesser extent to pig pancreatic elastase. Horse and human elastases differed somewhat in their interaction with some natural protein proteinase inhibitors. For example, in contrast with its action on human neutrophil elastase, aprotinin did not inhibit either of the horse proteinases. However, the Val15, alpha-aminobutyric acid-15 (Abu15), alpha-aminovaleric acid-15 (Nva15) and Ala15 reactive-site variants of aprotinin were good inhibitors of proteinase 2B (Ki < 10(-9) M) but only weak inhibitors of proteinase 2A (Ki > 10(-7) M). In summary, despite these differences, the horse neutrophil elastases were found to resemble closely their human counterparts, thus implicating them in the pathological degradation of connective tissue in chronic lung diseases in the equine species. PMID:7516152

  1. Directed Evolution and Structural Characterization of a Simvastatin Synthase

    SciTech Connect

    Gao, Xue; Xie, Xinkai; Pashkov, Inna; Sawaya, Michael R.; Laidman, Janel; Zhang, Wenjun; Cacho, Ralph; Yeates, Todd O.; Tang, Yi; UCLA

    2010-02-02

    Enzymes from natural product biosynthetic pathways are attractive candidates for creating tailored biocatalysts to produce semisynthetic pharmaceutical compounds. LovD is an acyltransferase that converts the inactive monacolin J acid (MJA) into the cholesterol-lowering lovastatin. LovD can also synthesize the blockbuster drug simvastatin using MJA and a synthetic {alpha}-dimethylbutyryl thioester, albeit with suboptimal properties as a biocatalyst. Here we used directed evolution to improve the properties of LovD toward semisynthesis of simvastatin. Mutants with improved catalytic efficiency, solubility, and thermal stability were obtained, with the best mutant displaying an {approx}11-fold increase in an Escherichia coli-based biocatalytic platform. To understand the structural basis of LovD enzymology, seven X-ray crystal structures were determined, including the parent LovD, an improved mutant G5, and G5 cocrystallized with ligands. Comparisons between the structures reveal that beneficial mutations stabilize the structure of G5 in a more compact conformation that is favorable for catalysis.

  2. Structural and magnetic characterization of YIG particles prepared using microemulsions

    NASA Astrophysics Data System (ADS)

    Baldomir, D.; Teijeiro, A. G.; Rivas, J.; Vaqueiro, P.; Paz, S. B.; López Quintela, A.

    1995-02-01

    Yttrium-iron-garnet (YIG) particles have been synthesized using the microemulsion technique. A comparison of ferrite powders obtained by this method and those prepared by sol-gel and solid state reactions is reported. We have studied both the magnetic and structural properties and have found a dependence on annealing temperatures.

  3. Topological characterization of crystalline ice structures from coordination sequences.

    PubMed

    Herrero, Carlos P; Ramírez, Rafael

    2013-10-21

    Topological properties of crystalline ice structures are studied by considering ring statistics, coordination sequences, and topological density of different ice phases. The coordination sequences (number of sites at topological distance k from a reference site) have been obtained by direct enumeration until at least 40 coordination spheres for different ice polymorphs. This allows us to study the asymptotic behavior of the mean number of sites in the k-th shell, Mk, for high values of k: Mk~ak(2), a being a structure-dependent parameter. Small departures from a strict parabolic dependence have been studied by considering first and second differences of the series {Mk} for each structure. The parameter a ranges from 2.00 for ice VI to 4.27 for ice XII, and is used to define a topological density for these solid phases of water. Correlations between such topological density and the actual volume of ice phases are discussed. Ices Ih and Ic are found to depart from the general trend in this correlation due to the large void space in their structures. PMID:23986009

  4. Structural and Mechanical Characterization of Thermally Treated Conch Shells

    NASA Astrophysics Data System (ADS)

    Li, Haoze; Jin, Dalai; Li, Rui; Li, Xiaodong

    2015-04-01

    Seashells are natural nanocomposite armors with an exceptional combination of strength and toughness. Conch shells have a crossed-lamellar structure constructed with aragonite and biopolymer. Thermal treatment uncovered a nanoscale hierarchical structure in shell's third-order lamellae. Individual third-order lamellae were found to consist of aragonite nanoparticles cemented with biopolymer. The biopolymer renders conch shells joint increase in strength, ductility and fracture energy, and especially the fracture energy increase is more remarkable. The shell's aragonite transformed to calcite at 407°C and lime at 607°C. The shell's biopolymer was burned out in the thermal treatment at 310°C, leading to 1.7% mass loss. The crossed-lamellar structure remained in the 500°C thermally treated shell. The 900°C heat treatment destroyed the crossed-lamellar architecture completely. Thermal treatment resulted in reduction in mechanical properties due to the joint effects—burning out of biopolymer, phase transformation, and destruction of structural integrity. The findings advance our understanding of conch shell's architecture and provide new guidelines for the design and manufacturing of bio-inspired materials.

  5. Structural and Functional Characterization of Pseudomonas aeruginosa AlgX

    PubMed Central

    Riley, Laura M.; Weadge, Joel T.; Baker, Perrin; Robinson, Howard; Codée, Jeroen D. C.; Tipton, Peter A.; Ohman, Dennis E.; Howell, P. Lynne

    2013-01-01

    The exopolysaccharide alginate, produced by mucoid Pseudomonas aeruginosa in the lungs of cystic fibrosis patients, undergoes two different chemical modifications as it is synthesized that alter the properties of the polymer and hence the biofilm. One modification, acetylation, causes the cells in the biofilm to adhere better to lung epithelium, form microcolonies, and resist the effects of the host immune system and/or antibiotics. Alginate biosynthesis requires 12 proteins encoded by the algD operon, including AlgX, and although this protein is essential for polymer production, its exact role is unknown. In this study, we present the X-ray crystal structure of AlgX at 2.15 Å resolution. The structure reveals that AlgX is a two-domain protein, with an N-terminal domain with structural homology to members of the SGNH hydrolase superfamily and a C-terminal carbohydrate-binding module. A number of residues in the carbohydrate-binding module form a substrate recognition “pinch point” that we propose aids in alginate binding and orientation. Although the topology of the N-terminal domain deviates from canonical SGNH hydrolases, the residues that constitute the Ser-His-Asp catalytic triad characteristic of this family are structurally conserved. In vivo studies reveal that site-specific mutation of these residues results in non-acetylated alginate. This catalytic triad is also required for acetylesterase activity in vitro. Our data suggest that not only does AlgX protect the polymer as it passages through the periplasm but that it also plays a role in alginate acetylation. Our results provide the first structural insight for a wide group of closely related bacterial polysaccharide acetyltransferases. PMID:23779107

  6. Fabrication and characterization of micro- /nano structures for nanophotonic applications

    NASA Astrophysics Data System (ADS)

    Jee, Hongsub

    The objective of this thesis is finding and developing fabrication methods to provide background techniques for potential applications with nanomaterials. The inclined UV lithography has announced to make three-dimensional fabrication process. With a movable stage, complex structures were achieved but difference of the refractive index, design of the final structures were limited. Refractive index matching medium between the substrate and the light source could reduce the refractive indices between the polymer and the substrate successfully. Nanoporous structures fabricated by multibeam interference lithography shows limitation of the usage since its periodicity. By insertion of the lift off resist layer between the patterned layer and the substrate, final photonic crystal structures could be partially removed for its own purpose and it provide potential application in the future. Two-step processing, combining with reactive ion etching system, nanoporous structures were on various substrates such as silicon and Polydimethylsiloxane. Photonic crystal template anodic aluminum oxide process has been described too. Large optical activity at visible wavelengths are of great attention in photonics. Dramatic enhancement of the optical activity of chiral poly(fluorene-alt-benzothiadiazole) with photoresist was demonstrated and successive photo patterning of chiral polymer shows the potential usage of this material for the photonics applications. Two photon lithography also used to pattern a photoresist-chiral polymer mixture into planar shapes and enhanced chirality can be realized by tuning the wavelength-dependent chiral response at both the molecular and geometric level. Near infrared light induced photopolymerization in-situ was demonstrated which can be applied everywhere where ultraviolet-polymerization is employed such as dentistry, coating industry. Use of the ultraviolet upconverting nanoparticles doped into the polymer, we show that expensive femtosecond pulsed

  7. Structural and Kinetic Characterization of Thymidine Kinase from Leishmania major

    PubMed Central

    Recio, Eliseo; Nettleship, Joanne E.; Rada, Heather; González-Pacanowska, Dolores; Wilson, Keith S.

    2015-01-01

    Leishmania spp. is a protozoan parasite and the causative agent of leishmaniasis. Thymidine kinase (TK) catalyses the transfer of the γ-phosphate of ATP to 2’-deoxythymidine (dThd) forming thymidine monophosphate (dTMP). L. major Type II TK (LmTK) has been previously shown to be important for infectivity of the parasite and therefore has potential as a drug target for anti-leishmanial therapy. In this study, we determined the enzymatic properties and the 3D structures of holo forms of the enzyme. LmTK efficiently phosphorylates dThd and dUrd and has high structural homology to TKs from other species. However, it significantly differs in its kinetic properties from Trypanosoma brucei TK since purines are not substrates of the enzyme and dNTPs such as dUTP inhibit LmTK. The enzyme had Km and kcat values for dThd of 1.1 μM and 2.62 s-1 and exhibits cooperative binding for ATP. Additionally, we show that the anti-retroviral prodrug zidovudine (3-azido-3-deoxythymidine, AZT) and 5’-modified dUrd can be readily phosphorylated by LmTK. The production of recombinant enzyme at a level suitable for structural studies was achieved by the construction of C-terminal truncated versions of the enzyme and the use of a baculoviral expression system. The structures of the catalytic core of LmTK in complex with dThd, the negative feedback regulator dTTP and the bi-substrate analogue AP5dT, were determined to 2.74, 3.00 and 2.40 Å, respectively, and provide the structural basis for exclusion of purines and dNTP inhibition. The results will aid the process of rational drug design with LmTK as a potential target for anti-leishmanial drugs. PMID:25978379

  8. Structural characterization of pharmaceutical heparins prepared from different animal tissues.

    PubMed

    Fu, Li; Li, Guoyun; Yang, Bo; Onishi, Akihiro; Li, Lingyun; Sun, Peilong; Zhang, Fuming; Linhardt, Robert J

    2013-05-01

    Although most pharmaceutical heparin used today is obtained from porcine intestine, heparin has historically been prepared from bovine lung and ovine intestine. There is some regulatory concern about establishing the species origin of heparin. This concern began with the outbreak of mad cow disease in the 1990s and was exacerbated during the heparin shortage in the 2000s and the heparin contamination crisis of 2007-2008. Three heparins from porcine, ovine, and bovine were characterized through state-of-the-art carbohydrate analysis methods with a view profiling their physicochemical properties. Differences in molecular weight, monosaccharide and disaccharide composition, oligosaccharide sequence, and antithrombin III-binding affinity were observed. These data provide some insight into the variability of heparins obtained from these three species and suggest some analytical approaches that may be useful in confirming the species origin of a heparin active pharmaceutical ingredient. PMID:23526651

  9. Structural and Electrical Characterization of Protonic Acid Doped Polyaniline

    NASA Astrophysics Data System (ADS)

    Shaktawat, Vinodini; Saxena, Narendra S.; Sharma, Kananbala; Sharma, Thaneshwar P.

    2008-04-01

    Polyaniline doped with different protonic acids were chemically synthesized using ammonium persulfate (APS) as an oxidant. These samples were characterized through X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy, which confirms the amorphous nature and acid doping, respectively. Electrical conduction in these samples has been studied through the measurement of I-V characteristics at room temperature as well as in the temperature range from 313 K to 413 K. So obtained characteristic curves were found to be nonlinear. The conductivity of phosphoric acid doped polyaniline sample is higher as compared to HCl doped polyaniline and pure polyaniline. Temperature dependence of conductivity suggests a semiconducting nature with increase in temperature. Activation energies have been found to be 50.86, 25.74 and 21.05 meV for pure polyaniline (base), polyaniline doped with hydrochloric, phosphoric acid, respectively.

  10. Material characterization of structural adhesives in the lap shear mode

    NASA Technical Reports Server (NTRS)

    Sancaktar, E.; Schenck, S. C.

    1983-01-01

    A general method for characterizing structual adhesives in the bonded lap shear mode is proposed. Two approaches in the form of semiempirical and theoretical approaches are used. The semiempirical approach includes Ludwik's and Zhurkov's equations to describe respectively, the failure stresses in the constant strain rate and constant stress loading modes with the inclusion of the temperature effects. The theoretical approach is used to describe adhesive shear stress-strain behavior with the use of viscoelastic or nonlinear elastic constitutive equations. Two different model adhesives are used in the single lap shear mode with titanium adherends. These adhesives (one of which was developed at NASA Langley Research Center) are currently considered by NASA for possible aerospace applications. Use of different model adhesives helps in assessment of the generality of the method.

  11. Internal structural characterization. Final report, September 1988-March 1992

    SciTech Connect

    Klaassen, R.; Bashyam, M.

    1992-08-01

    The nondestructive evaluation (NDE) techniques most appropriate for the detection of a variety of defects in metal- and ceramic matrix composites (MMC and CMC's) are described. NDE techniques which were investigated for application to these materials include acoustic microscopy, ultrasonic pulse-echo, ultrasonic through-transmission, ultrasonic velocity, ultrasonic backscatter, ultrasonic surface wave velocity, ultrasonic surface wave attenuation, film radiography, microtomographic radiography, and dual-energy microtomographic radiography. Types of defects for which optimized techniques are summarized include delaminations, broken fibers, fiber spacing, fiber orientation, fiber/matrix interface, matrix cracks and voids/porosity. Further NDE development is needed for these materials in the areas of basic development for other NDE modalities, advanced development for nondestructive material characterization, and the scale-up of proven NDE techniques for full scale components, to accommodate cost and geometry limitations.

  12. Structural characterization of human heparanase reveals insights into substrate recognition

    PubMed Central

    Wu, Liang; Viola, Cristina M.; Brzozowski, Andrzej M.; Davies, Gideon J.

    2016-01-01

    Heparan Sulfate (HS) is a glycosaminoglycan (GAG) which forms a key component of the extracellular matrix (ECM). Breakdown of HS is carried out by heparanase (HPSE), an endo-β-glucuronidase of the glycoside hydrolase (GH)79 family. Overexpression of HPSE is strongly linked to cancer metastases - reflecting breakdown of extracellular HS and release of stored growth factors. Here we present crystal structures of human HPSE at 1.6-1.9 Å resolution reveal how an endo-acting binding cleft is exposed by proteolytic activation of latent proHPSE. Oligosaccharide complexes map the substrate-binding and sulfate recognition motifs. These data shed light on the structure and interactions for a key enzyme involved in ECM maintenance, and provide a starting point for design of HPSE inhibitors as biochemical tools and anti-cancer therapeutics. PMID:26575439

  13. Characterization of the structure of PM-16E furnace black

    SciTech Connect

    Varlakov, V.P.; Fialkov, A.S.; Smirnov, B.N.

    1982-01-01

    An investigation of the structure of PM-16E furnace black in the initial and graphitized states has been carried out with the aid of phase-contact electron microscopy with direct resolution of the carbon layers (002). A two-stage mechanism of the formation of furnace black has been confirmed. In the first stage there is a free-radical mechanism of the formation of the particles of carbon black. In the second stage the orientated deposition of pyrolysis products takes place on the particles and their aggregates in the form of planar carbon layers. The structure of graphitized carbon black is represented in the form of a hollow polyhedron the faces of which consist of packets of continuous closed carbon layers.

  14. Structural characterization of human heparanase reveals insights into substrate recognition.

    PubMed

    Wu, Liang; Viola, Cristina M; Brzozowski, Andrzej M; Davies, Gideon J

    2015-12-01

    Heparan sulfate (HS) is a glycosaminoglycan that forms a key component of the extracellular matrix (ECM). Breakdown of HS is carried out by heparanase (HPSE), an endo-β-glucuronidase of the glycoside hydrolase 79 (GH79) family. Overexpression of HPSE results in breakdown of extracellular HS and release of stored growth factors and hence is strongly linked to cancer metastasis. Here we present crystal structures of human HPSE at 1.6-Å to 1.9-Å resolution that reveal how an endo-acting binding cleft is exposed by proteolytic activation of latent proHPSE. We used oligosaccharide complexes to map the substrate-binding and sulfate-recognition motifs. These data shed light on the structure and interactions of a key enzyme involved in ECM maintenance and provide a starting point for the design of HPSE inhibitors for use as biochemical tools and anticancer therapeutics. PMID:26575439

  15. Structural characterization of gel-derived calcium silicate systems.

    PubMed

    Meiszterics, Anikó; Rosta, László; Peterlik, Herwig; Rohonczy, János; Kubuki, Shiro; Henits, Péter; Sinkó, Katalin

    2010-09-30

    The main aim of this study is to synthesize calcium silicate ceramics that exhibit suitable properties to be used for biomedical applications. In the present work, attention was paid to the understanding of processing-structure relationships. A particular effort was made to clarify the identification of Ca-O-Si bonds by means of spectroscopy. The calcium silicate systems were prepared via a sol-gel route, varying the chemical compositions, the catalyst concentration, and the temperature and time of aging and heat treatment. The processes and the phases evolved during the sol-gel procedure were determined. The bond systems were investigated by Fourier transform infrared (FTIR) and (29)Si magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy and the aggregate structures by scanning electron microscopy (SEM), small-angle neutron scattering (SANS), small-angle X-ray scattering (SAXS), wide-angle X-ray scattering (WAXS), and X-ray diffraction (XRD) measurements. PMID:20828114

  16. Nanoscale structural and mechanical characterization of natural nanocomposites: Seashells

    NASA Astrophysics Data System (ADS)

    Li, Xiaodong

    2007-03-01

    Seashells are natural nanocomposites with superior mechanical strength and toughness. What is the secret recipe that Mother Nature uses to fabricate seashells? What roles do the nanoscale structures play in the inelasticity and toughening of seashells? Can we learn from this to produce seashell-like nanocomposites? The focus of this article is nacre (mother-of-pearl). The recent discovery of nanoparticles in nacre is summarized, and the role these nanoparticles play in nacre’s toughness is elucidated. It was found that rotation and deformation of aragonite nanoparticles are the two prominent mechanisms contributing to energy dissipation in nacre. The biopolymer spacing between nanoparticles facilitates the particle rotation process. This article also presents future challenges in the study of nacre’s nanoscale structure and mechanical properties.

  17. Chemical and structural characterization of carbon nanotube surfaces.

    PubMed

    Wepasnick, Kevin A; Smith, Billy A; Bitter, Julie L; Howard Fairbrother, D

    2010-02-01

    To utilize carbon nanotubes (CNTs) in various commercial and scientific applications, the graphene sheets that comprise CNT surfaces are often modified to tailor properties, such as dispersion. In this article, we provide a critical review of the techniques used to explore the chemical and structural characteristics of CNTs modified by covalent surface modification strategies that involve the direct incorporation of specific elements and inorganic or organic functional groups into the graphene sidewalls. Using examples from the literature, we discuss not only the popular techniques such as TEM, XPS, IR, and Raman spectroscopy but also more specialized techniques such as chemical derivatization, Boehm titrations, EELS, NEXAFS, TPD, and TGA. The chemical or structural information provided by each technique discussed, as well as their strengths and limitations. Particular emphasis is placed on XPS and the application of chemical derivatization in conjunction with XPS to quantify functional groups on CNT surfaces in situations where spectral deconvolution of XPS lineshapes is ambiguous. PMID:20052581

  18. Structural characterization of the packings of granular regular polygons.

    PubMed

    Wang, Chuncheng; Dong, Kejun; Yu, Aibing

    2015-12-01

    By using a recently developed method for discrete modeling of nonspherical particles, we simulate the random packings of granular regular polygons with three to 11 edges under gravity. The effects of shape and friction on the packing structures are investigated by various structural parameters, including packing fraction, the radial distribution function, coordination number, Voronoi tessellation, and bond-orientational order. We find that packing fraction is generally higher for geometrically nonfrustrated regular polygons, and can be increased by the increase of edge number and decrease of friction. The changes of packing fraction are linked with those of the microstructures, such as the variations of the translational and orientational orders and local configurations. In particular, the free areas of Voronoi tessellations (which are related to local packing fractions) can be described by log-normal distributions for all polygons. The quantitative analyses establish a clearer picture for the packings of regular polygons. PMID:26764678

  19. Structural Characterization of Novel Gemini Non-viral DNA

    SciTech Connect

    Foldvari,M.; Badea, I.; Wettig, S.; Verrall, R.; Bagonluri, M.

    2006-01-01

    The structural and physicochemical properties of novel cationic lipid-based DNA complexes have been investigated for the purpose of designing micro/nano-scale self-assembling delivery systems for cutaneous gene therapy. DNA/gemini surfactant (spacer n = 3-16; chain m = 12 or 16) complexes (1 : 10 charge ratio), with or without dioleoylphosphatidyl-ethanolamine (DOPE), designed for cellular transfection, were generally in the range of 100-200 nm as demonstrated by atomic force microscopy and particle size analysis. Small-angle X-ray scattering measurements indicated that the DNA/gemini complexes lacked long-range order, whereas DNA/gemini/DOPE complexes exhibited lamellar and polymorphic phases other than hexagonal. Correlation studies using transfection efficiency data in PAM 212 keratinocytes and in vitro skin absorption indicated that formulations containing gemini surfactants having the ability to induce structures other than lamellar in the resulting complexes, generally exhibited greater transfection activity and cutaneous absorption.

  20. Characterization of GPR101 transcript structure and expression patterns.

    PubMed

    Trivellin, Giampaolo; Bjelobaba, Ivana; Daly, Adrian F; Larco, Darwin O; Palmeira, Leonor; Faucz, Fabio R; Thiry, Albert; Leal, Letícia F; Rostomyan, Liliya; Quezado, Martha; Schernthaner-Reiter, Marie Helene; Janjic, Marija M; Villa, Chiara; Wu, T John; Stojilkovic, Stanko S; Beckers, Albert; Feldman, Benjamin; Stratakis, Constantine A

    2016-08-01

    We recently showed that Xq26.3 microduplications cause X-linked acrogigantism (X-LAG). X-LAG patients mainly present with growth hormone and prolactin-secreting adenomas and share a minimal duplicated region containing at least four genes. GPR101 was the only gene highly expressed in their pituitary lesions, but little is known about its expression patterns. In this work, GPR101 transcripts were characterized in human tissues by 5'-Rapid Amplification of cDNA Ends (RACE) and RNAseq, while the putative promoter was bioinformatically predicted. We investigated GPR101 mRNA and protein expression by RT-quantitative PCR (qPCR), whole-mount in situ hybridization, and immunostaining, in human, rhesus monkey, rat and zebrafish. We identified four GPR101 isoforms characterized by different 5'-untranslated regions (UTRs) and a common 6.1kb long 3'UTR. GPR101 expression was very low or absent in almost all adult human tissues examined, except for specific brain regions. Strong GPR101 staining was observed in human fetal pituitary and during adolescence, whereas very weak/absent expression was detected during childhood and adult life. In contrast to humans, adult monkey and rat pituitaries expressed GPR101, but in different cell types. Gpr101 is expressed in the brain and pituitary during rat and zebrafish development; in rat pituitary, Gpr101 is expressed only after birth and shows sexual dimorphism. This study shows that different GPR101 transcripts exist and that the brain is the major site of GPR101 expression across different species, although divergent species- and temporal-specific expression patterns are evident. These findings suggest an important role for GPR101 in brain and pituitary development and likely reflect the very different growth, development and maturation patterns among species. PMID:27282544

  1. Structural Characterization of Novel Pseudomonas aeruginosa Type IV Pilins

    SciTech Connect

    Nguyen, Y.; Jackson, S; Aidoo, F; Junop, M; Burrows, L

    2010-01-01

    Pseudomonas aeruginosa type IV pili, composed of PilA subunits, are used for attachment and twitching motility on surfaces. P. aeruginosa strains express one of five phylogenetically distinct PilA proteins, four of which are associated with accessory proteins that are involved either in pilin posttranslational modification or in modulation of pilus retraction dynamics. Full understanding of pilin diversity is crucial for the development of a broadly protective pilus-based vaccine. Here, we report the 1.6-{angstrom} X-ray crystal structure of an N-terminally truncated form of the novel PilA from strain Pa110594 (group V), which represents the first non-group II pilin structure solved. Although it maintains the typical T4a pilin fold, with a long N-terminal {alpha}-helix and four-stranded antiparallel {beta}-sheet connected to the C-terminus by a disulfide-bonded loop, the presence of an extra helix in the {alpha}{beta}-loop and a disulfide-bonded loop with helical character gives the structure T4b pilin characteristics. Despite the presence of T4b features, the structure of PilA from strain Pa110594 is most similar to the Neisseria gonorrhoeae pilin and is also predicted to assemble into a fiber similar to the GC pilus, based on our comparative pilus modeling. Interactions between surface-exposed areas of the pilin are suggested to contribute to pilus fiber stability. The non-synonymous sequence changes between group III and V pilins are clustered in the same surface-exposed areas, possibly having an effect on accessory protein interactions. However, based on our high-confidence model of group III PilA{sub PA14}, compensatory changes allow for maintenance of a similar shape.

  2. A structurally-characterized NbCl5-NHC adduct.

    PubMed

    Bortoluzzi, Marco; Ferretti, Eleonora; Marchetti, Fabio; Pampaloni, Guido; Zacchini, Stefano

    2014-05-01

    The selective reactions of niobium pentachloride with two bulky NHC carbenes afforded NbCl5(NHC) complexes, bearing the highest oxidation state ever found for a metal centre in a transition metal halide-NHC adduct. The X-ray structure of 2a is the first one reported for a monodentate NHC-niobium species, and exhibits an abnormally long Nb-C bond. PMID:24658260

  3. Pore structure characterization of catalyst supports via low field NMR

    SciTech Connect

    Smith, D.M.; Glaves, C.L.; Gallegos, D.P.; Brinker, C.J.

    1988-01-01

    In this paper, the application of low-field NMR to both surface area and pore structure analysis of catalyst supports will be presented. Low-field (20 MHz) spin-lattice relaxation (T/sub 1/) experiments are performed on fluids contained in alumina and silica catalyst supports. Pore size distributions (PSD) calculated from these NMR experiments are compared to those obtained from mercury porosimetry and nitrogen condensation. 18 refs., 4 figs., 2 tabs.

  4. Structural and Histone Binding Ability Characterizations of Human PWWP Domains

    SciTech Connect

    Wu, Hong; Zeng, Hong; Lam, Robert; Tempel, Wolfram; Amaya, Maria F.; Xu, Chao; Dombrovski, Ludmila; Qiu, Wei; Wang, Yanming; Min, Jinrong

    2013-09-25

    The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.

  5. Raman lidar characterization of PBL structure during COPS

    NASA Astrophysics Data System (ADS)

    Summa, D.; Di Girolamo, P.; Stelitano, D.; Di Iorio, T.

    2012-04-01

    The planetary boundary layer includes the portion of the atmosphere which is directly influenced by the presence of the Earth's surface. Aerosol particles trapped within the PBL can be used as tracers to study boundary-layer vertical structure and time variability. Aerosols can be dispersed out of the PBL during strong convection or temporary breaks of the capping temperature inversion. As a result of this, elastic backscatter signals collected by lidar systems can be used to determine the height and the internal structure of the PBL. Our analysis considers a method based on the first order derivative of the range-corrected elastic signal (RCS), which is a modified version of the method defined by Seibert et al. (2000) and Sicard et al. (2006). The analysis is focused on selected case studies collected by the Raman lidar system BASIL during the Convective and Orographically-induced Precipitation Study (COPS), held in Southern Germany and Eastern France in the period 01 June - 31 August 2007. Measurements were performed by the Raman lidar system BASIL, which was operational in Achern (Black Forest, Lat: 48.64 ° N, Long: 8.06 ° E, Elev.: 140 m). During COPS, BASIL collected more than 500 hours of measurements, distributed over 58 measurement days and 34 intensive observation periods (IOPs), covering both night-time and daytime and the transitions between the two. Therefore BASIL data during COPS represent a unique source of information for the study of the boundary layer structure and evolution. Potential temperature profiles obtained from the radiosonde data were used to get an additional estimate of the boundary layer height. Estimates of the PBL height and structure for specific case studies obtained from the lidar data and their comparison with estimates obtained from the radiosonde data will be illustrated and discussed at the Conference.

  6. Purification and structural characterization of herpes simplex virus glycoprotein C

    SciTech Connect

    Kikuchi, G.E.; Baker, S.A.; Merajver, S.D.; Coligan, J.E.; Levine, M.; Glorioso, J.C.; Nairn, R.

    1987-01-27

    Purification of herpes simplex virus glycoprotein C (gC) in microgram amounts yielded sufficient material for an analysis of its secondary structure. Purification was facilitated by using the mutant virus gC-3, which bears a point mutation that interrupts the putative hydrophobic membrane anchor sequence, causing the secretion of gC-3 protein into the cell culture medium. gC-3 protein was purified by size fractionation of concentrated culture medium from infected cells on a gel filtration column of Sephacryl S-200, followed by immunoaffinity chromatography on a column constructed of gC-specific monoclonal antibodies cross-linked to a protein A-Sepharose CL-4B matrix. Purified gC-3 had a molecular weight of 130,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the size expected for gC, was reactive with gC-specific monoclonal antibodies in protein immunoblots, and contained amino acid sequences characteristic of gC as determined by radiochemical amino acid microsequence analyses. Polyclonal antisera obtained from a rabbit immunized with gC-3 reacted with wild-type gC in immunoprecipitation, enzyme immunoassay, and immunoelectroblot (western blot) assays. Deglycosylation by treatment with trifluoromethanesulfonic acid reduced the molecular weight of gC-3 by approximately 35%. Analyses of both native and deglycosylated gC-3 by Raman spectroscopy showed that the native molecule consists of about 17%..cap alpha..-helix, 24% ..beta..-sheet, and 60% disordered secondary structures, whereas deglycosylated gC-3 consists of about 8% ..cap alpha..-helix, 10% ..beta..-sheet, 81% disordered structures. These data were in good agreement with the 11% ..cap alpha..-helix, 18% ..beta..-sheet, 61% ..beta..-turn, and 9% disordered structures calculated from Chou-Fasman analysis of the primary sequence of gC-3.

  7. Structure and Biochemical Characterization of Protein Acetyltransferase from Sulfolobus solfataricus

    SciTech Connect

    Brent, Michael M.; Iwata, Ayaka; Carten, Juliana; Zhao, Kehao; Marmorstein, Ronen

    2009-09-02

    The Sulfolobus solfataricus protein acetyltransferase (PAT) acetylates ALBA, an abundant nonspecific DNA-binding protein, on Lys{sup 16} to reduce its DNA affinity, and the Sir2 deacetylase reverses the modification to cause transcriptional repression. This represents a 'primitive' model for chromatin regulation analogous to histone modification in eukaryotes. We report the 1.84-{angstrom} crystal structure of PAT in complex with coenzyme A. The structure reveals homology to both prokaryotic GNAT acetyltransferases and eukaryotic histone acetyltransferases (HATs), with an additional 'bent helix' proximal to the substrate binding site that might play an autoregulatory function. Investigation of active site mutants suggests that PAT does not use a single general base or acid residue for substrate deprotonation and product reprotonation, respectively, and that a diffusional step, such as substrate binding, may be rate-limiting. The catalytic efficiency of PAT toward ALBA is low relative to other acetyltransferases, suggesting that there may be better, unidentified substrates for PAT. The structural similarity of PAT to eukaryotic HATs combined with its conserved role in chromatin regulation suggests that PAT is evolutionarily related to the eukaryotic HATs.

  8. Structural and thermodynamic characterization of Vibrio fischeri CcdB.

    PubMed

    De Jonge, Natalie; Hohlweg, Walter; Garcia-Pino, Abel; Respondek, Michal; Buts, Lieven; Haesaerts, Sarah; Lah, Jurij; Zangger, Klaus; Loris, Remy

    2010-02-19

    CcdB(Vfi) from Vibrio fischeri is a member of the CcdB family of toxins that poison covalent gyrase-DNA complexes. In solution CcdB(Vfi) is a dimer that unfolds to the corresponding monomeric components in a two-state fashion. In the unfolded state, the monomer retains a partial secondary structure. This observation correlates well with the crystal and NMR structures of the protein, which show a dimer with a hydrophobic core crossing the dimer interface. In contrast to its F plasmid homologue, CcdB(Vfi) possesses a rigid dimer interface, and the apparent relative rotations of the two subunits are due to structural plasticity of the monomer. CcdB(Vfi) shows a number of non-conservative substitutions compared with the F plasmid protein in both the CcdA and the gyrase binding sites. Although variation in the CcdA interaction site likely determines toxin-antitoxin specificity, substitutions in the gyrase-interacting region may have more profound functional implications. PMID:19959472

  9. Structural and Thermodynamic Characterization of Vibrio fischeri CcdB*

    PubMed Central

    De Jonge, Natalie; Hohlweg, Walter; Garcia-Pino, Abel; Respondek, Michal; Buts, Lieven; Haesaerts, Sarah; Lah, Jurij; Zangger, Klaus; Loris, Remy

    2010-01-01

    CcdBVfi from Vibrio fischeri is a member of the CcdB family of toxins that poison covalent gyrase-DNA complexes. In solution CcdBVfi is a dimer that unfolds to the corresponding monomeric components in a two-state fashion. In the unfolded state, the monomer retains a partial secondary structure. This observation correlates well with the crystal and NMR structures of the protein, which show a dimer with a hydrophobic core crossing the dimer interface. In contrast to its F plasmid homologue, CcdBVfi possesses a rigid dimer interface, and the apparent relative rotations of the two subunits are due to structural plasticity of the monomer. CcdBVfi shows a number of non-conservative substitutions compared with the F plasmid protein in both the CcdA and the gyrase binding sites. Although variation in the CcdA interaction site likely determines toxin-antitoxin specificity, substitutions in the gyrase-interacting region may have more profound functional implications. PMID:19959472

  10. Structural and functional characterization of Mycobacterium tuberculosis triosephosphate isomerase

    SciTech Connect

    Connor, Sean E.; Capodagli, Glenn C.; Deaton, Michelle K.; Pegan, Scott D.

    2012-04-18

    Tuberculosis (TB) is a major infectious disease that accounts for over 1.7 million deaths every year. Mycobacterium tuberculosis, the causative agent of tuberculosis, enters the human host by the inhalation of infectious aerosols. Additionally, one third of the world's population is likely to be infected with latent TB. The incidence of TB is on the rise owing in part to the emergence of multidrug-resistant strains. As a result, there is a growing need to focus on novel M. tuberculosis enzyme targets. M. tuberculosis triosephosphate isomerase (MtTPI) is an essential enzyme for gluconeogenetic pathways, making it a potential target for future therapeutics. In order to determine its structure, the X-ray crystal structure of MtTPI has been determined, as well as that of MtTPI bound with a reaction-intermediate analog. As a result, two forms of the active site were revealed. In conjunction with the kinetic parameters obtained for the MtTPI-facilitated conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (D-GAP), this provides a greater structural and biochemical understanding of this enzyme. Additionally, isothermal titration calorimetry was used to determine the binding constant for a reaction-intermediate analog bound to the active site of MtTPI.

  11. [STRUCTURAL CHARACTERIZATION OF PLATELETS AND PLATELET-DERIVED MICROVESICLES].

    PubMed

    Ponomareva, A A; Nevzorova, T A; Mordakhanova, E R; Andrianova, I A; Litvinov, R I

    2016-01-01

    Platelets are the anucleated blood cells, wich together with the fibrin stop bleeding (hemostasis). Cellular microvesicles are membrane-surrounded microparticles released into extracellular space upon activation and/or apoptosis of various cells. Platelet-derived macrovesicles from the major population of circulating blood microparticles that play an important role in hemostasis and thrombosis. Despite numerous studies on the pathophysiology of platelet-derived macrovesicles, mechanisms of their formation and structural details remain poorly understood. Here we investigated the ultrastructure of parental platelets and platelet-derived microvesicles formed in vitro by quiescent cells as well as by cells stimulated with one of the following activators: arachidonic acid, ADP, thrombin, calcium ionophore A23187. Using transmission electron microscopy of human platelets and isolated microvesicles, we analyzed the intracellular origin, steps of formation, structural diversity, and size distributions of the subcellular particles. We have revealed that thrombin, unlike other stimuli, not only induced vesiculation of the plasma membrane but also caused break-up of the cells followed by formation of microparticles that are comparable with microvesicles by size. A fraction of these microparticles contained cellular organelles surrounded by a thin membrane. The size of platelet-derived macrovesicles varied from 30 nm to 500 nm, however, the size distributions depended on the nature of a cell-activating stimulus. The results obtained provide new information about the formation of platelet-derived macrovesicles and their structural diversity, wich is important to understand their multiple functions in normal and disease states. PMID:27228656

  12. Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

    PubMed Central

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-01-01

    Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological material embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as the relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. PMID:21842467

  13. Isolation, Characterization, and Aggregation of a Structured Bacterial Matrix Precursor*

    PubMed Central

    Chai, Liraz; Romero, Diego; Kayatekin, Can; Akabayov, Barak; Vlamakis, Hera; Losick, Richard; Kolter, Roberto

    2013-01-01

    Biofilms are surface-associated groups of microbial cells that are embedded in an extracellular matrix (ECM). The ECM is a network of biopolymers, mainly polysaccharides, proteins, and nucleic acids. ECM proteins serve a variety of structural roles and often form amyloid-like fibers. Despite the extensive study of the formation of amyloid fibers from their constituent subunits in humans, much less is known about the assembly of bacterial functional amyloid-like precursors into fibers. Using dynamic light scattering, atomic force microscopy, circular dichroism, and infrared spectroscopy, we show that our unique purification method of a Bacillus subtilis major matrix protein component results in stable oligomers that retain their native α-helical structure. The stability of these oligomers enabled us to control the external conditions that triggered their aggregation. In particular, we show that stretched fibers are formed on a hydrophobic surface, whereas plaque-like aggregates are formed in solution under acidic pH conditions. TasA is also shown to change conformation upon aggregation and gain some β-sheet structure. Our studies of the aggregation of a bacterial matrix protein from its subunits shed new light on assembly processes of the ECM within bacterial biofilms. PMID:23632024

  14. Detailed glycan structural characterization by electronic excitation dissociation.

    PubMed

    Yu, Xiang; Jiang, Yan; Chen, Yajie; Huang, Yiqun; Costello, Catherine E; Lin, Cheng

    2013-11-01

    The structural complexity and diversity of glycans parallel their multilateral functions in living systems. To better understand the vital roles glycans play in biological processes, it is imperative to develop analytical tools that can provide detailed glycan structural information. This was conventionally achieved by multistage tandem mass spectrometry (MS(n)) analysis using collision-induced dissociation (CID) as the fragmentation method. However, the MS(n) approach lacks the sensitivity and throughput needed to analyze complex glycan mixtures from biological sources, often available in limited quantities. We define herein the critical parameters for a recently developed fragmentation technique, electronic excitation dissociation (EED), which can yield rich structurally informative fragment ions during liquid chromatographic (LC)-MS/MS analysis of glycans. We further demonstrate that permethylation, reducing end labeling and judicious selection of the metal charge carrier, can greatly facilitate spectral interpretation. With its high sensitivity, throughput, and compatibility with online chromatographic separation techniques, EED appears to hold great promise for large-scale glycomics studies. PMID:24080071

  15. Structural characterization and magnetic properties of steels subjected to fatigue

    NASA Astrophysics Data System (ADS)

    Lo, C. C. H.; Tang, F.; Biner, S. B.; Jiles, D. C.

    2000-05-01

    Studies have been made on the effects of residual stress and microstructure on the variations of magnetic properties of steels during fatigue. Strain-controlled fatigue tests have been conducted on 0.2wt% C steel samples which were (1) cold-worked, (2) cold-worked and annealed at 500 °C to relieve residual stress, and (3) annealed at 905 °C to produce a ferrite/pearlite structure. The changes of surface microstructure were studied by SEM replica technique. The dislocation structures of samples fatigued for different numbers of cycle were studied by TEM. In the initial stage of fatigue coercivity was found to behave differently for samples which have different residual stress levels. In the intermediate stage the magnetic hysteresis parameters became stable as the dislocation cell structure developed in the samples. In the final stage the magnetic parameters decreased dramatically. The decrease rate is related to the propagation rate of fatigue cracks observed in the SEM study, which was found to be dependent on the sample microstructure. The present results indicate that the magnetic inspection technique is able to differentiate the residual stress effects from the fatigue damage induced by cyclic loading, and therefore it is possible to detect the onset of fatigue failure in steel components via measurements of the changes in magnetic properties.—This work was sponsored by the National Science Foundation, under grant number CMS-9532056.

  16. Characterization of structural response to hypersonic boundary-layer transition

    DOE PAGESBeta

    Riley, Zachary B.; Deshmukh, Rohit; Miller, Brent A.; McNamara, Jack J.; Casper, Katya M.

    2016-05-24

    The inherent relationship between boundary-layer stability, aerodynamic heating, and surface conditions makes the potential for interaction between the structural response and boundary-layer transition an important and challenging area of study in high-speed flows. This paper phenomenologically explores this interaction using a fundamental two-dimensional aerothermoelastic model under the assumption of an aluminum panel with simple supports. Specifically, an existing model is extended to examine the impact of transition onset location, transition length, and transitional overshoot in heat flux and fluctuating pressure on the structural response of surface panels. Transitional flow conditions are found to yield significantly increased thermal gradients, and theymore » can result in higher maximum panel temperatures compared to turbulent flow. Results indicate that overshoot in heat flux and fluctuating pressure reduces the flutter onset time and increases the strain energy accumulated in the panel. Furthermore, overshoot occurring near the midchord can yield average temperatures and peak displacements exceeding those experienced by the panel subject to turbulent flow. Lastly, these results suggest that fully turbulent flow does not always conservatively predict the thermo-structural response of surface panels.« less

  17. Chemical and structural characterization of copper adsorbed on mosses (Bryophyta).

    PubMed

    González, Aridane G; Jimenez-Villacorta, Felix; Beike, Anna K; Reski, Ralf; Adamo, Paola; Pokrovsky, Oleg S

    2016-05-01

    The adsorption of copper on passive biomonitors (devitalized mosses Hypnum sp., Sphagnum denticulatum, Pseudoscleropodium purum and Brachythecium rutabulum) was studied under different experimental conditions such as a function of pH and Cu concentration in solution. Cu assimilation by living Physcomitrella patents was also investigated. Molecular structure of surface adsorbed and incorporated Cu was studied by X-ray Absorption Spectroscopy (XAS). Devitalized mosses exhibited the universal adsorption pattern of Cu as a function of pH, with a total binding sites number 0.05-0.06 mmolg(dry)(-1) and a maximal adsorption capacity of 0.93-1.25 mmolg(dry)(-1) for these devitalized species. The Extended X-ray Absorption Fine Structure (EXAFS) fit of the first neighbor demonstrated that for all studied mosses there are ∼4.5 O/N atoms around Cu at ∼1.95 Å likely in a pseudo-square geometry. The X-ray Absorption Near Edge Structure (XANES) analysis demonstrated that Cu(II)-cellulose (representing carboxylate groups) and Cu(II)-phosphate are the main moss surface binding moieties, and the percentage of these sites varies as a function of solution pH. P. patens exposed during one month to Cu(2+) yielded ∼20% of Cu(I) in the form of Cu-S(CN) complexes, suggesting metabolically-controlled reduction of adsorbed and assimilated Cu(2+). PMID:26852210

  18. The synthesis and structural characterization of novel transition metal fluorides

    SciTech Connect

    Casteel, W.J. Jr.

    1992-09-01

    High purity KMF[sub 6] and K[sub 2]MF[sub 6] salts (M = Mo,Re, Ru, Os, Ir, Pt) are obtained from reduction hexafluorides. A rhombohedral unit cell is observed for KReF[sub 6]. Fluoride ion capture by Lewis acids from the hexafluorometallate (IV) salts affords high purity tetrafluorides for M = Mo, Re, Ru, Os, and Pd. The structure of RuF[sub 4] is determined from X-ray synchrotron and neutron powder data. Unit cells based on theorthorhombic PdF[sub 4] type cell are derived from X-ray powder data for ReF[sub 4] and OsF[sub 4]. Fluoride ion capture from KAgF[sub 4] provides the thermally unstable trifluoride as a bright, red, diamagnetic solid. The structure solution of AgF[sub 3] and redetermination of the AuF[sub 3] structure from X-ray synchrotron and neutron powder data demonstrate that the two are isostnictural. Thermal decomposition product of AgF[sub 3] is the mixed valence compound Ag[sup II]Ag[sub 2][sup III]F[sub 8]. Several new salts containing the (Ag - F)[sub n][sup n+] chain cation are prepared. The first linear (Ag - F)[sub n][sup n+] chain is observed in AgF[sup +]BF[sub 4 [sup [minus

  19. Characterization of irradiated test structures for the CMS tracker upgrade

    NASA Astrophysics Data System (ADS)

    Lutzer, Bernhard

    2013-12-01

    The CMS collaboration is currently conducting a campaign to identify radiation-hard materials for an upgrade of the CMS tracker. This upgrade is needed to be able to cope with the higher radiation background of the future HL-LHC; additionally the performance of the current tracker will be significantly degraded at the time of the upgrade, requiring a replacement. Several different test structures (TSs) and sensors have been designed for a 6 in. wafer layout. These wafers were produced by an industrial supplier (Hamamatsu Photonics K.K.) and differ by their bulk material (Float Zone, Magnetic Czochralski and CVD-Epi), thickness (from 50 μm to 320 μm) and N-P type doping. These TSs consist of different microelectronic devices including diodes, resistors or MOS structures. They enable the extraction of parameters which are not accessible in a silicon detector and allow the assessment of the quality of the sensors produced on the same wafer. The TSs have been irradiated with protons and neutrons to emulate the radiation damage caused by the particle fluence inside the future CMS tracker after 10 years of operation. This contribution will present measurements of non-irradiated and irradiated test structures at different fluences. The changes of the properties of the microelectronic devices will be discussed as well as the design of the TSs.

  20. Synthesis, structure, and magnetic characterization of Cr4US8

    NASA Astrophysics Data System (ADS)

    Ward, Matthew D.; Chan, Ian Y.; Malliakas, Christos D.; Lee, Minseong; Choi, Eun Sang; Ibers, James A.

    2016-01-01

    The compound Cr4US8 has been synthesized at 1073 K and its crystal structure has been determined at 100 K. The structure is modulated with a two-fold commensurate supercell. The subcell may be indexed in an orthorhombic cell but weak supercell reflections lead to the monoclinic superspace group P21/c(α0γ)0s with two Cr sites, one U site, and four S sites. The structure comprises a three-dimensional framework of CrS6 octahedra with channels that are partially occupied by U atoms. Each U atom in these channels is coordinated by eight S atoms in a bicapped trigonal-prismatic arrangement. The magnetic behavior of Cr4US8 is complex. At temperatures above ~120 K at all measured fields, there is little difference between field-cooled and zero field-cooled data and χ(T) decreases monotonously with temperature, which is reminiscent of the Curie-Weiss law. At lower temperatures, the temperature dependence of χ(T) is complex and strongly dependent on the magnetic field strength.

