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Sample records for ring domain reveal

  1. Vortex Ring Dynamics in Radially Confined Domains

    Science.gov (United States)

    Stewart, Kelley; Niebel, Casandra; Jung, Sunghwan; Vlachos, Pavlos

    2010-11-01

    Vortex ring dynamics have been studied extensively in semi-infinite quiescent volumes. However, very little is known about vortex-ring formation in wall-bounded domains where vortex wall interaction will affect both the vortex ring pinch-off and propagation velocity. This study addresses this limitation and studies vortex formation in radially confined domains to analyze the affect of vortex-ring wall interaction on the formation and propagation of the vortex ring. Vortex rings were produced using a pneumatically driven piston cylinder arrangement and were ejected into a long cylindrical tube which defined the confined downstream domain. A range of confinement domains were studied with varying confinement diameters Velocity field measurements were performed using planar Time Resolved Digital Particle Image Velocimetry (TRDPIV) and were processed using an in-house developed cross-correlation PIV algorithm. The experimental analysis was used to facilitate the development of a theoretical model to predict the variations in vortex ring circulation over time within confined domains.

  2. Multiplicative Structure and Hecke Rings of Generator Matrices for Codes over Quotient Rings of Euclidean Domains

    Directory of Open Access Journals (Sweden)

    Hajime Matsui

    2017-12-01

    Full Text Available In this study, we consider codes over Euclidean domains modulo their ideals. In the first half of the study, we deal with arbitrary Euclidean domains. We show that the product of generator matrices of codes over the rings mod a and mod b produces generator matrices of all codes over the ring mod a b , i.e., this correspondence is onto. Moreover, we show that if a and b are coprime, then this correspondence is one-to-one, i.e., there exist unique codes over the rings mod a and mod b that produce any given code over the ring mod a b through the product of their generator matrices. In the second half of the study, we focus on the typical Euclidean domains such as the rational integer ring, one-variable polynomial rings, rings of Gaussian and Eisenstein integers, p-adic integer rings and rings of one-variable formal power series. We define the reduced generator matrices of codes over Euclidean domains modulo their ideals and show their uniqueness. Finally, we apply our theory of reduced generator matrices to the Hecke rings of matrices over these Euclidean domains.

  3. Cytoplasmic tethering of a RING protein RBCK1 by its splice variant lacking the RING domain

    International Nuclear Information System (INIS)

    Yoshimoto, Nobuo; Tatematsu, Kenji; Koyanagi, Tomoyoshi; Okajima, Toshihide; Tanizawa, Katsuyuki; Kuroda, Shun'ichi

    2005-01-01

    RBCC protein interacting with PKC 1 (RBCK1) is a transcription factor belonging to the RING-IBR protein family and has been shown to shuttle between the nucleus and cytoplasm, possessing both the nuclear export and localization signals within its amino acid sequence. RBCK2, lacking the C-terminal half of RBCK1 including the RING-IBR domain, has also been identified as an alternative splice variant of RBCK1. RBCK2 shows no transcriptional activity and instead it represses the transcriptional activity of RBCK1. Here, we show that RBCK2 is present usually in the cytoplasm containing two Leu-rich regions that presumably serve as a nuclear export signal (NES). Moreover, an NES-disrupted RBCK1 that is mostly localized within the nucleus is translocated to the cytoplasm when coexpressed with RBCK2, suggesting that RBCK2 serves as a cytoplasmic tethering protein for RBCK1. We propose a novel and general function of RING-lacking splice variants of RING proteins to control the intracellular localization and functions of the parental RING proteins by forming a hetero-oligomeric complex

  4. NMR characterization of foldedness for the production of E3 RING domains

    NARCIS (Netherlands)

    Huang, A.; de Jong, R.N.; Folkers, G.E.; Boelens, R.

    2010-01-01

    We summarize the use of NMR spectroscopy in the production and the screening of stability and foldedness of protein domains, and apply it to the RING domains of E3 ubiquitin-ligases. RING domains are involved in specific interactions with E2 ubiquitin-conjugating enzymes and thus play an essential

  5. A common Greenlandic Inuit BRCA1 RING domain founder mutation

    DEFF Research Database (Denmark)

    Hansen, T.v.O.; Ejlertsen, B.; Albrechtsen, Anders

    2009-01-01

    of the families had members with ovarian cancer, suggesting that the RING domain may be an ovarian cancer hotspot. By SNP array analysis, we find that all 13 families share a 4.5 Mb genomic fragment containing the BRCA1 gene, showing that the mutation originates from a founder. Finally, analysis of 1152 Inuit......, representing almost ~2% of the total Greenlandic Inuit population, showed that the frequency of the mutation was 1.0%. We conclude that the BRCA1 nucleotide 234 T > G is a common Greenlandic Inuit founder mutation. The relative high frequency in the general population, together with the ease of screening...... and possibility to reduce mortality in gene carriers, may warrant screening of the Greenlandic Inuit population. Provided screening is efficient, about 5% of breast- and 13% of ovarian cancers, respectively, may be prevented Udgivelsesdato: 2009/5...

  6. Multi-domain electromagnetic absorption of triangular quantum rings.

    Science.gov (United States)

    Sitek, Anna; Thorgilsson, Gunnar; Gudmundsson, Vidar; Manolescu, Andrei

    2016-06-03

    We present a theoretical study of the unielectronic energy spectra, electron localization, and optical absorption of triangular core-shell quantum rings. We show how these properties depend on geometric details of the triangle, such as side thickness or corners' symmetry. For equilateral triangles, the lowest six energy states (including spin) are grouped in an energy shell, are localized only around corner areas, and are separated by a large energy gap from the states with higher energy which are localized on the sides of the triangle. The energy levels strongly depend on the aspect ratio of the triangle sides, i.e., thickness/length ratio, in such a way that the energy differences are not monotonous functions of this ratio. In particular, the energy gap between the group of states localized in corners and the states localized on the sides strongly decreases with increasing the side thickness, and then slightly increases for thicker samples. With increasing the thickness the low-energy shell remains distinct but the spatial distribution of these states spreads. The behavior of the energy levels and localization leads to a thickness-dependent absorption spectrum where one transition may be tuned in the THz domain and a second transition can be tuned from THz to the infrared range of electromagnetic spectrum. We show how these features may be further controlled with an external magnetic field. In this work the electron-electron Coulomb repulsion is neglected.

  7. Multi-domain electromagnetic absorption of triangular quantum rings

    Science.gov (United States)

    Sitek, Anna; Thorgilsson, Gunnar; Gudmundsson, Vidar; Manolescu, Andrei

    2016-06-01

    We present a theoretical study of the unielectronic energy spectra, electron localization, and optical absorption of triangular core-shell quantum rings. We show how these properties depend on geometric details of the triangle, such as side thickness or corners’ symmetry. For equilateral triangles, the lowest six energy states (including spin) are grouped in an energy shell, are localized only around corner areas, and are separated by a large energy gap from the states with higher energy which are localized on the sides of the triangle. The energy levels strongly depend on the aspect ratio of the triangle sides, i.e., thickness/length ratio, in such a way that the energy differences are not monotonous functions of this ratio. In particular, the energy gap between the group of states localized in corners and the states localized on the sides strongly decreases with increasing the side thickness, and then slightly increases for thicker samples. With increasing the thickness the low-energy shell remains distinct but the spatial distribution of these states spreads. The behavior of the energy levels and localization leads to a thickness-dependent absorption spectrum where one transition may be tuned in the THz domain and a second transition can be tuned from THz to the infrared range of electromagnetic spectrum. We show how these features may be further controlled with an external magnetic field. In this work the electron-electron Coulomb repulsion is neglected.

  8. Extreme Drought Events Revealed in Amazon Tree Ring Records

    Science.gov (United States)

    Jenkins, H. S.; Baker, P. A.; Guilderson, T. P.

    2010-12-01

    The Amazon basin is a center of deep atmospheric convection and thus acts as a major engine for global hydrologic circulation. Yet despite its significance, a full understanding of Amazon rainfall variability remains elusive due to a poor historical record of climate. Temperate tree rings have been used extensively to reconstruct climate over the last thousand years, however less attention has been given to the application of dendrochronology in tropical regions, in large part due to a lower frequency of tree species known to produce annual rings. Here we present a tree ring record of drought extremes from the Madre de Dios region of southeastern Peru over the last 190 years. We confirm that tree ring growth in species Cedrela odorata is annual and show it to be well correlated with wet season precipitation. This correlation is used to identify extreme dry (and wet) events that have occurred in the past. We focus on drought events identified in the record as drought frequency is expected to increase over the Amazon in a warming climate. The Cedrela chronology records historic Amazon droughts of the 20th century previously identified in the literature and extends the record of drought for this region to the year 1816. Our analysis shows that there has been an increase in the frequency of extreme drought (mean recurrence interval = 5-6 years) since the turn of the 20th century and both Atlantic and Pacific sea surface temperature (SST) forcing mechanisms are implicated.

  9. Frequency-domain analysis of resonant-type ring magnet power supplies

    International Nuclear Information System (INIS)

    Kim, J.M.S.; Reiniger, K.W.

    1993-01-01

    For fast-cycling synchrotrons, resonant-type ring magnet power supplies are commonly used to provide a dc-biased ac excitation for the ring magnets. Up to the present, this power supply system has been analyzed using simplified analytical approximation, namely assuming the resonant frequency of the ring magnet network is fixed and equal to the accelerator frequency. This paper presents a frequency-domain analysis technique for a more accurate analysis of resonant-type ring magnet power supplies. This approach identifies that, with the variation of the resonant frequency, the operating conditions of the power supply changes quite dramatically because of the high Q value of the resonant network. The analytical results are verified, using both experimental results and simulation results

  10. Spatial and frequency domain ring source models for the single muscle fiber action potential

    DEFF Research Database (Denmark)

    Henneberg, Kaj-åge; R., Plonsey

    1994-01-01

    In the paper, single-fibre models for the extracellular action potential are developed that will allow the potential to the evaluated at an arbitrary field point in the extracellular space. Fourier-domain models are restricted in that they evaluate potentials at equidistant points along a line...... parallel to the fibre axis. Consequently, they cannot easily evaluate the potential at the boundary nodes of a boundary-element electrode model. The Fourier-domain models employ axial-symmetric ring source models, and thereby provide higher accuracy that the line source model, where the source is lumped...... including anisotropy show that the spatial models require extreme care in the integration procedure owing to the singularity in the weighting functions. With adequate sampling, the spatial models can evaluate extracellular potentials with high accuracy....

  11. THREE-DIMENSIONAL DUST MAPPING REVEALS THAT ORION FORMS PART OF A LARGE RING OF DUST

    International Nuclear Information System (INIS)

    Schlafly, E. F.; Rix, H.-W.; Martin, N. F.; Green, G.; Finkbeiner, D. P.; Burgett, W. S.; Chambers, K. C.; Kaiser, N.; Morgan, J. S.; Tonry, J. L.; Wainscoat, R. J.; Waters, C.; Draper, P. W.; Metcalfe, N.; Price, P. A.

    2015-01-01

    The Orion Molecular Complex is the nearest site of ongoing high-mass star formation, making it one of the most extensively studied molecular complexes in the Galaxy. We have developed a new technique for mapping the three-dimensional distribution of dust in the Galaxy using Pan-STARRS1 photometry. We isolate the dust at the distance to Orion using this technique, revealing a large (100 pc, 14° diameter), previously unrecognized ring of dust, which we term the ''Orion dust ring''. The ring includes Orion A and B, and is not coincident with current Hα features. The circular morphology suggests formation as an ancient bubble in the interstellar medium, though we have not been able to conclusively identify the source of the bubble. This hint at the history of Orion may have important consequences for models of high-mass star formation and triggered star formation

  12. Convergent solid-phase and solution approaches in the synthesis of the cysteine-rich Mdm2 RING finger domain.

    Science.gov (United States)

    Vasileiou, Zoe; Barlos, Kostas; Gatos, Dimitrios

    2009-12-01

    The RING finger domain of the Mdm2, located at the C-terminus of the protein, is necessary for regulation of p53, a tumor suppressor protein. The 48-residues long Mdm2 peptide is an important target for studying its interaction with small anticancer drug candidates. For the chemical synthesis of the Mdm2 RING finger domain, the fragment condensation on solid-phase and the fragment condensation in solution were studied. The latter method was performed using either protected or free peptides at the C-terminus as the amino component. Best results were achieved using solution condensation where the N-component was applied with the C-terminal carboxyl group left unprotected. The developed method is well suited for large-scale synthesis of Mdm2 RING finger domain, combining the advantages of both solid-phase and solution synthesis. (c) 2009 European Peptide Society and John Wiley & Sons, Ltd.

  13. Time-domain electric field enhancement on micrometer scale in coupled split ring resonator upon terahertz radiation

    DEFF Research Database (Denmark)

    Lange, Simon Lehnskov; Iwaszczuk, Krzysztof; Hoffmann, Matthias

    2016-01-01

    We present here a novel design for a coupled split ring resonator antenna optimized for time-domain electric field enhancement in the 0.1 to 1 terahertz (THz) range. The antenna is designed to be sensitive to the incident field polarization and seeks to avoid metal damage due to electron bombardm...

  14. Cyclic phosphopeptides for interference with Grb2 SH2 domain signal transduction prepared by ring-closing metathesis and phosphorylation

    NARCIS (Netherlands)

    Dekker, Frank J; de Mol, Nico J; Fischer, Marcel J E; Kemmink, Johan; Liskamp, Rob M J; Dekker, Frank

    2003-01-01

    Cyclic phosphopeptides were prepared using ring-closing metathesis followed by phosphorylation. These cyclic phosphopeptides were designed to interact with the SH2 domain of Grb2, which is a signal transduction protein of importance as a target for antiproliferative drug development. Binding of

  15. WW domain folding complexity revealed by infrared spectroscopy.

    Science.gov (United States)

    Davis, Caitlin M; Dyer, R Brian

    2014-09-02

    Although the intrinsic tryptophan fluorescence of proteins offers a convenient probe of protein folding, interpretation of the fluorescence spectrum is often difficult because it is sensitive to both global and local changes. Infrared (IR) spectroscopy offers a complementary measure of structural changes involved in protein folding, because it probes changes in the secondary structure of the protein backbone. Here we demonstrate the advantages of using multiple probes, infrared and fluorescence spectroscopy, to study the folding of the FBP28 WW domain. Laser-induced temperature jumps coupled with fluorescence or infrared spectroscopy have been used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation dynamics of the β-sheets and β-turn were measured independently by probing the corresponding IR bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe three kinetics phases, with the fastest process corresponding to the relaxation kinetics of the turns. In contrast, fluorescence measurements of the wild-type WW domain and tryptophan mutants exhibit single-exponential kinetics with a lifetime that corresponds to the slowest phase observed by infrared spectroscopy. Mutant sequences provide evidence of an intermediate dry molten globule state. The slowest step in the folding of this WW domain is the tight packing of the side chains in the transition from the dry molten globule intermediate to the native structure. This study demonstrates that using multiple complementary probes enhances the interpretation of protein folding dynamics.

  16. Rings and gaps in the disc around Elias 24 revealed by ALMA

    Science.gov (United States)

    Dipierro, G.; Ricci, L.; Pérez, L.; Lodato, G.; Alexander, R. D.; Laibe, G.; Andrews, S.; Carpenter, J. M.; Chandler, C. J.; Greaves, J. A.; Hall, C.; Henning, T.; Kwon, W.; Linz, H.; Mundy, L.; Sargent, A.; Tazzari, M.; Testi, L.; Wilner, D.

    2018-04-01

    We present Atacama Large Millimeter/sub-millimeter Array (ALMA) Cycle 2 observations of the 1.3-mm dust continuum emission of the protoplanetary disc surrounding the T Tauri star Elias 24 with an angular resolution of ˜0.2 arcsec (˜28 au). The dust continuum emission map reveals a dark ring at a radial distance of 0.47 arcsec (˜65 au) from the central star, surrounded by a bright ring at 0.58 arcsec (˜81 au). In the outer disc, the radial intensity profile shows two inflection points at 0.71 and 0.87 arcsec (˜99 and 121 au, respectively). We perform global three-dimensional smoothed particle hydrodynamic gas/dust simulations of discs hosting a migrating and accreting planet. Combining the dust density maps of small and large grains with three-dimensional radiative transfer calculations, we produce synthetic ALMA observations of a variety of disc models in order to reproduce the gap- and ring-like features observed in Elias 24. We find that the dust emission across the disc is consistent with the presence of an embedded planet with a mass of ˜0.7 MJ at an orbital radius of ˜ 60 au. Our model suggests that the two inflection points in the radial intensity profile are due to the inward radial motion of large dust grains from the outer disc. The surface brightness map of our disc model provides a reasonable match to the gap- and ring-like structures observed in Elias 24, with an average discrepancy of ˜5 per cent of the observed fluxes around the gap region.

  17. Potential for tree rings to reveal spatial patterns of past drought variability across western Australia

    Science.gov (United States)

    O'Donnell, Alison J.; Cook, Edward R.; Palmer, Jonathan G.; Turney, Chris S. M.; Grierson, Pauline F.

    2018-02-01

    Proxy records have provided major insights into the variability of past climates over long timescales. However, for much of the Southern Hemisphere, the ability to identify spatial patterns of past climatic variability is constrained by the sparse distribution of proxy records. This is particularly true for mainland Australia, where relatively few proxy records are located. Here, we (1) assess the potential to use existing proxy records in the Australasian region—starting with the only two multi-century tree-ring proxies from mainland Australia—to reveal spatial patterns of past hydroclimatic variability across the western third of the continent, and (2) identify strategic locations to target for the development of new proxy records. We show that the two existing tree-ring records allow robust reconstructions of past hydroclimatic variability over spatially broad areas (i.e. > 3° × 3°) in inland north- and south-western Australia. Our results reveal synchronous periods of drought and wet conditions between the inland northern and southern regions of western Australia as well as a generally anti-phase relationship with hydroclimate in eastern Australia over the last two centuries. The inclusion of 174 tree-ring proxy records from Tasmania, New Zealand and Indonesia and a coral record from Queensland did not improve the reconstruction potential over western Australia. However, our findings suggest that the addition of relatively few new proxy records from key locations in western Australia that currently have low reconstruction skill will enable the development of a comprehensive drought atlas for the region, and provide a critical link to the drought atlases of monsoonal Asia and eastern Australia and New Zealand.

  18. Monte Carlo simulation for thermal assisted reversal process of micro-magnetic torus ring with bistable closure domain structure

    Energy Technology Data Exchange (ETDEWEB)

    Terashima, Kenichi; Suzuki, Kenji; Yamaguchi, Katsuhiko, E-mail: yama@sss.fukushima-u.ac.jp

    2016-04-01

    Monte Carlo simulations were performed for temperature dependences of closure domain parameter for a magnetic micro-torus ring cluster under magnetic field on limited temperature regions. Simulation results show that magnetic field on tiny limited temperature region can reverse magnetic closure domain structures when the magnetic field is applied at a threshold temperature corresponding to intensity of applied magnetic field. This is one of thermally assisted switching phenomena through a self-organization process. The results show the way to find non-wasteful pairs between intensity of magnetic field and temperature region for reversing closure domain structure by temperature dependence of the fluctuation of closure domain parameter. Monte Carlo method for this simulation is very valuable to optimize the design of thermally assisted switching devices.

  19. SNOW AVALANCHE ACTIVITY IN PARÂNG SKI AREA REVEALED BY TREE-RINGS

    Directory of Open Access Journals (Sweden)

    F. MESEȘAN

    2014-11-01

    Full Text Available Snow Avalanche Activity in Parâng Ski Area Revealed by Tree-Rings. Snow avalanches hold favorable conditions to manifest in Parâng Mountains but only one event is historically known, without destructive impact upon infrastructure or fatalities and this region wasn’t yet the object of avalanche research. The existing ski infrastructure of Parâng resort located in the west of Parâng Mountains is proposed to be extended in the steep slopes of subalpine area. Field evidence pinpoints that these steep slopes were affected by snow avalanches in the past. In this study we analyzed 11 stem discs and 31 increment cores extracted from 22 spruces (Picea abies (L. Karst impacted by avalanches, in order to obtain more information about past avalanches activity. Using the dendrogeomorphological approach we found 13 avalanche events that occurred along Scărița avalanche path, since 1935 until 2012, nine of them produced in the last 20 years. The tree-rings data inferred an intense snow avalanche activity along this avalanche path. This study not only calls for more research in the study area but also proves that snow avalanches could constitute an important restrictive factor for the tourism infrastructure and related activities in the area. It must be taken into consideration by the future extension of tourism infrastructure. Keywords: snow avalanche, Parâng Mountains, dendrogeomorphology, ski area.

  20. Iterative image-domain ring artifact removal in cone-beam CT

    Science.gov (United States)

    Liang, Xiaokun; Zhang, Zhicheng; Niu, Tianye; Yu, Shaode; Wu, Shibin; Li, Zhicheng; Zhang, Huailing; Xie, Yaoqin

    2017-07-01

    Ring artifacts in cone beam computed tomography (CBCT) images are caused by pixel gain variations using flat-panel detectors, and may lead to structured non-uniformities and deterioration of image quality. The purpose of this study is to propose a method of general ring artifact removal in CBCT images. This method is based on the polar coordinate system, where the ring artifacts manifest as stripe artifacts. Using relative total variation, the CBCT images are first smoothed to generate template images with fewer image details and ring artifacts. By subtracting the template images from the CBCT images, residual images with image details and ring artifacts are generated. As the ring artifact manifests as a stripe artifact in a polar coordinate system, the artifact image can be extracted by mean value from the residual image; the image details are generated by subtracting the artifact image from the residual image. Finally, the image details are compensated to the template image to generate the corrected images. The proposed framework is iterated until the differences in the extracted ring artifacts are minimized. We use a 3D Shepp-Logan phantom, Catphan©504 phantom, uniform acrylic cylinder, and images from a head patient to evaluate the proposed method. In the experiments using simulated data, the spatial uniformity is increased by 1.68 times and the structural similarity index is increased from 87.12% to 95.50% using the proposed method. In the experiment using clinical data, our method shows high efficiency in ring artifact removal while preserving the image structure and detail. The iterative approach we propose for ring artifact removal in cone-beam CT is practical and attractive for CBCT guided radiation therapy.

  1. Inter-ring rotations of AAA ATPase p97 revealed by electron cryomicroscopy.

    Science.gov (United States)

    Yeung, Heidi O; Förster, Andreas; Bebeacua, Cecilia; Niwa, Hajime; Ewens, Caroline; McKeown, Ciarán; Zhang, Xiaodong; Freemont, Paul S

    2014-03-05

    The type II AAA+ protein p97 is involved in numerous cellular activities, including endoplasmic reticulum-associated degradation, transcription activation, membrane fusion and cell-cycle control. These activities are at least in part regulated by the ubiquitin system, in which p97 is thought to target ubiquitylated protein substrates within macromolecular complexes and assist in their extraction or disassembly. Although ATPase activity is essential for p97 function, little is known about how ATP binding or hydrolysis is coupled with p97 conformational changes and substrate remodelling. Here, we have used single-particle electron cryomicroscopy (cryo-EM) to study the effect of nucleotides on p97 conformation. We have identified conformational heterogeneity within the cryo-EM datasets from which we have resolved two major p97 conformations. A comparison of conformations reveals inter-ring rotations upon nucleotide binding and hydrolysis that may be linked to the remodelling of target protein complexes.

  2. The physics of highly charged heavy ions revealed by storage/cooler rings

    International Nuclear Information System (INIS)

    Mokler, P.H.; Stoehlker, T.

    1996-01-01

    With the successful commissioning of storage and cooler rings for bright beams of very heavy ions near the threshold of the last decade of this century, not only did a prosperous development in heavy ion accelerator technology come to its present summit, but also fundamental fields in heavy ion physics were opened widely for exciting explorations. Now, essential aspects in this area are accessible, aspects one only dared to dream of another decade ago. In the meantime, great progress already has been made in the fundamental physics in this field. This is particularly true for achievements in the atomic physics of highly charged heavy ions. In this chapter, we present a review of the current advances in this rapidly developing field. There are two general domains to be considered in the atomic physics of highly charged heavy ions: the fields of collisions and of atomic structure. Both aspects have to be explored equally, as they are strongly interconnected. One has to investigate the interaction processes to know, for instance, the population of excited states to help answer questions on the atomic structure; and conversely, one has to know the structure to understand the interactions. In both the fields, fundamental principles can be studied uniquely. This is in particular true for the heaviest ion species with only a few- or even zero-electrons left. 140 refs., 39 figs

  3. The crystal structures of EAP domains from Staphylococcus aureus reveal an unexpected homology to bacterial superantigens.

    Science.gov (United States)

    Geisbrecht, Brian V; Hamaoka, Brent Y; Perman, Benjamin; Zemla, Adam; Leahy, Daniel J

    2005-04-29

    The Eap (extracellular adherence protein) of Staphylococcus aureus functions as a secreted virulence factor by mediating interactions between the bacterial cell surface and several extracellular host proteins. Eap proteins from different Staphylococcal strains consist of four to six tandem repeats of a structurally uncharacterized domain (EAP domain). We have determined the three-dimensional structures of three different EAP domains to 1.8, 2.2, and 1.35 A resolution, respectively. These structures reveal a core fold that is comprised of an alpha-helix lying diagonally across a five-stranded, mixed beta-sheet. Comparison of EAP domains with known structures reveals an unexpected homology with the C-terminal domain of bacterial superantigens. Examination of the structure of the superantigen SEC2 bound to the beta-chain of a T-cell receptor suggests a possible ligand-binding site within the EAP domain (Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K., and Mariuzza, R. (1996) Nature 384, 188-192). These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships.

  4. Initial Reactivity of Linkages and Monomer Rings in Lignin Pyrolysis Revealed by ReaxFF Molecular Dynamics.

    Science.gov (United States)

    Zhang, Tingting; Li, Xiaoxia; Guo, Li

    2017-10-24

    The initial conversion pathways of linkages and their linked monomer units in lignin pyrolysis were investigated comprehensively by ReaxFF MD simulations facilitated by the unique VARxMD for reaction analysis. The simulated molecular model contains 15 920 atoms and was constructed on the basis of Adler's softwood lignin model. The simulations uncover the initial conversion ratio of various linkages and their linked aryl monomers. For linkages and their linked monomer aryl rings of α-O-4, β-O-4 and α-O-4 & β-5, the C α /C β ether bond cracking dominates the initial pathway accounting for at least up to 80% of their consumption. For the linkage of β-β & γ-O-α, both the C α -O ether bond cracking and its linked monomer aryl ring opening are equally important. Ring-opening reactions dominate the initial consumption of other 4-O-5, 5-5, β-1, β-2, and β-5 linkages and their linked monomers. The ether bond cracking of C α -O and C β -O occurs at low temperature, and the aryl ring-opening reactions take place at relatively high temperature. The important intermediates leading to the stable aryl ring opening are the phenoxy radicals, the bridged five-membered and three-membered rings and the bridged six-membered and three-membered rings. In addition, the reactivity of a linkage and its monomer aryl ring may be affected by other linkages. The ether bond cracking of α-O-4 and β-O-4 linkages can activate its neighboring linkage or monomer ring through the formed phenoxy radicals as intermediates. The important intermediates revealed in this article should be of help in deepening the understanding of the controlling mechanism for producing aromatic chemicals from lignin pyrolysis.

  5. Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring.

    Science.gov (United States)

    Mountassif, Driss; Fabre, Lucien; Zaid, Younes; Halawani, Dalia; Rouiller, Isabelle

    2015-12-25

    Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Comparison of S. cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site

    Science.gov (United States)

    Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R.; Kenniston, Jon A.; Mendrola, Jeannine M.; Ferguson, Kathryn M.; Lemmon, Mark A.

    2015-01-01

    SUMMARY F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here, we compare membrane-binding properties of the S. cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound to an inositol phosphate. The structures explain phospholipid-binding selectivity differences, and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip, and is partly retained in certain other F-BAR domains. Our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity, and provide a basis for its prediction from sequence. PMID:25620000

  7. Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring

    Energy Technology Data Exchange (ETDEWEB)

    Mountassif, Driss; Fabre, Lucien [Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d' Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7 (Canada); Zaid, Younes [Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d' Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7 (Canada); Current address: Laboratory of Thrombosis and Hemostasis, Montreal Heart Institute, Montreal, Quebec (Canada); Halawani, Dalia [Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d' Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7 (Canada); Current address: Department of Cell Biology, Lerner Research Institute, 9500 Euclid Avenue NC10, Cleveland, OH 44195 (United States); Rouiller, Isabelle, E-mail: isabelle.rouiller@mcgill.ca [Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d' Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7 (Canada)

    2015-12-25

    Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring. - Highlights: • p97{sub R155P} and p97{sub A232E} decrease the ability of p97 to bind to its co-factor Npl4. • p97{sub R155P} has a different isoelectric point than that of p97{sub R95G}, p97{sub A232E} and p97{sub WT}. • Mutation R155P changes principally the conformation of the D2 ring. • Mutation R155P modifies the interface between two protomers within the D2 ring.

  8. Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring

    International Nuclear Information System (INIS)

    Mountassif, Driss; Fabre, Lucien; Zaid, Younes; Halawani, Dalia; Rouiller, Isabelle

    2015-01-01

    Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring. - Highlights: • p97 R155P and p97 A232E decrease the ability of p97 to bind to its co-factor Npl4. • p97 R155P has a different isoelectric point than that of p97 R95G , p97 A232E and p97 WT . • Mutation R155P changes principally the conformation of the D2 ring. • Mutation R155P modifies the interface between two protomers within the D2 ring.

  9. Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions

    International Nuclear Information System (INIS)

    Eibl, Clarissa; Hessenberger, Manuel; Wenger, Julia; Brandstetter, Hans

    2014-01-01

    Pyrin domains (PYDs) recruit downstream effector molecules in NLR signalling. A specific charge-relay system suggests a the formation of a signalling complex involving a PYD dimer. The cytosolic tripartite NLR receptors serve as important signalling platforms in innate immunity. While the C-terminal domains act as sensor and activation modules, the N-terminal death-like domain, e.g. the CARD or pyrin domain, is thought to recruit downstream effector molecules by homotypic interactions. Such homotypic complexes have been determined for all members of the death-domain superfamily except for pyrin domains. Here, crystal structures of human NLRP14 pyrin-domain variants are reported. The wild-type protein as well as the clinical D86V mutant reveal an unexpected rearrangement of the C-terminal helix α6, resulting in an extended α5/6 stem-helix. This reordering mediates a novel symmetric pyrin-domain dimerization mode. The conformational switching is controlled by a charge-relay system with a drastic impact on protein stability. How the identified charge relay allows classification of NLRP receptors with respect to distinct recruitment mechanisms is discussed

  10. A time-domain digitally controlled oscillator composed of a free running ring oscillator and flying-adder

    International Nuclear Information System (INIS)

    Liu Wei; Zhang Shengdong; Wang Yangyuan; Li Wei; Ren Peng; Lin Qinglong

    2009-01-01

    A time-domain digitally controlled oscillator (DCO) is proposed. The DCO is composed of a free-running ring oscillator (FRO) and a two lap-selectors integrated flying-adder (FA). With a coiled cell array which allows uniform loading capacitances of the delay cells, the FRO produces 32 outputs with consistent tap spacing for the FA as reference clocks. The FA uses the outputs from the FRO to generate the output of the DCO according to the control number, resulting in a linear dependence of the output period, instead of the frequency on the digital controlling word input. Thus the proposed DCO ensures a good conversion linearity in a time-domain, and is suitable for time-domain all-digital phase locked loop applications. The DCO was implemented in a standard 0.13 μm digital logic CMOS process. The measurement results show that the DCO has a linear and monotonic tuning curve with gain variation of less than 10%, and a very low root mean square period jitter of 9.3 ps in the output clocks. The DCO works well at supply voltages ranging from 0.6 to 1.2 V, and consumes 4 mW of power with 500 MHz frequency output at 1.2 V supply voltage.

  11. Mutational analysis of TRAF6 reveals a conserved functional role of the RING dimerization interface and a potentially necessary but insufficient role of RING-dependent TRAF6 polyubiquitination towards NF-κB activation.

    Science.gov (United States)

    Megas, Charilaos; Hatzivassiliou, Eudoxia G; Yin, Qian; Marinopoulou, Elli; Hadweh, Paul; Vignali, Dario A A; Mosialos, George

    2011-05-01

    TRAF6 is an E3 ubiquitin ligase that plays a pivotal role in the activation of NF-κB by innate and adaptive immunity stimuli. TRAF6 consists of a highly conserved carboxyl terminal TRAF-C domain which is preceded by a coiled coil domain and an amino terminal region that contains a RING domain and a series of putative zinc-finger motifs. The TRAF-C domain contributes to TRAF6 oligomerization and mediates the interaction of TRAF6 with upstream signaling molecules whereas the RING domain comprises the core of the ubiquitin ligase catalytic domain. In order to identify structural elements that are important for TRAF6-induced NF-κB activation, mutational analysis of the TRAF-C and RING domains was performed. Alterations of highly conserved residues of the TRAF-C domain of TRAF6 did not affect significantly the ability of the protein to activate NF-κB. On the other hand a number of functionally important residues (L77, Q82, R88, F118, N121 and E126) for the activation of NF-κB were identified within the RING domain of TRAF6. Interestingly, several homologues of these residues in TRAF2 were shown to have a conserved functional role in TRAF2-induced NF-κB activation and lie at the dimerization interface of the RING domain. Finally, whereas alteration of Q82, R88 and F118 compromised both the K63-linked polyubiquitination of TRAF6 and its ability to activate NF-κB, alteration of L77, N121 and E126 diminished the NF-κB activating function of TRAF6 without affecting TRAF6 K63-linked polyubiquitination. Our results support a conserved functional role of the TRAF RING domain dimerization interface and a potentially necessary but insufficient role for RING-dependent TRAF6 K63-linked polyubiquitination towards NF-κB activation in cells. Copyright © 2010 Elsevier Inc. All rights reserved.

  12. Patterns of Storage, Synthesis and Changing Light Levels Revealed by Carbon Isotope Microsampling within Eocene Metasequoia Tree Rings

    Science.gov (United States)

    Jahren, H.; Sternberg, L.

    2005-12-01

    Fossil tree rings from Axel Heiberg Island were microanalyzed for δ13C value in order to assess patterns of tree growth and carbon storage within the Middle Eocene (~45 Ma) Arctic paleoenvironment. Wood from four Metasequoia-type individuals was subsampled for analysis: each individual fossil consisted of between 4 and 10 large (~1 cm thick) consecutive tree rings. One of the fossils displayed an obvious concentric pattern, allowing for the determination of the direction of growth with isotopic pattern. Each ring was divided into ~1 mm thick subsamples, resulting in 5-10 δ13C value determinations per period of ring growth (i.e., growing season). All rings revealed a distinct pattern that was characteristic across growing seasons and across individual fossils. Early in the season, δ13C was at its highest value but descended systematically and sharply to its lowest value at the end of the growing season. Total decrease ranged between 3 and 5 ‰ over the course of each growing season. Identical patterns were observed in the δ13C value of alpha-cellulose isolated from each subsample, indicating that the trends observed did not represent changing levels of secondary metabolites, but rather a seasonal adjustment in the bulk source of carbon used during biosynthesis. Our results are consistent with the following annual pattern of wood synthesis 1.) complete dependence on the mobilization of stored carbon compounds early in the growing season; 2.) systematically increasing use of actively-acquired photosynthate during the growing season; 3.) complete reliance on active photosynthate by the end of the growing season. An additional and significant source of 13C discrimination is declining light levels late in the growing season, and likely contributes to the extreme pattern of δ13C decrease seen across each ring. Our results mimic those seen from modern broadleaf deciduous trees (Helle & Schlesser 2004), but differ from those seen in modern conifers (Barbour et al 2002

  13. Data for increase of Lymantria dispar male survival after topical application of single-stranded RING domain fragment of IAP-3 gene of its nuclear polyhedrosis virus

    Science.gov (United States)

    Oberemok, Volodymyr V.; Laikova, Kateryna V.; Zaitsev, Aleksei S.; Gushchin, Vladimir A.; Skorokhod, Oleksii A.

    2016-01-01

    This data article is related to the research article entitled “The RING for gypsy moth control: topical application of fragment of its nuclear polyhedrosis virus anti-apoptosis gene as insecticide” [1]. This article reports on significantly higher survival of gypsy moth Lymantria dispar male individuals in response to topical application of single-stranded DNA, based on RING (really interesting new gene) domain fragment of LdMNPV (L. dispar multicapsid nuclear polyhedrosis virus) IAP-3 (inhibitor of apoptosis) gene and acted as DNA insecticide. PMID:27054151

  14. Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid.

    Directory of Open Access Journals (Sweden)

    Neil J Ball

    2016-11-01

    Full Text Available The Spumaretrovirinae, or foamy viruses (FVs are complex retroviruses that infect many species of monkey and ape. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. However, there is a paucity of structural information for FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. To probe the functional overlap of FV and orthoretroviral Gag we have determined the structure of a central region of Gag from the Prototype FV (PFV. The structure comprises two all α-helical domains NtDCEN and CtDCEN that although they have no sequence similarity, we show they share the same core fold as the N- (NtDCA and C-terminal domains (CtDCA of archetypal orthoretroviral capsid protein (CA. Moreover, structural comparisons with orthoretroviral CA align PFV NtDCEN and CtDCEN with NtDCA and CtDCA respectively. Further in vitro and functional virological assays reveal that residues making inter-domain NtDCEN-CtDCEN interactions are required for PFV capsid assembly and that intact capsid is required for PFV reverse transcription. These data provide the first information that relates the Gag proteins of Spuma and Orthoretrovirinae and suggests a common ancestor for both lineages containing an ancient CA fold.

  15. Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid

    Science.gov (United States)

    Dutta, Moumita; Pollard, Dominic J.; Goldstone, David C.; Ramos, Andres; Müllers, Erik; Stirnnagel, Kristin; Stanke, Nicole; Lindemann, Dirk; Taylor, William R.; Rosenthal, Peter B.

    2016-01-01

    The Spumaretrovirinae, or foamy viruses (FVs) are complex retroviruses that infect many species of monkey and ape. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. However, there is a paucity of structural information for FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. To probe the functional overlap of FV and orthoretroviral Gag we have determined the structure of a central region of Gag from the Prototype FV (PFV). The structure comprises two all α-helical domains NtDCEN and CtDCEN that although they have no sequence similarity, we show they share the same core fold as the N- (NtDCA) and C-terminal domains (CtDCA) of archetypal orthoretroviral capsid protein (CA). Moreover, structural comparisons with orthoretroviral CA align PFV NtDCEN and CtDCEN with NtDCA and CtDCA respectively. Further in vitro and functional virological assays reveal that residues making inter-domain NtDCEN—CtDCEN interactions are required for PFV capsid assembly and that intact capsid is required for PFV reverse transcription. These data provide the first information that relates the Gag proteins of Spuma and Orthoretrovirinae and suggests a common ancestor for both lineages containing an ancient CA fold. PMID:27829070

  16. Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.

    Science.gov (United States)

    Lang, Tiange; Yin, Kangquan; Liu, Jinyu; Cao, Kunfang; Cannon, Charles H; Du, Fang K

    2014-01-01

    Predicting protein domains is essential for understanding a protein's function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated with de novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.

  17. Functional analysis of SH3 domain containing ring finger 2 during the myogenic differentiation of quail myoblast cells

    Directory of Open Access Journals (Sweden)

    Si Won Kim

    2017-08-01

    Full Text Available Objective Owing to the public availability of complete genome sequences, including avian species, massive bioinformatics analyses may be conducted for computational gene prediction and the identification of gene regulatory networks through various informatics tools. However, to evaluate the biofunctional activity of a predicted target gene, in vivo and in vitro functional genomic analyses should be a prerequisite. Methods Due to a lack of quail genomic sequence information, we first identified the partial genomic structure and sequences of the quail SH3 domain containing ring finger 2 (SH3RF2 gene. Subsequently, SH3RF2 was knocked out using clustered regularly interspaced short palindromic repeat/Cas9 technology and single cell-derived SH3RF2 mutant sublines were established to study the biofunctional activity of SH3RF2 in quail myoblast (QM7 cells during muscle differentiation. Results Through a T7 endonuclease I assay and genotyping analysis, we established an SH3RF2 knockout (KO QM7#4 subline with 61 and 155 nucleotide deletion mutations in SH3RF2. After the induction of myotube differentiation, the expression profiles were analyzed and compared between regular QM7 and SH3RF2 KO QM7#4 cells by global RNA sequencing and bioinformatics analysis. Conclusion We did not detect any statistically significant role of SH3RF2 during myotube differentiation in QM7 myoblast cells. However, additional experiments are necessary to examine the biofunctional activity of SH3RF2 in cell proliferation and muscle growth.

  18. Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare).

    Science.gov (United States)

    Pandey, Bharati; Grover, Abhinav; Sharma, Pradeep

    2018-02-12

    The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. So far, the crystal structure of WRKY from barley has not been resolved; moreover, knowledge of the three-dimensional structure of WRKY domain is pre-requisites for exploring the protein-DNA recognition mechanisms. Homology modelling based approach was used to generate structures for WRKY DNA binding domain (DBD) and its variants using AtWRKY1 as a template. Finally, the stability and conformational changes of the generated model in unbound and bound form was examined through atomistic molecular dynamics (MD) simulations for 100 ns time period. In this study, we investigated the comparative binding pattern of WRKY domain and its variants with W-box cis-regulatory element using molecular docking and dynamics (MD) simulations assays. The atomic insight into WRKY domain exhibited significant variation in the intermolecular hydrogen bonding pattern, leading to the structural anomalies in the variant type and differences in the DNA-binding specificities. Based on the MD analysis, residual contribution and interaction contour, wild-type WRKY (HvWRKY46) were found to interact with DNA through highly conserved heptapeptide in the pre- and post-MD simulated complexes, whereas heptapeptide interaction with DNA was missing in variants (I and II) in post-MD complexes. Consequently, through principal component analysis, wild-type WRKY was also found to be more stable by obscuring a reduced conformational space than the variant I (HvWRKY34). Lastly, high binding free energy for wild-type and variant II allowed us to conclude that wild-type WRKY-DNA complex was more stable relative to variants I. The results of our study revealed complete dynamic and structural information

  19. Isolation of Chromatin from Dysfunctional Telomeres Reveals an Important Role for Ring1b in NHEJ-Mediated Chromosome Fusions

    Directory of Open Access Journals (Sweden)

    Cristina Bartocci

    2014-05-01

    Full Text Available When telomeres become critically short, DNA damage response factors are recruited at chromosome ends, initiating a cellular response to DNA damage. We performed proteomic isolation of chromatin fragments (PICh in order to define changes in chromatin composition that occur upon onset of acute telomere dysfunction triggered by depletion of the telomere-associated factor TRF2. This unbiased purification of telomere-associated proteins in functional or dysfunctional conditions revealed the dynamic changes in chromatin composition that take place at telomeres upon DNA damage induction. On the basis of our results, we describe a critical role for the polycomb group protein Ring1b in nonhomologous end-joining (NHEJ-mediated end-to-end chromosome fusions. We show that cells with reduced levels of Ring1b have a reduced ability to repair uncapped telomeric chromatin. Our data represent an unbiased isolation of chromatin undergoing DNA damage and are a valuable resource to map the changes in chromatin composition in response to DNA damage activation.

  20. Domain swapping reveals that the N-terminal domain of the sensor kinase KdpD in Escherichia coli is important for signaling

    Directory of Open Access Journals (Sweden)

    Lippert Marie-Luise

    2009-07-01

    Full Text Available Abstract Background The KdpD/KdpE two-component system of Escherichia coli regulates expression of the kdpFABC operon encoding the high affinity K+ transport system KdpFABC. The input domain of KdpD comprises a domain that belongs to the family of universal stress proteins (Usp. It has been previously demonstrated that UspC binds to this domain, resulting in KdpD/KdpE scaffolding under salt stress. However the mechanistic significance of this domain for signaling remains unclear. Here, we employed a "domain swapping" approach to replace the KdpD-Usp domain with four homologous domains or with the six soluble Usp proteins of E. coli. Results Full response to salt stress was only achieved with a chimera that contains UspC, probably due to unaffected scaffolding of the KdpD/KdpE signaling cascade by soluble UspC. Unexpectedly, chimeras containing either UspF or UspG not only prevented kdpFABC expression under salt stress but also under K+ limiting conditions, although these hybrid proteins exhibited kinase and phosphotransferase activities in vitro. These are the first KdpD derivatives that do not respond to K+ limitation due to alterations in the N-terminal domain. Analysis of the KdpD-Usp tertiary structure revealed that this domain has a net positively charged surface, while UspF and UspG are characterized by net negative surface charges. Conclusion The Usp domain within KdpD not only functions as a binding surface for the scaffold UspC, but it is also important for KdpD signaling. We propose that KdpD sensing/signaling involves alterations of electrostatic interactions between the large N- and C-terminal cytoplasmic domains.

  1. Structure of the Human FANCL RING-Ube2T Complex Reveals Determinants of Cognate E3-E2 Selection

    Science.gov (United States)

    Hodson, Charlotte; Purkiss, Andrew; Miles, Jennifer Anne; Walden, Helen

    2014-01-01

    Summary The combination of an E2 ubiquitin-conjugating enzyme with an E3 ubiquitin-ligase is essential for ubiquitin modification of a substrate. Moreover, the pairing dictates both the substrate choice and the modification type. The molecular details of generic E3-E2 interactions are well established. Nevertheless, the determinants of selective, specific E3-E2 recognition are not understood. There are ∼40 E2s and ∼600 E3s giving rise to a possible ∼24,000 E3-E2 pairs. Using the Fanconi Anemia pathway exclusive E3-E2 pair, FANCL-Ube2T, we report the atomic structure of the FANCL RING-Ube2T complex, revealing a specific and extensive network of additional electrostatic and hydrophobic interactions. Furthermore, we show that these specific interactions are required for selection of Ube2T over other E2s by FANCL. PMID:24389026

  2. Growth of solid domains in model membranes: quantitative image analysis reveals a strong correlation between domain shape and spatial position

    DEFF Research Database (Denmark)

    Bernchou, Uffe; Ipsen, John Hjort; Simonsen, Adam Cohen

    2009-01-01

    . To analyze this effect, the nucleation points were used as generators in a Voronoi construction. Associated with each generator is a Voronoi polygon that contains all points closer to this generator than to any other. Through a detailed quantitative analysis of the Voronoi cells and the domains, we have...

  3. Study of the individual cytochrome b5 and cytochrome b5 reductase domains of Ncb5or reveals a unique heme pocket and a possible role of the CS domain.

    Science.gov (United States)

    Deng, Bin; Parthasarathy, Sudharsan; Wang, WenFang; Gibney, Brian R; Battaile, Kevin P; Lovell, Scott; Benson, David R; Zhu, Hao

    2010-09-24

    NADH cytochrome b(5) oxidoreductase (Ncb5or) is found in animals and contains three domains similar to cytochrome b(5) (b(5)), CHORD-SGT1 (CS), and cytochrome b(5) reductase (b(5)R). Ncb5or has an important function, as suggested by the diabetes and lipoatrophy phenotypes in Ncb5or null mice. To elucidate the structural and functional properties of human Ncb5or, we generated its individual b(5) and b(5)R domains (Ncb5or-b(5) and Ncb5or-b(5)R, respectively) and compared them with human microsomal b(5) (Cyb5A) and b(5)R (Cyb5R3). A 1.25 Å x-ray crystal structure of Ncb5or-b(5) reveals nearly orthogonal planes of the imidazolyl rings of heme-ligating residues His(89) and His(112), consistent with a highly anisotropic low spin EPR spectrum. Ncb5or is the first member of the cytochrome b(5) family shown to have such a heme environment. Like other b(5) family members, Ncb5or-b(5) has two helix-loop-helix motifs surrounding heme. However, Ncb5or-b(5) differs from Cyb5A with respect to location of the second heme ligand (His(112)) and of polypeptide conformation in its vicinity. Electron transfer from Ncb5or-b(5)R to Ncb5or-b(5) is much less efficient than from Cyb5R3 to Cyb5A, possibly as a consequence of weaker electrostatic interactions. The CS linkage probably obviates the need for strong interactions between b(5) and b(5)R domains in Ncb5or. Studies with a construct combining the Ncb5or CS and b(5)R domains suggest that the CS domain facilitates docking of the b(5) and b(5)R domains. Trp(114) is an invariant surface residue in all known Ncb5or orthologs but appears not to contribute to electron transfer from the b(5)R domain to the b(5) domain.

  4. Volumetric flow imaging reveals the importance of vortex ring formation in squid swimming tail-first and arms-first.

    Science.gov (United States)

    Bartol, Ian K; Krueger, Paul S; Jastrebsky, Rachel A; Williams, Sheila; Thompson, Joseph T

    2016-02-01

    Squids use a pulsed jet and fin movements to swim both arms-first (forward) and tail-first (backward). Given the complexity of the squid multi-propulsor system, 3D velocimetry techniques are required for the comprehensive study of wake dynamics. Defocusing digital particle tracking velocimetry, a volumetric velocimetry technique, and high-speed videography were used to study arms-first and tail-first swimming of brief squid Lolliguncula brevis over a broad range of speeds [0-10 dorsal mantle lengths (DML) s(-1)] in a swim tunnel. Although there was considerable complexity in the wakes of these multi-propulsor swimmers, 3D vortex rings and their derivatives were prominent reoccurring features during both tail-first and arms-first swimming, with the greatest jet and fin flow complexity occurring at intermediate speeds (1.5-3.0 DML s(-1)). The jet generally produced the majority of thrust during rectilinear swimming, increasing in relative importance with speed, and the fins provided no thrust at speeds >4.5 DML s(-1). For both swimming orientations, the fins sometimes acted as stabilizers, producing negative thrust (drag), and consistently provided lift at low/intermediate speeds (swimming orientation, and η for swimming sequences with clear isolated jet vortex rings was significantly greater (η=78.6±7.6%, mean±s.d.) than that for swimming sequences with clear elongated regions of concentrated jet vorticity (η=67.9±19.2%). This study reveals the complexity of 3D vortex wake flows produced by nekton with hydrodynamically distinct propulsors. © 2016. Published by The Company of Biologists Ltd.

  5. Groups, rings, modules

    CERN Document Server

    Auslander, Maurice

    2014-01-01

    This classic monograph is geared toward advanced undergraduates and graduate students. The treatment presupposes some familiarity with sets, groups, rings, and vector spaces. The four-part approach begins with examinations of sets and maps, monoids and groups, categories, and rings. The second part explores unique factorization domains, general module theory, semisimple rings and modules, and Artinian rings. Part three's topics include localization and tensor products, principal ideal domains, and applications of fundamental theorem. The fourth and final part covers algebraic field extensions

  6. In vivo structure of the E. coli FtsZ-ring revealed by photoactivated localization microscopy (PALM).

    Science.gov (United States)

    Fu, Guo; Huang, Tao; Buss, Jackson; Coltharp, Carla; Hensel, Zach; Xiao, Jie

    2010-09-13

    The FtsZ protein, a tubulin-like GTPase, plays a pivotal role in prokaryotic cell division. In vivo it localizes to the midcell and assembles into a ring-like structure-the Z-ring. The Z-ring serves as an essential scaffold to recruit all other division proteins and generates contractile force for cytokinesis, but its supramolecular structure remains unknown. Electron microscopy (EM) has been unsuccessful in detecting the Z-ring due to the dense cytoplasm of bacterial cells, and conventional fluorescence light microscopy (FLM) has only provided images with limited spatial resolution (200-300 nm) due to the diffraction of light. Hence, given the small sizes of bacteria cells, identifying the in vivo structure of the Z-ring presents a substantial challenge. Here, we used photoactivated localization microscopy (PALM), a single molecule-based super-resolution imaging technique, to characterize the in vivo structure of the Z-ring in E. coli. We achieved a spatial resolution of ∼35 nm and discovered that in addition to the expected ring-like conformation, the Z-ring of E. coli adopts a novel compressed helical conformation with variable helical length and pitch. We measured the thickness of the Z-ring to be ∼110 nm and the packing density of FtsZ molecules inside the Z-ring to be greater than what is expected for a single-layered flat ribbon configuration. Our results strongly suggest that the Z-ring is composed of a loose bundle of FtsZ protofilaments that randomly overlap with each other in both longitudinal and radial directions of the cell. Our results provide significant insight into the spatial organization of the Z-ring and open the door for further investigations of structure-function relationships and cell cycle-dependent regulation of the Z-ring.

  7. In vivo structure of the E. coli FtsZ-ring revealed by photoactivated localization microscopy (PALM.

    Directory of Open Access Journals (Sweden)

    Guo Fu

    2010-09-01

    Full Text Available The FtsZ protein, a tubulin-like GTPase, plays a pivotal role in prokaryotic cell division. In vivo it localizes to the midcell and assembles into a ring-like structure-the Z-ring. The Z-ring serves as an essential scaffold to recruit all other division proteins and generates contractile force for cytokinesis, but its supramolecular structure remains unknown. Electron microscopy (EM has been unsuccessful in detecting the Z-ring due to the dense cytoplasm of bacterial cells, and conventional fluorescence light microscopy (FLM has only provided images with limited spatial resolution (200-300 nm due to the diffraction of light. Hence, given the small sizes of bacteria cells, identifying the in vivo structure of the Z-ring presents a substantial challenge. Here, we used photoactivated localization microscopy (PALM, a single molecule-based super-resolution imaging technique, to characterize the in vivo structure of the Z-ring in E. coli. We achieved a spatial resolution of ∼35 nm and discovered that in addition to the expected ring-like conformation, the Z-ring of E. coli adopts a novel compressed helical conformation with variable helical length and pitch. We measured the thickness of the Z-ring to be ∼110 nm and the packing density of FtsZ molecules inside the Z-ring to be greater than what is expected for a single-layered flat ribbon configuration. Our results strongly suggest that the Z-ring is composed of a loose bundle of FtsZ protofilaments that randomly overlap with each other in both longitudinal and radial directions of the cell. Our results provide significant insight into the spatial organization of the Z-ring and open the door for further investigations of structure-function relationships and cell cycle-dependent regulation of the Z-ring.

  8. Structure of the Z Ring-associated Protein, ZapD, Bound to the C-terminal Domain of the Tubulin-like Protein, FtsZ, Suggests Mechanism of Z Ring Stabilization through FtsZ Cross-linking.

    Science.gov (United States)

    Schumacher, Maria A; Huang, Kuo-Hsiang; Zeng, Wenjie; Janakiraman, Anuradha

    2017-03-03

    Cell division in most bacteria is mediated by the tubulin-like FtsZ protein, which polymerizes in a GTP-dependent manner to form the cytokinetic Z ring. A diverse repertoire of FtsZ-binding proteins affects FtsZ localization and polymerization to ensure correct Z ring formation. Many of these proteins bind the C-terminal domain (CTD) of FtsZ, which serves as a hub for FtsZ regulation. FtsZ ring-associated proteins, ZapA-D (Zaps), are important FtsZ regulatory proteins that stabilize FtsZ assembly and enhance Z ring formation by increasing lateral assembly of FtsZ protofilaments, which then form the Z ring. There are no structures of a Zap protein bound to FtsZ; therefore, how these proteins affect FtsZ polymerization has been unclear. Recent data showed ZapD binds specifically to the FtsZ CTD. Thus, to obtain insight into the ZapD-CTD interaction and how it may mediate FtsZ protofilament assembly, we determined the Escherichia coli ZapD-FtsZ CTD structure to 2.67 Å resolution. The structure shows that the CTD docks within a hydrophobic cleft in the ZapD helical domain and adopts an unusual structure composed of two turns of helix separated by a proline kink. FtsZ CTD residue Phe-377 inserts into the ZapD pocket, anchoring the CTD in place and permitting hydrophobic contacts between FtsZ residues Ile-374, Pro-375, and Leu-378 with ZapD residues Leu-74, Trp-77, Leu-91, and Leu-174. The structural findings were supported by mutagenesis coupled with biochemical and in vivo studies. The combined data suggest that ZapD acts as a molecular cross-linking reagent between FtsZ protofilaments to enhance FtsZ assembly. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Domain activities of PapC usher reveal the mechanism of action of an Escherichia coli molecular machine.

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    Volkan, Ender; Ford, Bradley A; Pinkner, Jerome S; Dodson, Karen W; Henderson, Nadine S; Thanassi, David G; Waksman, Gabriel; Hultgren, Scott J

    2012-06-12

    P pili are prototypical chaperone-usher pathway-assembled pili used by Gram-negative bacteria to adhere to host tissues. The PapC usher contains five functional domains: a transmembrane β-barrel, a β-sandwich Plug, an N-terminal (periplasmic) domain (NTD), and two C-terminal (periplasmic) domains, CTD1 and CTD2. Here, we delineated usher domain interactions between themselves and with chaperone-subunit complexes and showed that overexpression of individual usher domains inhibits pilus assembly. Prior work revealed that the Plug domain occludes the pore of the transmembrane domain of a solitary usher, but the chaperone-adhesin-bound usher has its Plug displaced from the pore, adjacent to the NTD. We demonstrate an interaction between the NTD and Plug domains that suggests a biophysical basis for usher gating. Furthermore, we found that the NTD exhibits high-affinity binding to the chaperone-adhesin (PapDG) complex and low-affinity binding to the major tip subunit PapE (PapDE). We also demonstrate that CTD2 binds with lower affinity to all tested chaperone-subunit complexes except for the chaperone-terminator subunit (PapDH) and has a catalytic role in dissociating the NTD-PapDG complex, suggesting an interplay between recruitment to the NTD and transfer to CTD2 during pilus initiation. The Plug domain and the NTD-Plug complex bound all of the chaperone-subunit complexes tested including PapDH, suggesting that the Plug actively recruits chaperone-subunit complexes to the usher and is the sole recruiter of PapDH. Overall, our studies reveal the cooperative, active roles played by periplasmic domains of the usher to initiate, grow, and terminate a prototypical chaperone-usher pathway pilus.

  10. The Bmi-1 helix–turn and ring finger domains are required for Bmi-1 antagonism of (–) epigallocatechin-3-gallate suppression of skin cancer cell survival

    Science.gov (United States)

    Balasubramanian, Sivaprakasam; Scharadin, Tiffany M.; Han, Bingshe; Xu, Wen; Eckert, Richard L.

    2016-01-01

    The Bmi-1 Polycomb group (PcG) protein is an important epigenetic regulator of chromatin status. Elevated Bmi-1 expression is observed in skin cancer and contributes to cancer cell survival. (–) Epigallocatechin-3-gallate (EGCG), an important green tea-derived cancer prevention agent, reduces Bmi-1 level resulting in reduced skin cancer cell survival. This is associated with increased p21Cip1 and p27Kip1 expression, reduced cyclin, and cyclin dependent kinase expression, and increased cleavage of apoptotic markers. These EGCG-dependent changes are attenuated by vector-mediated maintenance of Bmi-1 expression. In the present study, we identify Bmi-1 functional domains that are required for this response. Bmi-1 expression reverses the EGCG-dependent reduction in SCC-13 cell survival, but Bmi-1 mutants lacking the helix–turn–helix–turn–helix–turn (Bmi-1ΔHT) or ring finger (Bmi-1ΔRF) domains do not reverse the EGCG impact. The reduction in Ring1B ubiquitin ligase activity, observed in the presence of mutant Bmi-1, is associated with reduced ability of these mutants to interact with and activate Ring1B ubiquitin ligase, the major ligase responsible for the ubiquitination of histone H2A during chromatin condensation. This results in less chromatin condensation leading to increased tumor suppressor gene expression and reduced cell survival; thereby making the cells more susceptible to the anti-survival action of EGCG. We further show that these mutants act in a dominant-negative manner to inhibit the action of endogenous Bmi-1. Our results suggest that the HT and RF domains are required for Bmi-1 ability to maintain skin cancer cell survival in response to cancer preventive agents. PMID:25843776

  11. Structural-Functional Analysis Reveals a Specific Domain Organization in Family GH20 Hexosaminidases.

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    Val-Cid, Cristina; Biarnés, Xevi; Faijes, Magda; Planas, Antoni

    2015-01-01

    Hexosaminidases are involved in important biological processes catalyzing the hydrolysis of N-acetyl-hexosaminyl residues in glycosaminoglycans and glycoconjugates. The GH20 enzymes present diverse domain organizations for which we propose two minimal model architectures: Model A containing at least a non-catalytic GH20b domain and the catalytic one (GH20) always accompanied with an extra α-helix (GH20b-GH20-α), and Model B with only the catalytic GH20 domain. The large Bifidobacterium bifidum lacto-N-biosidase was used as a model protein to evaluate the minimal functional unit due to its interest and structural complexity. By expressing different truncated forms of this enzyme, we show that Model A architectures cannot be reduced to Model B. In particular, there are two structural requirements general to GH20 enzymes with Model A architecture. First, the non-catalytic domain GH20b at the N-terminus of the catalytic GH20 domain is required for expression and seems to stabilize it. Second, the substrate-binding cavity at the GH20 domain always involves a remote element provided by a long loop from the catalytic domain itself or, when this loop is short, by an element from another domain of the multidomain structure or from the dimeric partner. Particularly, the lacto-N-biosidase requires GH20b and the lectin-like domain at the N- and C-termini of the catalytic GH20 domain to be fully soluble and functional. The lectin domain provides this remote element to the active site. We demonstrate restoration of activity of the inactive GH20b-GH20-α construct (model A architecture) by a complementation assay with the lectin-like domain. The engineering of minimal functional units of multidomain GH20 enzymes must consider these structural requirements.

  12. Structure of the nucleotide-binding domain of a dipeptide ABC transporter reveals a novel iron-sulfur cluster-binding domain.

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    Li, Xiaolu; Zhuo, Wei; Yu, Jie; Ge, Jingpeng; Gu, Jinke; Feng, Yue; Yang, Maojun; Wang, Linfang; Wang, Na

    2013-02-01

    Dipeptide permease (Dpp), which belongs to an ABC transport system, imports peptides consisting of two or three L-amino acids from the matrix to the cytoplasm in microbes. Previous studies have indicated that haem competes with dipeptides to bind DppA in vitro and in vivo and that the Dpp system can also translocate haem. Here, the crystal structure of DppD, the nucleotide-binding domain (NBD) of the ABC-type dipeptide/oligopeptide/nickel-transport system from Thermoanaerobacter tengcongensis, bound with ATP, Mg(2+) and a [4Fe-4S] iron-sulfur cluster is reported. The N-terminal domain of DppD shares a similar structural fold with the NBDs of other ABC transporters. Interestingly, the C-terminal domain of DppD contains a [4Fe-4S] cluster. The UV-visible absorbance spectrum of DppD was consistent with the presence of a [4Fe-4S] cluster. A search with DALI revealed that the [4Fe-4S] cluster-binding domain is a novel structural fold. Structural analysis and comparisons with other ABC transporters revealed that this iron-sulfur cluster may act as a mediator in substrate (dipeptide or haem) binding by electron transfer and may regulate the transport process in Dpp ABC transport systems. The crystal structure provides a basis for understanding the properties of ABC transporters and will be helpful in investigating the functions of NBDs in the regulation of ABC transporter activity.

  13. Organization of Subunits in the Membrane Domain of the Bovine F-ATPase Revealed by Covalent Cross-linking.

    Science.gov (United States)

    Lee, Jennifer; Ding, ShuJing; Walpole, Thomas B; Holding, Andrew N; Montgomery, Martin G; Fearnley, Ian M; Walker, John E

    2015-05-22

    The F-ATPase in bovine mitochondria is a membrane-bound complex of about 30 subunits of 18 different kinds. Currently, ∼85% of its structure is known. The enzyme has a membrane extrinsic catalytic domain, and a membrane intrinsic domain where the turning of the enzyme's rotor is generated from the transmembrane proton-motive force. The domains are linked by central and peripheral stalks. The central stalk and a hydrophobic ring of c-subunits in the membrane domain constitute the enzyme's rotor. The external surface of the catalytic domain and membrane subunit a are linked by the peripheral stalk, holding them static relative to the rotor. The membrane domain contains six additional subunits named ATP8, e, f, g, DAPIT (diabetes-associated protein in insulin-sensitive tissues), and 6.8PL (6.8-kDa proteolipid), each with a single predicted transmembrane α-helix, but their orientation and topography are unknown. Mutations in ATP8 uncouple the enzyme and interfere with its assembly, but its roles and the roles of the other five subunits are largely unknown. We have reacted accessible amino groups in the enzyme with bifunctional cross-linking agents and identified the linked residues. Cross-links involving the supernumerary subunits, where the structures are not known, show that the C terminus of ATP8 extends ∼70 Å from the membrane into the peripheral stalk and that the N termini of the other supernumerary subunits are on the same side of the membrane, probably in the mitochondrial matrix. These experiments contribute significantly toward building up a complete structural picture of the F-ATPase. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Organization of Subunits in the Membrane Domain of the Bovine F-ATPase Revealed by Covalent Cross-linking*

    Science.gov (United States)

    Lee, Jennifer; Ding, ShuJing; Walpole, Thomas B.; Holding, Andrew N.; Montgomery, Martin G.; Fearnley, Ian M.; Walker, John E.

    2015-01-01

    The F-ATPase in bovine mitochondria is a membrane-bound complex of about 30 subunits of 18 different kinds. Currently, ∼85% of its structure is known. The enzyme has a membrane extrinsic catalytic domain, and a membrane intrinsic domain where the turning of the enzyme's rotor is generated from the transmembrane proton-motive force. The domains are linked by central and peripheral stalks. The central stalk and a hydrophobic ring of c-subunits in the membrane domain constitute the enzyme's rotor. The external surface of the catalytic domain and membrane subunit a are linked by the peripheral stalk, holding them static relative to the rotor. The membrane domain contains six additional subunits named ATP8, e, f, g, DAPIT (diabetes-associated protein in insulin-sensitive tissues), and 6.8PL (6.8-kDa proteolipid), each with a single predicted transmembrane α-helix, but their orientation and topography are unknown. Mutations in ATP8 uncouple the enzyme and interfere with its assembly, but its roles and the roles of the other five subunits are largely unknown. We have reacted accessible amino groups in the enzyme with bifunctional cross-linking agents and identified the linked residues. Cross-links involving the supernumerary subunits, where the structures are not known, show that the C terminus of ATP8 extends ∼70 Å from the membrane into the peripheral stalk and that the N termini of the other supernumerary subunits are on the same side of the membrane, probably in the mitochondrial matrix. These experiments contribute significantly toward building up a complete structural picture of the F-ATPase. PMID:25851905

  15. Theoretical Insights Reveal Novel Motions in Csk's SH3 Domain That Control Kinase Activation.

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    Sulyman Barkho

    Full Text Available The Src family of tyrosine kinases (SFKs regulate numerous aspects of cell growth and differentiation and are under the principal control of the C-terminal Src Kinase (Csk. Although Csk and SFKs share conserved kinase, SH2 and SH3 domains, they differ considerably in three-dimensional structure, regulatory mechanism, and the intrinsic kinase activities. Although the SH2 and SH3 domains are known to up- or down-regulate tyrosine kinase function, little is known about the global motions in the full-length kinase that govern these catalytic variations. We use a combination of accelerated Molecular Dynamics (aMD simulations and experimental methods to provide a new view of functional motions in the Csk scaffold. These computational studies suggest that high frequency vibrations in the SH2 domain are coupled through the N-terminal lobe of the kinase domain to motions in the SH3 domain. The effects of these reflexive movements on the kinase domain can be viewed using both Deuterium Exchange Mass Spectrometry (DXMS and steady-state kinetic methods. Removal of several contacts, including a crystallographically unobserved N-terminal segment, between the SH3 and kinase domains short-circuit these coupled motions leading to reduced catalytic efficiency and stability of N-lobe motifs within the kinase domain. The data expands the model of Csk's activation whereby separate domains productively interact with two diametrically opposed surfaces of the kinase domain. Such reversible transitions may organize the active structure of the tyrosine kinase domain of Csk.

  16. Molecular dynamics simulation reveals insights into the mechanism of unfolding by the A130T/V mutations within the MID1 zinc-binding Bbox1 domain.

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    Yunjie Zhao

    Full Text Available The zinc-binding Bbox1 domain in protein MID1, a member of the TRIM family of proteins, facilitates the ubiquitination of the catalytic subunit of protein phosphatase 2A and alpha4, a protein regulator of PP2A. The natural mutation of residue A130 to a valine or threonine disrupts substrate recognition and catalysis. While NMR data revealed the A130T mutant Bbox1 domain failed to coordinate both structurally essential zinc ions and resulted in an unfolded structure, the unfolding mechanism is unknown. Principle component analysis revealed that residue A130 served as a hinge point between the structured β-strand-turn-β-strand (β-turn-β and the lasso-like loop sub-structures that constitute loop1 of the ββα-RING fold that the Bbox1 domain adopts. Backbone RMSD data indicate significant flexibility and departure from the native structure within the first 5 ns of the molecular dynamics (MD simulation for the A130V mutant (>6 Å and after 30 ns for A130T mutant (>6 Å. Overall RMSF values were higher for the mutant structures and showed increased flexibility around residues 125 and 155, regions with zinc-coordinating residues. Simulated pKa values of the sulfhydryl group of C142 located near A130 suggested an increased in value to ~9.0, paralleling the increase in the apparent dielectric constants for the small cavity near residue A130. Protonation of the sulfhydryl group would disrupt zinc-coordination, directly contributing to unfolding of the Bbox1. Together, the increased motion of residues of loop 1, which contains four of the six zinc-binding cysteine residues, and the increased pKa of C142 could destabilize the structure of the zinc-coordinating residues and contribute to the unfolding.

  17. Structures of the Gasdermin D C-Terminal Domains Reveal Mechanisms of Autoinhibition.

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    Liu, Zhonghua; Wang, Chuanping; Rathkey, Joseph K; Yang, Jie; Dubyak, George R; Abbott, Derek W; Xiao, Tsan Sam

    2018-05-01

    Pyroptosis is an inflammatory form of programmed cell death that plays important roles in immune protection against infections and in inflammatory disorders. Gasdermin D (GSDMD) is an executor of pyroptosis upon cleavage by caspases-1/4/5/11 following canonical and noncanonical inflammasome activation. GSDMD N-terminal domain assembles membrane pores to induce cytolysis, whereas its C-terminal domain inhibits cell death through intramolecular association with the N domain. The molecular mechanisms of autoinhibition for GSDMD are poorly characterized. Here we report the crystal structures of the human and murine GSDMD C-terminal domains, which differ from those of the full-length murine GSDMA3 and the human GSDMB C-terminal domain. Mutations of GSDMD C-domain residues predicted to locate at its interface with the N-domain enhanced pyroptosis. Our results suggest that GSDMDs may employ a distinct mode of intramolecular domain interaction and autoinhibition, which may be relevant to its unique role in pyroptosis downstream of inflammasome activation. Copyright © 2018 Elsevier Ltd. All rights reserved.

  18. Structural Characterization of Maize SIRK1 Kinase Domain Reveals an Unusual Architecture of the Activation Segment

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    Bruno Aquino

    2017-05-01

    Full Text Available Kinases are primary regulators of plant metabolism and excellent targets for plant breeding. However, most kinases, including the abundant receptor-like kinases (RLK, have no assigned role. SIRK1 is a leucine-rich repeat receptor-like kinase (LRR-RLK, the largest family of RLK. In Arabidopsis thaliana, SIRK1 (AtSIRK1 is phosphorylated after sucrose is resupplied to sucrose-starved seedlings and it modulates the sugar response by phosphorylating several substrates. In maize, the ZmSIRK1 expression is altered in response to drought stress. In neither Arabidopsis nor in maize has the function of SIRK1 been completely elucidated. As a first step toward the biochemical characterization of ZmSIRK1, we obtained its recombinant kinase domain, demonstrated that it binds AMP-PNP, a non-hydrolysable ATP-analog, and solved the structure of ZmSIRK1- AMP-PNP co-crystal. The ZmSIRK1 crystal structure revealed a unique conformation for the activation segment. In an attempt to find inhibitors for ZmSIRK1, we screened a focused small molecule library and identified six compounds that stabilized ZmSIRK1 against thermal melt. ITC analysis confirmed that three of these compounds bound to ZmSIRK1 with low micromolar affinity. Solving the 3D structure of ZmSIRK1-AMP-PNP co-crystal provided information on the molecular mechanism of ZmSIRK1 activity. Furthermore, the identification of small molecules that bind this kinase can serve as initial backbone for development of new potent and selective ZmSIRK1 antagonists.

  19. Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap.

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    Gu, Shuang; Sushko, Oleksandr; Deery, Evelyne; Warren, Martin J; Pickersgill, Richard W

    2015-11-30

    CobK catalyzes the essential reduction of the precorrin ring in the cobalamin biosynthetic pathway. The crystal structure of CobK reveals that the enzyme, despite not having the signature sequence, comprises two Rossmann fold domains which bind coenzyme and substrate respectively. The two parallel β-sheets have swapped their last β-strands giving a novel sheet topology which is an interesting variation on the Rossmann-fold. The trapped ternary complex with coenzyme and product reveals five conserved basic residues that bind the carboxylates of the tetrapyrrole tightly anchoring the product. A loop, disordered in both the apoenzyme and holoenzyme structures, closes around the product further tightening binding. The structure is consistent with a mechanism involving protonation of C18 and pro-R hydride transfer from NADPH to C19 of precorrin-6A and reveals the interactions responsible for the specificity of CobK. The almost complete burial of the reduced precorrin product suggests a remarkable form of metabolite channeling where the next enzyme in the biosynthetic pathway triggers product release.

  20. Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers.

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    Finnerty, John R; Mazza, Maureen E; Jezewski, Peter A

    2009-01-20

    Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between MSX1 and MSX2 reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (Hmx, NK1, Emx) in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal), were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion. Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies.

  1. Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers

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    Finnerty John R

    2009-01-01

    Full Text Available Abstract Background Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. Results Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between MSX1 and MSX2 reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (Hmx, NK1, Emx in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal, were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion. Conclusion Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies.

  2. Residues 240-250 in the C-terminus of the Pirh2 protein complement the function of the RING domain in self-ubiquitination of the Pirh2 protein.

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    Rami Abou Zeinab

    Full Text Available Pirh2 is a p53 inducible gene that encodes a RING-H2 domain and is proposed to be a main regulator of p53 protein, thus fine tuning the DNA damage response. Pirh2 interacts physically with p53 and promotes its MDM2-independent ubiquitination and subsequent degradation as well as participates in an auto-regulatory feedback loop that controls p53 function. Pirh2 also self-ubiquitinates. Interestingly, Pirh2 is overexpressed in a wide range of human tumors. In this study, we investigated the domains and residues essential for Pirh2 self-ubiquitination. Deletions were made in each of the three major domains of Pirh2: the N-terminal domain (NTD, Ring domain (RING, and C-terminal domain (CTD. The effects of these deletions on Pirh2 self-ubiquitination were then assessed using in vitro ubiquitination assays. Our results demonstrate that the RING domain is essential, but not sufficient, for Pirh2 self-ubiquitination and that residues 240-250 of the C-terminal domain are also essential. Our results demonstrate that Pirh2 mediated p53 polyubiquitination occurs mainly through the K48 residue of ubiquitin in vitro. Our data further our understanding of the mechanism of Pirh2 self-ubiquitination and may help identify valuable therapeutic targets that play roles in reducing the effects of the overexpression of Pirh2, thus maximizing p53's response to DNA damage.

  3. Rare RNF213 variants in the C-terminal region encompassing the RING-finger domain are associated with moyamoya angiopathy in Caucasians.

    Science.gov (United States)

    Guey, Stéphanie; Kraemer, Markus; Hervé, Dominique; Ludwig, Thomas; Kossorotoff, Manoëlle; Bergametti, Françoise; Schwitalla, Jan Claudius; Choi, Simone; Broseus, Lucile; Callebaut, Isabelle; Genin, Emmanuelle; Tournier-Lasserve, Elisabeth

    2017-08-01

    Moyamoya angiopathy (MMA) is a cerebral angiopathy affecting the terminal part of internal carotid arteries. Its prevalence is 10 times higher in Japan and Korea than in Europe. In East Asian countries, moyamoya is strongly associated to the R4810K variant in the RNF213 gene that encodes for a protein containing a RING-finger and two AAA+ domains. This variant has never been detected in Caucasian MMA patients, but several rare RNF213 variants have been reported in Caucasian cases. Using a collapsing test based on exome data from 68 European MMA probands and 573 ethnically matched controls, we showed a significant association between rare missense RNF213 variants and MMA in European patients (odds ratio (OR)=2.24, 95% confidence interval (CI)=(1.19-4.11), P=0.01). Variants specific to cases had higher pathogenicity predictive scores (median of 24.2 in cases versus 9.4 in controls, P=0.029) and preferentially clustered in a C-terminal hotspot encompassing the RING-finger domain of RNF213 (P<10 -3 ). This association was even stronger when restricting the analysis to childhood-onset and familial cases (OR=4.54, 95% CI=(1.80-11.34), P=1.1 × 10 -3 ). All clinically affected relatives who were genotyped were carriers. However, the need for additional factors to develop MMA is strongly suggested by the fact that only 25% of mutation carrier relatives were clinically affected.

  4. Structural characterization of the bacterial proteasome homolog BPH reveals a tetradecameric double-ring complex with unique inner cavity properties.

    Science.gov (United States)

    Fuchs, Adrian C D; Maldoner, Lorena; Hipp, Katharina; Hartmann, Marcus D; Martin, Jörg

    2018-01-19

    Eukaryotic and archaeal proteasomes are paradigms for self-compartmentalizing proteases. To a large extent, their function requires interplay with hexameric ATPases associated with diverse cellular activities (AAA+) that act as substrate unfoldases. Bacteria have various types of self-compartmentalizing proteases; in addition to the proteasome itself, these include the proteasome homolog HslV, which functions together with the AAA+ HslU; the ClpP protease with its partner AAA+ ClpX; and Anbu, a recently characterized ancestral proteasome variant. Previous bioinformatic analysis has revealed a novel bacterial member of the proteasome family Betaproteobacteria proteasome homolog (BPH). Using cluster analysis, we here affirmed that BPH evolutionarily descends from HslV. Crystal structures of the Thiobacillus denitrificans and Cupriavidus metallidurans BPHs disclosed a homo-oligomeric double-ring architecture in which the active sites face the interior of the cylinder. Using small-angle X-ray scattering (SAXS) and electron microscopy averaging, we found that BPH forms tetradecamers in solution, unlike the dodecamers seen in HslV. Although the highly acidic inner surface of BPH was in striking contrast to the cavity characteristics of the proteasome and HslV, a classical proteasomal reaction mechanism could be inferred from the covalent binding of the proteasome-specific inhibitor epoxomicin to BPH. A ligand-bound structure implied that the elongated BPH inner pore loop may be involved in substrate recognition. The apparent lack of a partner unfoldase and other unique features, such as Ser replacing Thr as the catalytic residue in certain BPH subfamilies, suggest a proteolytic function for BPH distinct from those of known bacterial self-compartmentalizing proteases. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Sequence and structural analysis of the chitinase insertion domain reveals two conserved motifs involved in chitin-binding.

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    Hai Li

    2010-01-01

    Full Text Available Chitinases are prevalent in life and are found in species including archaea, bacteria, fungi, plants, and animals. They break down chitin, which is the second most abundant carbohydrate in nature after cellulose. Hence, they are important for maintaining a balance between carbon and nitrogen trapped as insoluble chitin in biomass. Chitinases are classified into two families, 18 and 19 glycoside hydrolases. In addition to a catalytic domain, which is a triosephosphate isomerase barrel, many family 18 chitinases contain another module, i.e., chitinase insertion domain. While numerous studies focus on the biological role of the catalytic domain in chitinase activity, the function of the chitinase insertion domain is not completely understood. Bioinformatics offers an important avenue in which to facilitate understanding the role of residues within the chitinase insertion domain in chitinase function.Twenty-seven chitinase insertion domain sequences, which include four experimentally determined structures and span five kingdoms, were aligned and analyzed using a modified sequence entropy parameter. Thirty-two positions with conserved residues were identified. The role of these conserved residues was explored by conducting a structural analysis of a number of holo-enzymes. Hydrogen bonding and van der Waals calculations revealed a distinct subset of four conserved residues constituting two sequence motifs that interact with oligosaccharides. The other conserved residues may be key to the structure, folding, and stability of this domain.Sequence and structural studies of the chitinase insertion domains conducted within the framework of evolution identified four conserved residues which clearly interact with the substrates. Furthermore, evolutionary studies propose a link between the appearance of the chitinase insertion domain and the function of family 18 chitinases in the subfamily A.

  6. fMRI reveals reciprocal inhibition between social and physical cognitive domains

    Science.gov (United States)

    Jack, Anthony I.; Dawson, Abigail; Begany, Katelyn; Leckie, Regina L.; Barry, Kevin; Ciccia, Angela; Snyder, Abraham

    2012-01-01

    Two lines of evidence indicate that there exists a reciprocal inhibitory relationship between opposed brain networks. First, most attention-demanding cognitive tasks activate a stereotypical set of brain areas, known as the task-positive network and simultaneously deactivate a different set of brain regions, commonly referred to as the task negative or default mode network. Second, functional connectivity analyses show that these same opposed networks are anti-correlated in the resting state. We hypothesize that these reciprocally inhibitory effects reflect two incompatible cognitive modes, each of which is directed towards understanding the external world. Thus, engaging one mode activates one set of regions and suppresses activity in the other. We test this hypothesis by identifying two types of problem-solving task which, on the basis of prior work, have been consistently associated with the task positive and task negative regions: tasks requiring social cognition, i.e., reasoning about the mental states of other persons, and tasks requiring physical cognition, i.e., reasoning about the causal/mechanical properties of inanimate objects. Social and mechanical reasoning tasks were presented to neurologically normal participants during fMRI. Each task type was presented using both text and video clips. Regardless of presentation modality, we observed clear evidence of reciprocal suppression: social tasks deactivated regions associated with mechanical reasoning and mechanical tasks deactivated regions associated with social reasoning. These findings are not explained by self-referential processes, task engagement, mental simulation, mental time travel or external vs. internal attention, all factors previously hypothesized to explain default mode network activity. Analyses of resting state data revealed a close match between the regions our tasks identified as reciprocally inhibitory and regions of maximal anti-correlation in the resting state. These results indicate

  7. fMRI reveals reciprocal inhibition between social and physical cognitive domains.

    Science.gov (United States)

    Jack, Anthony I; Dawson, Abigail J; Begany, Katelyn L; Leckie, Regina L; Barry, Kevin P; Ciccia, Angela H; Snyder, Abraham Z

    2013-02-01

    Two lines of evidence indicate that there exists a reciprocal inhibitory relationship between opposed brain networks. First, most attention-demanding cognitive tasks activate a stereotypical set of brain areas, known as the task-positive network and simultaneously deactivate a different set of brain regions, commonly referred to as the task negative or default mode network. Second, functional connectivity analyses show that these same opposed networks are anti-correlated in the resting state. We hypothesize that these reciprocally inhibitory effects reflect two incompatible cognitive modes, each of which may be directed towards understanding the external world. Thus, engaging one mode activates one set of regions and suppresses activity in the other. We test this hypothesis by identifying two types of problem-solving task which, on the basis of prior work, have been consistently associated with the task positive and task negative regions: tasks requiring social cognition, i.e., reasoning about the mental states of other persons, and tasks requiring physical cognition, i.e., reasoning about the causal/mechanical properties of inanimate objects. Social and mechanical reasoning tasks were presented to neurologically normal participants during fMRI. Each task type was presented using both text and video clips. Regardless of presentation modality, we observed clear evidence of reciprocal suppression: social tasks deactivated regions associated with mechanical reasoning and mechanical tasks deactivated regions associated with social reasoning. These findings are not explained by self-referential processes, task engagement, mental simulation, mental time travel or external vs. internal attention, all factors previously hypothesized to explain default mode network activity. Analyses of resting state data revealed a close match between the regions our tasks identified as reciprocally inhibitory and regions of maximal anti-correlation in the resting state. These results

  8. Planetary Rings

    Science.gov (United States)

    Nicholson, P. D.

    2001-11-01

    A revolution in the studies in planetary rings studies occurred in the period 1977--1981, with the serendipitous discovery of the narrow, dark rings of Uranus, the first Voyager images of the tenuous jovian ring system, and the many spectacular images returned during the twin Voyager flybys of Saturn. In subsequent years, ground-based stellar occultations, HST observations, and the Voyager flybys of Uranus (1986) and Neptune (1989), as well as a handful of Galileo images, provided much additional information. Along with the completely unsuspected wealth of detail these observations revealed came an unwelcome problem: are the rings ancient or are we privileged to live at a special time in history? The answer to this still-vexing question may lie in the complex gravitational interactions recent studies have revealed between the rings and their retinues of attendant satellites. Among the four known ring systems, we see elegant examples of Lindblad and corotation resonances (first invoked in the context of galactic disks), electromagnetic resonances, spiral density waves and bending waves, narrow ringlets which exhibit internal modes due to collective instabilities, sharp-edged gaps maintained via tidal torques from embedded moonlets, and tenuous dust belts created by meteoroid impact onto parent bodies. Perhaps most puzzling is Saturn's multi-stranded, clumpy F ring, which continues to defy a simple explanation 20 years after it was first glimpsed in grainy images taken by Pioneer 11. Voyager and HST images reveal a complex, probably chaotic, dynamical interaction between unseen parent bodies within this ring and its two shepherd satellites, Pandora and Prometheus. The work described here reflects contributions by Joe Burns, Jeff Cuzzi, Luke Dones, Dick French, Peter Goldreich, Colleen McGhee, Carolyn Porco, Mark Showalter, and Bruno Sicardy, as well as those of the author. This research has been supported by NASA's Planetary Geology and Geophysics program and the

  9. Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

    Directory of Open Access Journals (Sweden)

    Matteo Vietri Rudan

    2015-03-01

    Full Text Available Topological domains are key architectural building blocks of chromosomes, but their functional importance and evolutionary dynamics are not well defined. We performed comparative high-throughput chromosome conformation capture (Hi-C in four mammals and characterized the conservation and divergence of chromosomal contact insulation and the resulting domain architectures within distantly related genomes. We show that the modular organization of chromosomes is robustly conserved in syntenic regions and that this is compatible with conservation of the binding landscape of the insulator protein CTCF. Specifically, conserved CTCF sites are co-localized with cohesin, are enriched at strong topological domain borders, and bind to DNA motifs with orientations that define the directionality of CTCF’s long-range interactions. Conversely, divergent CTCF binding between species is correlated with divergence of internal domain structure, likely driven by local CTCF binding sequence changes, demonstrating how genome evolution can be linked to a continuous flux of local conformation changes. We also show that large-scale domains are reorganized during genome evolution as intact modules.

  10. Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape.

    Science.gov (United States)

    Yokoyama, Takao; Miura, Fumihito; Araki, Hiromitsu; Okamura, Kohji; Ito, Takashi

    2015-08-12

    Base-resolution methylome data generated by whole-genome bisulfite sequencing (WGBS) is often used to segment the genome into domains with distinct methylation levels. However, most segmentation methods include many parameters to be carefully tuned and/or fail to exploit the unsurpassed resolution of the data. Furthermore, there is no simple method that displays the composition of the domains to grasp global trends in each methylome. We propose to use changepoint detection for domain demarcation based on base-resolution methylome data. While the proposed method segments the methylome in a largely comparable manner to conventional approaches, it has only a single parameter to be tuned. Furthermore, it fully exploits the base-resolution of the data to enable simultaneous detection of methylation changes in even contrasting size ranges, such as focal hypermethylation and global hypomethylation in cancer methylomes. We also propose a simple plot termed methylated domain landscape (MDL) that globally displays the size, the methylation level and the number of the domains thus defined, thereby enabling one to intuitively grasp trends in each methylome. Since the pattern of MDL often reflects cell lineages and is largely unaffected by data size, it can serve as a novel signature of methylome. Changepoint detection in base-resolution methylome data followed by MDL plotting provides a novel method for methylome characterization and will facilitate global comparison among various WGBS data differing in size and even species origin.

  11. High-resolution 2-D Bragg diffraction reveal heterogeneous domain transformation behavior in a bulk relaxor ferroelectric

    Energy Technology Data Exchange (ETDEWEB)

    Pramanick, Abhijit, E-mail: apramani@cityu.edu.hk [Department of Physics and Materials Science, City University of Hong Kong, Kowloon (Hong Kong); Stoica, Alexandru D.; An, Ke [Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States)

    2016-08-29

    In-situ measurement of fine-structure of neutron Bragg diffraction peaks from a relaxor single-crystal using a time-of-flight instrument reveals highly heterogeneous mesoscale domain transformation behavior under applied electric fields. It is observed that only ∼25% of domains undergo reorientation or phase transition contributing to large average strains, while at least 40% remain invariant and exhibit microstrains. Such insights could be central for designing new relaxor materials with better performance and longevity. The current experimental technique can also be applied to resolve complex mesoscale phenomena in other functional materials.

  12. The structure of a conserved Piezo channel domain reveals a novel beta sandwich fold

    Science.gov (United States)

    Kamajaya, Aron; Kaiser, Jens; Lee, Jonas; Reid, Michelle; Rees, Douglas C.

    2014-01-01

    Summary Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a novel beta sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in Dehydrated Hereditary Stomatocytosis (DHS) patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels. PMID:25242456

  13. Increase in platinum group elements in Mexico City as revealed from growth rings of Taxodium mucronatum ten.

    Science.gov (United States)

    Morton-Bermea, Ofelia; Beramendi-Orosco, Laura; Martínez-Reyes, Ángeles; Hernández-Álvarez, Elizabeth; González-Hernández, Galia

    2016-02-01

    Tree rings may be used as indicators of contamination events providing information on the chronology and the elemental composition of the contamination. In this framework, we report PGEs enrichment in growth rings of Taxodium mucronatum ten for trees growing in the central area of Mexico City as compared to trees growing in a non-urban environment. Concentrations of PGE were determined by ICP-MS analysis on microwave-digested tree rings. The element found in higher concentrations was Pd (1.13-87.98 μg kg(-1)), followed by Rh (0.28-36.81 μg kg(-1)) and Pt (0.106-7.21 μg kg(-1)). The concentration trends of PGEs in the tree-ring sequences from the urban area presented significant correlation values when comparing between trees (r between 0.618 and 0.98, P < 0.025) and between elements within individual trees (r between 0.76 and 0.994, P < 0.01). Furthermore, a clear increase was observed for rings after 1997, with enrichment of up to 60 times the mean concentration found for the sequence from the non-urban area and up to 40 times the mean concentration for the pre-1991 period in the urban trees. These results also demonstrate the feasibility of applying T. mucronatum ten to be used as a bioindicator of the increase in PGE in urban environments.

  14. Hydrogen-deuterium exchange and mass spectrometry reveal the pH-dependent conformational changes of diphtheria toxin T domain.

    Science.gov (United States)

    Li, Jing; Rodnin, Mykola V; Ladokhin, Alexey S; Gross, Michael L

    2014-11-04

    The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our "standard condition" (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W(+)-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8-9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8-9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain.