  1. Hydrothermal Synthesis and Structural Characterization of Organically Templated Uranyl Diphosphonates

    SciTech Connect

    Adelani, Pius O.; Oliver, Allen G.; Albrecht-Schmitt, Thomas E.

    2011-03-09

    The hydrothermal treatment of uranyl nitrate and 1,4-benzenebisphosphonic acid with a variety of aliphatic amines (tetramethylammonium hydroxide, tetraethylammonium hydroxide, and diethyldimethylammonium hydroxide) and small quantities of hydrofluoric acid at 200 °C results in the crystallization of a series of layered uranyl diphosphonate compounds, [(CH3)4N][(UO2)3(O3PC6H4PO3H)2F(H2O)]·0.5H2O (Me4Ubbp), [(CH3CH2)4N](UO2)[C6H4(PO3H)(PO3H1.5)]2(H2O) (Et4Ubbp), and [(CH3CH2)2N(CH3)2][(UO2)3(O3PC6H4PO3H)2F(H2O)] (Et2Me2Ubbp). All these new compounds have layered structures, but the structures of Me4Ubbp and Et2Me2Ubbp are similar in that they both contain UO6F and UO7 pentagonal bipyramids within dimers that are bridged by the phosphonate into a three-dimensional structure. The structure of Et4Ubbp contains a single crystallographically unique UO7 unit. The edge-sharing pentagonal bipyramids are linked into chains formulated as (UO2)[C6H4(PO3H)(PO3H1.5)]2(H2O)1-. The voids in these structures are filled with the organic templates so that the overall charge balance is maintained. Intense fluorescence was observed from these compounds at room temperature.

  2. Synthesis and characterization of JBW structure and its thermal transformation

    SciTech Connect

    Hegazy, Eman Z.; Kosa, Samia A.; Abd El Maksod, Islam Hamdy

    2012-12-15

    In this paper, JBW zeolite prepared from Egyptian kaolin was investigated by means of XRD, IR, SEM, EDX and ion exchange of some heavy metals. Adsorption isotherms were used to investigate the structure and properties of the prepared zeolite. XRD analysis showed that the JBW was a pure crystalline phase with orthorhombic crystal symmetry. Thermal treatment showed that the JBW transformed into the It-Carn phase at 1000 Degree-Sign C through an intermediate crystalline alumino silicate phase. SEM images showed that the JBW crystallised in a cylindrical shape. However, spherical agglomerates were observed at lower magnifications. The ion exchange isotherms with Cu{sup 2+}, Ni{sup 2+} and Co{sup 2+} were found to follow a Freundlich isotherm. In addition, it shows higher affinity towards Cu{sup 2+} than other ions. - Graphical abstract: JBW zeolite structure was prepared from Egyptian kaolin and characterised. XRD analysis showed that the JBW was a pure crystalline phase with orthorhombic crystal symmetry. Thermal treatment showed that the JBW transformed into the It-Carn phase at 1000 Degree-Sign C through an intermediate crystalline alumino silicate phase. Highlights: Black-Right-Pointing-Pointer Egyptian kaolin was successfully used to prepare pure phase of JBW Structure. Black-Right-Pointing-Pointer JBW is stable till <300 Degree-Sign C. Black-Right-Pointing-Pointer JBW phase crystallizes as cylindrical shape but agglomerates in a Nano spherical shape. Black-Right-Pointing-Pointer The ion exchange isotherms of Cu{sup 2+}, Ni{sup 2+}, and Co{sup 2+} followed up Freundlich isotherm. Black-Right-Pointing-Pointer Selectivity towards Cu{sup 2+} is much higher than Co{sup 2+} or Ni{sup 2+}.

  3. Structural characterization of a karstified limestone formation using GPR

    NASA Astrophysics Data System (ADS)

    Rousset, D.; Sénéchal, G.; Gaffet, S.

    2009-12-01

    The Laboratoire Souterrain à Bas Bruit (LSBB) at Rustrel - Pays d'Apt, France, is an Inter-disciplinary Underground Science and Technology Laboratory buried in a karstified limestone formation. A multidisciplinary program focused on water circulation monitoring is presently performed inside the tunnels. This program comprises the investigation of faults, fractures, karstification and stratigraphy ofthe limestone massif using GPR. We present the main results obtained from these data. The tunnel has been dug in lower cretaceous limestone which is characterized by a low clay content, high electrical resistivity which results in generally very low attenuation of electro-magnetic waves. 90% of the tunnels floor are made of concrete whereas other are made of bare limestone. This experimental site offers a unique opportunity of perfoming measurements within an unweathered limestone massif. The whole 3km long tunnel has been investigated using single offset shielded 250 MHz antennas in May 2009. Processing includes : DC and very low frequency removal, amplitude compensation preserving lateral variations, migration and time to depth conversion. When necessary predictive deconvolution has been applied to remove ringing effects. These data sets are characterized by good signal to noise ratio and a signal penetration down to 18 meters. These data allow us to accurately map the stratigraphy of the surrounding rocks across the concrete walls of the tunnel. Some 20 m deep vertical wells have been drilled inside the tunnel through observed reflectors. This is a strong validation of the GPR images. The estimated resolution is centimetric to decimetric and matches the required geologic accuracy. The GPR data set allows to extend previous geological results in depth, particularly in the concrete coated parts of the tunnel where conventional geological surveying is impossible. Thanks to the processing which preserves lateral amplitude variations, GPR sections exhibit prominent

  4. Characterizing phonatory aeroacoustic sources using Lagrangian Coherent Structures

    NASA Astrophysics Data System (ADS)

    McPhail, Michael; Krane, Michael

    2014-11-01

    Voice disorders that lead to changes in vocal fold geometry, or posturing, are known to substantially affect phonatory airflow topology. How these topology changes affect aeroacoustic sound sources is not well understood, however. This talk presents modelling aeroacoustic sources with Lagrangian Coherent Structures (LCS). Here we use the motion of dynamically distinct fluid regions, identified by the LCS, to predict sound. This approach provides a means to connect phonatory airflow topology changes to resulting changes in sound production. Simple validation cases of this approach will be shown. The application of LCS analysis to phonatory flows will be also presented.

  5. Nanosized Ni–Al layered double hydroxides—Structural characterization

    SciTech Connect

    Jitianu, Mihaela; Gunness, Darren C.; Aboagye, Doreen E.; Zaharescu, Maria; Jitianu, Andrei

    2013-05-15

    Highlights: ► The takovite anionic clays were obtained using the sol–gel method. ► The effect of samples’ composition on the structural and textural characteristics has been investigated. ► X-ray analysis. ► FTIR spectroscopy evidenced a disordered interlayer structure. ► FESEM and TEM analysis showed that the samples have high porosity. - Abstract: Takovite, a natural mineral with the formula Ni{sub 6}Al{sub 2}(OH){sub 6}CO{sub 3}·5H{sub 2}O belongs to the large class of layered double hydroxides (LDHs) and contains positively charged Ni(II) and Al(III) layers alternating with layers containing carbonate ions and water molecules. Mesoporous takovite-type layered double hydroxides (LDH) of the general formula [Ni{sub 1−x}Al{sub x}(OH){sub 2}]{sup x+}(CO{sub 3}{sup 2−}){sub x/2}·nH{sub 2}O with different Ni/Al molar ratios (1.9–2.8) have been successfully synthesized by the sol–gel method, followed by anionic exchange using nickel acetylacetonate and aluminum isopropylate as cation precursors. A single LDH phase and an anisotropic growth of very small crystallites (below 4 nm) have been evidenced by X-ray diffraction. The effect of samples’ composition on their structural and textural characteristics has been investigated. The BET surface area values are in the range of 100–122 m{sup 2}/g. BJH pore radius decreased with increase in the Al(III) content in the LDHs. FESEM micrographs show large aggregates of highly porous LDH particles, while TEM analysis reveals irregular agglomerates of crystallites, among which some of them displayed a developing hexagonal shape. The average particle size variation with the Al(III) content in the samples follows the same trend as the pore radius, the sample with the highest Ni/Al ratio displaying also the smallest particle size. This sample becomes even more interesting, since TEM analysis shows agglomerates with inside circular structures, feature not observed for the other Ni/Al ratios investigated.

  6. System and process for ultrasonic characterization of deformed structures

    DOEpatents

    Panetta, Paul D.; Morra, Marino; Johnson, Kenneth I.

    2011-11-22

    Generally speaking, the method of the present invention is performed by making various ultrasonic scans at preselected orientations along the length of a material being tested. Data from the scans are then plotted together with various calculated parameters that are calculated from this data. Lines or curves are then fitted to the respective plotted points. Review of these plotted curves allows the location and severity of defects within these sections to be determined and quantified. With this information various other decisions related to how, when or whether repair or replacement of a particular portion of a structure can be made.

  7. Electrical and Structural Characterization of Web Dendrite Crystals

    NASA Technical Reports Server (NTRS)

    Schwuttke, G. H.; Koliwad, K.; Dumas, K. A.

    1985-01-01

    Minority carrier lifetime distributions in silicon web dendrites are measured. Emphasis is placed on measuring areal homogeneity of lifetime, show its dependency on structural defects, and its unique change during hot processing. The internal gettering action of defect layers present in web crystals and their relation to minority carrier lifetime distributions is discussed. Minority carrier lifetime maps of web dendrites obtained before and after high temperature heat treatment are compared to similar maps obtained from 100 mm diameter Czochralski silicon wafers. Such maps indicate similar or superior areal homogeneity of minority carrier lifetime in webs.

  8. Purification, structural characterization, and modification of organosolv wheat straw lignin.

    PubMed

    Mbotchak, Laurie; Le Morvan, Clara; Duong, Khanh Linh; Rousseau, Brigitte; Tessier, Martine; Fradet, Alain

    2015-06-01

    Biolignin, a wheat straw lignin produced by acetic acid/formic acid/water hydrolysis, was characterized by (31)P and (13)C-(1)H 2D NMR spectroscopy and by size-exclusion chromatography. Biolignin is a mixture of low molar mass compounds (Mn = 1660 g/mol) made up of S, G, and H units and of coumaric and ferulic acid units. β-5 and β-O-4 interunit linkages are partially acylated in the γ-position by acetate and p-coumarate groups. Deacylated samples with a low content of contaminants were obtained by combining alkaline hydrolysis and solvent extraction. The high phenolic OH content found by (31)P NMR reflects the presence of condensed aromatic units, such as 5-5 units. Reaction of purified lignin with ethanol and ethane-1,2-diol yielded esterified lignins much more soluble than Biolignin in common organic solvents. During this reaction, the secondary OH of β-O-4 linkages was simultaneously etherified. Phenol hydroxyethylation by 2-chloroethanol yielded samples containing only aliphatic hydroxyl groups. PMID:25961961

  9. Structural characterization and electrochemical properties of novel salicylidene phosphonate derivatives

    NASA Astrophysics Data System (ADS)

    Dolaz, Mustafa; McKee, Vickie; Köse, Muhammet; Gölcü, Ayşegül; Tümer, Mehmet

    2010-09-01

    In this study, three novel salicylidene phosphonate ligands, diethyl (4-{[(1 E)-(2-hydroxyphenyl)methylidene]amino}benzyl)phosphonate (HL 1), diethyl (4-{[(1 E)-(2-hydroxy-3-methoxyphenyl)methylidene]amino}benzyl)phosphonate (HL 2) and diethyl (4-{[(1 E)-(2,4-dihydroxyphenyl)methylidene]amino}benzyl)phosphonate (HL 3) were synthesized and characterized by the analytical and spectroscopic techniques. We obtained their single crystals from the ethanolic solution. There are intramolecular phenol-imine hydrogen bonds in all three compounds between O1 and N1 atoms. The ligand HL 3 contains a second phenol group and this is makes an intermolecular hydrogen bond with the phosphine oxide of a neighbouring molecule O2-O3 (under symmetry operation - x, 0.5 + y, 0.5 - z). In order to investigate the redox behaviours of the salicylidene phosphonate ligands (HL 1-HL 3), we were studied electrochemical properties of the ligands at the different pH and scan rates.

  10. Synthesis, physicochemical, structural and rheological characterizations of carboxymethyl xanthan derivatives.

    PubMed

    Yahoum, Madiha M; Moulai-Mostefa, Nadji; Le Cerf, Didier

    2016-12-10

    The aim of this work was to synthesize a carboxymethylated xanthan (CMXG) via an etherification reaction between different ratios (2, 4, and 6) of xanthan gum (XG) and monochloroacetic acid (MCAA) using the Williamson synthesis method. The synthetized products were characterized in terms of their physico-chemical and rheological properties. Both FTIR and proton nuclear magnetic resonance (H(1) NMR) analyses confirmed the grafting of carboxymethyl groups on xanthan hydroxyl groups. The obtained results demonstrated that the degree of substitution was proportional to the chloroacetic acid and xanthan gum ratios. The obtained carboxymethyl derivatives presented greater hydrophilicity and lower molecular weights with increasing degrees of substitution than native xanthan gum. The rheological study revealed that the viscosity of the CMXG derivatives decreased with the degree of substitution and with the conservation of the shear-thinning and weak gel behaviours. The flow curves suggested the existence of two different populations of particles consisting of CMXG particles with a smaller average size and a second population formed by the residual fractions of native XG particles. It was also found that the elastic modulus of XG was largely higher than that of the CMXG derivatives and decreased with increasing DS. For the CMXG derivatives, two regions of viscoelastic behaviour were observed, which were separated by a crossover point corresponding to the critical frequency and relaxation time, i.e., the time required for stress relaxation. PMID:27577918

  11. Spectral characterization and crystal structure of tetrahydropyran-4-one thiosemicarbazones

    NASA Astrophysics Data System (ADS)

    Umamatheswari, S.; Jaya Pratha, J.; Kabilan, S.

    2011-03-01

    ( E)-1-(Tetrahydro-3-methyl-2,6-diphenylpyran-4-ylidene) thiosemicarbazide ( 3) and ( E)-1-(2,6- bis(4-chlorophenyl)-tetrahydro-3,5-dimethylpyran-4-ylidene) thiosemicarbazide ( 4) were obtained and characterized by FT-IR, 1H NMR, 13C NMR, NOESY spectroscopy and X-ray single-crystal diffraction analysis. Molecular orbital calculations have been carried out for 3 and 4 by using an ab initio method (HF) and also density functional method (B3LYP) at 6-31G basis set. Compound 4 crystallizes in the monoclinic system, space group P2 1/c, with a = 11.9645(3) Å, b = 20.0690(6) Å, c = 8.7441(2) Å, β = 105.5220(10)°, V = 2023.02(9) Å 3, and Z = 4. Compounds 3 and 4 exist in chair conformation with equatorial orientation of all the substituents at pyran ring except the methyl group at C-5 of compound 4 which is oriented at axial disposition to stabilise the chair conformation and the configuration about the C dbnd N double bond is syn to C-5 carbon ( E-form).

  12. Spectroscopic studies of anthracyclines: Structural characterization and in vitro tracking.

    PubMed

    Szafraniec, Ewelina; Majzner, Katarzyna; Farhane, Zeineb; Byrne, Hugh J; Lukawska, Malgorzata; Oszczapowicz, Irena; Chlopicki, Stefan; Baranska, Malgorzata

    2016-12-01

    A broad spectroscopic characterization, using ultraviolet-visible (UV-vis) and Fourier transform infrared absorption as well as Raman scattering, of two commonly used anthracyclines antibiotics (DOX) daunorubicin (DNR), their epimers (EDOX, EDNR) and ten selected analogs is presented. The paper serves as a comprehensive spectral library of UV-vis, IR and Raman spectra of anthracyclines in the solid state and in solution. The particular advantage of Raman spectroscopy for the measurement and analysis of individual antibiotics is demonstrated. Raman spectroscopy can be used to monitor the in vitro uptake and distribution of the drug in cells, using both 488nm and 785nm as source wavelengths, with submicrometer spatial resolution, although the cellular accumulation of the drug is different in each case. The high information content of Raman spectra allows studies of the drug-cell interactions, and so the method seems very suitable for monitoring drug uptake and mechanisms of interaction with cellular compartments at the subcellular level. PMID:27372511

  13. Characterizing the non-reducing end structure of heparan sulfate.

    PubMed

    Wu, Zhengliang L; Lech, Miroslaw

    2005-10-01

    The reducing end of heparan sulfate has been known for a long time, but information on the non-reducing end has been lacking. Recent studies indicate that the non-reducing end of heparan sulfate might be the place where fibroblast growth factor signaling complex forms. The non-reducing end also changes with heparanase digestion and, thus, might serve as a marker for tumor pathology. Using high performance liquid chromatography-coupled mass spectrometry, we have identified and characterized the non-reducing end of bovine kidney heparan sulfate. We find that the non-reducing end region is highly sulfated and starts with a glucuronic acid (GlcA) residue. The likely sequence of the non-reducing end hexasaccharides is GlcA-GlcNS6S-UA+/-2S-GlcNS+/-6S-Ido2S-GlcNS+/-6S (where GlcNS is N-sulfate-D-glucosamine, S is sulfate, UA is uronic acid, and Ido is iduronic acid). Our data suggests that the non-reducing end of bovine kidney heparan sulfate is not trimmed by heparanase and is capable of supporting fibroblast growth factor signaling complex formation. PMID:16079142

  14. Characterization of Nora Virus Structural Proteins via Western Blot Analysis

    PubMed Central

    Ericson, Brad L.; Carlson, Darby J.

    2016-01-01

    Nora virus is a single stranded RNA picorna-like virus with four open reading frames (ORFs). The coding potentials of the ORFs are not fully characterized, but ORF3 and ORF4 are believed to encode the capsid proteins (VP3, VP4a, VP4b, and VP4c) comprising the virion. To determine the polypeptide composition of Nora virus virions, polypeptides from purified virus were compared to polypeptides detected in Nora virus infected Drosophila melanogaster. Nora virus was purified from infected flies and used to challenge mice for the production of antisera. ORF3, ORF4a, ORF4b, and ORF4c were individually cloned and expressed in E. coli; resultant recombinant proteins purified and were used to make monospecific antisera. Antisera were evaluated via Western blot against whole virus particles and Nora virus infected fly lysates. Viral purification yielded two particle types with densities of ~1.31 g/mL (empty particles) and ~1.33 g/mL (complete virions). Comparison of purified virus polypeptide composition to Nora virus infected D. melanogaster lysate showed the number of proteins in infected cell lysates is less than purified virus. Our results suggest the virion is composed of 6 polypeptides, VP3, VP4a, two forms of VP4b, and two forms of VP4c. This polypeptide composition is similar to other small RNA insect viruses. PMID:27298753

  15. Characterization of Nora Virus Structural Proteins via Western Blot Analysis.

    PubMed

    Ericson, Brad L; Carlson, Darby J; Carlson, Kimberly A

    2016-01-01

    Nora virus is a single stranded RNA picorna-like virus with four open reading frames (ORFs). The coding potentials of the ORFs are not fully characterized, but ORF3 and ORF4 are believed to encode the capsid proteins (VP3, VP4a, VP4b, and VP4c) comprising the virion. To determine the polypeptide composition of Nora virus virions, polypeptides from purified virus were compared to polypeptides detected in Nora virus infected Drosophila melanogaster. Nora virus was purified from infected flies and used to challenge mice for the production of antisera. ORF3, ORF4a, ORF4b, and ORF4c were individually cloned and expressed in E. coli; resultant recombinant proteins purified and were used to make monospecific antisera. Antisera were evaluated via Western blot against whole virus particles and Nora virus infected fly lysates. Viral purification yielded two particle types with densities of ~1.31 g/mL (empty particles) and ~1.33 g/mL (complete virions). Comparison of purified virus polypeptide composition to Nora virus infected D. melanogaster lysate showed the number of proteins in infected cell lysates is less than purified virus. Our results suggest the virion is composed of 6 polypeptides, VP3, VP4a, two forms of VP4b, and two forms of VP4c. This polypeptide composition is similar to other small RNA insect viruses. PMID:27298753

  16. Synthesis and structural characterization of base-stabilized oligomeric heterovinylidenes.

    PubMed

    Leung, Wing-Por; Chiu, Wang-Kin; Mak, Thomas C W

    2013-08-19

    Metalation of the (iminophosphoranyl)phosphine PPh2CH2(PPh2═NSiMe3) (1) with an equimolar amount of n-BuLi afforded the monolithium salt [Li{CH(PPh2)(PPh2═NSiMe3)}(THF)2] (2). The reaction of 2 with GeCl2·1,4-dioxane has led to the formation of a germavinylene moiety, which trimerized to form a new heterocyclic cage compound, [{(PPh2═NSiMe3)(PPh2)C═Ge:}{(PPh2═NSiMe3)(PPh2)C}2Ge→Ge:] (3). A similar reaction of the lithium methanide complex 2 with SnCl2 afforded the stannavinylidene moiety, which underwent a "head-to-tail" cycloaddition to form a stable 1,3-distannacyclobutane, 4. A trapping reaction of 4 with diiron nonacarbonyl gave the novel iron stannavinylidene complex 5. The solid-state structure analysis of 5 reveals that it contains two stannavinylidene moieties bonded in a Sn-P "head-to-tail" fashion, with one of the tin(II) centers coordinating to a Fe(CO)4 moiety. The X-ray structures of 2-5 have been determined by X-ray crystallography. In addition, the dynamic behavior of 5 has been studied by means of variable-temperature (31)P and (119)Sn NMR spectroscopy. PMID:23924072

  17. Structural characterization of anti-inflammatory Immunoglobulin G Fc proteins

    PubMed Central

    Ahmed, Alysia A.; Giddens, John; Pincetic, Andrew; Lomino, Joseph V.; Ravetch, Jeffrey V.; Wang, Lai-Xi; Bjorkman, Pamela J.

    2014-01-01

    Immunoglobulin G (IgG) is a central mediator of host defense due to its ability to recognize and eliminate pathogens. The recognition and effector responses are encoded on distinct regions of IgGs. The diversity of the antigen recognition Fab domains accounts for IgG's ability to bind with high specificity to essentially any antigen. Recent studies have indicated that the Fc effector domain also displays considerable heterogeneity, accounting for its complex effector functions of inflammation, modulation and immune suppression. Therapeutic anti-tumor antibodies, for example, require the pro-inflammatory properties of the IgG Fc to eliminate tumor cells, while the anti-inflammatory activity of Intravenous Immunoglobulin G (IVIG) requires specific Fc glycans for activity. In particular, the anti-inflammatory activity of IVIG is ascribed to a small population of IgGs in which the Asn297-linked complex N-glycans attached to each Fc CH2 domain include terminal α2,6-linked sialic acids. We used chemoenzymatic glycoengineering to prepare fully di-sialylated IgG Fc and solved its crystal structure. Comparison of the structures of asialylated Fc, sialylated Fc, and F241A Fc, a mutant that displays increased glycan sialylation, suggests that increased conformational flexibility of the CH2 domain is associated with the switch from pro- to anti-inflammatory activity of the Fc. PMID:25036289

  18. Structural Characterization of Sodium Alginate and Calcium Alginate.

    PubMed

    Hecht, Hadas; Srebnik, Simcha

    2016-06-13

    Alginate readily aggregates and forms a physical gel in the presence of cations. The association of the chains, and ultimately gel structure and mechanics, depends not only on ion type, but also on the sequence and composition of the alginate chain that ultimately determines its stiffness. Chain flexibility is generally believed to decrease with guluronic residue content, but it is also known that both polymannuronate and polyguluronate blocks are stiffer than heteropolymeric blocks. In this work, we use atomistic molecular dynamics simulation to primarily explore the association and aggregate structure of different alginate chains under various Ca(2+) concentrations and for different alginate chain composition. We show that Ca(2+) ions in general facilitate chain aggregation and gelation. However, aggregation is predominantly affected by alginate monomer composition, which is found to correlate with chain stiffness under certain solution conditions. In general, greater fractions of mannuronic monomers are found to increase chain flexibility of heteropolymer chains. Furthermore, differences in chain guluronic acid content are shown to lead to different interchain association mechanisms, such as lateral association, zipper mechanism, and entanglement, where the mannuronic residues are shown to operate as an elasticity moderator and therefore promote chain association. PMID:27177209

  19. Structural characterization of the mitomycin 7-O-methyltransferase

    SciTech Connect

    Singh, Shanteri; Chang, Aram; Goff, Randal D.; Bingman, Craig A.; Grüschow, Sabine; Sherman, David H.; Phillips, Jr., George N.; Thorson, Jon S.

    2014-10-02

    Mitomycins are quinone-containing antibiotics, widely used as antitumor drugs in chemotherapy. Mitomycin-7-O-methyltransferase (MmcR), a key tailoring enzyme involved in the biosynthesis of mitomycin in Streptomyces lavendulae, catalyzes the 7-O-methylation of both C9{beta}- and C9{alpha}-configured 7-hydroxymitomycins. We have determined the crystal structures of the MmcR-S-adenosylhomocysteine (SAH) binary complex and MmcR-SAH-mitomycin A (MMA) ternary complex at resolutions of 1.9 and 2.3 {angstrom}, respectively. The study revealed MmcR to adopt a common S-adenosyl-L-methionine-dependent O-methyltransferase fold and the presence of a structurally conserved active site general acid-base pair is consistent with a proton-assisted methyltransfer common to most methyltransferases. Given the importance of C7 alkylation to modulate mitomycin redox potential, this study may also present a template toward the future engineering of catalysts to generate uniquely bioactive mitomycins.

  20. Pore structure characterization of catalyst supports via low field NMR

    SciTech Connect

    Smith, D.M.; Glaves, C.L.; Gallegos, D.P. )

    1988-09-01

    The pore structures of two types of catalyst support material were studied: {gamma}-alumina and silica aerogel. The alumina samples were commercial catalyst supports made in 1/8 inch diameter pellet form by Harshaw Chemical. Aerogels were prepared by forming a gel in a two-step, base-catalyzed process using TEOS, followed by supercritical drying to form the aerogel. Two different aerogels were made, one undergoing the drying process immediately after gel formation (non-aged), and the other being aged in the gel state for two weeks in a basic solution of 0.1 molar NH{sub 4}OH at 323 K before being supercritically dried (aged). The aging process is believed to alter the aerogel pore structure. The pore size distribution of the alumina material was determined via NMR and compared to results obtained by mercury intrusion and nitrogen adsorption/condensation techniques. The pore size distributions of the two aerogel samples were measured via NMR and nitrogen adsorption/condensation; the material was too compressible for porosimetry.

  1. Structural characterization of some sol-gel derived phosphosilicate glasses

    NASA Astrophysics Data System (ADS)

    Todan, L.; Anghel, E. M.; Osiceanu, P.; Turcu, R. V. F.; Atkinson, I.; Simon, S.; Zaharescu, M.

    2015-04-01

    A comparative study of three phosphosilicate gels of the 90SiO2-10P2O5 composition obtained from tetraethoxysilane and three phosphorous precursors: triethylphosphate (TEP), triethylphosphite (TEPI) and H3PO4 is performed. 29Si and 31P Magic Angle Spining NMR, X-ray Photoelectron, X-ray Fluorescence and Raman spectroscopies as well as TG analysis are used in order to establish phosphorous precursors and annealing influence on composition and structure of the outcome materials. Unlike the three dimensional silicate network made of Si(OSi)x(OH)4-x species, unreacted TEP (100% Q1 condensed phosphorous units) from TEP derived gel and a large amount of isolated phosphorous species (39.7% Q0) in the H3PO4 derived gel are identified. Annealing at 700 °C of the three gels give similar structure with the 90SiO2-10P2O5 glass, excepting the triethylphosphate derived glass that has a much lower P content. Thus, the H3PO4 derived glass at 700 and 1000 °C shows 1.89 and 1.94 times higher P2O5/SiO2 ratios than in the case of the TEP derived one.

  2. Isomerism of Cyanomethanimine: Accurate Structural, Energetic, and Spectroscopic Characterization.

    PubMed

    Puzzarini, Cristina

    2015-11-25

    The structures, relative stabilities, and rotational and vibrational parameters of the Z-C-, E-C-, and N-cyanomethanimine isomers have been evaluated using state-of-the-art quantum-chemical approaches. Equilibrium geometries have been calculated by means of a composite scheme based on coupled-cluster calculations that accounts for the extrapolation to the complete basis set limit and core-correlation effects. The latter approach is proved to provide molecular structures with an accuracy of 0.001-0.002 Å and 0.05-0.1° for bond lengths and angles, respectively. Systematically extrapolated ab initio energies, accounting for electron correlation through coupled-cluster theory, including up to single, double, triple, and quadruple excitations, and corrected for core-electron correlation and anharmonic zero-point vibrational energy, have been used to accurately determine relative energies and the Z-E isomerization barrier with an accuracy of about 1 kJ/mol. Vibrational and rotational spectroscopic parameters have been investigated by means of hybrid schemes that allow us to obtain rotational constants accurate to about a few megahertz and vibrational frequencies with a mean absolute error of ∼1%. Where available, for all properties considered, a very good agreement with experimental data has been observed. PMID:26529434

  3. Structure and Mixing Characterization of Variable Density Transverse Jet Flows

    NASA Astrophysics Data System (ADS)

    Gevorkyan, Levon

    This dissertation describes an experimental study of the structural and mixing characteristics of transverse jets, or jets in crossfiow (JICF). Hot-wire anemometry, stereo particle image velocimetry (PIV), and acetone planar laser-induced fiuorescence (PLIF) measurements were utilized to illuminate and quantify the wind-ward (upstream) jet shear layer instability characteristics and their relationship to the velocity field evolution, as well as the effect of the overall velocity field on the scalar field distribution and resulting mixing characteristics. Transverse jets of various jet-to-crossfiow momentum flux ratios in the range 41 ≥ J ≥ 2, and jet-to-crossfiow density ratios in the range 1.00 ≥ S ≥ 0.35, were generated using mixtures of helium and nitrogen in the jet fluid. Jets were injected from one of three different injectors explored: a convergent nozzle with circular geometry which was mounted flush with the wind tunnel floor, another convergent nozzle with circular geometry whose exit plane lies above the crossfiow boundary layer, and a flush-mounted straight pipe injector with a circular orifice. Jet Reynolds number was kept constant for the majority of the mixing and structural exploration experiments at Rej = 1900, except when the effect of Reynolds number on cross-sectional jet structure was explored. Previous hot-wire based measurements at UCLA suggest that the upstream jet shear layer transitions from convective instability to absolute instability, giving rise to self-excited nonlinear states, as either the momentum flux ratio is lowered below J ≈10, or the density ratio is lowered below S ≈ 0.45 for the JICF injected from the flush nozzle injector. A similar transition to absolute instability when lowering momentum flux ratio was found in this work for the flush-mounted pipe injector. Cross-sectional PLIF measurements in the present studies suggested clear correspondence between the formation of a symmetric counter-rotating vortex pair

  4. Materials and characterization using acoustic nonlinearity parameters and harmonic generation - Effects of crystalline and amorphous structures

    NASA Technical Reports Server (NTRS)

    Cantrell, John H.; Yost, William T.

    1990-01-01

    The effects of material structure on the nonlinearity parameters are reviewed. Problems discussed include definition of nonlinearity parameters, square-law nonlinearity and collinear beam-mixing, structure dependence of the nonlinearity parameters, negative nonlinearity parameters, and implications for materials characterization.

  5. Structure Characterization and Properties of K-Containing Copper Hexacyanoferrate

    DOE PAGESBeta

    Ojwang, Dickson O.; Grins, Jekabs; Wardecki, Dariusz; Valvo, Mario; Renman, Viktor; Häggström, Lennart; Ericsson, Tore; Gustafsson, Torbjörn; Mahmoud, Abdelfattah; Hermann, Raphaël P.; et al

    2016-06-03

    Copper hexacyanoferrate, CuII[FeIII(CN)6]2/3 nH2O, was synthesized, and varied amounts of K+ ions were inserted via reduction by K2S2O3 (aq). Ideally, the reaction can be written as CuII[FeIII(CN)6]2/3∙ nH2O + 2x/3K+ + 2x/3e⁻ ↔K2x/3CuII[FeIIxFeIII1- x(CN)6]2/3 nH2O. Infrared, Raman, and Mössbauer spectroscopy studies show that FeIII is continuously reduced to FeII with increasing x, accompanied by a decrease of the a-axis of the cubic Fmore » $$m\\bar{3}$$m unit cell. Elemental analysis of K by inductively coupled plasma shows that the insertion only begins when a significant fraction, ~20% of the FeIII, has already been reduced. Thermogravimetric analysis shows a fast exchange of water with ambient atmosphere and a total weight loss of ~26 wt % upon heating to 180 °C, above which the structure starts to decompose. The crystal structures of CuII[FeIII(CN)6]2/3∙ nH2O and K2/3Cu[Fe(CN)6]2/3∙ nH2O were refined using synchrotron X-ray powder diffraction data. In both, one-third of the Fe(CN)6 groups are vacant, and the octahedron around CuII is completed by water molecules. In the two structures, difference Fourier maps reveal three additional zeolitic water sites (8c, 32f, and 48g) in the center of the cavities formed by the Cu N C Fe framework. In conclusion, the K-containing compound shows an increased electron density at two of these sites (32f and 48g), indicating them to be the preferred positions for the K+ ions.« less

  6. Structure Characterization and Properties of K-Containing Copper Hexacyanoferrate.

    PubMed

    Ojwang, Dickson O; Grins, Jekabs; Wardecki, Dariusz; Valvo, Mario; Renman, Viktor; Häggström, Lennart; Ericsson, Tore; Gustafsson, Torbjörn; Mahmoud, Abdelfattah; Hermann, Raphaël P; Svensson, Gunnar

    2016-06-20

    Copper hexacyanoferrate, Cu(II)[Fe(III)(CN)6]2/3·nH2O, was synthesized, and varied amounts of K(+) ions were inserted via reduction by K2S2O3 (aq). Ideally, the reaction can be written as Cu(II)[Fe(III)(CN)6]2/3·nH2O + 2x/3K(+) + 2x/3e(-) ↔ K2x/3Cu(II)[Fe(II)xFe(III)1-x(CN)6]2/3·nH2O. Infrared, Raman, and Mössbauer spectroscopy studies show that Fe(III) is continuously reduced to Fe(II) with increasing x, accompanied by a decrease of the a-axis of the cubic Fm3̅m unit cell. Elemental analysis of K by inductively coupled plasma shows that the insertion only begins when a significant fraction, ∼20% of the Fe(III), has already been reduced. Thermogravimetric analysis shows a fast exchange of water with ambient atmosphere and a total weight loss of ∼26 wt % upon heating to 180 °C, above which the structure starts to decompose. The crystal structures of Cu(II)[Fe(III)(CN)6]2/3·nH2O and K2/3Cu[Fe(CN)6]2/3·nH2O were refined using synchrotron X-ray powder diffraction data. In both, one-third of the Fe(CN)6 groups are vacant, and the octahedron around Cu(II) is completed by water molecules. In the two structures, difference Fourier maps reveal three additional zeolitic water sites (8c, 32f, and 48g) in the center of the cavities formed by the -Cu-N-C-Fe- framework. The K-containing compound shows an increased electron density at two of these sites (32f and 48g), indicating them to be the preferred positions for the K(+) ions. PMID:27258790

  7. The synthesis and structural characterization of novel transition metal fluorides

    SciTech Connect

    Casteel, W.J. Jr.

    1992-09-01

    High purity KMF{sub 6} and K{sub 2}MF{sub 6} salts (M = Mo,Re, Ru, Os, Ir, Pt) are obtained from reduction hexafluorides. A rhombohedral unit cell is observed for KReF{sub 6}. Fluoride ion capture by Lewis acids from the hexafluorometallate (IV) salts affords high purity tetrafluorides for M = Mo, Re, Ru, Os, and Pd. The structure of RuF{sub 4} is determined from X-ray synchrotron and neutron powder data. Unit cells based on theorthorhombic PdF{sub 4} type cell are derived from X-ray powder data for ReF{sub 4} and OsF{sub 4}. Fluoride ion capture from KAgF{sub 4} provides the thermally unstable trifluoride as a bright, red, diamagnetic solid. The structure solution of AgF{sub 3} and redetermination of the AuF{sub 3} structure from X-ray synchrotron and neutron powder data demonstrate that the two are isostnictural. Thermal decomposition product of AgF{sub 3} is the mixed valence compound Ag{sup II}Ag{sub 2}{sup III}F{sub 8}. Several new salts containing the (Ag - F){sub n}{sup n+} chain cation are prepared. The first linear (Ag - F){sub n}{sup n+} chain is observed in AgF{sup +}BF{sub 4 {sup {minus}}} which crystallizes in a tetragonal unit. AgFAuF{sub 4} has a triclinic unit cell and is isostructural with CuFAuF{sub 4}. AgFAuF{sub 6} has an orthorhombic unit cell and appears to be isostructural with AgFAsF{sub 6}. A second mixed valence silver fluoride, Ag{sup II}Ag{sup III}F{sub 5}, is prepared, which magnetic measurements indicate is probably an AgF{sup +} salt. Magnetic data for all of the AgF{sup +} salts exhibit low magnitude, temperature independent paramagnetism characteristic of metallic systems. Cationic AG(II) in acidic AHF solutions is a powerful oxidizer, capable of oxidizing Xe to Xe(II) and O{sub 2} to O{sub 2}{sup +}. Reactions with C{sub 6}F{sub 6} and C{sub 3}F{sub 6} suggest an electron capture mechanism for cationic AG(II) oxidations.

  8. The characterization of widespread fatigue damage in fuselage structure

    NASA Technical Reports Server (NTRS)

    Piascik, Robert S.; Willard, Scott A.; Miller, Matthew

    1994-01-01

    The characteristics of widespread fatigue damage (WSFD) in fuselage riveted structure were established by detailed nondestructive and destructive examinations of fatigue damage contained in a full size fuselage test article. The objectives of this were to establish an experimental data base for validating emerging WSFD analytical prediction methodology and to identify first order effects that contribute to fatigue crack initiation and growth. Detailed examinations were performed on a test panel containing four bays of a riveted lap splice joint. The panel was removed from a full scale fuselage test article after receiving 60,000 full pressurization cycles. The results of in situ examinations document the progression of fuselage skin fatigue crack growth through crack linkup. Detailed tear down examinations and fractography of the lap splice joint region revealed fatigue crack initiation sites, crack morphology, and crack linkup geometry. From this large data base, distributions of crack size and locations are presented and discussions of operative damage mechanisms are offered.

  9. Structure and Functional Characterization of Vibrio parahaemolyticus Thermostable Direct Hemolysin*

    PubMed Central

    Yanagihara, Itaru; Nakahira, Kumiko; Yamane, Tsutomu; Kaieda, Shuji; Mayanagi, Kouta; Hamada, Daizo; Fukui, Takashi; Ohnishi, Kiyouhisa; Kajiyama, Shin'ichiro; Shimizu, Toshiyuki; Sato, Mamoru; Ikegami, Takahisa; Ikeguchi, Mitsunori; Honda, Takeshi; Hashimoto, Hiroshi

    2010-01-01

    Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic foodborne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 Å resolution. The TDH tetramer forms a central pore with dimensions of 23 Å in diameter and ∼50 Å in depth. π-Cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside of the pore. Molecular dynamic simulations suggested that water molecules permeate freely through the central and side channel pores. Electron micrographs showed that tetrameric TDH attached to liposomes, and some of the tetramer associated with liposome via one protomer. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin. PMID:20335168

  10. Structural characterization of Mumps virus fusion protein core

    SciTech Connect

    Liu Yueyong; Xu Yanhui; Lou Zhiyong; Zhu Jieqing; Hu Xuebo; Gao, George F.; Qiu Bingsheng . E-mail: Qiubs@sun.im.ac.cn; Rao Zihe . E-mail: raozh@xtal.tsinghua.edu.cn; Tien, Po . E-mail: tienpo@sun.im.ac.cn

    2006-09-29

    The fusion proteins of enveloped viruses mediating the fusion between the viral and cellular membranes comprise two discontinuous heptad repeat (HR) domains located at the ectodomain of the enveloped glycoproteins. The crystal structure of the fusion protein core of Mumps virus (MuV) was determined at 2.2 A resolution. The complex is a six-helix bundle in which three HR1 peptides form a central highly hydrophobic coiled-coil and three HR2 peptides pack against the hydrophobic grooves on the surface of central coiled-coil in an oblique antiparallel manner. Fusion core of MuV, like those of simian virus 5 and human respiratory syncytium virus, forms typical 3-4-4-4-3 spacing. The similar charecterization in HR1 regions, as well as the existence of O-X-O motif in extended regions of HR2 helix, suggests a basic rule for the formation of the fusion core of viral fusion proteins.

  11. Genetic structure characterization of Chileans reflects historical immigration patterns.

    PubMed

    Eyheramendy, Susana; Martinez, Felipe I; Manevy, Federico; Vial, Cecilia; Repetto, Gabriela M

    2015-01-01

    Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography. PMID:25778948

  12. Performance characterization of structured light-based fingerprint scanner

    NASA Astrophysics Data System (ADS)

    Hassebrook, Laurence G.; Wang, Minghao; Daley, Raymond C.

    2013-05-01

    Our group believes that the evolution of fingerprint capture technology is in transition to include 3-D non-contact fingerprint capture. More specifically we believe that systems based on structured light illumination provide the highest level of depth measurement accuracy. However, for these new technologies to be fully accepted by the biometric community, they must be compliant with federal standards of performance. At present these standards do not exist for this new biometric technology. We propose and define a set of test procedures to be used to verify compliance with the Federal Bureau of Investigation's image quality specification for Personal Identity Verification single fingerprint capture devices. The proposed test procedures include: geometric accuracy, lateral resolution based on intensity or depth, gray level uniformity and flattened fingerprint image quality. Several 2-D contact analogies, performance tradeoffs and optimization dilemmas are evaluated and proposed solutions are presented.

  13. Features and characterization needs of rubber composite structures

    NASA Technical Reports Server (NTRS)

    Tabaddor, Farhad

    1989-01-01

    Some of the major unique features of rubber composite structures are outlined. The features covered are those related to the material properties, but the analytical features are also briefly discussed. It is essential to recognize these features at the planning stage of any long-range analytical, experimental, or application program. The development of a general and comprehensive program which fully accounts for all the important characteristics of tires, under all the relevant modes of operation, may present a prohibitively expensive and impractical task at the near future. There is therefore a need to develop application methodologies which can utilize the less general models, beyond their theoretical limitations and yet with reasonable reliability, by proper mix of analytical, experimental, and testing activities.

  14. Genetic structure characterization of Chileans reflects historical immigration patterns

    PubMed Central

    Eyheramendy, Susana; Martinez, Felipe I.; Manevy, Federico; Vial, Cecilia; Repetto, Gabriela M.

    2015-01-01

    Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography. PMID:25778948

  15. Biosynthesis and structural characterization of silver nanoparticles from bacterial isolates

    SciTech Connect

    Zaki, Sahar; El Kady, M.F.; Abd-El-Haleem, Desouky

    2011-10-15

    Graphical abstract: In this study five bacterial isolates belong to different genera were found to be able to biosynthesize silver nanoparticles. Biosynthesis and spectral characterization are reported here. Highlights: {yields} About 300 bacterial isolates were screened for their ability to produce nanosilvers {yields} Five of them were potential candidates for synthesis of silver nanoparticles {yields} Production of silver nanoparticles was examined using UV-Vis, XRD, SEM and EDS. {yields} The presence of nanoparticles with all five bacterial isolates was confirmed. -- Abstract: This study aimed to develop a green process for biosynthesis of silver nanomaterials by some Egyptian bacterial isolates. This target was achieved by screening an in-house culture collection consists of 300 bacterial isolates for silver nanoparticle formation. Through screening process, it was observed that strains belonging to Escherichia coli (S30, S78), Bacillus megaterium (S52), Acinetobacter sp. (S7) and Stenotrophomonas maltophilia (S54) were potential candidates for synthesis of silver nanoparticles. The extracellular production of silver nanoparticles by positive isolates was investigated by UV-Vis spectroscopy, X-ray diffraction (XRD), transmission electron microscope (TEM), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The results demonstrated that UV-visible spectrum of the aqueous medium containing silver ion showed a peak at 420 nm corresponding to the plasmon absorbance of silver nanoparticles. Scanning electron microscopy micrograph showed formation of silver nanoparticles in the range of 15-50 nm. XRD-spectrum of the silver nanoparticles exhibited 2{theta} values corresponding to the silver nanocrystal that produce in hexagonal and cubic crystal configurations with different plane of orientation. In addition, the signals of the silver atoms were observed by EDS-spectrum analysis that confirms the presence of silver nanoparticles (Ag

  16. Synthesis and Characterization of Elastomeric Heptablock Terpolymers Structured by Crystallization

    SciTech Connect

    Alfonzo, C.Guillermo; Fleury, Guillaume; Chaffin, Kimberly A.; Bates, Frank S.

    2010-12-07

    We report the synthesis and characterization of fully saturated hydrocarbon block copolymer thermoplastic elastomers with competitive mechanical properties and attractive processing features. Block copolymers containing glassy poly(cyclohexylethylene) (C), elastomeric poly(ethylene-alt-propylene) (P), and semicrystalline poly(ethylene) (E) were produced in a CEC-P-CEC heptablock architecture, denoted XPX, by anionic polymerization and catalytic hydrogenation. The X blocks contain equal volume fractions of C and E, totaling 40%-60% of the material overall. All the XPX polymers are disordered above the melt temperature for E (T{sub m,E} {approx_equal} 95 C) as evidenced by SAXS and dynamic mechanical spectroscopy measurements. Cooling below T{sub m,E} results in crystallization of the E blocks, which induces microphase segregation of E, C, and P into a complex morphology with a continuous rubbery domain and randomly arranged hard domains as shown by TEM. This mechanism of segregation decouples the processing temperature from the XPX molecular weight up to a limiting value. Tensile mechanical testing (simple extension and cyclic loading) demonstrates that the tensile strength (ca. 30 MPa) and strain at break (>500%) are comparable to the behavior of CPC triblock thermoplastic elastomers of similar molecular weight and glass content. However, in the CPC materials, processability is constrained by the order-disorder transition temperature, limiting the applications of these materials. Elastic recovery of the XPX materials following seven cycles of tensile deformation is correlated with the fraction of X in the heptablock copolymer, and the residual strain approaches that of CPC when the fraction of hard blocks f{sub X} {le} 0.39.

  17. Structural characterization of human general transcription factor TFIIF in solution

    PubMed Central

    Akashi, Satoko; Nagakura, Shinjiro; Yamamoto, Seiji; Okuda, Masahiko; Ohkuma, Yoshiaki; Nishimura, Yoshifumi

    2008-01-01

    Human general transcription factor IIF (TFIIF), a component of the transcription pre-initiation complex (PIC) associated with RNA polymerase II (Pol II), was characterized by size-exclusion chromatography (SEC), electrospray ionization mass spectrometry (ESI-MS), and chemical cross-linking. Recombinant TFIIF, composed of an equimolar ratio of α and β subunits, was bacterially expressed, purified to homogeneity, and found to have a transcription activity similar to a natural one in the human in vitro transcription system. SEC of purified TFIIF, as previously reported, suggested that this protein has a size >200 kDa. In contrast, ESI-MS of the purified sample gave a molecular size of 87 kDa, indicating that TFIIF is an αβ heterodimer, which was confirmed by matrix-assisted laser desorption/ionization (MALDI) MS of the cross-linked TFIIF components. Recent electron microscopy (EM) and photo-cross-linking studies showed that the yeast TFIIF homolog containing Tfg1 and Tfg2, corresponding to the human α and β subunits, exists as a heterodimer in the PIC, so the human TFIIF is also likely to exist as a heterodimer even in the PIC. In the yeast PIC, EM and photo-cross-linking studies showed different results for the mutual location of TFIIE and TFIIF along DNA. We have examined the direct interaction between human TFIIF and TFIIE by ESI-MS, SEC, and chemical cross-linking; however, no direct interaction was observed, at least in solution. This is consistent with the previous photo-cross-linking observation that TFIIF and TFIIE flank DNA separately on both sides of the Pol II central cleft in the yeast PIC. PMID:18218714

  18. Hierarchical manufacture and characterization of multifunctional nanocomposite structures

    NASA Astrophysics Data System (ADS)

    Veedu, Vinod P. V.