  15. Hydrogen–Deuterium Exchange and Mass Spectrometry Reveal the pH-Dependent Conformational Changes of Diphtheria Toxin T Domain

    Science.gov (United States)

    2015-01-01

    The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen–deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our “standard condition” (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W+-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8–9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8–9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain. PMID:25290210

  16. Flow patterns on spectral-domain optical coherence tomography reveal flow directions at retinal vessel bifurcations

    DEFF Research Database (Denmark)

    Willerslev, Anne; Li, Xiao Q; Munch, Inger C

    2014-01-01

    PURPOSE: To study intravascular characteristics of flowing blood in retinal vessels using spectral-domain optical coherence tomography (SD-OCT). METHODS: Examination of selected arterial bifurcations and venous sites of confluence in 25 healthy 11-year-old children recruited as an ad hoc subsample...

  17. The identification of FANCD2 DNA binding domains reveals nuclear localization sequences.

    Science.gov (United States)

    Niraj, Joshi; Caron, Marie-Christine; Drapeau, Karine; Bérubé, Stéphanie; Guitton-Sert, Laure; Coulombe, Yan; Couturier, Anthony M; Masson, Jean-Yves

    2017-08-21

    Fanconi anemia (FA) is a recessive genetic disorder characterized by congenital abnormalities, progressive bone-marrow failure, and cancer susceptibility. The FA pathway consists of at least 21 FANC genes (FANCA-FANCV), and the encoded protein products interact in a common cellular pathway to gain resistance against DNA interstrand crosslinks. After DNA damage, FANCD2 is monoubiquitinated and accumulates on chromatin. FANCD2 plays a central role in the FA pathway, using yet unidentified DNA binding regions. By using synthetic peptide mapping and DNA binding screen by electromobility shift assays, we found that FANCD2 bears two major DNA binding domains predominantly consisting of evolutionary conserved lysine residues. Furthermore, one domain at the N-terminus of FANCD2 bears also nuclear localization sequences for the protein. Mutations in the bifunctional DNA binding/NLS domain lead to a reduction in FANCD2 monoubiquitination and increase in mitomycin C sensitivity. Such phenotypes are not fully rescued by fusion with an heterologous NLS, which enable separation of DNA binding and nuclear import functions within this domain that are necessary for FANCD2 functions. Collectively, our results enlighten the importance of DNA binding and NLS residues in FANCD2 to activate an efficient FA pathway. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

    DEFF Research Database (Denmark)

    Sükösd, Zsuzsanna; Andersen, Ebbe Sloth; Seemann, Ernst Stefan

    2015-01-01

    of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping...

  19. Fra Angelico’s painting technique revealed by terahertz time-domain imaging (THz-TDI)

    DEFF Research Database (Denmark)

    Dandolo, Corinna Ludovica Koch; Picollo, Marcello; Cucci, Costanza

    2016-01-01

    We have investigated with terahertz time-domain imaging (THz-TDI) the well-known Lamentation over the dead Christ panel painting (San Marco Museum, Florence) painted by Fra Giovanni Angelico within 1436 and 1441. The investigation provided a better understanding of the construction and gilding te...

  20. Molecular Dynamics Simulations of the STAS Domains of Rat Prestin and Human Pendrin Reveal Conformational Motions in Conserved Flexible Regions

    Directory of Open Access Journals (Sweden)

    Alok K. Sharma

    2014-02-01

    domain in solution structure may be more dynamic than rat prestin STAS. Regions of prestin and pendrin identified by RMS fluctuation data as exhibiting larger atomic fluctuations corresponded to nominal GDP-binding regions of the aligned Rv1739c STAS domain of M. tuberculosis. Conclusions: MD simulations of mammalian STAS domains reveal substantial predicted conformational heterogeneity. These predicted conformational dynamics serve to supplement the reported crystal structure of the rat prestin STAS domain, and extend our understanding of the roles of STAS domains in SLC26 anion transporter function.

  1. Mechanism of SOS PR-domain autoinhibition revealed by single-molecule assays on native protein from lysate.

    Science.gov (United States)

    Lee, Young Kwang; Low-Nam, Shalini T; Chung, Jean K; Hansen, Scott D; Lam, Hiu Yue Monatrice; Alvarez, Steven; Groves, Jay T

    2017-04-28

    The guanine nucleotide exchange factor (GEF) Son of Sevenless (SOS) plays a critical role in signal transduction by activating Ras. Here we introduce a single-molecule assay in which individual SOS molecules are captured from raw cell lysate using Ras-functionalized supported membrane microarrays. This enables characterization of the full-length SOS protein, which has not previously been studied in reconstitution due to difficulties in purification. Our measurements on the full-length protein reveal a distinct role of the C-terminal proline-rich (PR) domain to obstruct the engagement of allosteric Ras independently of the well-known N-terminal domain autoinhibition. This inhibitory role of the PR domain limits Grb2-independent recruitment of SOS to the membrane through binding of Ras·GTP in the SOS allosteric binding site. More generally, this assay strategy enables characterization of the functional behaviour of GEFs with single-molecule precision but without the need for purification.

  2. Crystal structure of the UBR-box from UBR6/FBXO11 reveals domain swapping mediated by zinc binding.

    Science.gov (United States)

    Muñoz-Escobar, Juliana; Kozlov, Guennadi; Gehring, Kalle

    2017-10-01

    The UBR-box is a 70-residue zinc finger domain present in the UBR family of E3 ubiquitin ligases that directly binds N-terminal degradation signals in substrate proteins. UBR6, also called FBXO11, is an UBR-box containing E3 ubiquitin ligase that does not bind N-terminal signals. Here, we present the crystal structure of the UBR-box domain from human UBR6. The dimeric crystal structure reveals a unique form of domain swapping mediated by zinc coordination, where three independent protein chains come together to regenerate the topology of the monomeric UBR-box fold. Analysis of the structure suggests that the absence of N-terminal residue binding arises from the lack of an amino acid binding pocket. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  3. Characterization of a Fasciola gigantica protein carrying two DM9 domains reveals cellular relocalization property.

    Science.gov (United States)

    Phadungsil, Wansika; Smooker, Peter M; Vichasri-Grams, Suksiri; Grams, Rudi

    2016-01-01

    Even at the present age of whole-organism analysis, e.g., genomics, transcriptomics, and proteomics, the biological roles of many proteins remain unresolved. Classified among the proteins of unknown function is a family of proteins harboring repeats of the DM9 domain, a 60-75 amino acids motif first described in a small number of Drosophila melanogaster proteins. Proteins may carry two or more DM9 domains either in combination with other domains or as their sole constituent. Here we have characterized a 16.8 kDa Fasciola gigantica protein comprising two tandem repeated DM9 domains (FgDM9-1). The protein was located in the parenchyma of the immature and mature parasite and consequently it was not detected in the ES product of the parasite but only in the whole worm extract. Interestingly, extraction with SDS yielded a substantially higher amount of the protein suggesting association with insoluble cell components. In Sf9 insect cells a heterologously expressed EGFP-FgDM9-1 chimera showed cell-wide distribution but relocated to vesicle-like structures in the cytoplasm after stimulating cellular stress by bacteria, heat shock or chloroquine. These structures did not colocalize with the markers of endocytosis/phagocytosis ubiquitin, RAB7, GABARAP. The same behavior was noted for Aedes aegypti PRS1, a homologous mosquito DM9 protein as a positive control while EGFP did not exhibit such relocation in the insect cells. Cross-linking experiments on soluble recombinant FgDM9-1 indicated that the protein can undergo specific oligomerization. It is speculated that proteins carrying the DM9 domain have a role in vesicular transport in flatworms and insects. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Estrogen receptor alpha regulates expression of the breast cancer 1 associated ring domain 1 (BARD1) gene through intronic DNA sequence.

    Science.gov (United States)

    Creekmore, Amy L; Ziegler, Yvonne S; Bonéy, Jamie L; Nardulli, Ann M

    2007-03-15

    We have used a chromatin immunoprecipitation (ChIP)-based cloning strategy to isolate and identify genes associated with estrogen receptor alpha (ERalpha) in MCF-7 human breast cancer cells. One of the gene regions isolated was a 288bp fragment from the ninth intron of the breast cancer 1 associated ring domain (BARD1) gene. We demonstrated that ERalpha associated with this region of the endogenous BARD 1 gene in MCF-7 cells, that ERalpha bound to three of five ERE half sites located in the 288bp BARD1 region, and that this 288bp BARD1 region conferred estrogen responsiveness to a heterologous promoter. Importantly, treatment of MCF-7 cells with estrogen increased BARD1 mRNA and protein levels. These findings demonstrate that ChIP cloning strategies can be utilized to successfully isolate regulatory regions that are far removed from the transcription start site and assist in identifying cis elements involved in conferring estrogen responsiveness.

  5. NMR spectroscopic and bioinformatic analyses of the LTBP1 C-terminus reveal a highly dynamic domain organisation.

    Directory of Open Access Journals (Sweden)

    Ian B Robertson

    Full Text Available Proteins from the LTBP/fibrillin family perform key structural and functional roles in connective tissues. LTBP1 forms the large latent complex with TGFβ and its propeptide LAP, and sequesters the latent growth factor to the extracellular matrix. Bioinformatics studies suggest the main structural features of the LTBP1 C-terminus are conserved through evolution. NMR studies were carried out on three overlapping C-terminal fragments of LTBP1, comprising four domains with characterised homologues, cbEGF14, TB3, EGF3 and cbEGF15, and three regions with no homology to known structures. The NMR data reveal that the four domains adopt canonical folds, but largely lack the interdomain interactions observed with homologous fibrillin domains; the exception is the EGF3-cbEGF15 domain pair which has a well-defined interdomain interface. (15N relaxation studies further demonstrate that the three interdomain regions act as flexible linkers, allowing a wide range of motion between the well-structured domains. This work is consistent with the LTBP1 C-terminus adopting a flexible "knotted rope" structure, which may facilitate cell matrix interactions, and the accessibility to proteases or other factors that could contribute to TGFβ activation.

  6. Complex structure of the fission yeast SREBP-SCAP binding domains reveals an oligomeric organization.

    Science.gov (United States)

    Gong, Xin; Qian, Hongwu; Shao, Wei; Li, Jingxian; Wu, Jianping; Liu, Jun-Jie; Li, Wenqi; Wang, Hong-Wei; Espenshade, Peter; Yan, Nieng

    2016-11-01

    Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. SREBP C-terminus binds to the WD40 domain of SREBP cleavage-activating protein (SCAP), which confers sterol regulation by controlling the ER-to-Golgi transport of the SREBP-SCAP complex and access to the activating proteases in the Golgi. Here, we biochemically and structurally show that the carboxyl terminal domains (CTD) of Sre1 and Scp1, the fission yeast SREBP and SCAP, form a functional 4:4 oligomer and Sre1-CTD forms a dimer of dimers. The crystal structure of Sre1-CTD at 3.5 Å and cryo-EM structure of the complex at 5.4 Å together with in vitro biochemical evidence elucidate three distinct regions in Sre1-CTD required for Scp1 binding, Sre1-CTD dimerization and tetrameric formation. Finally, these structurally identified domains are validated in a cellular context, demonstrating that the proper 4:4 oligomeric complex formation is required for Sre1 activation.

  7. The structure of a conserved piezo channel domain reveals a topologically distinct β sandwich fold.

    Science.gov (United States)

    Kamajaya, Aron; Kaiser, Jens T; Lee, Jonas; Reid, Michelle; Rees, Douglas C

    2014-10-07

    Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2,000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a topologically distinct β sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in dehydrated hereditary stomatocytosis patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be-identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Internal Domains of Natural Porous Media Revealed: Critical Locations for Transport, Storage, and Chemical Reaction

    Energy Technology Data Exchange (ETDEWEB)

    Zachara, John M.; Brantley, Susan L.; Chorover, Jon D.; Ewing, Robert P.; Kerisit, Sebastien N.; Liu, Chongxuan; Perfect, E.; Rother, Gernot; Stack, Andrew G.

    2016-03-16

    Internal pore domains exist within rocks, lithic fragments, subsurface sediments and soil aggregates. These domains, which we term internal domains in porous media (IDPM), contain a significant fraction of their porosity as nanopores, dominate the reactive surface area of diverse porous media types, and are important locations for chemical reactivity and hydrocarbon storage. Traditionally difficult to interrogate, advances in instrumentation and imaging methods are providing new insights on the physical structures and chemical attributes of IDPM. In this review we: discuss analytical methods to characterize IDPM, evaluate what has been learned about their size distributions, connectivity, and extended structures; determine whether they exhibit unique chemical reactivity; and assess potential for their inclusion in reactive transport models. Three key findings are noteworthy. 1) A combination of methods now allows complete characterization of the porosity spectrum of natural materials and its connectivity; while imaging microscopies are providing three dimensional representations of the interconnected pore network. 2) Chemical reactivity in pores <10 nm is expected to be different from micro and macropores, yet research performed to date is inconclusive on the nature, direction, and magnitude of effect. 3) Existing continuum reactive transport models treat IDPM as a sub-grid feature with average, empirical, scale-dependent parameters; and are not formulated to include detailed information on pore networks. Overall we find that IDPM are key features controlling hydrocarbon release from shales in hydrofracking systems, organic matter stabilization and recalcitrance in soil, weathering and soil formation, and long term inorganic and organic contaminant behavior in the vadose zone and groundwater. We conclude with an assessment of impactful research opportunities to advance understanding of IDPM, and to incorporate their important effects in reactive transport models

  9. The DNA translocase RAD5A acts independently of the other main DNA repair pathways, and requires both its ATPase and RING domain for activity in Arabidopsis thaliana.

    Science.gov (United States)

    Klemm, Tobias; Mannuß, Anja; Kobbe, Daniela; Knoll, Alexander; Trapp, Oliver; Dorn, Annika; Puchta, Holger

    2017-08-01

    Multiple pathways exist to repair DNA damage induced by methylating and crosslinking agents in Arabidopsis thaliana. The SWI2/SNF2 translocase RAD5A, the functional homolog of budding yeast Rad5 that is required for the error-free branch of post-replicative repair, plays a surprisingly prominent role in the repair of both kinds of lesions in Arabidopsis. Here we show that both the ATPase domain and the ubiquitination function of the RING domain of the Arabidopsis protein are essential for the cellular response to different forms of DNA damage. To define the exact role of RAD5A within the complex network of DNA repair pathways, we crossed the rad5a mutant line with mutants of different known repair factors of Arabidopsis. We had previously shown that RAD5A acts independently of two main pathways of replication-associated DNA repair defined by the helicase RECQ4A and the endonuclease MUS81. The enhanced sensitivity of all double mutants tested in this study indicates that the repair of damaged DNA by RAD5A also occurs independently of nucleotide excision repair (AtRAD1), single-strand break repair (AtPARP1), as well as microhomology-mediated double-strand break repair (AtTEB). Moreover, RAD5A can partially complement for a deficient AtATM-mediated DNA damage response in plants, as the double mutant shows phenotypic growth defects. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  10. Relativistic, QED and nuclear effects in highly charged ions revealed by resonant electron-ion recombination in storage rings

    OpenAIRE

    Schippers, Stefan

    2008-01-01

    Dielectronic recombination (DR) of few-electron ions has evolved into a sensitive spectroscopic tool for highly charged ions. This is due to technological advances in electron-beam preparation and ion-beam cooling techniques at heavy-ion storage rings. Recent experiments prove unambiguously that DR collision spectroscopy has become sensitive to 2nd order QED and to nuclear effects. This review discusses the most recent developments in high-resolution spectroscopy of low-energy DR resonances, ...

  11. Function of the ATR N-terminal domain revealed by an ATM/ATR chimera

    International Nuclear Information System (INIS)

    Chen Xinping; Zhao Runxiang; Glick, Gloria G.; Cortez, David

    2007-01-01

    The ATM and ATR kinases function at the apex of checkpoint signaling pathways. These kinases share significant sequence similarity, phosphorylate many of the same substrates, and have overlapping roles in initiating cell cycle checkpoints. However, they sense DNA damage through distinct mechanisms. ATR primarily senses single stranded DNA (ssDNA) through its interaction with ATRIP, and ATM senses double strand breaks through its interaction with Nbs1. We determined that the N-terminus of ATR contains a domain that binds ATRIP. Attaching this domain to ATM allowed the fusion protein (ATM*) to bind ATRIP and associate with RPA-coated ssDNA. ATM* also gained the ability to localize efficiently to stalled replication forks as well as double strand breaks. Despite having normal kinase activity when tested in vitro and being phosphorylated on S1981 in vivo, ATM* is defective in checkpoint signaling and does not complement cellular deficiencies in either ATM or ATR. These data indicate that the N-terminus of ATR is sufficient to bind ATRIP and to promote localization to sites of replication stress

  12. Apple ring rot-responsive putative microRNAs revealed by high-throughput sequencing in Malus × domestica Borkh.

    Science.gov (United States)

    Yu, Xin-Yi; Du, Bei-Bei; Gao, Zhi-Hong; Zhang, Shi-Jie; Tu, Xu-Tong; Chen, Xiao-Yun; Zhang, Zhen; Qu, Shen-Chun

    2014-08-01

    MicroRNAs (miRNAs) are small non-coding RNAs, which silence target mRNA via cleavage or translational inhibition to function in regulating gene expression. MiRNAs act as important regulators of plant development and stress response. For understanding the role of miRNAs responsive to apple ring rot stress, we identified disease-responsive miRNAs using high-throughput sequencing in Malus × domestica Borkh.. Four small RNA libraries were constructed from two control strains in M. domestica, crabapple (CKHu) and Fuji Naga-fu No. 6 (CKFu), and two disease stress strains, crabapple (DSHu) and Fuji Naga-fu No. 6 (DSFu). A total of 59 miRNA families were identified and five miRNAs might be responsive to apple ring rot infection and validated via qRT-PCR. Furthermore, we predicted 76 target genes which were regulated by conserved miRNAs potentially. Our study demonstrated that miRNAs was responsive to apple ring rot infection and may have important implications on apple disease resistance.

  13. HYPERAUTOFLUORESCENT RING IN AUTOIMMUNE RETINOPATHY

    Science.gov (United States)

    LIMA, LUIZ H.; GREENBERG, JONATHAN P.; GREENSTEIN, VIVIENNE C.; SMITH, R. THEODORE; SALLUM, JULIANA M. F.; THIRKILL, CHARLES; YANNUZZI, LAWRENCE A.; TSANG, STEPHEN H.

    2015-01-01

    Purpose To report the presence of a hyperautofluorescent ring and corresponding spectral-domain optical coherence tomography (SD-OCT) features seen in patients with autoimmune retinopathy. Methods All eyes were evaluated by funduscopic examination, full-fleld electroretinography, fundus autofluorescence, and SD-OCT. Further confirmation of the diagnosis was obtained with immunoblot and immunohistochemistry testing of the patient’s serum. Humphrey visual fields and microperimetry were also performed. Results Funduscopic examination showed atrophic retinal pigment epithelium (RPE) associated with retinal artery narrowing but without pigment deposits. The scotopic and photopic full-field electroretinograms were nondetectable in three patients and showed a cone–rod pattern of dysfunction in one patient. Fundus autofluorescence revealed a hyperautofluorescent ring in the parafoveal region, and the corresponding SD-OCT demonstrated loss of the photoreceptor inner segment–outer segment junction with thinning of the outer nuclear layer from the region of the hyperautofluorescent ring toward the retinal periphery. The retinal layers were generally intact within the hyperautofluorescent ring, although the inner segment–outer segment junction was disrupted, and the outer nuclear layer and photoreceptor outer segment layer were thinned. Conclusion This case series revealed the structure of the hyperautofluorescent ring in autoimmune retinopathy using SD-OCT. Fundus autofluorescence and SD-OCT may aid in the diagnosis of autoimmune retinopathy and may serve as a tool to monitor its progression. PMID:22218149

  14. RING finger and WD repeat domain 3 (RFWD3) associates with replication protein A (RPA) and facilitates RPA-mediated DNA damage response.

    Science.gov (United States)

    Liu, Shangfeng; Chu, Jessica; Yucer, Nur; Leng, Mei; Wang, Shih-Ya; Chen, Benjamin P C; Hittelman, Walter N; Wang, Yi

    2011-06-24

    DNA damage response is crucial for maintaining genomic integrity and preventing cancer by coordinating the activation of checkpoints and the repair of damaged DNA. Central to DNA damage response are the two checkpoint kinases ATM and ATR that phosphorylate a wide range of substrates. RING finger and WD repeat domain 3 (RFWD3) was initially identified as a substrate of ATM/ATR from a proteomic screen. Subsequent studies showed that RFWD3 is an E3 ubiquitin ligase that ubiquitinates p53 in vitro and positively regulates p53 levels in response to DNA damage. We report here that RFWD3 associates with replication protein A (RPA), a single-stranded DNA-binding protein that plays essential roles in DNA replication, recombination, and repair. Binding of RPA to single-stranded DNA (ssDNA), which is generated by DNA damage and repair, is essential for the recruitment of DNA repair factors to damaged sites and the activation of checkpoint signaling. We show that RFWD3 is physically associated with RPA and rapidly localizes to sites of DNA damage in a RPA-dependent manner. In vitro experiments suggest that the C terminus of RFWD3, which encompass the coiled-coil domain and the WD40 domain, is necessary for binding to RPA. Furthermore, DNA damage-induced phosphorylation of RPA and RFWD3 is dependent upon each other. Consequently, loss of RFWD3 results in the persistent foci of DNA damage marker γH2AX and the repair protein Rad51 in damaged cells. These findings suggest that RFWD3 is recruited to sites of DNA damage and facilitates RPA-mediated DNA damage signaling and repair.

  15. Edge morphology evolution of graphene domains during chemical vapor deposition cooling revealed through hydrogen etching.

    Science.gov (United States)

    Zhang, Haoran; Zhang, Yanhui; Zhang, Yaqian; Chen, Zhiying; Sui, Yanping; Ge, Xiaoming; Yu, Guanghui; Jin, Zhi; Liu, Xinyu

    2016-02-21

    During cooling, considerable changes such as wrinkle formation and edge passivation occur in graphene synthesized on the Cu substrate. Wrinkle formation is caused by the difference in the thermal expansion coefficients of graphene and its substrate. This work emphasizes the cooling-induced edge passivation. The graphene-edge passivation can limit the regrowth of graphene at the domain edge. Our work shows that silicon-containing particles tend to accumulate at the graphene edge, and the formation of these particles is related to cooling. Furthermore, a clear curvature can be observed at the graphene edge on the Cu substrate, indicating the sinking of the graphene edge into the Cu substrate. Both the sinking of the graphene edge and the accumulation of silicon-containing particles are responsible for edge passivation. In addition, two kinds of graphene edge morphologies are observed after etching, which were explained by different etching mechanisms that illustrate the changes of the graphene edge during cooling.

  16. Image-Based Modeling Reveals Dynamic Redistribution of DNA Damageinto Nuclear Sub-Domains

    Energy Technology Data Exchange (ETDEWEB)

    Costes Sylvain V., Ponomarev Artem, Chen James L.; Nguyen, David; Cucinotta, Francis A.; Barcellos-Hoff, Mary Helen

    2007-08-03

    Several proteins involved in the response to DNA doublestrand breaks (DSB) f orm microscopically visible nuclear domains, orfoci, after exposure to ionizing radiation. Radiation-induced foci (RIF)are believed to be located where DNA damage occurs. To test thisassumption, we analyzed the spatial distribution of 53BP1, phosphorylatedATM, and gammaH2AX RIF in cells irradiated with high linear energytransfer (LET) radiation and low LET. Since energy is randomly depositedalong high-LET particle paths, RIF along these paths should also berandomly distributed. The probability to induce DSB can be derived fromDNA fragment data measured experimentally by pulsed-field gelelectrophoresis. We used this probability in Monte Carlo simulations topredict DSB locations in synthetic nuclei geometrically described by acomplete set of human chromosomes, taking into account microscope opticsfrom real experiments. As expected, simulations produced DNA-weightedrandom (Poisson) distributions. In contrast, the distributions of RIFobtained as early as 5 min after exposure to high LET (1 GeV/amu Fe) werenon-random. This deviation from the expected DNA-weighted random patterncan be further characterized by "relative DNA image measurements." Thisnovel imaging approach shows that RIF were located preferentially at theinterface between high and low DNA density regions, and were morefrequent than predicted in regions with lower DNA density. The samepreferential nuclear location was also measured for RIF induced by 1 Gyof low-LET radiation. This deviation from random behavior was evidentonly 5 min after irradiation for phosphorylated ATM RIF, while gammaH2AXand 53BP1 RIF showed pronounced deviations up to 30 min after exposure.These data suggest that DNA damage induced foci are restricted to certainregions of the nucleus of human epithelial cells. It is possible that DNAlesions are collected in these nuclear sub-domains for more efficientrepair.

  17. Structure of the cold-shock domain protein from Neisseria meningitidis reveals a strand-exchanged dimer

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Jingshan [The Oxford Protein Production Facility, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Nettleship, Joanne E.; Sainsbury, Sarah [The Oxford Protein Production Facility, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Saunders, Nigel J. [Bacterial Pathogenesis and Functional Genomics Group, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE (United Kingdom); Owens, Raymond J., E-mail: ray@strubi.ox.ac.uk [The Oxford Protein Production Facility, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom)

    2008-04-01

    The X-ray crystal structure of the cold-shock domain protein from N. meningitidis reveals a strand-exchanged dimer. The structure of the cold-shock domain protein from Neisseria meningitidis has been solved to 2.6 Å resolution and shown to comprise a dimer formed by the exchange of two β-strands between protein monomers. The overall fold of the monomer closely resembles those of other bacterial cold-shock proteins. The neisserial protein behaved as a monomer in solution and was shown to bind to a hexathymidine oligonucleotide with a stoichiometry of 1:1 and a K{sub d} of 1.25 µM.

  18. Characterization of Zebrafish von Willebrand Factor Reveals Conservation of Domain Structure, Multimerization, and Intracellular Storage

    Directory of Open Access Journals (Sweden)

    Arunima Ghosh

    2012-01-01

    Full Text Available von Willebrand disease (VWD is the most common inherited human bleeding disorder and is caused by quantitative or qualitative defects in von Willebrand factor (VWF. VWF is a secreted glycoprotein that circulates as large multimers. While reduced VWF is associated with bleeding, elevations in overall level or multimer size are implicated in thrombosis. The zebrafish is a powerful genetic model in which the hemostatic system is well conserved with mammals. The ability of this organism to generate thousands of offspring and its optical transparency make it unique and complementary to mammalian models of hemostasis. Previously, partial clones of zebrafish vwf have been identified, and some functional conservation has been demonstrated. In this paper we clone the complete zebrafish vwf cDNA and show that there is conservation of domain structure. Recombinant zebrafish Vwf forms large multimers and pseudo-Weibel-Palade bodies (WPBs in cell culture. Larval expression is in the pharyngeal arches, yolk sac, and intestinal epithelium. These results provide a foundation for continued study of zebrafish Vwf that may further our understanding of the mechanisms of VWD.

  19. A synthetic prestin reveals protein domains and molecular operation of outer hair cell piezoelectricity.

    Science.gov (United States)

    Schaechinger, Thorsten J; Gorbunov, Dmitry; Halaszovich, Christian R; Moser, Tobias; Kügler, Sebastian; Fakler, Bernd; Oliver, Dominik

    2011-06-24

    Prestin, a transporter-like protein of the SLC26A family, acts as a piezoelectric transducer that mediates the fast electromotility of outer hair cells required for cochlear amplification and auditory acuity in mammals. Non-mammalian prestin orthologues are anion transporters without piezoelectric activity. Here, we generated synthetic prestin (SynPres), a chimera of mammalian and non-mammalian prestin exhibiting both, piezoelectric properties and anion transport. SynPres delineates two distinct domains in the protein's transmembrane core that are necessary and sufficient for generating electromotility and associated non-linear charge movement (NLC). Functional analysis of SynPres showed that the amplitude of NLC and hence electromotility are determined by the transport of monovalent anions. Thus, prestin-mediated electromotility is a dual-step process: transport of anions by an alternate access cycle, followed by an anion-dependent transition generating electromotility. The findings define structural and functional determinants of prestin's piezoelectric activity and indicate that the electromechanical process evolved from the ancestral transport mechanism.

  20. The Structure of a Conserved Domain of TamB Reveals a Hydrophobic β Taco Fold.

    Science.gov (United States)

    Josts, Inokentijs; Stubenrauch, Christopher James; Vadlamani, Grishma; Mosbahi, Khedidja; Walker, Daniel; Lithgow, Trevor; Grinter, Rhys

    2017-12-05

    The translocation and assembly module (TAM) plays a role in the transport and insertion of proteins into the bacterial outer membrane. TamB, a component of this system spans the periplasmic space to engage with its partner protein TamA. Despite efforts to characterize the TAM, the structure and mechanism of action of TamB remained enigmatic. Here we present the crystal structure of TamB amino acids 963-1,138. This region represents half of the conserved DUF490 domain, the defining feature of TamB. TamB 963-1138 consists of a concave, taco-shaped β sheet with a hydrophobic interior. This β taco structure is of dimensions capable of accommodating and shielding the hydrophobic side of an amphipathic β strand, potentially allowing TamB to chaperone nascent membrane proteins from the aqueous environment. In addition, sequence analysis suggests that the structure of TamB 963-1138 is shared by a large portion of TamB. This architecture could allow TamB to act as a conduit for membrane proteins. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  1. Ring Theory

    CERN Document Server

    Jara, Pascual; Torrecillas, Blas

    1988-01-01

    The papers in this proceedings volume are selected research papers in different areas of ring theory, including graded rings, differential operator rings, K-theory of noetherian rings, torsion theory, regular rings, cohomology of algebras, local cohomology of noncommutative rings. The book will be important for mathematicians active in research in ring theory.

  2. Probing adenine rings and backbone linkages using base specific isotope-edited Raman spectroscopy: application to group II intron ribozyme domain V.

    Science.gov (United States)

    Chen, Yuanyuan; Eldho, Nadukkudy V; Dayie, T Kwaku; Carey, Paul R

    2010-04-27

    Raman difference spectroscopy is used to probe the properties of a 36-nt RNA molecule, "D5", which lies at the heart of the catalytic apparatus in group II introns. For D5 that has all of its adenine residues labeled with (13)C and (15)N and utilizing Raman difference spectroscopy, we identify the conformationally sensitive -C-O-P-O-C- stretching modes of the unlabeled bonds adjacent to adenine bases, as well as the adenine ring modes themselves. The phosphodiester modes can be assigned to individual adenine residues based on earlier NMR data. The effect of Mg(2+) binding was explored by analyzing the Raman difference spectra for [D5 + Mg(2+)] minus [D5 no Mg(2+)], for D5 unlabeled, or D5 labeled with (13)C/(15)N-enriched adenine. In both sets of data we assign differential features to G ring modes perturbed by Mg(2+) binding at the N7 position. In the A-labeled spectra we attribute a Raman differential near 1450 cm(-1) and changes of intensity at 1296 cm(-1) to Mg binding at the N7 position of adenine bases. The A and G bases involved in Mg(2+) binding again can be identified using earlier NMR results. For the unlabeled D5, a change in the C-O-P-O-C stretch profile at 811 cm(-1) upon magnesium binding is due to a "tightening up" (in the sense of a more rigid molecule with less dynamic interchange among competing ribose conformers) of the D5 structure. For adenine-labeled D5, small changes in the adenine backbone bond signatures in the 810-830 cm(-1) region suggest that small conformational changes occur in the tetraloop and bulge regions upon binding of Mg(2+). The PO(2)(-) stretching vibration, near 1100 cm(-1), from the nonbridging phosphate groups, probes the effect of Mg(2+)-hydrate inner-sphere interactions that cause an upshift. In turn, the upshift is modulated by the presence of monovalent cations since in the presence of Na(+) and Li(+) the upshift is 23 +/- 2 cm(-1) while in the presence of K(+) and Cs(+) it is 13 +/- 3 cm(-1), a finding that correlates

  3. The crystal structure of the Dachshund domain of human SnoN reveals flexibility in the putative protein interaction surface.

    Directory of Open Access Journals (Sweden)

    Tomas Nyman

    2010-09-01

    Full Text Available The human SnoN is an oncoprotein that interacts with several transcription-regulatory proteins such as the histone-deacetylase, N-CoR containing co-repressor complex and Smad proteins. This study presents the crystal structure of the Dachshund homology domain of human SnoN. The structure reveals a groove composed of conserved residues with characteristic properties of a protein-interaction surface. A comparison of the 12 monomers in the asymmetric unit reveals the presence of two major conformations: an open conformation with a well accessible groove and a tight conformation with a less accessible groove. The variability in the backbone between the open and the tight conformations matches the differences seen in previously determined structures of individual Dachshund homology domains, suggesting a general plasticity within this fold family. The flexibility observed in the putative protein binding groove may enable SnoN to recognize multiple interaction partners.This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

  4. Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3'-5' exonuclease activity.

    Science.gov (United States)

    Nakane, Shuhei; Nakagawa, Noriko; Kuramitsu, Seiki; Masui, Ryoji

    2009-04-01

    The X-family DNA polymerases (PolXs) comprise a highly conserved DNA polymerase family found in all kingdoms. Mammalian PolXs are known to be involved in several DNA-processing pathways including repair, but the cellular functions of bacterial PolXs are less known. Many bacterial PolXs have a polymerase and histidinol phosphatase (PHP) domain at their C-termini in addition to a PolX core (POLXc) domain, and possess 3'-5' exonuclease activity. Although both domains are highly conserved in bacteria, their molecular functions, especially for a PHP domain, are unknown. We found Thermus thermophilus HB8 PolX (ttPolX) has Mg(2+)/Mn(2+)-dependent DNA/RNA polymerase, Mn(2+)-dependent 3'-5' exonuclease and DNA-binding activities. We identified the domains of ttPolX by limited proteolysis and characterized their biochemical activities. The POLXc domain was responsible for the polymerase and DNA-binding activities but exonuclease activity was not detected for either domain. However, the POLXc and PHP domains interacted with each other and a mixture of the two domains had Mn(2+)-dependent 3'-5' exonuclease activity. Moreover, site-directed mutagenesis revealed catalytically important residues in the PHP domain for the 3'-5' exonuclease activity. Our findings provide a molecular insight into the functional domain organization of bacterial PolXs, especially the requirement of the PHP domain for 3'-5' exonuclease activity.

  5. Synchronous multi-decadal climate variability of the whole Pacific areas revealed in tree rings since 1567

    Science.gov (United States)

    Fang, Keyan; Cook, Edward; Guo, Zhengtang; Chen, Deliang; Ou, Tinghai; Zhao, Yan

    2018-02-01

    Oceanic and atmospheric patterns play a crucial role in modulating climate variability from interannual to multi-decadal timescales by causing large-scale co-varying climate changes. The brevity of the existing instrumental records hinders the ability to recognize climate patterns before the industrial era, which can be alleviated using proxies. Unfortunately, proxy based reconstructions of oceanic and atmospheric modes of the past millennia often have modest agreements with each other before the instrumental period, raising questions about the robustness of the reconstructions. To ensure the stability of climate signals in proxy data through time, we first identified tree-ring datasets from distant regions containing coherent variations in Asia and North America, and then interpreted their climate information. We found that the multi-decadal covarying climate patterns of the middle and high latitudinal regions around the northern Pacific Ocean agreed quite well with the climate reconstructions of the tropical and southern Pacific areas. This indicates a synchronous variability at the multi-decadal timescale of the past 430 years for the entire Pacific Ocean. This pattern is closely linked to the dominant mode of the Pacific sea surface temperature (SST) after removing the warming trend. This Pacific multi-decadal SST variability resembles the Interdecadal Pacific Oscillation.

  6. STRUCTURAL ASSESSMENT OF HYPERAUTOFLUORESCENT RING IN PATIENTS WITH RETINITIS PIGMENTOSA

    Science.gov (United States)

    LIMA, LUIZ H.; CELLA, WENER; GREENSTEIN, VIVIENNE C.; WANG, NAN-KAI; BUSUIOC, MIHAI; THEODORE SMITH, R.; YANNUZZI, LAWRENCE A.; TSANG, STEPHEN H.

    2009-01-01

    Purpose To analyze the retinal structure underlying the hyperautofluorescent ring visible on fundus autofluorescence in patients with retinitis pigmentosa. Methods Twenty-four eyes of 13 patients with retinitis pigmentosa, aged 13 years to 67 years, were studied. The integrity of the photoreceptor cilia, also known as the inner/outer segment junction of the photoreceptors, the outer nuclear layer, and retinal pigment epithelium, was evaluated outside, across, and inside the ring with spectral-domain optical coherence tomography (OCT). Results Inside the foveal area, fundus autofluorescence did not detect abnormalities. Outside the ring, fundus autofluorescence revealed hypoautofluorescence compatible with the photoreceptor/retinal pigment epithelium degeneration. Spectral-domain OCT inside the ring, in the area of normal foveal fundus autofluorescence, revealed an intact retinal structure in all eyes and total retinal thickness values that were within normal limits. Across the ring, inner/outer segment junction disruption was observed and the outer nuclear layer was decreased in thickness in a centrifugal direction in all eyes. Outside the hyperautofluorescent ring, the inner/outer segment junction and the outer nuclear layer appeared to be absent and there were signs of retinal pigment epithelium degeneration. Conclusion Disruption of the inner/outer segment junction and a decrease in outer retinal thickness were found across the central hyperautofluorescent ring seen in retinitis pigmentosa. Outer segment phagocytosis by retinal pigment epithelium is necessary for the formation of an hyperautofluorescent ring. PMID:19584660

  7. Magnetic domain structures and stray fields of individual elongated magnetite grains revealed by magnetic force microscopy (MFM)

    DEFF Research Database (Denmark)

    Frandsen, Cathrine; Stipp, S. L. S.; McEnroe, S. A.

    2004-01-01

    ), the internal domain structure was determined for individual grains. In general, the lamellae were pseudo-single-domain grains with open-flux domain magnetisations parallel to their long axes. The domain sizes were, in cross-section, on the order of a micrometer for the longer lamellae and about 300 nm...

  8. The structure of the nucleoprotein binding domain of lyssavirus phosphoprotein reveals a structural relationship between the N-RNA binding domains of Rhabdoviridae and Paramyxoviridae.

    Science.gov (United States)

    Delmas, Olivier; Assenberg, Rene; Grimes, Jonathan M; Bourhy, Hervé

    2010-01-01

    The phosphoprotein P of non-segmented negative-sense RNA viruses is an essential component of the replication and transcription complex and acts as a co-factor for the viral RNA-dependent RNA polymerase. P recruits the viral polymerase to the nucleoprotein-bound viral RNA (N-RNA) via an interaction between its C-terminal domain and the N-RNA complex. We have obtained the structure of the C-terminal domain of P of Mokola virus (MOKV), a lyssavirus that belongs to the Rhabdoviridae family and mapped at the amino acid level the crucial positions involved in interaction with N and in the formation of the viral replication complex. Comparison of the N-RNA binding domains of P solved to date suggests that the N-RNA binding domains are structurally conserved among paramyxoviruses and rhabdoviruses in spite of low sequence conservation. We also review the numerous other functions of this domain and more generally of the phosphoprotein.

  9. Greenhouse Gas Dynamics in a Salt-Wedge Estuary Revealed by High Resolution Cavity Ring-Down Spectroscopy Observations.

    Science.gov (United States)

    Tait, Douglas R; Maher, Damien T; Wong, WeiWen; Santos, Isaac R; Sadat-Noori, Mahmood; Holloway, Ceylena; Cook, Perran L M

    2017-12-05

    Estuaries are an important source of greenhouse gases to the atmosphere, but uncertainties remain in the flux rates and production pathways of greenhouse gases in these dynamic systems. This study performs simultaneous high resolution measurements of the three major greenhouse gases (carbon dioxide, methane, and nitrous oxide) as well as carbon stable isotope ratios of carbon dioxide and methane, above and below the pycnocline along a salt wedge estuary (Yarra River estuary, Australia). We identified distinct zones of elevated greenhouse gas concentrations. At the tip of salt wedge, average CO 2 and N 2 O concentrations were approximately five and three times higher than in the saline mouth of the estuary. In anaerobic bottom waters, the natural tracer radon ( 222 Rn) revealed that porewater exchange was the likely source of the highest methane concentrations (up to 1302 nM). Isotopic analysis of CH 4 showed a dominance of acetoclastic production in fresh surface waters and hydrogenotrophic production occurring in the saline bottom waters. The atmospheric flux of methane (in CO 2 equivalent units) was a major (35-53%) contributor of atmospheric radiative forcing from the estuary, while N 2 O contributed <2%. We hypothesize that the release of bottom water gases when stratification episodically breaks down will release large pulses of greenhouse gases to the atmosphere.

  10. Crystal structure of Src-like adaptor protein 2 reveals close association of SH3 and SH2 domains through β-sheet formation.

    Science.gov (United States)

    Wybenga-Groot, Leanne E; McGlade, C Jane

    2013-12-01

    The Src-like adaptor proteins (SLAP/SLAP2) are key components of Cbl-dependent downregulation of antigen receptor, cytokine receptor, and receptor tyrosine kinase signaling in hematopoietic cells. SLAP and SLAP2 consist of adjacent SH3 and SH2 domains that are most similar in sequence to Src family kinases (SFKs). Notably, the SH3-SH2 connector sequence is significantly shorter in SLAP/SLAP2 than in SFKs. To understand the structural implication of a short SH3-SH2 connector sequence, we solved the crystal structure of a protein encompassing the SH3 domain, SH3-SH2 connector, and SH2 domain of SLAP2 (SLAP2-32). While both domains adopt typical folds, the short SH3-SH2 connector places them in close association. Strand βe of the SH3 domain interacts with strand βA of the SH2 domain, resulting in the formation of a continuous β sheet that spans the length of the protein. Disruption of the SH3/SH2 interface through mutagenesis decreases SLAP-32 stability in vitro, consistent with inter-domain binding being an important component of SLAP2 structure and function. The canonical peptide binding pockets of the SH3 and SH2 domains are fully accessible, in contrast to other protein structures that display direct interaction between SH3 and SH2 domains, in which either peptide binding surface is obstructed by the interaction. Our results reveal potential sites of novel interaction for SH3 and SH2 domains, and illustrate the adaptability of SH2 and SH3 domains in mediating interactions. As well, our results suggest that the SH3 and SH2 domains of SLAP2 function interdependently, with implications on their mode of substrate binding. © 2013.

  11. The Structure of the Poxvirus A33 Protein Reveals a Dimer of Unique C-Type Lectin-Like Domains

    Energy Technology Data Exchange (ETDEWEB)

    Su, Hua-Poo; Singh, Kavita; Gittis, Apostolos G.; Garboczi, David N. (NIH)

    2010-11-03

    The current vaccine against smallpox is an infectious form of vaccinia virus that has significant side effects. Alternative vaccine approaches using recombinant viral proteins are being developed. A target of subunit vaccine strategies is the poxvirus protein A33, a conserved protein in the Chordopoxvirinae subfamily of Poxviridae that is expressed on the outer viral envelope. Here we have determined the structure of the A33 ectodomain of vaccinia virus. The structure revealed C-type lectin-like domains (CTLDs) that occur as dimers in A33 crystals with five different crystal lattices. Comparison of the A33 dimer models shows that the A33 monomers have a degree of flexibility in position within the dimer. Structural comparisons show that the A33 monomer is a close match to the Link module class of CTLDs but that the A33 dimer is most similar to the natural killer (NK)-cell receptor class of CTLDs. Structural data on Link modules and NK-cell receptor-ligand complexes suggest a surface of A33 that could interact with viral or host ligands. The dimer interface is well conserved in all known A33 sequences, indicating an important role for the A33 dimer. The structure indicates how previously described A33 mutations disrupt protein folding and locates the positions of N-linked glycosylations and the epitope of a protective antibody.

  12. Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2008-12-01

    Full Text Available Abstract Background Phosphorylation by protein kinases is a common event in many cellular processes. Further, many kinases perform specialized roles and are regulated by non-kinase domains tethered to kinase domain. Perturbation in the regulation of kinases leads to malignancy. We have identified and analysed putative protein kinases encoded in the genome of chimpanzee which is a close evolutionary relative of human. Result The shared core biology between chimpanzee and human is characterized by many orthologous protein kinases which are involved in conserved pathways. Domain architectures specific to chimp/human kinases have been observed. Chimp kinases with unique domain architectures are characterized by deletion of one or more non-kinase domains in the human kinases. Interestingly, counterparts of some of the multi-domain human kinases in chimp are characterized by identical domain architectures but with kinase-like non-kinase domain. Remarkably, out of 587 chimpanzee kinases no human orthologue with greater than 95% sequence identity could be identified for 160 kinases. Variations in chimpanzee kinases compared to human kinases are brought about also by differences in functions of domains tethered to the catalytic kinase domain. For example, the heterodimer forming PB1 domain related to the fold of ubiquitin/Ras-binding domain is seen uniquely tethered to PKC-like chimpanzee kinase. Conclusion Though the chimpanzee and human are evolutionary very close, there are chimpanzee kinases with no close counterpart in the human suggesting differences in their functions. This analysis provides a direction for experimental analysis of human and chimpanzee protein kinases in order to enhance our understanding on their specific biological roles.