    The objective of this work is to develop multifunctional 3-D nanocomposite structures in an attempt to solve the shortcomings of the traditional composite materials. To achieve this goal, at first a detailed analysis of the properties of the basic nano reinforcement, carbon nanotube, was performed in terms of mechanical behavior, thermoelastic responses and thermal conductivity using an analytical technique, namely, asymptotic homogenization method. In our initial experimental works, different polymer resins were reinforced with nanotubes as well as nanoparticles and their mechanical performances were investigated. These experiments reveal that at higher weight percentage loading of the nanoparticles and nanotubes there are dominant issues such as alignment and dispersion, which would weaken the material. This led us to seek a novel approach to nanocomposites. In this report, two multifunctional nanocomposite structures are introduced: nanotube based brushes and hierarchical 3-D nanocomposite. The nanotube brushes were fabricated using chemical vapor deposition. Functions performed by these brushes such as mechanical and chemical cleaning, painting and electrical contacts will be discussed. Also, we unveil a novel approach to the 3-D composite challenge, without altering the existing 2-D stack design, based on the concept of interlaminar carbon nanotube forests that would provide enhanced multifunctional properties in the thickness direction. The nanotube coated fabric cloths serve as building blocks for the multi-layered 3-D composites with the nanotubes forests providing much needed interlaminar strength and toughness under various loading conditions. For the fabricated 3-D composites with nanotube forests, we demonstrate remarkable improvements in the interlaminar fracture toughness, delamination resistance, in-plane mechanical properties, damping, thermoelastic behavior, and thermal and electrical conductivities providing truly three-dimensional multifunctional

  19. Production and characterization of carbon structures derived from wood

    NASA Astrophysics Data System (ADS)

    Xie, Xinfeng

    The objective of this research was to produce structural carbon materials from wood, a renewable biomaterial, for advanced material application. A broad range of materials were produced for study including carbonized wood, resin infused carbon composites made from carbonized wood, and carbon nanotubes from wood fibers. The effect of slow heating on the properties of carbonized wood was studied and important carbonized wood properties were found to be produced over a range of heating rates and peak temperatures. Slow heating rates promoted the formation and growth of graphene sheets in turbostratic crystallites, which had a significant influence on the electrical resistivity and Young's modulus of the carbonized wood. A reduction in the rate of heating may be beneficial with respect to carbon properties and the prevention of crack production during the manufacture of large monolithic carbon specimens from wood and wood-based materials. Investigation of selected physical and mechanical properties of resin-infused porous carbon composites made from medium density fiberboard demonstrated that the infused material can be used in specific applications, where high mechanical strength is not required but high dimensional stability at elevated-use temperatures, fire safety, or static dissipation and shielding is required. A unique cyclic heating process has been developed to produce carbon nanotubes directly from wood fibers. Study on the oxidative behavior of carbons derived from cellulose and lignin showed that cellulose carbon ablates faster at a lower temperature in air than lignin carbon when they were prepared at temperatures lower than 500°C due to cellulose carbon's lower content of aromatic structures. It is hypothesized that the formation of carbon nanotubes during the cyclic heating process occurred via template synthesis, with the nanochannels formed from the ablation of cellulose fibrils functioning as a template. Evidence of formation of nanochannels has been

  20. Mechanical characterization and structural assessment of biocomposites for construction

    NASA Astrophysics Data System (ADS)

    Christian, Sarah Jane

    The objective of this dissertation is to assess whether or not two particular biocomposite materials, made from hemp fabric and cellulose acetate or polyhydroxybutyrate matrices, are capable of being used for structural and/or construction purposes within in the construction and building industry. The objective of this dissertation was addressed by conducting research to meet the following three goals: (1) to measure the basic mechanical properties of hemp/cellulose acetate and hemp/PHB biocomposites and evaluate if they suitable for use in construction applications, (2) to determine how quickly moisture diffuses into the biocomposite materials and how the moisture affects the mechanical behavior, and (3) to determine how well simple models can predict behavior of structural scale laminates in tension and flexure using biocomposite ply behavior. Compression molding was used to manufacturing the biocomposites from hemp fabric and the themoplastic matrices: cellulose acetate and polyhydroxybutyrate. Four methods for determining the fiber volume fraction were evaluated, and the dissolution method, using different solvents for each matrix type, was used to determine the fiber volume fraction for each composite plate manufactured. Both types of biocomposite were tested in tension, compression, shear, and flexure and the measured properties were compared to wood and engineered wood products to assess whether the biocomposite properties are suitable for use in the construction industry. The biocomposites were conditioned in a humid environment to determine the rate of moisture diffusion into the materials. Then saturated specimens and specimens that were saturated and then dried were tested in tension to evaluate how moisture absorption affects the mechanical behavior of the biocomposites. Finally, simple models of laminate behavior based on laminate plate theory were evaluated to determine if ply level behavior could be used to predict structural scale laminate behavior

  1. Characterization and estimation of permeability correlation structure from performance data

    SciTech Connect

    Ershaghi, I.; Al-Qahtani, M.

    1997-08-01

    In this study, the influence of permeability structure and correlation length on the system effective permeability and recovery factors of 2-D cross-sectional reservoir models, under waterflood, is investigated. Reservoirs with identical statistical representation of permeability attributes are shown to exhibit different system effective permeability and production characteristics which can be expressed by a mean and variance. The mean and variance are shown to be significantly influenced by the correlation length. Detailed quantification of the influence of horizontal and vertical correlation lengths for different permeability distributions is presented. The effect of capillary pressure, P{sub c1} on the production characteristics and saturation profiles at different correlation lengths is also investigated. It is observed that neglecting P{sub c} causes considerable error at large horizontal and short vertical correlation lengths. The effect of using constant as opposed to variable relative permeability attributes is also investigated at different correlation lengths. Next we studied the influence of correlation anisotropy in 2-D reservoir models. For a reservoir under five-spot waterflood pattern, it is shown that the ratios of breakthrough times and recovery factors of the wells in each direction of correlation are greatly influenced by the degree of anisotropy. In fully developed fields, performance data can aid in the recognition of reservoir anisotropy. Finally, a procedure for estimating the spatial correlation length from performance data is presented. Both the production performance data and the system`s effective permeability are required in estimating the correlation length.

  2. Design and characterization of structured protein linkers with differing flexibilities

    PubMed Central

    Klein, Joshua S.; Jiang, Siduo; Galimidi, Rachel P.; Keeffe, Jennifer R.; Bjorkman, Pamela J.

    2014-01-01

    Engineered fusion proteins containing two or more functional polypeptides joined by a peptide or protein linker are important for many fields of biological research. The separation distance between functional units can impact epitope access and the ability to bind with avidity; thus the availability of a variety of linkers with different lengths and degrees of rigidity would be valuable for protein design efforts. Here, we report a series of designed structured protein linkers incorporating naturally occurring protein domains and compare their properties to commonly used Gly4Ser repeat linkers. When incorporated into the hinge region of an immunoglobulin G (IgG) molecule, flexible Gly4Ser repeats did not result in detectable extensions of the IgG antigen-binding domains, in contrast to linkers including more rigid domains such as β2-microglobulin, Zn-α2-glycoprotein and tetratricopeptide repeats. This study adds an additional set of linkers with varying lengths and rigidities to the available linker repertoire, which may be useful for the construction of antibodies with enhanced binding properties or other fusion proteins. PMID:25301959

  3. Multiaxial nonlinear viscoelastic characterization and modeling of a structural adhesive

    SciTech Connect

    Popelar, C.F.; Liechti, K.M.

    1997-07-01

    Many polymeric materials, including structural adhesives, exhibit a nonlinear viscoelastic response. The nonlinear free volume approach is based on the Doolittle concept that the free volume controls the mobility of polymer molecules and, thus, the inherent time scale of the material. It then follows that factors such as temperature and moisture, which change the free volume, will influence the time scale. Furthermore, stress-induced dilatation will also affect the free volume and, hence, the time scale. However, during this investigation dilatational effects alone were found to be insufficient in describing the response of near pure shear tests performed on a bisphenol A epoxy with an amido amine hardener. Thus, the free volume approach presented here has been modified to include distortional effects in the inherent time scale of the material. In addition to predicting the global response under a variety of multiaxial stress states, the modified free volume theory also accurately predicts the local displacement fields, including those associated with a localized region, as determined from geometric moire measurements at various stages of deformation.

  4. Structural and functional characterization of paramecium dynein: initial studies.

    PubMed

    Larsen, J; Barkalow, K; Hamasaki, T; Satir, P

    1991-01-01

    Dynein arms and isolated dynein from Paramecium tetraurelia ciliary axonemes are comparable in structure, direction of force generation, and microtubule translocation ability to other dyneins. In situ arms have dimensions and substructure similar to those of Tetrahymena. Based on spoke arrangement in intact axonemes, arms translocate axonemal microtubules in sliding such that active dynein arms are (-) end directed motors and the doublet to which the body and cape of the arms binds (N) translocates the adjacent doublet (N + 1) tipward. After salt extraction, based on ATPase activity, paramecium dynein is found as a 22S and a 14S species. The 22S dynein is a three-headed molecule that has unfolded from the in situ dimensions; the 14S dynein is single headed. Both dyneins can be photocleaved by UV light (350 nm) in the presence of Mg2+, ATP and vanadate; the photocleavage pattern of 22S dynein differs from that seen with Tetrahymena. Both isolated dyneins translocate taxol-stabilized, bovine brain microtubules in vitro. Under standard conditions, 22S dynein, like comparable dyneins from other organisms, translocates at velocities that are about three times faster than 14S dynein. PMID:1825507

  5. Characterization of Ion Dynamics in Structures for Lossless Ion Manipulations

    SciTech Connect

    Tolmachev, Aleksey V.; Webb, Ian K.; Ibrahim, Yehia M.; Garimella, Venkata BS; Zhang, Xinyu; Anderson, Gordon A.; Smith, Richard D.

    2014-08-23

    Structures for Lossless Ion Manipulation (SLIM) represent a novel class of ion optical devices based upon electrodes patterned on planar surfaces, and relying on a combined action of radio frequency and DC electric fields and specific buffer gas density conditions. Initial experimental studies have demonstrated the feasibility of the SLIM concept. This report offers an in-depth consideration of key ion dynamics properties in such devices based upon ion optics theory and computational modeling. The SLIM devices investigated are formed by two surfaces, each having an array of radio frequency (RF) "rung" electrodes, bordered by DC "guard" electrodes. Ion motion is confined by the RF effective potential in the direction orthogonal to the boards, and limited or controlled in the transversal direction by the guard DC potentials. Ions can be efficiently trapped and stored in SLIM devices where the confinement of ions can be ‘soft’ in regard to the extent of collisional activation, similarly to RF-only multipole ion guides and traps. The segmentation of the RF rung electrodes and guards along the axis makes it possible to apply electric field profiles to stimulate ion transfer within a SLIM. In the case of a linear DC gradient applied to RF rungs and guards, a virtually uniform electric field can be created along the axis of the device, enabling ion mobility separations.

  6. Characterization of Ion Dynamics in Structures for Lossless Ion Manipulations

    PubMed Central

    2015-01-01

    Structures for Lossless Ion Manipulation (SLIM) represent a novel class of ion optical devices based upon electrodes patterned on planar surfaces, and relying on a combined action of radiofrequency and DC electric fields and specific buffer gas density conditions. Initial experimental studies have demonstrated the feasibility of the SLIM concept. This report offers an in-depth consideration of key ion dynamics properties in such devices based upon ion optics theory and computational modeling. The SLIM devices investigated are formed by two surfaces, each having an array of radiofrequency (RF) “rung” electrodes, bordered by DC “guard” electrodes. Ion motion is confined by the RF effective potential in the direction orthogonal to the boards and limited or controlled in the transversal direction by the guard DC potentials. Ions can be efficiently trapped and stored in SLIM devices where the confinement of ions can be “soft” in regard to the extent of collisional activation, similarly to RF-only multipole ion guides and traps. The segmentation of the RF rung electrodes and guards along the axis makes it possible to apply static or transient electric field profiles to stimulate ion transfer within a SLIM. In the case of a linear DC gradient applied to RF rungs and guards, a virtually uniform electric field can be created along the axis of the device, enabling high quality ion mobility separations. PMID:25152178

  7. Characterizing Facesheet/Core Disbonding in Honeycomb Core Sandwich Structure

    NASA Technical Reports Server (NTRS)

    Rinker, Martin; Ratcliffe, James G.; Adams, Daniel O.; Krueger, Ronald

    2013-01-01

    Results are presented from an experimental investigation into facesheet core disbonding in carbon fiber reinforced plastic/Nomex honeycomb sandwich structures using a Single Cantilever Beam test. Specimens with three, six and twelve-ply facesheets were tested. Specimens with different honeycomb cores consisting of four different cell sizes were also tested, in addition to specimens with three different widths. Three different data reduction methods were employed for computing apparent fracture toughness values from the test data, namely an area method, a compliance calibration technique and a modified beam theory method. The compliance calibration and modified beam theory approaches yielded comparable apparent fracture toughness values, which were generally lower than those computed using the area method. Disbonding in the three-ply facesheet specimens took place at the facesheet/core interface and yielded the lowest apparent fracture toughness values. Disbonding in the six and twelve-ply facesheet specimens took place within the core, near to the facesheet/core interface. Specimen width was not found to have a significant effect on apparent fracture toughness. The amount of scatter in the apparent fracture toughness data was found to increase with honeycomb core cell size.

  8. Structural and functional characterization of human NAD kinase.

    PubMed

    Lerner, F; Niere, M; Ludwig, A; Ziegler, M

    2001-10-19

    NADP is essential for biosynthetic pathways, energy, and signal transduction. Its synthesis is catalyzed by NAD kinase. Very little is known about the structure, function, and regulation of this enzyme from multicellular organisms. We identified a human NAD kinase cDNA and the corresponding gene using available database information. A cDNA was amplified from a human fibroblast cDNA library and functionally overexpressed in Escherichia coli. The obtained cDNA, slightly different from that deposited in the database, encodes a protein of 49 kDa. The gene is expressed in most human tissues, but not in skeletal muscle. Human NAD kinase differs considerably from that of prokaryotes by subunit molecular mass (49 kDa vs 30-35 kDa). The catalytically active homotetramer is highly selective for its substrates, NAD and ATP. It did not phosphorylate the nicotinic acid derivative of NAD (NAAD) suggesting that the potent calcium-mobilizing pyridine nucleotide NAADP is synthesized by an alternative route. PMID:11594753

  9. Structural characterization of particle systems using spherical harmonics

    SciTech Connect

    Feinauer, Julian; Spettl, Aaron; Manke, Ingo; Strege, Stefan; Kwade, Arno; Pott, Andres; Schmidt, Volker

    2015-08-15

    Many important properties of particulate materials are heavily influenced by the size and shape of the constituent particles. Thus, in order to control and improve product quality, it is important to develop a good understanding of the shape and size of the particles that make up a given particulate material. In this paper, we show how the spherical harmonics expansion can be used to approximate particles obtained from tomographic 3D images. This yields an analytic representation of the particles which can be used to calculate structural characteristics. We present an estimation method for the optimal length of expansion depending on individual particle shapes, based on statistical hypothesis testing. A suitable choice of this parameter leads to a smooth approximation that preserves the main shape features of the original particle. To show the wide applicability of this procedure, we use it to approximate particles obtained from two different tomographic 3D datasets of particulate materials. The first one describes an anode material from lithium-ion cells that consists of sphere-like particles with different sizes. The second dataset describes a powder of highly non-spherical titanium dioxide particles. - Highlights: • Complex particle shapes are described analytically by spherical harmonics expansion. • The optimal length of the expansion is estimated for each particle individually. • Characteristics like, e.g., particle surface areas can be calculated efficiently. • The method is applied to two tomographic datasets of particulate materials.

  10. Valuation of brewers spent yeast polysaccharides: a structural characterization approach.

    PubMed

    Pinto, Mariana; Coelho, Elisabete; Nunes, Alexandra; Brandão, Tiago; Coimbra, Manuel A

    2015-02-13

    Brewers spent yeast (BSY) is a by-product from beer industry that can be exploited as source of glucans and mannoproteins, with potential biological activities. In order to solubilize these carbohydrate-rich polymeric materials, a sequential extraction with hot water and alkaline solutions (0.1-8 M KOH) was performed. Mannoproteins were mainly (85%) extracted with 4 M KOH whereas glucans were extracted with 8 M KOH and in an amount that accounted only for 34% of total glucose. Final residue still accounted for 34% of the initial glucans and contained 98% of glucose. Cellulase and α-amylase treatments showed the presence of both α- and β-(1→4)-Glc linkages. To promote total solubilization of these insoluble glucans, the final residue was submitted to a partial acid hydrolysis. This work is the first report showing that the most abundant polysaccharides in BSY are polymers that contain structural features similar to cellulose, thus justifying their resistance to alkaline extractions, acid hydrolysis, and insolubility in water. PMID:25458292

  11. Structural and Biochemical Characterization of Mycobacterium tuberculosis CYP142

    PubMed Central

    Driscoll, Max D.; McLean, Kirsty J.; Levy, Colin; Mast, Natalia; Pikuleva, Irina A.; Lafite, Pierre; Rigby, Stephen E. J.; Leys, David; Munro, Andrew W.

    2010-01-01

    The Mycobacterium tuberculosis cytochrome P450 enzyme CYP142 is encoded in a large gene cluster involved in metabolism of host cholesterol. CYP142 was expressed and purified as a soluble, low spin P450 hemoprotein. CYP142 binds tightly to cholesterol and its oxidized derivative cholest-4-en-3-one, with extensive shift of the heme iron to the high spin state. High affinity for azole antibiotics was demonstrated, highlighting their therapeutic potential. CYP142 catalyzes either 27-hydroxylation of cholesterol/cholest-4-en-3-one or generates 5-cholestenoic acid/cholest-4-en-3-one-27-oic acid from these substrates by successive sterol oxidations, with the catalytic outcome dependent on the redox partner system used. The CYP142 crystal structure was solved to 1.6 Å, revealing a similar active site organization to the cholesterol-metabolizing M. tuberculosis CYP125, but having a near-identical organization of distal pocket residues to the branched fatty acid oxidizing M. tuberculosis CYP124. The cholesterol oxidizing activity of CYP142 provides an explanation for previous findings that ΔCYP125 strains of Mycobacterium bovis and M. bovis BCG cannot grow on cholesterol, because these strains have a defective CYP142 gene. CYP142 is revealed as a cholesterol 27-oxidase with likely roles in host response modulation and cholesterol metabolism. PMID:20889498

  12. Electronic structure characterization and bandgap engineeringofsolar hydrogen materials

    SciTech Connect

    Guo, Jinghua

    2007-11-01

    Bandgap, band edge positions as well as the overall band structure of semiconductors are of crucial importance in photoelectrochemical and photocatalytic applications. The energy position of the band edge level can be controlled by the electronegativity of the dopants, the pH of the solution (flatband potential variation of 60 mV per pH unit), as well as by quantum confinement effects. Accordingly, band edges and bandgap can be tailored to achieve specific electronic, optical or photocatalytic properties. Synchrotron radiation with photon energy at or below 1 keV is giving new insight into such areas as condensed matter physics and extreme ultraviolet optics technology. In the soft x-ray region, the question tends to be, what are the electrons doing as they migrated between the atoms. In this paper, I will present a number of soft x-ray spectroscopic study of nanostructured 3d metal compounds Fe{sub 2}O{sub 3} and ZnO.

  13. Structural and Electrochemical Characterization of Lithium Transition Metal Phosphates

    NASA Astrophysics Data System (ADS)

    Hashambhoy, Ayesha Maria

    The lithium ion battery has emerged as one of the most promising hybrid vehicle energy storage systems of the future. Of the potential cathode chemistries explored, lithium transition metal phosphates have generated a significant amount of interest due to their low-cost precursors, potential ease of synthesis, stability, and their environmentally friendly nature. This is in contrast to layered oxide systems such as LiCoO2, which have long been considered state of the art, but are now being reevaluated due to their structural instability at elevated temperatures, and higher cost. In particular, LiFePO4 has an operating potential comparable to those batteries available on the market (˜3.5V vs. Li/Li+), and higher theoretical specific capacity (170mAh/g vs. that of LiCoO2 which is 140mAh/g). The manganese analog to LiFePO4, LiMnPO4, exhibits a higher operating potential (˜4.1V v Li/Li+), and the same theoretical capacity, however Li-ion diffusion through this structure is much more rate limited and its theoretical capacity cannot be realized at rates suitable for commercial applications. The purpose of this work was threefold: 1) To explore the impact of Fe substitution on Mn sites in LiMnPO 4. 2) To examine the effects of alterations to the particle/electrolyte interface on rate capability. 3) To explore a novel fabrication route for LiMnPO4 using microwaves, and determine an optimal power and time combination for best performance. The coexistence of Fe and Mn on the transition metal site M, of LiMPO 4 resulted in an improved apparent Li-ion diffusivity in both Fe and Mn regimes as compared to that observed for LiFePO4 and LiMnPO 4 respectively. Calculations made from two different analysis methods, cyclic voltammetry (CV) and galvanostatic intermittent titration (GITT) drew this same conclusion. The signature characteristics observed from the CVs pertaining to single and dual phase reactions led to a delithiation model of LiFe0.5Mn0.5PO4 proposing the localization

  14. Morphological, Mechanical and Structural Characterization of Damselfly Wing

    NASA Astrophysics Data System (ADS)

    Talucdher, ABSM Rupan Ali

    The damselfly belongs to the same insect family as the dragonfly that inspired the development of Micro Air Vehicles (MAVs). Understanding the morphological, mechanical and structural properties of wings, veins and membranes of fly would provide guidelines to develop efficient MAVs. Lack of test methodologies inhibited the progress. The objective of this research was to develop the above methodologies and then measure the properties of veins, membranes and wings of damselflies. The research yielded four test methodologies: fluorescence spectroscopic analysis to map the morphology of vein; axial nanoindentation test to measure indentation properties; micro tension test to measure tensile properties of microscopic components; and a unique vibration test of wings to measure natural frequency, stiffness and air damping factor. Axial indentation test contrasts the transverse indentation used in the past, whose results were corrupted by surface roughness and flexibility of veins. Veins were found to be made of two layered, elliptical tubular members. The thickness of inner and outer layers was about 8 and 5 microm, respectively and corresponding indentation moduli were 8.42 and 16.00 GPa. The modulus of veins agreed with those of human bones. The tensile modulus and strength of veins ranged from 14 to 17 GPa and 232 to 285 MPa, respectively. The damselfly wing was found to vibrate under bending and torsional deformations, the natural frequency (in air) ranged from 130 to 178 Hz, the wing stiffness ranged from 0.18 to 0.30 N/m with the air damping ratio from 0.67 to 0.79. Pathway to develop a material of matching properties is also presented.

  15. An automatic form error evaluation method for characterizing micro-structured surfaces

    NASA Astrophysics Data System (ADS)

    Yu, D. P.; Zhong, X.; Wong, Y. S.; Hong, G. S.; Lu, W. F.; Cheng, H. L.

    2011-01-01

    Ultra-precision micro-structured surfaces are becoming increasingly important in a range of application areas, including engineering optics, biological products, metrology artifacts, data storage, etc. However, there is a lack of surface characterization methods for the micro-structured surfaces with sub-nanometer accuracy. Although some research studies have been conducted on 3D surface characterization, most of them are on freeform surfaces, which are difficult to be applied on the micro-structured surfaces because of their limited characterization accuracy and the repeated surface feature patterns in the micro-structured surfaces. In this paper, an automatic form error evaluation method (AFEEM) is presented to characterize the form accuracy of the micro-structured surfaces. The machined micro-structured surface can be measured by any 3D high resolution measurement instrument. The measurement data are converted and pre-processed for the AFEEM, which mainly consists of a coarse registration and a fine registration process. The coarse registration estimates an initial position of the measured surface for the fine registration by extracting the most perceptually salient points in the surfaces, computing the integral volume descriptor for each salient point, searching for the best triplet-point correspondence and calculating the coarse registration matrix. The fine registration aligns the measured surface to the designed surface by a proposed adaptive iterative closest point algorithm to guarantee sub-nanometer accuracy for surface characterization. A series of computer simulations and experimental studies were conducted to verify the AFEEM. Results demonstrate the accuracy and effectiveness of the AFEEM for characterizing the micro-structured surfaces.

  16. Posttraumatic Stress Disorder: Structural Characterization with 3-T MR Imaging.

    PubMed

    Li, Shiguang; Huang, Xiaoqi; Li, Lingjiang; Du, Fei; Li, Jing; Bi, Feng; Lui, Su; Turner, Jessica A; Sweeney, John A; Gong, Qiyong

    2016-08-01

    Purpose To explore cerebral alterations related to the emergence of posttraumatic stress disorder (PTSD) by using three-dimensional T1-weighted imaging and also to explore the relationship of gray and white matter abnormalities and the anatomic changes with clinical severity and duration of time since the trauma. Materials and Methods Informed consent was provided, and the prospective study was approved by the ethics committee of the West China Hospital. Recruited were 67 patients with PTSD and 78 adult survivors without PTSD 7-15 months after a devastating earthquake in western China. All participants underwent magnetic resonance (MR) imaging with a 3-T imager to obtain anatomic images. Cortical thickness and volumes of 14 subcortical gray matter structures and five subregions of the corpus callosum were analyzed with software. Statistical differences between patients with PTSD and healthy survivors were evaluated with a general linear model. Averaged data from the regions with volumetric or cortical thickness differences between groups were extracted in each individual to examine correlations between morphometric measures and clinical profiles. Results Patients with PTSD showed greater cortical thickness in the right superior temporal gyrus, inferior parietal lobule, and left precuneus (P < .05; Monte Carlo null-z simulation corrected) and showed reduced volume in the posterior portion of the corpus callosum (F = 6.167; P = .014) compared with healthy survivors of the earthquake. PTSD severity was positively correlated with cortical thickness in the left precuneus (r = 0.332; P = .008). The volumes of posterior corpus callosum were negatively correlated with PTSD ratings in all survivors (r = -0.210; P = .013) and with cortical thickness of the left precuneus in patients with PTSD (r = -0.302; P = .017). Conclusion Results indicate that patients with PTSD had alterations in both cerebral gray matter and white matter compared with individuals who experienced

  17. Analysis and characterizations of planar transmission structures and components for superconducting and monolithic integrated circuits

    NASA Technical Reports Server (NTRS)

    Itoh, Tatsuo

    1992-01-01

    The research effort was continued to design and characterize superconducting transmission line structures. The research during this period was concentrated on the implementation of a superconductor into coplanar waveguide structures. First, the superconducting coplanar waveguide was examined, and compared with a superconducting microstrip line in terms of loss characteristics and their design aspects. Then, the research was carried on the design and characterization of the coplanar waveguide family in the packaging environment. The transition between the coaxial line to the conductor backed coplanar waveguide was also designed for the measurement of the superconducting conductor backed coplanar waveguide.

  18. Structural and Magnetic Characterization of the ``Gaspar'' Meteorite from Betéitiva, Boyacá, Colombia

    NASA Astrophysics Data System (ADS)

    Flor, L. M.; Pérez, G. A.

    2013-09-01

    In this work we reported the structural and magnetic characterization of the “Gaspar” meteorite from Beteitiva, Boyacá, Colombia. The meteorite was characterized by XRD, Mössbauer spectrometry and scanning electron microscopy.

  19. Identification and Structural Characterization of an Intermediate in the Folding of the Measles Virus X Domain.

    PubMed

    Bonetti, Daniela; Camilloni, Carlo; Visconti, Lorenzo; Longhi, Sonia; Brunori, Maurizio; Vendruscolo, Michele; Gianni, Stefano

    2016-05-13

    Although most proteins fold by populating intermediates, the transient nature of such states makes it difficult to characterize their structures. In this work we identified and characterized the structure of an intermediate of the X domain of phosphoprotein (P) of measles virus. We obtained this result by a combination of equilibrium and kinetic measurements and NMR chemical shifts used as structural restraints in replica-averaged metadynamics simulations. The structure of the intermediate was then validated by rationally designing four mutational variants predicted to affect the stability of this state. These results provide a detailed view of an intermediate state and illustrate the opportunities offered by a synergistic use of experimental and computational methods to describe non-native states at atomic resolution. PMID:27002146

  20. Electrochemical characterization of p(+)n and n(+)p diffused InP structures

    NASA Technical Reports Server (NTRS)

    Wilt, David M.; Faur, Maria; Faur, Mircea; Goradia, M.; Vargas-Aburto, Carlos

    1993-01-01

    The relatively well documented and widely used electrolytes for characterization and processing of Si and GaAs-related materials and structures by electrochemical methods are of little or no use with InP because the electrolytes presently used either dissolve the surface preferentially at the defect areas or form residual oxides and introduce a large density of surface states. Using an electrolyte which was newly developed for anodic dissolution of InP, and was named the 'FAP' electrolyte, accurate characterization of InP related structures including nature and density of surface states, defect density, and net majority carrier concentration, all as functions of depth was performed. A step-by-step optimization of n(+)p and p(+)n InP structures made by thermal diffusion was done using the electrochemical techniques, and resulted in high performance homojunction InP structures.

  1. Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus

    PubMed Central

    Duong-ly, Krisna C.; Schoeffield, Andrew J.; Pizarro-Dupuy, Mario A.; Zarr, Melissa; Pineiro, Silvia A.; Amzel, L. Mario; Gabelli, Sandra B.

    2015-01-01

    Given the broad range of substrates hydrolyzed by Nudix (nucleoside diphosphate linked to X) enzymes, identification of sequence and structural elements that correctly predict a Nudix substrate or characterize a family is key to correctly annotate the myriad of Nudix enzymes. Here, we present the structure determination and characterization of Bd3179 –- a Nudix hydrolase from Bdellovibrio bacteriovorus–that we show localized in the periplasmic space of this obligate Gram-negative predator. We demonstrate that the enzyme is a nucleoside diphosphate sugar hydrolase (NDPSase) and has a high degree of sequence and structural similarity to a canonical ADP-ribose hydrolase and to a nucleoside diphosphate sugar hydrolase (1.4 and 1.3 Å Cα RMSD respectively). Examination of the structural elements conserved in both types of enzymes confirms that an aspartate-X-lysine motif on the C-terminal helix of the α-β-α NDPSase fold differentiates NDPSases from ADPRases. PMID:26524597

  2. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.

    PubMed

    Watters, Kyle E; Abbott, Timothy R; Lucks, Julius B

    2016-01-29

    Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure-function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA-RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA-RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell. PMID:26350218

  3. μ-COMPUTED Tomography for Micro-Structure Characterization of Carbon Fiber Reinforced Plastic (cfrp)

    NASA Astrophysics Data System (ADS)

    Stoessel, R.; Guenther, T.; Dierig, T.; Schladitz, K.; Godehardt, M.; Kessling, P.-M.; Fuchs, T.

    2011-06-01

    Non-destructive testing is of major importance for quality assurance of carbon fiber reinforced plastic (CFRP) in aerospace industry. It is of interest to obtain information of the 3D inner micro-structure of CFRP. A promising option is the usage of μ-CT inspection. State-of-the art software tools are used to characterize the 3D inner micro-structure and to gather knowledge about porosity, cracks, and fiber orientation.

  4. First structurally characterized mixed-halogen nickel(III) NCN-pincer complex

    NASA Astrophysics Data System (ADS)

    Kozhanov, Konstantin A.; Bubnov, Michael P.; Cherkasov, Vladimir K.; Fukin, Georgy K.; Vavilina, Nina N.; Efremova, Larisa Yu.; Abakumov, Gleb A.

    2009-03-01

    A square-pyramidal mixed-halogen nickel(III) NCN-pincer complex (PipeNCN)NiClBr (where PipeNCN = 2,6-bis(piperidinomethyl)phenyl) was structurally characterized. Bromine occupies apical position; pincer ligand and chlorine atom are in the basal plane. EPR detects that complex in solution exists as a mixture of two structural isomers with bromine or chlorine atoms in the top of pyramid.

  5. Characterization of small thermal structures in RFX-mod electron temperature profiles

    NASA Astrophysics Data System (ADS)

    Fassina, A.; Gobbin, M.; Spagnolo, S.; Franz, P.; Terranova, D.

    2016-05-01

    In the RFX-mod reverse field pinch (RFP) experiment, electron temperature profiles often feature structures and fluctuations at fine scale. The present work aims at characterizing their occurrence and their localization, in particular by linking them to underlying tearing modes magnetic islands. The confinement characteristics are discussed, identifying analogies with respect to high scale T e structures. Finally, high frequency magnetic activity (i.e. microtearing instabilities) is confirmed to be closely correlated to the presence and proximity of temperature gradients.

  6. X-ray diffraction characterization of suspended structures forMEMS applications

    SciTech Connect

    Goudeau, P.; Tamura, N.; Lavelle, B.; Rigo, S.; Masri, T.; Bosseboeuf, A.; Sarnet, T.; Petit, J.-A.; Desmarres, J.-M.

    2005-09-15

    Mechanical stress control is becoming one of the major challenges for the future of micro and nanotechnologies. Micro scanning X-ray diffraction is one of the promising techniques that allows stress characterization in such complex structures at sub micron scales. Two types of MEMS structure have been studied: a bilayer cantilever composed of a gold film deposited on poly-silicon and a boron doped silicon bridge. X-ray diffraction results are discussed in view of numerical simulation experiments.

  7. Using the Structure-Function Linkage Database to Characterize Functional Domains in Enzymes

    PubMed Central

    Brown, Shoshana; Babbitt, Patricia

    2015-01-01

    The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a web-accessible database designed to link enzyme sequence, structure and functional information. This unit describes the protocol by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. It is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases. PMID:25501940

  8. Characterization of pore structure of polymer blended films used for controlled drug release.

    PubMed

    Häbel, Henrike; Andersson, Helene; Olsson, Anna; Olsson, Eva; Larsson, Anette; Särkkä, Aila

    2016-01-28

    The characterization of the pore structure in pharmaceutical coatings is crucial for understanding and controlling mass transport properties and function in controlled drug release. Since the drug release rate can be associated with the film permeability, the effect of the pore structure on the permeability is important to study. In this paper, a new approach for characterizing the pore structure in polymer blended films was developed based on an image processing procedure for given two-dimensional scanning electron microscopy images of film cross-sections. The focus was on different measures for characterizing the complexity of the shape of a pore. The pore characterization developed was applied to ethyl cellulose (EC) and hydroxypropyl cellulose (HPC) blended films, often used as pharmaceutical coatings, where HPC acts as the pore former. It was studied how two different HPC viscosity grades influence the pore structure and, hence, mass transport through the respective films. The film with higher HPC viscosity grade had been observed to be more permeable than the other in a previous study; however, experiments had failed to show a difference between their pore structures. By instead characterizing the pore structures using tools from image analysis, statistically significant differences in pore area fraction and pore shape were identified. More specifically, it was found that the more permeable film with higher HPC viscosity grade seemed to have more extended and complex pore shapes than the film with lower HPC viscosity grade. This result indicates a greater degree of connectivity in the film with higher permeability and statistically confirms hypotheses on permeability from related experimental studies. PMID:26686080

  9. Mass Spectrometry Combinations for Structural Characterization of Sulfated-Steroid Metabolites

    NASA Astrophysics Data System (ADS)

    Yan, Yuetian; Rempel, Don L.; Holy, Timothy E.; Gross, Michael L.

    2014-05-01

    Steroid conjugates, which often occur as metabolites, are challenging to characterize. One application is female-mouse urine, where steroid conjugates serve as important ligands for the pheromone-sensing neurons. Although the two with the highest abundance in mouse urine were previously characterized with mass spectrometry (MS) and NMR to be sulfated steroids, many more exist but remain structurally unresolved. Given that their physical and chemical properties are similar, they are likely to have a sulfated steroid ring structure. Because these compounds occur in trace amounts in mouse urine and elsewhere, their characterization by NMR will be difficult. Thus, MS methods become the primary approach for determining structure. Here, we show that a combination of MS tools is effective for determining the structures of sulfated steroids. Using 4-pregnene analogs, we explored high-resolving power MS (HR-MS) to determine chemical formulae; HD exchange MS (HDX-MS) to determine number of active, exchangeable hydrogens (e.g., OH groups); methoxyamine hydrochloride (MOX) derivatization MS, or reactive desorption electrospray ionization with hydroxylamine to determine the number of carbonyl groups; and tandem MS (MSn), high-resolution tandem MS (HRMS/MS), and GC-MS to obtain structural details of the steroid ring. From the fragmentation studies, we deduced three major fragmentation rules for this class of sulfated steroids. We also show that a combined MS approach is effective for determining structure of steroid metabolites, with important implications for targeted metabolomics in general and for the study of mouse social communication in particular.

  10. 2D and 3D reconstruction and geomechanical characterization of kilometre-scale complex folded structures

    NASA Astrophysics Data System (ADS)

    Zanchi, Andrea; Agliardi, Federico; Crosta, Giovanni B.; Villa, Alberto; Bistacchi, Andrea; Iudica, Gaetano

    2015-04-01

    The geometrical, structural and geomechanical characterization of large-scale folded structures in sedimentary rocks is an important issue for different geological and geo-hazard applications (e.g. hydrocarbon and geothermal reservoir exploitation, natural rock slope stability, mining, and tunnelling). Fold geometry controls topography and the spatial distribution of rock types with different strength and permeability. Fold-related fracture systems condition the fracture intensity, degree of freedom, and overall strength of rock masses. Nevertheless, scale issues and limited accessibility or partial exposure of structures often hamper a complete characterization of these complex structures. During the last years, advances in remote survey techniques as terrestrial Lidar (TLS) allowed significant improvements in the geometrical and geological characterization of large or inaccessible outcrops. However, sound methods relating structures to rock mass geomechanical properties are yet to be developed. Here we present results obtained by integrating remote survey and field assessment techniques to characterize a folded sedimentary succession exposed in unreachable vertical rock walls. The study area is located in the frontal part of the Southern Alps near Bergamo, Italy. We analysed large-scale detachment folds developed in the Upper Triassic sedimentary cover in the Zu Limestone. Folds are parallel and disharmonic, with regular wavelengths and amplitudes of about 200-250 m. We used a Riegl VZ-1000 long-range laser scanner to obtain points clouds with nominal spacings between 5 cm and 20 cm from 9 scan positions characterized by range between 350 m and 1300 m. We fixed shadowing and occlusion effects related to fold structure exposure by filling point clouds with data collected by terrestrial digital photogrammetry (TDP). In addition, we carried out field surveys of fold-related brittle structures and their geomechanical attributes at key locations. We classified cloud

  11. Concept Definition Study for In-Space Structural Characterization of a Lightweight Solar Array

    NASA Technical Reports Server (NTRS)

    Woods-Vedeler, Jessica A.; Pappa, Richard S.; Jones, Thomas W.; Spellman, Regina; Scott, Willis; Mockensturm, Eric M.; Liddle, Donn; Oshel, Ed; Snyder, Michael

    2002-01-01

    A Concept Definition Study (CDS) was conducted to develop a proposed "Lightweight High-Voltage Stretched-Lens Concentrator Solar Array Experiment" under NASA's New Millennium Program Space Technology-6 (NMP ST-6) activity. As part of a multi-organizational team, NASA Langley Research Center's role in this proposed experiment was to lead Structural Characterization of the solar array during the flight experiment. In support of this role, NASA LaRC participated in the CDS to de.ne an experiment for static, dynamic, and deployment characterization of the array. In this study, NASA LaRC traded state-of-the-art measurement approaches appropriate for an in-space, STS-based flight experiment, provided initial analysis and testing of the lightweight solar array and lens elements, performed a lighting and photogrammetric simulation in conjunction with JSC, and produced an experiment concept definition to meet structural characterization requirements.

  12. Structural characterization and IgE epitope analysis of arginine kinase from Scylla paramamosain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Arginine kinase (AK) has been reported as the pan-allergen of shellfish, however, there is limited information about its IgE epitopes and structural characteristics. In this study, AK from Scylla paramamosain was purified and characterized. The purified AK was a glycoprotein with the molecular weigh...

  13. Mechanical, biological and structural characterization of human atherosclerotic femoral plaque tissue.

    PubMed

    Cunnane, E M; Mulvihill, J J E; Barrett, H E; Healy, D A; Kavanagh, E G; Walsh, S R; Walsh, M T

    2015-01-01

    The failure of endovascular treatments of peripheral arterial disease represents a critical clinical issue. Specialized data are required to tailor such procedures to account for the mechanical response of the diseased femoral arterial tissue to medical device deployment. The purpose of this study is to characterize the mechanical response of atherosclerotic femoral arterial tissue to large deformation, the conditions typical of angioplasty and stenting, and also to determine the mechanically induced failure properties and to relate this behaviour to biological content and structural composition using uniaxial testing, Fourier transform infrared spectroscopy and scanning electron microscopy. Mechanical and biological characterization of 20 plaque samples obtained from femoral endarterectomy identified three distinct classifications. "Lightly calcified" samples display linear mechanical responses and fail at relatively high stretch. "Moderately calcified" samples undergo an increase in stiffness and ultimate strength coupled with a decrease in ductility. Structural characterization reveals calcified nodules within this group that may be acting to reinforce the tissue matrix, thus increasing the stiffness and ultimate strength. "Heavily calcified" samples account for the majority of samples tested and exhibit significantly reduced ultimate strength and ductility compared to the preceding groups. Structural characterization of this group reveals large areas of calcified tissue dominating the failure cross-sections of the samples. The frequency and structural dominance of these features solely within this group offers an explanation as to the reduced ultimate strength and ductility and highlights the need for modern peripheral endovascular devices to account for this behaviour during novel medical device design. PMID:25242646

  14. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq

    PubMed Central

    Watters, Kyle E.; Abbott, Timothy R.; Lucks, Julius B.

    2016-01-01

    Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure–function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA–RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA–RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell. PMID:26350218

  15. Characterization of the geometry of microscale periodic structures using acoustic microscopy.

    PubMed

    Shaw, Anurupa; Liu, Jingfei; Yoon, Suk Wang; Declercq, Nico F

    2016-08-01

    Periodic structures are very common in both scientific investigations and engineering applications. The geometry of the periodic structure is important for its designed functionality. Although the techniques such as optical and electron microscopy are capable of measuring the periodicity of microscale periodically-corrugated structures, they cannot be used to measure the height or depth of the corrugation. The technique of acoustic microscopy has been developed rapidly and it has been applied in the studies of steel integrated structures, ferro-elastic ceramics, human retina, semiconductors, composites, etc. In acoustic microscopy, V(z) curves have been used to investigate the visco-elastic parameters of thin sliced samples of composites, animal tissue, etc., while in this work it is applied in characterizing the geometry of periodically corrugated structures. The measurements of the geometry of periodic structures obtained using acoustic microscopy are compared with those obtained using optical microscopy, and the reliability of this acoustic technique is also examined. PMID:27259118

  16. Structural and electronic characterization of self-assembled molecular nanoarchitectures by X-ray photoelectron spectroscopy.

    PubMed

    Gulino, Antonino

    2013-02-01

    Molecular monolayers and similar nanoarchitectures are indicative of the promising future of nanotechnology. Therefore, many scientists recently devoted their efforts to the synthesis, characterization, and properties of mono- and multilayer-based systems. In this context, X-ray photoelectron spectroscopy is an important technique for the in-depth chemical and structural characterization of nanoscopic systems. In fact, it is a surface technique suitable for probing thicknesses of the same order of the photoelectron inelastic mean free paths (a few tens of ångströms) and allows one to immediately obtain qualitative and quantitative data, film thickness, surface coverage, molecule footprint, oxidation states, and presence of functional groups. Nevertheless, other techniques are important in obtaining a complete spectroscopic characterization of the investigated systems. Therefore, in the present review we report on X-ray photoelectron spectroscopy of self-assembled molecular mono- and multilayer materials including some examples on which other characterization techniques produced important results. PMID:23014858

  17. Electrical network method for the thermal or structural characterization of a conducting material sample or structure

    DOEpatents

    Ortiz, M.G.

    1993-06-08

    A method for modeling a conducting material sample or structure system, as an electrical network of resistances in which each resistance of the network is representative of a specific physical region of the system. The method encompasses measuring a resistance between two external leads and using this measurement in a series of equations describing the network to solve for the network resistances for a specified region and temperature. A calibration system is then developed using the calculated resistances at specified temperatures. This allows for the translation of the calculated resistances to a region temperature. The method can also be used to detect and quantify structural defects in the system.

  18. Electrical network method for the thermal or structural characterization of a conducting material sample or structure

    DOEpatents

    Ortiz, Marco G.

    1993-01-01

    A method for modeling a conducting material sample or structure system, as an electrical network of resistances in which each resistance of the network is representative of a specific physical region of the system. The method encompasses measuring a resistance between two external leads and using this measurement in a series of equations describing the network to solve for the network resistances for a specified region and temperature. A calibration system is then developed using the calculated resistances at specified temperatures. This allows for the translation of the calculated resistances to a region temperature. The method can also be used to detect and quantify structural defects in the system.

  19. Optoelectronic characterization of carrier extraction in a hot carrier photovoltaic cell structure

    NASA Astrophysics Data System (ADS)

    Dimmock, James A. R.; Kauer, Matthias; Smith, Katherine; Liu, Huiyun; Stavrinou, Paul N.; Ekins-Daukes, Nicholas J.

    2016-07-01

    A hot carrier photovoltaic cell requires extraction of electrons on a timescale faster than they can lose energy to the lattice. We optically and optoelectronically characterize two resonant tunneling structures, showing their compatability with hot carrier photovoltaic operation, demonstrating structural and carrier extraction properties necessary for such a device. In particular we use time resolved and temperature dependent photoluminescence to determine extraction timescales and energy levels in the structures and demonstrate fast carrier extraction by tunneling. We also show that such devices are capable of extracting photo-generated electrons at high carrier densities, with an open circuit voltage in excess of 1 V.

  20. Fabrication and Structure Characterization of Alumina-Aluminum Interpenetrating Phase Composites

    NASA Astrophysics Data System (ADS)

    Dolata, Anna J.

    2016-01-01

    Alumina-Aluminum composites with interpenetrating networks structure belong to advanced materials with potentially better properties when compared with composites reinforced by particles or fibers. The paper presents the experimental results of fabrication and structure characterization of Al matrix composites locally reinforced via Al2O3 ceramic foam. The composites were obtained using centrifugal infiltration of porous ceramics by liquid aluminum alloy. Both scanning electron microscopy (SEM + EDS) and x-ray tomography were used to determine the structure of foams and composites especially in reinforced areas. The quality of castings, degree of pore filling in ceramic foams by Al alloy, and microstructure in area of interface were assessed.

  1. Scanning tunneling microscopy characterization of the geometric and electronic structure of hydrogen-terminated silicon surfaces

    NASA Technical Reports Server (NTRS)

    Kaiser, W. J.; Bell, L. D.; Hecht, M. H.; Grunthaner, F. J.

    1988-01-01

    Scanning tunneling microscopy (STM) methods are used to characterize hydrogen-terminated Si surfaces prepared by a novel method. The surface preparation method is used to expose the Si-SiO2 interface. STM images directly reveal the topographic structure of the Si-SiO2 interface. The dependence of interface topography on oxide preparation conditions observed by STM is compared to the results of conventional surface characterization methods. Also, the electronic structure of the hydrogen-terminated surface is studied by STM spectroscopy. The near-ideal electronic structure of this surface enables direct tunnel spectroscopy measurements of Schottky barrier phenomena. In addition, this method enables probing of semiconductor subsurface properties by STM.

  2. Solid state NMR: The essential technology for helical membrane protein structural characterization

    PubMed Central

    Cross, Timothy A.; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

    2014-01-01

    NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed – neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins. PMID:24412099

  3. Solid state NMR: The essential technology for helical membrane protein structural characterization

    NASA Astrophysics Data System (ADS)

    Cross, Timothy A.; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

    2014-02-01

    NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins.

  4. Solid state NMR: The essential technology for helical membrane protein structural characterization.

    PubMed

    Cross, Timothy A; Ekanayake, Vindana; Paulino, Joana; Wright, Anna

    2014-02-01

    NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins. PMID:24412099

  5. Identification, characterization and evolution of non-local quasi-Lagrangian structures in turbulence

    NASA Astrophysics Data System (ADS)

    Yang, Yue

    2016-02-01

    The recent progress on non-local Lagrangian and quasi-Lagrangian structures in turbulence is reviewed. The quasi-Lagrangian structures, e.g., vortex surfaces in viscous flow, gas-liquid interfaces in multi-phase flow, and flame fronts in premixed combustion, can show essential Lagrangian following properties, but they are able to have topological changes in the temporal evolution. In addition, they can represent or influence the turbulent flow field. The challenges for the investigation of the non-local structures include their identification, characterization, and evolution. The improving understanding of the quasi-Lagrangian structures is expected to be helpful to elucidate crucial dynamics and develop structure-based predictive models in turbulence.

  6. Theoretical Characterization of the Minimum-Energy Structure of (SF6)2.

    PubMed

    Vazhappilly, Tijo; Marjolin, Aude; Jordan, Kenneth D

    2016-03-01

    MP2 and symmetry-adapted perturbation theory calculations are used in conjunction with the aug-cc-pVQZ basis set to characterize the SF6 dimer. Both theoretical methods predict the global minimum structure to be of C2 symmetry, lying 0.07-0.16 kJ/mol below a C2h saddle point structure, which, in turn, is predicted to lie energetically 0.4-0.5 kJ/mol below the lowest-energy D2d structure. This is in contrast with IR spectroscopic studies that infer an equilibrium D2d structure. It is proposed that the inclusion of vibrational zero-point motion gives an averaged structure of D2d symmetry. PMID:26619257

  7. Synthesis and characterization of high temperature curable poly(arylene ether) structural adhesive and composite matrices

    SciTech Connect

    Mecham, S.J.; Jayaraman, S.; Bobbitt, M.M.

    1996-12-31

    Crosslinked poly(arylene ether) systems are projected to display many desirable properties suitable for aerospace structural adhesive and composite matrix applications. The synthesis and characterization of a series of processable high temperature curing poly(arylene ether) oligomers incorporating terminally reactive phenylethynyl endgroups will be discussed. Characterization of the oligomers includes NMR, intrinsic viscosity, parallel plate rheological behavior, TGA, and DSC. Curing of these oligomers was conducted at or above 380{degrees}C, providing a large processing window. Thermal stability is very good and the melt viscosity of the oligomers in the processing temperature range is exceptionally low.

  8. Test method development for structural characterization of fiber composites at high temperatures

    NASA Technical Reports Server (NTRS)

    Mandell, J. F.; Grande, D. H.; Edwards, B.

    1985-01-01

    Test methods used for structural characterization of polymer matrix composites can be applied to glass and ceramic matrix composites only at low temperatures. New test methods are required for tensile, compressive, and shear properties of fiber composites at high temperatures. A tensile test which should be useful to at least 1000 C has been developed and used to characterize the properties of a Nicalon/glass composite up to the matrix limiting temperature of 600 C. Longitudinal and transverse unidirectional composite data are presented and discussed.

  9. Structural and Biochemical Characterization of AidC, a Quorum-Quenching Lactonase with Atypical Selectivity.

    PubMed

    Mascarenhas, Romila; Thomas, Pei W; Wu, Chun-Xiang; Nocek, Boguslaw P; Hoang, Quyen Q; Liu, Dali; Fast, Walter

    2015-07-21

    Quorum-quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-l-homoserine lactone (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is the most efficient wild-type quorum-quenching enzymes characterized to date, with a kcat/KM value of approximately 2 × 10(6) M(-1) s(-1) for N-heptanoyl-l-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) compared to those of typical AHL lactonases (ca. >1 mM). X-ray crystal structures of AidC alone and with the product N-hexanoyl-l-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multiangle light scattering. The structures reveal two atypical features as compared to previously characterized AHL lactonases: a "kinked" α-helix that forms part of a closed binding pocket that provides affinity and enforces selectivity for AHL substrates and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. Implications for the catalytic mechanism of AHL lactonases are discussed. PMID:26115006

  10. Raman and structural characterization of LuAlO{sub 3}

    SciTech Connect

    Casu, Alberto; Ricci, Pier Carlo

    2011-11-15

    The structural and vibrational properties of lutetium orthoaluminate perovskite (LuAlO{sub 3}) were investigated by means of Raman spectroscopy and EXAFS measurements. The analysis of Raman spectra taken in four different polarized configurations along the principal axes at 20 K and room temperature conditions permits to assign the principal vibrational modes in LuAP single crystals and to confirm the belonging to the D{sub 2h}{sup 16} space group. EXAFS measurements were performed at room temperature in order to obtain local structural informations on the first and next nearest neighbors around lutetium absorptions sites. Unit cell parameters and bond lengths were determined by the analysis of the EXAFS spectroscopy at the L{sub 3} absorption edge of lutetium. The informations thus gathered on this compound can offer a useful addition in the framework of a full structural characterization of LuAlO{sub 3}. - Graphical abstract: Raman active mode in LuAP crystal. Highlights: > Structural characterization of LuAlO{sub 3} is obtained by Raman and EXAFS spectroscopies. > Vibrational modes, temperature-dependent variations studied by Raman spectroscopy. > Cell parameters and local characterization obtained by EXAFS spectroscopy.

  11. Structural and spectroscopic characterization of ZrO2:Eu3+ nanoparticles.

    PubMed

    Salas, P; Nava, N; Angeles-Chavez, C; De la Rosa, E; Díaz-Torres, L A

    2008-12-01

    ZrO2:Eu3+ nanocrystals were prepared by the sol-gel technique. The structural and luminescence properties of europium doped zirconia with 0.5 to 2 mol% were studied by Mössbauer spectroscopy, Raman spectroscopy, X-ray diffraction (XRD), High Resolution Transmission Electron Microscopy (HRTEM) and photoluminescence (PL) under UV excitation. Structural characterization shows a crystallite size between 16 to 55 nm and monoclinic and tetragonal zirconia phases as the main crystalline structure. XRD patterns shown that the content of the active ions stabilizes the tetragonal structure of ZrO2 at 1000 degrees C, being 100% for 2 mol% Eu2O3 doped sample. Such results are in agreement with HRTEM and Raman spectroscopy. The Mössbauer spectra of the ZrO2:Eu3+ samples show a single peak near zero velocity which is attributed to Eu+3. Luminescence characterization shows the typical emission band centered at 595 and 611 nm. Change in the structure of such band was observed and explained in terms of crystalline phase change. The dependence between the fluorescence emission and the crystalline structure is discussed. PMID:19205217

  12. Microfluidic-based fabrication, characterization and magnetic functionalization of microparticles with novel internal anisotropic structure

    PubMed Central

    Qiu, Yang; Wang, Fei; Liu, Ying-Mei; Wang, Wei; Chu, Liang-Yin; Wang, Hua-Lin

    2015-01-01

    Easy fabrication and independent control of the internal and external morphologies of core-shell microparticles still remain challenging. Core-shell microparticle comprised of a previously unknown internal anisotropic structure and a spherical shell was fabricated by microfluidic-based emulsificaiton and photopolymerization. The interfacial and spatial 3D morphology of the anisotropic structure were observed by SEM and micro-CT respectively. Meanwhile, a series of layer-by-layer scans of the anisotropic structure were obtained via the micro-CT, which enhanced the detail characterization and analysis of micro materials. The formation mechanism of the internal anisotropic structure may be attributed to solution-directed diffusion caused by the semipermeable membrane structure and chemical potential difference between inside and outside of the semipermeable membrane-like polymerized shell. The morphology evolution of the anisotropic structure was influenced and controlled by adjusting reaction parameters including polymerization degree, polymerization speed, and solute concentration difference. The potential applications of these microparticles in microrheological characterization and image enhancement were also proposed by embedding magnetic nanoparticles in the inner core. PMID:26268148

  13. Microfluidic-based fabrication, characterization and magnetic functionalization of microparticles with novel internal anisotropic structure

    NASA Astrophysics Data System (ADS)

    Qiu, Yang; Wang, Fei; Liu, Ying-Mei; Wang, Wei; Chu, Liang-Yin; Wang, Hua-Lin

    2015-08-01

    Easy fabrication and independent control of the internal and external morphologies of core-shell microparticles still remain challenging. Core-shell microparticle comprised of a previously unknown internal anisotropic structure and a spherical shell was fabricated by microfluidic-based emulsificaiton and photopolymerization. The interfacial and spatial 3D morphology of the anisotropic structure were observed by SEM and micro-CT respectively. Meanwhile, a series of layer-by-layer scans of the anisotropic structure were obtained via the micro-CT, which enhanced the detail characterization and analysis of micro materials. The formation mechanism of the internal anisotropic structure may be attributed to solution-directed diffusion caused by the semipermeable membrane structure and chemical potential difference between inside and outside of the semipermeable membrane-like polymerized shell. The morphology evolution of the anisotropic structure was influenced and controlled by adjusting reaction parameters including polymerization degree, polymerization speed, and solute concentration difference. The potential applications of these microparticles in microrheological characterization and image enhancement were also proposed by embedding magnetic nanoparticles in the inner core.

  14. Pathological tendons maintain sufficient aligned fibrillar structure on ultrasound tissue characterization (UTC).

    PubMed

    Docking, S I; Cook, J

    2016-06-01

    Structural disorganization in the tendon is associated with tendinopathy, with little research investigating whether disorganization overwhelms the overall structural integrity of the tendon. This study investigated the mean cross-sectional area (CSA) of aligned fibrillar structure as detected by ultrasound tissue characterization (UTC) in the pathological and normal Achilles and patellar tendons. Ninety-one participants had their Achilles and/or patellar tendons scanned using UTC to capture a three-dimensional image of the tendon and allow a semi-quantification of the echopattern. The mean CSA of aligned fibrillar structure (echo type I + II) and disorganized structure (echo type III + IV) was calculated based on UTC algorithms. Each tendon was classified as either pathological or normal based solely on gray-scale ultrasound. The mean CSA of aligned fibrillar structure was significantly greater (P ≤ 0.001) in the pathological tendon compared with the normal tendon, despite the pathological tendon containing greater amounts of disorganized structure (P ≤ 0.001). A significant relationship was observed between the mean CSA of disorganized structure and anteroposterior diameter of the Achilles (R(2)  = 0.587) and patellar (R(2)  = 0.559) tendons. This study is the first to show that pathological tendons have sufficient levels of aligned fibrillar structure. Pathological tendons may compensate for areas of disorganization by increasing in tendon thickness. PMID:26059532

  15. Structure characterization of the non-crystalline complexes of copper salts with native cyclodextrins.

    PubMed

    Velasco, Manuel I; Krapacher, Claudio R; de Rossi, Rita H; Rossi, Laura I

    2016-06-28

    The characterization of non-crystalline complexes is particularly difficult when techniques like X-ray diffraction or NMR cannot be used. We propose a simple procedure to characterize the physicochemical properties of amorphous new coordination compounds between cyclodextrins (CD) and Cu(2+) salts, by means of the integration of the information provided by several techniques including elemental analysis, flame atomic absorption, TGA, UV-Vis diffuse reflectance, colorimetry, FT-IR and EPR. On the basis of these procedures, we suggest geometrical and structural approximations resulting in an octahedral or distorted octahedral geometry with diverse positions for the metallic centre. According to the EPR spectrum, only one of the complexes may have rhombic symmetry. We also analyzed enthalpy-entropy compensation and the isokinetic effect. In addition, general trends in thermal stability, spectroscopic properties and inclusion in the cavity were analysed. This complete characterization methodology becomes essential for their future application as catalysts. PMID:27272478

  16. An inverse display color characterization model based on an optimized geometrical structure

    NASA Astrophysics Data System (ADS)

    Thomas, Jean-Baptiste; Colantoni, Philippe; Hardeberg, Jon Y.; Foucherot, Irène; Gouton, Pierre

    2008-01-01

    We have defined an inverse model for colorimetric characterization of additive displays. It is based on an optimized three-dimensional tetrahedral structure. In order to minimize the number of measurements, the structure is defined using a forward characterization model. Defining a regular grid in the device-dependent destination color space leads to heterogeneous interpolation errors in the device-independent source color space. The parameters of the function used to define the grid are optimized using a globalized Nelder-Mead simplex downhill algorithm. Several cost functions are tested on several devices. We have performed experiments with a forward model which assumes variation in chromaticities (PLVC), based on one-dimensional interpolations for each primary ramp along X, Y and Z (3×3×1-D). Results on 4 devices (2 LCD and a DLP projection devices, one LCD monitor) are shown and discussed.

  17. Nondestructive techniques for characterizing mechanical properties of structural materials - An overview

    NASA Technical Reports Server (NTRS)

    Vary, A.; Klima, S. J.

    1986-01-01

    An overview of nondestructive evaluation (NDE) is presented to indicate the availability and application potentials of techniques for quantitative characterization of the mechanical properties of structural materials. The purpose is to review NDE techniques that go beyond the usual emphasis on flow detection and characterization. Discussed are current and emerging NDE techniques that can verify and monitor entrinsic properties (e.g., tensile, shear, and yield strengths; fracture toughness, hardness, ductility; elastic moduli) and underlying microstructural and morphological factors. Most of the techniques described are, at present, neither widely applied nor widely accepted in commerce and industry because they are still emerging from the laboratory. The limitations of the techniques may be overcome by advances in applications research and instrumentation technology and perhaps by accommodations for their use in the design of structural parts.

  18. Nondestructive techniques for characterizing mechanical properties of structural materials: An overview

    NASA Technical Reports Server (NTRS)

    Vary, A.; Klima, S. J.

    1985-01-01

    An overview of nondestructive evaluation (NDE) is presented to indicate the availability and application potentials of techniques for quantitative characterization of the mechanical properties of structural materials. The purpose is to review NDE techniques that go beyond the usual emphasis on flaw detection and characterization. Discussed are current and emerging NDE techniques that can verify and monitor entrinsic properties (e.g., tensile, shear, and yield strengths; fracture toughness, hardness, ductility; elastic moduli) and underlying microstructural and morphological factors. Most of the techniques described are, at present, neither widely applied nor widely accepted in commerce and industry because they are still emerging from the laboratory. The limitations of the techniques may be overcome by advances in applications research and instrumentation technology and perhaps by accommodations for their use in the design of structural parts.

  19. Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif.

    PubMed

    Kim, Kuglae; Kwon, Soon-Kyeong; Jun, Sung-Hoon; Cha, Jeong Seok; Kim, Hoyoung; Lee, Weontae; Kim, Jihyun F; Cho, Hyun-Soo

    2016-01-01

    A novel light-driven chloride-pumping rhodopsin (ClR) containing an 'NTQ motif' in its putative ion conduction pathway has been discovered and functionally characterized in a genomic analysis study of a marine bacterium. Here we report the crystal structure of ClR from the flavobacterium Nonlabens marinus S1-08(T) determined under two conditions at 2.0 and 1.56 Å resolutions. The structures reveal two chloride-binding sites, one around the protonated Schiff base and the other on a cytoplasmic loop. We identify a '3 omega motif' formed by three non-consecutive aromatic amino acids that is correlated with the B-C loop orientation. Detailed ClR structural analyses with functional studies in E. coli reveal the chloride ion transduction pathway. Our results help understand the molecular mechanism and physiological role of ClR and provide a structural basis for optogenetic applications. PMID:27554809

  20. Characterization of Effect of Support Structures in Laser Additive Manufacturing of Stainless Steel

    NASA Astrophysics Data System (ADS)

    Järvinen, Jukka-Pekka; Matilainen, Ville; Li, Xiaoyun; Piili, Heidi; Salminen, Antti; Mäkelä, Ismo; Nyrhilä, Olli

    Laser additive manufacturing (LAM) of stainless steel is a layer wisetechnology for fabricating 3D parts from metal powder via selectively melting powder with laser beam. Support structures play a significant role in LAM process as they help to remove heat away from the process and on the other hand hold the work piece in its place. A successful design of support structures can help to achievea building process fast and inexpensive with high quality. Aimof this study was to characterize the usability of two types of support structures: web and tube supports. Purpose of this studywas also to analyze how suitable they are in two industrial application cases: case for dental application and case for jewelry application. It was concluded that the removability of web supports was much better than tube supports. It was noticed that support structures are an important part of LAM process and they strongly affect the manufacturability and the end quality of the part.

  1. Growth and characterization of periodically polarity-inverted ZnO structures on sapphire substrates

    SciTech Connect

    Park, Jinsub; Yao, Takafumi

    2012-10-15

    We report on the fabrication and characterization of periodically polarity inverted (PPI) ZnO heterostructures on (0 0 0 1) Al{sub 2}O{sub 3} substrates. For the periodically inverted array of ZnO polarity, CrN and Cr{sub 2}O{sub 3} polarity selection buffer layers are used for the Zn- and O-polar ZnO films, respectively. The change of polarity and period in fabricated ZnO structures is evaluated by diffraction patterns and polarity sensitive piezo-response microscopy. Finally, PPI ZnO structures with subnanometer scale period are demonstrated by using holographic lithography and regrowth techniques.

  2. Cobalt Molybdenum Oxynitrides: Synthesis, Structural, Characterization, and Catalytic Activity for the Oxygen Reduction Reaction

    SciTech Connect

    Cao, Bingfei; Veith, Gabriel M; Diaz, Rosa; Liu, Jue; Stach, Eric; Adzic, Radoslav R.; Khalifah, P.

    2013-01-01

    Here, we report the synthesis and characterization of CoxMo1 xOyNz compounds supported on carbon black as potential cathode catalysts for ORR. They were prepared by a conventional impregnation method. Their ORR activities in both acid and alkaline electrolytes were evaluated via half-cell measurements. The synthesis temperature and sample composition both strongly impacted their physical and chemical properties. Factors influencing their crystal structures, morphologies and ORR activities will be discussed based on the results of structural and spectroscopic studies.

  3. Acoustic characterization of nanoswitch structures: application to the DNA Holliday Junction.

    PubMed

    Papadakis, George; Tsortos, Achilleas; Gizeli, Electra

    2010-12-01

    A novel biophysical approach in combination with an acoustic device is demonstrated as a sensitive, rapid, and label-free technique for characterizing various structures of the DNA Holliday Junction (J1) nanoswitch. We were successful in discriminating the "closed" from the "open" state, as well as confirming that the digestion of the J1 junction resulted in the two, anticipated, rod-shaped, 20 bp long fragments. Furthermore, we propose a possible structure for the ∼10 nm long (DNA58) component participating in the J1 assembly. This work reveals the potential of acoustic devices as a powerful tool for molecular conformation studies. PMID:21038866

  4. Automated wind load characterization of wind turbine structures by embedded model updating

    NASA Astrophysics Data System (ADS)

    Swartz, R. Andrew; Zimmerman, Andrew T.; Lynch, Jerome P.

    2010-04-01

    The continued development of renewable energy resources is for the nation to limit its carbon footprint and to enjoy independence in energy production. Key to that effort are reliable generators of renewable energy sources that are economically competitive with legacy sources. In the area of wind energy, a major contributor to the cost of implementation is large uncertainty regarding the condition of wind turbines in the field due to lack of information about loading, dynamic response, and fatigue life of the structure expended. Under favorable circumstances, this uncertainty leads to overly conservative designs and maintenance schedules. Under unfavorable circumstances, it leads to inadequate maintenance schedules, damage to electrical systems, or even structural failure. Low-cost wireless sensors can provide more certainty for stakeholders by measuring the dynamic response of the structure to loading, estimating the fatigue state of the structure, and extracting loading information from the structural response without the need of an upwind instrumentation tower. This study presents a method for using wireless sensor networks to estimate the spectral properties of a wind turbine tower loading based on its measured response and some rudimentary knowledge of its structure. Structural parameters are estimated via model-updating in the frequency domain to produce an identification of the system. The updated structural model and the measured output spectra are then used to estimate the input spectra. Laboratory results are presented indicating accurate load characterization.

  5. Characterization of Structural and Pigmentary Colors in Common Emigrant (Catopsilia Pomona) Butterfly

    SciTech Connect

    Ghate, Ekata; Kulkarni, G. R.; Bhoraskar, S. V.; Adhi, K. P.

    2011-10-20

    Study of structural colors in case of insects and butterflies is important for their biomimic and biophotonics applications. Structural color is the color which is produced by physical structures and their interaction with light while pigmentary color is produced by absorption of light by pigments. Common Emigrant butterfly is widely distributed in India. It is of moderate size with wing span of about 60-80 mm. The wings are broadly white with yellow or sulphur yellow coloration at places as well as few dark black patches. It belongs to family Pieridae. A study of structural color in case of Common Emigrant butterfly has been carried out in the present work. The characterization of wing color was performed using absorption spectroscopy. Scanning electron microscopic study of the wings of Common Emigrant butterfly showed that three different types of scales are present on the wing surface dorsally. Diffracting structures are present in certain parts of the surfaces of the various scales. Bead like structures are embedded in the intricate structures of the scales. Absorption spectra revealed that a strong absorption peak is seen in the UV-range. Crystalline structure of beads was confirmed by the X-ray diffraction analysis.

  6. Foam injection molding of thermoplastic elastomers: Blowing agents, foaming process and characterization of structural foams

    NASA Astrophysics Data System (ADS)

    Ries, S.; Spoerrer, A.; Altstaedt, V.

    2014-05-01

    Polymer foams play an important role caused by the steadily increasing demand to light weight design. In case of soft polymers, like thermoplastic elastomers (TPE), the haptic feeling of the surface is affected by the inner foam structure. Foam injection molding of TPEs leads to so called structural foam, consisting of two compact skin layers and a cellular core. The properties of soft structural foams like soft-touch, elastic and plastic behavior are affected by the resulting foam structure, e.g. thickness of the compact skins and the foam core or density. This inner structure can considerably be influenced by different processing parameters and the chosen blowing agent. This paper is focused on the selection and characterization of suitable blowing agents for foam injection molding of a TPE-blend. The aim was a high density reduction and a decent inner structure. Therefore DSC and TGA measurements were performed on different blowing agents to find out which one is appropriate for the used TPE. Moreover a new analyzing method for the description of processing characteristics by temperature dependent expansion measurements was developed. After choosing suitable blowing agents structural foams were molded with different types of blowing agents and combinations and with the breathing mold technology in order to get lower densities. The foam structure was analyzed to show the influence of the different blowing agents and combinations. Finally compression tests were performed to estimate the influence of the used blowing agent and the density reduction on the compression modulus.

  7. Structural and morphological characterization of hemozoin produced by Schistosoma mansoni and Rhodnius prolixus.

    PubMed

    Oliveira, Marcus F; Kycia, Stefan W; Gomez, Ariel; Kosar, Aaron J; Bohle, D Scott; Hempelmann, Ernst; Menezes, Diego; Vannier-Santos, Marcos André; Oliveira, Pedro L; Ferreira, Sérgio T

    2005-11-01

    Hemozoin (Hz) is a heme crystal produced upon the digestion of hemoglobin (Hb) by blood-feeding organisms as a main mechanism of heme disposal. The structure of Hz consists of heme dimers bound by reciprocal iron-carboxylate interactions and stabilized by hydrogen bonds. We have recently described heme crystals in the blood fluke, Schistosoma mansoni, and in the kissing bug, Rhodnius prolixus. Here, we characterized the structures and morphologies of the heme crystals from those two organisms and compared them to synthetic beta-hematin (betaH). Synchrotron radiation X-ray powder diffraction showed that all heme crystals share the same unit cell and structure. The heme crystals isolated from S. mansoni and R. prolixus consisted of very regular units assembled in multicrystalline spherical structures exhibiting remarkably distinct surface morphologies compared to betaH. In both organisms, Hz formation occurs inside lipid droplet-like particles or in close association to phospholipid membranes. These results show, for the first time, the structural and morphological characterization of natural Hz samples obtained from these two blood-feeding organisms. Moreover, Hz formation occurring in close association to a hydrophobic environment seems to be a common trend for these organisms and may be crucial to produce very regular shaped phases, allowing the formation of multicrystalline assemblies in the guts of S. mansoni and R. prolixus. PMID:16229843

  8. Characterization and structural analysis of an active particulate methane monooxygenase trimer from Methylococcus capsulatus (Bath).

    PubMed

    Kitmitto, Ashraf; Myronova, Natalia; Basu, Piku; Dalton, Howard

    2005-08-23

    The oxidation of methane to methanol in methanotrophs is catalyzed by the enzyme methane monooxygenase (MMO). Two distinct forms of this enzyme exist, a soluble cytoplasmic MMO (sMMO) and a membrane-bound particulate form (pMMO). We describe here the biochemical characterization of a stable and active purified pMMO hydroxylase (pMMO-H) and report a three-dimensional (3D) structure, determined by electron microscopy and single-particle analysis at 23 A resolution. Both biochemical and structural data indicate that pMMO hydroxylase is trimeric, with each monomer unit comprised of three polypeptides of 47, 26, and 23 kDa. Comparison of the recent crystal structure [Lieberman, R. L., and Rosenzweig, A. C. (2005) Nature 434, 177] of an uncharacterized pMMO-H complex with the three-dimensional (3D) structure determined here yielded a good match between the principal features and the organization of the enzyme monomers into trimers. The data presented here advance our current understanding of particulate methane monooxygenase function by the characterization of an active form of the enzyme and the corresponding 3D structure. PMID:16101279

  9. Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways

    PubMed Central

    Boucher, Benjamin; Lee, Anna Y.; Hallett, Michael; Jenna, Sarah

    2016-01-01

    A genetic interaction (GI) is defined when the mutation of one gene modifies the phenotypic expression associated with the mutation of a second gene. Genome-wide efforts to map GIs in yeast revealed structural and functional properties of a GI network. This provided insights into the mechanisms underlying the robustness of yeast to genetic and environmental insults, and also into the link existing between genotype and phenotype. While a significant conservation of GIs and GI network structure has been reported between distant yeast species, such a conservation is not clear between unicellular and multicellular organisms. Structural and functional characterization of a GI network in these latter organisms is consequently of high interest. In this study, we present an in-depth characterization of ~1.5K GIs in the nematode Caenorhabditis elegans. We identify and characterize six distinct classes of GIs by examining a wide-range of structural and functional properties of genes and network, including co-expression, phenotypical manifestations, relationship with protein-protein interaction dense subnetworks (PDS) and pathways, molecular and biological functions, gene essentiality and pleiotropy. Our study shows that GI classes link genes within pathways and display distinctive properties, specifically towards PDS. It suggests a model in which pathways are composed of PDS-centric and PDS-independent GIs coordinating molecular machines through two specific classes of GIs involving pleiotropic and non-pleiotropic connectors. Our study provides the first in-depth characterization of a GI network within pathways of a multicellular organism. It also suggests a model to understand better how GIs control system robustness and evolution. PMID:26871911

  10. Using multispecies occupancy models to improve the characterization and understanding of metacommunity structure.

    PubMed

    Mihaljevic, Joseph R; Joseph, Maxwell B; Johnson, Pieter T J

    2015-07-01

    Two of the most prominent frameworks to develop in ecology over the past decade are metacommunity ecology, which seeks to characterize multispecies distributions across space, and occupancy modeling, which corrects for imperfect detection in an effort to better understand species occurrence patterns. Although their goals are complementary, metacommunity theory and statistical occupancy modeling methods have developed independently. For instance, the elements of metacommunity structure (EMS) framework uses species occurrence data to classify metacommunity structure and link it to underlying environmental gradients. While the efficacy of this approach relies on the quality of the data, few studies have considered how imperfect detection, which is widespread in ecological surveys and the major focus of occupancy modeling, affects the outcome. We introduce a framework that integrates multispecies occupancy models with the current EMS framework, detection error-corrected EMS (DECEMS). This method offers two distinct advantages. First, DECEMS reduces bias in characterizing metacommunity structure by using repeated surveys and occupancy models to disentangle species-specific occupancy and detection probabilities, ultimately bringing metacommunity structure classification into a more probabilistic framework. Second, occupancy modeling allows estimation of species-specific responses to environmental covariates, which will increase our ability to link species-level effects to metacommunity-wide patterns. After reviewing the EMS framework, we introduce a simple multispecies occupancy model and show how DECEMS can work in practice, highlighting that detection error often causes EMS to assign incorrect structures. To emphasize the broader applicability of this approach, we further illustrate that DECEMS can reduce the rate of structure misclassification by more than 20% in some cases, even proving useful when detection error rates are quite low (-10%). Integrating occupancy

  11. Large-Scale Production and Structural and Biophysical Characterizations of the Human Hepatitis B Virus Polymerase

    PubMed Central

    Vörös, Judit; Urbanek, Annika; Rautureau, Gilles Jean Philippe; O'Connor, Maggie; Fisher, Henry C.; Ashcroft, Alison E.

    2014-01-01

    ABSTRACT Hepatitis B virus (HBV) is a major human pathogen that causes serious liver disease and 600,000 deaths annually. Approved therapies for treating chronic HBV infections usually target the multifunctional viral polymerase (hPOL). Unfortunately, these therapies—broad-spectrum antivirals—are not general cures, have side effects, and cause viral resistance. While hPOL remains an attractive therapeutic target, it is notoriously difficult to express and purify in a soluble form at yields appropriate for structural studies. Thus, no empirical structural data exist for hPOL, and this impedes medicinal chemistry and rational lead discovery efforts targeting HBV. Here, we present an efficient strategy to overexpress recombinant hPOL domains in Escherichia coli, purifying them at high yield and solving their known aggregation tendencies. This allowed us to perform the first structural and biophysical characterizations of hPOL domains. Apo-hPOL domains adopt mainly α-helical structures with small amounts of β-sheet structures. Our recombinant material exhibited metal-dependent, reverse transcriptase activity in vitro, with metal binding modulating the hPOL structure. Calcomine orange 2RS, a small molecule that inhibits duck HBV POL activity, also inhibited the in vitro priming activity of recombinant hPOL. Our work paves the way for structural and biophysical characterizations of hPOL and should facilitate high-throughput lead discovery for HBV. IMPORTANCE The viral polymerase from human hepatitis B virus (hPOL) is a well-validated therapeutic target. However, recombinant hPOL has a well-deserved reputation for being extremely difficult to express in a soluble, active form in yields appropriate to the structural studies that usually play an important role in drug discovery programs. This has hindered the development of much-needed new antivirals for HBV. However, we have solved this problem and report here procedures for expressing recombinant hPOL domains in

  12. Dispersed metal cluster catalysts by design. Synthesis, characterization, structure, and performance

    SciTech Connect

    Arslan, Ilke; Dixon, David A.; Gates, Bruce C.; Katz, Alexander

    2015-09-30

    To understand the class of metal cluster catalysts better and to lay a foundation for the prediction of properties leading to improved catalysts, we have synthesized metal catalysts with well-defined structures and varied the cluster structures and compositions systematically—including the ligands bonded to the metals. These ligands include supports and bulky organics that are being tuned to control both the electron transfer to or from the metal and the accessibility of reactants to influence catalytic properties. We have developed novel syntheses to prepare these well-defined catalysts with atomic-scale control the environment by choice and placement of ligands and applied state-of-the art spectroscopic, microscopic, and computational methods to determine their structures, reactivities, and catalytic properties. The ligands range from nearly flat MgO surfaces to enveloping zeolites to bulky calixarenes to provide controlled coverages of the metal clusters, while also enforcing unprecedented degrees of coordinative unsaturation at the metal site—thereby facilitating bonding and catalysis events at exposed metal atoms. With this wide range of ligand properties and our arsenal of characterization tools, we worked to achieve a deep, fundamental understanding of how to synthesize robust supported and ligand-modified metal clusters with controlled catalytic properties, thereby bridging the gap between active site structure and function in unsupported and supported metal catalysts. We used methods of organometallic and inorganic chemistry combined with surface chemistry for the precise synthesis of metal clusters and nanoparticles, characterizing them at various stages of preparation and under various conditions (including catalytic reaction conditions) and determining their structures and reactivities and how their catalytic properties depend on their compositions and structures. Key characterization methods included IR, NMR, and EXAFS spectroscopies to identify

  13. Synthesis, spectroscopic characterizations, crystal structures and DFT studies of nalidixic acid carbonyl hydrazones derivatives

    NASA Astrophysics Data System (ADS)

    Bergamini, F. R. G.; Ribeiro, M. A.; Lancellotti, M.; Machado, D.; Miranda, P. C. M. L.; Cuin, A.; Formiga, A. L. B.; Corbi, P. P.

    2016-09-01

    This article describes the synthesis and characterization of the 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carbohydrazide (hzd) and six carbonyl hydrazones derivatives of the nalidixic with 1H-pyrrol-2-ylmethylidene (hpyrr), 1H-imidazol-2-ylmethylidene (h2imi), pyridin-2-ylmethylidene (h2py), pyridin-3-ylmethylidene (h3py), pyridin-4-ylmethylidene(h4py) and (2-hydroxyphenyl)methylidene (hsali). The carbonyl hydrazones were characterized by elemental and ESI-QTOF-MS analyses, IR and detailed NMR spectroscopic measurements. The 2D NMR experiments allowed the unambiguous assignment of the hydrogen, carbon and nitrogen atoms, which have not been reported for nalidixic acid carbonyl hydrazone derivatives so far. Crystal structures of hzd and the new carbonyl hydrazones h2imi, hpyrr and h3py were determined by X-ray diffraction studies. Although the synthesis of hzd was reported decades ago, the hzd crystal structure have not been reported yet. Geometric optimizations of all the characterized structures were performed with the aid of DFT studies. Despite the fact that the hydrazones with 2-pyridine carboxylic acid (h2py) and salicyl aldehyde (hsali) were already reported by literature, a detailed spectroscopic study followed by DFT studies are also reported for such compounds in this manuscript. Antimicrobial studies of the compounds are also presented.

  14. Structures and characterizations of bundles of collapsed double-walled carbon nanotubes.

    PubMed

    Zhong, X H; Wang, R; Liu, L B; Kang, M; Wen, Y Y; Hou, F; Feng, J M; Li, Y L

    2012-12-21

    The performance of carbon nanotube fibers (CNTFs) significantly depends on the packing styles of carbon nanotube (CNT) bundles. Revealing the structures and characterizations of CNT bundles is contributive to understanding the structures, properties and even the formation of CNTFs during chemical vapor deposition (CVD) processing. In this paper, bundles consisting of collapsed double-walled carbon nanotubes (CDWNT) in continuous CNTFs fabricated from CVD processing were characterized and analyzed by transmission electronic microscopy (TEM) and x-ray diffraction (XRD). TEM observations show that the continuous CNTFs are composed of CDWNT-bundle units. CDWNT-bundle units of 10-20 nm in thickness contain near numbers of collapsed tubes. The degree of collapse of the CDWNTs varies with their location in the bundle and their own diameter. CDWNT-bundle units pack side by side or face to face, assembling into super-bundles with diameters of 200-300 nm. XRD patterns show that three novel and strong peaks appear at 10°-15°, 21.3° and 23.7°, respectively, corresponding to CDWNT two side pores (10°-15°) and CDWNT layers (21.3° and 23.7°), which indicates the collapsed tube structures in CNTFs are common characterizations. Finally, a collapse mechanism is discussed from the observation and analysis. PMID:23196759

  15. Characterizing Electrical and Thermal Breakdown of Metamaterial Structures for HPM Applications

    NASA Astrophysics Data System (ADS)

    Wynkoop, T.; Gilmore, M.; Lynn, A. G.; Prasad, S.; Schamiloglu, E.

    2013-10-01

    The use of metamaterials (MTMs) has been proposed to increase the performance and efficiency of high power microwave (HPM) sources. However, by nature, MTMs are composed of subwavelength structures and are prone to electrical breakdown. In order to investigate the survivability of potential MTM structures in an HPM environment, two test stands are being constructed to characterize MTM electrical and thermal response. First, the SINUS-6 electron beam accelerator with maximum deliverable power of 4.2 GW(700 kV, 6 kA) , and pulse duration of 12 ns will be utilized. MTM's will be placed in close proximity to the beam, and breakdown will be characterized via fast imaging, and survey and high resolution spectroscopy. Secondly, a low current electron gun with Vbeam <= 50 kV, that can operate from ns pulsed to steady state, will investigate thermal loading and charging. Ultimately, results of this characterization will be used to develop robust MTM resonant/slow wave structures for HPM applications. Work supported by US AFOSR MURI Grant FA9550-12-1-0489.

  16. Characterization of a Novel Water Pocket Inside the Human Cx26 Hemichannel Structure

    PubMed Central

    Araya-Secchi, Raul; Perez-Acle, Tomas; Kang, Seung-gu; Huynh, Tien; Bernardin, Alejandro; Escalona, Yerko; Garate, Jose-Antonio; Martínez, Agustin D.; García, Isaac E.; Sáez, Juan C.; Zhou, Ruhong

    2014-01-01

    Connexins (Cxs) are a family of vertebrate proteins constituents of gap junction channels (GJCs) that connect the cytoplasm of adjacent cells by the end-to-end docking of two Cx hemichannels. The intercellular transfer through GJCs occurs by passive diffusion allowing the exchange of water, ions, and small molecules. Despite the broad interest to understand, at the molecular level, the functional state of Cx-based channels, there are still many unanswered questions regarding structure-function relationships, perm-selectivity, and gating mechanisms. In particular, the ordering, structure, and dynamics of water inside Cx GJCs and hemichannels remains largely unexplored. In this work, we describe the identification and characterization of a believed novel water pocket—termed the IC pocket—located in-between the four transmembrane helices of each human Cx26 (hCx26) monomer at the intracellular (IC) side. Using molecular dynamics (MD) simulations to characterize hCx26 internal water structure and dynamics, six IC pockets were identified per hemichannel. A detailed characterization of the dynamics and ordering of water including conformational variability of residues forming the IC pockets, together with multiple sequence alignments, allowed us to propose a functional role for this cavity. An in vitro assessment of tracer uptake suggests that the IC pocket residue Arg-143 plays an essential role on the modulation of the hCx26 hemichannel permeability. PMID:25099799

  17. Structural characterization of a first-generation articulated-truss joint for space crane application

    NASA Technical Reports Server (NTRS)

    Sutter, Thomas R.; Wu, K. Chauncey; Riutort, Kevin T.; Laufer, Joseph B.; Phelps, James E.

    1992-01-01

    A first-generation space crane articulated-truss joint was statically and dynamically characterized in a configuration that approximated an operational environment. The articulated-truss joint was integrated into a test-bed for structural characterization. Static characterization was performed by applying known loads and measuring the corresponding deflections to obtain load-deflection curves. Dynamic characterization was performed using modal testing to experimentally determine the first six mode shapes, frequencies, and modal damping values. Static and dynamic characteristics were also determined for a reference truss that served as a characterization baseline. Load-deflection curves and experimental frequency response functions are presented for the reference truss and the articulated-truss joint mounted in the test-bed. The static and dynamic experimental results are compared with analytical predictions obtained from finite element analyses. Load-deflection response is also presented for one of the linear actuators used in the articulated-truss joint. Finally, an assessment is presented for the predictability of the truss hardware used in the reference truss and articulated-truss joint based upon hardware stiffness properties that were previously obtained during the Precision Segmented Reflector (PSR) Technology Development Program.

  18. Structure of dehaloperoxidase B at 1.58 Å resolution and structural characterization of the AB dimer from Amphitrite ornata

    SciTech Connect

    Serrano, Vesna de; D’Antonio, Jennifer; Franzen, Stefan; Ghiladi, Reza A.

    2010-05-01

    The crystal structure of dehaloperoxidase (DHP) isoenzyme B from the terebellid polychaete A. ornata, which exhibits both hemoglobin and peroxidase functions, has been determined at 1.58 Å resolution. As members of the globin superfamily, dehaloperoxidase (DHP) isoenzymes A and B from the marine annelid Amphitrite ornata possess hemoglobin function, but they also exhibit a biologically relevant peroxidase activity that is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. Here, a comprehensive structural study of recombinant DHP B, both by itself and cocrystallized with isoenzyme A, using X-ray diffraction is presented. The structure of DHP B refined to 1.58 Å resolution exhibits the same distal histidine (His55) conformational flexibility as that observed in isoenzyme A, as well as additional changes to the distal and proximal hydrogen-bonding networks. Furthermore, preliminary characterization of the DHP AB heterodimer is presented, which exhibits differences in the AB interface that are not observed in the A-only or B-only homodimers. These structural investigations of DHP B provide insights that may relate to the mechanistic details of the H{sub 2}O{sub 2}-dependent oxidative dehalogenation reaction catalyzed by dehaloperoxidase, present a clearer description of the function of specific residues in DHP at the molecular level and lead to a better understanding of the paradigms of globin structure–function relationships.

  19. Structure of dehaloperoxidase B at 1.58 Å resolution and structural characterization of the AB dimer from Amphitrite ornata

    SciTech Connect

    de Serrano, Vesna; D; Antonio, Jennifer; Franzen, Stefan; Ghiladi, Reza A.

    2012-04-18

    As members of the globin superfamily, dehaloperoxidase (DHP) isoenzymes A and B from the marine annelid Amphitrite ornata possess hemoglobin function, but they also exhibit a biologically relevant peroxidase activity that is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. Here, a comprehensive structural study of recombinant DHP B, both by itself and cocrystallized with isoenzyme A, using X-ray diffraction is presented. The structure of DHP B refined to 1.58 {angstrom} resolution exhibits the same distal histidine (His55) conformational flexibility as that observed in isoenzyme A, as well as additional changes to the distal and proximal hydrogen-bonding networks. Furthermore, preliminary characterization of the DHP AB heterodimer is presented, which exhibits differences in the AB interface that are not observed in the A-only or B-only homodimers. These structural investigations of DHP B provide insights that may relate to the mechanistic details of the H{sub 2}O{sub 2}-dependent oxidative dehalogenation reaction catalyzed by dehaloperoxidase, present a clearer description of the function of specific residues in DHP at the molecular level and lead to a better understanding of the paradigms of globin structure-function relationships.

  20. PREFACE: Symposium 1: Advanced Structure Analysis and Characterization of Ceramic Materials

    NASA Astrophysics Data System (ADS)

    Yashima, Masatomo

    2011-05-01

    Preface to Symposium 1 (Advanced Structure Analysis and Characterization of Ceramic Materials) of the International Congress of Ceramics III, held 14-18 November 2010 in Osaka, Japan Remarkable developments have been made recently in the structural analysis and characterization of inorganic crystalline and amorphous materials, such as x-ray, neutron, synchrotron and electron diffraction, x-ray/neutron scattering, IR/Raman scattering, NMR, XAFS, first-principle calculations, computer simulations, Rietveld analysis, the maximum-entropy method, in situ measurements at high temperatures/pressures and electron/nuclear density analysis. These techniques enable scientists to study not only static and long-range periodic structures but also dynamic and short-/intermediate-range structures. Multi-scale characterization from the electron to micrometer levels is becoming increasingly important as a means of understanding phenomena at the interfaces, grain boundaries and surfaces of ceramic materials. This symposium has discussed the structures and structure/property relationships of various ceramic materials (electro, magnetic and optical ceramics; energy and environment related ceramics; bio-ceramics; ceramics for reliability secure society; traditional ceramics) through 38 oral presentations including 8 invited lectures and 49 posters. Best poster awards were given to six excellent poster presentations (Y-C Chen, Tokyo Institute of Technology; C-Y Chung, Tohoku University; T Stawski, University of Twente; Y Hirano, Nagoya Institute of Technology; B Bittova, Charles University Prague; Y Onodera, Kyoto University). I have enjoyed working with my friends in the ICC3 conference. I would like to express special thanks to other organizers: Professor Scott T Misture, Alfred University, USA, Professor Xiaolong Chen, Institute of Physics, CAS, China, Professor Takashi Ida, Nagoya Institute of Technology, Japan, Professor Isao Tanaka, Kyoto University, Japan. I also acknowledge the

  1. Structural characterization of sol-gel derived oxide nanostuctures using synchrotron x-ray techniques

    NASA Astrophysics Data System (ADS)

    Sun, Tao

    Ceramic oxides possess extraordinarily rich functionalities. With the advent of nanofabrication techniques, it is now possible to grow nanostructured oxides with precise control of composition, morphology, and microstructure, which has re-vitalized the research in the field of traditional ceramics. The unexpected behavior and enhanced properties of oxide nanostructures have been extensively reported. However, knowledge about the underlying mechanisms as well as structural implications is still quite limited. Therefore, it is imperative to develop and employ sophisticated characterization tools for unraveling the structure-property relationships for oxide nanostructures. The present thesis work aims at addressing the critical issues associated with fabrication, and more importantly, structural characterization of functional oxide nanostructures. The dissertation starts with introducing the strategy for synthesizing phase-pure and highly controlled oxide nanostructures using sol-gel deposition and an innovative approach called "soft" electron beam lithography. Some specific oxides are chosen for the present study, such as BiFeO3, CoFe2O4, and SnO2, because of their scientific and technological significance. Subsequent to fabrication of tailored oxide nanostructures, advanced synchrotron x-ray scattering techniques have been applied for structural characterization. The nucleation and growth behavior of BiFeO3 thin film was investigated using in situ grazing-incidence small-angle x-ray scattering (GISAXS) technique. The results reveal that the kinetics for early-stage nuclei growth are governed by the oriented-attachment model. Moreover, the porous structures of undoped and Pd-doped semiconducting SnOx thin films were quantitatively characterized using GISAXS. By correlating the structural parameters with H2 sensitivity of SnOx films, it is found out that the microstructure of doped film is favorable for gas sensing, but it is not the major reason for the overall

  2. Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics

    PubMed Central

    Cherkasov, Artem; Ho Sui, Shannan J; Brunham, Robert C; Jones, Steven JM

    2004-01-01

    Background We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, maintainability and safety work to model time-to-failure of mechanical devices, mechanisms, building constructions and equipment. Results We have found that the Weibull function describes protein fold distribution within and among genomes more accurately than conventional power functions which have been used in a number of structural genomic studies reported to date. It has also been found that the Weibull reliability parameter β for protein fold distributions varies between genomes and may reflect differences in rates of gene duplication in evolutionary history of organisms. Conclusions The results of this work demonstrate that reliability analysis can provide useful insights and testable predictions in the fields of comparative and structural genomics. PMID:15274750

  3. Structural characterization of wind-sheared turbulent flow using self-organized mapping

    NASA Astrophysics Data System (ADS)

    Scott, Nicholas V.; Handler, Robert A.