  13. Black rings

    International Nuclear Information System (INIS)

    Emparan, Roberto; Reall, Harvey S

    2006-01-01

    A black ring is a five-dimensional black hole with an event horizon of topology S 1 x S 2 . We provide an introduction to the description of black rings in general relativity and string theory. Novel aspects of the presentation include a new approach to constructing black ring coordinates and a critical review of black ring microscopics. (topical review)

  14. Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain

    Energy Technology Data Exchange (ETDEWEB)

    Miller, D.J.; Ouellette, N.; Evodokimova, E.; Savchenko, A.; Edwards, A.; Anderson, W.F. (Toronto); (NWU)

    2010-03-08

    S-adenosyl-L-methionine-dependent methyltransferases (MTs) are abundant, and highly conserved across phylogeny. These enzymes use the cofactor AdoMet to methylate a wide variety of molecular targets, thereby modulating important cellular and metabolic activities. Thermotoga maritima protein 0872 (TM0872) belongs to a large sequence family of predicted MTs, ranging phylogenetically from relatively simple bacteria to humans. The genes for many of the bacterial homologs are located within operons involved in cell wall synthesis and cell division. Despite preliminary biochemical studies in E. coli and B. subtilis, the substrate specificity of this group of more than 150 proteins is unknown. As part of the Midwest Center for Structural Genomics initiative (www.mcsg.anl.gov), we have determined the structure of TM0872 in complexes with AdoMet and with S-adenosyl-L-homocysteine (AdoHcy). As predicted, TM0872 has a typical MT domain, and binds endogenous AdoMet, or co-crystallized AdoHcy, in a manner consistent with other known MT structures. In addition, TM0872 has a second domain that is novel among MTs in both its location in the sequence and its structure. The second domain likely acts in substrate recognition and binding, and there is a potential substrate-binding cleft spanning the two domains. This long and narrow cleft is lined with positively charged residues which are located opposite the S{sup +}-CH{sub 3} bond, suggesting that a negatively charged molecule might be targeted for catalysis. However, AdoMet and AdoHcy are both buried, and access to the methyl group would presumably require structural rearrangement. These TM0872 crystal structures offer the first structural glimpses at this phylogenetically conserved sequence family.

  15. Recognition of ERK MAP kinase by PEA-15 reveals a common docking site within the death domain and death effector domain

    OpenAIRE

    Hill, Justine M.; Vaidyanathan, Hema; Ramos, Joe W.; Ginsberg, Mark H.; Werner, Milton H.

    2002-01-01

    PEA-15 is a multifunctional protein that modulates signaling pathways which control cell proliferation and cell death. In particular, PEA-15 regulates the actions of the ERK MAP kinase cascade by binding to ERK and altering its subcellular localization. The three-dimensional structure of PEA-15 has been determined using NMR spectroscopy and its interaction with ERK defined by characterization of mutants that modulate ERK function. PEA-15 is composed of an N-terminal death effector domain (DED...

  16. Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain

    International Nuclear Information System (INIS)

    Parent, Kristin N.; Tang, Jinghua; Cardone, Giovanni; Gilcrease, Eddie B.; Janssen, Mandy E.; Olson, Norman H.; Casjens, Sherwood R.; Baker, Timothy S.

    2014-01-01

    CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the “HK97-fold” shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain (“I-domain”), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently. - Highlights: • Asymmetric and symmetric three-dimensional reconstructions of phage CUS-3 are presented. • CUS-3 major capsid protein has a conserved I-domain, which is found in all three categories of “P22-like phage”. • CUS-3 has very different tailspike receptor binding domain from those of P22 and Sf6. • The CUS-3 tailspike likely was acquired by horizontal gene transfer

  17. Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved Dynamic Interface

    Directory of Open Access Journals (Sweden)

    Justin W. Chartron

    2012-12-01

    Full Text Available In the cytoplasm, the correct delivery of membrane proteins is an essential and highly regulated process. The posttranslational targeting of the important tail-anchor membrane (TA proteins has recently been under intense investigation. A specialized pathway, called the guided entry of TA proteins (GET pathway in yeast and the transmembrane domain recognition complex (TRC pathway in vertebrates, recognizes endoplasmic-reticulum-targeted TA proteins and delivers them through a complex series of handoffs. An early step is the formation of a complex between Sgt2/SGTA, a cochaperone with a presumed ubiquitin-like-binding domain (UBD, and Get5/UBL4A, a ubiquitin-like domain (UBL-containing protein. We structurally characterize this UBD/UBL interaction for both yeast and human proteins. This characterization is supported by biophysical studies that demonstrate that complex formation is mediated by electrostatics, generating an interface that has high-affinity with rapid kinetics. In total, this work provides a refined model of the interplay of Sgt2 homologs in TA targeting.

  18. Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain

    Energy Technology Data Exchange (ETDEWEB)

    Parent, Kristin N., E-mail: kparent@msu.edu [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378 (United States); Tang, Jinghua; Cardone, Giovanni [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378 (United States); Gilcrease, Eddie B. [University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 84112 (United States); Janssen, Mandy E.; Olson, Norman H. [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378 (United States); Casjens, Sherwood R., E-mail: sherwood.casjens@path.utah.edu [University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 84112 (United States); Baker, Timothy S., E-mail: tsb@ucsd.edu [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378 (United States); University of California, San Diego, Division of Biological Sciences, La Jolla, CA, 92093 (United States)

    2014-09-15

    CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the “HK97-fold” shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain (“I-domain”), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently. - Highlights: • Asymmetric and symmetric three-dimensional reconstructions of phage CUS-3 are presented. • CUS-3 major capsid protein has a conserved I-domain, which is found in all three categories of “P22-like phage”. • CUS-3 has very different tailspike receptor binding domain from those of P22 and Sf6. • The CUS-3 tailspike likely was acquired by horizontal gene transfer.

  19. Revealing the Raft Domain Organization in the Plasma Membrane by Single-Molecule Imaging of Fluorescent Ganglioside Analogs.

    Science.gov (United States)

    Suzuki, Kenichi G N; Ando, Hiromune; Komura, Naoko; Konishi, Miku; Imamura, Akihiro; Ishida, Hideharu; Kiso, Makoto; Fujiwara, Takahiro K; Kusumi, Akihiro

    2018-01-01

    Gangliosides have been implicated in a variety of physiological processes, particularly in the formation and function of raft domains in the plasma membrane. However, the scarcity of suitable fluorescent ganglioside analogs had long prevented us from determining exactly how gangliosides perform their functions in the live-cell plasma membrane. With the development of new fluorescent ganglioside analogs, as described by Komura et al. (2017), this barrier has been broken. We can now address the dynamic behaviors of gangliosides in the live-cell plasma membrane, using fluorescence microscopy, particularly by single-fluorescent molecule imaging and tracking. Single-molecule tracking of fluorescent GM1 and GM3 revealed that these molecules are transiently and dynamically recruited to monomers (monomer-associated rafts) and homodimer rafts of the raftophilic GPI-anchored protein CD59 in quiescent cells, with exponential residency times of 12 and 40ms, respectively, in a manner dependent on raft-lipid interactions. Upon CD59 stimulation, which induces CD59-cluster signaling rafts, the fluorescent GM1 and GM3 analogs were recruited to the signaling rafts, with a lifetime of 48ms. These results represent the first direct evidence that GPI-anchored receptors and gangliosides interact in a cholesterol-dependent manner. Furthermore, they show that gangliosides continually move in and out of rafts that contain CD59 in an extremely dynamic manner, with much higher frequency than expected previously. Such studies would not have been possible without fluorescent ganglioside probes, which exhibit native-like behavior and single-molecule tracking. In this chapter, we review the methods for single-molecule tracking of fluorescent ganglioside analogs and the results obtained by applying these methods. © 2018 Elsevier Inc. All rights reserved.

  20. The Structures of Coiled-Coil Domains from Type III Secretion System Translocators Reveal Homology to Pore-Forming Toxins

    Energy Technology Data Exchange (ETDEWEB)

    Barta, Michael L.; Dickenson, Nicholas E.; Patil, Mrinalini; Keightley, Andrew; Wyckoff, Gerald J.; Picking, William D.; Picking, Wendy L.; Geisbrecht, Brian V. (UMKC); (OKLU)

    2012-03-26

    Many pathogenic Gram-negative bacteria utilize type III secretion systems (T3SSs) to alter the normal functions of target cells. Shigella flexneri uses its T3SS to invade human intestinal cells to cause bacillary dysentery (shigellosis) that is responsible for over one million deaths per year. The Shigella type III secretion apparatus is composed of a basal body spanning both bacterial membranes and an exposed oligomeric needle. Host altering effectors are secreted through this energized unidirectional conduit to promote bacterial invasion. The active needle tip complex of S. flexneri is composed of a tip protein, IpaD, and two pore-forming translocators, IpaB and IpaC. While the atomic structure of IpaD has been elucidated and studied, structural data on the hydrophobic translocators from the T3SS family remain elusive. We present here the crystal structures of a protease-stable fragment identified within the N-terminal regions of IpaB from S. flexneri and SipB from Salmonella enterica serovar Typhimurium determined at 2.1 {angstrom} and 2.8 {angstrom} limiting resolution, respectively. These newly identified domains are composed of extended-length (114 {angstrom} in IpaB and 71 {angstrom} in SipB) coiled-coil motifs that display a high degree of structural homology to one another despite the fact that they share only 21% sequence identity. Further structural comparisons also reveal substantial similarity to the coiled-coil regions of pore-forming proteins from other Gram-negative pathogens, notably, colicin Ia. This suggests that these mechanistically separate and functionally distinct membrane-targeting proteins may have diverged from a common ancestor during the course of pathogen-specific evolutionary events.

  1. Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center

    Directory of Open Access Journals (Sweden)

    Leybourne Matthew

    2006-12-01

    Full Text Available Abstract Background The protein encoded by the SA1388 gene from Staphylococcus aureus was chosen for structure determination to elucidate its domain organization and confirm our earlier remote homology based prediction that it housed a nitrogen regulatory PII protein-like domain. SA1388 was predicted to contain a central PII-like domain and two flanking regions, which together belong to the NIF3-like protein family. Proteins like SA1388 remain a poorly studied group and their structural characterization could guide future investigations aimed at understanding their function. Results The structure of SA1388 has been solved to 2.0Å resolution by single wavelength anomalous dispersion phasing method using selenium anomalous signals. It reveals a canonical NIF3-like fold containing two domains with a PII-like domain inserted in the middle of the polypeptide. The N and C terminal halves of the NIF3-like domains are involved in dimerization, while the PII domain forms trimeric contacts with symmetry related monomers. Overall, the NIF3-like domains of SA1388 are organized as a hexameric toroid similar to its homologs, E. coli ybgI and the hypothetical protein SP1609 from Streptococcus pneumoniae. The openings on either side of the toroid are partially covered by trimeric "lids" formed by the PII domains. The junction of the two NIF3 domains has two zinc ions bound at what appears to be a histidine rich active site. A well-defined electron density corresponding to an endogenously bound ligand of unknown identity is observed in close proximity to the metal site. Conclusion SA1388 is the third member of the NIF3-like family of proteins to be structurally characterized, the other two also being hypothetical proteins of unknown function. The structure of SA1388 confirms our earlier prediction that the inserted domain that separates the two NIF3 domains adopts a PII-like fold and reveals an overall capped toroidal arrangement for the protein hexamer. The

  2. White Ring; White ring

    Energy Technology Data Exchange (ETDEWEB)

    Aoki, H.; Yuzawa, H. [Nikken Sekkei Ltd., Osaka (Japan)

    1998-01-05

    White Ring is a citizen`s gymnasium used for figure skating and short track speed skating games of 18th Winter Olympic Games in 1998. White Ring is composed of a main-arena and a sub-arena. For the main-arena with an area 41mtimes66m, an ice link can be made by disengaging the potable floor and by flowing brine in the bridged polystyrene pipes embedded in the concrete floor. Due to the fortunate groundwater in this site, well water is used for the outside air treatment energy in 63% during heating and in 35% during cooling. Ammonia is used as a cooling medium for refrigerating facility. For the heating of audience area in the large space, heat load from the outside is reduced by enhancing the heat insulation performance of the roof of arena. The audience seats are locally heated using heaters. For the White Ring, high quality environment is realized for games through various functions of the large-scale roof of the large space. Success of the big event was expected. 15 figs., 4 tabs.

  3. Comprehensive Binary Interaction Mapping of SH2 Domains via Fluorescence Polarization Reveals Novel Functional Diversification of ErbB Receptors

    Science.gov (United States)

    Ciaccio, Mark F.; Chuu, Chih-pin; Jones, Richard B.

    2012-01-01

    First-generation interaction maps of Src homology 2 (SH2) domains with receptor tyrosine kinase (RTK) phosphosites have previously been generated using protein microarray (PM) technologies. Here, we developed a large-scale fluorescence polarization (FP) methodology that was able to characterize interactions between SH2 domains and ErbB receptor phosphosites with higher fidelity and sensitivity than was previously achieved with PMs. We used the FP assay to query the interaction of synthetic phosphopeptides corresponding to 89 ErbB receptor intracellular tyrosine sites against 93 human SH2 domains and 2 phosphotyrosine binding (PTB) domains. From 358,944 polarization measurements, the affinities for 1,405 unique biological interactions were determined, 83% of which are novel. In contrast to data from previous reports, our analyses suggested that ErbB2 was not more promiscuous than the other ErbB receptors. Our results showed that each receptor displays unique preferences in the affinity and location of recruited SH2 domains that may contribute to differences in downstream signaling potential. ErbB1 was enriched versus the other receptors for recruitment of domains from RAS GEFs whereas ErbB2 was enriched for recruitment of domains from tyrosine and phosphatidyl inositol phosphatases. ErbB3, the kinase inactive ErbB receptor family member, was predictably enriched for recruitment of domains from phosphatidyl inositol kinases and surprisingly, was enriched for recruitment of domains from tyrosine kinases, cytoskeletal regulatory proteins, and RHO GEFs but depleted for recruitment of domains from phosphatidyl inositol phosphatases. Many novel interactions were also observed with phosphopeptides corresponding to ErbB receptor tyrosines not previously reported to be phosphorylated by mass spectrometry, suggesting the existence of many biologically relevant RTK sites that may be phosphorylated but below the detection threshold of standard mass spectrometry procedures. This

  4. Comprehensive binary interaction mapping of SH2 domains via fluorescence polarization reveals novel functional diversification of ErbB receptors.

    Directory of Open Access Journals (Sweden)

    Ronald J Hause

    Full Text Available First-generation interaction maps of Src homology 2 (SH2 domains with receptor tyrosine kinase (RTK phosphosites have previously been generated using protein microarray (PM technologies. Here, we developed a large-scale fluorescence polarization (FP methodology that was able to characterize interactions between SH2 domains and ErbB receptor phosphosites with higher fidelity and sensitivity than was previously achieved with PMs. We used the FP assay to query the interaction of synthetic phosphopeptides corresponding to 89 ErbB receptor intracellular tyrosine sites against 93 human SH2 domains and 2 phosphotyrosine binding (PTB domains. From 358,944 polarization measurements, the affinities for 1,405 unique biological interactions were determined, 83% of which are novel. In contrast to data from previous reports, our analyses suggested that ErbB2 was not more promiscuous than the other ErbB receptors. Our results showed that each receptor displays unique preferences in the affinity and location of recruited SH2 domains that may contribute to differences in downstream signaling potential. ErbB1 was enriched versus the other receptors for recruitment of domains from RAS GEFs whereas ErbB2 was enriched for recruitment of domains from tyrosine and phosphatidyl inositol phosphatases. ErbB3, the kinase inactive ErbB receptor family member, was predictably enriched for recruitment of domains from phosphatidyl inositol kinases and surprisingly, was enriched for recruitment of domains from tyrosine kinases, cytoskeletal regulatory proteins, and RHO GEFs but depleted for recruitment of domains from phosphatidyl inositol phosphatases. Many novel interactions were also observed with phosphopeptides corresponding to ErbB receptor tyrosines not previously reported to be phosphorylated by mass spectrometry, suggesting the existence of many biologically relevant RTK sites that may be phosphorylated but below the detection threshold of standard mass spectrometry

  5. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation

    International Nuclear Information System (INIS)

    Das, Debanu; Grishin, Nick V.; Kumar, Abhinav; Carlton, Dennis; Bakolitsa, Constantina; Miller, Mitchell D.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Burra, Prasad; Chen, Connie; Chiu, Hsiu-Ju; Chiu, Michelle; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Ernst, Dustin; Farr, Carol L.; Feuerhelm, Julie; Grzechnik, Anna; Grzechnik, Slawomir K.; Grant, Joanna C.; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Johnson, Hope A.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; Bedem, Henry van den; Weekes, Dana; Wooten, Tiffany; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2009-01-01

    The crystal structure of the NGO1945 gene product from N. gonorrhoeae (UniProt Q5F5IO) reveals that the N-terminal domain assigned as a domain of unknown function (DUF2063) is likely to bind DNA and that the protein may be involved in transcriptional regulation. Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (∼40–99% sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention

  6. Crystal structure of Arabidopsis thaliana Dawdle forkhead-associated domain reveals a conserved phospho-threonine recognition cleft for dicer-like 1 binding.

    Science.gov (United States)

    Machida, Satoru; Yuan, Y Adam

    2013-07-01

    Dawdle (DDL) is a microRNA processing protein essential for the development of Arabidopsis. DDL contains a putative nuclear localization signal at its amino-terminus and forkhead-associated (FHA) domain at the carboxyl-terminus. Here, we report the crystal structure of the FHA domain of Arabidopsis Dawdle, determined by multiple-wavelength anomalous dispersion method at 1.7-Å resolution. DDL FHA structure displays a seven-stranded β-sandwich architecture that contains a unique structural motif comprising two long anti-parallel strands. Strikingly, crystal packing of the DDL FHA domain reveals that a glutamate residue from the symmetry-related DDL FHA domain, a structural mimic of the phospho-threonine, is specifically recognized by the structurally conserved phospho-threonine binding cleft. Consistently with the structural observations, co-immuno-precipitation experiments performed in Nicotiana benthamiana show that the DDL FHA domain co-immuno-precipitates with DCL1 fragments containing the predicted pThr+3(Ile/Val/Leu/Asp) motif. Taken together, we count the recognition of the target residue by the canonical binding cleft of the DDL FHA domain as the key molecular event to instate FHA domain-mediated protein-protein interaction in plant miRNA processing.

  7. Crystal structure of the enzyme-product complex reveals sugar ring distortion during catalysis by family 63 inverting α-glycosidase.

    Science.gov (United States)

    Miyazaki, Takatsugu; Nishikawa, Atsushi; Tonozuka, Takashi

    2016-12-01

    Glycoside hydrolases are divided into two groups, known as inverting and retaining enzymes, based on their hydrolytic mechanisms. Glycoside hydrolase family 63 (GH63) is composed of inverting α-glycosidases, which act mainly on α-glucosides. We previously found that Escherichia coli GH63 enzyme, YgjK, can hydrolyze 2-O-α-d-glucosyl-d-galactose. Two constructed glycosynthase mutants, D324N and E727A, which catalyze the transfer of a β-glucosyl fluoride donor to galactose, lactose, and melibiose. Here, we determined the crystal structures of D324N and E727A soaked with a mixture of glucose and lactose at 1.8- and 2.1-Å resolutions, respectively. Because glucose and lactose molecules are found at the active sites in both structures, it is possible that these structures mimic the enzyme-product complex of YgjK. A glucose molecule found at subsite -1 in both structures adopts an unusual 1 S 3 skew-boat conformation. Comparison between these structures and the previously determined enzyme-substrate complex structure reveals that the glucose pyranose ring might be distorted immediately after nucleophilic attack by a water molecule. These structures represent the first enzyme-product complex for the GH63 family, as well as the structurally-related glycosidases, and it may provide insight into the catalytic mechanism of these enzymes. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Structure-Activity Relationship and Molecular Mechanics Reveal the Importance of Ring Entropy in the Biosynthesis and Activity of a Natural Product.

    Science.gov (United States)

    Tran, Hai L; Lexa, Katrina W; Julien, Olivier; Young, Travis S; Walsh, Christopher T; Jacobson, Matthew P; Wells, James A

    2017-02-22

    Macrocycles are appealing drug candidates due to their high affinity, specificity, and favorable pharmacological properties. In this study, we explored the effects of chemical modifications to a natural product macrocycle upon its activity, 3D geometry, and conformational entropy. We chose thiocillin as a model system, a thiopeptide in the ribosomally encoded family of natural products that exhibits potent antimicrobial effects against Gram-positive bacteria. Since thiocillin is derived from a genetically encoded peptide scaffold, site-directed mutagenesis allows for rapid generation of analogues. To understand thiocillin's structure-activity relationship, we generated a site-saturation mutagenesis library covering each position along thiocillin's macrocyclic ring. We report the identification of eight unique compounds more potent than wild-type thiocillin, the best having an 8-fold improvement in potency. Computational modeling of thiocillin's macrocyclic structure revealed a striking requirement for a low-entropy macrocycle for activity. The populated ensembles of the active mutants showed a rigid structure with few adoptable conformations while inactive mutants showed a more flexible macrocycle which is unfavorable for binding. This finding highlights the importance of macrocyclization in combination with rigidifying post-translational modifications to achieve high-potency binding.

  9. The Hi-Ring DCN Architecture

    DEFF Research Database (Denmark)

    Galili, Michael; Kamchevska, Valerija; Ding, Yunhong

    2016-01-01

    We will review recent work on the proposed hierarchical ring-based architecture (HiRing) proposed for data center networks. We will discuss the architecture and initial demonstrations of optical switching performance and time-domain synchronization......We will review recent work on the proposed hierarchical ring-based architecture (HiRing) proposed for data center networks. We will discuss the architecture and initial demonstrations of optical switching performance and time-domain synchronization...

  10. Vortex rings

    CERN Document Server

    Akhmetov, D G

    2009-01-01

    This text on vortex rings covers their theoretical foundation, systematic investigations, and practical applications such as the extinction of fires at gushing oil wells. It pays special attention to the formation and motion of turbulent vortex rings.

  11. Architecture of the nitric-oxide synthase holoenzyme reveals large conformational changes and a calmodulin-driven release of the FMN domain.

    Science.gov (United States)

    Yokom, Adam L; Morishima, Yoshihiro; Lau, Miranda; Su, Min; Glukhova, Alisa; Osawa, Yoichi; Southworth, Daniel R

    2014-06-13

    Nitric-oxide synthase (NOS) is required in mammals to generate NO for regulating blood pressure, synaptic response, and immune defense. NOS is a large homodimer with well characterized reductase and oxygenase domains that coordinate a multistep, interdomain electron transfer mechanism to oxidize l-arginine and generate NO. Ca(2+)-calmodulin (CaM) binds between the reductase and oxygenase domains to activate NO synthesis. Although NOS has long been proposed to adopt distinct conformations that alternate between interflavin and FMN-heme electron transfer steps, structures of the holoenzyme have remained elusive and the CaM-bound arrangement is unknown. Here we have applied single particle electron microscopy (EM) methods to characterize the full-length of the neuronal isoform (nNOS) complex and determine the structural mechanism of CaM activation. We have identified that nNOS adopts an ensemble of open and closed conformational states and that CaM binding induces a dramatic rearrangement of the reductase domain. Our three-dimensional reconstruction of the intact nNOS-CaM complex reveals a closed conformation and a cross-monomer arrangement with the FMN domain rotated away from the NADPH-FAD center, toward the oxygenase dimer. This work captures, for the first time, the reductase-oxygenase structural arrangement and the CaM-dependent release of the FMN domain that coordinates to drive electron transfer across the domains during catalysis. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Effects of clinically relevant MPL mutations in the transmembrane domain revealed at the atomic level through computational modeling.

    Science.gov (United States)

    Lee, Tai-Sung; Kantarjian, Hagop; Ma, Wanlong; Yeh, Chen-Hsiung; Giles, Francis; Albitar, Maher

    2011-01-01

    Mutations in the thrombopoietin receptor (MPL) may activate relevant pathways and lead to chronic myeloproliferative neoplasms (MPNs). The mechanisms of MPL activation remain elusive because of a lack of experimental structures. Modern computational biology techniques were utilized to explore the mechanisms of MPL protein activation due to various mutations. Transmembrane (TM) domain predictions, homology modeling, ab initio protein structure prediction, and molecular dynamics (MD) simulations were used to build structural dynamic models of wild-type and four clinically observed mutants of MPL. The simulation results suggest that S505 and W515 are important in keeping the TM domain in its correct position within the membrane. Mutations at either of these two positions cause movement of the TM domain, altering the conformation of the nearby intracellular domain in unexpected ways, and may cause the unwanted constitutive activation of MPL's kinase partner, JAK2. Our findings represent the first full-scale molecular dynamics simulations of the wild-type and clinically observed mutants of the MPL protein, a critical element of the MPL-JAK2-STAT signaling pathway. In contrast to usual explanations for the activation mechanism that are based on the relative translational movement between rigid domains of MPL, our results suggest that mutations within the TM region could result in conformational changes including tilt and rotation (azimuthal) angles along the membrane axis. Such changes may significantly alter the conformation of the adjacent and intrinsically flexible intracellular domain. Hence, caution should be exercised when interpreting experimental evidence based on rigid models of cytokine receptors or similar systems.

  13. Structural Dynamics of the GW182 Silencing Domain Including its RNA Recognition motif (RRM) Revealed by Hydrogen-Deuterium Exchange Mass Spectrometry

    Science.gov (United States)

    Cieplak-Rotowska, Maja K.; Tarnowski, Krzysztof; Rubin, Marcin; Fabian, Marc R.; Sonenberg, Nahum; Dadlez, Michal; Niedzwiecka, Anna

    2018-01-01

    The human GW182 protein plays an essential role in micro(mi)RNA-dependent gene silencing. miRNA silencing is mediated, in part, by a GW182 C-terminal region called the silencing domain, which interacts with the poly(A) binding protein and the CCR4-NOT deadenylase complex to repress protein synthesis. Structural studies of this GW182 fragment are challenging due to its predicted intrinsically disordered character, except for its RRM domain. However, detailed insights into the properties of proteins containing disordered regions can be provided by hydrogen-deuterium exchange mass spectrometry (HDX/MS). In this work, we applied HDX/MS to define the structural state of the GW182 silencing domain. HDX/MS analysis revealed that this domain is clearly divided into a natively unstructured part, including the CCR4-NOT interacting motif 1, and a distinct RRM domain. The GW182 RRM has a very dynamic structure, since water molecules can penetrate the whole domain in 2 h. The finding of this high structural dynamics sheds new light on the RRM structure. Though this domain is one of the most frequently occurring canonical protein domains in eukaryotes, these results are - to our knowledge - the first HDX/MS characteristics of an RRM. The HDX/MS studies show also that the α2 helix of the RRM can display EX1 behavior after a freezing-thawing cycle. This means that the RRM structure is sensitive to environmental conditions and can change its conformation, which suggests that the state of the RRM containing proteins should be checked by HDX/MS in regard of the conformational uniformity. [Figure not available: see fulltext.

  14. Genome-wide comparisons reveal a clinal species pattern within a holobenthic octopod-the Australian Southern blue-ringed octopus, Hapalochlaena maculosa (Cephalopoda: Octopodidae).

    Science.gov (United States)

    Morse, Peter; Kjeldsen, Shannon R; Meekan, Mark G; Mccormick, Mark I; Finn, Julian K; Huffard, Christine L; Zenger, Kyall R

    2018-02-01

    The southern blue-ringed octopus, Hapalochlaena maculosa (Hoyle, 1883) lacks a planktonic dispersal phase, yet ranges across Australia's southern coastline. This species' brief and holobenthic life history suggests gene flow might be limited, leaving distant populations prone to strong genetic divergence. This study used 17,523 genome-wide SNP loci to investigate genetic structuring and local adaptation patterns of H. maculosa among eight sampling sites along its reported range. Within sites, interrelatedness was very high, consistent with the limited dispersal of this taxon. However, inbreeding coefficients were proportionally lower among sites where substructuring was not detected, suggesting H. maculosa might possess a mechanism for inbreeding avoidance. Genetic divergence was extremely high among all sites, with the greatest divergence observed between both ends of the distribution, Fremantle, WA, and Stanley, TAS. Genetic distances closely followed an isolation by geographic distance pattern. Outlier analyses revealed distinct selection signatures at all sites, with the strongest divergence reported between Fremantle and the other Western Australian sites. Phylogenetic reconstructions using the described sister taxon H. fasciata (Hoyle, 1886) further supported that the genetic divergence between distal H. maculosa sites in this study was equivalent to that of between established heterospecifics within this genus. However, it is advocated that taxonomic delineations within this species should be made with caution. These data indicate that H. maculosa forms a clinal species pattern across its geographic range, with gene flow present through allele sharing between adjacent populations. Morphological investigations are recommended for a robust resolution of the taxonomic identity and ecotype boundaries of this species.

  15. Site-Specific Phosphorylation of PSD-95 PDZ Domains Reveals Fine-Tuned Regulation of Protein-Protein Interactions

    DEFF Research Database (Denmark)

    Pedersen, Søren W; Albertsen, Louise; Moran, Griffin E

    2017-01-01

    The postsynaptic density protein of 95 kDa (PSD-95) is a key scaffolding protein that controls signaling at synapses in the brain through interactions of its PDZ domains with the C-termini of receptors, ion channels, and enzymes. PSD-95 is highly regulated by phosphorylation. To explore the effec...

  16. Structure of the mouse galectin-4 N-terminal carbohydrate-recognition domain reveals the mechanism of oligosaccharide recognition

    Energy Technology Data Exchange (ETDEWEB)

    Krejciríková, Veronika; Pachl, Petr; Fábry, Milan; Malý, Petr; Rezácová, Pavlína; Brynda, Jirí (Czech Academy)

    2011-11-18

    Galectin-4, a member of the tandem-repeat subfamily of galectins, participates in cell-membrane interactions and plays an important role in cell adhesion and modulation of immunity and malignity. The oligosaccharide specificity of the mouse galectin-4 carbohydrate-recognition domains (CRDs) has been reported previously. In this work, the structure and binding properties of the N-terminal domain CRD1 were further investigated and the crystal structure of CRD1 in complex with lactose was determined at 2.1 {angstrom} resolution. The lactose-binding affinity was characterized by fluorescence measurements and two lactose-binding sites were identified: a high-affinity site with a K{sub d} value in the micromolar range (K{sub d1} = 600 {+-} 70 {mu}M) and a low-affinity site with K{sub d2} = 28 {+-} 10 mM.

  17. Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family

    Czech Academy of Sciences Publication Activity Database

    Trempe, J. F.; Grantz Šašková, Klára; Sivá, Monika; Ratcliffe, C. D. H.; Veverka, Václav; Hoegl, A.; Ménade, M.; Feng, X.; Shenker, S.; Svoboda, Michal; Kožíšek, Milan; Konvalinka, Jan; Gehring, K.

    2016-01-01

    Roč. 6, Sep 20 (2016), č. článku 33671. ISSN 2045-2322 R&D Projects: GA MŠk(CZ) LK11205; GA MŠk(CZ) LO1304 Institutional support: RVO:61388963 Keywords : ubiquitin-associated domains * ray solution scattering * torsion angle dynamics Subject RIV: CE - Biochemistry Impact factor: 4.259, year: 2016 http://www.nature.com/articles/srep33671

  18. Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain

    DEFF Research Database (Denmark)

    Midtgaard, Søren Fuglsang; Assenholt, Jannie; Jonstrup, Anette Thyssen

    2006-01-01

    The multisubunit eukaryotic exosome is an essential RNA processing and degradation machine. In its nuclear form, the exosome associates with the auxiliary factor Rrp6p, which participates in both RNA processing and degradation reactions. The crystal structure of Saccharomyces cerevisiae Rrp6p...... ribonucleotides and their bases. Finally, in vivo mutational studies show the importance of the domain contacts for the processing function of Rrp6p and highlight fundamental differences between the protein and its prokaryotic RNase D counterparts....

  19. Mutational analysis of the RNA-binding domain of the Prunus necrotic ringspot virus (PNRSV) movement protein reveals its requirement for cell-to-cell movement

    OpenAIRE

    Herranz, M. Carmen; Sánchez Navarro, Jesús A.; Saurí Peris, Ana; Mingarro Muñoz, Ismael; Pallás Benet, Vicente

    2005-01-01

    The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is required for cell-to-cell movement. MP subcellular localization studies using a GFP fusion protein revealed highly punctate structures between neighboring cells, believed to represent plasmodesmata. Deletion of the RNA-binding domain (RBD) of PNRSV MP abolishes the cell-to-cell movement. A mutational analysis on this RBD was performed in order to identify in vivo the features that govern viral transport. Loss of positive c...

  20. The host-binding domain of the P2 phage tail spike reveals a trimeric iron-binding structure

    International Nuclear Information System (INIS)

    Yamashita, Eiki; Nakagawa, Atsushi; Takahashi, Junichi; Tsunoda, Kin-ichi; Yamada, Seiko; Takeda, Shigeki

    2011-01-01

    The C-terminal domain of a bacteriophage P2 tail-spike protein, gpV, was crystallized and its structure was solved at 1.27 Å resolution. The refined model showed a triple β-helix structure and the presence of iron, calcium and chloride ions. The adsorption and infection of bacteriophage P2 is mediated by tail fibres and tail spikes. The tail spikes on the tail baseplate are used to irreversibly adsorb to the host cells. Recently, a P2 phage tail-spike protein, gpV, was purified and it was shown that a C-terminal domain, Ser87–Leu211, is sufficient for the binding of gpV to host Escherichia coli membranes [Kageyama et al. (2009 ▶), Biochemistry, 48, 10129–10135]. In this paper, the crystal structure of the C-terminal domain of P2 gpV is reported. The structure is a triangular pyramid and looks like a spearhead composed of an intertwined β-sheet, a triple β-helix and a metal-binding region containing iron, calcium and chloride ions

  1. The Role of Chaperone-subunit Usher Domain Interactions in the Mechanism of Bacterial Pilus Biogenesis Revealed by ESI-MS*

    Science.gov (United States)

    Morrissey, Bethny; Leney, Aneika C.; Toste Rêgo, Ana; Phan, Gilles; Allen, William J.; Verger, Denis; Waksman, Gabriel; Ashcroft, Alison E.; Radford, Sheena E.

    2012-01-01

    The PapC usher is a β-barrel outer membrane protein essential for assembly and secretion of P pili that are required for adhesion of pathogenic E. coli, which cause the development of pyelonephritis. Multiple protein subunits form the P pilus, the highly specific assembly of which is coordinated by the usher. Despite a wealth of structural knowledge, how the usher catalyzes subunit polymerization and orchestrates a correct and functional order of subunit assembly remain unclear. Here, the ability of the soluble N-terminal (UsherN), C-terminal (UsherC2), and Plug (UsherP) domains of the usher to bind different chaperone-subunit (PapDPapX) complexes is investigated using noncovalent electrospray ionization mass spectrometry. The results reveal that each usher domain is able to bind all six PapDPapX complexes, consistent with an active role of all three usher domains in pilus biogenesis. Using collision induced dissociation, combined with competition binding experiments and dissection of the adhesin subunit, PapG, into separate pilin and adhesin domains, the results reveal why PapG has a uniquely high affinity for the usher, which is consistent with this subunit always being displayed at the pilus tip. In addition, we show how the different soluble usher domains cooperate to coordinate and control efficient pilus assembly at the usher platform. As well as providing new information about the protein-protein interactions that determine pilus biogenesis, the results highlight the power of noncovalent MS to interrogate biological mechanisms, especially in complex mixtures of species. PMID:22371487

  2. The role of chaperone-subunit usher domain interactions in the mechanism of bacterial pilus biogenesis revealed by ESI-MS.

    Science.gov (United States)

    Morrissey, Bethny; Leney, Aneika C; Toste Rêgo, Ana; Phan, Gilles; Allen, William J; Verger, Denis; Waksman, Gabriel; Ashcroft, Alison E; Radford, Sheena E

    2012-07-01

    The PapC usher is a β-barrel outer membrane protein essential for assembly and secretion of P pili that are required for adhesion of pathogenic E. coli, which cause the development of pyelonephritis. Multiple protein subunits form the P pilus, the highly specific assembly of which is coordinated by the usher. Despite a wealth of structural knowledge, how the usher catalyzes subunit polymerization and orchestrates a correct and functional order of subunit assembly remain unclear. Here, the ability of the soluble N-terminal (UsherN), C-terminal (UsherC2), and Plug (UsherP) domains of the usher to bind different chaperone-subunit (PapDPapX) complexes is investigated using noncovalent electrospray ionization mass spectrometry. The results reveal that each usher domain is able to bind all six PapDPapX complexes, consistent with an active role of all three usher domains in pilus biogenesis. Using collision induced dissociation, combined with competition binding experiments and dissection of the adhesin subunit, PapG, into separate pilin and adhesin domains, the results reveal why PapG has a uniquely high affinity for the usher, which is consistent with this subunit always being displayed at the pilus tip. In addition, we show how the different soluble usher domains cooperate to coordinate and control efficient pilus assembly at the usher platform. As well as providing new information about the protein-protein interactions that determine pilus biogenesis, the results highlight the power of noncovalent MS to interrogate biological mechanisms, especially in complex mixtures of species.

  3. The Structure of Plasmodium falciparum Blood-Stage 6-Cys Protein Pf41 Reveals an Unexpected Intra-Domain Insertion Required for Pf12 Coordination.

    Directory of Open Access Journals (Sweden)

    Michelle L Parker

    Full Text Available Plasmodium falciparum is an apicomplexan parasite and the etiological agent of severe human malaria. The complex P. falciparum life cycle is supported by a diverse repertoire of surface proteins including the family of 6-Cys s48/45 antigens. Of these, Pf41 is localized to the surface of the blood-stage merozoite through its interaction with the glycophosphatidylinositol-anchored Pf12. Our recent structural characterization of Pf12 revealed two juxtaposed 6-Cys domains (D1 and D2. Pf41, however, contains an additional segment of 120 residues predicted to form a large spacer separating its two 6-Cys domains. To gain insight into the assembly mechanism and overall architecture of the Pf12-Pf41 complex, we first determined the 2.45 Å resolution crystal structure of Pf41 using zinc single-wavelength anomalous dispersion. Structural analysis revealed an unexpected domain organization where the Pf41 6-Cys domains are, in fact, intimately associated and the additional residues instead map predominately to an inserted domain-like region (ID located between two β-strands in D1. Notably, the ID is largely proteolyzed in the final structure suggesting inherent flexibility. To assess the contribution of the ID to complex formation, we engineered a form of Pf41 where the ID was replaced by a short glycine-serine linker and showed by isothermal titration calorimetry that binding to Pf12 was abrogated. Finally, protease protection assays showed that the proteolytic susceptibility of the ID was significantly reduced in the complex, consistent with the Pf41 ID directly engaging Pf12. Collectively, these data establish the architectural organization of Pf41 and define an essential role for the Pf41 ID in promoting assembly of the Pf12-Pf41 heterodimeric complex.

  4. A crystal structure of the Dengue virus NS5 protein reveals a novel inter-domain interface essential for protein flexibility and virus replication.

    Directory of Open Access Journals (Sweden)

    Yongqian Zhao

    2015-03-01

    Full Text Available Flavivirus RNA replication occurs within a replication complex (RC that assembles on ER membranes and comprises both non-structural (NS viral proteins and host cofactors. As the largest protein component within the flavivirus RC, NS5 plays key enzymatic roles through its N-terminal methyltransferase (MTase and C-terminal RNA-dependent-RNA polymerase (RdRp domains, and constitutes a major target for antivirals. We determined a crystal structure of the full-length NS5 protein from Dengue virus serotype 3 (DENV3 at a resolution of 2.3 Å in the presence of bound SAH and GTP. Although the overall molecular shape of NS5 from DENV3 resembles that of NS5 from Japanese Encephalitis Virus (JEV, the relative orientation between the MTase and RdRp domains differs between the two structures, providing direct evidence for the existence of a set of discrete stable molecular conformations that may be required for its function. While the inter-domain region is mostly disordered in NS5 from JEV, the NS5 structure from DENV3 reveals a well-ordered linker region comprising a short 310 helix that may act as a swivel. Solution Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS analysis reveals an increased mobility of the thumb subdomain of RdRp in the context of the full length NS5 protein which correlates well with the analysis of the crystallographic temperature factors. Site-directed mutagenesis targeting the mostly polar interface between the MTase and RdRp domains identified several evolutionarily conserved residues that are important for viral replication, suggesting that inter-domain cross-talk in NS5 regulates virus replication. Collectively, a picture for the molecular origin of NS5 flexibility is emerging with profound implications for flavivirus replication and for the development of therapeutics targeting NS5.

  5. Solution Structure of the Tandem Acyl Carrier Protein Domains from a Polyunsaturated Fatty Acid Synthase Reveals Beads-on-a-String Configuration

    KAUST Repository

    Trujillo, Uldaeliz

    2013-02-28

    The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP

  6. Solution Structure of the Tandem Acyl Carrier Protein Domains from a Polyunsaturated Fatty Acid Synthase Reveals Beads-on-a-String Configuration

    KAUST Repository

    Trujillo, Uldaeliz; Vá zquez-Rosa, Edwin; Oyola-Robles, Delise; Stagg, Loren J.; Vassallo, David A.; Vega, Irving E.; Arold, Stefan T.; Baerga-Ortiz, Abel

    2013-01-01

    The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP

  7. Solution structure of the tandem acyl carrier protein domains from a polyunsaturated fatty acid synthase reveals beads-on-a-string configuration.

    Directory of Open Access Journals (Sweden)

    Uldaeliz Trujillo

    Full Text Available The polyunsaturated fatty acid (PUFA synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect and in structural stabilization of the multidomain protein (synergistic effect. While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of

  8. Analysis of Metal-Binding Features of the Wild Type and Two Domain-Truncated Mutant Variants of Littorina littorea Metallothionein Reveals Its Cd-Specific Character

    Directory of Open Access Journals (Sweden)

    Òscar Palacios

    2017-07-01

    Full Text Available After the resolution of the 3D structure of the Cd9-aggregate of the Littorina littorea metallothionein (MT, we report here a detailed analysis of the metal binding capabilities of the wild type MT, LlwtMT, and of two truncated mutants lacking either the N-terminal domain, Lltr2MT, or both the N-terminal domain, plus four extra flanking residues (SSVF, Lltr1MT. The recombinant synthesis and in vitro studies of these three proteins revealed that LlwtMT forms unique M9-LlwtMT complexes with Zn(II and Cd(II, while yielding a complex mixture of heteronuclear Zn,Cu-LlwtMT species with Cu(I. As expected, the truncated mutants gave rise to unique M6-LltrMT complexes and Zn,Cu-LltrMT mixtures of lower stoichiometry with respect to LlwtMT, with the SSVF fragment having an influence on their metal binding performance. Our results also revealed a major specificity, and therefore a better metal-coordinating performance of the three proteins for Cd(II than for Zn(II, although the analysis of the Zn(II/Cd(II displacement reaction clearly demonstrates a lack of any type of cooperativity in Cd(II binding. Contrarily, the analysis of their Cu(I binding abilities revealed that every LlMT domain is prone to build Cu4-aggregates, the whole MT working by modules analogously to, as previously described, certain fungal MTs, like those of C. neoformans and T. mesenterica. It is concluded that the Littorina littorea MT is a Cd-specific protein that (beyond its extended binding capacity through an additional Cd-binding domain confers to Littorina littorea a particular adaptive advantage in its changeable marine habitat.

  9. Vortex and source rings

    DEFF Research Database (Denmark)

    Branlard, Emmanuel Simon Pierre

    2017-01-01

    The velocity field, vector potential and velocity gradient of a vortex ring is derived in this chapter. The Biot-Savart law for the vector potential and velocity is expressed in a first section. Then, the flow is derived at specific locations: on the axis, near the axis and in the far field where...... the analogy to a doublet field is made. The following section derive the value of the vector potential and velocity field in the full domain. The expression for the velocity gradient is also provided since it may be relevant in a simulation with vortex particles and vortex rings. Most of this chapter...

  10. Tree-ring chronologies and stable carbon isotopic composition reveal impacts of hydro-climate change on bottomland hardwood forests of South-Central Texas

    Science.gov (United States)

    Deshpande, A. G.; Lafon, C. W.; Hyodo, A.; Boutton, T. W.; Moore, G. W.

    2017-12-01

    Over the last three decades, South-Central Texas has experienced an increase in frequency and intensity of hydro-climatic anomalies such as extreme droughts and floods. These extreme events can have negative impacts on forest health and can strongly alter a wide range of ecosystem processes. Tree increment growth in bottomland hardwood forests is influenced by droughts and floods, which affects the carbon isotope values (δ13C) in tree-ring cellulose. This study aims to assess the impacts of hydro-climate change on the growth and physiological response of bottomland hardwood forests by investigating variations in radial growth and tree-ring carbon isotopic composition. Annual ring-width chronologies for 41 years (1975-2016) were developed from 24 water oak (Quercus nigra) trees at 4 sites along a 25 km transect located in the San Bernard River watershed. The δ13C values in cellulose were measured from 4-year ring composites including years with anomalously high and low precipitation. Dendroclimatology analysis involved correlating ring-width index with precipitation records and Palmer Drought Sensitivity Index (PDSI). Radial growth was more closely associated with spring-summer (Feb-Aug) precipitation (R2 = 0.42, pstress, as indicated by narrower growth rings and increased cellulose δ13C. However, the inter-site variation in δ13C indicated large hydro-climatic variation between sites (2.79-4.24‰ for wet years and 0.53-1.50‰ for drought years). δ13C values showed an increase of 0.78‰ and 2.40‰ from the wettest (1991-1994) to the driest period (2008-2011) at two of our sites, possibly due to drought-induced moisture-deficit-stress. However, at the other two sites, the δ13C values of tree rings from the same periods decreased by 0.65‰ and 1.19‰, possibly emanating from flooding-induced stress caused by waterlogging. This study provides insights on how hydro-climatic variations affect riparian forest health in the region and acts as a baseline for

  11. Comparative genomic analysis of SET domain family reveals the origin, expansion, and putative function of the arthropod-specific SmydA genes as histone modifiers in insects.