    2016-05-01

    A nonlinear cluster analysis algorithm is used to characterize the spatial structure of a wind-sheared turbulent flow obtained from the direct numerical simulation (DNS) of the three-dimensional temperature and momentum fields. The application of self-organizing mapping to DNS data for data reduction is utilized because of the dimensional similitude in structure between DNS data and remotely sensed hyperspectral and multispectral data where the technique has been used extensively. For the three Reynolds numbers of 150, 180, and 220 used in the DNS, self-organized mapping is successful in the extraction of boundary layer streaky structures from the turbulent temperature and momentum fields. In addition, it preserves the cross-wind scale structure of the streaks exhibited in both fields which loosely scale with the inverse of the Reynolds number. Self-organizing mapping of the along wind component of the helicity density shows a layer of the turbulence field which is spotty suggesting significant direct coupling between the large and small-scale turbulent structures. The spatial correlation of the temperature and momentum fields allows for the possibility of the remote extrapolation of the momentum structure from thermal structure.

  4. Quantitative characterization of the atomic-scale structure of oxyhydroxides in rusts formed on steel surfaces

    SciTech Connect

    Saito, M.; Suzuki, S. . E-mail: ssuzuki@tagen.tohoku.ac.jp; Kimura, M.; Suzuki, T.; Kihira, H.; Waseda, Y.

    2005-11-15

    Quantitative X-ray structural analysis coupled with anomalous X-ray scattering has been used for characterizing the atomic-scale structure of rust formed on steel surfaces. Samples were prepared from rust layers formed on the surfaces of two commercial steels. X-ray scattered intensity profiles of the two samples showed that the rusts consisted mainly of two types of ferric oxyhydroxide, {alpha}-FeOOH and {gamma}-FeOOH. The amounts of these rust components and the realistic atomic arrangements in the components were estimated by fitting both the ordinary and the environmental interference functions with a model structure calculated using the reverse Monte Carlo simulation technique. The two rust components were found to be the network structure formed by FeO{sub 6} octahedral units, the network structure itself deviating from the ideal case. The present results also suggest that the structural analysis method using anomalous X-ray scattering and the reverse Monte Carlo technique is very successful in determining the atomic-scale structure of rusts formed on the steel surfaces.

  5. Comparative metabolomics and structural characterizations illuminate colibactin pathway-dependent small molecules.

    PubMed

    Vizcaino, Maria I; Engel, Philipp; Trautman, Eric; Crawford, Jason M

    2014-07-01

    The gene cluster responsible for synthesis of the unknown molecule "colibactin" has been identified in mutualistic and pathogenic Escherichia coli. The pathway endows its producer with a long-term persistence phenotype in the human bowel, a probiotic activity used in the treatment of ulcerative colitis, and a carcinogenic activity under host inflammatory conditions. To date, functional small molecules from this pathway have not been reported. Here we implemented a comparative metabolomics and targeted structural network analyses approach to identify a catalog of small molecules dependent on the colibactin pathway from the meningitis isolate E. coli IHE3034 and the probiotic E. coli Nissle 1917. The structures of 10 pathway-dependent small molecules are proposed based on structural characterizations and network relationships. The network will provide a roadmap for the structural and functional elucidation of a variety of other small molecules encoded by the pathway. From the characterized small molecule set, in vitro bacterial growth inhibitory and mammalian CNS receptor antagonist activities are presented. PMID:24932672

  6. Processing and characterization of porous structures from chitosan and starch for tissue engineering scaffolds.

    PubMed

    Nakamatsu, Javier; Torres, Fernando G; Troncoso, Omar P; Min-Lin, Yuan; Boccaccini, Aldo R

    2006-12-01

    Natural biodegradable polymers were processed by different techniques for the production of porous structures for tissue engineering scaffolds. Potato, corn, and sweet potato starches and chitosan, as well as blends of these, were characterized and used in the experiments. The techniques used to produce the porous structures included a novel solvent-exchange phase separation technique and the well-established thermally induced phase separation method. Characterization of the open pore structures was performed by measuring pore size distribution, density, and porosity of the samples. A wide range of pore structures ranging from 1 to 400 microm were obtained. The mechanisms of pore formation are discussed for starch and chitosan scaffolds. Pore morphology in starch scaffolds seemed to be determined by the initial freezing temperature/freezing rate, whereas in chitosan scaffolds the shape and size of pores may have been determined by the processing route used. The mechanical properties of the scaffolds were assessed by indentation tests, showing that the indentation collapse strength depends on the pore geometry and the material type. Bioactivity and degradation of the potential scaffolds were assessed by immersion in simulated body fluid. PMID:17154462

  7. Structural and biochemical characterization of engineered tissue using FTIR spectroscopic imaging: melanoma progression as an example

    NASA Astrophysics Data System (ADS)

    Bhargava, Rohit; Kong, Rong

    2008-02-01

    Engineered tissue represents a convenient path to providing models for imaging and disease progression. The use of these models or phantoms is becoming increasingly prevalent. While structural characterization of these systems is well-documented, a combination of biochemical and structural knowledge is often helpful. Fourier transform infrared (FTIR) spectroscopic imaging is a rapidly emerging technique that combines the molecular selectivity of spectroscopy with the spatial specificity of optical microscopy. Here, we report on the application of FTIR spectroscopic for analysis of a melanoma model in engineered skin. We first characterize the biochemical properties, consistency and spectral changes in different layers of growing skin. Results provide simple indices for monitoring tissue consistency and reproducibility as a function of time. Second, we introduce malignant melanocytes to simulate tumor formation and growth. Both cellular changes associated with tumor formation and growth can be observed. FTIR images indicate holistic chemical changes during the tumor growth, allowing for the development of automated pathology protocols. FTIR imaging being non-destructive, further, samples remain entirely compatible with downstream tissue processing or staining. We specifically examined the correlation of structural changes, molecular content and reproducibility of the model systems. The development of analysis, integrating spectroscopy, imaging and computation will allow for quality control and standardization of both the structural and biochemical properties of tissue phantoms.

  8. Structural and Enzymatic Characterization of the Phosphotriesterase OPHC2 from Pseudomonas pseudoalcaligenes

    PubMed Central

    Gonzalez, Daniel; Elias, Mikael; Chabriere, Eric

    2013-01-01

    Background Organophosphates (OPs) are neurotoxic compounds for which current methods of elimination are unsatisfactory; thus bio-remediation is considered as a promising alternative. Here we provide the structural and enzymatic characterization of the recently identified enzyme isolated from Pseudomonas pseudoalcaligenes dubbed OPHC2. OPHC2 belongs to the metallo-β-lactamase superfamily and exhibits an unusual thermal resistance and some OP degrading abilities. Principal findings The X-ray structure of OPHC2 has been solved at 2.1 Å resolution. The enzyme is roughly globular exhibiting a αβ/βα topology typical of the metallo-β-lactamase superfamily. Several structural determinants, such as an extended dimerization surface and an intramolecular disulfide bridge, common features in thermostable enzymes, are consistent with its high Tm (97.8°C). Additionally, we provide the enzymatic characterization of OPHC2 against a wide range of OPs, esters and lactones. Significance OPHC2 possesses a broad substrate activity spectrum, since it hydrolyzes various phosphotriesters, esters, and a lactone. Because of its organophosphorus hydrolase activity, and given its intrinsic thermostability, OPHC2 is an interesting candidate for the development of an OPs bio-decontaminant. Its X-ray structure shed light on its active site, and provides key information for the understanding of the substrate binding mode and catalysis. PMID:24223749

  9. Structural and dynamic characterization of eukaryotic gene regulatory protein domains in solution

    SciTech Connect

    Lee, A L

    1996-05-01

    Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the {delta}-Al-{var_epsilon} activation domain from c-jun and the Drosophila RNA-binding protein Sex-lethal. The second system is the Drosophila Sex-lethal (Sxl) protein, an RNA-binding protein which is the ``master switch`` in sex determination. Sxl contains two adjacent RNA-binding domains (RBDs) of the RNP consensus-type. The NMR spectrum of the second RBD (Sxl-RBD2) was assigned using multidimensional heteronuclear NMR, and an intermediate-resolution family of structures was calculated from primarily NOE distance restraints. The overall fold was determined to be similar to other RBDs: a {beta}{alpha}{beta}-{beta}{alpha}{beta} pattern of secondary structure, with the two helices packed against a 4-stranded anti-parallel {beta}-sheet. In addition {sup 15}N T{sub 1}, T{sub 2}, and {sup 15}N/{sup 1}H NOE relaxation measurements were carried out to characterize the backbone dynamics of Sxl-RBD2 in solution. RNA corresponding to the polypyrimidine tract of transformer pre-mRNA was generated and titrated into 3 different Sxl-RBD protein constructs. Combining Sxl-RBD1+2 (bht RBDs) with this RNA formed a specific, high affinity protein/RNA complex that is amenable to further NMR characterization. The backbone {sup 1}H, {sup 13}C, and {sup 15}N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and {sup 15}N relaxation experiments were carried out to characterize the backbone dynamics of this complex. The changes in chemical shift in Sxl-RBD1+2 upon binding RNA are observed using Sxl-RBD2 as a substitute for unbound Sxl-RBD1+2. This allowed the binding interface to be qualitatively mapped for the second domain.

  10. Engineering characterization of ground motion. Task II. Effects of ground motion characteristics on structural response considering localized structural nonlinearities and soil-structure interaction effects. Volume 2

    SciTech Connect

    Kennedy, R.P.; Kincaid, R.H.; Short, S.A.

    1985-03-01

    This report presents the results of part of a two-task study on the engineering characterization of earthquake ground motion for nuclear power plant design. Task I of the study, which is presented in NUREG/CR-3805, Vol. 1, developed a basis for selecting design response spectra taking into account the characteristics of free-field ground motion found to be significant in causing structural damage. Task II incorporates additional considerations of effects of spatial variations of ground motions and soil-structure interaction on foundation motions and structural response. The results of Task II are presented in four parts: (1) effects of ground motion characteristics on structural response of a typical PWR reactor building with localized nonlinearities and soil-structure interaction effects; (2) empirical data on spatial variations of earthquake ground motion; (3) soil-structure interaction effects on structural response; and (4) summary of conclusions and recommendations based on Tasks I and II studies. This report presents the results of the first part of Task II. The results of the other parts will be presented in NUREG/CR-3805, Vols. 3 to 5.

  11. Characterization and crystal structure of lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase (cDHDPS) protein

    SciTech Connect

    Rice, E.A.; Bannon, G.A.; Glenn, K.C.; Jeong, S.S.; Sturman, E.J.; Rydel, T.J.

    2008-11-21

    The lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase enzyme (cDHDPS) was recently successfully introduced into maize plants to enhance the level of lysine in the grain. To better understand lysine insensitivity of the cDHDPS, we expressed, purified, kinetically characterized the protein, and solved its X-ray crystal structure. The cDHDPS enzyme has a fold and overall structure that is highly similar to other DHDPS proteins. A noteworthy feature of the active site is the evidence that the catalytic lysine residue forms a Schiff base adduct with pyruvate. Analyses of the cDHDPS structure in the vicinity of the putative binding site for S-lysine revealed that the allosteric binding site in the Escherichia coli DHDPS protein does not exist in cDHDPS due to three non-conservative amino acids substitutions, and this is likely why cDHDPS is not feedback inhibited by lysine.

  12. Raman spectroscopic characterization of the core-rim structure in reaction bonded boron carbide ceramics

    SciTech Connect

    Jannotti, Phillip; Subhash, Ghatu; Zheng, James Q.; Halls, Virginia; Karandikar, Prashant G.; Salamone, S.; Aghajanian, Michael K.

    2015-01-26

    Raman spectroscopy was used to characterize the microstructure of reaction bonded boron carbide ceramics. Compositional and structural gradation in the silicon-doped boron carbide phase (rim), which develops around the parent boron carbide region (core) due to the reaction between silicon and boron carbide, was evaluated using changes in Raman peak position and intensity. Peak shifting and intensity variation from the core to the rim region was attributed to changes in the boron carbide crystal structure based on experimental Raman observations and ab initio calculations reported in literature. The results were consistent with compositional analysis determined by energy dispersive spectroscopy. The Raman analysis revealed the substitution of silicon atoms first into the linear 3-atom chain, and then into icosahedral units of the boron carbide structure. Thus, micro-Raman spectroscopy provided a non-destructive means of identifying the preferential positions of Si atoms in the boron carbide lattice.

  13. Stationary phases with special structural properties for high-throughput separation techniques: preparation, characterization and applications.

    PubMed

    Buszewski, Boguslaw; Welerowicz, Tomasz

    2004-06-01

    Stationary phases with specific structural properties for high-throughput liquid chromatographic (LC) techniques are described. Special attention was paid to phases with special structural properties, mainly containing internal functional group (e.g. amide). Such materials are generally called "embedded phases". There are phases created in amidation process of aminopropylated silica gel, especially phases based on biological compounds, like phospholipids and cholesterol, which are called immobilized artificial membranes (IAM's). The synthesis and applications of polar embedded amide LC stationary phases were also reviewed. Methods of characterization of synthesized packing materials were presented, with general focusing on spectroscopic measurements like (13C and 29Si CP/MAS NMR and FT-IR), elemental and thermal analysis as well as chromatographic quantitative structure-retention relationships (QSRR) and extended chemometric tests. The potential applications of various dedicated stationary phases in a high-throughput LC screening procedures were also presented. PMID:15200378

  14. Raman spectroscopic characterization of the core-rim structure in reaction bonded boron carbide ceramics

    NASA Astrophysics Data System (ADS)

    Jannotti, Phillip; Subhash, Ghatu; Zheng, James Q.; Halls, Virginia; Karandikar, Prashant G.; Salamone, S.; Aghajanian, Michael K.

    2015-01-01

    Raman spectroscopy was used to characterize the microstructure of reaction bonded boron carbide ceramics. Compositional and structural gradation in the silicon-doped boron carbide phase (rim), which develops around the parent boron carbide region (core) due to the reaction between silicon and boron carbide, was evaluated using changes in Raman peak position and intensity. Peak shifting and intensity variation from the core to the rim region was attributed to changes in the boron carbide crystal structure based on experimental Raman observations and ab initio calculations reported in literature. The results were consistent with compositional analysis determined by energy dispersive spectroscopy. The Raman analysis revealed the substitution of silicon atoms first into the linear 3-atom chain, and then into icosahedral units of the boron carbide structure. Thus, micro-Raman spectroscopy provided a non-destructive means of identifying the preferential positions of Si atoms in the boron carbide lattice.

  15. Metal-organic frameworks: structure, properties, methods of synthesis and characterization

    NASA Astrophysics Data System (ADS)

    Butova, V. V.; Soldatov, M. A.; Guda, A. A.; Lomachenko, K. A.; Lamberti, C.

    2016-03-01

    This review deals with key methods of synthesis and characterization of metal-organic frameworks (MOFs). The modular structure affords a wide variety of MOFs with different active metal sites and organic linkers. These compounds represent a new stage of development of porous materials in which the pore size and the active site structure can be modified within wide limits. The set of experimental methods considered in this review is sufficient for studying the short-range and long-range order of the MOF crystal structure, determining the morphology of samples and elucidating the processes that occur at the active metal site in the course of chemical reactions. The interest in metal-organic frameworks results, first of all, from their numerous possible applications, ranging from gas separation and storage to chemical reactions within the pores. The bibliography includes 362 references.

  16. Novel aldehyde and thiosemicarbazone derivatives: Synthesis, spectroscopic characterization, structural studies and molecular docking studies

    NASA Astrophysics Data System (ADS)

    Karakurt, Tuncay; Tahtaci, Hakan; Subasi, Nuriye Tuna; Er, Mustafa; Ağar, Erbil

    2016-12-01

    In this study our purpose is that, synthesis and characterization of compounds containing the aldehyde and thiosemicarbazone groups and comparison of the theoretical results with the experimental results. The structures of all synthesized compounds were elucidated by IR, 1H NMR, 13C NMR, elemental analyses techniques. The structure of compound (4) (C9H8N4O2S) was also elucidated by X-ray diffraction analysis. In addition, the theoretical IR spectrum, 1H NMR and 13C NMR chemical shift values, frontier molecular orbital values (FMO) of these molecules were analyzed by using Becke-3- Lee-Yang-Parr (B3LYP) method with LanL2DZ basis set. Finally, molecular docking studies were performed on synthesized compounds using the 4DKI beta-lactam protein structure to determine the potential binding mode of inhibitors.

  17. Inflight Characterization of the Cassini Spacecraft Propellant Slosh and Structural Frequencies

    NASA Technical Reports Server (NTRS)

    Lee, Allan Y.; Stupik, Joan

    2015-01-01

    While there has been extensive theoretical and analytical research regarding the characterization of spacecraft propellant slosh and structural frequencies, there have been limited studies to compare the analytical predictions with measured flight data. This paper uses flight telemetry from the Cassini spacecraft to get estimates of high-g propellant slosh frequencies and the magnetometer boom frequency characteristics, and compares these values with those predicted by theoretical works. Most Cassini attitude control data are available at a telemetry frequency of 0.5 Hz. Moreover, liquid sloshing is attenuated by propellant management device and attitude controllers. Identification of slosh and structural frequency are made on a best-effort basis. This paper reviews the analytical approaches that were used to predict the Cassini propellant slosh frequencies. The predicted frequencies are then compared with those estimated using telemetry from selected Cassini burns where propellant sloshing was observed (such as the Saturn Orbit Insertion burn). Determination of the magnetometer boom structural frequency is also discussed.

  18. Characterization and crystal structure determination of β-1,2-mannobiose phosphorylase from Listeria innocua.

    PubMed

    Tsuda, Tomohiro; Nihira, Takanori; Chiku, Kazuhiro; Suzuki, Erika; Arakawa, Takatoshi; Nishimoto, Mamoru; Kitaoka, Motomitsu; Nakai, Hiroyuki; Fushinobu, Shinya

    2015-12-21

    Glycoside hydrolase family 130 consists of phosphorylases and hydrolases for β-mannosides. Here, we characterized β-1,2-mannobiose phosphorylase from Listeria innocua (Lin0857) and determined its crystal structures complexed with β-1,2-linked mannooligosaccharides. β-1,2-Mannotriose was bound in a U-shape, interacting with a phosphate analog at both ends. Lin0857 has a unique dimer structure connected by a loop, and a significant open-close loop displacement was observed for substrate entry. A long loop, which is exclusively present in Lin0857, covers the active site to limit the pocket size. A structural basis for substrate recognition and phosphorolysis was provided. PMID:26632508

  19. Characterization of multiple twinned structural units in pulse-electrodeposited nickel

    NASA Astrophysics Data System (ADS)

    Klement, U.; Kahrimanidis, A.; Yao, Y.

    2015-04-01

    The investigation was performed on pulse-electrodeposited Nickel with submicrocrystalline microstructure containing slightly elongated grains having a <110> fibre texture in growth direction. Structural units in form of groups of elongated grains possessing a common <110>-zone axis in growth direction and CSL boundaries (in some cases twins) between them have been found in the microstructure by use of EBSD. Grain growth sets in above 325°C but the texture is conserved up to at least 600°C. This means that the arrangement of twins and other CSL boundaries stabilized the structural units; there is no orientation change (by further twinning) when grain growth occurs as seen in previous studies on Ni and Ni-Fe of different initial texture. The observed structural units were characterized in detail and the occurring grains and grain boundaries are described.

  20. Structural and Biochemical Characterization of AidC, a Quorum-Quenching Lactonase With Atypical Selectivity

    PubMed Central

    Mascarenhas, Romila; Thomas, Pei W.; Wu, Chun-Xiang; Nocek, Boguslaw P.; Hoang, Quyen Q.; Liu, Dali; Fast, Walter

    2015-01-01

    Quorum-quenching catalysts are of interest for potential application as biochemical tools to interrogate interbacterial communication pathways, as anti-biofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-L-homoserine (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is one of the most efficient wild-type quorum-quenching enzymes characterized to date, with a kcat/KM value of approximately 2 × 106 M−1s−1 for N-heptanoyl-L-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) than typical AHL lactonases (ca. > 1 mM). X-ray crystal structures of AidC alone, and with the product N-hexanoyl-L-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multi-angle light scattering. The structures reveal two atypical features as compared to previously characterized AHL lactonases: a ‘kinked’ α-helix that forms part of a closed binding pocket which provides affinity and enforces selectivity for AHL substrates, and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. Implications for the catalytic mechanism of AHL lactonases are discussed. PMID:26115006

  1. Structural and biochemical characterization of AidC, a quorum-quenching lactonase with atypical selectivity

    SciTech Connect

    Mascarenhas, Romila; Thomas, Pei W.; Wu, Chun -Xiang; Nocek, Boguslaw P.; Hoang, Quyen Q.; Liu, Dali; Fast, Walter

    2015-06-26

    Quorum-quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-l-homoserine lactone (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is the most efficient wild-type quorum-quenching enzymes characterized to date, with a kcat/KM value of approximately 2 × 106 M-1 s-1 for N-heptanoyl-l-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) compared to those of typical AHL lactonases (ca. >1 mM). X-ray crystal structures of AidC alone and with the product N-hexanoyl-l-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multiangle light scattering. Lastly, the structures reveal two atypical features as compared to previously characterized AHL lactonases: a "kinked" α-helix that forms part of a closed binding pocket that provides affinity and enforces selectivity for AHL substrates and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. We discuss implications for the catalytic mechanism of AHL lactonases.

  2. Structural and biochemical characterization of AidC, a quorum-quenching lactonase with atypical selectivity

    DOE PAGESBeta

    Mascarenhas, Romila; Thomas, Pei W.; Wu, Chun -Xiang; Nocek, Boguslaw P.; Hoang, Quyen Q.; Liu, Dali; Fast, Walter

    2015-06-26

    Quorum-quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-l-homoserine lactone (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is the most efficient wild-type quorum-quenching enzymes characterized to date, with a kcat/KM value of approximately 2 × 106 M-1 s-1 for N-heptanoyl-l-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) compared to those of typical AHL lactonases (ca. >1 mM).more » X-ray crystal structures of AidC alone and with the product N-hexanoyl-l-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multiangle light scattering. Lastly, the structures reveal two atypical features as compared to previously characterized AHL lactonases: a "kinked" α-helix that forms part of a closed binding pocket that provides affinity and enforces selectivity for AHL substrates and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. We discuss implications for the catalytic mechanism of AHL lactonases.« less

  3. Comparative structural characterization of 7 commercial galacto-oligosaccharide (GOS) products.

    PubMed

    van Leeuwen, Sander S; Kuipers, Bas J H; Dijkhuizen, Lubbert; Kamerling, Johannis P

    2016-04-29

    Many β-galactosidase enzymes convert lactose into a mixture of galacto-oligosaccharides (GOS) when incubated under the right conditions. Recently, the composition of commercial Vivinal GOS produced by Bacillus circulans β-galactosidase was studied in much detail in another study by van Leeuwen et al. As a spin-off of this study, we used the developed analytical strategy for the evaluation of 6 anonymous commercial GOS products, in comparison with Vivinal GOS. These GOS products were first subjected to HPLC-SEC, calibrated HPAEC-PAD profiling (glucose units in relation to a malto-oligosaccharide ladder), and 1D (1)H NMR spectroscopy. For a more detailed analysis and support of the conclusions based on the initial analysis, the GOS products were separated into DP-pure subpools on Bio-Gel P-2 (MALDI-TOF-MS analysis), which were subjected to calibrated HPAEC-PAD profiling and (1)H NMR analysis. Unidentified peaks from different GOS products, not present in Vivinal GOS, were isolated for detailed structural characterization. In this way, the differences between the various GOS products in terms of DP distribution and type of glycosidic linkages were established. A total of 13 new GOS structures were characterized, adding structural-reporter-group signals and HPAEC-PAD based glucose unit G.U. values to the analytical toolbox. The newly characterized products enhance the quality of the database with GOS structures up to DP4. The combined data provide a firm basis for the rapid profiling of the GOS products of microbial β-galactosidase enzymes. PMID:27035911

  4. Structural dynamic characterization of a vehicle seat coupled with human occupant

    NASA Astrophysics Data System (ADS)

    Lo, Leon; Fard, Mohammad; Subic, Aleksandar; Jazar, Reza

    2013-02-01

    Predicting the responses of the combined human body-seat structure to vibration excitation is still a challenging task. This is mainly due to the complex dynamics behaviour of the seated human body in response to vibration. It is however essential to characterize and predict the critical frequencies and the corresponding vibration patterns of the seat when it is coupled with a human occupant. This study provides important knowledge to predict the structural resonant frequencies and corresponding vibration mode shapes of the vehicle seat coupled with occupant from the seat alone or seat bare-frame (seat without foam cushion). An experiment is designed to measure the frequency responses, resonant frequencies, and corresponding mode shapes of the three different selected vehicle seats when mounted on the test rig. Six volunteers have participated in the experiments. The experiment data for each of the seats were collected for the seat bare-frames, seat alone (seat with foam cushion), and seat with human occupant. The results indicate that the vehicle seat bare-frame, seat alone, and seat with occupant have similar main seatback lateral, seatback fore-aft, and seat twisting structural resonant frequencies below 80 Hz. The coupling of the seated human body with the seat shows that the human occupant is not adding any new structural resonant frequency or mode shape to the seat below 80 Hz. It is therefore possible to characterize and predict the key vibration attributes such as occupied seat structural resonant frequencies and mode shapes from their corresponding unoccupied seat or bare frame characteristics. This alleviates the need for complex modelling or detailed analysis of the human body structure itself.

  5. Predicting X-ray absorption spectra of semiconducting polymers for electronic structure and morphology characterization

    NASA Astrophysics Data System (ADS)

    Su, Gregory; Patel, Shrayesh; Pemmaraju, C. Das; Kramer, Edward; Prendergast, David; Chabinyc, Michael

    2015-03-01

    Core-level X-ray absorption spectroscopy (XAS) reveals important information on the electronic structure of materials and plays a key role in morphology characterization. Semiconducting polymers are the active component in many organic electronics. Their electronic properties are critically linked to device performance, and a proper understanding of semiconducting polymer XAS is crucial. Techniques such as resonant X-ray scattering rely on core-level transitions to gain materials contrast and probe orientational order. However, it is difficult to identify these transitions based on experiments alone, and complementary simulations are required. We show that first-principles calculations can capture the essential features of experimental XAS of semiconducting polymers, and provide insight into which molecular model, such as oligomers or periodic boundary conditions, are best suited for XAS calculations. Simulated XAS can reveal contributions from individual atoms and be used to visualize molecular orbitals. This allows for improved characterization of molecular orientation and scattering analysis. These predictions lay the groundwork for understanding how chemical makeup is linked to electronic structure, and to properly utilize experiments to characterize semiconducting polymers.

  6. Synthesis, structural characterization and catalytic activity of a multifunctional enzyme mimetic oxoperoxovanadium(V) complex.

    PubMed

    Si, Tapan K; Paul, Shiv S; Drew, Michael G B; Mukherjea, Kalyan K

    2012-05-21

    The synthesis and structural characterization of a novel oxoperoxovanadium(V) complex [VO(O(2))(PAH)(phen)] containing the ligands 2-phenylacetohydroxamic acid (PAHH) and 1,10-phenanthroline (phen) has been accomplished. The oxoperoxovanadium(V) complex was found to mimic both vanadate-dependent haloperoxidase (VHPO) activity as well as nuclease activity through effective interaction with DNA. The complex is the first example of a structurally characterized stable oxoperoxovanadium(V) complex with a coordinated bi-dentate hydroximate moiety (-CONHO(-)) from 2-phenylacetohydroximate (PAH). The oxoperoxovanadium(V) complex has been used as catalyst for the peroxidative bromination reaction of some unsaturated alcohols (e.g. 4-pentene-1-ol, 1-octene-3-ol and 9-decene-1-ol) in the presence of H(2)O(2) and KBr. The catalytic products have been characterized by GC-MS analysis and spectrophotometric methods. The DNA binding of this complex has been established with CT DNA whereas the DNA cleavage was demonstrated with plasmid DNA. The interactions of the complex with DNA have been monitored by electronic absorption and fluorescence emission spectroscopy. Viscometric measurements suggest that the compound is a DNA intercalator. The nuclease activity of this complex was confirmed by gel electrophoresis studies. PMID:22441646

  7. Combined No Dig techniques for the characterization of historical buildings' structural elements in Abruzzo

    NASA Astrophysics Data System (ADS)

    Ranalli, Danilo; Santacroce, Cristina

    2013-04-01

    Non destructive investigation techniques, No Dig Techniques, have been applied in engineering field since over fifty years, and their employment innovations increase proportionally to the technological development. Actually, for existing buildings, is possible to employ several non destructive investigation techniques, according to current national and local regulations. The application of an indirect survey campaign, enable to extend the result obtained by a confined e/o local destructive investigation method to the whole studied object. It offers a more complete structure knowledge, in terms of physics, chemistry and mechanical characterization, in despite of using less invasive investigation methods. In this paper the attention is pointed on structures characterization, belonging to historic and architectonic Italian heritage, using minimal impact investigation methods. The proposed method consists of the combined employing of Georadar technique, using high frequencies antennas unit, and sonic method, setting an impulsive mass centred on low frequencies. The result of this combined method, employed in the Abruzzi Region post seismic context (6th april 2009 Earthquake), are exposed treating two case-studies of masonry pillars characterization in the "De Amicis" school courtyard (L'Aquila old town centre), and in the naves of Valvense Basilica di San Pelino (Corfinio).

  8. Property characterization of AlN thin films in composite resonator structure

    NASA Astrophysics Data System (ADS)

    Chen, Qingming; Qin, Lifen; Wang, Qing-Ming

    2007-04-01

    AlN thin films with c-axis orientation have been investigated for fabricating thin film bulk acoustic wave resonators in the past few years. Characterization of thin film material properties including density, elastic modulus, and piezoelectric coefficient is essential in processing study and for predicting the performance of the acoustic devices. In this paper, we present our results on the fabrication of highly c-axis oriented AlN thin films on Pt /Ti/Si (100) substrates by dc reactive magnetron sputtering method. The crystalline structure and the surface morphology of AlN films are characterized by x-ray diffraction and scanning electron microscopy. The effective piezoelectric coefficient d33eff of the AlN films was measured by a laser interferometer method and the piezoelectric coefficient d33 was estimated. A recently developed resonance spectrum method is applied to characterize the electromechanical properties of AlN thin films based on the input electrical impedance equation derived by one-dimensional transmission line theory for composite resonators. Using the experimental impedance spectrum data, the density and elastic constant of the piezoelectric AlN thin film in the four-layer composite resonator structure are evaluated. The calculated results reveal that the piezoelectric coefficient d33, density, and velocity of the c-axis oriented AlN thin film are 4.19pm/V, 3187.3kg/m3, and 10631m/s, respectively.

  9. Studies in dynamic characterization and control of a flexible structure and optical beampath

    NASA Astrophysics Data System (ADS)

    Schulthess, Marcus R.

    The dynamic characterization and control of a flexible structure and optical beampath is explored. The experiment is motivated by the expanding demand for structurally mounted space based laser pointing and tracking systems. The setup of the cantilevered UWAA planar truss is based on a similar setup at the Air Force Academy. An existing finite element model is modified to reflect the characteristics of the UWAA truss and experimentally validated. A reduced order truss model suitable for simulation is developed and validated with the hardware. The formulation of linear and nonlinear models for the AJT and tilting mirror actuators are explored. The design and implementation of the mirror and structural control is manifested in the form of proportional-integral (PI) feedback to a tilting control mirror to actively reject line of sight disturbances and velocity feedback to on-off AJT actuators to supress large amplitude low frequency lateral structural vibrations. Good line of sight disturbance rejection is demonstrated for the first four lateral modes of the flexible truss structure. The AJT velocity feedback controller was used to supress large amplitude low frequency oscillations to bring structural vibrational motions to within limited range of the tilting mirror platform. A baseline theoretical model of the reduced order truss and control actuators was constructed in SIMULAB and thoroughly validated.

  10. Characterization of dermal plates from armored catfish Pterygoplichthys pardalis reveals sandwich-like nanocomposite structure.

    PubMed

    Ebenstein, Donna; Calderon, Carlos; Troncoso, Omar P; Torres, Fernando G

    2015-05-01

    Dermal plates from armored catfish are bony structures that cover their body. In this paper we characterized structural, chemical, and nanomechanical properties of the dermal plates from the Amazonian fish Pterygoplichthys pardalis. Analysis of the morphology of the plates using scanning electron microscopy (SEM) revealed that the dermal plates have a sandwich-like structure composed of an inner porous matrix surrounded by two external dense layers. This is different from the plywood-like laminated structure of elasmoid fish scales but similar to the structure of osteoderms found in the dermal armour of some reptiles and mammals. Chemical analysis performed using Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and X-ray diffraction (XRD) results revealed similarities between the composition of P. pardalis plates and the elasmoid fish scales of Arapaima gigas. Reduced moduli of P. pardalis plates measured using nanoindentation were also consistent with reported values for A. gigas scales, but further revealed that the dermal plate is an anisotropic and heterogeneous material, similar to many other fish scales and osteoderms. It is postulated that the sandwich-like structure of the dermal plates provides a lightweight and tough protective layer. PMID:25732181

  11. Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames)

    PubMed Central

    Couñago, Rafael M; Davlieva, Milya; Strych, Ulrich; Hill, Ryan E; Krause, Kurt L

    2009-01-01

    Background Bacillus anthracis is the causative agent of anthrax and a potential bioterrorism threat. Here we report the biochemical and structural characterization of B. anthracis (Ames) alanine racemase (AlrBax), an essential enzyme in prokaryotes and a target for antimicrobial drug development. We also compare the native AlrBax structure to a recently reported structure of the same enzyme obtained through reductive lysine methylation. Results B. anthracis has two open reading frames encoding for putative alanine racemases. We show that only one, dal1, is able to complement a D-alanine auxotrophic strain of E. coli. Purified Dal1, which we term AlrBax, is shown to be a dimer in solution by dynamic light scattering and has a Vmax for racemization (L- to D-alanine) of 101 U/mg. The crystal structure of unmodified AlrBax is reported here to 1.95 Å resolution. Despite the overall similarity of the fold to other alanine racemases, AlrBax makes use of a chloride ion to position key active site residues for catalysis, a feature not yet observed for this enzyme in other species. Crystal contacts are more extensive in the methylated structure compared to the unmethylated structure. Conclusion The chloride ion in AlrBax is functioning effectively as a carbamylated lysine making it an integral and unique part of this structure. Despite differences in space group and crystal form, the two AlrBax structures are very similar, supporting the case that reductive methylation is a valid rescue strategy for proteins recalcitrant to crystallization, and does not, in this case, result in artifacts in the tertiary structure. PMID:19695097

  12. Non-destructive testing for the structures and civil infrastructures characterization

    NASA Astrophysics Data System (ADS)

    Capozzoli, L.; Rizzo, E.

    2012-04-01

    This work evaluates the ability of non-conventional NDT techniques such as GPR, geoelectrical method and conventional ones such as infrared thermography (IRT) and sonic test for the characterization of building structures in laboratory and in-situ. Moreover, the integration of the different techniques were evaluated in order to reduce the degree of uncertainties associated. The presence of electromagnetic, resistivity or thermal anomalies in the behavior may be related to the presence of defects, crack, decay or moisture. The research was conducted in two phases: the first phase was performed in laboratory and the second one mainly in the field work. The laboratory experiments proceeded to calibrate the geophysical techniques GPR and geoelectrical method on building structures. A multi-layer structure was reconstructed in laboratory, in order to simulate a back-bridge: asphalt, reinforced concrete, sand and gravel layers. In the deep sandy layer, PVC, aluminum and steel pipes were introduced. This structure has also been brought to crack in a predetermined area and hidden internal fractures were investigated. GPR has allowed to characterize the panel in a non-invasive mode; radar maps were developed using various algorithms during post-process about 2D maps and 3D models with aerial acquisition of 400 MHz, 900MHz, 1500MHz, 2000MHz. Geoelectrical testing was performed with a network of 25 electrodes spaced at mutual distance of 5 cm. Two different configurations were used dipole-dipole and pole-dipole approaches. In the second phase, we proceeded to the analysis of pre-tensioned concrete in order to detect the possible presence of criticality in the structure. For this purpose by GPR 2GHz antenna, a '70 years precast bridge characterized by a high state of decay was studied; then were also analyzed a pillar and a beam of recent production directly into the processing plant. Moreover, results obtained using GPR were compared with those obtained through the use of

  13. Integrating structural and functional connectivity to characterize sediment dynamics in a small Alpine catchment

    NASA Astrophysics Data System (ADS)

    Cavalli, Marco; Crema, Stefano; Blok, Michiel; Lucía, Ana; Comiti, Francesco; Marchi, Lorenzo; Keesstra, Saskia

    2016-04-01

    Sediment connectivity can be regarded as a descriptor of the internal linkages between different landscape components within a catchment. The recent focus of the scientific community on connectivity related topics, both concerning hydrological and sediment connectivity, stresses the importance of understanding the main active pathways for a better estimation of energy and matter transfer at catchment scale. This task can be addressed using topography-based indices that analyse the linkages between landscape units. This approach to characterize connectivity is known as structural connectivity. The main limitation of structural connectivity is that it does not account for the processes driving sediment and energy fluxes (i.e., functional connectivity). In this work the integration between structural and functional approaches is proposed for characterizing sediment connectivity in mountain catchments. The structural approach, based on a topography-based sediment connectivity index, was used for assessing hillslope-to-channel connectivity. Since field data on processes driving sediment transport along the channel network are available, a functional approach has been devised to estimate within-channel connectivity. An index of unit stream power computed from the hydraulic properties of the channel (i.e., discharge, slope and channel width) has been compared with the critical unit stream power computed from incipient motion thresholds derived from field data to identify the cells of the Digital Terrain Model (DTM) in which sediment can be mobilized under near-bankfull conditions. The index expressing the within-channel connectivity is given by the length of the reaches consisting of contiguous cells that exceed the critical unit stream power. During high-magnitude floods, when unit stream power values exceed the threshold for incipient motion, channels experience an increase in both hydrological and sediment connectivity. The proposed index characterizes those sections

  14. Joint application of non-invasive techniques to characterize the dynamic behaviuor of engineering structures

    NASA Astrophysics Data System (ADS)

    Gallipoli, M. R.; Perrone, A.; Stabile, T. A.; Ponzo, F. C.; Ditommaso, R.

    2012-04-01

    The systematic monitoring of strategic civil infrastructures such as bridges, large dams or high-rise buildings in order to ensure their structural stability is a strategic issue particularly in earthquake-prone regions. Nevertheless, in areas less exposed to seismic hazard, the monitoring is also an important tool for civil engineers, for instance if they have to deal with structures exposed to heavy operational demands for extended periods of time and whose structural integrity might be in question or at risk. A continuous monitoring of such structures allows the identification of their fundamental response characteristics and the changes of these over time, the latter representing indicators for potential structural degradation. The aim of this paper is the estimation of fundamental dynamic parameters of some civil infrastructures by the joint application of fast executable, non-invasive techniques such as the Ambient Noise Standard Spectral Ratio, and Ground-Based microwave Radar Interferometer techniques. The joint approach combine conventional, non-conventional and innovative techniques in order to set up a non destructive evaluation procedure allowing for a multi-sensing monitoring at a multi-scale and multi-depth levels (i.e. with different degrees of spatial resolution and different subsurface depths). In particular, techniques based on ambient vibration recordings have become a popular tool for characterizing the seismic response and state-of-health of strategic civil infrastructure. The primary advantage of these approaches lies in the fact that no transient earthquake signals or even active excitation of the structure under investigation are required. The microwave interferometry radar technology, it has proven to be a powerful remote sensing tool for vibration measurement of structures, such as bridge, heritage architectural structures, vibrating stay cables, and engineering structures. The main advantage of this radar technique is the possibility to

  15. Image-based characterization of cement pore structure using Wood`s metal intrusion

    SciTech Connect

    Willis, K.L.; Abell, A.B.; Lange, D.A.

    1998-12-01

    Mercury intrusion porosimetry is a widely used technique for characterization of the pore size distribution of cement-based materials. However, the technique has several limitations, among which are the ink bottle effect and a cylindrical pore geometry assumption that lead to inaccurate pore size distribution curves. By substituting Wood`s metal for mercury as the intruding liquid, scanning electron microscopy and imaging techniques can be applied to the sample after intrusion. The molten Wood`s metal solidifies within the pore structure of the sample, which allows it to be sectioned and observed in the scanning electron microscopy. From here, the sample can be analyzed both qualitatively, by observing the changes in the appearance of the sample as the intrusion process progresses, and quantitatively, by applying image analysis techniques. This study provides insight for better interpretation of mercury intrusion porosimetry results and the possibility for quantitative characterization of the spatial geometry of pores in cement-based materials.

  16. Novel pyridinium based cobalt carbonyl ionic liquids: synthesis, full characterization, crystal structure and application in catalysis.

    PubMed

    Deng, Fan-Guo; Hu, Bin; Sun, Wei; Chen, Jing; Xia, Chun-Gu

    2007-10-10

    Through an optimized synthetic strategy, a series of novel alkylpyridinium cobalt tetracarbonyl salts, [C(1)Py][Co(CO)(4)] (), [C(4)Py][Co(CO)(4)] () and [C(16)Py][Co(CO)(4)] () (C(n)Py = N-C(n)H(2n+1)-pyridinium), were successfully prepared in good yields, using a water-organic biphasic system. All the three compounds melt well below 100 degrees C and could be classified as ionic liquids. The compounds were fully characterized using IR, UV-Vis, (1)H NMR, (13)C NMR, ESI-MS and elemental analysis, and was structurally characterized by X-ray single crystal analysis. Compound has been found to be an efficient and reusable catalyst for the alkoxycarbonylation of propylene oxide without the aid of a base additive. PMID:17893815

  17. The Preparation and Structural Characterization of Three Structural Types of Gallium Compounds Derived from Gallium (II) Chloride

    NASA Technical Reports Server (NTRS)

    Gordon, Edward M.; Hepp, Aloysius F.; Duraj. Stan A.; Habash, Tuhfeh S.; Fanwick, Phillip E.; Schupp, John D.; Eckles, William E.; Long, Shawn

    1997-01-01

    The three compounds Ga2Cl4(4-mepy)2 (1),[GaCl2(4-mepy)4]GaCl4x1/2(4-mepy); (2) and GaCl2(4-mepy)2(S2CNEt2); (3) (4-mepy= 4-methylpyridine) have been prepared from reactions of gallium (II) chloride in 4-methylpyridine and characterized by single-crystal X-ray analysis. Small variations in the reaction conditions for gallium(II) chloride can produce crystals with substantially different structural properties. The three compounds described here encompass a neutral gallium(II) dimer in which each gallium is four-coordinate, an ionic compound containing both anionic and cationic gallium complex ions with different coordination numbers and a neutral six-coordinate heteroleptic

  18. Technical decision making with higher order structure data: higher order structure characterization during protein therapeutic candidate screening.

    PubMed

    Jiang, Yijia; Li, Cynthia; Li, Jenny; Gabrielson, John P; Wen, Jie

    2015-04-01

    Protein therapeutics differ considerably from small molecule drugs because of the presence of higher order structure (HOS), post-translational modifications, inherent molecular heterogeneity, and unique stability profiles. At early stages of development, multiple molecular candidates are often produced for the same biological target. In order to select the most promising molecule for further development, studies are carried out to compare and rank order the candidates in terms of their manufacturability, purity, and stability profiles. This note reports a case study on the use of selected HOS characterization methods for candidate selection and the role of HOS data in identifying potential challenges that may be avoided by selecting the optimal molecular entity for continued development. PMID:25716705

  19. Advanced analysis of complex seismic waveforms to characterize the subsurface Earth structure

    NASA Astrophysics Data System (ADS)

    Jia, Tianxia

    2011-12-01

    This thesis includes three major parts, (1) Body wave analysis of mantle structure under the Calabria slab, (2) Spatial Average Coherency (SPAC) analysis of microtremor to characterize the subsurface structure in urban areas, and (3) Surface wave dispersion inversion for shear wave velocity structure. Although these three projects apply different techniques and investigate different parts of the Earth, their aims are the same, which is to better understand and characterize the subsurface Earth structure by analyzing complex seismic waveforms that are recorded on the Earth surface. My first project is body wave analysis of mantle structure under the Calabria slab. Its aim is to better understand the subduction structure of the Calabria slab by analyzing seismograms generated by natural earthquakes. The rollback and subduction of the Calabrian Arc beneath the southern Tyrrhenian Sea is a case study of slab morphology and slab-mantle interactions at short spatial scale. I analyzed the seismograms traversing the Calabrian slab and upper mantle wedge under the southern Tyrrhenian Sea through body wave dispersion, scattering and attenuation, which are recorded during the PASSCAL CAT/SCAN experiment. Compressional body waves exhibit dispersion correlating with slab paths, which is high-frequency components arrivals being delayed relative to low-frequency components. Body wave scattering and attenuation are also spatially correlated with slab paths. I used this correlation to estimate the positions of slab boundaries, and further suggested that the observed spatial variation in near-slab attenuation could be ascribed to mantle flow patterns around the slab. My second project is Spatial Average Coherency (SPAC) analysis of microtremors for subsurface structure characterization. Shear-wave velocity (Vs) information in soil and rock has been recognized as a critical parameter for site-specific ground motion prediction study, which is highly necessary for urban areas located

  20. Ion beam-based characterization of multicomponent oxide thin films and thin film layered structures

    SciTech Connect

    Krauss, A.R.; Rangaswamy, M.; Lin, Yuping; Gruen, D.M.; Schultz, J.A.; Schmidt, H.K.; Chang, R.P.H.

    1992-11-01

    Fabrication of thin film layered structures of multi-component materials such as high temperature superconductors, ferroelectric and electro-optic materials, and alloy semiconductors, and the development of hybrid materials requires understanding of film growth and interface properties. For High Temperature Superconductors, the superconducting coherence length is extremely short (5--15 {Angstrom}), and fabrication of reliable devices will require control of film properties at extremely sharp interfaces; it will be necessary to verify the integrity of thin layers and layered structure devices over thicknesses comparable to the atomic layer spacing. Analytical techniques which probe the first 1--2 atomic layers are therefore necessary for in-situ characterization of relevant thin film growth processes. However, most surface-analytical techniques are sensitive to a region within 10--40 {Angstrom} of the surface and are physically incompatible with thin film deposition and are typically restricted to ultra high vacuum conditions. A review of ion beam-based analytical methods for the characterization of thin film and multi-layered thin film structures incorporating layers of multicomponent oxides is presented. Particular attention will be paid to the use of time-of-flight techniques based on the use of 1- 15 key ion beams which show potential for use as nondestructive, real-time, in-situ surface diagnostics for the growth of multicomponent metal and metal oxide thin films.

  1. Biochemical and Structural Characterization of the Human TL1A Ectodomain

    SciTech Connect

    Zhan, C.; Yan, Q; Patskovsky, Y; Li, Z; Toro, R; Meyer, A; Cheng, H; Brenowitz, M; Nathenson, S; Almo, S

    2009-01-01

    TNF-like 1A (TL1A) is a newly described member of the TNF superfamily that is directly implicated in the pathogenesis of autoimmune diseases, including inflammatory bowel disease, atherosclerosis, and rheumatoid arthritis. We report the crystal structure of the human TL1A extracellular domain at a resolution of 2.5 {angstrom}, which reveals a jelly-roll fold typical of the TNF superfamily. This structural information, in combination with complementary mutagenesis and biochemical characterization, provides insights into the binding interface and the specificity of the interactions between TL1A and the DcR3 and DR3 receptors. These studies suggest that the mode of interaction between TL1A and DcR3 differs from other characterized TNF ligand/receptor complexes. In addition, we have generated functional TL1A mutants with altered disulfide bonding capability that exhibit enhanced solution properties, which will facilitate the production of materials for future cell-based and whole animal studies. In summary, these studies provide insights into the structure and function of TL1A and provide the basis for the rational manipulation of its interactions with cognate receptors.

  2. Structural characterization of some oxalato-bridged copper(II) and nickel(II) complexes

    NASA Astrophysics Data System (ADS)

    Mautner, Franz A.; Louka, Febee R.; Massoud, Salah S.

    2009-03-01

    A new series of dinuclear oxalato-bridged copper(II) and nickel(II) complexes derived from tridentate amines: [Cu 2(Medpt) 2(μ-C 2O 4)](ClO 4) 2 ( 1), [Cu 2(pmedien) 2(μ-C 2O 4)](ClO 4) 2 ( 2), [Cu 2(DPA) 2(μ-C 2O 4)(ClO 4) 2]·2H 2O (3), and [Ni 2(Et 2dien) 2(μ-C 2O 4)(H 2O) 2](ClO 4) 2·2H 2O ( 4) (C 2O 42- = oxalate dianion, Medpt = 3,3'-diamino- N-methyldipropylmine, pmedien = N, N, N', N'', N''-pentamethyldiethylenetriamine, DPA = di(2-pyridylmethyl)amine and Et 2dien = N, N-diethyldiethylenetriamine) were synthesized and structurally characterized by X-ray crystallography. The spectral and structural characterizations of these complexes are reported. In this series, structures consist of the C 2O 42- bridging the two M(II) centers in a bis-bidentate bonding mode. The Cu 2+ centers are coordinated to the tridentate amines Medpt or pmedien in distorted SP geometry in 1 and 2, respectively, with the ClO 4- groups as counter ions. In the other two complexes, distorted octahedral geometries were achieved by the three nitrogen donors of the DPA and by an oxygen atom from coordinated perchlorate ion in 3 and by the Et 2dien and one water molecule in 4.

  3. Mechanical and structural characterizations of gamma- and alpha-alumina nanofibers

    SciTech Connect

    Vahtrus, Mikk; Umalas, Madis; Polyakov, Boris; Dorogin, Leonid; Saar, Rando; Tamme, Maret; Saal, Kristjan; Lõhmus, Rünno; Vlassov, Sergei

    2015-09-15

    We investigate the applicability of alumina nanofibers as a potential reinforcement material in ceramic matrix compounds by comparing the mechanical properties of individual nanofibers before and after annealing at 1400 °C. Mechanical testing is performed inside a scanning electron microscope (SEM), which enables observation in real time of the deformation and fracture of the fibers under loading, thereby providing a close-up inspection of the freshly fractured area in vacuum. Improvement of both the Young's modulus and the breaking strength for annealed nanofibers is demonstrated. Mechanical testing is supplemented with the structural characterization of the fibers before and after annealing using SEM, transmission electron microscopy and X-ray diffraction methods. - Highlights: • Mechanical properties of individual alumina nanofibers were measured using in situ SEM cantilevered beam bending technique. • Improvement of mechanical properties of the alumina fibers after annealing at 1400 °C is demonstrated. • Formation of branched structures is demonstrated and their mechanical properties are studied. • XRD and electron microscopy were used for structural characterization of untreated and annealed nanofibers.

  4. Structural characterization and aging of glassy pharmaceuticals made using acoustic levitation.

    PubMed

    Benmore, Chris J; Weber, J K R; Tailor, Amit N; Cherry, Brian R; Yarger, Jeffery L; Mou, Qiushi; Weber, Warner; Neuefeind, Joerg; Byrn, Stephen R

    2013-04-01

    Here, we report the structural characterization of several amorphous drugs made using the method of quenching molten droplets suspended in an acoustic levitator. (13) C NMR, X-ray, and neutron diffraction results are discussed for glassy cinnarizine, carbamazepine, miconazole nitrate, probucol, and clotrimazole. The (13) C NMR results did not find any change in chemical bonding induced by the amorphization process. High-energy X-ray diffraction results were used to characterize the ratio of crystalline to amorphous material present in the glasses over a period of 8 months. All the glasses were stable for at least 6 months except carbamazepine, which has a strong tendency to crystallize within a few months. Neutron and X-ray pair distribution function analyses were applied to the glassy materials, and the results were compared with their crystalline counterparts. The two diffraction techniques yielded similar results in most cases and identified distinct intramolecular and intermolecular correlations. The intramolecular scattering was calculated based on the crystal structure and fit to the measured X-ray structure factor. The resulting intermolecular pair distribution functions revealed broad-nearest and next-nearest neighbor molecule-molecule correlations. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 102:1290-1300, 2013. PMID:23381910

  5. Structural characterization of ANGPTL8 (betatrophin) with its interacting partner lipoprotein lipase.

    PubMed

    Siddiqa, Amnah; Ahmad, Jamil; Ali, Amjad; Paracha, Rehan Zafar; Bibi, Zurah; Aslam, Babar

    2016-04-01

    Angiopoietin-like protein 8 (ANGPTL8) (also known as betatrophin) is a newly identified secretory protein with a potential role in autophagy, lipid metabolism and pancreatic beta-cell proliferation. Its structural characterization is required to enhance our current understanding of its mechanism of action which could help in identifying its receptor and/or other binding partners. Based on the physiological significance and necessity of exploring structural features of ANGPTL8, the present study is conducted with a specific aim to model the structure of ANGPTL8 and study its possible interactions with Lipoprotein Lipase (LPL). To the best of our knowledge, this is the first attempt to predict 3-dimensional (3D) structure of ANGPTL8. Three different approaches were used for modeling of ANGPTL8 including homology modeling, de-novo structure prediction and their amalgam which is then proceeded by structure verification using ERRATT, PROSA, Qmean and Ramachandran plot scores. The selected models of ANGPTL8 were further evaluated for protein-protein interaction (PPI) analysis with LPL using CPORT and HADDOCK server. Our results have shown that the crystal structure of iSH2 domain of Phosphatidylinositol 3-kinase (PI3K) p85β subunit (PDB entry: 3mtt) is a good candidate for homology modeling of ANGPTL8. Analysis of inter-molecular interactions between the structure of ANGPTL8 and LPL revealed existence of several non-covalent interactions. The residues of LPL involved in these interactions belong from its lid region, thrombospondin (TSP) region and heparin binding site which is suggestive of a possible role of ANGPTL8 in regulating the proteolysis, motility and localization of LPL. Besides, the conserved residues of SE1 region of ANGPTL8 formed interactions with the residues around the hinge region of LPL. Overall, our results support a model of inhibition of LPL by ANGPTL8 through the steric block of its catalytic site which will be further explored using wet lab

  6. Biochemical and structural characterization of polyphosphate kinase 2 from the intracellular pathogen Francisella tularensis

    PubMed Central

    Batten, Laura E.; Parnell, Alice E.; Wells, Neil J.; Murch, Amber L.; Oyston, Petra C. F.; Roach, Peter L.

    2015-01-01

    The metabolism of polyphosphate is important for the virulence of a wide range of pathogenic bacteria and the enzymes of polyphosphate metabolism have been proposed as an anti-bacterial target. In the intracellular pathogen Francisella tularensis, the product of the gene FTT1564 has been identified as a polyphosphate kinase from the polyphosphate kinase 2 (PPK2) family. The isogenic deletion mutant was defective for intracellular growth in macrophages and was attenuated in mice, indicating an important role for polyphosphate in the virulence of Francisella. Herein, we report the biochemical and structural characterization of F. tularensis polyphosphate kinase (FtPPK2) with a view to characterizing the enzyme as a novel target for inhibitors. Using an HPLC-based activity assay, the substrate specificity of FtPPK2 was found to include purine but not pyrimidine nts. The activity was also measured using 31P-NMR. FtPPK2 has been crystallized and the structure determined to 2.23 Å (1 Å=0.1 nm) resolution. The structure consists of a six-stranded parallel β-sheet surrounded by 12 α-helices, with a high degree of similarity to other members of the PPK2 family and the thymidylate kinase superfamily. Residues proposed to be important for substrate binding and catalysis have been identified in the structure, including a lid-loop and the conserved Walker A and B motifs. The ΔFTT1564 strain showed significantly increased sensitivity to a range of antibiotics in a manner independent of the mode of action of the antibiotic. This combination of biochemical, structural and microbiological data provide a sound foundation for future studies targeting the development of PPK2 small molecule inhibitors. PMID:26582818

  7. Biochemical and structural characterization of polyphosphate kinase 2 from the intracellular pathogen Francisella tularensis.

    PubMed

    Batten, Laura E; Parnell, Alice E; Wells, Neil J; Murch, Amber L; Oyston, Petra C F; Roach, Peter L

    2016-01-01

    The metabolism of polyphosphate is important for the virulence of a wide range of pathogenic bacteria and the enzymes of polyphosphate metabolism have been proposed as an anti-bacterial target. In the intracellular pathogen Francisella tularensis, the product of the gene FTT1564 has been identified as a polyphosphate kinase from the polyphosphate kinase 2 (PPK2) family. The isogenic deletion mutant was defective for intracellular growth in macrophages and was attenuated in mice, indicating an important role for polyphosphate in the virulence of Francisella. Herein, we report the biochemical and structural characterization of F. tularensis polyphosphate kinase (FtPPK2) with a view to characterizing the enzyme as a novel target for inhibitors. Using an HPLC-based activity assay, the substrate specificity of FtPPK2 was found to include purine but not pyrimidine nts. The activity was also measured using (31)P-NMR. FtPPK2 has been crystallized and the structure determined to 2.23 Å (1 Å=0.1 nm) resolution. The structure consists of a six-stranded parallel β-sheet surrounded by 12 α-helices, with a high degree of similarity to other members of the PPK2 family and the thymidylate kinase superfamily. Residues proposed to be important for substrate binding and catalysis have been identified in the structure, including a lid-loop and the conserved Walker A and B motifs. The ΔFTT1564 strain showed significantly increased sensitivity to a range of antibiotics in a manner independent of the mode of action of the antibiotic. This combination of biochemical, structural and microbiological data provide a sound foundation for future studies targeting the development of PPK2 small molecule inhibitors. PMID:26582818

  8. Characterizing structural association alterations within brain networks in normal aging using Gaussian Bayesian networks

    PubMed Central

    Guo, Xiaojuan; Wang, Yan; Chen, Kewei; Wu, Xia; Zhang, Jiacai; Li, Ke; Jin, Zhen; Yao, Li

    2014-01-01

    Recent multivariate neuroimaging studies have revealed aging-related alterations in brain structural networks. However, the sensory/motor networks such as the auditory, visual and motor networks, have obtained much less attention in normal aging research. In this study, we used Gaussian Bayesian networks (BN), an approach investigating possible inter-regional directed relationship, to characterize aging effects on structural associations between core brain regions within each of these structural sensory/motor networks using volumetric MRI data. We then further examined the discriminability of BN models for the young (N = 109; mean age =22.73 years, range 20–28) and old (N = 82; mean age =74.37 years, range 60–90) groups. The results of the BN modeling demonstrated that structural associations exist between two homotopic brain regions from the left and right hemispheres in each of the three networks. In particular, compared with the young group, the old group had significant connection reductions in each of the three networks and lesser connection numbers in the visual network. Moreover, it was found that the aging-related BN models could distinguish the young and old individuals with 90.05, 73.82, and 88.48% accuracy for the auditory, visual, and motor networks, respectively. Our findings suggest that BN models can be used to investigate the normal aging process with reliable statistical power. Moreover, these differences in structural inter-regional interactions may help elucidate the neuronal mechanism of anatomical changes in normal aging. PMID:25324771

  9. Crystal Structure and Characterization of Particulate Methane Monooxygenase from Methylocystis species Strain M

    PubMed Central

    Smith, Stephen M.; Rawat, Swati; Telser, Joshua; Hoffman, Brian M.; Stemmler, Timothy L.; Rosenzweig, Amy C.

    2012-01-01

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Previous biochemical and structural studies of pMMO have focused on preparations from Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b. A pMMO from a third organism, Methylocystis species strain M, has been isolated and characterized. Both membrane-bound and solubilized Methylocystis sp. strain M pMMO contain ~2 copper ions per 100 kDa protomer and exhibit copper-dependent propylene epoxidation activity. Spectroscopic data indicate that Methylocystis sp. strain M pMMO contains a mixture of CuI and CuII, of which the latter exhibits two distinct type 2 CuII electron paramagnetic resonance (EPR) signals. Extended X-ray absorption fine structure (EXAFS) data are best fit with a mixture of Cu–O/N and Cu–Cu ligand environments with a Cu–Cu interaction at 2.52–2.64 Å. The crystal structure of Methylocystis sp. strain M pMMO was determined to 2.68 Å resolution and is the best quality pMMO structure obtained to date. It provides a revised model for the pmoA and pmoC subunits and has led to an improved model of M. capsulatus (Bath) pMMO. In these new structures, the intramembrane zinc/copper binding site has a different coordination environment from that in previous models. PMID:22013879

  10. Characterization of the Local Structure in Liquid Water by Various Order Parameters

    PubMed Central

    2015-01-01

    A wide range of geometric order parameters have been suggested to characterize the local structure of liquid water and its tetrahedral arrangement, but their respective merits have remained elusive. Here, we consider a series of popular order parameters and analyze molecular dynamics simulations of water, in the bulk and in the hydration shell of a hydrophobic solute, at 298 and 260 K. We show that these parameters are weakly correlated and probe different distortions, for example the angular versus radial disorders. We first combine these complementary descriptions to analyze the structural rearrangements leading to the density maximum in liquid water. Our results reveal no sign of a heterogeneous mixture and show that the density maximum arises from the depletion in interstitial water molecules upon cooling. In the hydration shell of the hydrophobic moiety of propanol, the order parameters suggest that the water local structure is similar to that in the bulk, with only a very weak depletion in ordered configurations, thus confirming the absence of any iceberg-type structure. Finally, we show that the main structural fluctuations that affect water reorientation dynamics in the bulk are angular distortions, which we explain by the jump hydrogen-bond exchange mechanism. PMID:26054933

  11. Comprehensive comparison of the chemical and structural characterization of landfill leachate and leonardite humic fractions.

    PubMed

    Tahiri, Abdelghani; Richel, Aurore; Destain, Jacqueline; Druart, Philippe; Thonart, Philippe; Ongena, Marc

    2016-03-01

    Humic substances (HS) are complex and heterogeneous mixtures of organic compounds that occur everywhere in the environment. They represent most of the dissolved organic matter in soils, sediments (fossil), water, and landfills. The exact structure of HS macromolecules has not yet been determined because of their complexity and heterogeneity. Various descriptions of HS are used depending on specific environments of origin and research interests. In order to improve the understanding of the structure of HS extracted from landfill leachate (LHS) and commercial HS from leonardite (HHS), this study sought to compare the composition and characterization of the structure of LHS and HHS using elemental composition, chromatographic (high-performance liquid chromatography (HPLC)), and spectroscopic techniques (UV-vis, FTIR, NMR, and MALDI-TOF). The results showed that LHS molecules have a lower molecular weight and less aromatic structure than HHS molecules. The characteristics of functional groups of both LHS and HHS, however, were basically similar, but there was some differences in absorbance intensity. There were also less aliphatic and acidic functional groups and more aromatic and polyphenolic compounds in the humic acid (HA) fraction than in the fulvic acid (FA) and other molecules (OM) fractions of both origins. The differences between LHS and HHS might be due to the time course of humification. Combining the results obtained from these analytical techniques cold improve our understanding of the structure of HS of different origins and thus enhance their potential use. PMID:26781101

  12. Synthesis, structure, characterization and fluorescent properties of Ag+ complexes with extended π⋯π interactions

    NASA Astrophysics Data System (ADS)

    Huang, Ting-Hong; Yan, Jie; Yang, Hu; Qiang, Liu; Du, Huai-Ming

    2015-12-01

    Two mixed-ligand Ag (I) complexes, [Ag2(Phterpy)2(NO3)2(dppe)]·CH3CN (1) and [Ag4(Phterpy)2(NO3)2(dppp)2](NO3)2·6H2O (2) (dppe = 1, 2-bis (diphenylphosphino) ethane, dppp = 1, 3-bis (diphenylphosphino) propane, Phterpy = 4‧-phenyl-2, 2‧:6‧, 2″-terpyridine), have been synthesized and structurally characterized by IR, 1H-NMR, 31P-NMR, elemental analysis and X-ray crystal structure analysis. Structural analysis reveals that the change of bridging ligands from dppe to dppp lead to the formation of centrosymmetric cations [Ag2(Phterpy)2(NO3)2(dppe)] and [Ag4(Phterpy)2 (NO3)2(dppp)2]2+, especially complex 2 containing two independent centrosymmetric tetramers with the central (obligate) Ag2O2 planes. Complexes 1 and 2 consist of the 1D infinite chains, with different variations in π-stacking patterns. Crystal structure of 1 contains 1D infinite chains constructed by π⋯π interactions between Phterpy, while 2 is built by π⋯π interaction of phenylene rings from dppp. All these reveal that the change of phosphine ligands might be the key of construction of different types of polynuclear structures and 1D π-stacking chain. Moreover, the solid-state emission spectra of complexes 1 and 2 display broad emission bands at 420-600 nm.

  13. Crystal structure and characterization of particulate methane monooxygenase from Methylocystis species strain M.

    PubMed

    Smith, Stephen M; Rawat, Swati; Telser, Joshua; Hoffman, Brian M; Stemmler, Timothy L; Rosenzweig, Amy C

    2011-11-29

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Previous biochemical and structural studies of pMMO have focused on preparations from Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b. A pMMO from a third organism, Methylocystis species strain M, has been isolated and characterized. Both membrane-bound and solubilized Methylocystis sp. strain M pMMO contain ~2 copper ions per 100 kDa protomer and exhibit copper-dependent propylene epoxidation activity. Spectroscopic data indicate that Methylocystis sp. strain M pMMO contains a mixture of Cu(I) and Cu(II), of which the latter exhibits two distinct type 2 Cu(II) electron paramagnetic resonance (EPR) signals. Extended X-ray absorption fine structure (EXAFS) data are best fit with a mixture of Cu-O/N and Cu-Cu ligand environments with a Cu-Cu interaction at 2.52-2.64 Å. The crystal structure of Methylocystis sp. strain M pMMO was determined to 2.68 Å resolution and is the best quality pMMO structure obtained to date. It provides a revised model for the pmoA and pmoC subunits and has led to an improved model of M. capsulatus (Bath) pMMO. In these new structures, the intramembrane zinc/copper binding site has a different coordination environment from that in previous models. PMID:22013879

  14. Crystal Structure and Characterization of Particulate Methane Monooxygenase from Methylocystis species Strain M

    SciTech Connect

    Smith, Stephen M.; Rawat, Swati; Telser, Joshua; Hoffman, Brian M.; Stemmler, Timothy L.; Rosenzweig, Amy C.

    2012-02-08

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. Previous biochemical and structural studies of pMMO have focused on preparations from Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b. A pMMO from a third organism, Methylocystis species strain M, has been isolated and characterized. Both membrane-bound and solubilized Methylocystis sp. strain M pMMO contain {approx}2 copper ions per 100 kDa protomer and exhibit copper-dependent propylene epoxidation activity. Spectroscopic data indicate that Methylocystis sp. strain M pMMO contains a mixture of Cu{sup I} and Cu{sup II}, of which the latter exhibits two distinct type 2 Cu{sup II} electron paramagnetic resonance (EPR) signals. Extended X-ray absorption fine structure (EXAFS) data are best fit with a mixture of Cu-O/N and Cu-Cu ligand environments with a Cu-Cu interaction at 2.52-2.64 {angstrom}. The crystal structure of Methylocystis sp. strain M pMMO was determined to 2.68 {angstrom} resolution and is the best quality pMMO structure obtained to date. It provides a revised model for the pmoA and pmoC subunits and has led to an improved model of M. capsulatus (Bath) pMMO. In these new structures, the intramembrane zinc/copper binding site has a different coordination environment from that in previous models.

  15. Uranyl Sequestration: Synthesis and Structural Characterization of Uranyl Complexes with a Tetradentate Methylterephthalamide Ligand

    SciTech Connect

    Ni, Chengbao; Shuh, David; Raymond, Kenneth

    2011-03-07

    Uranyl complexes of a bis(methylterephthalamide) ligand (LH{sub 4}) have been synthesized and characterized by X-ray crystallography. The structure is an unexpected [Me{sub 4}N]{sub 8}[L(UO{sub 2})]{sub 4} tetramer, formed via coordination of the two MeTAM units of L to two uranyl moieties. Addition of KOH to the tetramer gave the corresponding monomeric uranyl methoxide species [Me{sub 4}N]K{sub 2}[LUO{sub 2}(OMe)].

  16. Characterization of coherent structures in a turbulent mixing layer by digital image analysis

    NASA Technical Reports Server (NTRS)

    Bernal, L. P.; Hernan, M. A.; Sarohia, V.

    1985-01-01

    Digital image analysis has been applied to a shadowgraph motion picture of a helium nitrogen mixing layer in order to characterize the coherent vortex structures in the flow. Both the primary spanwise coherent vortices and secondary streamwise vortices are considered. Pattern recognition algorithms were designed to take advantage of the more pronounced features of the vortices and of their temporal coherence to isolate them and to measure their characteristics. The resulting data base permits a deterministic description of the evolution of primary and seconary vortices.

  17. Surface chemical functionalized single-walled carbon nanotube with anchored phenol structures: Physical and chemical characterization

    NASA Astrophysics Data System (ADS)

    Bae, Jong Hyun; Shanmugharaj, A. M.; Noh, Woo Hyun; Choi, Won Seok; Ryu, Sung Hun

    2007-02-01

    Surface functionalization of single-walled carbon nanotube was carried out by introducing ylides groups containing anchored phenol structures. The functionalized nanotube is characterized using elemental analysis, Fourier transform infrared spectroscopy, field emission scanning electron microscopy, thermogravimetric analysis, Raman spectroscopy and zeta potential measurements. Elemental and FT-IR analysis reveal the successful functionalization of azomethine ylides. Raman spectroscopic studies corroborates that the surface functionalization does not affect the basic crystal domain size of the nanotubes. Functionalized carbon nanotubes exhibit higher zeta potential values showing its higher dispersant ability in water and acetone solvent in comparison to pure carbon nanotube.

  18. Synthesis and structural characterization of vertical ferromagnetic MnAs/semiconducting InAs heterojunction nanowires

    NASA Astrophysics Data System (ADS)

    Kodaira, Ryutaro; Hara, Shinjiro; Kabamoto, Kyohei; Fujimagari, Hiromu

    2016-07-01

    The purpose of this study is to synthesize vertical ferromagnetic/semiconducting heterojunction nanowires by combing the catalyst-free selective-area growth of InAs nanowires and the endotaxial nanoclustering of MnAs and to structurally and magnetically characterize them. MnAs penetrates the InAs nanowires to form nanoclusters. The surface migration length of manganese adatoms on the nanowires, which is estimated to be 600 nm at 580 °C, is a key to the successful fabrication of vertical MnAs/InAs heterojunction nanowires with atomically abrupt heterointerfaces.

  19. First structural characterization of a protactinium(V) single oxo bond in aqueous media.

    PubMed

    Le Naour, Claire; Trubert, Didier; Di Giandomenico, Maria V; Fillaux, Clara; Den Auwer, Christophe; Moisy, Philippe; Hennig, Christoph

    2005-12-12

    The present work describes the first structural studies of protactinium(V) in sulfuric and hydrofluoric acid media using X-ray absorption spectroscopy. The results show unambiguously the absence of the trans-dioxo bond that characterizes the other early actinide elements such as U and Np. In concentrated sulfuric acid (13 M), Pa(V) is proved to exhibit a single oxo bond as postulated in the literature for species in more dilute media. In a 0.5 M HF medium, XANES and EXAFS spectra indicate the absence of any oxo bond: Pa(V) exists in the form of a pure fluoro complex. PMID:16323942

  20. A facile approach towards synthesis, characterization, single crystal structure, and DFT study of 5-bromosalicylalcohol

    NASA Astrophysics Data System (ADS)

    Rastogi, Rupali; Tarannum, Nazia; Butcher, R. J.

    2016-03-01

    5-Bromosalicylalcohol was prepared by the interaction of NaBH4 and 5-bromosalicylaldehyde. The use of sodium borohydride makes the reaction easy, facile, economic and does not require any toxic catalyst. The compound is characterized by FTIR, 1H NMR, 13C NMR, TEM and ESI-mass spectra. Crystal structure is determined by single crystal X-ray analysis. Quantum mechanical calculations of geometries, energies and thermodynamic parameters are carried out using density functional theory (DFT/B3LYP) method with 6-311G( d, p) basis set. The optimized geometrical parameters obtained by B3LYP method show good agreement with experimental data.

  1. Quantitative void characterization in structural ceramics using scanning laser acoustic microscopy

    NASA Technical Reports Server (NTRS)

    Roth, D. J.; Generazio, E. R.; Baaklini, G. Y.

    1986-01-01

    The ability of scanning laser acoustic microscopy (SLAM) to characterize artificially seeded voids in sintered silicon nitride structural ceramic specimens was investigated. Using trigonometric relationships and Airy's diffraction theory, predictions of internal void depth and size were obtained from acoustic diffraction patterns produced by the voids. Agreement was observed between actual and predicted void depths. However, predicted void diameters were generally much greater than actual diameters. Precise diameter predictions are difficult to obtain due to measurement uncertainty and the limitations of 100 MHz SLAM applied to typical ceramic specimens.

  2. Holey-structured metamaterial lens for subwavelength resolution in ultrasonic characterization of metallic components

    NASA Astrophysics Data System (ADS)

    Amireddy, Kiran Kumar; Balasubramaniam, Krishnan; Rajagopal, Prabhu

    2016-05-01

    This paper presents the implementation of holey structured metamaterial lens for ultrasonic characterization of subwavelength subsurface defects in metallic components. Experimental results are presented, demonstrating ultrasound-based resolution of side drilled through-holes spaced (λ/5) in an aluminum block. Numerical simulation is then used to investigate the parameters that can help improve the resolution performance of the metamaterial lens, particularly, the addition of end-conditions. This work has important implications for higher resolution ultrasonic imaging in the context of practical non-destructive imaging and non-invasive material diagnostics.

  3. Structural characterization and dehydration kinetics of Kirka inderite mineral: Application of non-isothermal models

    SciTech Connect

    Figen, Aysel Kantuerk; Yilmaz, Muege Sari; Piskin, Sabriye

    2010-06-15

    Coats-Redfern, Arrhenius, Ozawa, Kissinger, and Doyle non-isothermal kinetic models were used to calculate the dynamic kinetic parameters for dehydration reaction of Mg-borate mineral, inderite (Kirka - Turkey) based on thermogravimetric analysis, derivative thermogravimetric analysis and differential thermal analysis. Dehydration experiments were carried out at different heating rates of 2, 5, 10, 15, and 20 deg. C/min in a pure nitrogen atmosphere. Structural and morphological properties have been characterized by X-Ray diffraction, Fourier transform-infrared spectroscopy, Scanning electron microscopy-energy dispersive spectroscopy, and Inductively coupled plasma-optical emission spectroscopy techniques.

  4. Synthesis, molecular modeling and structural characterization of vanillin derivatives as antimicrobial agents

    NASA Astrophysics Data System (ADS)

    Sun, Juan; Yin, Yong; Sheng, Gui-Hua; Yang, Zhi-Bo; Zhu, Hai-Liang

    2013-05-01

    Two vanillin derivatives have been designed and synthesized and their biological activities were also evaluated for antimicrobial activity. Their chemical structures are characterized by single crystal X-ray diffraction studies, 1H NMR, MS, and elemental analysis. Structural stabilization of them followed by intramolecular as well as intermolecular H-bonds makes these molecules as perfect examples in molecular recognition with self-complementary donor and acceptor units within a single molecule. Docking simulations have been performed to position compounds into the FtsZ active site to determine their probable binding model. Compound 3a shows the most potent biological activity, which may be a promising antimicrobial leading compound for the further research.

  5. Synthesis and structure characterization of chromium oxide prepared by solid thermal decomposition reaction.

    PubMed

    Li, Li; Yan, Zi F; Lu, Gao Q; Zhu, Zhong H

    2006-01-12

    Mesoporous chromium oxide (Cr2O3) nanocrystals were first synthesized by the thermal decomposition reaction of Cr(NO3)3.9H2O using citric acid monohydrate (CA) as the mesoporous template agent. The texture and chemistry of chromium oxide nanocrystals were characterized by N2 adsorption-desorption isotherms, FTIR, X-ray diffraction (XRD), UV-vis, and thermoanalytical methods. It was shown that the hydrate water and CA are the crucial factors in influencing the formation of mesoporous Cr2O3 nanocrystals in the mixture system. The decomposition of CA results in the formation of a mesoporous structure with wormlike pores. The hydrate water of the mixture provides surface hydroxyls that act as binders, making the nanocrystals aggregate. The pore structures and phases of chromium oxide are affected by the ratio of precursor-to-CA, thermal temperature, and time. PMID:16471518

  6. Functional and Structural Characterization of the Antiphagocytic Properties of a Novel Transglutaminase from Streptococcus suis*

    PubMed Central

    Yu, Jie; Pian, Yaya; Ge, Jingpeng; Guo, Jie; Zheng, Yuling; Jiang, Hua; Hao, Huaijie; Yuan, Yuan; Jiang, Yongqiang; Yang, Maojun

    2015-01-01

    Streptococcus suis serotype 2 (Ss2) is an important swine and human zoonotic pathogen. In the present study, we identified a novel secreted immunogenic protein, SsTGase, containing a highly conserved eukaryotic-like transglutaminase (TGase) domain at the N terminus. We found that inactivation of SsTGase significantly reduced the virulence of Ss2 in a pig infection model and impaired its antiphagocytosis in human blood. We further solved the crystal structure of the N-terminal portion of the protein in homodimer form at 2.1 Å. Structure-based mutagenesis and biochemical studies suggested that disruption of the homodimer directly resulted in the loss of its TGase activity and antiphagocytic ability. Characterization of SsTGase as a novel virulence factor of Ss2 by acting as a TGase would be beneficial for developing new therapeutic agents against Ss2 infections. PMID:26085092

  7. Synthesis, characterization and crystal structures of new organic compounds containing cyanoacrylic acid

    NASA Astrophysics Data System (ADS)

    Khalaji, Aliakbar Dehno; Mogheiseh, Mohsen; Eigner, Václav; Dusek, Michal; Chow, Tahsin J.; Maddahi, Elham

    2015-10-01

    New organic compounds, cin-aa (1) and mecin-aa (2), containing cyanoacrylic acid as an acceptor were synthesized by the reaction of cinnamaldehyde or α-methylcinnamaldehyde with cyanoaceticacid in acetonitrile. The compounds 1 and 2 were characterized by elemental analyses (CHN), FT-IR, UV-Vis and 1H NMR spectroscopy, and their monoclinic centrosymmetric structures were determined by single crystal X-ray diffraction. In addition, they were tested for their potential use as photosensitizers in dye-sensitized solar cells (DSSC). Overall conversion efficiencies of 1 and 2 were determined as 0.04 and 0.09, respectively, under full sunlight irradiation. To get further insight into the molecular structure of 1 and 2, their geometry and energies of HOMO and LUMO were optimized by density functional theory calculation at the B3LYP/6-31G(d) level with Gaussian 03.

  8. Structural Characterization of the Catalytic Subunit of a Novel RNA Splicing Endonuclease

    SciTech Connect

    Calvin, Kate; Hall, Michelle D.; Xu, Fangmin; Xue, Song; Li, Hong

    2010-07-13

    The RNA splicing endonuclease is responsible for recognition and excision of nuclear tRNA and all archaeal introns. Despite the conserved RNA cleavage chemistry and a similar enzyme assembly, currently known splicing endonuclease families have limited RNA specificity. Different from previously characterized splicing endonucleases in Archaea, the splicing endonuclease from archaeum Sulfolobus solfataricus was found to contain two different subunits and accept a broader range of substrates. Here, we report a crystal structure of the catalytic subunit of the S. solfataricus endonuclease at 3.1 {angstrom} resolution. The structure, together with analytical ultracentrifugation analysis, identifies the catalytic subunit as an inactive but stable homodimer, thus suggesting the possibility of two modes of functional assembly for the active enzyme.

  9. Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments.

    PubMed

    He, Didi; Hughes, Sam; Vanden-Hehir, Sally; Georgiev, Atanas; Altenbach, Kirsten; Tarrant, Emma; Mackay, C Logan; Waldron, Kevin J; Clarke, David J; Marles-Wright, Jon

    2016-01-01

    Ferritins are ubiquitous proteins that oxidise and store iron within a protein shell to protect cells from oxidative damage. We have characterized the structure and function of a new member of the ferritin superfamily that is sequestered within an encapsulin capsid. We show that this encapsulated ferritin (EncFtn) has two main alpha helices, which assemble in a metal dependent manner to form a ferroxidase center at a dimer interface. EncFtn adopts an open decameric structure that is topologically distinct from other ferritins. While EncFtn acts as a ferroxidase, it cannot mineralize iron. Conversely, the encapsulin shell associates with iron, but is not enzymatically active, and we demonstrate that EncFtn must be housed within the encapsulin for iron storage. This encapsulin nanocompartment is widely distributed in bacteria and archaea and represents a distinct class of iron storage system, where the oxidation and mineralization of iron are distributed between two proteins. PMID:27529188

  10. Biochemical and structural characterization of Klebsiella pneumoniae oxamate amidohydrolase in the uric acid degradation pathway.

    PubMed

    Hicks, Katherine A; Ealick, Steven E

    2016-06-01

    HpxW from the ubiquitous pathogen Klebsiella pneumoniae is involved in a novel uric acid degradation pathway downstream from the formation of oxalurate. Specifically, HpxW is an oxamate amidohydrolase which catalyzes the conversion of oxamate to oxalate and is a member of the Ntn-hydrolase superfamily. HpxW is autoprocessed from an inactive precursor to form a heterodimer, resulting in a 35.5 kDa α subunit and a 20 kDa β subunit. Here, the structure of HpxW is presented and the substrate complex is modeled. In addition, the steady-state kinetics of this enzyme and two active-site variants were characterized. These structural and biochemical studies provide further insight into this class of enzymes and allow a mechanism for catalysis consistent with other members of the Ntn-hydrolase superfamily to be proposed. PMID:27303801

  11. Phenanthro[4,5-fgh]quinoxaline-Fused Subphthalocyanines: Synthesis, Structure, and Spectroscopic Characterization.

    PubMed

    Pan, Houhe; Liu, Wenbo; Wang, Chiming; Wang, Kang; Jiang, Jianzhuang

    2016-07-01

    A series of four phenanthro[4,5-fgh]quinoxaline-fused subphthalocyanine derivatives 0-3 containing zero, one, two, and three phenanthro[4,5-fgh]quinoxaline moieties, respectively, were isolated from the mixed cyclotrimerization reaction of 2,9-di-tert-butylphenanthro[4,5-fgh]quinoxaline-5,6-dicarbonitrile with 4,5-bis(2,6-diisopropylphenoxy)phthalonitrile and characterized by a series of spectroscopic methods including MALDI-TOF mass, (1) H NMR, electronic absorption, magnetic circular dichroism (MCD), and fluorescence spectroscopy. The molecular structures for the compounds 0 and 2 were clearly revealed on the basis of single-crystal X-ray diffraction analysis. Their electrochemical properties were also studied by cyclic voltammetry. In particular, theoretical calculations in combination with the electronic absorption and electrochemical analyses revealed the significant influence of the fused-phenanthro[4,5-fgh]quinoxaline units on the electronic structures. PMID:27123546

  12. Structure and biochemical characterization of proliferating cellular nuclear antigen from a parasitic protozoon

    SciTech Connect

    Cardona-Felix, Cesar S.; Lara-Gonzalez, Samuel; Brieba, Luis G.

    2012-02-08

    Proliferating cellular nuclear antigen (PCNA) is a toroidal-shaped protein that is involved in cell-cycle control, DNA replication and DNA repair. Parasitic protozoa are early-diverged eukaryotes that are responsible for neglected diseases. In this work, a PCNA from a parasitic protozoon was identified, cloned and biochemically characterized and its crystal structure was determined. Structural and biochemical studies demonstrate that PCNA from Entamoeba histolytica assembles as a homotrimer that is able to interact with and stimulate the activity of a PCNA-interacting peptide-motif protein from E. histolytica, EhDNAligI. The data indicate a conservation of the biochemical mechanisms of PCNA-mediated interactions between metazoa, yeast and parasitic protozoa.

  13. Structural characterization and antioxidant activities of polysaccharides from Citrus aurantium L.

    PubMed

    Wang, Qiu Hong; Shu, Zun Peng; Xu, Bing Qing; Xing, Na; Jiao, Wen Juan; Yang, Bing You; Kuang, Hai Xue

    2014-06-01

    Three polysaccharide fractions were obtained from Citrus aurantium L. (CAL) by sequential extraction with cold water, hot water, and 1.0M NaOH, respectively. The fractions were denoted CALA, CALB, and CALC. Structural characterization was conducted by physicochemical property, FTIR, and SEM analyses. Antioxidant activities in vivo and in vitro were also evaluated. CALB, which showed the highest activity, was further isolated to afford four purified polysaccharides (CALB-1-4) by various ion exchange and gel-filtration chromatography. Meanwhile, the purified polysaccharides were subjected to composition analysis and screened by antioxidant activity in vitro. Among the four purified polysaccharides, CALB-3 had the highest antioxidant activity and its structure was analyzed by FTIR, SEM and AFM microscopy. Overall, these results indicated that polysaccharides from CAL had potential therapeutic applications in the medical and food industries because of their antioxidant activities. PMID:24631547

  14. Structural and compositional characterization of the adhesive produced by reef building oysters.

    PubMed

    Alberts, Erik M; Taylor, Stephen D; Edwards, Stephanie L; Sherman, Debra M; Huang, Chia-Ping; Kenny, Paul; Wilker, Jonathan J

    2015-04-29

    Oysters have an impressive ability to overcome difficulties of life within the stressful intertidal zone. These shellfish produce an adhesive for attaching to each other and building protective reef communities. With their reefs often exceeding kilometers in length, oysters play a major role in balancing the health of coastal marine ecosystems. Few details are available to describe oyster adhesive composition or structure. Here several characterization methods were applied to describe the nature of this material. Microscopy studies indicated that the glue is comprised of organic fiber-like and sheet-like structures surrounded by an inorganic matrix. Phospholipids, cross-linking chemistry, and conjugated organics were found to differentiate this adhesive from the shell. Symbiosis in material synthesis could also be present, with oysters incorporating bacterial polysaccharides into their adhesive. Oyster glue shows that an organic-inorganic composite material can provide adhesion, a property especially important when constructing a marine ecosystem. PMID:25843147

  15. Structural characterization of P1′-diversified urea-based inhibitors of glutamate carboxypeptidase II

    PubMed Central

    Pavlicek, Jiri; Ptacek, Jakub; Cerny, Jiri; Byun, Youngjoo; Skultetyova, Lubica; Pomper, Martin G.; Lubkowski, Jacek; Barinka, Cyril

    2014-01-01

    Urea-based inhibitors of human glutamate carboxypeptidase II (GCPII) have advanced into clinical trials for imaging metastatic prostate cancer. In parallel efforts, agents with increased lipophilicity have been designed and evaluated for targeting GCPII residing within the neuraxis. Here we report the structural and computational characterization of six complexes between GCPII and P1′-diversified urea-based inhibitors that have the C-terminal glutamate replaced by more hydrophobic moieties. The X-ray structures are complemented by quantum mechanics calculations that provide a quantitative insight into the GCPII/inhibitor interactions. These data can be used for the rational design of novel glutamate-free GCPII inhibitors with tailored physicochemical properties. PMID:24731280

  16. Structural characterization and anti-fatigue activity of polysaccharides from the roots of Morinda officinalis.

    PubMed

    Zhang, Hua-Lin; Li, Jun; Li, George; Wang, Dong-mei; Zhu, Long-ping; Yang, De-po

    2009-04-01

    Three polysaccharides MP-1, MP-2, and MP-3 were isolated from hot water extract of Chinese medicine Morinda officinalis through 95% ethanol precipitation and gel-filtration chromatography (DEAE-Sepharose CL-6B column and Sephadex G-75 or G-100 column). MP-1 was identified as an inulin-type fructan with simple linear (2-->1)-linked structure. Both MP-2 and MP-3 were acidic polysaccharides which consisted predominantly of galacturonic acid, arabinose and galactose. Partial structure characterization of MP-3 was carried out by partial acid hydrolysis and periodate oxidation. The total polysaccharides of the herb were tested in mice weight-loaded swimming model and were found to have anti-fatigue activity. PMID:19150459

  17. Structural and optical characterization of MOCVD-grown ZnO thin films

    NASA Astrophysics Data System (ADS)

    Pagni, O.; James, G. R.; Leitch, A. W. R.

    2004-03-01

    We report on the characterization of ZnO thin films grown by metal organic chemical vapor deposition (MOCVD) using diethyl zinc (DEZ) and tert-butanol (TBOH) as precursors. Substrate temperature proved to be a crucial factor in the crystallization process, as it vastly impacted the structural properties of the samples studied. Highly c-axis oriented films with large grain size (52 nm), low tensile strain (0.6%), uniform substrate coverage and a columnar structure devoid of hexagonal needles were successfully deposited on n-Si (100) substrates. The temperature-dependent luminescence spectra recorded confirmed the excellent quality of the material obtained in this work. Our results so far set TBOH apart as an outstanding oxygen source for the MOCVD growth of ZnO.

  18. Characterization of Microgravity Effects on Bone Structure and Strength Using Fractal Analysis

    NASA Technical Reports Server (NTRS)

    Acharya, Raj S.; Shackelford, Linda

    1996-01-01

    Protecting humans against extreme environmental conditions requires a thorough understanding of the pathophysiological changes resulting from the exposure to those extreme conditions. Knowledge of the degree of medical risk associated with the exposure is of paramount importance in the design of effective prophylactic and therapeutic measures for space exploration. Major health hazards due o musculoskeletal systems include the signs and symptoms of hypercalciuria, lengthy recovery of lost bone tissue after flight, the possibility of irreversible trabecular bone loss, the possible effect of calcification in the soft tissues, and the possible increase in fracture potential. In this research, we characterize the trabecular structure with the aid of fractal analysis. Our research to relate local trabecular structural information to microgravity conditions is an important initial step in understanding the effect of microgravity and countermeasures on bone condition and strength. The proposed research is also closely linked with Osteoporosis and will benefit the general population.

  19. Proposed structures for poorly characterized phases in C2M carbonaceous chondrite meteorites

    NASA Technical Reports Server (NTRS)

    Mackinnon, I. D. R.; Zolensky, M. E.

    1984-01-01

    A recent investigation of C2M carbonaceous chondrite meteorite matrices using electron microscopy and High-Resolution Transmission Electron Microscopy (HRTEM) has provided data on the structure and chemistry of Poorly Characterized Phases (PCP). It is suggested that a dominant matrix variety (10 A PCP) has a structure equivalent to iron-rich tochinilite (6Fe0.9S5/Fe, Mg//OHO2/), which consists of coherently intrastratified mackinawite and brucite sheets. In addition, it is proposed that 17 A PCP is a commensurate intergrowth of serpentine and tochinilite layers. Various forms of PCP observed in carbonaceous chondrites appear to be intergrowths of tochinilite, serpentine, and tochinilite-serpentine minerals.

  20. Structural and Energetic Characterization of Prebiotic Molecules: The Case Study of Formamide and Its Dimer.

    PubMed

    Alessandrini, Silvia; Puzzarini, Cristina

    2016-07-14

    State-of-the-art quantum-chemical computations have been employed to determine the accurate equilibrium structure of formamide and its symmetric dimer as well as the interaction energy of the latter, thus extending available reference data for the peptide (also denoted as amide) bond and the hydrogen-bond interaction that characterizes peptides and proteins. Equilibrium geometries and electronic energies have been evaluated by means of a composite scheme based on coupled-cluster calculations, including up to triple excitations, which also accounts for extrapolation to the complete basis set limit and core-correlation effects. This approach provides molecular structures with an accuracy of 0.001-0.002 Å and 0.05-0.1° for bond lengths and angles, respectively, and relative energies with an accuracy of about 1-2 kJ/mol. PMID:26981715

  1. Characterizing pore sizes and water structure in stimuli-responsive hydrogels

    SciTech Connect

    Hoffman, A.S.; Antonsen, K.P.; Ashida, T.; Bohnert, J.L.; Dong, L.C.; Nabeshima, Y.; Nagamatsu, S.; Park, T.G.; Sheu, M.S.; Wu, X.S.; Yan, Q.

    1993-12-31

    Hydrogels have been extensively investigated as potential matrices for drug delivery. In particular, hydrogels responsive to pH and temperature changes have been of greatest interest most recently. Proteins and peptide drugs are especially relevant for delivery from such hydrogel matrices due to the relatively {open_quotes}passive{close_quotes} and biocompatible microenvironment which should exist within the hydrogel aqueous pores. The large molecular size of many proteins requires an interconnected large pore structure. Furthermore, the gel pore {open_quotes}walls{close_quotes} should not provide hydrophobic sites for strong interactions with proteins. In the special case of ion exchange release the protein would be attracted by opposite charges on the polymer backbones. Therefore, it is important both to control and to characterize the pore structure and the water character within a hydrogel to be used or protein or peptide drug delivery. This talk will critically review techniques for estimating these two key parameters in hydrogels.

  2. Inflight Characterization of the Cassini Spacecraft Propellant Slosh and Structural Frequencies

    NASA Technical Reports Server (NTRS)

    Lee, Allan Y.; Stupik, Joan

    2015-01-01

    While there has been extensive theoretical and analytical research regarding the characterization of spacecraft propellant slosh and structural frequencies, there have been limited studies to compare the analytical predictions with measured flight data. This paper uses flight telemetry from the Cassini spacecraft to get estimates of high-g propellant slosh frequencies and the magnetometer boom frequency characteristics, and compares these values with those predicted by theoretical works. Most Cassini attitude control data are available at a telemetry frequency of 0.5 Hz. Moreover, liquid sloshing is attenuated by propellant management device and attitude controllers. Identification of slosh and structural frequency are made on a best-effort basis. This paper reviews the analytical approaches that were used to predict the Cassini propellant slosh frequencies. The predicted frequencies are then compared with those estimated using telemetry from selected Cassini burns where propellant sloshing was observed (such as the Saturn Orbit Insertion burn).