    Science.gov (United States)

    Jiang, Feng; Liu, Qing; Wang, Yanli; Zhang, Jie; Wang, Huimin; Song, Tianqi; Yang, Meiling; Wang, Xianhui; Kang, Le

    2017-06-01

    The SET domain is an evolutionarily conserved motif present in histone lysine methyltransferases, which are important in the regulation of chromatin and gene expression in animals. In this study, we searched for SET domain-containing genes (SET genes) in all of the 147 arthropod genomes sequenced at the time of carrying out this experiment to understand the evolutionary history by which SET domains have evolved in insects. Phylogenetic and ancestral state reconstruction analysis revealed an arthropod-specific SET gene family, named SmydA, that is ancestral to arthropod animals and specifically diversified during insect evolution. Considering that pseudogenization is the most probable fate of the new emerging gene copies, we provided experimental and evolutionary evidence to demonstrate their essential functions. Fluorescence in situ hybridization analysis and in vitro methyltransferase activity assays showed that the SmydA-2 gene was transcriptionally active and retained the original histone methylation activity. Expression knockdown by RNA interference significantly increased mortality, implying that the SmydA genes may be essential for insect survival. We further showed predominantly strong purifying selection on the SmydA gene family and a potential association between the regulation of gene expression and insect phenotypic plasticity by transcriptome analysis. Overall, these data suggest that the SmydA gene family retains essential functions that may possibly define novel regulatory pathways in insects. This work provides insights into the roles of lineage-specific domain duplication in insect evolution. © The Authors 2017. Published by Oxford University Press.

  12. Interface-induced chiral domain walls, spin spirals and skyrmions revealed by spin-polarized scanning tunneling microscopy.

    Science.gov (United States)

    von Bergmann, Kirsten; Kubetzka, André; Pietzsch, Oswald; Wiesendanger, Roland

    2014-10-01

    The spin textures of ultra-thin magnetic layers exhibit surprising variety. The loss of inversion symmetry at the interface of the magnetic layer and substrate gives rise to the so-called Dzyaloshinskii-Moriya interaction which favors non-collinear spin arrangements with unique rotational sense. Here we review the application of spin-polarized scanning tunneling microscopy to such systems, which has led to the discovery of interface-induced chiral domain walls and spin spirals. Recently, different interface-driven skyrmion lattices have been found, and the writing as well as the deleting of individual skyrmions based on local spin-polarized current injection has been demonstrated. These interface-induced non-collinear magnetic states offer new exciting possibilities to study fundamental magnetic interactions and to tailor material properties for spintronic applications.

  13. Pharmacology of the Nav1.1 domain IV voltage sensor reveals coupling between inactivation gating processes.

    Science.gov (United States)

    Osteen, Jeremiah D; Sampson, Kevin; Iyer, Vivek; Julius, David; Bosmans, Frank

    2017-06-27

    The Na v 1.1 voltage-gated sodium channel is a critical contributor to excitability in the brain, where pathological loss of function leads to such disorders as epilepsy, Alzheimer's disease, and autism. This voltage-gated sodium (Na v ) channel subtype also plays an important role in mechanical pain signaling by primary afferent somatosensory neurons. Therefore, pharmacologic modulation of Na v 1.1 represents a potential strategy for treating excitability disorders of the brain and periphery. Inactivation is a complex aspect of Na v channel gating and consists of fast and slow components, each of which may involve a contribution from one or more voltage-sensing domains. Here, we exploit the Hm1a spider toxin, a Na v 1.1-selective modulator, to better understand the relationship between these temporally distinct modes of inactivation and ask whether they can be distinguished pharmacologically. We show that Hm1a inhibits the gating movement of the domain IV voltage sensor (VSDIV), hindering both fast and slow inactivation and leading to an increase in Na v 1.1 availability during high-frequency stimulation. In contrast, ICA-121431, a small-molecule Na v 1.1 inhibitor, accelerates a subsequent VSDIV gating transition to accelerate entry into the slow inactivated state, resulting in use-dependent block. Further evidence for functional coupling between fast and slow inactivation is provided by a Na v 1.1 mutant in which fast inactivation removal has complex effects on slow inactivation. Taken together, our data substantiate the key role of VSDIV in Na v channel fast and slow inactivation and demonstrate that these gating processes are sequential and coupled through VSDIV. These findings provide insight into a pharmacophore on VSDIV through which modulation of inactivation gating can inhibit or facilitate Na v 1.1 function.

  14. The medaka novel immune-type receptor (NITR gene clusters reveal an extraordinary degree of divergence in variable domains

    Directory of Open Access Journals (Sweden)

    Litman Gary W

    2008-06-01

    Full Text Available Abstract Background Novel immune-type receptor (NITR genes are members of diversified multigene families that are found in bony fish and encode type I transmembrane proteins containing one or two extracellular immunoglobulin (Ig domains. The majority of NITRs can be classified as inhibitory receptors that possess cytoplasmic immunoreceptor tyrosine-based inhibition motifs (ITIMs. A much smaller number of NITRs can be classified as activating receptors by the lack of cytoplasmic ITIMs and presence of a positively charged residue within their transmembrane domain, which permits partnering with an activating adaptor protein. Results Forty-four NITR genes in medaka (Oryzias latipes are located in three gene clusters on chromosomes 10, 18 and 21 and can be organized into 24 families including inhibitory and activating forms. The particularly large dataset acquired in medaka makes direct comparison possible to another complete dataset acquired in zebrafish in which NITRs are localized in two clusters on different chromosomes. The two largest medaka NITR gene clusters share conserved synteny with the two zebrafish NITR gene clusters. Shared synteny between NITRs and CD8A/CD8B is limited but consistent with a potential common ancestry. Conclusion Comprehensive phylogenetic analyses between the complete datasets of NITRs from medaka and zebrafish indicate multiple species-specific expansions of different families of NITRs. The patterns of sequence variation among gene family members are consistent with recent birth-and-death events. Similar effects have been observed with mammalian immunoglobulin (Ig, T cell antigen receptor (TCR and killer cell immunoglobulin-like receptor (KIR genes. NITRs likely diverged along an independent pathway from that of the somatically rearranging antigen binding receptors but have undergone parallel evolution of V family diversity.

  15. A chimeric prokaryotic-eukaryotic pentameric ligand gated ion channel reveals interactions between the extracellular and transmembrane domains shape neurosteroid modulation.

    Science.gov (United States)

    Ghosh, Borna; Tsao, Tzu-Wei; Czajkowski, Cynthia

    2017-10-01

    Pentameric ligand-gated ion channels (pLGICs) are the targets of several clinical and endogenous allosteric modulators including anesthetics and neurosteroids. Molecular mechanisms underlying allosteric drug modulation are poorly understood. Here, we constructed a chimeric pLGIC by fusing the extracellular domain (ECD) of the proton-activated, cation-selective bacterial channel GLIC to the transmembrane domain (TMD) of the human ρ1 chloride-selective GABA A R, and tested the hypothesis that drug actions are regulated locally in the domain that houses its binding site. The chimeric channels were proton-gated and chloride-selective demonstrating the GLIC ECD was functionally coupled to the GABAρ TMD. Channels were blocked by picrotoxin and inhibited by pentobarbital, etomidate and propofol. The point mutation, ρ TMD W328M, conferred positive modulation and direct gating by pentobarbital. The data suggest that the structural machinery mediating general anesthetic modulation resides in the TMD. Proton-activation and neurosteroid modulation of the GLIC-ρ chimeric channels, however, did not simply mimic their respective actions on GLIC and GABAρ revealing that across domain interactions between the ECD and TMD play important roles in determining their actions. Proton-induced current responses were biphasic suggesting that the chimeric channels contain an additional proton sensor. Neurosteroid modulation of the GLIC-ρ chimeric channels by the stereoisomers, 5α-THDOC and 5β-THDOC, were swapped compared to their actions on GABAρ indicating that positive versus negative neurosteroid modulation is not encoded solely in the TMD nor by neurosteroid isomer structure but is dependent on specific interdomain connections between the ECD and TMD. Our data reveal a new mechanism for shaping neurosteroid modulation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.

    Science.gov (United States)

    van Koningsbruggen, Silvana; Gierlinski, Marek; Schofield, Pietá; Martin, David; Barton, Geoffey J; Ariyurek, Yavuz; den Dunnen, Johan T; Lamond, Angus I

    2010-11-01

    The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

  17. Structure of N-Terminal Domain of NPC1 Reveals Distinct Subdomains for Binding and Transfer of Cholesterol

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Hyock Joo; Abi-Mosleh, Lina; Wang, Michael L.; Deisenhofer, Johann; Goldstein, Joseph L.; Brown, Michael S.; Infante, Rodney E.; (UTSMC)

    2010-09-21

    LDL delivers cholesterol to lysosomes by receptor-mediated endocytosis. Exit of cholesterol from lysosomes requires two proteins, membrane-bound Niemann-Pick C1 (NPC1) and soluble NPC2. NPC2 binds cholesterol with its isooctyl side chain buried and its 3{beta}-hydroxyl exposed. Here, we describe high-resolution structures of the N-terminal domain (NTD) of NPC1 and complexes with cholesterol and 25-hydroxycholesterol. NPC1(NTD) binds cholesterol in an orientation opposite to NPC2: 3{beta}-hydroxyl buried and isooctyl side chain exposed. Cholesterol transfer from NPC2 to NPC1(NTD) requires reorientation of a helical subdomain in NPC1(NTD), enlarging the opening for cholesterol entry. NPC1 with point mutations in this subdomain (distinct from the binding subdomain) cannot accept cholesterol from NPC2 and cannot restore cholesterol exit from lysosomes in NPC1-deficient cells. We propose a working model wherein after lysosomal hydrolysis of LDL-cholesteryl esters, cholesterol binds NPC2, which transfers it to NPC1(NTD), reversing its orientation and allowing insertion of its isooctyl side chain into the outer lysosomal membranes.

  18. Interactions between Metal-binding Domains Modulate Intracellular Targeting of Cu(I)-ATPase ATP7B, as Revealed by Nanobody Binding*

    Science.gov (United States)

    Huang, Yiping; Nokhrin, Sergiy; Hassanzadeh-Ghassabeh, Gholamreza; Yu, Corey H.; Yang, Haojun; Barry, Amanda N.; Tonelli, Marco; Markley, John L.; Muyldermans, Serge; Dmitriev, Oleg Y.; Lutsenko, Svetlana

    2014-01-01

    The biologically and clinically important membrane transporters are challenging proteins to study because of their low level of expression, multidomain structure, and complex molecular dynamics that underlies their activity. ATP7B is a copper transporter that traffics between the intracellular compartments in response to copper elevation. The N-terminal domain of ATP7B (N-ATP7B) is involved in binding copper, but the role of this domain in trafficking is controversial. To clarify the role of N-ATP7B, we generated nanobodies that interact with ATP7B in vitro and in cells. In solution NMR studies, nanobodies revealed the spatial organization of N-ATP7B by detecting transient functionally relevant interactions between metal-binding domains 1–3. Modulation of these interactions by nanobodies in cells enhanced relocalization of the endogenous ATP7B toward the plasma membrane linking molecular and cellular dynamics of the transporter. Stimulation of ATP7B trafficking by nanobodies in the absence of elevated copper provides direct evidence for the important role of N-ATP7B structural dynamics in regulation of ATP7B localization in a cell. PMID:25253690

  19. Roles for SH2 and SH3 domains in Lyn kinase association with activated FcepsilonRI in RBL mast cells revealed by patterned surface analysis.

    Science.gov (United States)

    Hammond, Stephanie; Wagenknecht-Wiesner, Alice; Veatch, Sarah L; Holowka, David; Baird, Barbara

    2009-10-01

    In mast cells, antigen-mediated cross-linking of IgE bound to its high-affinity surface receptor, FcepsilonRI, initiates a signaling cascade that culminates in degranulation and release of allergic mediators. Antigen-patterned surfaces, in which the antigen is deposited in micron-sized features on a silicon substrate, were used to examine the spatial relationship between clustered IgE-FcepsilonRI complexes and Lyn, the signal-initiating tyrosine kinase. RBL mast cells expressing wild-type Lyn-EGFP showed co-redistribution of this protein with clustered IgE receptors on antigen-patterned surfaces, whereas Lyn-EGFP containing an inhibitory point mutation in its SH2 domain did not significantly accumulate with the patterned antigen, and Lyn-EGFP with an inhibitory point mutation in its SH3 domain exhibited reduced interactions. Our results using antigen-patterned surfaces and quantitative cross-correlation image analysis reveal that both the SH2 and SH3 domains contribute to interactions between Lyn kinase and cross-linked IgE receptors in stimulated mast cells.

  20. ring system

    African Journals Online (AJOL)

    1,3,2-DIAZABORACYCLOALKANE. RING SYSTEM. Negussie Retta" and Robert H. Neilson. 'Department of Chemistry, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia. Department of Chemistry, Texas Christian University.

  1. Tree ring δ18O reveals no long-term change of atmospheric water demand since 1800 in the northern Great Hinggan Mountains, China

    Science.gov (United States)

    Liu, Xiaohong; Zhang, Xuanwen; Zhao, Liangju; Xu, Guobao; Wang, Lixin; Sun, Weizhen; Zhang, Qiuliang; Wang, Wenzhi; Zeng, Xiaomin; Wu, Guoju

    2017-07-01

    Global warming will significantly increase transpirational water demand, which could dramatically affect plant physiology and carbon and water budgets. Tree ring δ18O is a potential index of the leaf-to-air vapor-pressure deficit (VPD) and therefore has great potential for long-term climatic reconstruction. Here we developed δ18O chronologies of two dominant native trees, Dahurian larch (Larix gmelinii Rupr.) and Mongolian pine (Pinus sylvestris var. mongolica), from a permafrost region in the Great Hinggan Mountains of northeastern China. We found that the July-August VPD and relative humidity were the dominant factors that controlled tree ring δ18O in the study region, indicating strong regulation of stomatal conductance. Based on the larch and pine tree ring δ18O chronologies, we developed a reliable summer (July-August) VPD reconstruction since 1800. Warming growing season temperatures increase transpiration and enrich cellulose 18O, but precipitation seemed to be the most important influence on VPD changes in this cold region. Periods with stronger transpirational demand occurred around the 1850s, from 1914 to 1925, and from 2005 to 2010. However, we found no overall long-term increasing or decreasing trends for VPD since 1800, suggesting that despite the increasing temperatures and thawing permafrost throughout the region, forest transpirational demand has not increased significantly during the past two centuries. Under current climatic conditions, VPD did not limit growth of larch and pine, even during extremely drought years. Our findings will support more realistic evaluations and reliable predictions of the potential influences of ongoing climatic change on carbon and water cycles and on forest dynamics in permafrost regions.

  2. cAMP control of HCN2 channel Mg2+ block reveals loose coupling between the cyclic nucleotide-gating ring and the pore.

    Directory of Open Access Journals (Sweden)

    Alex K Lyashchenko

    Full Text Available Hyperpolarization-activated cyclic nucleotide-regulated HCN channels underlie the Na+-K+ permeable IH pacemaker current. As with other voltage-gated members of the 6-transmembrane KV channel superfamily, opening of HCN channels involves dilation of a helical bundle formed by the intracellular ends of S6 albeit this is promoted by inward, not outward, displacement of S4. Direct agonist binding to a ring of cyclic nucleotide-binding sites, one of which lies immediately distal to each S6 helix, imparts cAMP sensitivity to HCN channel opening. At depolarized potentials, HCN channels are further modulated by intracellular Mg2+ which blocks the open channel pore and blunts the inhibitory effect of outward K+ flux. Here, we show that cAMP binding to the gating ring enhances not only channel opening but also the kinetics of Mg2+ block. A combination of experimental and simulation studies demonstrates that agonist acceleration of block is mediated via acceleration of the blocking reaction itself rather than as a secondary consequence of the cAMP enhancement of channel opening. These results suggest that the activation status of the gating ring and the open state of the pore are not coupled in an obligate manner (as required by the often invoked Monod-Wyman-Changeux allosteric model but couple more loosely (as envisioned in a modular model of protein activation. Importantly, the emergence of second messenger sensitivity of open channel rectification suggests that loose coupling may have an unexpected consequence: it may endow these erstwhile "slow" channels with an ability to exert voltage and ligand-modulated control over cellular excitability on the fastest of physiologically relevant time scales.

  3. Crystal Structure of Marburg Virus VP40 Reveals a Broad, Basic Patch for Matrix Assembly and a Requirement of the N-Terminal Domain for Immunosuppression.

    Science.gov (United States)

    Oda, Shun-Ichiro; Noda, Takeshi; Wijesinghe, Kaveesha J; Halfmann, Peter; Bornholdt, Zachary A; Abelson, Dafna M; Armbrust, Tammy; Stahelin, Robert V; Kawaoka, Yoshihiro; Saphire, Erica Ollmann

    2016-02-15

    Marburg virus (MARV), a member of the filovirus family, causes severe hemorrhagic fever with up to 90% lethality. MARV matrix protein VP40 is essential for assembly and release of newly copied viruses and also suppresses immune signaling in the infected cell. Here we report the crystal structure of MARV VP40. We found that MARV VP40 forms a dimer in solution, mediated by N-terminal domains, and that formation of this dimer is essential for budding of virus-like particles. We also found the N-terminal domain to be necessary and sufficient for immune antagonism. The C-terminal domains of MARV VP40 are dispensable for immunosuppression but are required for virus assembly. The C-terminal domains are only 16% identical to those of Ebola virus, differ in structure from those of Ebola virus, and form a distinct broad and flat cationic surface that likely interacts with the cell membrane during virus assembly. Marburg virus, a cousin of Ebola virus, causes severe hemorrhagic fever, with up to 90% lethality seen in recent outbreaks. Molecular structures and visual images of the proteins of Marburg virus are essential for the development of antiviral drugs. One key protein in the Marburg virus life cycle is VP40, which both assembles the virus and suppresses the immune system. Here we provide the molecular structure of Marburg virus VP40, illustrate differences from VP40 of Ebola virus, and reveal surfaces by which Marburg VP40 assembles progeny and suppresses immune function. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  4. Interaction of a putative BH3 domain of clusterin with anti-apoptotic Bcl-2 family proteins as revealed by NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dong-Hwa; Ha, Ji-Hyang [Medical Proteomics Research Center, KRIBB, Daejeon 305-806 (Korea, Republic of); Kim, Yul [Department of Bio and Brain Engineering, KAIST, Daejeon 305-701 (Korea, Republic of); Bae, Kwang-Hee [Medical Proteomics Research Center, KRIBB, Daejeon 305-806 (Korea, Republic of); Park, Jae-Yong [Department of Physiology, Institute of Health Science, School of Medicine, Gyeongsang National University, Jinju, Gyeongnam 660-751 (Korea, Republic of); Choi, Wan Sung [Department of Anatomy and Neurobiology, Institute of Health Science, School of Medicine, Gyeongsang National University, Jinju, Gyeongnam 660-751 (Korea, Republic of); Yoon, Ho Sup [Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637511 (Singapore); Park, Sung Goo; Park, Byoung Chul [Medical Proteomics Research Center, KRIBB, Daejeon 305-806 (Korea, Republic of); Yi, Gwan-Su, E-mail: gsyi@kaist.ac.kr [Department of Bio and Brain Engineering, KAIST, Daejeon 305-701 (Korea, Republic of); Chi, Seung-Wook, E-mail: swchi@kribb.re.kr [Medical Proteomics Research Center, KRIBB, Daejeon 305-806 (Korea, Republic of)

    2011-05-20

    Highlights: {yields} Identification of a conserved BH3 motif in C-terminal coiled coil region of nCLU. {yields} The nCLU BH3 domain binds to BH3 peptide-binding grooves in both Bcl-X{sub L} and Bcl-2. {yields} A conserved binding mechanism of nCLU BH3 and the other pro-apoptotic BH3 peptides with Bcl-X{sub L}. {yields} The absolutely conserved Leu323 and Asp328 of nCLU BH3 domain are critical for binding to Bcl-X{sub L.} {yields} Molecular understanding of the pro-apoptotic function of nCLU as a novel BH3-only protein. -- Abstract: Clusterin (CLU) is a multifunctional glycoprotein that is overexpressed in prostate and breast cancers. Although CLU is known to be involved in the regulation of apoptosis and cell survival, the precise molecular mechanism underlying the pro-apoptotic function of nuclear CLU (nCLU) remains unclear. In this study, we identified a conserved BH3 motif in C-terminal coiled coil (CC2) region of nCLU by sequence analysis and characterized the molecular interaction of the putative nCLU BH3 domain with anti-apoptotic Bcl-2 family proteins by nuclear magnetic resonance (NMR) spectroscopy. The chemical shift perturbation data demonstrated that the nCLU BH3 domain binds to pro-apoptotic BH3 peptide-binding grooves in both Bcl-X{sub L} and Bcl-2. A structural model of the Bcl-X{sub L}/nCLU BH3 peptide complex reveals that the binding mode is remarkably similar to those of other Bcl-X{sub L}/BH3 peptide complexes. In addition, mutational analysis confirmed that Leu323 and Asp328 of nCLU BH3 domain, absolutely conserved in the BH3 motifs of BH3-only protein family, are critical for binding to Bcl-X{sub L}. Taken altogether, our results suggest a molecular basis for the pro-apoptotic function of nCLU by elucidating the residue specific interactions of the BH3 motif in nCLU with anti-apoptotic Bcl-2 family proteins.

  5. Storage Rings

    International Nuclear Information System (INIS)

    Fischer, W.

    2010-01-01

    Storage rings are circular machines that store particle beams at a constant energy. Beams are stored in rings without acceleration for a number of reasons (Tab. 1). Storage rings are used in high-energy, nuclear, atomic, and molecular physics, as well as for experiments in chemistry, material and life sciences. Parameters for storage rings such as particle species, energy, beam intensity, beam size, and store time vary widely depending on the application. The beam must be injected into a storage ring but may not be extracted (Fig. 1). Accelerator rings such as synchrotrons are used as storage rings before and after acceleration. Particles stored in rings include electrons and positrons; muons; protons and anti-protons; neutrons; light and heavy, positive and negative, atomic ions of various charge states; molecular and cluster ions, and neutral polar molecules. Spin polarized beams of electrons, positrons, and protons were stored. The kinetic energy of the stored particles ranges from 10 -6 eV to 3.5 x 10 12 eV (LHC, 7 x 10 12 eV planned), the number of stored particles from one (ESR) to 1015 (ISR). To store beam in rings requires bending (dipoles) and transverse focusing (quadrupoles). Higher order multipoles are used to correct chromatic aberrations, to suppress instabilities, and to compensate for nonlinear field errors of dipoles and quadrupoles. Magnetic multipole functions can be combined in magnets. Beams are stored bunched with radio frequency systems, and unbunched. The magnetic lattice and radio frequency system are designed to ensure the stability of transverse and longitudinal motion. New technologies allow for better storage rings. With strong focusing the beam pipe dimensions became much smaller than previously possible. For a given circumference superconducting magnets make higher energies possible, and superconducting radio frequency systems allow for efficient replenishment of synchrotron radiation losses of large current electron or positron beams

  6. Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins*

    Science.gov (United States)

    Inaba, Satomi; Numoto, Nobutaka; Ogawa, Shuhei; Morii, Hisayuki; Ikura, Teikichi; Abe, Ryo; Ito, Nobutoshi; Oda, Masayuki

    2017-01-01

    Full activation of T cells and differentiation into effector T cells are essential for many immune responses and require co-stimulatory signaling via the CD28 receptor. Extracellular ligand binding to CD28 recruits protein-tyrosine kinases to its cytoplasmic tail, which contains a YMNM motif. Following phosphorylation of the tyrosine, the proteins growth factor receptor-bound protein 2 (Grb2), Grb2-related adaptor downstream of Shc (Gads), and p85 subunit of phosphoinositide 3-kinase may bind to pYMNM (where pY is phosphotyrosine) via their Src homology 2 (SH2) domains, leading to downstream signaling to distinct immune pathways. These three adaptor proteins bind to the same site on CD28 with variable affinity, and all are important for CD28-mediated co-stimulatory function. However, the mechanism of how these proteins recognize and compete for CD28 is unclear. To visualize their interactions with CD28, we have determined the crystal structures of Gads SH2 and two p85 SH2 domains in complex with a CD28-derived phosphopeptide. The high resolution structures obtained revealed that, whereas the CD28 phosphopeptide bound to Gads SH2 is in a bent conformation similar to that when bound to Grb2 SH2, it adopts a more extended conformation when bound to the N- and C-terminal SH2 domains of p85. These differences observed in the peptide-protein interactions correlated well with the affinity and other thermodynamic parameters for each interaction determined by isothermal titration calorimetry. The detailed insight into these interactions reported here may inform the development of compounds that specifically inhibit the association of CD28 with these adaptor proteins to suppress excessive T cell responses, such as in allergies and autoimmune diseases. PMID:27927989

  7. Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins.

    Science.gov (United States)

    Inaba, Satomi; Numoto, Nobutaka; Ogawa, Shuhei; Morii, Hisayuki; Ikura, Teikichi; Abe, Ryo; Ito, Nobutoshi; Oda, Masayuki

    2017-01-20

    Full activation of T cells and differentiation into effector T cells are essential for many immune responses and require co-stimulatory signaling via the CD28 receptor. Extracellular ligand binding to CD28 recruits protein-tyrosine kinases to its cytoplasmic tail, which contains a YMNM motif. Following phosphorylation of the tyrosine, the proteins growth factor receptor-bound protein 2 (Grb2), Grb2-related adaptor downstream of Shc (Gads), and p85 subunit of phosphoinositide 3-kinase may bind to pYMNM (where pY is phosphotyrosine) via their Src homology 2 (SH2) domains, leading to downstream signaling to distinct immune pathways. These three adaptor proteins bind to the same site on CD28 with variable affinity, and all are important for CD28-mediated co-stimulatory function. However, the mechanism of how these proteins recognize and compete for CD28 is unclear. To visualize their interactions with CD28, we have determined the crystal structures of Gads SH2 and two p85 SH2 domains in complex with a CD28-derived phosphopeptide. The high resolution structures obtained revealed that, whereas the CD28 phosphopeptide bound to Gads SH2 is in a bent conformation similar to that when bound to Grb2 SH2, it adopts a more extended conformation when bound to the N- and C-terminal SH2 domains of p85. These differences observed in the peptide-protein interactions correlated well with the affinity and other thermodynamic parameters for each interaction determined by isothermal titration calorimetry. The detailed insight into these interactions reported here may inform the development of compounds that specifically inhibit the association of CD28 with these adaptor proteins to suppress excessive T cell responses, such as in allergies and autoimmune diseases. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Topological rings

    CERN Document Server

    Warner, S

    1993-01-01

    This text brings the reader to the frontiers of current research in topological rings. The exercises illustrate many results and theorems while a comprehensive bibliography is also included. The book is aimed at those readers acquainted with some very basic point-set topology and algebra, as normally presented in semester courses at the beginning graduate level or even at the advanced undergraduate level. Familiarity with Hausdorff, metric, compact and locally compact spaces and basic properties of continuous functions, also with groups, rings, fields, vector spaces and modules, and with Zorn''s Lemma, is also expected.

  9. Ring accelerators

    International Nuclear Information System (INIS)

    Gisler, G.; Faehl, R.

    1983-01-01

    We present two-dimensional simulations in (r-z) and r-theta) cylinderical geometries of imploding-liner-driven accelerators of rings of charged particles. We address issues of azimuthal and longitudinal stability of the rings. We discuss self-trapping designs in which beam injection and extraction is aided by means of external cusp fields. Our simulations are done with the 2-1/2-D particle-in-cell plasma simulation code CLINER, which combines collisionless, electromagnetic PIC capabilities with a quasi-MHD finite element package

  10. Identification of nucleolus-associated chromatin domains reveals the role of the nucleolus in the 3D organisation of the A. thaliana genome

    Science.gov (United States)

    Pontvianne, Frédéric; Carpentier, Marie-Christine; Durut, Nathalie; Pavlištová, Veronika; Jaške, Karin; Schořová, Šárka; Parrinello, Hugues; Rohmer, Marine; Pikaard, Craig S; Fojtová, Miloslava; Fajkus, Jiří; Saez-Vasquez, Julio

    2017-01-01

    The nucleolus is the site of ribosomal RNA (rRNA) gene transcription, rRNA processing and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli by Fluorescence Activated Cell Sorting (FACS) and identified Nucleolus-Associated Chromatin Domains (NADs) by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein, NUCLEOLIN 1 (NUC1). NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions and mostly inactive protein-coding genes. However, NADs also include active ribosomal RNA genes, and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance. PMID:27477271

  11. Ring interferometry

    CERN Document Server

    Malykin, Grigorii B; Zhurov, Alexei

    2013-01-01

    This monograph is devoted to the creation of a comprehensive formalism for quantitative description of polarized modes' linear interaction in modern single-mode optic fibers. The theory of random connections between polarized modes, developed in the monograph, allows calculations of the zero shift deviations for a fiber ring interferometer. The monograph addresses also the

  12. Congruence between distribution modelling and phylogeographical analyses reveals Quaternary survival of a toadflax species (Linaria elegans) in oceanic climate areas of a mountain ring range.

    Science.gov (United States)

    Fernández-Mazuecos, Mario; Vargas, Pablo

    2013-06-01

    · The role of Quaternary climatic shifts in shaping the distribution of Linaria elegans, an Iberian annual plant, was investigated using species distribution modelling and molecular phylogeographical analyses. Three hypotheses are proposed to explain the Quaternary history of its mountain ring range. · The distribution of L. elegans was modelled using the maximum entropy method and projected to the last interglacial and to the last glacial maximum (LGM) using two different paleoclimatic models: the Community Climate System Model (CCSM) and the Model for Interdisciplinary Research on Climate (MIROC). Two nuclear and three plastid DNA regions were sequenced for 24 populations (119 individuals sampled). Bayesian phylogenetic, phylogeographical, dating and coalescent-based population genetic analyses were conducted. · Molecular analyses indicated the existence of northern and southern glacial refugia and supported two routes of post-glacial recolonization. These results were consistent with the LGM distribution as inferred under the CCSM paleoclimatic model (but not under the MIROC model). Isolation between two major refugia was dated back to the Riss or Mindel glaciations, > 100 kyr before present (bp). · The Atlantic distribution of inferred refugia suggests that the oceanic (buffered)-continental (harsh) gradient may have played a key and previously unrecognized role in determining Quaternary distribution shifts of Mediterranean plants. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  13. Mutational analysis of the RNA-binding domain of the Prunus necrotic ringspot virus (PNRSV) movement protein reveals its requirement for cell-to-cell movement.

    Science.gov (United States)

    Carmen Herranz, Ma; Sanchez-Navarro, Jesús-Angel; Saurí, Ana; Mingarro, Ismael; Pallás, Vicente

    2005-08-15

    The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is required for cell-to-cell movement. MP subcellular localization studies using a GFP fusion protein revealed highly punctate structures between neighboring cells, believed to represent plasmodesmata. Deletion of the RNA-binding domain (RBD) of PNRSV MP abolishes the cell-to-cell movement. A mutational analysis on this RBD was performed in order to identify in vivo the features that govern viral transport. Loss of positive charges prevented the cell-to-cell movement even though all mutants showed a similar accumulation level in protoplasts to those observed with the wild-type (wt) MP. Synthetic peptides representing the mutants and wild-type RBDs were used to study RNA-binding affinities by EMSA assays being approximately 20-fold lower in the mutants. Circular dichroism analyses revealed that the secondary structure of the peptides was not significantly affected by mutations. The involvement of the affinity changes between the viral RNA and the MP in the viral cell-to-cell movement is discussed.

  14. Mutational analysis of the RNA-binding domain of the Prunus necrotic ringspot virus (PNRSV) movement protein reveals its requirement for cell-to-cell movement

    International Nuclear Information System (INIS)

    Carmen Herranz, Ma; Sanchez-Navarro, Jesus-Angel; Sauri, Ana; Mingarro, Ismael; Pallas, Vicente

    2005-01-01

    The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is required for cell-to-cell movement. MP subcellular localization studies using a GFP fusion protein revealed highly punctate structures between neighboring cells, believed to represent plasmodesmata. Deletion of the RNA-binding domain (RBD) of PNRSV MP abolishes the cell-to-cell movement. A mutational analysis on this RBD was performed in order to identify in vivo the features that govern viral transport. Loss of positive charges prevented the cell-to-cell movement even though all mutants showed a similar accumulation level in protoplasts to those observed with the wild-type (wt) MP. Synthetic peptides representing the mutants and wild-type RBDs were used to study RNA-binding affinities by EMSA assays being approximately 20-fold lower in the mutants. Circular dichroism analyses revealed that the secondary structure of the peptides was not significantly affected by mutations. The involvement of the affinity changes between the viral RNA and the MP in the viral cell-to-cell movement is discussed

  15. Applicability of a particularly simple model to nonlinear elasticity of slide-ring gels with movable cross-links as revealed by unequal biaxial deformation.

    Science.gov (United States)

    Kondo, Yuuki; Urayama, Kenji; Kidowaki, Masatoshi; Mayumi, Koichi; Takigawa, Toshikazu; Ito, Kohzo

    2014-10-07

    The strain energy density function (F) of the polyrotaxane-based slide-ring (SR) gels with movable cross-links along the network strands is characterized by unequal biaxial stretching which can achieve various types of deformation. The SR gels as prepared without any post-preparation complication exhibit considerably smaller values of the ratio of the stresses (σy/σx) in the stretched (x) and constrained (y) directions in planar extension than classical chemical gels with heterogeneous and nearly homogeneous network structures do. This feature of the SR gels leads to the peculiar characteristic that the strain energy density function (F) has no explicit cross term of strains in different directions, which is in contrast to F with explicit strain cross terms for most chemical gels and elastomers. The biaxial stress-strain data of the SR gels are successfully described by F of the Gent model with only two parameters (small-strain shear modulus and a parameter representing ultimate elongation), which introduces the finite extensibility effect into the neo-Hookean model with no explicit cross term of strain. The biaxial data of the deswollen SR gels examined in previous study, which underwent a considerable reduction in volume from the preparation state, are also well described by the Gent model, which is in contrast to the case of the classical chemical gels that the stress-strain relations before and after large deswelling are not described by a common type of F due to a significant degree of collapse of the network strands in the deswollen state. These intriguing features of nonlinear elasticity of the SR gels originate from a novel function of the slidable cross-links that can maximize the arrangement entropy of cross-linked and non-cross-linked cyclic molecules in the deformed networks.

  16. The Rings of Saturn

    Science.gov (United States)

    Cuzzi, J. N.; Filacchione, G.; Marouf, E. A.

    2018-03-01

    One could become an expert on Saturn's iconic rings pretty easily in the early 1970s, as very little was known about them beyond the distinction between the A, B, and C rings, and the Cassini Division or "gap" between rings A and B (Alexander, 1962; Bobrov, 1970). Water ice was discovered spectroscopically on the ring particle surfaces, and radar and microwave emission observations proved that the particles must be centimeters to meters in size, consisting primarily, not just superficially, of water ice (Pollack, 1975). While a 2:1 orbital resonance with Mimas had long been suspected of having something to do with the Cassini Division, computers of the time were unable to model the subtle dynamical effects that we now know to dominate ring structure. This innocent state of affairs was exploded by the Voyager 1 and 2 encounters in 1980 and 1981. Spectacular images revealed filigree structure and odd regional color variations, and exquisitely detailed radial profiles of fluctuating particle abundance were obtained from the first stellar and radio occultations, having resolution almost at the scale of single particles. Voyager-era understanding was reviewed by Cuzzi et al. (1984) and Esposito et al. (1984). While the Voyager data kept ring scientists busy for decades, planning which led to the monumentally successful NASA-ESA-ASI Cassini mission, which arrived in 2004, had been under way even before Voyager got to Saturn. A review of pre-Cassini knowledge of Saturn's Rings can be found in Orton et al. (2009). This chapter will build on recent topical and process-specific reviews that treat the gamut of ring phenomena and its underlying physics in considerable detail (Colwell et al., 2009; Cuzzi et al., 2009; Horányi et al., 2009; Schmidt et al., 2009; Esposito, 2010; Tiscareno, 2013b; Esposito, 2014). We will follow and extend the general organization of Cuzzi et al. (2010), the most recent general discussion of Saturn's rings. For brevity and the benefit of the

  17. Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome

    Directory of Open Access Journals (Sweden)

    Frédéric Pontvianne

    2016-08-01

    Full Text Available The nucleolus is the site of rRNA gene transcription, rRNA processing, and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli using fluorescence-activated cell sorting (FACS and identified nucleolus-associated chromatin domains (NADs by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein NUCLEOLIN 1 (NUC1. NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs, sub-telomeric regions, and mostly inactive protein-coding genes. However, NADs also include active rRNA genes and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased, and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance.

  18. Change of Retinal Nerve Layer Thickness in Non-Arteritic Anterior Ischemic Optic Neuropathy Revealed by Fourier Domain Optical Coherence Tomography.

    Science.gov (United States)

    Han, Mei; Zhao, Chen; Han, Quan-Hong; Xie, Shiyong; Li, Yan

    2016-08-01

    To examine the changes of non-arteritic anterior ischemic optic neuropathy (NAION) by serial morphometry using Fourier domain optical coherence tomography (FD-OCT). Retrospective study in patients with newly diagnosed NAION (n=33, all unilateral) and controls (n=75 unilateral NAION patients with full contralateral eye vision) who underwent FD-OCT of the optic disk, optic nerve head (ONH), and macula within 1 week of onset and again 1, 3, 6, and 12 months later. The patients showed no improvement in vision during follow-up. Within 1 week of onset, all NAION eyes exhibited severe ONH fiber crowding and peripapillary retinal nerve fiber layer (RNFL) edema. Four had subretinal fluid accumulation and 12 had posterior vitreous detachment (PVD) at the optic disc surface. Ganglion cell complex (GCC) and RNFL thicknesses were reduced at 1 and 3 months (p < 0.05), with no deterioration thereafter. Initial RNFL/GCC contraction magnitude in the superior hemisphere correlated with the severity of inferior visual field deficits. NAION progression is characterized by an initial phase of accelerated RNFL and GCC deterioration. These results reveal that the kinetic change of neural retina in NAION and may have implication on the time window for treatment of NAION. FD-OCT is useful in the evaluation of NAION.

  19. Identification of Nucleolus-Associated Chromatin Domains Reveals a Role for the Nucleolus in 3D Organization of the A. thaliana Genome.

    Science.gov (United States)

    Pontvianne, Frédéric; Carpentier, Marie-Christine; Durut, Nathalie; Pavlištová, Veronika; Jaške, Karin; Schořová, Šárka; Parrinello, Hugues; Rohmer, Marine; Pikaard, Craig S; Fojtová, Miloslava; Fajkus, Jiří; Sáez-Vásquez, Julio

    2016-08-09

    The nucleolus is the site of rRNA gene transcription, rRNA processing, and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli using fluorescence-activated cell sorting (FACS) and identified nucleolus-associated chromatin domains (NADs) by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein NUCLEOLIN 1 (NUC1). NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions, and mostly inactive protein-coding genes. However, NADs also include active rRNA genes and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased, and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  20. Structures of the APC–ARM domain in complexes with discrete Amer1/WTX fragments reveal that it uses a consensus mode to recognize its binding partners

    Science.gov (United States)

    Zhang, Zhenyi; Akyildiz, Senem; Xiao, Yafei; Gai, Zhongchao; An, Ying; Behrens, Jürgen; Wu, Geng

    2015-01-01

    The tumor suppressor APC employs its conserved armadillo repeat (ARM) domain to recognize many of its binding partners, including Amer1/WTX, which is mutated in Wilms' tumor and bone overgrowth syndrome. The APC–Amer1 complex has important roles in regulating Wnt signaling and cell adhesion. Three sites A1, A2, and A3 of Amer1 have been reported to mediate its interaction with APC-ARM. In this study, crystal structures of APC–ARM in complexes with Amer1-A1, -A2, and -A4, which is newly identified in this work, were determined. Combined with our GST pull-down, yeast two-hybrid, and isothermal titration calorimetry (ITC) assay results using mutants of APC and Amer1 interface residues, our structures demonstrate that Amer1-A1, -A2, and -A4, as well as other APC-binding proteins such as Asef and Sam68, all employ a common recognition pattern to associate with APC–ARM. In contrast, Amer1-A3 binds to the C-terminal side of APC–ARM through a bipartite interaction mode. Composite mutations on either APC or Amer1 disrupting all four interfaces abrogated their association in cultured cells and impaired the membrane recruitment of APC by Amer1. Our study thus comprehensively elucidated the recognition mechanism between APC and Amer1, and revealed a consensus recognition sequence employed by various APC–ARM binding partners. PMID:27462415

  1. Structures of the APC-ARM domain in complexes with discrete Amer1/WTX fragments reveal that it uses a consensus mode to recognize its binding partners.

    Science.gov (United States)

    Zhang, Zhenyi; Akyildiz, Senem; Xiao, Yafei; Gai, Zhongchao; An, Ying; Behrens, Jürgen; Wu, Geng

    2015-01-01

    The tumor suppressor APC employs its conserved armadillo repeat (ARM) domain to recognize many of its binding partners, including Amer1/WTX, which is mutated in Wilms' tumor and bone overgrowth syndrome. The APC-Amer1 complex has important roles in regulating Wnt signaling and cell adhesion. Three sites A1, A2, and A3 of Amer1 have been reported to mediate its interaction with APC-ARM. In this study, crystal structures of APC-ARM in complexes with Amer1-A1, -A2, and -A4, which is newly identified in this work, were determined. Combined with our GST pull-down, yeast two-hybrid, and isothermal titration calorimetry (ITC) assay results using mutants of APC and Amer1 interface residues, our structures demonstrate that Amer1-A1, -A2, and -A4, as well as other APC-binding proteins such as Asef and Sam68, all employ a common recognition pattern to associate with APC-ARM. In contrast, Amer1-A3 binds to the C-terminal side of APC-ARM through a bipartite interaction mode. Composite mutations on either APC or Amer1 disrupting all four interfaces abrogated their association in cultured cells and impaired the membrane recruitment of APC by Amer1. Our study thus comprehensively elucidated the recognition mechanism between APC and Amer1, and revealed a consensus recognition sequence employed by various APC-ARM binding partners.

  2. Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and CryoEM modeling.

    Science.gov (United States)

    Rizzo, Alessandro A; Suhanovsky, Margaret M; Baker, Matthew L; Fraser, LaTasha C R; Jones, Lisa M; Rempel, Don L; Gross, Michael L; Chiu, Wah; Alexandrescu, Andrei T; Teschke, Carolyn M

    2014-06-10

    Some capsid proteins built on the ubiquitous HK97-fold have accessory domains imparting specific functions. Bacteriophage P22 coat protein has a unique insertion domain (I-domain). Two prior I-domain models from subnanometer cryoelectron microscopy (cryoEM) reconstructions differed substantially. Therefore, the I-domain's nuclear magnetic resonance structure was determined and also used to improve cryoEM models of coat protein. The I-domain has an antiparallel six-stranded β-barrel fold, not previously observed in HK97-fold accessory domains. The D-loop, which is dynamic in the isolated I-domain and intact monomeric coat protein, forms stabilizing salt bridges between adjacent capsomers in procapsids. The S-loop is important for capsid size determination, likely through intrasubunit interactions. Ten of 18 coat protein temperature-sensitive-folding substitutions are in the I-domain, indicating its importance in folding and stability. Several are found on a positively charged face of the β-barrel that anchors the I-domain to a negatively charged surface of the coat protein HK97-core. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role

    International Nuclear Information System (INIS)

    Krishna, S. Sri; Aravind, L.; Bakolitsa, Constantina; Caruthers, Jonathan; Carlton, Dennis; Miller, Mitchell D.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C.; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Reyes, Ron; Rife, Christopher L.; Bedem, Henry van den; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    The crystal structure of SSO2064, the first structural representative of Pfam family PF01796 (DUF35), reveals a two-domain architecture comprising an N-terminal zinc-ribbon domain and a C-terminal OB-fold domain. Analysis of the domain architecture, operon organization and bacterial orthologs combined with the structural features of SSO2064 suggests a role involving acyl-CoA binding for this family of proteins. SSO2064 is the first structural representative of PF01796 (DUF35), a large prokaryotic family with a wide phylogenetic distribution. The structure reveals a novel two-domain architecture comprising an N-terminal, rubredoxin-like, zinc ribbon and a C-terminal, oligonucleotide/oligosaccharide-binding (OB) fold domain. Additional N-terminal helical segments may be involved in protein–protein interactions. Domain architectures, genomic context analysis and functional evidence from certain bacterial representatives of this family suggest that these proteins form a novel fatty-acid-binding component that is involved in the biosynthesis of lipids and polyketide antibiotics and that they possibly function as acyl-CoA-binding proteins. This structure has led to a re-evaluation of the DUF35 family, which has now been split into two entries in the latest Pfam release (v.24.0)

  4. Unique structure and dynamics of the EphA5 ligand binding domain mediate its binding specificity as revealed by X-ray crystallography, NMR and MD simulations.