  3. Synthesis and characterization of DC magnetron sputtered nano structured molybdenum thin films

    NASA Astrophysics Data System (ADS)

    Rondiya, S. R.; Rokade, A. V.; Jadhavar, A. A.; Pandharkar, S. M.; Kulkarni, R. R.; Karpe, S. D.; Diwate, K. D.; Jadkar, S. R.

    2016-04-01

    Molybdenum (Mo) thin films were deposited on corning glass (#7059) substrates using DC magnetron sputtering system. The effect of substrate temperature on the structural, morphology and topological properties have been investigated. Films were characterized by variety of techniques such as low angle x-ray diffraction (low angle XRD), field emission scanning electron microscopy (FE-SEM), atomic force microscopy (AFM). The low angle XRD analysis revealed that the synthesized Mo films are nanocrystalline having cubic crystal structure with (110) preferential orientation. The microstructure of the deposited Mo thin films observed with FE-SEM images indicated that films are homogeneous and uniform with randomly oriented leaf shape morphology. The AFM analysis shows that with increase in substrate temperature the rms roughness of Mo films increases. The obtained results suggest that the synthesized nanostructured Mo thin films have potential application as a back contact material for high efficiency solar cells like CdTe, CIGS, CZTS etc.

  4. Structural characterization of selenosubtilisin by sup 77 Se-NMR spectroscopy

    SciTech Connect

    House, K.L.; Dunlap, R.B.; Odom, J.D.; Wu, Z.P.; Hilvert. D. Research Inst. of Scripps Clinic, La Jolla, CA )

    1991-03-15

    Selenosubtilisin is an artificial enzyme containing an active site selenocysteine residue. In this environment the selenium atom is a valuable probe of structure-function relationships and also confers novel redox and hydrolytic properties to the original protease template. The authors have used {sup 77}Se NMR spectroscopy to characterize different oxidation states of {sup 77}Se isotopically enriched selenosubtilisin. The oxidized form of the enzyme exhibits a {sup 77}Se resonance at 1,189 ppm. This is in good agreement with the {sup 77}Se chemical shifts for model seleninic acids, confirming that the prosthetic group is in the seleninic acid oxidation state. On treatment of the oxidized enzyme with three equivalents of 3-carboxy-4-nitrobenzenethiol at pH 5.0, they observe the enzyme bound selenenyl sulfide at 388.5 ppm. This work demonstrates the utility of {sup 77}Se NMR spectroscopy for examining structure-function relationships of selenium containing proteins.

  5. Structural and Catalytic Characterization of a Fungal Baeyer-Villiger Monooxygenase

    PubMed Central

    Ferroni, Felix Martin; Tolmie, Carmien; Smit, Martha Sophia; Opperman, Diederik Johannes

    2016-01-01

    Baeyer-Villiger monooxygenases (BVMOs) are biocatalysts that convert ketones to esters. Due to their high regio-, stereo- and enantioselectivity and ability to catalyse these reactions under mild conditions, they have gained interest as alternatives to chemical Baeyer-Villiger catalysts. Despite their widespread occurrence within the fungal kingdom, most of the currently characterized BVMOs are from bacterial origin. Here we report the catalytic and structural characterization of BVMOAFL838 from Aspergillus flavus. BVMOAFL838 converts linear and aryl ketones with high regioselectivity. Steady-state kinetics revealed BVMOAFL838 to show significant substrate inhibition with phenylacetone, which was more pronounced at low pH, enzyme and buffer concentrations. Para substitutions on the phenyl group significantly improved substrate affinity and increased turnover frequencies. Steady-state kinetics revealed BVMOAFL838 to preferentially oxidize aliphatic ketones and aryl ketones when the phenyl group are separated by at least two carbons from the carbonyl group. The X-ray crystal structure, the first of a fungal BVMO, was determined at 1.9 Å and revealed the typical overall fold seen in type I bacterial BVMOs. The active site Arg and Asp are conserved, with the Arg found in the “in” position. Similar to phenylacetone monooxygenase (PAMO), a two residue insert relative to cyclohexanone monooxygenase (CHMO) forms a bulge within the active site. Approximately half of the “variable” loop is folded into a short α-helix and covers part of the active site entry channel in the non-NADPH bound structure. This study adds to the current efforts to rationalize the substrate scope of BVMOs through comparative catalytic and structural investigation of different BVMOs. PMID:27472055

  6. High resolution structural characterization of Aβ42 amyloid fibrils by magic angle spinning NMR.

    PubMed

    Colvin, Michael T; Silvers, Robert; Frohm, Birgitta; Su, Yongchao; Linse, Sara; Griffin, Robert G

    2015-06-17

    The presence of amyloid plaques composed of amyloid beta (Aβ) fibrils is a hallmark of Alzheimer's disease (AD). The Aβ peptide is present as several length variants with two common alloforms consisting of 40 and 42 amino acids, denoted Aβ1-40 and Aβ1-42, respectively. While there have been numerous reports that structurally characterize fibrils of Aβ1-40, very little is known about the structure of amyloid fibrils of Aβ1-42, which are considered the more toxic alloform involved in AD. We have prepared isotopically (13)C/(15)N labeled AβM01-42 fibrils in vitro from recombinant protein and examined their (13)C-(13)C and (13)C-(15)N magic angle spinning (MAS) NMR spectra. In contrast to several other studies of Aβ fibrils, we observe spectra with excellent resolution and a single set of chemical shifts, suggesting the presence of a single fibril morphology. We report the initial structural characterization of AβM01-42 fibrils utilizing (13)C and (15)N shift assignments of 38 of the 43 residues, including the backbone and side chains, obtained through a series of cross-polarization based 2D and 3D (13)C-(13)C, (13)C-(15)N MAS NMR experiments for rigid residues along with J-based 2D TOBSY experiments for dynamic residues. We find that the first ∼5 residues are dynamic and most efficiently detected in a J-based TOBSY spectrum. In contrast, residues 16-42 are easily observed in cross-polarization experiments and most likely form the amyloid core. Calculation of ψ and φ dihedral angles from the chemical shift assignments indicate that 4 β-strands are present in the fibril's secondary structure. PMID:26001057

  7. High Resolution Structural Characterization of Aβ42 Amyloid Fibrils by Magic Angle Spinning NMR

    PubMed Central

    2015-01-01

    The presence of amyloid plaques composed of amyloid beta (Aβ) fibrils is a hallmark of Alzheimer’s disease (AD). The Aβ peptide is present as several length variants with two common alloforms consisting of 40 and 42 amino acids, denoted Aβ1–40 and Aβ1–42, respectively. While there have been numerous reports that structurally characterize fibrils of Aβ1–40, very little is known about the structure of amyloid fibrils of Aβ1–42, which are considered the more toxic alloform involved in AD. We have prepared isotopically 13C/15N labeled AβM01–42 fibrils in vitro from recombinant protein and examined their 13C–13C and 13C–15N magic angle spinning (MAS) NMR spectra. In contrast to several other studies of Aβ fibrils, we observe spectra with excellent resolution and a single set of chemical shifts, suggesting the presence of a single fibril morphology. We report the initial structural characterization of AβM01–42 fibrils utilizing 13C and 15N shift assignments of 38 of the 43 residues, including the backbone and side chains, obtained through a series of cross-polarization based 2D and 3D 13C–13C, 13C–15N MAS NMR experiments for rigid residues along with J-based 2D TOBSY experiments for dynamic residues. We find that the first ∼5 residues are dynamic and most efficiently detected in a J-based TOBSY spectrum. In contrast, residues 16–42 are easily observed in cross-polarization experiments and most likely form the amyloid core. Calculation of ψ and φ dihedral angles from the chemical shift assignments indicate that 4 β-strands are present in the fibril’s secondary structure. PMID:26001057

  8. Structural and Catalytic Characterization of a Fungal Baeyer-Villiger Monooxygenase.

    PubMed

    Ferroni, Felix Martin; Tolmie, Carmien; Smit, Martha Sophia; Opperman, Diederik Johannes

    2016-01-01

    Baeyer-Villiger monooxygenases (BVMOs) are biocatalysts that convert ketones to esters. Due to their high regio-, stereo- and enantioselectivity and ability to catalyse these reactions under mild conditions, they have gained interest as alternatives to chemical Baeyer-Villiger catalysts. Despite their widespread occurrence within the fungal kingdom, most of the currently characterized BVMOs are from bacterial origin. Here we report the catalytic and structural characterization of BVMOAFL838 from Aspergillus flavus. BVMOAFL838 converts linear and aryl ketones with high regioselectivity. Steady-state kinetics revealed BVMOAFL838 to show significant substrate inhibition with phenylacetone, which was more pronounced at low pH, enzyme and buffer concentrations. Para substitutions on the phenyl group significantly improved substrate affinity and increased turnover frequencies. Steady-state kinetics revealed BVMOAFL838 to preferentially oxidize aliphatic ketones and aryl ketones when the phenyl group are separated by at least two carbons from the carbonyl group. The X-ray crystal structure, the first of a fungal BVMO, was determined at 1.9 Å and revealed the typical overall fold seen in type I bacterial BVMOs. The active site Arg and Asp are conserved, with the Arg found in the "in" position. Similar to phenylacetone monooxygenase (PAMO), a two residue insert relative to cyclohexanone monooxygenase (CHMO) forms a bulge within the active site. Approximately half of the "variable" loop is folded into a short α-helix and covers part of the active site entry channel in the non-NADPH bound structure. This study adds to the current efforts to rationalize the substrate scope of BVMOs through comparative catalytic and structural investigation of different BVMOs. PMID:27472055

  9. Characterizing Woody Vegetation Spectral and Structural Parameters with a 3-D Scene Model

    NASA Astrophysics Data System (ADS)

    Qin, W.; Yang, L.

    2004-05-01

    Quantification of structural and biophysical parameters of woody vegetation is of great significance in understanding vegetation condition, dynamics and functionality. Such information over a landscape scale is crucial for global and regional land cover characterization, global carbon-cycle research, forest resource inventories, and fire fuel estimation. While great efforts and progress have been made in mapping general land cover types over large area, at present, the ability to quantify regional woody vegetation structural and biophysical parameters is limited. One approach to address this research issue is through an integration of physically based 3-D scene model with multiangle and multispectral remote sensing data and in-situ measurements. The first step of this work is to model woody vegetation structure and its radiation regime using a physically based 3-D scene model and field data, before a robust operational algorithm can be developed for retrieval of important woody vegetation structural/biophysical parameters. In this study, we use an advanced 3-D scene model recently developed by Qin and Gerstl (2000), based on L-systems and radiosity theories. This 3-D scene model has been successfully applied to semi-arid shrubland to study structure and radiation regime at a regional scale. We apply this 3-D scene model to a more complicated and heterogeneous forest environment dominated by deciduous and coniferous trees. The data used in this study are from a field campaign conducted by NASA in a portion of the Superior National Forest (SNF) near Ely, Minnesota during the summers of 1983 and 1984, and supplement data collected during our revisit to the same area of SNF in summer of 2003. The model is first validated with reflectance measurements at different scales (ground observations, helicopter, aircraft, and satellite). Then its ability to characterize the structural and spectral parameters of the forest scene is evaluated. Based on the results from this study

  10. Mechanical and structural characterization of tibial prosthetic interfaces before and after aging under simulated service conditions.

    PubMed

    Cavaco, A; Ramalho, A; Pais, S; Durães, L

    2015-03-01

    Prosthesis interface is one of the most important components to promote individual׳s health and comfort, as it establishes direct contact with the skin and transfers loads generated during gait. The aim of this study was to mechanically characterize, three commercial interfaces (block copolymer, silicone gel and silicone elestomer), under static and dynamic conditions, before and after undergoing a process of chemical aging in synthetic sweat for periods up to 90 days. Static mechanical compression tests were performed on the materials, as well as fatigue tests to assess their static and dynamic mechanical behaviors, respectively. For the second, a sinusoidal load was applied with an appropriate range of deformation for each material. Several analytical techniques were also used to characterize the materials, namely Fourier Transform Infrared Spectroscopy (FTIR), X-ray diffraction (XRD), and morphology characterization by Scanning Electron Microscopy (SEM). All the tested materials have strong viscoelastic behavior, showing a linear response for small deformations, followed by a nonlinear behavior for higher deformation. The block copolymer and the silicone gel are affected by aging in synthetic sweat in a similar way, with a significant increase of their rigidity after 30 days, followed by a progressive reduction. The silicone elastomer displays a continuous increase of rigidity along the 90 days of storage, being the most sensitive to aging affects. It also exhibits the lowest stiffness value, being suitable for uses that require maximum comfort. All materials demonstrate chemical and structural stability under service simulated conditions. PMID:25554916

  11. Structural and magnetic characterization of (TM=Co, Fe) doped SnO2 nanostructures

    NASA Astrophysics Data System (ADS)

    Parra Palomino, A.; Rzchowski, M. S.; Perales Perez, O.

    2009-03-01

    Recent indications of intrinsic room-temperature (RT) ferromagnetism in transition metal doped-SnO2 have increased its attractiveness as promising material for nano-optoelectronic and spintronics-based devices. A control over dopant speciation and the determination of the size-dependence of the properties at the nanoscale, become then indispensable. We present here the conditions for the room-temperature synthesis of doped SnO2 in ethanol using SnCl2 and LiHO precursors, and the characterization of the resulting bare, Co and Fe- doped SnO2 powders. X-ray diffraction patterns of bare and doped SnO2 showed the formation of an amorphous structure from the produced powder at RT. However, a pure phase of rutile structure was observed when the samples were annealed in air or Ar at 400^oC. 100nm diameter wires were observed after annealing using scanning electron microscopy (SEM). The results of magnetic characterization of the materials using a vibrating sample magnetometer (VSM) will also be presented and discussed.

  12. Structure Characterization and Properties of Metal-Surfactant Complexes Dispersed in Organic Solvents.

    PubMed

    de la Iglesia, Pablo; Jaeger, Vance W; Xi, Yuyin; Pfaendtner, Jim; Pozzo, Lilo D

    2015-08-25

    This work describes the synthesis and characterization of metal-surfactant complexes. Dioctyl sulfosuccinate and dodecylbenzenesulfonate are associated with multivalent aluminum, iron, and vanadium ions using an ion exchange reaction. The metal complexes are dispersible in various organic solvents. In solvents with low polarity, the complexes form "inverse" macromolecular structures with multiple metal ions. In contrast, in alcohols, the complex size is reduced, showing a more disperse conformation. The metal and surfactant ions are still strongly bonded to each other in all the solvents probed. Small-angle X-ray and neutron scattering (SAXS and SANS) are used to characterize the structures. Simultaneous fitting of neutron and X-ray scattering spectra is performed in order to obtain an accurate description of the system. Scattering results are also validated by performing molecular dynamics (MD) simulations. The conductive and electrochemical properties of the complexes in solution are also evaluated. The dispersion of metal-organic complexes significantly increases electric conductivity, and some metal ions in the core of the complexes are shown to be electrochemically active in apolar solvents. PMID:26212253

  13. Structural and kinetic characterization of two 4-oxalocrotonate tautomerases in Methylibium petroleiphilum strain PM1

    PubMed Central

    Terrell, Cassidy R.; Burks, Elizabeth A.; Whitman, Christian P.; Hoffman, David W.

    2013-01-01

    Methylibium petroleiphilumstrain PM1 uses various petroleum products including the fuel additive methyl tert-butyl ether and straight chain and aromatic hydrocarbons as sole carbon and energy sources. It has two operons, dmpI and dmpII, that code for the enzymes in a pair of parallel meta-fission pathways. In order to understand the roles of the pathways, the 4-oxalocrotonate tautomerase (4-OT) isozyme from each pathway was characterized. Tautomerase I and tautomerase II have the lowest pairwise sequence identity (35%) among the isozyme pairs in the parallel pathways, and could offer insight into substrate preferences and pathway functions. The kinetic parameters of tautomerase I and tautomerase II were determined using 2-hydroxymuconate and 5-(methyl)-2-hydroxymuconate. Both tautomerase I and tautomerase II process the substrates, but with different efficiencies. Crystal structures were determined for both tautomerase I and tautomerase II, at 1.57 and 1.64 Å resolution, respectively. The backbones of tautomerase I and tautomerase II are highly similar, but have distinct active site environments. The results, in combination with those for other structurally and kinetically characterized 4-OT isozymes, suggest that tautomerase I catalyzes the tautomerization of both 2-hydroxymuconate and alkyl derivatives, whereas tautomerase II might specialize in other aromatic hydrocarbon metabolites. PMID:23831510

  14. On the characterization of coherent structures within a neutrally-stratified atmospheric boundary layer

    NASA Astrophysics Data System (ADS)

    Rosi, Giuseppe; Le Bastide, Benen; Gaebler, Julia; Kinzel, Matias; Rival, David

    2012-11-01

    Up to this point, a clear characterization of wind turbulence and extreme gust events through experimentation has frustrated countless researchers. The statistical analysis of fluctuating components has been exhausted while the conditional analysis of extreme events, though insightful, often results in constricted conclusions that cannot be bridged from study to study. Thus the current study shifts towards an understanding of the fundamental turbulent flow structures within a neutrally-stratified atmospheric boundary layer. Two approaches to characterize coherent wind structures are presented. The first approach identifies hairpin-vortex heads by correlating three-dimensional, fluctuating data from two high-speed anemometers situated at 40m and 50m heights on a wind mast. The model assumes that a hairpin-vortex head can be approximated as a transverse vortex with a Vatistas viscous core of assumed radius when the hairpin-vortex head impinges onto the two anemometers. The second approach employs large-scale particle tracking velocimetry to follow seeded bubbles next to the wind mast. The results obtained with both approaches are then compared, and the advantages and shortcomings of each method are discussed.

  15. Characterization by XDR of amorphous SiCx/c-Si structures at high temperatures

    NASA Astrophysics Data System (ADS)

    Torres, I.

    2011-09-01

    By annealing thin hydrogenated amorphous silicon carbide (a-SiCx:H) films deposited by Plasma Enhanced Chemical Vapor Deposition (PECVD) on crystalline silicon (c-Si) wafers, pn-junctions with very low inverse saturation current can be formed. This has been shown in heterojunction bipolar transistors and solar cells with +/- 400°C for this process. The characterization of these structures indicates that a-SiCx:H films partially re-crystallize during the annealing process forming Si-nanocrystals embedded in the amorphous film. Understanding this process and further improving the pn-junction the study of the re-crystallization process by X-Ray Diffraction (XRD) measurements has been done. This paper deals with the characterization of amorphous SiCx/c-Si structures with 100 and 300 nm thickness measured by XRD with the temperature chamber with an annealing process at 900°C. Both intrinsic and phosphorus-doped a-SiCx:H films were deposited on a c-Si substrate p-type of 300um-thickness with crystallographic orientation <100> using the PECVD reactor. From the in-situ measurements using the XDR, the crystallization phase was obtained; this was done by taking the maximum value of intensity at the dominant peak in the orientation <111> and normalization. Fitting this with the Avrami-Mehl-Johnson Theory the incubation as well as the crystallization time were obtained to study the thermally activated process.

  16. Solvate Structures and Computational/Spectroscopic Characterization of LiBF4 Electrolytes

    SciTech Connect

    Seo, D. M.; Boyle, Paul D.; Allen, Joshua L.; Han, Sang D.; Jonsson, Erlendur; Johansson, Patrik; Henderson, Wesley A.

    2014-07-21

    Crystal structures have been determined for both LiBF4 and HBF4 solvates—(acetonitrile)2:LiBF4, (ethylene glycol diethyl ether)1:LiBF4, (diethylene glycol diethyl ether)1:LiBF4, (tetrahydrofuran)1:LiBF4, (methyl methoxyacetate)1:LiBF4, (suc-cinonitrile)1:LiBF4, (N,N,N',N",N"-pentamethyldiethylenetriamine)1:HBF4, (N,N,N',N'-tetramethylethylenediamine)3/2:HBF4 and (phenanthroline)2:HBF4. These, as well as other known LiBF4 solvate structures, have been characterized by Raman vibrational spectroscopy to unambiguously assign the anion Raman band positions to specific forms of BF4-...Li+ cation coordination. In addition, complementary DFT calculations of BF4-...Li+ cation complexes have provided additional insight into the challenges associated with accurately interpreting the anion interactions from experimental Raman spectra. This information provides a crucial tool for the characterization of the ionic association interactions within electrolytes.

  17. Syntheses and structural characterization of two new nanostructured Bi(III) supramolecular polymers via sonochemical method.

    PubMed

    Yan, Xiao-Wei; Haji-Hasani, Ensieh; Morsali, Ali

    2016-07-01

    Two new bismuth(III) coordination supramolecular polymers, {[Bi2(Hbpp)(bpp)(μ-I)2I6](Hbpp)·MeOH}n (1) and [Bi(Hbpp)(Br4)] (2), (bpp=1,3-di(pyridin-4-yl)propane) were prepared and were structurally characterized by single crystal X-ray diffraction. Single crystalline one-dimensional materials were prepared using a heat gradient applied a solution of the reagents using the branched tube method. The structural determination by single crystal X-ray crystallography shows that compounds 1 and 2 form monoclinic polymers with symmetry space group P21 in the solid state. These new nanostructured Bi(III) supramolecular compounds, {[Bi2(Hbpp)(bpp)(μ-I)2I6](Hbpp)·MeOH} (1) and [Bi(Hbpp)(Br4)] (2), were also synthesized by sonochemical method. The nanostructures were characterized by Field Emission-scanning electron microscopy (FE-SEM), powder X-ray diffraction (PXRD) and IR spectroscopy. PMID:26964932

  18. Compositional and Structural Characterization by TEM of Lattice-Mismatched III-V Epilayers

    SciTech Connect

    Ahrenkiel, S. P.; Rathi, M.; Nesheim, R.; Zheng, N.; Vunnam, S.; Carapella, J. J.; Wanlass, M. W.

    2011-01-01

    We discuss compositional and structural transmission electron microscopy (TEM) characterization of lattice-mismatched (LMM) III-V epilayers grown on GaAs by metalorganic chemical vapor deposition (MOCVD), with possible applications in high-efficiency multijunction solar cells. In addition to the use of TEM imaging to survey layer thicknesses and defect morphology, our analysis emphasizes the particular methods of energy-dispersive X-ray spectrometry (EDX) and convergent-beam electron diffraction (CBED). Outlined here is a standards-based method for extracting compositions by EDX, which uses principal-component analysis (PCA) [1], combined with the zeta-factor approach of Watanabe and Williams [2]. A procedure is described that uses the coordinates of high-order Laue zone (HOLZ) lines, which are found in the bright-field disks of CBED patterns, to extract composition and strain parameters from embedded epilayers. The majority of the crystal growth for this work was performed at NREL, which has accommodated the development at SDSM&T of the characterization techniques described. However, epilayer deposition capability at SDSM&T has recently been achieved, using a home-built system, which is presently being used to examine new lattice-mismatched structures relevant to photovoltaic technology.

  19. Human exonuclease 1 (EXO1) activity characterization and its function on flap structures

    PubMed Central

    Keijzers, Guido; Bohr, Vilhelm A.; Rasmussen, Lene Juel

    2015-01-01

    Human exonuclease 1 (EXO1) is involved in multiple DNA metabolism processes, including DNA repair and replication. Most of the fundamental roles of EXO1 have been described in yeast. Here, we report a biochemical characterization of human full-length EXO1. Prior to assay EXO1 on different DNA flap structures, we determined factors essential for the thermodynamic stability of EXO1. We show that enzymatic activity and stability of EXO1 on DNA is modulated by temperature. By characterization of EXO1 flap activity using various DNA flap substrates, we show that EXO1 has a strong capacity for degrading double stranded DNA and has a modest endonuclease or 5′ flap activity. Furthermore, we report novel mechanistic insights into the processing of flap structures, showing that EXO1 preferentially cleaves one nucleotide inwards in a double stranded region of a forked and nicked DNA flap substrates, suggesting a possible role of EXO1 in strand displacement. PMID:26182368

  20. Synthesis, fine structural characterization, and CO2 adsorption capacity of metal organic frameworks-74.

    PubMed

    Adhikari, Abhijit Krishna; Lin, Kuen-Song

    2014-04-01

    Two metal organic frameworks of MOF-74 group (zinc and copper-based) were successfully synthesized, characterized, and evaluated for CO2 adsorption. The both samples such as MOF-74(Zn) and MOF-74(Cu) were characterized with FE-SEM for morphology and particle size, XRD patterns for phase structure, FTIR for organic functional groups, nitrogen adsorption for pore textural properties, and X-ray absorption spectroscopy for fine structural parameters and oxidation states of central metal atoms. CO2 adsorption isotherms of MOF-74 samples were measured in a volumetric adsorption unit at 273 K and pressure up to 1.1 bar. The MOF-74(Zn) and MOF-74(Cu) adsorbents have the pore widths of 8.58 and 8.04 angstroms with the BET specific surface areas of 1,474 and 1,345 m2 g(-1), respectively. CO2 adsorption capacities of MOF-74(Zn) and MOF-74(Cu) were 4.10 and 3.38 mmol x g(-1), respectively measured at 273 K and 1.1 bar. The oxidation state of central atoms in MOF-74(Zn) was Zn(II) confirmed by XANES spectra while MOF-74(Cu) was composed of Cu(I) and Cu(II) central atoms. The bond distances of Zn--O and Cu--O were 1.98 and 1.94 angstroms, respectively. PMID:24734683

  1. Structural characterization of nanoscale intermetallic precipitates in highly neutron irradiated reactor pressure vessel steels

    SciTech Connect

    Sprouster, D. J.; Sinsheimer, J.; Dooryhee, E.; Ghose, S.; Wells, P.; Stan, T.; Almirall, N.; Odette, G. R.; Ecker, L. E.

    2015-10-21

    Here, massive, thick-walled pressure vessels are permanent nuclear reactor structures that are exposed to a damaging flux of neutrons from the adjacent core. The neutrons cause embrittlement of the vessel steel that increases with dose (fluence or service time), as manifested by an increasing temperature transition from ductile-to-brittle fracture. Moreover, extending reactor life requires demonstrating that large safety margins against brittle fracture are maintained at the higher neutron fluence associated with 60 to 80 years of service. Here synchrotron-based x-ray diffraction and small angle x-ray scattering measurements are used to characterize a new class of highly embrittling nm-scale Mn-Ni-Si precipitates that develop in the irradiated steels at high fluence. Furthermore, these precipitates can lead to severe embrittlement that is not accounted for in current regulatory models. Application of the complementarity techniques has, for the very first time, successfully characterized the crystal structures of the nanoprecipitates, while also yielding self-consistent compositions, volume fractions and size distributions.

  2. Structural characterization of nanoscale intermetallic precipitates in highly neutron irradiated reactor pressure vessel steels

    DOE PAGESBeta

    Sprouster, D. J.; Sinsheimer, J.; Dooryhee, E.; Ghose, S.; Wells, P.; Stan, T.; Almirall, N.; Odette, G. R.; Ecker, L. E.

    2015-10-21

    Here, massive, thick-walled pressure vessels are permanent nuclear reactor structures that are exposed to a damaging flux of neutrons from the adjacent core. The neutrons cause embrittlement of the vessel steel that increases with dose (fluence or service time), as manifested by an increasing temperature transition from ductile-to-brittle fracture. Moreover, extending reactor life requires demonstrating that large safety margins against brittle fracture are maintained at the higher neutron fluence associated with 60 to 80 years of service. Here synchrotron-based x-ray diffraction and small angle x-ray scattering measurements are used to characterize a new class of highly embrittling nm-scale Mn-Ni-Si precipitatesmore » that develop in the irradiated steels at high fluence. Furthermore, these precipitates can lead to severe embrittlement that is not accounted for in current regulatory models. Application of the complementarity techniques has, for the very first time, successfully characterized the crystal structures of the nanoprecipitates, while also yielding self-consistent compositions, volume fractions and size distributions.« less

  3. A Polyhedral Oligomeric Silsesquioxane-Polyoxometalate Hybrid Shape Amphiphile: Facile Synthesis, Characterization and Crystal Structure

    NASA Astrophysics Data System (ADS)

    Liu, Hao; Wang, Jing; Yue, Kan; Jiang, Jing; Zhang, Wen-Bin; Cheng, Stephen

    2013-03-01

    This study contains the synthesis and characterization of a novel shape amphiphile composed of two covalently conjugated inorganic nanoparticles, i.e. an isobutyl substituted polyhedral oligomeric silsesquioxane (BPOSS) cage and a Lindqvist-type hexamolybdate ([Mo6O19]2-) cluster, and its crystal structure. The facile one-step coupling strategy was realized via the highly efficient palladium-catalyzed Sonogashira reaction between an alkyne-bearing POSS derivative (BPOSS-Alkyne) and an iodo-functionalized Lindqvist precursor (Lind-Iodide) in high yield. The precisely defined molecular structure was thoroughly characterized by combination of routine techniques, such as 1H and 13C NMR, FT-IR, and MALDI-TOF mass spectroscopy. The persistent shape and chemical incompatibility of the two building blocks, as well as the rigid p-phenylene ethynylene linker, drive BPOSS-Lind to pack into a monoclinic lattice, which was confirmed by bright field transmission electron microscopy (TEM), selected area electron diffraction (SAED), small angle X-ray scattering (SAXS) and wide angle X-ray scattering (WAXS). This work introduces a new dumbbell-shaped giant hybrid molecule (BPOSS-Lind) and shed light on the packing behavior of this shape amphiphile.

  4. Structural and optical characterizations of chemically deposited cadmium selenide thin films

    SciTech Connect

    Khomane, A.S.

    2011-10-15

    Highlights: {yields} CdSe thin films deposited first time using formic acid as a complexing agent. {yields} The deposited thin films were characterized by XRD, SEM, UV-vis-NIR and electrical techniques. {yields} X-ray diffraction analysis shows presence of zinc blende crystal structure. -- Abstract: Synthesis of cadmium selenide thin films by CBD method has been presented. The deposited film samples were subjected to XRD, SEM, UV-vis-NIR and TEP characterization. X-ray diffraction analysis showed that CdSe film sample crystallized in zinc blende or cubic phase structure. SEM studies reveal that the grains are spherical in shape and uniformly distributed all over the surface of the substrates. The optical band gap energy of as deposited film sample was found to be in the order of 1.8 eV. The electrical conductivity of the film sample was found to be 10{sup -6} ({Omega} cm){sup -1} with n-type of conduction mechanism.

  5. Structural evolution and characterization of heteroepitaxial GaSb thin films on Si(111) substrates

    NASA Astrophysics Data System (ADS)

    Nguyen, Thang; Varhue, Walter; Cross, Michael; Pino, Robinson; Adams, Edward; Lavoie, Mark; Lee, Jaichan

    2007-04-01

    This paper describes the structural evolution and characterization of heteroepitaxial GaSb thin films on Si(111) substrates. The growth process used a combination of atomic sources which included the rf sputtering of Sb and the thermal effusion of Ga. The formation of crystalline GaSb thin films required that initially a monolayer thick Sb buffer layer be applied directly to a clean H-passivated Si(111) substrate surface. The resulting film was characterized by high resolution x-ray diffraction, Rutherford backscattering spectrometry, transmission electron microscopy, secondary ion mass spectroscopy, and atomic force microscopy (AFM). The AFM images were taken from the material after several periods of growth to determine the evolution of crystal structure with thickness. Atomic force microscopy images of the film surface showed that the heteroepitaxial layers were formed via the Stranski-Krastanov growth mechanism. This result is consistent with the heteroepitaxial growth of systems representing large differences in lattice constant. The hole mobility and carrier concentration in the deposited material were determined by the Hall measurement, performed at room temperature and on a 140nm thick sample, to be 66cm2/Vsec and 3×1019 cm-3, respectively. The carrier mobility was relatively low as expected for measurements taken at room temperature.

  6. Effects of structural characterizations on fragility functions of bridges subject to seismic shaking and lateral spreading

    NASA Astrophysics Data System (ADS)

    Zhang, Jian; Huo, Yili; Brandenberg, Scott J.; Kashighandi, Pirooz

    2008-12-01

    This paper evaluates the seismic vulnerability of different classes of typical bridges in California when subjected to seismic shaking or liquefaction-induced lateral spreading. The detailed structural configurations in terms of superstructure type, connection, continuity at support and foundation type, etc. render different damage resistant capability. Six classes of bridges are established based on their anticipated failure mechanisms under earthquake shaking. The numerical models that are capable of simulating the complex soil-structure interaction effects, nonlinear behavior of columns and connections are developed for each bridge class. The dynamic responses are obtained using nonlinear time history analyses for a suite of 250 earthquake motions with increasing intensity. An equivalent static analysis procedure is also implemented to evaluate the vulnerability of the bridges when subjected to liquefaction-induced lateral spreading. Fragility functions for each bridge class are derived and compared for both seismic shaking (based on nonlinear dynamic analyses) and lateral spreading (based on equivalent static analyses) for different performance states. The study finds that the fragility functions due to either ground shaking or lateral spreading show significant correlation with the structural characterizations, but differences emerge for ground shaking and lateral spreading conditions. Structural properties that will mostly affect the bridges’ damage resistant capacity are also identified.

  7. Deployment, Foam Rigidization, and Structural Characterization of Inflatable Thin-Film Booms

    NASA Technical Reports Server (NTRS)

    Schnell, Andrew R.; Leigh, Larry M., Jr.; Tinker, Michael L.; McConnaughey, Paul R. (Technical Monitor)

    2002-01-01

    Detailed investigation of the construction, packaging/deployment, foam rigidization, and structural characterization of polyimide film inflatable booms is described. These structures have considerable potential for use in space with solar concentrators, solar sails, space power systems including solar arrays, and other future missions. Numerous thin-film booms or struts were successfully constructed, inflated, injected with foam, and rigidized. Both solid-section and annular test articles were fabricated, using Kapton polyimide film, various adhesives, Styrofoam end plugs, and polyurethane pressurized foam. Numerous inflation/deployment experiments were conducted and compared to computer simulations using the MSC/DYTRAN code. Finite element models were developed for several foam-rigidized struts and compared to model test results. Several problems encountered in the construction, deployment, and foam injection/rigidization process are described. Areas of difficulty included inadequate adhesive strength, cracking of the film arid leakage, excessive bending of the structure during deployment, problems with foam distribution and curing properties, and control of foam leakage following injection into the structure. Many of these problems were overcome in the course of the research.

  8. Amino-Functionalized Layered Crystalline Zirconium Phosphonates: Synthesis, Crystal Structure, and Spectroscopic Characterization.

    PubMed

    Taddei, Marco; Sassi, Paola; Costantino, Ferdinando; Vivani, Riccardo

    2016-06-20

    Two new layered zirconium phosphonates functionalized with amino groups were synthesized starting from aminomethylphosphonic acid in the presence of different mineralizers, and their structures were solved from powder X-ray diffraction data. Their topologies are unprecedented in zirconium phosphonate chemistry: the first, of formula ZrH[F3(O3PCH2NH2)], prepared in the presence of hydrofluoric acid, features uncommon ZrO2F4 units and a remarkable thermal stability; the second, of formula Zr2H2[(C2O4)3(O3PCH2NH2)2]·2H2O, prepared in the presence of oxalic acid, is based on ZrO7 units with oxalate anions coordinated to the metal atom, which were never observed before in any zirconium phosphonate. In addition, the structure of another compound based on (2-aminoethyl)phosphonic acid is reported, which was the object of a previously published study. This compound has layered α-type structure with -NH3(+) groups located in the interlayer space. All of the reported compounds were further characterized by means of vibrational spectroscopy, which provided important information on fine structural details that cannot be deduced from the powder X-ray diffraction data. PMID:27254781

  9. Structural characterization of Turtle Mountain anticline (Alberta, Canada) and impact on rock slope failure

    NASA Astrophysics Data System (ADS)

    Humair, Florian; Pedrazzini, Andrea; Epard, Jean-Luc; Froese, Corey R.; Jaboyedoff, Michel

    2013-10-01

    This paper proposes a structural investigation of the Turtle Mountain anticline (Alberta, Canada) to better understand the role of the different tectonic features on the development of both local and large scale rock slope instabilities occurring in Turtle Mountain. The study area is investigated by combining remote methods with detailed field surveys. In particular, the benefit of Terrestrial Laser Scanning for ductile and brittle tectonic structure interpretations is illustrated. The proposed tectonic interpretation allows the characterization of the fracturing pattern, the fold geometry and the role of these tectonic features in rock slope instability development. Ten discontinuity sets are identified in the study area, their local variations permitting the differentiation of the study zone into 20 homogenous structural domains. The anticline is described as an eastern verging fold that displays considerable geometry differences along its axis and developed by both flexural slip and tangential longitudinal strain folding mechanisms. Moreover, the origins of the discontinuity sets are determined according to the tectonic phases affecting the region (pre-folding, folding, post-folding). The localization and interpretation of kinematics of the different instabilities revealed the importance of considering the discrete brittle planes of weakness, which largely control the kinematic release of the local instabilities, and also the rock mass damage induced by large tectonic structures (fold hinge, thrust).

  10. A hirshfeld surface analysis, crystal structure and physicochemical characterization of 1-ethylpiperazinium trichlorocadmate(II)

    NASA Astrophysics Data System (ADS)

    Soudani, S.; Jeanneau, E.; Jelsch, C.; Lefebvre, F.; Ben Nasr, C.

    2016-07-01

    A novel organic-inorganic hybrid material, C6H15N2CdCl3.H2O, was synthesized, and its structure was determined at room temperature in the monoclinic space group P21/n with the following parameters: a = 10.3829 (17), b = 7.7459 (12), c = 14.905 (2) Å, β = 98.801 (15), and Z = 4. Its crystal structure is characterized by one-dimensional polymeric chains of edge-sharing CdCl5N distorted octahedra. These chains are linked to the water molecules via Osbnd H … Cl hydrogen bonds to form layers parallel to the (b, a + c) plane. The crystal structure was stabilized by an extensive network of Nsbnd H … Cl, Osbnd H … Cl and Nsbnd H … O hydrogen bonds. The differential scanning calorimetry (DSC) reveals that the title compound is stable until 101.6 °C. The optimized geometry parameters, normal mode frequencies, and corresponding vibrational assignments of the present compound were theoretically examined by DFT/B3LYP method with the Lanl2dz basis set. The FT-IR spectrum of the polycrystalline sample was examined and compared to the calculated spectrum. The calculated results showed that the optimized geometry could well reproduce the crystal structure and that the theoretical vibrational frequency values were in good agreement with their experimental counterparts.

  11. Prospect for characterizing interacting soft colloidal structures using spin-echo small angle neutron scattering

    SciTech Connect

    Chen, Wei-Ren; Herwig, Kenneth W; Li, Xin; Liu, Emily; Liu, Yun; Pynn, Roger; Robertson, J. L.; Shew, Chwen-Yang; Smith, Gregory Scott

    2011-01-01

    Spin-echo small angle neutron scattering (SESANS) presents a new experimental tool for structural investigation. Regarding the material study using neutron scattering it is of particular novel: Due to the action of spin echo encoding, SESANS registers the spatial correlations function in real space, which is distinct from the measurables of conventional elastic neutron scattering techniques. To make viable the use of SESANS in structural characterization, particularly for the interacting colloidal suspensions, we have conducted a theoretical study focusing on understanding the essential features of the SESANS correlation functions obtained from different model systems consisting of particles with uniform density profile (J. Chem. Phys. 132, 174509 (2010)). Within the same framework, we continue to explore the prospect of using SESANS to investigate the structural characteristics of colloid systems consisting of particle with non-uniform intra-particle mass distribution. As an example, a Gaussian model of interacting soft colloids is put forward in our mean-field calculations to investigate the manifestation of structural softness in SESANS measurement. The exploration shows a characteristically different SESANS correlation function for interacting soft colloids, in comparison to that of the referential uniform hard sphere system, due to the Abel transform imbedded in the mathematical formalism bridging the SESANS spectra and the spatial autocorrelation.

  12. Analytical and Experimental Characterization of Gravity Induced Deformations In Subscale Gossamer Structures

    NASA Technical Reports Server (NTRS)

    Johnston, John D.; Blandino, Joseph R.; McEvoy, Kiley C.

    2004-01-01

    The development of gossamer space structures such as solar sails and sunshields presents many challenges due to their large size and extreme flexibility. The post-deployment structural geometry exhibited during ground testing may significantly depart from the in-space configuration due to the presence of gravity-induced deformations (gravity sag) of lightly preloaded membranes. This paper describes a study carried out to characterize gravity sag in two subscale gossamer structures: a single quadrant from a 2 m, 4 quadrant square solar sail and a 1.7 m membrane layer from a multi-layer sunshield The behavior of the test articles was studied over a range of preloads and in several orientations with respect to gravity. An experimental study was carried out to measure the global surface profiles using photogrammetry, and nonlinear finite element analysis was used to predict the behavior of the test articles. Comparison of measured and predicted surface profiles shows that the finite dement analysis qualitatively predicts deformed shapes comparable to those observed in the laboratory. Quantitatively, finite element analysis predictions for peak gravity-induced deformations in both test articles were within 10% of measured values. Results from this study provide increased insight into gravity sag behavior in gossamer structures, and demonstrates the potential to analytically predict gravity-induced deformations to within reasonable accuracy.

  13. Low-resolution characterization of the 3D structure of the Euglena gracilis photoreceptor

    SciTech Connect

    Barsanti, Laura; Coltelli, Primo; Evangelista, Valtere; Passarelli, Vincenzo; Frassanito, Anna Maria; Vesentini, Nicoletta; Gualtieri, Paolo

    2008-10-24

    This paper deals with the first characterization of the structure of the photoreceptive organelle of the unicellular alga Euglena gracilis (Euglenophyta). This organelle has a three-dimensional organization consisting of up to 50 closely stacked membrane lamellae. Ionically induced unstacking of the photoreceptor lamellae revealed ordered arrays well suited to structural analysis by electron microscopy and image analysis, which ultimately yielded a low-resolution picture of the structure. Each lamella is formed by the photoreceptive membrane protein of the cell assembled within the membrane layer in a hexagonal lattice. The first order diffraction spots in the calculated Fourier transform reveals the presence of 6-fold symmetrized topography (better resolution about 90 A). The 2D and 3D structural data are very similar with those recently published on proteorodopsin, a membrane protein used by marine bacterio-plankton as light-driven proton pump. In our opinion these similarity indicate that a photoreceptive protein belonging to the same superfamily of proteorodopsin could form the Euglena photoreceptor.