    Directory of Open Access Journals (Sweden)

    Xuelu Huan

    Full Text Available The 16 EphA and EphB receptors represent the largest family of receptor tyrosine kinases, and their interactions with 9 ephrin-A and ephrin-B ligands initiate bidirectional signals controlling many physiological and pathological processes. Most interactions occur between receptor and ephrins of the same class, and only EphA4 can bind all A and B ephrins. To understand the structural and dynamic principles that enable Eph receptors to utilize the same jellyroll β-sandwich fold to bind ephrins, the VAPB-MSP domain, peptides and small molecules, we have used crystallography, NMR and molecular dynamics (MD simulations to determine the first structure and dynamics of the EphA5 ligand-binding domain (LBD, which only binds ephrin-A ligands. Unexpectedly, despite being unbound, the high affinity ephrin-binding pocket of EphA5 resembles that of other Eph receptors bound to ephrins, with a helical conformation over the J-K loop and an open pocket. The openness of the pocket is further supported by NMR hydrogen/deuterium exchange data and MD simulations. Additionally, the EphA5 LBD undergoes significant picosecond-nanosecond conformational exchanges over the loops, as revealed by NMR and MD simulations, but lacks global conformational exchanges on the microsecond-millisecond time scale. This is markedly different from the EphA4 LBD, which shares 74% sequence identity and 87% homology. Consequently, the unbound EphA5 LBD appears to comprise an ensemble of open conformations that have only small variations over the loops and appear ready to bind ephrin-A ligands. These findings show how two proteins with high sequence homology and structural similarity are still able to achieve distinctive binding specificities through different dynamics, which may represent a general mechanism whereby the same protein fold can serve for different functions. Our findings also suggest that a promising strategy to design agonists/antagonists with high affinity and selectivity

  5. Interaction of ring dark solitons with ring impurities in Bose-Einstein condensates

    International Nuclear Information System (INIS)

    Xue Jukui

    2005-01-01

    The interaction of ring dark solitons/vortexes with the ring-shaped repulsive and attractive impurities in two-dimensional Bose-Einstein condensates is investigated numerically. Very rich interaction phenomena are obtained, i.e., not only the interaction between the ring soliton and the impurity, but also the interaction between vortexes and the impurity. The interaction characters, i.e., snaking of ring soliton, quasitrapping or reflection of ring soliton and vortexes by the impurity, strongly depend on initial ring soliton velocity, impurity strength, initial position of ring soliton and impurity. The numerical results also reveal that ring dark solitons/vortexes can be trapped and dragged by an adiabatically moving attractive ring impurity

  6. High-resolution crystal structure reveals a HEPN domain at the C-terminal region of S. cerevisiae RNA endonuclease Swt1

    International Nuclear Information System (INIS)

    Peng, Shuxia; Zhou, Ke; Wang, Wenjia; Gao, Zengqiang; Dong, Yuhui; Liu, Quansheng

    2014-01-01

    Highlights: • Crystal structure of the C-terminal (CT) domain of Swt1 was determined at 2.3 Å. • Structure of the CT domain was identified as HEPN domain superfamily member. • Low-resolution envelope of Swt1 full-length in solution was analyzed by SAXS. • The middle and CT domains gave good fit to SAXS structural model. - Abstract: Swt1 is an RNA endonuclease that plays an important role in quality control of nuclear messenger ribonucleoprotein particles (mRNPs) in eukaryotes; however, its structural details remain to be elucidated. Here, we report the crystal structure of the C-terminal (CT) domain of Swt1 from Saccharomyces cerevisiae, which shares common characteristics of higher eukaryotes and prokaryotes nucleotide binding (HEPN) domain superfamily. To study in detail the full-length protein structure, we analyzed the low-resolution architecture of Swt1 in solution using small angle X-ray scattering (SAXS) method. Both the CT domain and middle domain exhibited a good fit upon superimposing onto the molecular envelope of Swt1. Our study provides the necessary structural information for detailed analysis of the functional role of Swt1, and its importance in the process of nuclear mRNP surveillance

  7. Receptor complementation and mutagenesis reveal SR-BI as an essential HCV entry factor and functionally imply its intra- and extra-cellular domains.

    Directory of Open Access Journals (Sweden)

    Marlène Dreux

    2009-02-01

    Full Text Available HCV entry into cells is a multi-step and slow process. It is believed that the initial capture of HCV particles by glycosaminoglycans and/or lipoprotein receptors is followed by coordinated interactions with the scavenger receptor class B type I (SR-BI, a major receptor of high-density lipoprotein (HDL, the CD81 tetraspanin, and the tight junction protein Claudin-1, ultimately leading to uptake and cellular penetration of HCV via low-pH endosomes. Several reports have indicated that HDL promotes HCV entry through interaction with SR-BI. This pathway remains largely elusive, although it was shown that HDL neither associates with HCV particles nor modulates HCV binding to SR-BI. In contrast to CD81 and Claudin-1, the importance of SR-BI has only been addressed indirectly because of lack of cells in which functional complementation assays with mutant receptors could be performed. Here we identified for the first time two cell types that supported HCVpp and HCVcc entry upon ectopic SR-BI expression. Remarkably, the undetectable expression of SR-BI in rat hepatoma cells allowed unambiguous investigation of human SR-BI functions during HCV entry. By expressing different SR-BI mutants in either cell line, our results revealed features of SR-BI intracellular domains that influence HCV infectivity without affecting receptor binding and stimulation of HCV entry induced by HDL/SR-BI interaction. Conversely, we identified positions of SR-BI ectodomain that, by altering HCV binding, inhibit entry. Finally, we characterized alternative ectodomain determinants that, by reducing SR-BI cholesterol uptake and efflux functions, abolish HDL-mediated infection-enhancement. Altogether, we demonstrate that SR-BI is an essential HCV entry factor. Moreover, our results highlight specific SR-BI determinants required during HCV entry and physiological lipid transfer functions hijacked by HCV to favor infection.

  8. Foundations of commutative rings and their modules

    CERN Document Server

    Wang, Fanggui

    2016-01-01

    This book provides an introduction to the basics and recent developments of commutative algebra. A glance at the contents of the first five chapters shows that the topics covered are ones that usually are included in any commutative algebra text. However, the contents of this book differ significantly from most commutative algebra texts: namely, its treatment of the Dedekind–Mertens formula, the (small) finitistic dimension of a ring, Gorenstein rings, valuation overrings and the valuative dimension, and Nagata rings. Going further, Chapter 6 presents w-modules over commutative rings as they can be most commonly used by torsion theory and multiplicative ideal theory. Chapter 7 deals with multiplicative ideal theory over integral domains. Chapter 8 collects various results of the pullbacks, especially Milnor squares and D+M constructions, which are probably the most important example-generating machines. In Chapter 9, coherent rings with finite weak global dimensions are probed, and the local ring of weak gl...

  9. On (m, n)-absorbing ideals of commutative rings

    Indian Academy of Sciences (India)

    with respect to various ring theoretic constructions and study (m, n)-absorbing ideals in several commutative rings. For example, in a Bézout ring or a Boolean ring, an ideal is an (m, n)-absorbing ideal if and only if it is an n-absorbing ideal, and in an almost. Dedekind domain every (m, n)-absorbing ideal is a product of at ...

  10. Domains and domain loss

    DEFF Research Database (Denmark)

    Haberland, Hartmut

    2005-01-01

    politicians and in the media, especially in the discussion whether some languages undergo ‘domain loss’ vis-à-vis powerful international languages like English. An objection that has been raised here is that domains, as originally conceived, are parameters of language choice and not properties of languages...

  11. The 1.75 Å resolution structure of fission protein Fis1 from Saccharomyces cerevisiae reveals elusive interactions of the autoinhibitory domain

    International Nuclear Information System (INIS)

    Tooley, James E.; Khangulov, Victor; Lees, Jonathan P. B.; Schlessman, Jamie L.; Bewley, Maria C.; Heroux, Annie; Bosch, Jürgen; Hill, R. Blake

    2011-01-01

    A 1.75 Å resolution crystal structure of the Fis1 cytoplasmic domain from Saccharomyces cerevisiae is reported which adopts a tetratricopeptide-repeat fold. Fis1 mediates mitochondrial and peroxisomal fission. It is tail-anchored to these organelles by a transmembrane domain, exposing a soluble cytoplasmic domain. Previous studies suggested that Fis1 is autoinhibited by its N-terminal region. Here, a 1.75 Å resolution crystal structure of the Fis1 cytoplasmic domain from Saccharomyces cerevisiae is reported which adopts a tetratricopeptide-repeat fold. It is observed that this fold creates a concave surface important for fission, but is sterically occluded by its N-terminal region. Thus, this structure provides a physical basis for autoinhibition and allows a detailed examination of the interactions that stabilize the inhibited state of this molecule

  12. Kayser-Fleischer Rings

    Science.gov (United States)

    ... Support Contacts Lab Tracker/Copper Calculator Stories Programs & Research ... About Everything you need to know about Wilson Disease Kayser-Fleischer Rings Definition Kayser-Fleischer Ring: Clinical sign. Brownish-yellow ring visible around the corneo- ...

  13. Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition.

    Directory of Open Access Journals (Sweden)

    Thomas Hoffmann

    2015-07-01

    Full Text Available T-cell receptors (TCR play an important role in the adaptive immune system as they recognize pathogen- or cancer-based epitopes and thus initiate the cell-mediated immune response. Therefore there exists a growing interest in the optimization of TCRs for medical purposes like adoptive T-cell therapy. However, the molecular mechanisms behind T-cell signaling are still predominantly unknown. For small sets of TCRs it was observed that the angle between their Vα- and Vβ-domains, which bind the epitope, can vary and might be important for epitope recognition. Here we present a comprehensive, quantitative study of the variation in the Vα/Vβ interdomain-angle and its influence on epitope recognition, performing a systematic bioinformatics analysis based on a representative set of experimental TCR structures. For this purpose we developed a new, cuboid-based superpositioning method, which allows a unique, quantitative analysis of the Vα/Vβ-angles. Angle-based clustering led to six significantly different clusters. Analysis of these clusters revealed the unexpected result that the angle is predominantly influenced by the TCR-clonotype, whereas the bound epitope has only a minor influence. Furthermore we could identify a previously unknown center of rotation (CoR, which is shared by all TCRs. All TCR geometries can be obtained by rotation around this center, rendering it a new, common TCR feature with the potential of improving the accuracy of TCR structure prediction considerably. The importance of Vα/Vβ rotation for signaling was confirmed as we observed larger variances in the Vα/Vβ-angles in unbound TCRs compared to epitope-bound TCRs. Our results strongly support a two-step mechanism for TCR-epitope: First, preformation of a flexible TCR geometry in the unbound state and second, locking of the Vα/Vβ-angle in a TCR-type specific geometry upon epitope-MHC association, the latter being driven by rotation around the unique center of rotation.

  14. ASSOCIATIVE RINGS SOLVED AS LIE RINGS

    Directory of Open Access Journals (Sweden)

    M. B. Smirnov

    2011-01-01

    Full Text Available The paper has proved that an associative ring which is solvable of a n- class as a Lie ring has a nilpotent ideal of the nilpotent class not more than 3×10n–2  and a corresponding quotient ring satisfies an identity [[x1, x2, [x3, x4

  15. Conserved intron positions in FGFR genes reflect the modular structure of FGFR and reveal stepwise addition of domains to an already complex ancestral FGFR.

    Science.gov (United States)

    Rebscher, Nicole; Deichmann, Christina; Sudhop, Stefanie; Fritzenwanker, Jens Holger; Green, Stephen; Hassel, Monika

    2009-10-01

    We have analyzed the evolution of fibroblast growth factor receptor (FGFR) tyrosine kinase genes throughout a wide range of animal phyla. No evidence for an FGFR gene was found in Porifera, but we tentatively identified an FGFR gene in the placozoan Trichoplax adhaerens. The gene encodes a protein with three immunoglobulin-like domains, a single-pass transmembrane, and a split tyrosine kinase domain. By superimposing intron positions of 20 FGFR genes from Placozoa, Cnidaria, Protostomia, and Deuterostomia over the respective protein domain structure, we identified ten ancestral introns and three conserved intron groups. Our analysis shows (1) that the position of ancestral introns correlates to the modular structure of FGFRs, (2) that the acidic domain very likely evolved in the last common ancestor of triploblasts, (3) that splicing of IgIII was enabled by a triploblast-specific insertion, and (4) that IgI is subject to substantial loss or duplication particularly in quickly evolving genomes. Moreover, intron positions in the catalytic domain of FGFRs map to the borders of protein subdomains highly conserved in other serine/threonine kinases. Nevertheless, these introns were introduced in metazoan receptor tyrosine kinases exclusively. Our data support the view that protein evolution dating back to the Cambrian explosion took place in such a short time window that only subtle changes in the domain structure are detectable in extant representatives of animal phyla. We propose that the first multidomain FGFR originated in the last common ancestor of Placozoa, Cnidaria, and Bilateria. Additional domains were introduced mainly in the ancestor of triploblasts and in the Ecdysozoa.

  16. The Structure of the RNA m5C Methyltransferase YebU from Escherichia coli Reveals a C-terminal RNA-recruiting PUA Domain

    DEFF Research Database (Denmark)

    Hallberg, B. Martin; Ericsson, Ulrika B.; Johnson, Kenneth A

    2006-01-01

    potential that differ from other RNA-MTase structures, suggesting that YebU interacts with its RNA target in a different manner. Docking of YebU onto the 30 S subunit indicates that the PUA and MTase domains make several contacts with 16 S rRNA as well as with the ribosomal protein S12. The ribosomal...... protein interactions would explain why the assembled 30 S subunit, and not naked 16 S rRNA, is the preferred substrate for YebU....... by X-ray crystallography, and we present a molecular model for how YebU specifically recognizes, binds and methylates its ribosomal substrate. The YebU protein has an N-terminal SAM-binding catalytic domain with structural similarity to the equivalent domains in several other m(5)C RNA MTases including...

  17. Threading structural model of the manganese-stabilizing protein PsbO reveals presence of two possible beta-sandwich domains.

    Science.gov (United States)

    Pazos, F; Heredia, P; Valencia, A; de las Rivas, J

    2001-12-01

    The manganese-stabilizing protein (PsbO) is an essential component of photosystem II (PSII) and is present in all oxyphotosynthetic organisms. PsbO allows correct water splitting and oxygen evolution by stabilizing the reactions driven by the manganese cluster. Despite its important role, its structure and detailed functional mechanism are still unknown. In this article we propose a structural model based on fold recognition and molecular modeling. This model has additional support from a study of the distribution of characteristics of the PsbO sequence family, such as the distribution of conserved, apolar, tree-determinants, and correlated positions. Our threading results consistently showed PsbO as an all-beta (beta) protein, with two homologous beta domains of approximately 120 amino acids linked by a flexible Proline-Glycine-Glycine (PGG) motif. These features are compatible with a general elongated and flexible architecture, in which the two domains form a sandwich-type structure with Greek key topology. The first domain is predicted to include 8 to 9 beta-strands, the second domain 6 to 7 beta-strands. An Ig-like beta-sandwich structure was selected as a template to build the 3-D model. The second domain has, between the strands, long-loops rich in Pro and Gly that are difficult to model. One of these long loops includes a highly conserved region (between P148 and P174) and a short alpha-helix (between E181 and N188)). These regions are characteristic parts of PsbO and show that the second domain is not so similar to the template. Overall, the model was able to account for much of the experimental data reported by several authors, and it would allow the detection of key residues and regions that are proposed in this article as essential for the structure and function of PsbO. Copyright 2001 Wiley-Liss, Inc.

  18. Novel human mutation and CRISPR/Cas genome-edited mice reveal the importance of C-terminal domain of MSX1 in tooth and palate development.

    Science.gov (United States)

    Mitsui, Silvia Naomi; Yasue, Akihiro; Masuda, Kiyoshi; Naruto, Takuya; Minegishi, Yoshiyuki; Oyadomari, Seiichi; Noji, Sumihare; Imoto, Issei; Tanaka, Eiji

    2016-12-05

    Several mutations, located mainly in the MSX1 homeodomain, have been identified in non-syndromic tooth agenesis predominantly affecting premolars and third molars. We identified a novel frameshift mutation of the highly conserved C-terminal domain of MSX1, known as Msx homology domain 6 (MH6), in a Japanese family with non-syndromic tooth agenesis. To investigate the importance of MH6 in tooth development, Msx1 was targeted in mice with CRISPR/Cas system. Although heterozygous MH6 disruption did not alter craniofacial development, homozygous mice exhibited agenesis of lower incisors with or without cleft palate at E16.5. In addition, agenesis of the upper third molars and the lower second and third molars were observed in 4-week-old mutant mice. Although the upper second molars were present, they were abnormally small. These results suggest that the C-terminal domain of MSX1 is important for tooth and palate development, and demonstrate that that CRISPR/Cas system can be used as a tool to assess causality of human disorders in vivo and to study the importance of conserved domains in genes.

  19. Swapping the N- and C-terminal domains of human apolipoprotein E3 and AI reveals insights into their structure/activity relationship.

    Directory of Open Access Journals (Sweden)

    Mark T Lek

    Full Text Available Apolipoprotein (apo E3 and apoAI are exchangeable apolipoproteins that play a dominant role in regulating plasma lipoprotein metabolism. ApoE3 (299 residues is composed of an N-terminal (NT domain bearing a 4-helix bundle and a C-terminal (CT domain bearing a series of amphipathic α-helices. ApoAI (243 residues also comprises a highly helical NT domain and a less structured CT tail. The objective of this study was to understand their structural and functional role by generating domain swapped chimeras: apoE3-NT/apoAI-CT and apoAI-NT/apoE-CT. The bacterially overexpressed chimeras were purified by affinity chromatography and their identity confirmed by immunoblotting and mass spectrometry. Their α-helical content was comparable to that of the parent proteins. ApoE3-NT/apoAI-CT retained the denaturation profile of apoE3 NT domain, with apoAI CT tail eliciting a relatively unstructured state; its lipid binding ability improved dramatically compared to apoE3 indicative of a significant role of apoAI CT tail in lipid binding interaction. The LDL receptor interaction and ability to promote ABCA1-mediated cholesterol efflux of apoE3-NT/apoAI-CT was comparable to that of apoE3. In contrast, apoAI-NT/apoE-CT elicited an unfolding pattern and lipid binding ability that were similar to that of apoAI. As expected, DMPC/apoAI-NT/apoE-CT discoidal particles did not elicit LDLr binding ability, and promoted SR-B1 mediated cellular uptake of lipids to a limited extent. However, apoAI-NT/apoE-CT displayed an enhanced ability to promote cholesterol efflux compared to apoAI, indicative of a significant role for apoE CT domain in mediating this function. Together, these results indicate that the functional attributes of apoAI and apoE3 can be conferred on each other and that NT-CT domain interactions significantly modulate their structure and function.

  20. Stirling engine piston ring

    Science.gov (United States)

    Howarth, Roy B.

    1983-01-01

    A piston ring design for a Stirling engine wherein the contact pressure between the piston and the cylinder is maintained at a uniform level, independent of engine conditions through a balancing of the pressure exerted upon the ring's surface and thereby allowing the contact pressure on the ring to be predetermined through the use of a preloaded expander ring.

  1. Alternative loop rings

    CERN Document Server

    Goodaire, EG; Polcino Milies, C

    1996-01-01

    For the past ten years, alternative loop rings have intrigued mathematicians from a wide cross-section of modern algebra. As a consequence, the theory of alternative loop rings has grown tremendously. One of the main developments is the complete characterization of loops which have an alternative but not associative, loop ring. Furthermore, there is a very close relationship between the algebraic structures of loop rings and of group rings over 2-groups. Another major topic of research is the study of the unit loop of the integral loop ring. Here the interaction between loop rings and group ri

  2. An Asymmetric Runaway Domain Swap Antithrombin Dimer as a Key Intermediate for Polymerization Revealed by Hydrogen/Deuterium-Exchange Mass Spectrometry

    DEFF Research Database (Denmark)

    Trelle, Morten Beck; Pedersen, Shona H; Østerlund, Eva Christina

    2017-01-01

    Antithrombin deficiency is associated with increased risk of venous thrombosis. In certain families, this condition is caused by pathogenic polymerization of mutated antithrombin in the blood. To facilitate future development of pharmaceuticals against antithrombin polymerization, an improved und...... strongly supports a β4A-β5A β-hairpin runaway domain swap mechanism for antithrombin polymerization. HDX-MS thus holds exceptional promise as an enabling analytical technique in the efforts toward future pharmacological intervention with protein polymerization and associated diseases....

  3. Crystal structure of ryanodine receptor N-terminal domain from Plutella xylostella reveals two potential species-specific insecticide-targeting sites.

    Science.gov (United States)

    Lin, Lianyun; Liu, Chen; Qin, Juan; Wang, Jie; Dong, Shengjie; Chen, Wei; He, Weiyi; Gao, Qingzhi; You, Minsheng; Yuchi, Zhiguang

    2018-01-01

    Ryanodine receptors (RyRs) are large calcium-release channels located in sarcoplasmic reticulum membrane. They play a central role in excitation-contraction coupling of muscle cells. Three commercialized insecticides targeting pest RyRs generate worldwide sales over 2 billion U.S. dollars annually, but the structure of insect RyRs remains elusive, hindering our understanding of the mode of action of RyR-targeting insecticides and the development of insecticide resistance in pests. Here we present the crystal structure of RyR N-terminal domain (NTD) (residue 1-205) at 2.84 Å resolution from the diamondback moth (DBM), Plutella xylostella, a destructive pest devouring cruciferous crops all over the world. Similar to its mammalian homolog, DBM RyR NTD consists of a beta-trefoil folding motif and a flanking alpha helix. Interestingly, two regions in NTD interacting with neighboring domains showed distinguished conformations in DBM relative to mammalian RyRs. Using homology modeling and molecular dynamics simulation, we created a structural model of the N-terminal three domains, showing two unique binding pockets that could be targeted by potential species-specific insecticides. Thermal melt experiment showed that the stability of DBM RyR NTD was higher than mammalian RyRs, probably due to a stable intra-domain disulfide bond observed in the crystal structure. Previously DBM NTD was shown to be one of the two critical regions to interact with insecticide flubendiamide, but isothermal titration calorimetry experiments negated DBM NTD alone as a major binding site for flubendiamide. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. 3.3 Å structure of Niemann–Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xiaochun; Lu, Feiran; Trinh, Michael N.; Schmiege, Philip; Seemann, Joachim; Wang, Jiawei; Blobel, Günter

    2017-08-07

    Niemann–Pick C1 (NPC1) and NPC2 proteins are indispensable for the export of LDL-derived cholesterol from late endosomes. Mutations in these proteins result in Niemann–Pick type C disease, a lysosomal storage disease. Despite recent reports of the NPC1 structure depicting its overall architecture, the function of its C-terminal luminal domain (CTD) remains poorly understood even though 45% of NPC disease-causing mutations are in this domain. Here, we report a crystal structure at 3.3 Å resolution of NPC1* (residues 314–1,278), which—in contrast to previous lower resolution structures—features the entire CTD well resolved. Notably, all eight cysteines of the CTD form four disulfide bonds, one of which (C909–C914) enforces a specific loop that in turn mediates an interaction with a loop of the N-terminal domain (NTD). Importantly, this loop and its interaction with the NTD were not observed in any previous structures due to the lower resolution. Our mutagenesis experiments highlight the physiological relevance of the CTD–NTD interaction, which might function to keep the NTD in the proper orientation for receiving cholesterol from NPC2. Additionally, this structure allows us to more precisely map all of the disease-causing mutations, allowing future molecular insights into the pathogenesis of NPC disease.

  5. C-Terminal Substitution of HBV Core Proteins with Those from DHBV Reveals That Arginine-Rich 167RRRSQSPRR175 Domain Is Critical for HBV Replication

    Science.gov (United States)

    Kim, Taeyeung; Shin, Bo-Hye; Park, Gil-Soon; Park, Sun; Chwae, Yong-Joon; Shin, Ho-Joon; Kim, Kyongmin

    2012-01-01

    To investigate the contributions of carboxyl-terminal nucleic acid binding domain of HBV core (C) protein for hepatitis B virus (HBV) replication, chimeric HBV C proteins were generated by substituting varying lengths of the carboxyl-terminus of duck hepatitis B virus (DHBV) C protein for the corresponding regions of HBV C protein. All chimeric C proteins formed core particles. A chimeric C protein with 221–262 amino acids of DHBV C protein, in place of 146–185 amino acids of the HBV C protein, supported HBV pregenomic RNA (pgRNA) encapsidation and DNA synthesis: 40% amino acid sequence identity or 45% homology in the nucleic-acid binding domain of HBV C protein was sufficient for pgRNA encapsidation and DNA synthesis, although we predominantly detected spliced DNA. A chimeric C protein with 221–241 and 251–262 amino acids of DHBV C, in place of HBV C 146–166 and 176–185 amino acids, respectively, could rescue full-length DNA synthesis. However, a reciprocal C chimera with 242–250 of DHBV C (242RAGSPLPRS 250) introduced in place of 167–175 of HBV C (167RRRSQSPRR 175) significantly decreased pgRNA encapsidation and DNA synthesis, and full-length DNA was not detected, demonstrating that the arginine-rich 167RRRSQSPRR175 domain may be critical for efficient viral replication. Five amino acids differing between viral species (underlined above) were tested for replication rescue; R169 and R175 were found to be important. PMID:22911745

  6. Dissection of an old protein reveals a novel application: domain D of Staphylococcus aureus Protein A (sSpAD as a secretion - tag

    Directory of Open Access Journals (Sweden)

    Paal Michael

    2010-11-01

    Full Text Available Abstract Background Escherichia coli as a frequently utilized host organism for recombinant protein production offers different cellular locations with distinct qualities. The periplasmic space is often favored for the production of complex proteins due to enhanced disulfide bond formation, increased target product stability and simplified downstream processing. To direct proteins to the periplasmic space rather small proteinaceus tags that can be used for affinity purification would be advantageous. Results We discovered that domain D of the Staphylococcus aureus protein A was sufficient for the secretion of various target proteins into the periplasmic space of E. coli. Our experiments indicated the Sec pathway as the mode of secretion, although N-terminal processing was not observed. Furthermore, the solubility of recombinant fusion proteins was improved for proteins prone to aggregation. The tag allowed a straightforward affinity purification of recombinant fusion protein via an IgG column, which was exemplified for the target protein human superoxide dismutase 1 (SOD. Conclusions In this work we present a new secretion tag that combines several advantages for the production of recombinant proteins in E. coli. Domain D of S. aureus protein A protects the protein of interest against N-terminal degradation, increases target protein solubility and enables a straight-forward purification of the recombinant protein using of IgG columns.

  7. IL-6/IL-12 Cytokine Receptor Shuffling of Extra- and Intracellular Domains Reveals Canonical STAT Activation via Synthetic IL-35 and IL-39 Signaling.

    Science.gov (United States)

    Floss, D M; Schönberg, M; Franke, M; Horstmeier, F C; Engelowski, E; Schneider, A; Rosenfeldt, E M; Scheller, J

    2017-11-09

    IL-35 and IL-39 are recently discovered shared members of the IL-6- and IL-12-type cytokine family with immune-suppressive capacity. IL-35 has been reported to induce the formation of four different receptor complexes: gp130:IL-12β2, gp130:gp130, IL-12β2:IL-12β2, and IL-12β2:WSX-1. IL-39 was proposed to form a gp130:IL-23R receptor complex. IL-35, but not IL-39, has been reported to activate non-conventional STAT signaling, depending on the receptor complex and target cell. Analyses of IL-35 and IL-39 are, however, hampered by the lack of biologically active recombinant IL-35 and IL-39 proteins. Therefore, we engineered chimeric cytokine receptors to accomplish synthetic IL-35 and IL- 39 signaling by shuffling the extra- and intracellular domains of IL-6/IL-12-type cytokine receptors, resulting in biological activity for all previously described IL-35 receptor complexes. Moreover, we found that the proposed IL-39 receptor complex is biologically active and discovered two additional biologically active synthetic receptor combinations, gp130/IL-12Rβ1 and IL-23R/IL-12Rβ2. Surprisingly, synthetic IL-35 activation led to more canonical STAT signaling of all receptor complexes. In summary, our receptor shuffling approach highlights an interchangeable, modular domain structure among IL-6- and IL-12-type cytokine receptors and enabled synthetic IL-35 and IL-39 signaling.

  8. Wear Analysis of Top Piston Ring to Reduce Top Ring Reversal Bore Wear

    Directory of Open Access Journals (Sweden)

    P. Ilanthirayan

    2017-12-01

    Full Text Available The piston rings are the most important part in engine which controls the lubricating oil consumption and blowby of the gases. The lubricating film of oil is provided to seal of gases towards crankcase and also to give smooth friction free translatory motion between rings and liner. Of the three rings present top ring is more crucial as it does the main work of restricting gases downwards the crankcase. Boundary lubrication is present at the Top dead centre (TDC and Bottom dead centre (BDC of the liner surface. In addition to this, top ring is exposed to high temperature gases which makes the oil present near the top ring to get evaporated and decreasing its viscosity, making metal-metal contact most of the time. Due to this at TDC, excess wear happens on the liner which is termed as Top ring reversal bore wear. The wear rate depends upon many parameters such as lubrication condition, viscosity index, contact type, normal forces acting on ring, geometry of ring face, surface roughness, material property. The present work explores the wear depth for different geometries of barrel ring using Finite Element model with the help of Archard wear law and the same is validated through experimentation. The study reveals that Asymmetric barrel rings have less contact pressure which in turn reduces the wear at Top dead centre.

  9. Accretion in Saturn's F Ring

    Science.gov (United States)

    Meinke, B. K.; Esposito, L. W.; Stewart, G.

    2012-12-01

    Saturn's F ring is the solar system's principal natural laboratory for direct observation of accretion and disruption processes. The ring resides in the Roche zone, where tidal disruption competes with self-gravity, which allows us to observe the lifecycle of moonlets. Just as nearby moons create structure at the B ring edge (Esposito et al. 2012) and the Keeler gap (Murray 2007), the F ring "shepherding" moons Prometheus and Pandora stir up ring material and create observably changing structures on timescales of days to decades. In fact, Beurle et al (2010) show that Prometheus makes it possible for "distended, yet gravitationally coherent clumps" to form in the F ring, and Barbara and Esposito (2002) predicted a population of ~1 km bodies in the ring. In addition to the observations over the last three decades, the Cassini Ultraviolet Imaging Spectrograph (UVIS) has detected 27 statistically significant features in 101 occultations by Saturn's F ring since July 2004. Seventeen of those 27 features are associated with clumps of ring material. Two features are opaque in occultation, which makes them candidates for solid objects, which we refer to as Moonlets. The 15 other features partially block stellar signal for 22 m to just over 3.7 km along the radial expanse of the occultation. Upon visual inspection of the occultation profile, these features resemble Icicles, thus we will refer to them as such here. The density enhancements responsible for such signal attenuations are likely due to transient clumping of material, evidence that aggregations of material are ubiquitous in the F ring. Our lengthy observing campaign reveals that Icicles are likely transient clumps, while Moonlets are possible solid objects. Optical depth is an indicator of clumping because more-densely aggregated material blocks more light; therefore, it is natural to imagine moonlets as later evolutionary stage of icicle, when looser clumps of material compact to form a feature that appears

  10. Rings in drugs.

    Science.gov (United States)

    Taylor, Richard D; MacCoss, Malcolm; Lawson, Alastair D G

    2014-07-24

    We have analyzed the rings, ring systems, and frameworks in drugs listed in the FDA Orange Book to understand the frequency, timelines, molecular property space, and the application of these rings in different therapeutic areas and target classes. This analysis shows that there are only 351 ring systems and 1197 frameworks in drugs that came onto the market before 2013. Furthermore, on average six new ring systems enter drug space each year and approximately 28% of new drugs contain a new ring system. Moreover, it is very unusual for a drug to contain more than one new ring system and the majority of the most frequently used ring systems (83%) were first used in drugs developed prior to 1983. These observations give insight into the chemical novelty of drugs and potentially efficient ways to assess compound libraries and develop compounds from hit identification to lead optimization and beyond.

  11. Birth Control Ring

    Science.gov (United States)

    ... Health Food & Fitness Diseases & Conditions Infections Drugs & Alcohol School & Jobs Sports Expert Answers (Q&A) Staying Safe Videos for Educators Search English Español Birth Control Ring KidsHealth / For Teens / Birth Control Ring What's ...

  12. Sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6, and V9 domains reveal highly species-specific variations within the genus Agrocybe.

    Science.gov (United States)

    Gonzalez, P; Labarère, J

    1998-11-01

    A comparative study of variable domains V4, V6, and V9 of the mitochondrial small-subunit (SSU) rRNA was carried out with the genus Agrocybe by PCR amplification of 42 wild isolates belonging to 10 species, Agrocybe aegerita, Agrocybe dura, Agrocybe chaxingu, Agrocybe erebia, Agrocybe firma, Agrocybe praecox, Agrocybe paludosa, Agrocybe pediades, Agrocybe alnetorum, and Agrocybe vervacti. Sequencing of the PCR products showed that the three domains in the isolates belonging to the same species were the same length and had the same sequence, while variations were found among the 10 species. Alignment of the sequences showed that nucleotide motifs encountered in the smallest sequence of each variable domain were also found in the largest sequence, indicating that the sequences evolved by insertion-deletion events. Determination of the secondary structure of each domain revealed that the insertion-deletion events commonly occurred in regions not directly involved in the secondary structure (i.e., the loops). Moreover, conserved sequences ranging from 4 to 25 nucleotides long were found at the beginning and end of each domain and could constitute genus-specific sequences. Comparisons of the V4, V6, and V9 secondary structures resulted in identification of the following four groups: (i) group I, which was characterized by the presence of additional P23-1 and P23-3 helices in the V4 domain and the lack of the P49-1 helix in V9 and included A. aegerita, A. chaxingu, and A. erebia; (ii) group II, which had the P23-3 helix in V4 and the P49-1 helix in V9 and included A. pediades; (iii) group III, which did not have additional helices in V4, had the P49-1 helix in V9 and included A. paludosa, A. firma, A. alnetorum, and A. praecox; and (iv) group IV, which lacked both the V4 additional helices and the P49-1 helix in V9 and included A. vervacti and A. dura. This grouping of species was supported by the structure of a consensus tree based on the variable domain sequences. The

  13. Forster Resonance Energy Transfer (FRET) Analysis of Dual CFP/YFP Labeled AMPA Receptors Reveals Structural Rearrangement within the C-Terminal Domain during Receptor Activation

    DEFF Research Database (Denmark)

    Zachariassen, Linda Grønborg; Katchan, Mila; Plested, Andrew

    2014-01-01

    that retain function and display intrareceptor FRET. This includes a construct (GluA2-6Y-10C) containing YFP in the intracellular loop between the M1 and M2 membrane-embedded segments and CFP inserted in the C-ter- minal domain (CTD). GluA2-6Y-10C displays FRET with an efficiency of 0.11 while retaining wild......-type receptor expression and kinetic properties. We have used GluA2-6Y-10C to study conformational changes in homomeric GluA2 receptors during receptor activation. Our results show that the FRET efficiency is dependent on functional state of GluA2-6Y-10C and hereby indi- cates that the intracellular CTD...

  14. Mechanism of Retinal Pigment Epithelium Tear Formation Following Intravitreal Anti–Vascular Endothelial Growth Factor Therapy Revealed by Spectral-Domain Optical Coherence Tomography

    DEFF Research Database (Denmark)

    Nagiel, Aaron; Freund, K Bailey; Spaide, Richard F

    2013-01-01

    to the retracted RPE. In all eyes, the RPE ruptured along a segment of bare RPE not in contact with the CNV or Bruch membrane. CONCLUSIONS: Eyes with vascularized PEDs secondary to AMD may show specific OCT findings that increase the risk for RPE tear following intravitreal anti-VEGF injection. Rapid involution......PURPOSE: To demonstrate the mechanism by which retinal pigment epithelium (RPE) tears occur in eyes with neovascular age-related macular degeneration (AMD) treated with intravitreal anti-vascular endothelial growth factor (VEGF) agents using spectral-domain optical coherence tomography (OCT......). DESIGN: Retrospective observational case series. METHODS: OCT images of 8 eyes that developed RPE tears following the administration of intravitreal anti-VEGF agents for neovascular AMD were evaluated. Pretear and posttear images were compared in order to elucidate the mechanism by which RPE tears occur...

  15. Interactions of an Arabidopsis RanBPM homologue with LisH-CTLH domain proteins revealed high conservation of CTLH complexes in eukaryotes

    Czech Academy of Sciences Publication Activity Database

    Tomaštíková, Eva; Cenklová, Věra; Kohoutová, Lucie; Petrovská, Beáta; Váchová, Lenka; Halada, Petr; Kočárová, Gabriela; Binarová, Pavla

    2012-01-01

    Roč. 12, č. 83 (2012) ISSN 1471-2229 R&D Projects: GA ČR(CZ) GA204/07/1169; GA ČR GP204/09/P155; GA ČR GAP501/12/2333; GA MŠk(CZ) LC06034; GA MŠk LC545; GA AV ČR IAA500200719 Grant - others:GA MŠk(CZ) ED0007/01/01 Program:ED Institutional research plan: CEZ:AV0Z50380511; CEZ:AV0Z50200510 Keywords : Arabidopsis homologue of RanBPM * CTLH-complex * LisH-CTLH domain proteins Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.354, year: 2012

  16. Crystal structure of inhibitor of growth 4 (ING4) dimerization domain reveals functional organization of ING family of chromatin-binding proteins.

    Science.gov (United States)

    Culurgioni, Simone; Muñoz, Inés G; Moreno, Alberto; Palacios, Alicia; Villate, Maider; Palmero, Ignacio; Montoya, Guillermo; Blanco, Francisco J

    2012-03-30

    The protein ING4 binds to histone H3 trimethylated at Lys-4 (H3K4me3) through its C-terminal plant homeodomain, thus recruiting the HBO1 histone acetyltransferase complex to target promoters. The structure of the plant homeodomain finger bound to an H3K4me3 peptide has been described, as well as the disorder and flexibility in the ING4 central region. We report the crystal structure of the ING4 N-terminal domain, which shows an antiparallel coiled-coil homodimer with each protomer folded into a helix-loop-helix structure. This arrangement suggests that ING4 can bind simultaneously two histone tails on the same or different nucleosomes. Dimerization has a direct impact on ING4 tumor suppressor activity because monomeric mutants lose the ability to induce apoptosis after genotoxic stress. Homology modeling based on the ING4 structure suggests that other ING dimers may also exist.

  17. Crystal structure of type I ryanodine receptor amino-terminal [beta]-trefoil domain reveals a disease-associated mutation 'hot spot' loop

    Energy Technology Data Exchange (ETDEWEB)

    Amador, Fernando J.; Liu, Shuang; Ishiyama, Noboru; Plevin, Michael J.; Wilson, Aaron; MacLennan, David H.; Ikura, Mitsuhiko; (Toronto)

    2009-12-01

    Muscle contraction and relaxation is regulated by transient elevations of myoplasmic Ca{sup 2+}. Ca{sup 2+} is released from stores in the lumen of the sarco(endo)plasmic reticulum (SER) to initiate formation of the Ca{sup 2+} transient by activation of a class of Ca{sup 2+} release channels referred to as ryanodine receptors (RyRs) and is pumped back into the SER lumen by Ca{sup 2+}-ATPases (SERCAs) to terminate the Ca{sup 2+} transient. Mutations in the type 1 ryanodine receptor gene, RYR1, are associated with 2 skeletal muscle disorders, malignant hyperthermia (MH), and central core disease (CCD). The evaluation of proposed mechanisms by which RyR1 mutations cause MH and CCD is hindered by the lack of high-resolution structural information. Here, we report the crystal structure of the N-terminal 210 residues of RyR1 (RyR{sub NTD}) at 2.5 {angstrom}. The RyR{sub NTD} structure is similar to that of the suppressor domain of type 1 inositol 1,4,5-trisphosphate receptor (IP3Rsup), but lacks most of the long helix-turn-helix segment of the 'arm' domain in IP3Rsup. The N-terminal {beta}-trefoil fold, found in both RyR and IP{sub 3}R, is likely to play a critical role in regulatory mechanisms in this channel family. A disease-associated mutation 'hot spot' loop was identified between strands 8 and 9 in a highly basic region of RyR1. Biophysical studies showed that 3 MH-associated mutations (C36R, R164C, and R178C) do not adversely affect the global stability or fold of RyRNTD, supporting previously described mechanisms whereby mutations perturb protein-protein interactions.

  18. Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin-binding protein PonA1 reveal potential mechanisms of antibiotic resistance.

    Science.gov (United States)

    Filippova, Ekaterina V; Kieser, Karen J; Luan, Chi-Hao; Wawrzak, Zdzislaw; Kiryukhina, Olga; Rubin, Eric J; Anderson, Wayne F

    2016-06-01

    Mycobacterium tuberculosis is a human respiratory pathogen that causes the deadly disease tuberculosis. The rapid global spread of antibiotic-resistant M. tuberculosis makes tuberculosis infections difficult to treat. To overcome this problem new effective antimicrobial strategies are urgently needed. One promising target for new therapeutic approaches is PonA1, a class A penicillin-binding protein, which is required for maintaining physiological cell wall synthesis and cell shape during growth in mycobacteria. Here, crystal structures of the transpeptidase domain, the enzymatic domain responsible for penicillin binding, of PonA1 from M. tuberculosis in the inhibitor-free form and in complex with penicillin V are reported. We used site-directed mutagenesis, antibiotic profiling experiments, and fluorescence thermal shift assays to measure PonA1's sensitivity to different classes of β-lactams. Structural comparison of the PonA1 apo-form and the antibiotic-bound form shows that binding of penicillin V induces conformational changes in the position of the loop β4'-α3 surrounding the penicillin-binding site. We have also found that binding of different antibiotics including penicillin V positively impacts protein stability, while other tested β-lactams such as clavulanate or meropenem resulted in destabilization of PonA1. Our antibiotic profiling experiments indicate that the transpeptidase activity of PonA1 in both M. tuberculosis and M. smegmatis mediates tolerance to specific cell wall-targeting antibiotics, particularly to penicillin V and meropenem. Because M. tuberculosis is an important human pathogen, these structural data provide a template to design novel transpeptidase inhibitors to treat tuberculosis infections. Structural data are available in the PDB database under the accession numbers 5CRF and 5CXW. © 2016 The Authors. The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

  19. Structural elucidation of transmembrane domain zero (TMD0) of EcdL: A multidrug resistance-associated protein (MRP) family of ATP-binding cassette transporter protein revealed by atomistic simulation.

    Science.gov (United States)

    Bera, Krishnendu; Rani, Priyanka; Kishor, Gaurav; Agarwal, Shikha; Kumar, Antresh; Singh, Durg Vijay

    2017-09-20

    ATP-Binding cassette (ABC) transporters play an extensive role in the translocation of diverse sets of biologically important molecules across membrane. EchnocandinB (antifungal) and EcdL protein of Aspergillus rugulosus are encoded by the same cluster of genes. Co-expression of EcdL and echinocandinB reflects tightly linked biological functions. EcdL belongs to Multidrug Resistance associated Protein (MRP) subfamily of ABC transporters with an extra transmembrane domain zero (TMD0). Complete structure of MRP subfamily comprising of TMD0 domain, at atomic resolution is not known. We hypothesized that the transportation of echonocandinB is mediated via EcdL protein. Henceforth, it is pertinent to know the topological arrangement of TMD0, with other domains of protein and its possible role in transportation of echinocandinB. Absence of effective template for TMD0 domain lead us to model by I-TASSER, further structure has been refined by multiple template modelling using homologous templates of remaining domains (TMD1, NBD1, TMD2, NBD2). The modelled structure has been validated for packing, folding and stereochemical properties. MD simulation for 0.1 μs has been carried out in the biphasic environment for refinement of modelled protein. Non-redundant structures have been excavated by clustering of MD trajectory. The structural alignment of modelled structure has shown Z-score -37.9; 31.6, 31.5 with RMSD; 2.4, 4.2, 4.8 with ABC transporters; PDB ID 4F4C, 4M1 M, 4M2T, respectively, reflecting the correctness of structure. EchinocandinB has been docked to the modelled as well as to the clustered structures, which reveals interaction of echinocandinB with TMD0 and other TM helices in the translocation path build of TMDs.

  20. Generation of Pet1210-Cre Transgenic Mouse Line Reveals Non-Serotonergic Expression Domains of Pet1 Both in CNS and Periphery

    Science.gov (United States)

    Pelosi, Barbara; Migliarini, Sara; Pacini, Giulia; Pratelli, Marta; Pasqualetti, Massimo

    2014-01-01

    Neurons producing serotonin (5-hydroxytryptamine, 5-HT) constitute one of the most widely distributed neuronal networks in the mammalian central nervous system (CNS) and exhibit a profuse innervation throughout the CNS already at early stages of development. Serotonergic neuron specification is controlled by a combination of secreted molecules and transcription factors such as Shh, Fgf4/8, Nkx2.2, Lmx1b and Pet1. In the mouse, Pet1 mRNA expression appears between 10 and 11 days post coitum (dpc) in serotonergic post-mitotic precursors and persists in serotonergic neurons up to adulthood, where it promotes the expression of genes defining the mature serotonergic phenotype such as tryptophan hydroxylase 2 (Tph2) and serotonin transporter (SERT). Hence, the generation of genetic tools based on Pet1 specific expression represents a valuable approach to study the development and function of the serotonergic system. Here, we report the generation of a Pet1210-Cre transgenic mouse line in which the Cre recombinase is expressed under the control of a 210 kb fragment from the Pet1 genetic locus to ensure a reliable and faithful control of somatic recombination in Pet1 cell lineage. Besides Cre-mediated recombination accurately occurred in the serotonergic system as expected and according to previous studies, Pet1210-Cre transgenic mouse line allowed us to identify novel, so far uncharacterized, Pet1 expression domains. Indeed, we showed that in the raphe Pet1 is expressed also in a non-serotonergic neuronal population intermingled with Tph2-expressing cells and mostly localized in the B8 and B9 nuclei. Moreover, we detected Cre-mediated recombination also in the developing pancreas and in the ureteric bud derivatives of the kidney, where it reflected a specific Pet1 expression. Thus, Pet1210-Cre transgenic mouse line faithfully drives Cre-mediated recombination in all Pet1 expression domains representing a valuable tool to genetically manipulate serotonergic and non

  1. Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation.

    Science.gov (United States)

    Corrada, Dario; Soshilov, Anatoly A; Denison, Michael S; Bonati, Laura

    2016-06-01

    The Aryl hydrocarbon Receptor (AhR) is a transcription factor that mediates the biochemical response to xenobiotics and the toxic effects of a number of environmental contaminants, including dioxins. Recently, endogenous regulatory roles for the AhR in normal physiology and development have also been reported, thus extending the interest in understanding its molecular mechanisms of activation. Since dimerization with the AhR Nuclear Translocator (ARNT) protein, occurring through the Helix-Loop-Helix (HLH) and PER-ARNT-SIM (PAS) domains, is needed to convert the AhR into its transcriptionally active form, deciphering the AhR:ARNT dimerization mode would provide insights into the mechanisms of AhR transformation. Here we present homology models of the murine AhR:ARNT PAS domain dimer developed using recently available X-ray structures of other bHLH-PAS protein dimers. Due to the different reciprocal orientation and interaction surfaces in the different template dimers, two alternative models were developed for both the PAS-A and PAS-B dimers and they were characterized by combining a number of computational evaluations. Both well-established hot spot prediction methods and new approaches to analyze individual residue and residue-pairwise contributions to the MM-GBSA binding free energies were adopted to predict residues critical for dimer stabilization. On this basis, a mutagenesis strategy for both the murine AhR and ARNT proteins was designed and ligand-dependent DNA binding ability of the AhR:ARNT heterodimer mutants was evaluated. While functional analysis disfavored the HIF2α:ARNT heterodimer-based PAS-B model, most mutants derived from the CLOCK:BMAL1-based AhR:ARNT dimer models of both the PAS-A and the PAS-B dramatically decreased the levels of DNA binding, suggesting this latter model as the most suitable for describing AhR:ARNT dimerization. These novel results open new research directions focused at elucidating basic molecular mechanisms underlying the

  2. Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation.

    Directory of Open Access Journals (Sweden)

    Dario Corrada

    2016-06-01

    Full Text Available The Aryl hydrocarbon Receptor (AhR is a transcription factor that mediates the biochemical response to xenobiotics and the toxic effects of a number of environmental contaminants, including dioxins. Recently, endogenous regulatory roles for the AhR in normal physiology and development have also been reported, thus extending the interest in understanding its molecular mechanisms of activation. Since dimerization with the AhR Nuclear Translocator (ARNT protein, occurring through the Helix-Loop-Helix (HLH and PER-ARNT-SIM (PAS domains, is needed to convert the AhR into its transcriptionally active form, deciphering the AhR:ARNT dimerization mode would provide insights into the mechanisms of AhR transformation. Here we present homology models of the murine AhR:ARNT PAS domain dimer developed using recently available X-ray structures of other bHLH-PAS protein dimers. Due to the different reciprocal orientation and interaction surfaces in the different template dimers, two alternative models were developed for both the PAS-A and PAS-B dimers and they were characterized by combining a number of computational evaluations. Both well-established hot spot prediction methods and new approaches to analyze individual residue and residue-pairwise contributions to the MM-GBSA binding free energies were adopted to predict residues critical for dimer stabilization. On this basis, a mutagenesis strategy for both the murine AhR and ARNT proteins was designed and ligand-dependent DNA binding ability of the AhR:ARNT heterodimer mutants was evaluated. While functional analysis disfavored the HIF2α:ARNT heterodimer-based PAS-B model, most mutants derived from the CLOCK:BMAL1-based AhR:ARNT dimer models of both the PAS-A and the PAS-B dramatically decreased the levels of DNA binding, suggesting this latter model as the most suitable for describing AhR:ARNT dimerization. These novel results open new research directions focused at elucidating basic molecular mechanisms

  3. Domain analysis

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2017-01-01

    The domain-analytic approach to knowledge organization (KO) (and to the broader field of library and information science, LIS) is outlined. The article reviews the discussions and proposals on the definition of domains, and provides an example of a domain-analytic study in the field of art studies....... Varieties of domain analysis as well as criticism and controversies are presented and discussed....

  4. Carboxyl-terminal-dependent recruitment of nonmuscle myosin II to megakaryocyte contractile ring during polyploidization.

    Science.gov (United States)

    Badirou, Idinath; Pan, Jiajia; Legrand, Céline; Wang, Aibing; Lordier, Larissa; Boukour, Siham; Roy, Anita; Vainchenker, William; Chang, Yunhua

    2014-10-16

    Endomitosis is a unique megakaryocyte (MK) differentiation process that is the consequence of a late cytokinesis failure associated with a contractile ring defect. Evidence from in vitro studies has revealed the distinct roles of 2 nonmuscle myosin IIs (NMIIs) on MK endomitosis: only NMII-B (MYH10), but not NMII-A (MYH9), is localized in the MK contractile ring and implicated in mitosis/endomitosis transition. Here, we studied 2 transgenic mouse models in which nonmuscle myosin heavy chain (NMHC) II-A was genetically replaced either by II-B or by a chimeric NMHCII that combined the head domain of II-A with the rod and tail domains of II-B. This study provides in vivo evidence on the specific role of NMII-B on MK polyploidization. It demonstrates that the carboxyl-terminal domain of the heavy chains determines myosin II localization to the MK contractile ring and is responsible for the specific role of NMII-B in MK polyploidization.

  5. A triclinic crystal structure of the carboxy-terminal domain of HIV-1 capsid protein with four molecules in the asymmetric unit reveals a novel packing interface

    International Nuclear Information System (INIS)

    Lampel, Ayala; Yaniv, Oren; Berger, Or; Bacharach, Eran; Gazit, Ehud; Frolow, Felix

    2013-01-01

    The triclinic structure of the HIV-1 capsid protein contains four molecules in the asymmetric unit that form a novel packing interface that could conceivably resemble an intermediate structure that is involved in the early steps of HIV-1 assembly. The Gag precursor is the major structural protein of the virion of human immunodeficiency virus-1 (HIV-1). Capsid protein (CA), a cleavage product of Gag, plays an essential role in virus assembly both in Gag-precursor multimerization and in capsid core formation. The carboxy-terminal domain (CTD) of CA contains 20 residues that are highly conserved across retroviruses and constitute the major homology region (MHR). Genetic evidence implies a role for the MHR in interactions between Gag precursors during the assembly of the virus, but the structural basis for this role remains elusive. This paper describes a novel triclinic structure of the HIV-1 CA CTD at 1.6 Å resolution with two canonical dimers of CA CTD in the asymmetric unit. The canonical dimers form a newly identified packing interface where interactions of four conserved MHR residues take place. This is the first structural indication that these MHR residues participate in the putative CTD–CTD interactions. These findings suggest that the molecules forming this novel interface resemble an intermediate structure that participates in the early steps of HIV-1 assembly. This interface may therefore provide a novel target for antiviral drugs

  6. The structure of a novel thermophilic esterase from the Planctomycetes species, Thermogutta terrifontis reveals an open active site due to a minimal ‘cap’ domain.

    Directory of Open Access Journals (Sweden)

    Jennifer Ann Littlechild

    2015-11-01

    Full Text Available A carboxyl esterase (TtEst2 has been identified in a novel thermophilic bacterium, Thermogutta terrifontis from the phylum Planctomycetes and has been cloned and over-expressed in Escherichia coli. The enzyme has been characterised biochemically and shown to have activity towards small p-nitrophenyl (pNP carboxylic esters with optimal activity for pNP-acetate. The enzyme shows moderate thermostability retaining 75% activity after incubation for 30 minutes at 70°C. The crystal structures have been determined for the native TtEst2 and its complexes with the carboxylic acid products propionate, butyrate and valerate. TtEst2 differs from most enzymes of the α/β-hydrolase family 3 as it lacks the majority of the ‘cap’ domain and its active site cavity is exposed to the solvent. The bound ligands have allowed the identification of the carboxyl pocket in the enzyme active site. Comparison of TtEst2 with structurally related enzymes has given insight into how differences in their substrate preference can be rationalised based upon the properties of their active site pockets.

  7. Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger

    International Nuclear Information System (INIS)

    Axelrod, Herbert L.; Das, Debanu; Abdubek, Polat; Astakhova, Tamara; Bakolitsa, Constantina; Carlton, Dennis; Chen, Connie; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Farr, Carol L.; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Lam, Winnie W.; Marciano, David; McMullan, Daniel; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Puckett, Christina; Reyes, Ron; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; Bedem, Henry van den; Weekes, Dana; Wooten, Tiffany; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    The first structures from the FmdE Pfam family (PF02663) reveal that some members of this family form tightly intertwined dimers consisting of two domains (N-terminal α+β core and C-terminal zinc-finger domains), whereas others contain only the core domain. The presence of the zinc-finger domain suggests that some members of this family may perform functions associated with transcriptional regulation, protein–protein interaction, RNA binding or metal-ion sensing. Examination of the genomic context for members of the FmdE Pfam family (PF02663), such as the protein encoded by the fmdE gene from the methanogenic archaeon Methanobacterium thermoautotrophicum, indicates that 13 of them are co-transcribed with genes encoding subunits of molybdenum formylmethanofuran dehydrogenase (EC 1.2.99.5), an enzyme that is involved in microbial methane production. Here, the first crystal structures from PF02663 are described, representing two bacterial and one archaeal species: B8FYU2-DESHY from the anaerobic dehalogenating bacterium Desulfitobacterium hafniense DCB-2, Q2LQ23-SYNAS from the syntrophic bacterium Syntrophus aciditrophicus SB and Q9HJ63-THEAC from the thermoacidophilic archaeon Thermoplasma acidophilum. Two of these proteins, Q9HJ63-THEAC and Q2LQ23-SYNAS, contain two domains: an N-terminal thioredoxin-like α+β core domain (NTD) consisting of a five-stranded, mixed β-sheet flanked by several α-helices and a C-terminal zinc-finger domain (CTD). B8FYU2-DESHY, on the other hand, is composed solely of the NTD. The CTD of Q9HJ63-THEAC and Q2LQ23-SYNAS is best characterized as a treble-clef zinc finger. Two significant structural differences between Q9HJ63-THEAC and Q2LQ23-SYNAS involve their metal binding. First, zinc is bound to the putative active site on the NTD of Q9HJ63-THEAC, but is absent from the NTD of Q2LQ23-SYNAS. Second, whereas the structure of the CTD of Q2LQ23-SYNAS shows four Cys side chains within coordination distance of the Zn atom, the structure

  8. Superbinder SH2 domains act as antagonists of cell signaling.

    Science.gov (United States)

    Kaneko, Tomonori; Huang, Haiming; Cao, Xuan; Li, Xing; Li, Chengjun; Voss, Courtney; Sidhu, Sachdev S; Li, Shawn S C

    2012-09-25

    Protein-ligand interactions mediated by modular domains, which often play important roles in regulating cellular functions, are generally of moderate affinities. We examined the Src homology 2 (SH2) domain, a modular domain that recognizes phosphorylated tyrosine (pTyr) residues, to investigate how the binding affinity of a modular domain for its ligand influences the structure and cellular function of the protein. We used the phage display method to perform directed evolution of the pTyr-binding residues in the SH2 domain of the tyrosine kinase Fyn and identified three amino acid substitutions that critically affected binding. We generated three SH2 domain triple-point mutants that were "superbinders" with much higher affinities for pTyr-containing peptides than the natural domain. Crystallographic analysis of one of these superbinders revealed that the superbinder SH2 domain recognized the pTyr moiety in a bipartite binding mode: A hydrophobic surface encompassed the phenyl ring, and a positively charged site engaged the phosphate. When expressed in mammalian cells, the superbinder SH2 domains blocked epidermal growth factor receptor signaling and inhibited anchorage-independent cell proliferation, suggesting that pTyr superbinders might be explored for therapeutic applications and useful as biological research tools. Although the SH2 domain fold can support much higher affinity for its ligand than is observed in nature, our results suggest that natural SH2 domains are not optimized for ligand binding but for specificity and flexibility, which are likely properties important for their function in signaling and regulatory processes.

  9. An anti-phospholipase A2 receptor quantitative immunoassay and epitope analysis in membranous nephropathy reveals different antigenic domains of the receptor.

    Directory of Open Access Journals (Sweden)

    Astrid Behnert

    Full Text Available The phospholipase A2 receptor (PLA2R was recently discovered as a target autoantigen in patients with idiopathic membranous nephropathy (IMN. Published evidence suggests that the autoantibodies directed towards a conformation dependent epitope are currently effectively detected by a cell based assay (CBA utilizing indirect immunofluorescence (IIF on tissue culture cells transfected with the PLA2R cDNA. Limitations of such IIF-CBA assays include observer dependent subjective evaluation of semi-quantitative test results and the protocols are not amenable to high throughput diagnostic testing. We developed a quantitative, observer independent, high throughput capture immunoassay for detecting PLA2R autoantibodies on an addressable laser bead immunoassay (ALBIA platform. Since reactive domains of PLA2R (i.e. epitopes could be used to improve diagnostic tests by using small peptides in various high throughput diagnostic platforms, we identified PLA2R epitopes that bound autoantibodies of IMN patients. These studies confirmed that inter-molecular epitope spreading occurs in IMN but use of the cognate synthetic peptides in immunoassays was unable to conclusively distinguish between IMN patients and normal controls. However, combinations of these peptides were able to effectively absorb anti-PLA2R reactivity in IIF-CBA and an immunoassay that employed a lysate derived from HEK cells tranfected with and overexpressing PLA2R. While we provide evidence of intermolecular epitope spreading, our data indicates that in addition to conformational epitopes, human anti-PLA2R reactivity in a commercially available CBA and an addressable laser bead immunoassay is significantly absorbed by peptides representing epitopes of PLA2R.

  10. Unconventional Cadherin Localization in Honey Bee Gonads Revealed Through Domain-Specific Apis mellifera E- and N-Cadherin Antibodies Indicates Alternative Functions

    Directory of Open Access Journals (Sweden)

    Klaus Hartfelder

    2012-11-01

    Full Text Available As key factors in intercellular adhesion processes, cadherins play important roles in a plethora of developmental processes, including gametogenesis. In a previous study on cadherin localization in the gonads of honey bees, performed with heterologous pan-cadherin antibodies, we detected these proteins as (i associated with cell membranes, (ii as homogeneously distributed throughout the cytoplasm, and (iii as nuclear foci in both somatic and germline cells, raising the possibility of alternative functions. To further investigate such unusual intracellular cadherin localization we produced specific antibodies against the N- and C-terminal domains of honey bee N- and E-cadherin. A 160 kDa protein was recognized by the E-cadherin antibodies as well as one of approximately 300 kDa from those raised against N-cadherin. In gonad preparations, both proteins were detected as dispersed throughout the cytoplasm and as nuclear foci in both germline and somatic cells of queen and worker ovarioles, as well as in the testioles of drones. This leads us to infer that cadherins may indeed be involved in certain signaling pathways and/or transcriptional regulation during gametogenesis. In late oogenesis stages, immunolabeling for both proteins was observed at the cell cortex, in conformity with a role in cell adhesion. In testioles, E-cadherin was seen in co-localization with fusomes, indicating a possible role in cyst organization. Taken together, the distribution of N- and E-cadherins in honey bee gonads is suggestive of alternative roles for cadherins in gametogenesis of both sexes.

  11. A polyether biotoxin binding site on the lipid-exposed face of the pore domain of Kv channels revealed by the marine toxin gambierol

    Science.gov (United States)

    Kopljar, Ivan; Labro, Alain J.; Cuypers, Eva; Johnson, Henry W. B.; Rainier, Jon D.; Tytgat, Jan; Snyders, Dirk J.

    2009-01-01

    Gambierol is a marine polycyclic ether toxin belonging to the group of ciguatera toxins. It does not activate voltage-gated sodium channels (VGSCs) but inhibits Kv1 potassium channels by an unknown mechanism. While testing whether Kv2, Kv3, and Kv4 channels also serve as targets, we found that Kv3.1 was inhibited with an IC50 of 1.2 ± 0.2 nM, whereas Kv2 and Kv4 channels were insensitive to 1 μM gambierol. Onset of block was similar from either side of the membrane, and gambierol did not compete with internal cavity blockers. The inhibition did not require channel opening and could not be reversed by strong depolarization. Using chimeric Kv3.1–Kv2.1 constructs, the toxin sensitivity was traced to S6, in which T427 was identified as a key determinant. In Kv3.1 homology models, T427 and other molecular determinants (L348, F351) reside in a space between S5 and S6 outside the permeation pathway. In conclusion, we propose that gambierol acts as a gating modifier that binds to the lipid-exposed surface of the pore domain, thereby stabilizing the closed state. This site may be the topological equivalent of the neurotoxin site 5 of VGSCs. Further elucidation of this previously undescribed binding site may explain why most ciguatoxins activate VGSCs, whereas others inhibit voltage-dependent potassium (Kv) channels. This previously undescribed Kv neurotoxin site may have wide implications not only for our understanding of channel function at the molecular level but for future development of drugs to alleviate ciguatera poisoning or to modulate electrical excitability in general. PMID:19482941

  12. Laser-scanning astrocyte mapping reveals increased glutamate-responsive domain size and disrupted maturation of glutamate uptake following neonatal cortical freeze-lesion

    Directory of Open Access Journals (Sweden)

    Mortiz eArmbruster

    2014-09-01

    Full Text Available Astrocytic uptake of glutamate shapes extracellular neurotransmitter dynamics, receptor activation, and synaptogenesis. During development, glutamate transport becomes more robust. How neonatal brain insult affects the functional maturation of glutamate transport remains unanswered. Neonatal brain insult can lead to developmental delays, cognitive losses, and epilepsy; the disruption of glutamate transport is known to cause changes in synaptogenesis, receptor activation, and seizure. Using the neonatal freeze-lesion (FL model, we have investigated how insult affects the maturation of astrocytic glutamate transport. As lesioning occurs on the day of birth, a time when astrocytes are still functionally immature, this model is ideal for identifying changes in astrocyte maturation following insult. Reactive astrocytosis, astrocyte proliferation, and in vitro hyperexcitability are known to occur in this model. To probe astrocyte glutamate transport with better spatial precision we have developed a novel technique, Laser Scanning Astrocyte Mapping (LSAM, which combines glutamate transport current (TC recording from astrocytes with laser scanning glutamate photolysis. LSAM allows us to identify the area from which a single astrocyte can transport glutamate and to quantify spatial heterogeneity in the rate of glutamate clearance kinetics within that domain. Using LSAM, we report that cortical astrocytes have an increased glutamate-responsive area following FL and that TCs have faster decay times in distal, as compared to proximal processes. Furthermore, the developmental shift from GLAST- to GLT-1-dominated clearance is disrupted following FL. These findings introduce a novel method to probe astrocyte glutamate uptake and show that neonatal cortical FL disrupts the functional maturation of cortical astrocytes.

  13. Imidazolopiperazines (IPZ) kill both rings and dormant rings in wild type and K13 artemisinin resistant Plasmodium falciparum in vitro.

    Science.gov (United States)

    Dembele, Laurent; Gupta, Devendra Kumar; Lim, Michelle Yi-Xiu; Ang, Xiaoman; Selva, Jeremy J; Chotivanich, Kesinee; Nguon, Chea; Dondorp, Arjen M; Bonamy, Ghislain M C; Diagana, Thierry T; Bifani, Pablo

    2018-03-12

    Artemisinin (ART) resistance has spread through Southeast Asia, posing serious threat to the control and elimination of malaria. ART resistance has been associated with mutations in the Plasmodium falciparum kelch-13 ( Pfk13 ) propeller domain. Phenotypically, ART resistance is defined as delayed parasite clearance in patients' due to the reduced susceptibility of early ring-stage parasites to the active metabolite of ART dihydroartemisinin (DHA). Early rings can enter a state of quiescence upon DHA exposure and resume growth in its absence. These quiescent rings are referred to as dormant rings or DHA-pretreated rings (called here dormant rings). The imidazolopiperazine (IPZ) is a novel class of antimalarial drugs, which has demonstrated efficacy in early clinical trials. Here, we characterized the stage of action of IPZ GNF179 and evaluated its activity against rings and dormant rings in wild type and ART resistant parasites. Unlike DHA, GNF179 does not induce dormancy. We show that GNF179 is more rapidly cidal against schizonts than ring and trophozoite stages. However, with 12 hours exposure, the compound effectively kills rings and dormant rings of both susceptible and ART resistant parasites within 72 hours. We further demonstrate that in combination with ART, GNF179 effectively prevent recrudescence of dormant rings including those bearing pfk13 propeller mutations. Copyright © 2018 Dembele et al.

  14. Ring faults and ring dikes around the Orientale basin on the Moon.

    Science.gov (United States)

    Andrews-Hanna, Jeffrey C; Head, James W; Johnson, Brandon; Keane, James T; Kiefer, Walter S; McGovern, Patrick J; Neumann, Gregory A; Wieczorek, Mark A; Zuber, Maria T

    2018-08-01

    The Orientale basin is the youngest and best-preserved multiring impact basin on the Moon, having experienced only modest modification by subsequent impacts and volcanism. Orientale is often treated as the type example of a multiring basin, with three prominent rings outside of the inner depression: the Inner Rook Montes, the Outer Rook Montes, and the Cordillera. Here we use gravity data from NASA's Gravity Recovery and Interior Laboratory (GRAIL) mission to reveal the subsurface structure of Orientale and its ring system. Gradients of the gravity data reveal a continuous ring dike intruded into the Outer Rook along the plane of the fault associated with the ring scarp. The volume of this ring dike is ~18 times greater than the volume of all extrusive mare deposits associated with the basin. The gravity gradient signature of the Cordillera ring indicates an offset along the fault across a shallow density interface, interpreted to be the base of the low-density ejecta blanket. Both gravity gradients and crustal thickness models indicate that the edge of the central cavity is shifted inward relative to the equivalent Inner Rook ring at the surface. Models of the deep basin structure show inflections along the crust-mantle interface at both the Outer Rook and Cordillera rings, indicating that the basin ring faults extend from the surface to at least the base of the crust. Fault dips range from 13-22° for the Cordillera fault in the northeastern quadrant, to 90° for the Outer Rook in the northwestern quadrant. The fault dips for both outer rings are lowest in the northeast, possibly due to the effects of either the direction of projectile motion or regional gradients in pre-impact crustal thickness. Similar ring dikes and ring faults are observed around the majority of lunar basins.

  15. Construction of synthetic nucleoli in human cells reveals how a major functional nuclear domain is formed and propagated through cell division.

    Science.gov (United States)

    Grob, Alice; Colleran, Christine; McStay, Brian

    2014-02-01

    Human cell nuclei are functionally organized into structurally stable yet dynamic bodies whose cell cycle inheritance is poorly understood. Here, we investigate the biogenesis and propagation of nucleoli, sites of ribosome biogenesis and key regulators of cellular growth. Nucleolar and cell cycles are intimately connected. Nucleoli disappear during mitosis, reforming around prominent uncharacterized chromosomal features, nucleolar organizer regions (NORs). By examining the effects of UBF depletion on both endogenous NORs and synthetic pseudo-NORs, we reveal its essential role in maintaining competency and establishing a bookmark on mitotic NORs. Furthermore, we demonstrate that neo-NORs, UBF-binding site arrays coupled with rDNA transcription units, direct the de novo biogenesis of functional compartmentalized neonucleoli irrespective of their site of chromosomal integration. For the first time, we establish the sequence requirements for nucleolar biogenesis and provide proof that this is a staged process where UBF-dependent mitotic bookmarking precedes function-dependent nucleolar assembly.

  16. Structural, stability, dynamic and binding properties of the ALS-causing T46I mutant of the hVAPB MSP domain as revealed by NMR and MD simulations.

    Directory of Open Access Journals (Sweden)

    Shixiong Lua

    Full Text Available T46I is the second mutation on the hVAPB MSP domain which was recently identified from non-Brazilian kindred to cause a familial amyotrophic lateral sclerosis (ALS. Here using CD, NMR and molecular dynamics (MD simulations, we characterized the structure, stability, dynamics and binding capacity of the T46I-MSP domain. The results reveal: 1 unlike P56S which we previously showed to completely eliminate the native MSP structure, T46I leads to no significant disruption of the native secondary and tertiary structures, as evidenced from its far-UV CD spectrum, as well as Cα and Cβ NMR chemical shifts. 2 Nevertheless, T46I does result in a reduced thermodynamic stability and loss of the cooperative urea-unfolding transition. As such, the T46I-MSP domain is more prone to aggregation than WT at high protein concentrations and temperatures in vitro, which may become more severe in the crowded cellular environments. 3 T46I only causes a 3-fold affinity reduction to the Nir2 peptide, but a significant elimination of its binding to EphA4. 4 EphA4 and Nir2 peptide appear to have overlapped binding interfaces on the MSP domain, which strongly implies that two signaling networks may have a functional interplay in vivo. 5 As explored by both H/D exchange and MD simulations, the MSP domain is very dynamic, with most loop residues and many residues on secondary structures highly fluctuated or/and exposed to bulk solvent. Although T46I does not alter overall dynamics, it does trigger increased dynamics of several local regions of the MSP domain which are implicated in binding to EphA4 and Nir2 peptide. Our study provides the structural and dynamic understanding of the T46I-causing ALS; and strongly highlights the possibility that the interplay of two signaling networks mediated by the FFAT-containing proteins and Eph receptors may play a key role in ALS pathogenesis.

  17. Token Ring Project

    Directory of Open Access Journals (Sweden)

    Adela Ionescu

    2007-01-01

    Full Text Available Ring topology is a simple configuration used to connect processes that communicate among themselves. A number of network standards such as token ring, token bus, and FDDI are based on the ring connectivity. This article will develop an implementation of a ring of processes that communicate among themselves via pipe links. The processes are nodes in the ring. Each process reads from its standard input and writes in its standard output. N-1 process redirects the its standard output to a standard input of the process through a pipe. When the ring-structure is designed, the project can be extended to simulate networks or to implement algorithms for mutual exclusion

  18. Characterization of heterocyclic rings through quantum chemical topology.

    Science.gov (United States)

    Griffiths, Mark Z; Popelier, Paul L A

    2013-07-22

    Five-membered rings are found in a myriad of molecules important in a wide range of areas such as catalysis, nutrition, and drug and agrochemical design. Systematic insight into their largely unexplored chemical space benefits from first principle calculations presented here. This study comprehensively investigates a grand total of 764 different rings, all geometry optimized at the B3LYP/6-311+G(2d,p) level, from the perspective of Quantum Chemical Topology (QCT). For the first time, a 3D space of local topological properties was introduced, in order to characterize rings compactly. This space is called RCP space, after the so-called ring critical point. This space is analogous to BCP space, named after the bond critical point, which compactly and successfully characterizes a chemical bond. The relative positions of the rings in RCP space are determined by the nature of the ring scaffold, such as the heteroatoms within the ring or the number of π-bonds. The summed atomic QCT charges of the five ring atoms revealed five features (number and type of heteroatom, number of π-bonds, substituent and substitution site) that dictate a ring's net charge. Each feature independently contributes toward a ring's net charge. Each substituent has its own distinct and systematic effect on the ring's net charge, irrespective of the ring scaffold. Therefore, this work proves the possibility of designing a ring with specific properties by fine-tuning it through manipulation of these five features.

  19. Concrete domains

    OpenAIRE

    Kahn, G.; Plotkin, G.D.

    1993-01-01

    This paper introduces the theory of a particular kind of computation domains called concrete domains. The purpose of this theory is to find a satisfactory framework for the notions of coroutine computation and sequentiality of evaluation.

  20. Token ring technology report

    CERN Document Server

    2013-01-01

    Please note this is a Short Discount publication. This report provides an overview of the IBM Token-Ring technology and products built by IBM and compatible vendors. It consists of two sections: 1. A summary of the design trade-offs for the IBM Token-Ring. 2. A summary of the products of the major token-ring compatible vendors broken down by adapters and components, wiring systems, testing, and new chip technology.

  1. Radioactive gold ring dermatitis

    International Nuclear Information System (INIS)

    Miller, R.A.; Aldrich, J.E.

    1990-01-01

    A superficial squamous cell carcinoma developed in a woman who wore a radioactive gold ring for more than 30 years. Only part of the ring was radioactive. Radiation dose measurements indicated that the dose to basal skin layer was 2.4 Gy (240 rad) per week. If it is assumed that the woman continually wore her wedding ring for 37 years since purchase, she would have received a maximum dose of approximately 4600 Gy

  2. Domain Engineering

    Science.gov (United States)

    Bjørner, Dines

    Before software can be designed we must know its requirements. Before requirements can be expressed we must understand the domain. So it follows, from our dogma, that we must first establish precise descriptions of domains; then, from such descriptions, “derive” at least domain and interface requirements; and from those and machine requirements design the software, or, more generally, the computing systems.

  3. Physics of quantum rings

    International Nuclear Information System (INIS)

    Fomin, Vladimir M.

    2014-01-01

    Presents the new class of materials of quantum rings. Provides an elemental basis for low-cost high-performance devices promising for electronics, optoelectronics, spintronics and quantum information processing. Explains the physical properties of quantum rings to cover a gap in scientific literature. Presents the application of most advanced nanoengineering and nanocharacterization techniques. This book deals with a new class of materials, quantum rings. Innovative recent advances in experimental and theoretical physics of quantum rings are based on the most advanced state-of-the-art fabrication and characterization techniques as well as theoretical methods. The experimental efforts allow to obtain a new class of semiconductor quantum rings formed by capping self-organized quantum dots grown by molecular beam epitaxy. Novel optical and magnetic properties of quantum rings are associated with non-trivial topologies at the nanoscale. An adequate characterization of quantum rings is possible on the basis of modern characterization methods of nanostructures, such as Scanning Tunneling Microscopy. A high level of complexity is demonstrated to be needed for a dedicated theoretical model to adequately represent the specific features of quantum rings. The findings presented in this book contribute to develop low-cost high-performance electronic, spintronic, optoelectronic and information processing devices based on quantum rings.

  4. Nanoscale Membrane Domain Formation Driven by Cholesterol

    DEFF Research Database (Denmark)

    Javanainen, Matti; Martinez-Seara, Hector; Vattulainen, Ilpo

    2017-01-01

    Biological membranes generate specific functions through compartmentalized regions such as cholesterol-enriched membrane nanodomains that host selected proteins. Despite the biological significance of nanodomains, details on their structure remain elusive. They cannot be observed via microscopic...... dipalmitoylphosphatidylcholine and cholesterol - the "minimal standard" for nanodomain formation. The simulations reveal how cholesterol drives the formation of fluid cholesterol-rich nanodomains hosting hexagonally packed cholesterol-poor lipid nanoclusters, both of which show registration between the membrane leaflets....... The complex nanodomain substructure forms when cholesterol positions itself in the domain boundary region. Here cholesterol can also readily flip-flop across the membrane. Most importantly, replacing cholesterol with a sterol characterized by a less asymmetric ring region impairs the emergence of nanodomains...

  5. Dewetting-mediated pattern formation inside the coffee ring

    Science.gov (United States)

    Li, Weibin; Lan, Ding; Wang, Yuren

    2017-04-01

    The rearrangement of particles in the final stage of droplet evaporation has been investigated by utilizing differential interference contrast microscopy and the formation mechanism of a network pattern inside a coffee ring has been revealed. A tailored substrate with a circular hydrophilic domain is prepared to obtain thin liquid film containing monolayer particles. Real-time bottom-view images show that the evolution of a dry patch could be divided into three stages: rupture initiation, dry patch expansion, and drying of the residual liquid. A growing number of dry patches will repeat these stages to form the network patterns inside the ringlike stain. It can be shown that the suction effect promotes the rupture of the liquid film and the formation of the dry patch. The particle-assembling process is totally controlled by the liquid film dewetting and dominated by the surface tension of the liquid film, which eventually determine the ultimate deposition patterns.

  6. EBT ring physics

    International Nuclear Information System (INIS)

    Uckan, N.A.

    1980-04-01

    This workshop attempted to evaluate the status of the current experimental and theoretical understanding of hot electron ring properties. The dominant physical processes that influence ring formation, scaling, and their optimal behavior are also studied. Separate abstracts were prepared for each of the 27 included papers

  7. A metamaterial terahertz modulator based on complementary planar double-split-ring resonator

    Science.gov (United States)

    Wang, Chang-hui; Kuang, Deng-feng; Chang, Sheng-jiang; Lin, Lie

    2013-07-01

    A metamaterial based on complementary planar double-split-ring resonator (DSRR) structure is presented and demonstrated, which can optically tune the transmission of the terahertz (THz) wave. Unlike the traditional DSRR metamaterials, the DSRR discussed in this paper consists of two split rings connected by two bridges. Numerical simulations with the finite-difference time-domain (FDTD) method reveal that the transmission spectra of the original and the complementary metamaterials are both in good agreement with Babinet's principle. Then by increasing the carrier density of the intrinsic GaAs substrate, the magnetic response of the complementary special DSRR metamaterial can be weakened or even turned off. This metamaterial structure is promised to be a narrow-band THz modulator with response time of several nanoseconds.

  8. Hereditary noetherian prime rings and idealizers

    CERN Document Server

    Levy, Lawrence S

    2011-01-01

    The direct sum behaviour of its projective modules is a fundamental property of any ring. Hereditary Noetherian prime rings are perhaps the only noncommutative Noetherian rings for which this direct sum behaviour (for both finitely and infinitely generated projective modules) is well-understood, yet highly nontrivial. This book surveys material previously available only in the research literature. It provides a re-worked and simplified account, with improved clarity, fresh insights and many original results about finite length modules, injective modules and projective modules. It culminates in the authors' surprisingly complete structure theorem for projective modules which involves two independent additive invariants: genus and Steinitz class. Several applications demonstrate its utility. The theory, extending the well-known module theory of commutative Dedekind domains and of hereditary orders, develops via a detailed study of simple modules. This relies upon the substantial account of idealizer subrings wh...

  9. Atomic structure of the sweet-tasting protein thaumatin I at pH 8.0 reveals the large disulfide-rich region in domain II to be sensitive to a pH change

    Energy Technology Data Exchange (ETDEWEB)

    Masuda, Tetsuya, E-mail: t2masuda@kais.kyoto-u.ac.jp [Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011 (Japan); Department of Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Gokasho, Uji, Kyoto 611-0011 (Japan); Ohta, Keisuke [Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011 (Japan); Department of Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Gokasho, Uji, Kyoto 611-0011 (Japan); Mikami, Bunzo [Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011 (Japan); Kitabatake, Naofumi [Department of Foods and Human Nutrition, Notre Dame Seishin University, Okayama 700-8516 (Japan); Tani, Fumito [Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011 (Japan); Department of Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Gokasho, Uji, Kyoto 611-0011 (Japan)

    2012-03-02

    Highlights: Black-Right-Pointing-Pointer Structure of a recombinant thaumatin at pH 8.0 determined at a resolution of 1.0 A. Black-Right-Pointing-Pointer Substantial fluctuations of a loop in domain II was found in the structure at pH 8.0. Black-Right-Pointing-Pointer B-factors for Lys137, Lys163, and Lys187 were significantly affected by pH change. Black-Right-Pointing-Pointer An increase in mobility might play an important role in the heat-induced aggregation. -- Abstract: Thaumatin, an intensely sweet-tasting plant protein, elicits a sweet taste at 50 nM. Although the sweetness remains when thaumatin is heated at 80 Degree-Sign C for 4 h under acid conditions, it rapidly declines when heating at a pH above 6.5. To clarify the structural difference at high pH, the atomic structure of a recombinant thaumatin I at pH 8.0 was determined at a resolution of 1.0 A. Comparison to the crystal structure of thaumatin at pH 7.3 and 7.0 revealed the root-mean square deviation value of a C{alpha} atom to be substantially greater in the large disulfide-rich region of domain II, especially residues 154-164, suggesting that a loop region in domain II to be affected by solvent conditions. Furthermore, B-factors of Lys137, Lys163, and Lys187 were significantly affected by pH change, suggesting that a striking increase in the mobility of these lysine residues, which could facilitate a reaction with a free sulfhydryl residue produced via the {beta}-elimination of disulfide bonds by heating at a pH above 7.0. The increase in mobility of lysine residues as well as a loop region in domain II might play an important role in the heat-induced aggregation of thaumatin above pH 7.0.

  10. On the Laurent polynomial rings

    International Nuclear Information System (INIS)

    Stefanescu, D.

    1985-02-01

    We describe some properties of the Laurent polynomial rings in a finite number of indeterminates over a commutative unitary ring. We study some subrings of the Laurent polynomial rings. We finally obtain two cancellation properties. (author)

  11. On the structure of order domains

    DEFF Research Database (Denmark)

    Geil, Olav; Pellikaan, Ruud

    2002-01-01

    The notion of an order domain is generalized. The behaviour of an order domain by taking a subalgebra, the extension of scalars, and the tensor product is studied. The relation of an order domain with valuation theory, Gröbner algebras, and graded structures is given. The theory of Gröbner bases...... for order domains is developed and used to show that the factor ring theorem and its converse, the presentation theorem, hold. The dimension of an order domain is related to the rank of its value semigroup....

  12. Ring enhancement in recurrent gliomas

    International Nuclear Information System (INIS)

    Ogashiwa, Motohide; Takeuchi, Kazuo; Akai, Keiichiro

    1981-01-01

    The clinical courses,CT scans, and postmortem reports for 6 glioma patients treated by surgery, radiation, and chemotherapy were reviewed. They underwent reoperation and/or retreatment with radiation or chemotherapy for recurrent tumors. CT scans taken at the time of recurrence or about one month prior to death showed ring enhancement of varied size and form after intensive treatment. The cases were examined histologically in correlation with the CT features and divided into two groups based on the pathological findings in the centers surrounded by areas of ring enhancement. The 1st group demonstrated a large necrotic area in the center, and the 2nd group, a cystic tumor. Tumor cells were found to have spread throughout the high-density areas around the necrotic area or cyst. However, gross differentiation between tumor and necrosis was difficult. In addition to an increase in cellularity, all cases demonstrated vascular proliferation, and dilatation of vessels in the sulci or sulci adjacent to gyri invaded by the tumor. The contrast enhancement corresponded well with the vascular proliferation in these areas. It is concluded that vascular proliferation or dilatation of vessels in and around the tumor is an important factor in demonstrating high-density areas in ring enhancement, while a cyst or necrosis in the tumor center is revealed as a low-density area in the CT scan of recurrent gliomas. (author)

  13. Ring enhancement in recurrent gliomas

    Energy Technology Data Exchange (ETDEWEB)

    Ogashiwa, M; Takeuchi, K; Akai, K [Kyorin Univ., Mitaka, Tokyo (Japan). School of Medicine

    1981-08-01

    The clinical courses,CT scans, and postmortem reports for 6 glioma patients treated by surgery, radiation, and chemotherapy were reviewed. They underwent reoperation and/or retreatment with radiation or chemotherapy for recurrent tumors. CT scans taken at the time of recurrence or about one month prior to death showed ring enhancement of varied size and form after intensive treatment. The cases were examined histologically in correlation with the CT features and divided into two groups based on the pathological findings in the centers surrounded by areas of ring enhancement. The 1st group demonstrated a large necrotic area in the center, and the 2nd group, a cystic tumor. Tumor cells were found to have spread throughout the high-density areas around the necrotic area or cyst. However, gross differentiation between tumor and necrosis was difficult. In addition to an increase in cellularity, all cases demonstrated vascular proliferation, and dilatation of vessels in the sulci or sulci adjacent to gyri invaded by the tumor. The contrast enhancement corresponded well with the vascular proliferation in these areas. It is concluded that vascular proliferation or dilatation of vessels in and around the tumor is an important factor in demonstrating high-density areas in ring enhancement, while a cyst or necrosis in the tumor center is revealed as a low-density area in the CT scan of recurrent gliomas.

  14. Heavy ion storage rings

    International Nuclear Information System (INIS)

    Schuch, R.

    1987-01-01

    A brief overview of synchrotron storage rings for heavy ions, which are presently under construction in different accelerator laboratories is given. Ions ranging from protons up to uranium ions at MeV/nucleon energies will be injected into these rings using multiturn injection from the accelerators available or being built in these laboratories. After injection, it is planned to cool the phase space distribution of the ions by merging them with cold electron beams or laser beams, or by using stochastic cooling. Some atomic physics experiments planned for these rings are presented. 35 refs

  15. Faithfully quadratic rings

    CERN Document Server

    Dickmann, M

    2015-01-01

    In this monograph the authors extend the classical algebraic theory of quadratic forms over fields to diagonal quadratic forms with invertible entries over broad classes of commutative, unitary rings where -1 is not a sum of squares and 2 is invertible. They accomplish this by: (1) Extending the classical notion of matrix isometry of forms to a suitable notion of T-isometry, where T is a preorder of the given ring, A, or T = A^2. (2) Introducing in this context three axioms expressing simple properties of (value) representation of elements of the ring by quadratic forms, well-known to hold in

  16. Saturn's Ring: Pre-Cassini Status and Mission Goals

    Science.gov (United States)

    Cuzzi, Jeff N.; DeVincenzi, Donald L. (Technical Monitor)

    1999-01-01

    In November 1980, and again in August 1981, identical Voyager spacecraft flew through the Saturn system, changing forever the way we think about planetary rings. Although Saturn's rings had been the only known ring system for three centuries, a ring system around Uranus had been discovered by stellar occultations from Earth in 1977, and the nearly transparent ring of Jupiter was imaged by Voyager in 1979 (the presence of material there had been inferred from charged particle experiments on Pioneer 10 and 11 several years earlier). While Saturn had thus temporarily lost its uniqueness as having the only ring system, with Voyager it handily recaptured the role of having the most fascinating one. The Voyager breakthroughs included spiral density and bending waves such as cause galactic structure; ubiquitous fine-scale radial 'irregular' structure, with the appearance of record-grooves; regional and local variations in particle color; complex, azimuthally variable ring structure; empty gaps in the rings, some containing very regular, sharp-edged, elliptical rings and one containing both a small moonlet and incomplete arcs of dusty material; and shadowy 'spokes' that flicker across the main rings. One of the paradigm shifts of this period was the realization that many aspects of planetary rings, and even the ring systems themselves, could be 'recent' on geological timescales. These early results are reviewed and summarized in the Arizona Space Science series volumes 'Saturn'. (An excellent review of ring dynamics at a formative stage is by Goldreich and Tremaine.) From the mid 1980's to the time of this writing, progress has been steady, while at a less heady pace, and some of the novel ring properties revealed by Voyager 1 and 2 are beginning to be better understood. It is clearly impossible to cite, much less review, every advance over the last decade; however, below we summarize the main advances in understanding of Saturn's rings since the mid 1980's, in the context

  17. Self-assembly and flux closure studies of magnetic nanoparticle rings

    DEFF Research Database (Denmark)

    Wei, Alexander; Kasama, Takeshi; Dunin-Borkowski, Rafal E.

    2011-01-01

    Thermoremanent magnetic nanoparticles (MNPs) can self-assemble into rings through dipolar interactions, when dispersed under appropriate conditions. Analysis of individual MNP rings and clusters by off-axis electron holography reveals bistable flux closure (FC) states at ambient temperatures...

  18. On arbitrarily graded rings

    Indian Academy of Sciences (India)

    58

    paper is devoted to the study of arbitrary rings graded through arbitrary sets. .... which recover certain multiplicative relations among the homogeneous components ... instance the case in which the grading set A is an Abelian group, where the ...

  19. The g-2 ring

    CERN Multimedia

    1974-01-01

    The precise measurement of "g-2", the anomalous magnetic moment of the muon, required a special muon storage ring with electrostatic focussing and very accurate knowledge of the magnetic bending field. For more details see under photo 7405430.

  20. [Liesegang's rings resembling helminthiasis].

    Science.gov (United States)

    Zámecník, M; Riedl, I

    1996-12-01

    So called Liesegang's rings are lamellar corpuscles which develop after periodical precipitation of oversaturated solutions in gel medium. They can occur in cysts, closed cavities, inflammatory exudates and necroses. They resemble parasitic eggs, larvae or adult forms. A case of 28-year-old woman is presented with many Liesegang's rings in a stuff from dilated renal calyx. Their preliminary evaluation considered helminths, especially Dioctophyma renale.

  1. Storage ring group summary

    International Nuclear Information System (INIS)

    King, N.M.

    1980-01-01

    The Storage Ring Group set out to identify and pursue salient problems in accelerator physics for heavy ion fusion, divorced from any particular reference design concept. However, it became apparent that some basic parameter framework was required to correlate the different study topics. As the Workshop progressed, ring parameters were modified and updated. Consequently, the accompanying papers on individual topics will be found to refer to slightly varied parameters, according to the stage at which the different problems were tackled

  2. The rings of Uranus

    Science.gov (United States)

    Elliot, J. L.; Dunham, E.; Mink, D.

    1977-01-01

    A description is given of the observation of five brief occultations of the star SAO 158687 which occurred both before and after its occultation by Uranus on March 10, 1977. The events were observed with a three-channel occultation photometer, attached to a 91-cm telescope. The observations indicate that at least five rings encircle the planet Uranus. Possible reasons for the narrowness of the Uranus rings are discussed.

  3. AN N-BODY INTEGRATOR FOR GRAVITATING PLANETARY RINGS, AND THE OUTER EDGE OF SATURN'S B RING

    International Nuclear Information System (INIS)

    Hahn, Joseph M.; Spitale, Joseph N.