  14. Structural and biochemical characterization of the Bacillus cereus 3-hydroxyisobutyrate dehydrogenase.

    PubMed

    Park, Sun Cheol; Kim, Pyeung-Hyeun; Lee, Geun-Shik; Kang, Seung Goo; Ko, Hyun-Jeong; Yoon, Sung-Il

    2016-06-01

    The 3-hydroxyisobutyrate dehydrogenase (HIBADH) family catalyzes the NAD(+)- or NADP(+)-dependent oxidation of various β-hydroxyacid substrates into their cognate semialdehydes for diverse metabolic pathways. Because HIBADH group members exhibit different substrate specificities, the substrate-recognition mode of each enzyme should be individually characterized. In the current study, we report the biochemical and structural analysis of a HIBADH group enzyme from Bacillus cereus (bcHIBADH). bcHIBADH mediates a dehydrogenation reaction on S-3-hydroxyisobutyrate substrate with high catalytic efficiency in an NAD(+)-dependent manner; it also oxidizes l-serine and 3-hydroxypropionate with lower activity. bcHIBADH consists of two domains and is further assembled into a functional dimer rather than a tetramer that has been commonly observed in other prokaryotic HIBADH group members. In the bcHIBADH structure, the interdomain cleft forms a putative active site and simultaneously accommodates both an NAD(+) cofactor and a substrate mimic. Our structure-based comparative analysis highlights structural motifs that are important in the cofactor and substrate recognition of the HIBADH group. PMID:27120461

  15. Characterizing the nonlinear growth of large-scale structure in the Universe

    PubMed

    Coles; Chiang

    2000-07-27

    The local Universe displays a rich hierarchical pattern of galaxy clusters and superclusters. The early Universe, however, was almost smooth, with only slight 'ripples' as seen in the cosmic microwave background radiation. Models of the evolution of cosmic structure link these observations through the effect of gravity, because the small initially overdense fluctuations are predicted to attract additional mass as the Universe expands. During the early stages of this expansion, the ripples evolve independently, like linear waves on the surface of deep water. As the structures grow in mass, they interact with each other in nonlinear ways, more like waves breaking in shallow water. We have recently shown how cosmic structure can be characterized by phase correlations associated with these nonlinear interactions, but it was not clear how to use that information to obtain quantitative insights into the growth of structures. Here we report a method of revealing phase information, and show quantitatively how this relates to the formation of filaments, sheets and clusters of galaxies by nonlinear collapse. We develop a statistical method based on information entropy to separate linear from nonlinear effects, and thereby are able to disentangle those aspects of galaxy clustering that arise from initial conditions (the ripples) from the subsequent dynamical evolution. PMID:10935627

  16. Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif

    PubMed Central

    Kim, Kuglae; Kwon, Soon-Kyeong; Jun, Sung-Hoon; Cha, Jeong Seok; Kim, Hoyoung; Lee, Weontae; Kim, Jihyun F.; Cho, Hyun-Soo

    2016-01-01

    A novel light-driven chloride-pumping rhodopsin (ClR) containing an ‘NTQ motif' in its putative ion conduction pathway has been discovered and functionally characterized in a genomic analysis study of a marine bacterium. Here we report the crystal structure of ClR from the flavobacterium Nonlabens marinus S1-08T determined under two conditions at 2.0 and 1.56 Å resolutions. The structures reveal two chloride-binding sites, one around the protonated Schiff base and the other on a cytoplasmic loop. We identify a ‘3 omega motif' formed by three non-consecutive aromatic amino acids that is correlated with the B–C loop orientation. Detailed ClR structural analyses with functional studies in E. coli reveal the chloride ion transduction pathway. Our results help understand the molecular mechanism and physiological role of ClR and provide a structural basis for optogenetic applications. PMID:27554809

  17. Structural characterization and DFT study of V(IV)O(acac)2 in imidazolium ionic liquids.

    PubMed

    Mota, Andreia; Hallett, Jason P; Kuznetsov, Maxim L; Correia, Isabel

    2011-09-01

    We report the structural characterization of vanadyl acetylacetonate in imidazolium room temperature ionic liquids--bbimNTf(2), bmimNTf(2), C(3)OmimNTf(2), bm(2)imNTf(2), bmimPF(6), bmimOTf, bmimBF(4), bmimMeCO(2), bmimMeSO(4), bmimMe(2)PO(4) and bmimN(CN)(2)--and organic solvents. The complex was characterized by visible electronic (Vis) and EPR spectroscopies. VO(acac)(2) shows solvatochromism in the selected ionic liquids and behaves as in organic solvents, evidencing coordination of the ionic liquid anion in the solvents with higher coordinating ability. The Lewis basicity order obtained for the IL anions was: PF(6)(-) < NTf(2)(-) < OTf(-)≈ MeCO(2)(-) < MeSO(4)(-) < BF(4)(-)≈ N(CN)(2)(-) < Me(2)PO(4)(-). The solvent effect on the spectroscopic data was tentatively examined using linear solvation energy relationships based on the Kamlet-Taft solvent scale (α, β and π*), however no suitable correlation was found with all data. The EPR characterization showed the presence of two isomers in bmimOTf, bmimMeCO(2) and bmimMe(2)PO(4), suggesting coordination of the ionic liquid anions in both equatorial and axial positions. The full geometry optimization of cis-/trans-VO(acac)(2)(OTf)(-) and cis-/trans-VO(acac)(2)(OTf)(mmim) structures was done at the B3P86/6-31G* level of theory. The calculations confirm that the anion OTf(-) is able to coordinate to VO(acac)(2) with the trans isomer being more stable than the cis by 4.8 kcal mol(-1). PMID:21789301

  18. Structural Characterization of Melanin Pigments from Commercial Preparations of the Edible Mushroom Auricularia auricula

    PubMed Central

    Prados-Rosales, Rafael; Toriola, Stacy; Nakouzi, Antonio; Chatterjee, Subhasish; Stark, Ruth; Gerfen, Gary; Tumpowsky, Paul; Dadachova, Ekaterina; Casadevall, Arturo

    2016-01-01

    Many of the most widely consumed edible mushrooms are pigmented, and these have been associated with some beneficial health effects. Nevertheless, the majority of the reported compounds associated with these desirable properties are non-pigmented. We have previously reported that melanin pigment from the edible mushroom Auricularia auricula can protect mice against ionizing radiation, although no physicochemical characterization was reported. Consequently, in this study we have characterized commercial A. auricula mushroom preparations for melanin content and carried out structural characterization of isolated insoluble melanin materials using a panel of sophisticated spectroscopic and physical/imaging techniques. Our results show that approximately 10% of the dry mass of A. auricula is melanin and that the pigment has physicochemical properties consistent with those of eumelanins, including hosting a stable free radical population. Electron microscopy studies show that melanin is associated with the mushroom cell wall in a manner similar to that of melanin from the model fungus C. neoformans. Elemental analysis of melanin indicated C, H, and N ratios consistent with 5,6-dihydroxyindole-2-carboxylic acid/5,6-dihydroxyindole and 1,8-dihydroxynaphthalene eumelanin. Validation of the identity of the isolated product as melanin was achieved by EPR analysis. A. auricula melanin manifested structural differences, relative to the C. neoformans melanin, with regard to the variable proportions of alkyl chains or oxygenated carbons. Given the necessity for new oral and inexpensive radioprotective materials coupled with the commercial availability of A. auricula mushrooms, this product may represent an excellent source of edible melanin. PMID:26244793

  19. Evaluation of water sampling methodologies for amplicon-based characterization of bacterial community structure.

    PubMed

    Staley, Christopher; Gould, Trevor J; Wang, Ping; Phillips, Jane; Cotner, James B; Sadowsky, Michael J

    2015-07-01

    Reduction in costs of next-generation sequencing technologies has allowed unprecedented characterization of bacterial communities from environmental samples including aquatic ecosystems. However, the extent to which extrinsic factors including sampling volume, sample replication, DNA extraction kits, and sequencing target affect the community structure inferred are poorly explored. Here, triplicate 1, 2, and 6L volume water samples from the Upper Mississippi River were processed to determine variation among replicates and sample volumes. Replicate variability significantly influenced differences in the community α-diversity (P=0.046), while volume significantly changed β-diversity (P=0.037). Differences in phylogenetic and taxonomic community structure differed both among triplicate samples and among the volumes filtered. Communities from 2L and 6L water samples showed similar clustering via discriminant analysis. To assess variation due to DNA extraction method, DNA was extracted from triplicate cell pellets from four sites along the Upper Mississippi River using the Epicentre Metagenomic DNA Isolation Kit for Water and MoBio PowerSoil kit. Operational taxonomic units representing ≤14% of sequence reads differed significantly among all sites and extraction kits used, although differences in diversity and community coverage were not significant (P≥0.057). Samples characterized using only the V6 region had significantly higher coverage and lower richness and α-diversity than those characterized using V4-V6 regions (P<0.001). Triplicate sampling of at least 2L of water provides robust representation of community variability, and these results indicate that DNA extraction kit and sequencing target displayed taxonomic biases that did not affect the overall biological conclusions drawn. PMID:25956022

  20. Structural Characterization of HIV gp41 with the Membrane-proximal External Region

    SciTech Connect

    Shi, W.; Bohon, J; Han, D; Habte, H; Qin, Y; Cho, M; Chance, M

    2010-01-01

    Human immunodeficiency virus, type 1 (HIV-1) envelope glycoprotein (gp120/gp41) plays a critical role in virus infection and pathogenesis. Three of the six monoclonal antibodies considered to have broadly neutralizing activities (2F5, 4E10, and Z13e1) bind to the membrane-proximal external region (MPER) of gp41. This makes the MPER a desirable template for developing immunogens that can elicit antibodies with properties similar to these monoclonal antibodies, with a long term goal of developing antigens that could serve as novel HIV vaccines. In order to provide a structural basis for rational antigen design, an MPER construct, HR1-54Q, was generated for x-ray crystallographic and x-ray footprinting studies to provide both high resolution atomic coordinates and verification of the solution state of the antigen, respectively. The crystal structure of HR1-54Q reveals a trimeric, coiled-coil six-helical bundle, which probably represents a postfusion form of gp41. The MPER portion extends from HR2 in continuation of a slightly bent long helix and is relatively flexible. The structures observed for the 2F5 and 4E10 epitopes agree well with existing structural data, and enzyme-linked immunosorbent assays indicate that the antigen binds well to antibodies that recognize the above epitopes. Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specifically protected and accessible regions consistent with the predictions based on the trimeric structure from the crystallographic data. Overall, the HR1-54Q antigen, as characterized by crystallography and footprinting, represents a postfusion, trimeric form of HIV gp41, and its structure provides a rational basis for gp41 antigen design suitable for HIV vaccine development.

  1. Structural characterization of HIV gp41 with the membrane-proximal external region.

    PubMed

    Shi, Wuxian; Bohon, Jen; Han, Dong P; Habte, Habtom; Qin, Yali; Cho, Michael W; Chance, Mark R

    2010-07-30

    Human immunodeficiency virus, type 1 (HIV-1) envelope glycoprotein (gp120/gp41) plays a critical role in virus infection and pathogenesis. Three of the six monoclonal antibodies considered to have broadly neutralizing activities (2F5, 4E10, and Z13e1) bind to the membrane-proximal external region (MPER) of gp41. This makes the MPER a desirable template for developing immunogens that can elicit antibodies with properties similar to these monoclonal antibodies, with a long term goal of developing antigens that could serve as novel HIV vaccines. In order to provide a structural basis for rational antigen design, an MPER construct, HR1-54Q, was generated for x-ray crystallographic and x-ray footprinting studies to provide both high resolution atomic coordinates and verification of the solution state of the antigen, respectively. The crystal structure of HR1-54Q reveals a trimeric, coiled-coil six-helical bundle, which probably represents a postfusion form of gp41. The MPER portion extends from HR2 in continuation of a slightly bent long helix and is relatively flexible. The structures observed for the 2F5 and 4E10 epitopes agree well with existing structural data, and enzyme-linked immunosorbent assays indicate that the antigen binds well to antibodies that recognize the above epitopes. Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specifically protected and accessible regions consistent with the predictions based on the trimeric structure from the crystallographic data. Overall, the HR1-54Q antigen, as characterized by crystallography and footprinting, represents a postfusion, trimeric form of HIV gp41, and its structure provides a rational basis for gp41 antigen design suitable for HIV vaccine development. PMID:20525690

  2. Structural Characterization of HIV gp41 with the Membrane-proximal External Region*

    PubMed Central

    Shi, Wuxian; Bohon, Jen; Han, Dong P.; Habte, Habtom; Qin, Yali; Cho, Michael W.; Chance, Mark R.

    2010-01-01

    Human immunodeficiency virus, type 1 (HIV-1) envelope glycoprotein (gp120/gp41) plays a critical role in virus infection and pathogenesis. Three of the six monoclonal antibodies considered to have broadly neutralizing activities (2F5, 4E10, and Z13e1) bind to the membrane-proximal external region (MPER) of gp41. This makes the MPER a desirable template for developing immunogens that can elicit antibodies with properties similar to these monoclonal antibodies, with a long term goal of developing antigens that could serve as novel HIV vaccines. In order to provide a structural basis for rational antigen design, an MPER construct, HR1-54Q, was generated for x-ray crystallographic and x-ray footprinting studies to provide both high resolution atomic coordinates and verification of the solution state of the antigen, respectively. The crystal structure of HR1-54Q reveals a trimeric, coiled-coil six-helical bundle, which probably represents a postfusion form of gp41. The MPER portion extends from HR2 in continuation of a slightly bent long helix and is relatively flexible. The structures observed for the 2F5 and 4E10 epitopes agree well with existing structural data, and enzyme-linked immunosorbent assays indicate that the antigen binds well to antibodies that recognize the above epitopes. Hydroxyl radical-mediated protein footprinting of the antigen in solution reveals specifically protected and accessible regions consistent with the predictions based on the trimeric structure from the crystallographic data. Overall, the HR1-54Q antigen, as characterized by crystallography and footprinting, represents a postfusion, trimeric form of HIV gp41, and its structure provides a rational basis for gp41 antigen design suitable for HIV vaccine development. PMID:20525690

  3. Mechanical characterization and structural analysis of recycled fiber-reinforced-polymer resin-transfer-molded beams

    NASA Astrophysics Data System (ADS)

    Tan, Eugene Wie Loon

    1999-09-01

    The present investigation was focussed on the mechanical characterization and structural analysis of resin-transfer-molded beams containing recycled fiber-reinforced polymers. The beams were structurally reinforced with continuous unidirectional glass fibers. The reinforcing filler materials consisted entirely of recycled fiber-reinforced polymer wastes (trim and overspray). The principal resin was a 100-percent dicyclo-pentadiene unsaturated polyester specially formulated with very low viscosity for resin transfer molding. Variations of the resin transfer molding technique were employed to produce specimens for material characterization. The basic materials that constituted the structural beams, continuous-glass-fiber-reinforced, recycled-trim-filled and recycled-overspray-filled unsaturated polyesters, were fully characterized in axial and transverse compression and tension, and inplane and interlaminar shear, to ascertain their strengths, ultimate strains, elastic moduli and Poisson's ratios. Experimentally determined mechanical properties of the recycled-trim-filled and recycled-overspray-filled materials from the present investigation were superior to those of unsaturated polyester polymer concretes and Portland cement concretes. Mechanical testing and finite element analyses of flexure (1 x 1 x 20 in) and beam (2 x 4 x 40 in) specimens were conducted. These structurally-reinforced specimens were tested and analyzed in four-point, third-point flexure to determine their ultimate loads, maximum fiber stresses and mid-span deflections. The experimentally determined load capacities of these specimens were compared to those of equivalent steel-reinforced Portland cement concrete beams computed using reinforced concrete theory. Mechanics of materials beam theory was utilized to predict the ultimate loads and mid-span deflections of the flexure and beam specimens. However, these predictions proved to be severely inadequate. Finite element (fracture propagation

  4. Characterization of Hertzian rolling microslip in precision revolute joints for deployable space structures

    NASA Astrophysics Data System (ADS)

    Jeon, Sungeun Ki

    2009-09-01

    The capabilities of space-born telescopes are primarily limited by their launch systems, dictating both light-gathering power and resolution, by constricting aperture size. Precision deployable space structure technology enables smaller stowed configurations for launch and a larger deployed operational state in space. The primary engineering difficulties arise from the accuracy and repeatability requirements of the deployed system, where an optical system requires tens of nanometers RMS surface displacement. Recent studies identify that instabilities and errors in a deployable space structure are primarily caused by the stick-slip friction between the contact interfaces of the latches and joints. The intent of this research is to model and characterize the nonlinearities of contact of a precision revolute joint for deployable space structures. The joint is a modified pin-clevis joint, where the deployment mechanism, load-path, and sources of instability are relegated to the contact interfaces of pair of angular contact bearings. This research presents a nonlinear lumped-parameter finite element modeling the nonlinear mechanics of contact to characterize the microdynamic behavior of the angular contact bearings for a precision revolute hinge. The mechanics of contact are based on Hertz contact theory and a numerical simulation subproblem based on the influence function method. The numerical simulation is rigorously validated and is shown to efficiently and effectively model transient rolling contact with varying normal contact forces, where current literature and numerical modeling techniques fail. The in uence of surface roughness and stochastic variations due to manufacturing and assembly are studied in regards to stiffness performance metrics. Rolling hysteresis is identified for various conditions, and a zero-loss rolling mechanism is discovered and investigated. Design implications, capabilities, recommendations, and optimal improvements for the precision hinge

  5. Structural and magnetic characterization of electro-crystallized magnetite nanoparticles under constant current

    SciTech Connect

    Mosivand, Saba; Kazeminezhad, Iraj

    2015-10-15

    Graphical abstract: Structural and magnetic properties of electro-crystallized magnetite nanoparticles under constant current were studied. All samples were characterized using XRD, SEM, VSM, and Mössbauer spectrometry. - Highlights: • The effect of applied current on morphology and properties of Fe{sub 3}O{sub 4} is studied. • The particle size and morphology are controllable by adjusting the current. • The magnetization depends on particle size, type of surfactant and applied current. • The clear correlation between magnetization and the mean particle size is observed. - Abstract: The effect of applied current on the morphology, particle size, structure, and magnetic properties of magnetite nanoparticles prepared by electro-crystallization method was studied. The synthesis was performed in an electrochemical cell containing two iron electrodes and an aqueous solution of sodium sulfate, and either thiourea, sodium butanoate, or β-cyclodextrine as organic stabilizer. All the samples were characterized by XRD, SEM, VSM, and Mössbauer spectroscopy. X-ray diffraction patterns, clearly confirmed that all products have the cubic spinel Fe{sub 3}O{sub 4} crystal structure. Electron microscope images of the samples showed that their mean particle size is in the range 20–80 nm, and depends critically on the applied current and type of the organic additives. Specific magnetization of the samples at room temperature ranges from 60 to 90 A m{sup 2} kg{sup −1}, depending on the growth conditions. Room temperature Mössbauer spectra are typical of nonstoichiometric Fe{sub 3−δ}O{sub 4}, with a small excess of Fe{sup 3+}, 0.06 ≤ δ ≤ 0.17.

  6. Remote Characterization of Forest Structure Using 5 and 10m SPOT-5 Satellite Data

    NASA Astrophysics Data System (ADS)

    Wolter, P. T.; Townsend, P. A.; Sturtevant, B. R.

    2008-12-01

    Comprehensive understanding of forest dynamics at regional or biome scales is linked to our ability to accurately characterize forest ecosystems over increasingly large areas using remote sensing. LIDAR technology, although promising, is currently not yet viable for repeated regional accounting, necessitating the development of methods which take advantage of existing spaceborne assets. As such, our objective is to estimate a comprehensive set of forest structural attributes at a finer spatial grain size (10 m) over a broader area than is currently available. We employ neighborhood statistics (standard deviation, variance, sill variance, and ratios of these metrics at 5 and 10m) calculated from SPOT-5 data and derivatives to estimate and map forest structural characteristics. A partial least squares (PLS) regression approach was used with the local statistics and field data to produce models for pixel-wise estimation and mapping of mean values, respectively, for deciduous and coniferous forest canopy diameter (R2 = 0.82 and 0.93), tree height (R2 = 0.69 and 0.92), height of live crown (R2 = 0.58 and 0.81), canopy closure (R2 = 0.52 and 0.68), bole diameter at breast height (R2 = 0.82 and 0.90), and basal area (R2 = 0.71 and 0.74) for a 3,660 km2 area in northeast Minnesota. This approach for quantifying forest structure is robust in the sense that a detailed forest cover type map is not required at any step in the process. Hence, we show that multi-resolution SPOT-5 data may be used as a practical alternative to LIDAR for regional characterization of forest biophysical parameters.

  7. Silver sulfadoxinate: Synthesis, structural and spectroscopic characterizations, and preliminary antibacterial assays in vitro

    NASA Astrophysics Data System (ADS)

    Zanvettor, Nina T.; Abbehausen, Camilla; Lustri, Wilton R.; Cuin, Alexandre; Masciocchi, Norberto; Corbi, Pedro P.

    2015-02-01

    The sulfa drug sulfadoxine (SFX) reacted with Ag+ ions in aqueous solution, affording a new silver(I) complex (AgSFX), which was fully characterized by chemical, spectroscopic and structural methods. Elemental, ESI-TOF mass spectrometric and thermal analyses of AgSFX suggested a [Ag(C12H13N4O2S)] empirical formula. Infrared spectroscopic measurements indicated ligand coordination to Ag(I) through the nitrogen atoms of the (deprotonated) sulfonamide group and by the pyrimidine ring, as well as through oxygen atom(s) of the sulfonamide group. These hypotheses were corroborated by 13C and 15N SS-NMR spectroscopy and by an unconventional structural characterization based on X-ray powder diffraction data. The latter showed that AgSFX crystallizes as centrosymmetric dimers with a strong Ag⋯Ag interaction of 2.7435(6) Å, induced by the presence of exo-bidentate N,N‧ bridging ligands and the formation of an eight-membered ring of [AgNCN]2 sequence, nearly planar. Participation of oxygen atoms of the sulfonamide residues generates in the crystal a 1D coordination polymer, likely responsible for its very limited solubility in all common solvents. Besides the analytical, spectroscopic and structural description, the antibacterial properties of AgSFX were assayed using disc diffusion methods against Escherichia coli and Pseudomonas aeruginosa (Gram-negative), and Staphylococcus aureus (Gram-positive) bacterial strains. The AgSFX complex showed to be active against Gram-positive and Gram-negative bacterial strains, being comparable to the activities of silver sulfadiazine.

  8. Structural and biochemical characterization of a novel aminopeptidase from human intestine.

    PubMed

    Tykvart, Jan; Bařinka, Cyril; Svoboda, Michal; Navrátil, Václav; Souček, Radko; Hubálek, Martin; Hradilek, Martin; Šácha, Pavel; Lubkowski, Jacek; Konvalinka, Jan

    2015-05-01

    N-acetylated α-linked acidic dipeptidase-like protein (NAALADase L), encoded by the NAALADL1 gene, is a close homolog of glutamate carboxypeptidase II, a metallopeptidase that has been intensively studied as a target for imaging and therapy of solid malignancies and neuropathologies. However, neither the physiological functions nor structural features of NAALADase L are known at present. Here, we report a thorough characterization of the protein product of the human NAALADL1 gene, including heterologous overexpression and purification, structural and biochemical characterization, and analysis of its expression profile. By solving the NAALADase L x-ray structure, we provide the first experimental evidence that it is a zinc-dependent metallopeptidase with a catalytic mechanism similar to that of glutamate carboxypeptidase II yet distinct substrate specificity. A proteome-based assay revealed that the NAALADL1 gene product possesses previously unrecognized aminopeptidase activity but no carboxy- or endopeptidase activity. These findings were corroborated by site-directed mutagenesis and identification of bestatin as a potent inhibitor of the enzyme. Analysis of NAALADL1 gene expression at both the mRNA and protein levels revealed the small intestine as the major site of protein expression and points toward extensive alternative splicing of the NAALADL1 gene transcript. Taken together, our data imply that the NAALADL1 gene product's primary physiological function is associated with the final stages of protein/peptide digestion and absorption in the human digestive system. Based on these results, we suggest a new name for this enzyme: human ileal aminopeptidase (HILAP). PMID:25752612

  9. Smart Fluids in Hydrology: Use of Non-Newtonian Fluids for Pore Structure Characterization

    NASA Astrophysics Data System (ADS)

    Abou Najm, Majdi; Atallah, Nabil; Selker, John; Roques, Clément; Stewart, Ryan; Rupp, David; Saad, George; El-Fadel, Mutasem

    2016-04-01

    Classic porous media characterization relies on typical infiltration experiments with Newtonian fluids (i.e., water) to estimate hydraulic conductivity. However, such experiments are generally not able to discern important characteristics such as pore size distribution or pore structure. We show that introducing non-Newtonian fluids provides additional unique flow signatures that can be used for improved pore structure characterization. We present a new method that transforms results of N infiltration experiments using water and N-1 non-Newtonian solutions into a system of equations that yields N representative radii (Ri) and their corresponding percent contribution to flow (wi). Those radii and weights are optimized in terms of flow and porosity to represent the functional hydraulic behavior of real porous media. The method also allows for estimating the soil retention curve using only saturated experiments. Experimental and numerical validation revealed the ability of the proposed method to represent the water retention and functional infiltration behavior of real soils. The experimental results showed the ability of such fluids to outsmart Newtonian fluids and infer pore size distribution and unsaturated behavior using simple saturated experiments. Specifically, we demonstrate using synthetic porous media composed of different combinations of sizes and numbers of capillary tubes that the use of different non-Newtonian fluids enables the prediction of the pore structure. The results advance the knowledge towards conceptualizing the complexity of porous media and can potentially impact applications in fields like irrigation efficiencies, vadose zone hydrology, soil-root-plant continuum, carbon sequestration into geologic formations, soil remediation, petroleum reservoir engineering, oil exploration and groundwater modeling.

  10. Structural Characterization of a Therapeutic Anti-Methamphetamine Antibody Fragment: Oligomerization and Binding of Active Metabolites

    PubMed Central

    Gokulan, Kuppan; Varughese, Kottayil I.

    2013-01-01

    Vaccines and monoclonal antibodies (mAb) for treatment of (+)-methamphetamine (METH) abuse are in late stage preclinical and early clinical trial phases, respectively. These immunotherapies work as pharmacokinetic antagonists, sequestering METH and its metabolites away from sites of action in the brain and reduce the rewarding and toxic effects of the drug. A key aspect of these immunotherapy strategies is the understanding of the subtle molecular interactions important for generating antibodies with high affinity and specificity for METH. We previously determined crystal structures of a high affinity anti-METH therapeutic single chain antibody fragment (scFv6H4, KD = 10 nM) in complex with METH and the (+) stereoisomer of 3,4-methylenedioxymethamphetamine (MDMA, or “ecstasy”). Here we report the crystal structure of scFv6H4 in homo-trimeric unbound (apo) form (2.60Å), as well as monomeric forms in complex with two active metabolites; (+)-amphetamine (AMP, 2.38Å) and (+)-4-hydroxy methamphetamine (p-OH-METH, 2.33Å). The apo structure forms a trimer in the crystal lattice and it results in the formation of an intermolecular composite beta-sheet with a three-fold symmetry. We were also able to structurally characterize the coordination of the His-tags with Ni2+. Two of the histidine residues of each C-terminal His-tag interact with Ni2+ in an octahedral geometry. In the apo state the CDR loops of scFv6H4 form an open conformation of the binding pocket. Upon ligand binding, the CDR loops adopt a closed formation, encasing the drug almost completely. The structural information reported here elucidates key molecular interactions important in anti-methamphetamine abuse immunotherapy. PMID:24349338

  11. Characterization of the Fe-Doped Mixed-Valent Tunnel Structure 2 Manganese Oxide KOMS-2

    SciTech Connect

    Hanson J. C.; Shen X.; Morey A.M.; Liu J.; Ding Y.; Cai J.; Durand J.; Wang Q.; Wen W.; Hines W.A.; Bai J.; Frenkel A.I.; Reiff W.; Aindow M.; Suib S.L.

    2011-11-10

    A sol-gel-assisted combustion method was used to prepare Fe-doped manganese oxide octahedral molecular sieve (Fe-KOMS-2) materials with the cryptomelane structure. Characterization of the nanopowder samples over a wide range of Fe-doping levels (0 {le} Fe/Mn {le} 1/2) was carried out using a variety of experimental techniques. For each sample, Cu K{alpha} XRD and ICP-AES were used to index the cryptomelane structure and determine the elemental composition, respectively. A combination of SEM and TEM images revealed that the morphology changes from nanoneedle to nanorod after Fe doping. Furthermore, TGA scans indicated that the thermal stability is also enhanced with the doping. Anomalous XRD demonstrated that the Fe ions replace the Mn ions in the cryptomelane structure, particularly in the (211) planes, and results in a lattice expansion along the c axis, parallel to the tunnels. Reasonable fits to EXAFS data were obtained using a model based on the cryptomelane structure. Moessbauer spectra for selected Fe-KOMS-2 samples indicated that the Fe is present as Fe{sup 3+} in an octahedral environment similar to Mn in the MnO{sub 6} building blocks of KOMS-2. Magnetization measurements detected a small amount of {gamma}-Fe{sub 2}O{sub 3} second phase (e.g., 0.6 wt % for the Fe/Mn = 1/10 sample), the vast majority of the Fe being in the structure as Fe{sup 3+} in the high-spin state.

  12. Structural Characterization and Epitope Mapping of the Glutamic Acid/Alanine-rich Protein from Trypanosoma congolense

    PubMed Central

    Loveless, Bianca C.; Mason, Jeremy W.; Sakurai, Tatsuya; Inoue, Noboru; Razavi, Morteza; Pearson, Terry W.; Boulanger, Martin J.

    2011-01-01

    Trypanosoma congolense is an African trypanosome that causes serious disease in cattle in Sub-Saharan Africa. The four major life cycle stages of T. congolense can be grown in vitro, which has led to the identification of several cell-surface molecules expressed on the parasite during its transit through the tsetse vector. One of these, glutamic acid/alanine-rich protein (GARP), is the first expressed on procyclic forms in the tsetse midgut and is of particular interest because it replaces the major surface coat molecule of bloodstream forms, the variant surface glycoprotein (VSG) that protects the parasite membrane, and is involved in antigenic variation. Unlike VSG, however, the function of GARP is not known, which necessarily limits our understanding of parasite survival in the tsetse. Toward establishing the function of GARP, we report its three-dimensional structure solved by iodide phasing to a resolution of 1.65 Å. An extended helical bundle structure displays an unexpected and significant degree of homology to the core structure of VSG, the only other major surface molecule of trypanosomes to be structurally characterized. Immunofluorescence microscopy and immunoaffinity-tandem mass spectrometry were used in conjunction with monoclonal antibodies to map both non-surface-disposed and surface epitopes. Collectively, these studies enabled us to derive a model describing the orientation and assembly of GARP on the surface of trypanosomes. The data presented here suggest the possible structure-function relationships involved in replacement of the bloodstream form VSG by GARP as trypanosomes differentiate in the tsetse vector after a blood meal. PMID:21471223

  13. Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions

    PubMed Central

    Malik, Radhika; Viola, Ronald E.

    2010-01-01

    The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2 Å resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg2+ and NADH. This TDH structure from Pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. How­ever, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identification of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate inter­mediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH. PMID:20516620

  14. Structural characterization of complex O-linked glycans from insect-derived material.

    PubMed

    Garenaux, Estelle; Maes, Emmanuel; Levêque, S; Brassart, Colette; Guerardel, Yann

    2011-07-01

    Although insects are among the most diverse groups of the animal kingdom and may be found in nearly all environments, one can observe an obvious lack of structural data on their glycosylation ability. Hymenoptera is the second largest of all insect orders with more than 110,000 identified species and includes the most famous examples of social insects' species such as wasps, bees and ants. In this report, the structural variety of O-glycans has been studied in two Hymenoptera species. In a previous study, we showed that major O-glycans from common wasp (Vespula germanica) salivary mucins correspond to T and Tn antigen, eventually substituted by phosphoethanolamine or phosphate groups. More detailed structural analysis performed by mass spectrometry revealed numerous minor O-glycan structures bearing Gal, GlcNAc, GalNAc and Fuc residues. Thus, in order to investigate glycosylation diversity in insects, we used common wasp nest (V. germanica) and hornet nest (Vespa cabro) as starting materials. These materials were submitted to reductive β-elimination and the released oligosaccharide-alditols further fractionated by multidimensional HPLC. Tandem mass spectrometry analyses combined with NMR data revealed the presence of various families of complex O-glycans differing accordingly to both core structures and external motifs. Glycans from wasp were characterized by the presence of core types 1 and 2, Lewis X and internal Gal-Gal motifs. We also observed unusual O-glycans containing a reducing GalNAc unit directly substituted by a fucose residue. In contrast, hornet O-glycans appeared as a rather homogeneous family of core 1 type O-glycans extended by galactose oligomers. PMID:21536259

  15. Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions

    SciTech Connect

    Malik, Radhika; Viola, Ronald E.

    2010-10-28

    The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2 {angstrom} resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg{sup 2+} and NADH. This TDH structure from Pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. However, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identification of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate intermediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH.

  16. The functional and structural characterization of a novel oncogene GIG47 involved in the breast tumorigenesis

    PubMed Central

    2012-01-01

    Background A candidate oncogene GIG47, previously known as a neudesin with a neurotrophic activity, was identified by applying the differential expression analysis method. Methods As a first step to understand the molecular role of GIG47, we analyzed the expression profile of GIG47 in multiple human cancers including the breast cancer and characterized its function related to human carcinogenesis. Based on this oncogenic role of GIG47, we then embarked on determining the high-resolution structure of GIG47. We have applied multidimensional heteronuclear NMR methods to GIG47. Results GIG47 was over-expressed in primary breast tumors as well as other human tumors including carcinomas of the uterine cervix, malignant lymphoma, colon, lung, skin, and leukemia. To establish its role in the pathogenesis of breast cancer in humans, we generated stable transfectants of MCF7 cells. The ectopic expression of GIG47 in MCF7 cells promoted the invasiveness in the presence of 50% serum. In addition, it also resulted in the increased tumorigenicity in in vivo tumor formation assay. The tumorigenesis mechanism involving GIG47 might be mediated by the activation of MAPK and PI3K pathways. These results indicate that GIG47 plays a role in the breast tumorigenesis, thus representing a novel target for the treatment of breast cancer. To facilitate the development of GIG47-targeted therapeutics, we determined the structural configuration of GIG47. The high-resolution structure of GIG47 was obtained by combination of NMR and homology modeling. The overall structure of GIG47 has four α-helices and 6 β-strands, arranged in a β1-α1-β2-β3-α2-β4-α3-α4-β5-β6 topology. There is a potential heme/steroid binding pocket formed between two helices α2 and α3. Conclusion The determined three-dimensional structure of GIG47 may facilitate the development of potential anti-cancer agents. PMID:22748190

  17. Automated metric characterization of urban structure using building decomposition from very high resolution imagery

    NASA Astrophysics Data System (ADS)

    Heinzel, Johannes; Kemper, Thomas

    2015-03-01

    Classification approaches for urban areas are mostly of qualitative and semantic nature. They produce interpreted classes similar to those from land cover and land use classifications. As a complement to those classes, quantitative measures directly derived from the image could lead to a metric characterization of the urban area. While these metrics lack of qualitative interpretation they are able to provide objective measure of the urban structures. Such quantitative measures are especially important in rapidly growing cities since, beside of the growth in area, they can provide structural information for specific areas and detect changes. Rustenburg, which serves as test area for the present study, is amongst the fastest growing cities in South Africa. It reveals a heterogeneous face of housing and building structures reflecting social and/or economic differences often linked to the spatial distribution of industrial and local mining sites. Up to date coverage with aerial photographs is provided by aerial surveys in regular intervals. Also recent satellite systems provide imagery with suitable resolution. Using such set of very high resolution images a fully automated algorithm has been developed which outputs metric classes by systematically combining important measures of building structure. The measurements are gained by decomposition of buildings directly from the imagery and by using methods from mathematical morphology. The decomposed building objects serve as basis for the computation of grid statistics. Finally a systematic combination of the single features leads to combined metrical classes. For the dominant urban structures verification results indicate an overall accuracy of at least 80% on the single feature level and 70% for the combined classes.

  18. Structural characterization of a neuroblast-specific phosphorylated region of MARCKS.

    PubMed

    Tinoco, Luzineide W; Fraga, Jully L; Anobom, Cristiane D; Zolessi, Flavio R; Obal, Gonzalo; Toledo, Andrea; Pritsch, Otto; Arruti, Cristina

    2014-04-01

    MARCKS (Myristoylated Alanine-Rich C Kinase substrate) is a natively unfolded protein that interacts with actin, Ca(2+)-Calmodulin, and some plasma membrane lipids. Such interactions occur at a highly conserved region that is specifically phosphorylated by PKC: the Effector Domain. There are two other conserved domains, MH1 (including a myristoylation site) and MH2, also located in the amino terminal region and whose structure and putative protein binding capabilities are currently unknown. MH2 sequence contains a serine that we described as being phosphorylated only in differentiating neurons (S25 in chick). Here, Circular Dichroism (CD) and Nuclear Magnetic Resonance (NMR) spectroscopy were used to characterize the phosphorylated and unphosphorylated forms of a peptide with the MARCKS sequence surrounding S25. The peptide phosphorylated at this residue is recognized by monoclonal antibody 3C3 (mAb 3C3). CD and NMR data indicated that S25 phosphorylation does not cause extensive modifications in the peptide structure. However, the sharper lines, the absence of multiple spin systems and relaxation dispersion data observed for the phosphorylated peptide suggested a more ordered structure. Surface Plasmon Resonance was employed to compare the binding properties of mAb 3C3 to MARCKS protein and peptide. SPR showed that mAb 3C3 binds to the whole protein and the peptide with a similar affinity, albeit different kinetics. The slightly ordered structure of the phosphorylated peptide might be at the origin of its ability to interact with mAb 3C3 antibody, but this binding did not noticeably modify the peptide structure. PMID:24590112

  19. Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ

    SciTech Connect

    Bargar, John; Fuller, Christopher; Marcus, Matthew A.; Brearley, Adrian J.; Perez De la Rosa, M.; Webb, Samuel M.; Caldwell, Wendel A.

    2008-03-19

    The microbial catalysis of Mn(II) oxidation is believed to be a dominant source of abundant sorption- and redox-active Mn oxides in marine, freshwater, and subsurface aquatic environments. In spite of their importance, environmental oxides of known biogenic origin have generally not been characterized in detail from a structural perspective. Hyporheic zone Mn oxide grain coatings at Pinal Creek, Arizona, a metals-contaminated stream, have been identified as being dominantly microbial in origin and are well studied from bulk chemistry and contaminant hydrology perspectives. This site thus presents an excellent opportunity to study the structures of terrestrial microbial Mn oxides in detail. XRD and EXAFS measurements performed in this study indicate that the hydrated Pinal Creek Mn oxide grain coatings are layer-type Mn oxides with dominantly hexagonal or pseudo-hexagonal layer symmetry. XRD and TEM measurements suggest the oxides to be nanoparticulate plates with average dimensions on the order of 11 nm thick x 35 nm diameter, but with individual particles exhibiting thickness as small as a single layer and sheets as wide as 500 nm. The hydrated oxides exhibit a 10-A basal-plane spacing and turbostratic disorder. EXAFS analyses suggest the oxides contain layer Mn(IV) site vacancy defects, and layer Mn(III) is inferred to be present, as deduced from Jahn-Teller distortion of the local structure. The physical geometry and structural details of the coatings suggest formation within microbial biofilms. The biogenic Mnoxides are stable with respect to transformation into thermodynamically more stable phases over a time scale of at least 5 months. The nanoparticulate layered structural motif, also observed in pure culture laboratory studies, appears to be characteristic of biogenic Mn oxides and may explain the common occurrence of this mineral habit in soils and sediments.

  20. Size-dependent characterization of embedded Ge nanocrystals: Structural and thermal properties

    NASA Astrophysics Data System (ADS)

    Araujo, L. L.; Giulian, R.; Sprouster, D. J.; Schnohr, C. S.; Llewellyn, D. J.; Kluth, P.; Cookson, D. J.; Foran, G. J.; Ridgway, M. C.

    2008-09-01

    A combination of conventional and synchrotron-based techniques has been used to characterize the size-dependent structural and thermal properties of Ge nanocrystals (NCs) embedded in a silica (a-SiO2) matrix. Ge NC size distributions with four different diameters ranging from 4.0 to 9.0 nm were produced by ion implantation and thermal annealing as characterized with small-angle x-ray scattering and transmission electron microscopy. The NCs were well represented by the superposition of bulklike crystalline and amorphous environments, suggesting the formation of an amorphous layer separating the crystalline NC core and the a-SiO2 matrix. The amorphous fraction was quantified with x-ray-absorption near-edge spectroscopy and increased as the NC diameter decreased, consistent with the increase in surface-to-volume ratio. The structural parameters of the first three nearest-neighbor shells were determined with extended x-ray-absorption fine-structure (EXAFS) spectroscopy and evolved linearly with inverse NC diameter. Specifically, increases in total disorder, interatomic distance, and the asymmetry in the distribution of distances were observed as the NC size decreased, demonstrating that finite-size effects govern the structural properties of embedded Ge NCs. Temperature-dependent EXAFS measurements in the range of 15-300 K were employed to probe the mean vibrational frequency and the variation of the interatomic distance distribution (mean value, variance, and asymmetry) with temperature for all NC distributions. A clear trend of increased stiffness (higher vibrational frequency) and decreased thermal expansion with decreasing NC size was evident, confirming the close relationship between the variation of structural and thermal/vibrational properties with size for embedded Ge NCs. The increase in surface-to-volume ratio and the presence of an amorphous Ge layer separating the matrix and crystalline NC core are identified as the main factors responsible for the observed

  1. Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria

    SciTech Connect

    Halavaty, Andrei S.; Kim, Youngchang; Minasov, George; Shuvalova, Ludmilla; Dubrovska, Ievgeniia; Winsor, James; Zhou, Min; Onopriyenko, Olena; Skarina, Tatiana; Papazisi, Leka; Kwon, Keehwan; Peterson, Scott N.; Joachimiak, Andrzej; Savchenko, Alexei; Anderson, Wayne F.

    2012-10-01

    The structural characterization of acyl-carrier-protein synthase (AcpS) from three different pathogenic microorganisms is reported. One interesting finding of the present work is a crystal artifact related to the activity of the enzyme, which fortuitously represents an opportunity for a strategy to design a potential inhibitor of a pathogenic AcpS. Some bacterial type II fatty-acid synthesis (FAS II) enzymes have been shown to be important candidates for drug discovery. The scientific and medical quest for new FAS II protein targets continues to stimulate research in this field. One of the possible additional candidates is the acyl-carrier-protein synthase (AcpS) enzyme. Its holo form post-translationally modifies the apo form of an acyl carrier protein (ACP), which assures the constant delivery of thioester intermediates to the discrete enzymes of FAS II. At the Center for Structural Genomics of Infectious Diseases (CSGID), AcpSs from Staphylococcus aureus (AcpS{sub SA}), Vibrio cholerae (AcpS{sub VC}) and Bacillus anthracis (AcpS{sub BA}) have been structurally characterized in their apo, holo and product-bound forms, respectively. The structure of AcpS{sub BA} is emphasized because of the two 3′, 5′-adenosine diphosphate (3′, 5′-ADP) product molecules that are found in each of the three coenzyme A (CoA) binding sites of the trimeric protein. One 3′, 5′-ADP is bound as the 3′, 5′-ADP part of CoA in the known structures of the CoA–AcpS and 3′, 5′-ADP–AcpS binary complexes. The position of the second 3′, 5′-ADP has never been described before. It is in close proximity to the first 3′, 5′-ADP and the ACP-binding site. The coordination of two ADPs in AcpS{sub BA} may possibly be exploited for the design of AcpS inhibitors that can block binding of both CoA and ACP.

  2. Active and passive infrared thermography applied to the detection and characterization of hidden defects in structure

    NASA Astrophysics Data System (ADS)

    Dumoulin, Jean

    2013-04-01

    Infrared thermography for Non Destructive Testing (NDT) has encountered a wide spreading this last 2 decades, in particular thanks to emergence on the market of low cost uncooled infrared camera. So, infrared thermography is not anymore a measurement technique limited to laboratory application. It has been more and more involved in civil engineering and cultural heritage applications, but also in many other domains, as indicated by numerous papers in the literature. Nevertheless, laboratory, measurements are done as much as possible in quite ideal conditions (good atmosphere conditions, known properties of materials, etc.), while measurement on real site requires to consider the influence of not controlled environmental parameters and additional unknown thermal properties. So, dedicated protocol and additional sensors are required for measurement data correction. Furthermore, thermal excitation is required to enhance the signature of defects in materials. Post-processing of data requires to take into account the protocol used for the thermal excitation and sometimes its nature to avoid false detection. This analysis step is based on signal and image processing tool and allows to carry out the detection. Characterization of anomalies detected at the previous step can be done by additional signal processing in particular for manufactured objects. The use of thermal modelling and inverse method allows to determine properties of the defective area. The present paper will first address a review of some protocols currently in use for field measurement with passive and/or active infrared measurements. Illustrations in various experiments carried out on civil engineering structure will be shown and discussed. In a second part, different post-processing approaches will be presented and discussed. In particular, a review of the most standard processing methods like Fast Fourier Analysis, Principal Components Analysis, Polynomial Decomposition, defect characterization using

  3. Biochemical and structural characterization of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-IV

    SciTech Connect

    Han, Q.; Robinson, H.; Cai, T.; Tagle, D. A.; Li, J.

    2011-10-01

    Mammalian mAspAT (mitochondrial aspartate aminotransferase) is recently reported to have KAT (kynurenine aminotransferase) activity and plays a role in the biosynthesis of KYNA (kynurenic acid) in rat, mouse and human brains. This study concerns the biochemical and structural characterization of mouse mAspAT. In this study, mouse mAspAT cDNA was amplified from mouse brain first stand cDNA and its recombinant protein was expressed in an Escherichia coli expression system. Sixteen oxo acids were tested for the co-substrate specificity of mouse mAspAT and 14 of them were shown to be capable of serving as co-substrates for the enzyme. Structural analysis of mAspAT by macromolecular crystallography revealed that the cofactor-binding residues of mAspAT are similar to those of other KATs. The substrate-binding residues of mAspAT are slightly different from those of other KATs. Our results provide a biochemical and structural basis towards understanding the overall physiological role of mAspAT in vivo and insight into controlling the levels of endogenous KYNA through modulation of the enzyme in the mouse brain.

  4. Molecular Characterization of Buffalo Haptoglobin: Sequence Based Structural Comparison Indicates Convergent Evolution Between Ruminants and Human.

    PubMed

    Niranjan, S K; Goyal, S; Dubey, P K; Vohra, V; Singh, S; Kathiravan, P; Kataria, R S

    2016-01-01

    Haptoglobin (Hp) protein has high affinity for hemoglobin (Hb) binding during intravascular hemolysis and scavenges the hemoglobin induced free radicals. Earlier reports indicate about uniqueness of Hp molecule in human and cattle, but in other animals, it is not much studied. In this paper, we characterized buffalo Hp molecule and determined its molecular structure, evolutionary importance, and tissue expression. Comparative analysis and predicted domain structure indicated that the buffalo Hp has an internal duplicated region in α-chain only similar to an alternate Hp2 allele in human. This duplicated part encoded for an extra complement control protein CCP domain. Phylogenetic analysis revealed that buffalo and other ruminants were found to group together separated from all other non-ruminants, including human. The key amino acid residues involved in Hp and Hb as well as Hp and macrophage scavenger receptor, CD163 interactions in buffalo, depicted a significant variation in comparison to other non-ruminant species. Constitutive expression of Hp was also confirmed across all the vital tissues of buffalo, for the first time. Results revealed that buffalo Hp is both structurally and functionally conserved, having internal duplication in α-chain similar to human Hp2 and other ruminant species, which might have evolved separately as a convergent evolutionary process. Furthermore, the presence of extra Hp CCP domain possibly in all ruminants may have an effect during dimerization of molecule in these species. PMID:26646629

  5. Fast Lamb wave energy shift approach using fully contactless ultrasonic system to characterize concrete structures

    NASA Astrophysics Data System (ADS)

    Ham, Suyun; Popovics, John S.

    2015-03-01

    Ultrasonic techniques provide an effective non-destructive evaluation (NDE) method to monitor concrete structures, but the need to perform rapid and accurate structural assessment requires evaluation of hundreds, or even thousands, of measurement datasets. Use of a fully contactless ultrasonic system can save time and labor through rapid implementation, and can enable automated and controlled data acquisition, for example through robotic scanning. Here we present results using a fully contactless ultrasonic system. This paper describes our efforts to develop a contactless ultrasonic guided wave NDE approach to detect and characterize delamination defects in concrete structures. The developed contactless sensors, controlled scanning system, and employed Multi-channel Analysis of Surface Waves (MASW) signal processing scheme are reviewed. Then a guided wave interpretation approach for MASW data is described. The presence of delamination is interpreted by guided plate wave (Lamb wave) behavior, where a shift in excited Lamb mode phase velocity, is monitored. Numerically simulated and experimental ultrasonic data collected from a concrete sample with simulated delamination defects are presented, where the occurrence of delamination is shown to be associated with a mode shift in Lamb wave energy.

  6. Structural Characterization of Inhibitors with Selectivity against Members of a Homologous Enzyme Family

    SciTech Connect

    Pavlovsky, Alexander G.; Liu, Xuying; Faehnle, Christopher R.; Potente, Nina; Viola, Ronald E.

    2013-01-31

    The aspartate biosynthetic pathway provides essential metabolites for many important biological functions, including the production of four essential amino acids. As this critical pathway is only present in plants and microbes, any disruptions will be fatal to these organisms. An early pathway enzyme, L-aspartate-{beta}-semialdehyde dehydrogenase, produces a key intermediate at the first branch point of this pathway. Developing potent and selective inhibitors against several orthologs in the L-aspartate-{beta}-semialdehyde dehydrogenase family can serve as lead compounds for antibiotic development. Kinetic studies of two small molecule fragment libraries have identified inhibitors that show good selectivity against L-aspartate-{beta}-semialdehyde dehydrogenases from two different bacterial species, Streptococcus pneumoniae and Vibrio cholerae, despite the presence of an identical constellation of active site amino acids in this homologous enzyme family. Structural characterization of enzyme-inhibitor complexes have elucidated different modes of binding between these structurally related enzymes. This information provides the basis for a structure-guided approach to the development of more potent and more selective inhibitors.

  7. In situ hydrodynamic spectroscopy for structure characterization of porous energy storage electrodes.

    PubMed

    Shpigel, Netanel; Levi, Mikhael D; Sigalov, Sergey; Girshevitz, Olga; Aurbach, Doron; Daikhin, Leonid; Pikma, Piret; Marandi, Margus; Jänes, Alar; Lust, Enn; Jäckel, Nicolas; Presser, Volker

    2016-05-01

    A primary atomic-scale effect accompanying Li-ion insertion into rechargeable battery electrodes is a significant intercalation-induced change of the unit cell volume of the crystalline material. This generates a variety of secondary multiscale dimensional changes and causes a deterioration in the energy storage performance stability. Although traditional in situ height-sensing techniques (atomic force microscopy or electrochemical dilatometry) are able to sense electrode thickness changes at a nanometre scale, they are much less informative concerning intercalation-induced changes of the porous electrode structure at a mesoscopic scale. Based on a electrochemical quartz-crystal microbalance with dissipation monitoring on multiple overtone orders, herein we introduce an in situ hydrodynamic spectroscopic method for porous electrode structure