    2013-01-01

    A new symplectic N-body integrator is introduced, one designed to calculate the global 360° evolution of a self-gravitating planetary ring that is in orbit about an oblate planet. This freely available code is called epi i nt, and it is distinct from other such codes in its use of streamlines to calculate the effects of ring self-gravity. The great advantage of this approach is that the perturbing forces arise from smooth wires of ring matter rather than discreet particles, so there is very little gravitational scattering and so only a modest number of particles are needed to simulate, say, the scalloped edge of a resonantly confined ring or the propagation of spiral density waves. The code is applied to the outer edge of Saturn's B ring, and a comparison of Cassini measurements of the ring's forced response to simulations of Mimas's resonant perturbations reveals that the B ring's surface density at its outer edge is σ 0 = 195 ± 60 g cm –2 , which, if the same everywhere across the ring, would mean that the B ring's mass is about 90% of Mimas's mass. Cassini observations show that the B ring-edge has several free normal modes, which are long-lived disturbances of the ring-edge that are not driven by any known satellite resonances. Although the mechanism that excites or sustains these normal modes is unknown, we can plant such a disturbance at a simulated ring's edge and find that these modes persist without any damping for more than ∼10 5 orbits or ∼100 yr despite the simulated ring's viscosity ν s = 100 cm 2 s –1 . These simulations also indicate that impulsive disturbances at a ring can excite long-lived normal modes, which suggests that an impact in the recent past by perhaps a cloud of cometary debris might have excited these disturbances, which are quite common to many of Saturn's sharp-edged rings

  4. The sequencing of the complete genome of a Tomato black ring virus (TBRV) and of the RNA2 of three Grapevine chrome mosaic virus (GCMV) isolates from grapevine reveals the possible recombinant origin of GCMV.

    Science.gov (United States)

    Digiaro, M; Yahyaoui, E; Martelli, G P; Elbeaino, T

    2015-02-01

    The complete genome of a Tomato black ring virus isolate (TBRV-Mirs) (RNA1, 7,366 nt and RNA2, 4,640 nt) and the RNA2 sequences (4,437; 4,445; and 4,442 nts) of three Grapevine chrome mosaic virus isolates (GCMV-H6, -H15, and -H27) were determined. All RNAs contained a single open reading frame encoding polyproteins of 254 kDa (p1) and 149 kDa (p2) for TBRV-Mirs RNA1 and RNA2, respectively, and 146 kDa for GCMV RNA2. p1 of TBRV-Mirs showed the highest identity with TBRV-MJ (94 %), Beet ringspot virus (BRSV, 82 %), and Grapevine Anatolian ringspot virus (GARSV, 66 %), while p2 showed the highest identity with TBRV isolates MJ (89 %) and ED (85 %), followed by BRSV (65 %), GCMV (58 %), and GARSV (57 %). The amino acid identity of RNA2 sequences of four GCMV isolates (three from this study and one from GenBank) ranged from 91 to 98 %, the homing protein being the most variable. The RDP3 program predicted putative intra-species recombination events for GCMV-H6 and recognized GCMV as a putative inter-species recombinant between GARSV and TBRV. In both cases, the recombination events were at the movement protein level.

  5. Some Aspects of Ring Theory

    CERN Document Server

    Herstein, IN

    2011-01-01

    S. Amitsur: Associative rings with identities.- I.N. Herstein: Topics in ring theory.- N. Jacobson: Representation theory of Jordan algebras.- I. Kaplansky: The theory of homological dimension.- D. Buchsbaum: Complexes in local ring theory.- P.H. Cohn: Two topics in ring theory.- A.W. Goldie: Non-commutative localisation.

  6. Ring correlations in random networks.

    Science.gov (United States)

    Sadjadi, Mahdi; Thorpe, M F

    2016-12-01

    We examine the correlations between rings in random network glasses in two dimensions as a function of their separation. Initially, we use the topological separation (measured by the number of intervening rings), but this leads to pseudo-long-range correlations due to a lack of topological charge neutrality in the shells surrounding a central ring. This effect is associated with the noncircular nature of the shells. It is, therefore, necessary to use the geometrical distance between ring centers. Hence we find a generalization of the Aboav-Weaire law out to larger distances, with the correlations between rings decaying away when two rings are more than about three rings apart.

  7. Mapping Ring Particle Cooling across Saturn's Rings with Cassini CIRS

    Science.gov (United States)

    Brooks, Shawn M.; Spilker, L. J.; Edgington, S. G.; Pilorz, S. H.; Deau, E.

    2010-10-01

    Previous studies have shown that the rings' thermal inertia, a measure of their response to changes in the thermal environment, varies from ring to ring. Thermal inertia can provide insight into the physical structure of Saturn's ring particles and their regoliths. Low thermal inertia and quick temperature responses are suggestive of ring particles that have more porous or fluffy regoliths or that are riddled with cracks. Solid, coherent particles can be expected to have higher thermal inertias (Ferrari et al. 2005). Cassini's Composite Infrared Spectrometer has recorded millions of spectra of Saturn's rings since its arrival at Saturn in 2004 (personal communication, M. Segura). CIRS records far infrared radiation between 10 and 600 cm-1 (16.7 and 1000 µm) at focal plane 1 (FP1), which has a field of view of 3.9 mrad. Thermal emission from Saturn's rings peaks in this wavelength range. FP1 spectra can be used to infer ring temperatures. By tracking how ring temperatures vary, we can determine the thermal inertia of the rings. In this work we focus on CIRS observations of the shadowed portion of Saturn's rings. The thermal budget of the rings is dominated by the solar radiation absorbed by its constituent particles. When ring particles enter Saturn's shadow this source of energy is abruptly cut off. As a result, ring particles cool as they traverse Saturn's shadow. From these shadow observations we can create cooling curves at specific locations across the rings. We will show that the rings' cooling curves and thus their thermal inertia vary not only from ring to ring, but by location within the individual rings. This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA. Copyright 2010 California Institute of Technology. Government sponsorship acknowledged.

  8. BERKELEY: ALS ring

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1993-06-15

    Everybody at Lawrence Berkeley Laboratory's Center for Beam Physics is pleased with the rapid progress in commissioning LBL's Advanced Light Source (ALS) electron storage ring, the foundation for this third-generation synchrotron radiation facility. Designed for a maximum current of 400 mA, the ALS storage ring reached 407 mA just 24 days after storing the first beam on 16 March. ALS construction as a US Department of Energy (DOE) national user facility to provide high-brightness vacuum ultra-violet and soft x-ray radiation began in October 1987. One technical requirement marking project completion was to accumulate a 50-mA current in the storage ring. The ALS passed this milestone on 24 March, a week ahead of the official deadline. Once injected, the electron beam decays quasi-exponentially primarily because of interactions with residual gas molecules in the storage-ring vacuum chamber. Eventually, when the pressure in the vacuum chamber with beam decreases toward the expected operating level of 1 nano Torr, it will only be necessary to refill the storage ring at intervals of four to eight hours. At present the vacuum is improving rapidly as surfaces are irradiated (scrubbed) by the synchrotron radiation itself. At 100 mA, beam lifetime was about one hour (9 April)

  9. Compressible Vortex Ring

    Science.gov (United States)

    Elavarasan, Ramasamy; Arakeri, Jayawant; Krothapalli, Anjaneyulu

    1999-11-01

    The interaction of a high-speed vortex ring with a shock wave is one of the fundamental issues as it is a source of sound in supersonic jets. The complex flow field induced by the vortex alters the propagation of the shock wave greatly. In order to understand the process, a compressible vortex ring is studied in detail using Particle Image Velocimetry (PIV) and shadowgraphic techniques. The high-speed vortex ring is generated from a shock tube and the shock wave, which precedes the vortex, is reflected back by a plate and made to interact with the vortex. The shadowgraph images indicate that the reflected shock front is influenced by the non-uniform flow induced by the vortex and is decelerated while passing through the vortex. It appears that after the interaction the shock is "split" into two. The PIV measurements provided clear picture about the evolution of the vortex at different time interval. The centerline velocity traces show the maximum velocity to be around 350 m/s. The velocity field, unlike in incompressible rings, contains contributions from both the shock and the vortex ring. The velocity distribution across the vortex core, core diameter and circulation are also calculated from the PIV data.

  10. BERKELEY: ALS ring

    International Nuclear Information System (INIS)

    Anon.

    1993-01-01

    Everybody at Lawrence Berkeley Laboratory's Center for Beam Physics is pleased with the rapid progress in commissioning LBL's Advanced Light Source (ALS) electron storage ring, the foundation for this third-generation synchrotron radiation facility. Designed for a maximum current of 400 mA, the ALS storage ring reached 407 mA just 24 days after storing the first beam on 16 March. ALS construction as a US Department of Energy (DOE) national user facility to provide high-brightness vacuum ultra-violet and soft x-ray radiation began in October 1987. One technical requirement marking project completion was to accumulate a 50-mA current in the storage ring. The ALS passed this milestone on 24 March, a week ahead of the official deadline. Once injected, the electron beam decays quasi-exponentially primarily because of interactions with residual gas molecules in the storage-ring vacuum chamber. Eventually, when the pressure in the vacuum chamber with beam decreases toward the expected operating level of 1 nano Torr, it will only be necessary to refill the storage ring at intervals of four to eight hours. At present the vacuum is improving rapidly as surfaces are irradiated (scrubbed) by the synchrotron radiation itself. At 100 mA, beam lifetime was about one hour (9 April)

  11. Almost ring theory

    CERN Document Server

    2003-01-01

    This book develops thorough and complete foundations for the method of almost etale extensions, which is at the basis of Faltings' approach to p-adic Hodge theory. The central notion is that of an "almost ring". Almost rings are the commutative unitary monoids in a tensor category obtained as a quotient V-Mod/S of the category V-Mod of modules over a fixed ring V; the subcategory S consists of all modules annihilated by a fixed ideal m of V, satisfying certain natural conditions. The reader is assumed to be familiar with general categorical notions, some basic commutative algebra and some advanced homological algebra (derived categories, simplicial methods). Apart from these general prerequisites, the text is as self-contained as possible. One novel feature of the book - compared with Faltings' earlier treatment - is the systematic exploitation of the cotangent complex, especially for the study of deformations of almost algebras.

  12. Compact electron storage rings

    International Nuclear Information System (INIS)

    Williams, G.P.

    1987-01-01

    There have been many recent developments in the area of compact storage rings. Such rings would have critical wavelengths of typically 10 A, achieved with beam energies of several hundreds of MeV and superconducting dipole fields of around 5 Tesla. Although the primary motivation for progress in this area is that of commercial x-ray lithography, such sources might be an attractive source for college campuses to operate. They would be useful for many programs in materials science, solid state, x-ray microscopy and other biological areas. We discuss the properties of such sources and review developments around the world, primarily in the USA, japan and W. Germany

  13. The covariant chiral ring

    Energy Technology Data Exchange (ETDEWEB)

    Bourget, Antoine; Troost, Jan [Laboratoire de Physique Théorique, École Normale Supérieure, 24 rue Lhomond, 75005 Paris (France)

    2016-03-23

    We construct a covariant generating function for the spectrum of chiral primaries of symmetric orbifold conformal field theories with N=(4,4) supersymmetry in two dimensions. For seed target spaces K3 and T{sup 4}, the generating functions capture the SO(21) and SO(5) representation theoretic content of the chiral ring respectively. Via string dualities, we relate the transformation properties of the chiral ring under these isometries of the moduli space to the Lorentz covariance of perturbative string partition functions in flat space.

  14. The Saturnian rings

    International Nuclear Information System (INIS)

    Alfven, H.

    1975-09-01

    The structure of the Saturnian rings is traditionally believed to be due to resonances caused by Mimas (and possibly other satellites). It is shown that both theoretical and observational evidence rule out this interpretation. The increased observational accuracy on one hand and the increased understanding of the cosmogonic processes on the other makes it possible to explain the structure of the ring system as a product of condensation from a partially corotating plasma. In certain respects the agreement between theory and observations is about 1%. (Auth.)

  15. RINGED ACCRETION DISKS: INSTABILITIES

    Energy Technology Data Exchange (ETDEWEB)

    Pugliese, D.; Stuchlík, Z., E-mail: d.pugliese.physics@gmail.com, E-mail: zdenek.stuchlik@physics.cz [Institute of Physics and Research Centre of Theoretical Physics and Astrophysics, Faculty of Philosophy and Science, Silesian University in Opava, Bezručovo náměstí 13, CZ-74601 Opava (Czech Republic)

    2016-04-01

    We analyze the possibility that several instability points may be formed, due to the Paczyński mechanism of violation of mechanical equilibrium, in the orbiting matter around a supermassive Kerr black hole. We consider a recently proposed model of a ringed accretion disk, made up by several tori (rings) that can be corotating or counter-rotating relative to the Kerr attractor due to the history of the accretion process. Each torus is governed by the general relativistic hydrodynamic Boyer condition of equilibrium configurations of rotating perfect fluids. We prove that the number of the instability points is generally limited and depends on the dimensionless spin of the rotating attractor.

  16. Vortex formation in narrow ferromagnetic rings

    International Nuclear Information System (INIS)

    Klaeui, M; Vaz, C A F; Lopez-Diaz, L; Bland, J A C

    2003-01-01

    The high-symmetry ring geometry is shown to exhibit a wide range of intriguing magnetostatic and magnetodynamic properties, which we survey in this topical review. We consider first the patterning and deposition techniques, which are used to fabricate ring structures (diameters between 0.1 and 2 μm) and discuss their respective advantages and disadvantages. The results of direct nanoscale imaging of the novel magnetization configurations present in rings with different geometrical parameters (including discs) are discussed. These results give valuable insight into the influence of the magnetic anisotropies governing the magnetic states. The different types of domain walls that arise are compared quantitatively to micromagnetic simulations. The magnetodynamic switching between the different magnetic states is described in detail. In particular we elaborate on the different geometry-dependent magnetic switchings, since the different transitions occurring allow us to determine which energy terms govern the reversal process. We discuss a process by which fast (sub-ns) and controlled switching can be achieved, therefore making rings an attractive geometry for applications, in addition to studying fundamental issues of nanomagnetism. (topical review)

  17. Fusion rings and fusion ideals

    DEFF Research Database (Denmark)

    Andersen, Troels Bak

    by the so-called fusion ideals. The fusion rings of Wess-Zumino-Witten models have been widely studied and are well understood in terms of precise combinatorial descriptions and explicit generating sets of the fusion ideals. They also appear in another, more general, setting via tilting modules for quantum......This dissertation investigates fusion rings, which are Grothendieck groups of rigid, monoidal, semisimple, abelian categories. Special interest is in rational fusion rings, i.e., fusion rings which admit a finite basis, for as commutative rings they may be presented as quotients of polynomial rings...

  18. Einstein Ring in Distant Universe

    Science.gov (United States)

    2005-06-01

    on the newly discovered Einstein ring. The image quality ("seeing") of the R-band image is exceptional (0.5") and the image reveals the lensing system in stunning details. The central dot is the lens, a quiescent massive galaxy that distort the light emitted by background sources. The large arc surrounding the central lens is a part of the Einstein-ring created by a background source finely aligned with the lens. The reddish colour indicates that the redshift of the system is very large. FORS2 spectroscopy of the lensing system yield a redshift close to 1 for the lens (we see the lens as it was when the universe was half its present size), and a record-breaking redshift z=3.8 for a background source of such brightness, hence we see the object (a star forming galaxy) as it was when the universe was only 12% of its present age. The lensing model indicates that the light of the source is magnified at least 13 times. The right panel shows the reconstructed image based on the model of the lens and the source, showing the ring to extend over 3/4 of a circle. "There are only a very few optical rings or arcs known, and even less so in which the lens and the source are at large distance, i.e. more than about 7,000 million light-years away (or half the present age of the Universe)", says Rémi Cabanac, former ESO Fellow and now working at the Canada-France-Hawaii Telescope. "Moreover, very few are nearly complete", he adds. But in the case of this newly found cosmic ring, the images show it to extend to almost 3/4 of a circle. The lensing galaxy is located at a distance of about 8,000 million light-years from us, while the source galaxy whose light is distorted, is much farther away, at 12,000 million light-years. Thus, we see this galaxy as it was when the universe was only 12% of its present age. The lens magnifies the source almost 13 times. The observations reveal the galaxy acting as a lens to be a rather quiet galaxy, 40,000 light-years wide, with an old stellar

  19. The cryogenic storage ring CSR

    Science.gov (United States)

    von Hahn, R.; Becker, A.; Berg, F.; Blaum, K.; Breitenfeldt, C.; Fadil, H.; Fellenberger, F.; Froese, M.; George, S.; Göck, J.; Grieser, M.; Grussie, F.; Guerin, E. A.; Heber, O.; Herwig, P.; Karthein, J.; Krantz, C.; Kreckel, H.; Lange, M.; Laux, F.; Lohmann, S.; Menk, S.; Meyer, C.; Mishra, P. M.; Novotný, O.; O'Connor, A. P.; Orlov, D. A.; Rappaport, M. L.; Repnow, R.; Saurabh, S.; Schippers, S.; Schröter, C. D.; Schwalm, D.; Schweikhard, L.; Sieber, T.; Shornikov, A.; Spruck, K.; Sunil Kumar, S.; Ullrich, J.; Urbain, X.; Vogel, S.; Wilhelm, P.; Wolf, A.; Zajfman, D.

    2016-06-01

    An electrostatic cryogenic storage ring, CSR, for beams of anions and cations with up to 300 keV kinetic energy per unit charge has been designed, constructed, and put into operation. With a circumference of 35 m, the ion-beam vacuum chambers and all beam optics are in a cryostat and cooled by a closed-cycle liquid helium system. At temperatures as low as (5.5 ± 1) K inside the ring, storage time constants of several minutes up to almost an hour were observed for atomic and molecular, anion and cation beams at an energy of 60 keV. The ion-beam intensity, energy-dependent closed-orbit shifts (dispersion), and the focusing properties of the machine were studied by a system of capacitive pickups. The Schottky-noise spectrum of the stored ions revealed a broadening of the momentum distribution on a time scale of 1000 s. Photodetachment of stored anions was used in the beam lifetime measurements. The detachment rate by anion collisions with residual-gas molecules was found to be extremely low. A residual-gas density below 140 cm-3 is derived, equivalent to a room-temperature pressure below 10-14 mbar. Fast atomic, molecular, and cluster ion beams stored for long periods of time in a cryogenic environment will allow experiments on collision- and radiation-induced fragmentation processes of ions in known internal quantum states with merged and crossed photon and particle beams.

  20. The cryogenic storage ring CSR.

    Science.gov (United States)

    von Hahn, R; Becker, A; Berg, F; Blaum, K; Breitenfeldt, C; Fadil, H; Fellenberger, F; Froese, M; George, S; Göck, J; Grieser, M; Grussie, F; Guerin, E A; Heber, O; Herwig, P; Karthein, J; Krantz, C; Kreckel, H; Lange, M; Laux, F; Lohmann, S; Menk, S; Meyer, C; Mishra, P M; Novotný, O; O'Connor, A P; Orlov, D A; Rappaport, M L; Repnow, R; Saurabh, S; Schippers, S; Schröter, C D; Schwalm, D; Schweikhard, L; Sieber, T; Shornikov, A; Spruck, K; Sunil Kumar, S; Ullrich, J; Urbain, X; Vogel, S; Wilhelm, P; Wolf, A; Zajfman, D

    2016-06-01

    An electrostatic cryogenic storage ring, CSR, for beams of anions and cations with up to 300 keV kinetic energy per unit charge has been designed, constructed, and put into operation. With a circumference of 35 m, the ion-beam vacuum chambers and all beam optics are in a cryostat and cooled by a closed-cycle liquid helium system. At temperatures as low as (5.5 ± 1) K inside the ring, storage time constants of several minutes up to almost an hour were observed for atomic and molecular, anion and cation beams at an energy of 60 keV. The ion-beam intensity, energy-dependent closed-orbit shifts (dispersion), and the focusing properties of the machine were studied by a system of capacitive pickups. The Schottky-noise spectrum of the stored ions revealed a broadening of the momentum distribution on a time scale of 1000 s. Photodetachment of stored anions was used in the beam lifetime measurements. The detachment rate by anion collisions with residual-gas molecules was found to be extremely low. A residual-gas density below 140 cm(-3) is derived, equivalent to a room-temperature pressure below 10(-14) mbar. Fast atomic, molecular, and cluster ion beams stored for long periods of time in a cryogenic environment will allow experiments on collision- and radiation-induced fragmentation processes of ions in known internal quantum states with merged and crossed photon and particle beams.

  1. The cryogenic storage ring CSR

    Energy Technology Data Exchange (ETDEWEB)

    Hahn, R. von; Becker, A.; Berg, F.; Blaum, K.; Fadil, H.; Fellenberger, F.; Froese, M.; George, S.; Göck, J.; Grieser, M.; Grussie, F.; Guerin, E. A.; Herwig, P.; Karthein, J.; Krantz, C.; Kreckel, H.; Lange, M.; Laux, F.; Lohmann, S.; Menk, S. [Max-Planck-Institut für Kernphysik, 69117 Heidelberg (Germany); and others

    2016-06-15

    An electrostatic cryogenic storage ring, CSR, for beams of anions and cations with up to 300 keV kinetic energy per unit charge has been designed, constructed, and put into operation. With a circumference of 35 m, the ion-beam vacuum chambers and all beam optics are in a cryostat and cooled by a closed-cycle liquid helium system. At temperatures as low as (5.5 ± 1) K inside the ring, storage time constants of several minutes up to almost an hour were observed for atomic and molecular, anion and cation beams at an energy of 60 keV. The ion-beam intensity, energy-dependent closed-orbit shifts (dispersion), and the focusing properties of the machine were studied by a system of capacitive pickups. The Schottky-noise spectrum of the stored ions revealed a broadening of the momentum distribution on a time scale of 1000 s. Photodetachment of stored anions was used in the beam lifetime measurements. The detachment rate by anion collisions with residual-gas molecules was found to be extremely low. A residual-gas density below 140 cm{sup −3} is derived, equivalent to a room-temperature pressure below 10{sup −14} mbar. Fast atomic, molecular, and cluster ion beams stored for long periods of time in a cryogenic environment will allow experiments on collision- and radiation-induced fragmentation processes of ions in known internal quantum states with merged and crossed photon and particle beams.

  2. Flushing Ring for EDM

    Science.gov (United States)

    Earwood, L.

    1985-01-01

    Removing debris more quickly lowers cutting time. Operation, cutting oil and pressurized air supplied to ring placed around workpiece. Air forces oil through small holes and agitates oil as it flows over workpiece. High flow rate and agitation dislodge and remove debris. Electrical discharge removes material from workpiece faster.

  3. Sector ring accelerator ''RESATRON''

    International Nuclear Information System (INIS)

    Schwabe, E.

    1980-01-01

    Project of sector ring accelerator RESATRON is described. The curiosity of this accelerator is the second cycle of acceleration of the beam after stripping it on the foil. In such an accelerator heavy ions with a different ratio Z to A can be accelerated. (S.B.)

  4. Ring chromosome 13

    DEFF Research Database (Denmark)

    Brandt, C A; Hertz, Jens Michael; Petersen, M B

    1992-01-01

    A stillborn male child with anencephaly and multiple malformations was found to have the karyotype 46,XY,r(13) (p11q21.1). The breakpoint at 13q21.1, determined by high resolution banding, is the most proximal breakpoint ever reported in patients with ring chromosome 13. In situ hybridisation...

  5. SXLS storage ring design

    International Nuclear Information System (INIS)

    Anon.

    1991-01-01

    X-ray lithography has emerged as a strong candidate to meet the demands of ever finer linewidths on integrated circuits, particularly for linewidths less than .25 microns. Proximity printing X-ray lithography makes use of soft X-rays to shadow print an image of a mask onto a semiconductor wafer to produce integrated circuits. To generate the required X-rays in sufficient quantities to make commercial production viable, electron storage rings have been proposed as the soft X-ray sources. Existing storage rings have been used to do the initial development work and the success of these efforts has led the lithographers to request that new rings be constructed that are dedicated to X-ray lithography. As a result of a series of workshops held at BNL [10.3] which were attended by both semiconductor and accelerator scientists, the following set of zeroth order specifications' on the light and electron beam of a storage ring for X-ray lithography were developed: critical wavelength of light: λ c = 6 to 10 angstroms, white light power: P = 0.25 to 2.5 watts/mrad, horizontal collection angle per port: θ = 10 to 50 mrad, electron beam sizes: σ x ∼ σ y y ' < 1 mrad

  6. Ring magnetron ionizer

    International Nuclear Information System (INIS)

    Alessi, J.G.

    1986-01-01

    A ring magnetron D - charge exchange ionizer has been built and tested. An H - current of 500 μA was extracted with an estimated H 0 density in the ionizer of 10 12 cm -3 . This exceeds the performance of ionizers presently in use on polarized H - sources. The ionizer will soon be tested with a polarized atomic beam

  7. Algebras, rings and modules

    CERN Document Server

    Hazewinkel, Michiel; Kirichenko, V V

    Provides both the classical aspects of the theory of groups and their representations as well as a general introduction to the modern theory of representations, including the representations of quivers and finite partially ordered sets. This volume provides the theory of semiprime Noetherian semiperfect and semidistributive rings.

  8. Lattices for antiproton rings

    International Nuclear Information System (INIS)

    Autin, B.

    1984-01-01

    After a description of the constraints imposed by the cooling of Antiprotons on the lattice of the rings, the reasons which motivate the shape and the structure of these machines are surveyed. Linear and non-linear beam optics properties are treated with a special amplification to the Antiproton Accumulator. (orig.)

  9. Domain crossing

    DEFF Research Database (Denmark)

    Schraefel, M. C.; Rouncefield, Mark; Kellogg, Wendy

    2012-01-01

    In CSCW, how much do we need to know about another domain/culture before we observe, intersect and intervene with designs. What optimally would that other culture need to know about us? Is this a “how long is a piece of string” question, or an inquiry where we can consider a variety of contexts a...

  10. Propellers in Saturn's rings

    Science.gov (United States)

    Sremcevic, M.; Stewart, G. R.; Albers, N.; Esposito, L. W.

    2013-12-01

    Theoretical studies and simulations have demonstrated the effects caused by objects embedded in planetary rings. Even if the objects are too small to be directly observed, each creates a much larger gravitational imprint on the surrounding ring material. These strongly depend on the mass of the object and range from "S" like propeller-shaped structures for about 100m-sized icy bodies to the opening of circumferential gaps as in the case of the embedded moons Pan and Daphnis and their corresponding Encke and Keeler Gaps. Since the beginning of the Cassini mission many of these smaller objects (~data from Cassini Ultraviolet Imaging Spectrograph (UVIS) and Imaging Science Subsystem (ISS) experiments. We show evidence that B ring seems to harbor two distinct populations of propellers: "big" propellers covering tens of degrees in azimuth situated in the densest part of B ring, and "small" propellers in less dense inner B ring that are similar in size and shape to known A ring propellers. The population of "big" propellers is exemplified with a single object which is observed for 5 years of Cassini data. The object is seen as a very elongated bright stripe (40 degrees wide) in unlit Cassini images, and dark stripe in lit geometries. In total we report observing the feature in images at 18 different epochs between 2005 and 2010. In UVIS occultations we observe this feature as an optical depth depletion in 14 out of 93 occultation cuts at corrotating longitudes compatible with imaging data. Combining the available Cassini data we infer that the object is a partial gap located at r=112,921km embedded in the high optical depth region of the B ring. The gap moves at Kepler speed appropriate for its radial location. Radial offsets of the gap locations in UVIS occultations are consistent with an asymmetric propeller shape. The asymmetry of the observed shape is most likely a consequence of the strong surface mass density gradient, as the feature is located at an edge between

  11. The glomuvenous malformation protein Glomulin binds Rbx1 and regulates cullin RING ligase-mediated turnover of Fbw7.

    Science.gov (United States)

    Tron, Adriana E; Arai, Takehiro; Duda, David M; Kuwabara, Hiroshi; Olszewski, Jennifer L; Fujiwara, Yuko; Bahamon, Brittany N; Signoretti, Sabina; Schulman, Brenda A; DeCaprio, James A

    2012-04-13

    Fbw7, a substrate receptor for Cul1-RING-ligase (CRL1), facilitates the ubiquitination and degradation of several proteins, including Cyclin E and c-Myc. In spite of much effort, the mechanisms underlying Fbw7 regulation are mostly unknown. Here, we show that Glomulin (Glmn), a protein found mutated in the vascular disorder glomuvenous malformation (GVM), binds directly to the RING domain of Rbx1 and inhibits its E3 ubiquitin ligase activity. Loss of Glmn in a variety of cells, tissues, and GVM lesions results in decreased levels of Fbw7 and increased levels of Cyclin E and c-Myc. The increased turnover of Fbw7 is dependent on CRL and proteasome activity, indicating that Glmn modulates the E3 activity of CRL1(Fbw7). These data reveal an unexpected functional connection between Glmn and Rbx1 and demonstrate that defective regulation of Fbw7 levels contributes to GVM. Copyright © 2012 Elsevier Inc. All rights reserved.

  12. FUZZY RINGS AND ITS PROPERTIES

    Directory of Open Access Journals (Sweden)

    Karyati Karyati

    2017-01-01

      One of algebraic structure that involves a binary operation is a group that is defined  an un empty set (classical with an associative binary operation, it has identity elements and each element has an inverse. In the structure of the group known as the term subgroup, normal subgroup, subgroup and factor group homomorphism and its properties. Classical algebraic structure is developed to algebraic structure fuzzy by the researchers as an example semi group fuzzy and fuzzy group after fuzzy sets is introduced by L. A. Zadeh at 1965. It is inspired of writing about semi group fuzzy and group of fuzzy, a research on the algebraic structure of the ring is held with reviewing ring fuzzy, ideal ring fuzzy, homomorphism ring fuzzy and quotient ring fuzzy with its properties. The results of this study are obtained fuzzy properties of the ring, ring ideal properties fuzzy, properties of fuzzy ring homomorphism and properties of fuzzy quotient ring by utilizing a subset of a subset level  and strong level  as well as image and pre-image homomorphism fuzzy ring.   Keywords: fuzzy ring, subset level, homomorphism fuzzy ring, fuzzy quotient ring

  13. Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase: DAWIDZIAK et al.

    Energy Technology Data Exchange (ETDEWEB)

    Dawidziak, Daria M. [Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville Virginia; Sanchez, Jacint G. [Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville Virginia; Wagner, Jonathan M. [Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville Virginia; Ganser-Pornillos, Barbie K. [Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville Virginia; Pornillos, Owen [Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville Virginia

    2017-07-24

    Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. An emerging general model is that TRIMs form elongated antiparallel coiled-coil dimers that prevent interaction of the two attendant RING domains. The RING domains themselves bind E2 conjugating enzymes as dimers, implying that an active TRIM ligase requires higher-order oligomerization of the basal coiled-coil dimers. Here, we report crystal structures of the TRIM23 RING domain in isolation and in complex with an E2–ubiquitin conjugate. Our results indicate that TRIM23 enzymatic activity requires RING dimerization, consistent with the general model of TRIM activation.

  14. Inorganic glass ceramic slip rings

    Science.gov (United States)

    Glossbrenner, E. W.; Cole, S. R.

    1972-01-01

    Prototypes of slip rings have been fabricated from ceramic glass, a material which is highly resistant to deterioration due to high temperature. Slip ring assemblies were not structurally damaged by mechanical tests and performed statisfactorily for 200 hours.

  15. Uniquely Strongly Clean Group Rings

    Institute of Scientific and Technical Information of China (English)

    WANG XIU-LAN

    2012-01-01

    A ring R is called clean if every element is the sum of an idempotent and a unit,and R is called uniquely strongly clean (USC for short) if every element is uniquely the sum of an idempotent and a unit that commute.In this article,some conditions on a ring R and a group G such that RG is clean are given.It is also shown that if G is a locally finite group,then the group ring RG is USC if and only if R is USC,and G is a 2-group.The left uniquely exchange group ring,as a middle ring of the uniquely clean ring and the USC ring,does not possess this property,and so does the uniquely exchange group ring.

  16. Trusted Domain

    DEFF Research Database (Denmark)

    Hjorth, Theis Solberg; Torbensen, Rune

    2012-01-01

    remote access via IP-based devices such as smartphones. The Trusted Domain platform fits existing legacy technologies by managing their interoperability and access controls, and it seeks to avoid the security issues of relying on third-party servers outside the home. It is a distributed system...... of wireless standards, limited resources of embedded systems, etc. Taking these challenges into account, we present a Trusted Domain home automation platform, which dynamically and securely connects heterogeneous networks of Short-Range Wireless devices via simple non-expert user. interactions, and allows......In the digital age of home automation and with the proliferation of mobile Internet access, the intelligent home and its devices should be accessible at any time from anywhere. There are many challenges such as security, privacy, ease of configuration, incompatible legacy devices, a wealth...

  17. Ring closure in actin polymers

    Energy Technology Data Exchange (ETDEWEB)

    Sinha, Supurna, E-mail: supurna@rri.res.in [Raman Research Institute, Bangalore 560080 (India); Chattopadhyay, Sebanti [Doon University, Dehradun 248001 (India)

    2017-03-18

    We present an analysis for the ring closure probability of semiflexible polymers within the pure bend Worm Like Chain (WLC) model. The ring closure probability predicted from our analysis can be tested against fluorescent actin cyclization experiments. We also discuss the effect of ring closure on bend angle fluctuations in actin polymers. - Highlights: • Ring closure of biopolymers. • Worm like chain model. • Predictions for experiments.

  18. Expansion of protein domain repeats.

    Directory of Open Access Journals (Sweden)

    Asa K Björklund

    2006-08-01

    Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

  19. Design of low energy ring(s)

    CERN Document Server

    Lachaize, Antoine

    During the last two years, several upgrades of the initial baseline scenario were studied with the aim of increasing the average intensity of ion beams in the accelerator chain of the Beta Beam complex. This is the reason why the Rapid Cycling Synchrotron (RCS) specifications were reconsidered many times [1], [2], [3].General considerations on the optical design were presented at the Beta Beam Task Meetings held at CERN and at Saclay in 2005 [4]. More detailed beam optics studies were performed during the next months. Lattices, RF system parameters, multi-turn injection scheme, fast extraction, closed orbit correction and chromaticity correction systems were proposed for different versions of the RCS [5], [6], [7].Finally, the RCS specifications have stabilized in November 2006 after the fourth Beta Beam Task Meeting when it was decided to fix the maximum magnetic rigidity of ion beams to 14.47 T.m (3.5 GeV equivalent proton energy) and to adopt a ring physical radius of 40 m in order to facilitate injectio...

  20. Fusion Rings for Quantum Groups

    DEFF Research Database (Denmark)

    Andersen, Henning Haahr; Stroppel, Catharina

    2012-01-01

    We study the fusion rings of tilting modules for a quantum group at a root of unity modulo the tensor ideal of negligible tilting modules. We identify them in type A with the combinatorial rings from [12] and give a similar description of the sp2n-fusion ring in terms of noncommutative symmetric...

  1. RINGED ACCRETION DISKS: EQUILIBRIUM CONFIGURATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Pugliese, D.; Stuchlík, Z., E-mail: d.pugliese.physics@gmail.com, E-mail: zdenek.stuchlik@physics.cz [Institute of Physics and Research Centre of Theoretical Physics and Astrophysics, Faculty of Philosophy and Science, Silesian University in Opava, Bezručovo náměstí 13, CZ-74601 Opava (Czech Republic)

    2015-12-15

    We investigate a model of a ringed accretion disk, made up by several rings rotating around a supermassive Kerr black hole attractor. Each toroid of the ringed disk is governed by the general relativity hydrodynamic Boyer condition of equilibrium configurations of rotating perfect fluids. Properties of the tori can then be determined by an appropriately defined effective potential reflecting the background Kerr geometry and the centrifugal effects. The ringed disks could be created in various regimes during the evolution of matter configurations around supermassive black holes. Therefore, both corotating and counterrotating rings have to be considered as being a constituent of the ringed disk. We provide constraints on the model parameters for the existence and stability of various ringed configurations and discuss occurrence of accretion onto the Kerr black hole and possible launching of jets from the ringed disk. We demonstrate that various ringed disks can be characterized by a maximum number of rings. We present also a perturbation analysis based on evolution of the oscillating components of the ringed disk. The dynamics of the unstable phases of the ringed disk evolution seems to be promising in relation to high-energy phenomena demonstrated in active galactic nuclei.

  2. Terahertz pulse imaging for tree-ring analysis: a preliminary study for dendrochronology applications

    International Nuclear Information System (INIS)

    Jackson, J B; Mourou, M; Whitaker, J F; Labaune, J; Mourou, G A; Duling, I N III; Williamson, S L; Lavier, C; Menu, M

    2009-01-01

    Time-domain terahertz reflection imaging is presented as a novel method of measuring otherwise inaccessible tree rings in wooden cultural heritage for the purpose of tree-ring crossdating. Axial and lateral two-dimensional terahertz images of obscured ring patterns are statistically validated with respect to their corresponding optical photographs via adapted dendrochronological methods. Results are compared to similar analysis of x-ray images of a wood specimen

  3. Graphene-based tunable terahertz filter with rectangular ring ...

    Indian Academy of Sciences (India)

    A plasmonic band-pass filter based on graphene rectangular ring resonator with double narrow gaps is proposed and numerically investigated by finite-difference time-domain (FDTD) simulations. For the filter with or without gaps, the resonant frequencies can be effectively adjusted by changing the width of the graphene ...

  4. Binary GCD like Algorithms for Some Complex Quadratic Rings

    DEFF Research Database (Denmark)

    Agarwal, Saurabh; Frandsen, Gudmund Skovbjerg

    2004-01-01

    On the lines of the binary gcd algorithm for rational integers, algorithms for computing the gcd are presented for the ring of integers in where . Thus a binary gcd like algorithm is presented for a unique factorization domain which is not Euclidean (case d=-19). Together with the earlier known b...

  5. Modified climate with long term memory in tree ring proxies

    Czech Academy of Sciences Publication Activity Database

    Zhang, H.; Yuan, N.; Esper, J.; Werner, J. P.; Xoplaki, E.; Büntgen, Ulf; Treydte, K.; Luterbacher, J.

    2015-01-01

    Roč. 10, č. 8 (2015), č. článku 084020. ISSN 1748-9326 Institutional support: RVO:67179843 Keywords : surface-temperature * northern-hemisphere * china * variability * persistence * precipitation * fluctuations * millennium * rainfall * model * climate reconstructions * tree-ring width * maximum latewood density * frequency domains Subject RIV: EH - Ecology, Behaviour Impact factor: 4.134, year: 2015

  6. Graphene-based tunable terahertz filter with rectangular ring ...

    Indian Academy of Sciences (India)

    WEI SU

    2017-08-16

    Aug 16, 2017 ... Abstract. A plasmonic band-pass filter based on graphene rectangular ring resonator with double narrow gaps is proposed and numerically investigated by finite-difference time-domain (FDTD) simulations. For the filter with or without gaps, the resonant frequencies can be effectively adjusted by changing ...

  7. A New GCD Algorithm for Quadratic Number Rings with Unique Factorization

    DEFF Research Database (Denmark)

    Agarwal, Saurabh; Frandsen, Gudmund Skovbjerg

    2006-01-01

    We present an algorithm to compute a greatest common divisor of two integers in a quadratic number ring that is a unique factorization domain. The algorithm uses bit operations in a ring of discriminant Δ. This appears to be the first gcd algorithm of complexity o(n 2) for any fixed non-Euclidean...

  8. Numerical Modelling of a Bidirectional Long Ring Raman Fiber Laser Dynamics

    Science.gov (United States)

    Sukhanov, S. V.; Melnikov, L. A.; Mazhirina, Yu A.

    2017-11-01

    The numerical model for the simulation of the dynamics of a bidirectional long ring Raman fiber laser is proposed. The model is based on the transport equations and Courant-Isaacson-Rees method. Different regimes of a bidirectional long ring Raman fiber laser and long time-domain realizations are investigated.

  9. Ring Confidential Transactions

    Directory of Open Access Journals (Sweden)

    Shen Noether

    2016-12-01

    Full Text Available This article introduces a method of hiding transaction amounts in the strongly decentralized anonymous cryptocurrency Monero. Similar to Bitcoin, Monero is a cryptocurrency which is distributed through a proof-of-work “mining” process having no central party or trusted setup. The original Monero protocol was based on CryptoNote, which uses ring signatures and one-time keys to hide the destination and origin of transactions. Recently the technique of using a commitment scheme to hide the amount of a transaction has been discussed and implemented by Bitcoin Core developer Gregory Maxwell. In this article, a new type of ring signature, A Multilayered Linkable Spontaneous Anonymous Group signature is described which allows one to include a Pedersen Commitment in a ring signature. This construction results in a digital currency with hidden amounts, origins and destinations of transactions with reasonable efficiency and verifiable, trustless coin generation. The author would like to note that early drafts of this were publicized in the Monero Community and on the #bitcoin-wizards IRC channel. Blockchain hashed drafts are available showing that this work was started in Summer 2015, and completed in early October 2015. An eprint is also available at http://eprint.iacr.org/2015/1098.

  10. Electron localization and optical absorption of polygonal quantum rings

    Science.gov (United States)

    Sitek, Anna; Serra, Llorenç; Gudmundsson, Vidar; Manolescu, Andrei

    2015-06-01

    We investigate theoretically polygonal quantum rings and focus mostly on the triangular geometry where the corner effects are maximal. Such rings can be seen as short core-shell nanowires, a generation of semiconductor heterostructures with multiple applications. We show how the geometry of the sample determines the electronic energy spectrum, and also the localization of electrons, with effects on the optical absorption. In particular, we show that irrespective of the ring shape low-energy electrons are always attracted by corners and are localized in their vicinity. The absorption spectrum in the presence of a magnetic field shows only two peaks within the corner-localized state domain, each associated with different circular polarization. This picture may be changed by an external electric field which allows previously forbidden transitions, and thus enables the number of corners to be determined. We show that polygonal quantum rings allow absorption of waves from distant ranges of the electromagnetic spectrum within one sample.

  11. Sequence and Secondary Structure of the Mitochondrial Small-Subunit rRNA V4, V6, and V9 Domains Reveal Highly Species-Specific Variations within the Genus Agrocybe

    OpenAIRE

    Gonzalez, Patrice; Labarère, Jacques

    1998-01-01

    A comparative study of variable domains V4, V6, and V9 of the mitochondrial small-subunit (SSU) rRNA was carried out with the genus Agrocybe by PCR amplification of 42 wild isolates belonging to 10 species, Agrocybe aegerita, Agrocybe dura, Agrocybe chaxingu, Agrocybe erebia, Agrocybe firma, Agrocybe praecox, Agrocybe paludosa, Agrocybe pediades, Agrocybe alnetorum, and Agrocybe vervacti. Sequencing of the PCR products showed that the three domains in the isolates belonging to the same specie...

  12. Somatic mutations, allele loss, and DNA methylation of the Cub and Sushi Multiple Domains 1 (CSMD1 gene reveals association with early age of diagnosis in colorectal cancer patients.

    Directory of Open Access Journals (Sweden)

    Austin Y Shull

    Full Text Available The Cub and Sushi Multiple Domains 1 (CSMD1 gene, located on the short arm of chromosome 8, codes for a type I transmembrane protein whose function is currently unknown. CSMD1 expression is frequently lost in many epithelial cancers. Our goal was to characterize the relationships between CSMD1 somatic mutations, allele imbalance, DNA methylation, and the clinical characteristics in colorectal cancer patients.We sequenced the CSMD1 coding regions in 54 colorectal tumors using the 454FLX pyrosequencing platform to interrogate 72 amplicons covering the entire coding sequence. We used heterozygous SNP allele ratios at multiple CSMD1 loci to determine allelic balance and infer loss of heterozygosity. Finally, we performed methylation-specific PCR on 76 colorectal tumors to determine DNA methylation status for CSMD1 and known methylation targets ALX4, RUNX3, NEUROG1, and CDKN2A.Using 454FLX sequencing and confirming with Sanger sequencing, 16 CSMD1 somatic mutations were identified in 6 of the 54 colorectal tumors (11%. The nonsynonymous to synonymous mutation ratio of the 16 somatic mutations was 15:1, a ratio significantly higher than the expected 2:1 ratio (p = 0.014. This ratio indicates a presence of positive selection for mutations in the CSMD1 protein sequence. CSMD1 allelic imbalance was present in 19 of 37 informative cases (56%. Patients with allelic imbalance and CSMD1 mutations were significantly younger (average age, 41 years than those without somatic mutations (average age, 68 years. The majority of tumors were methylated at one or more CpG loci within the CSMD1 coding sequence, and CSMD1 methylation significantly correlated with two known methylation targets ALX4 and RUNX3. C:G>T:A substitutions were significantly overrepresented (47%, suggesting extensive cytosine methylation predisposing to somatic mutations.Deep amplicon sequencing and methylation-specific PCR reveal that CSMD1 alterations can correlate with earlier clinical

  13. Fusion Rings for Quantum Groups

    DEFF Research Database (Denmark)

    Andersen, Henning Haahr; Stroppel, Catharina

    2014-01-01

    We study the fusion rings of tilting modules for a quantum group at a root of unity modulo the tensor ideal of negligible tilting modules. We identify them in type A with the combinatorial rings from Korff, C., Stroppel, C.: The sl(ˆn)k-WZNW fusion ring: a combinato-rial construction...... and a realisation as quotient of quantum cohomology. Adv. Math. 225(1), 200–268, (2010) and give a similar description of the sp2n-fusion ring in terms of non-commutative symmetric functions. Moreover we give a presentation of all fusion rings in classical types as quotients of polynomial rings. Finally we also...... compute the fusion rings for type G2....

  14. Dynamics of satellites, asteroids, and rings

    International Nuclear Information System (INIS)

    Dermott, S.F.

    1987-01-01

    Work is reported on: (1) the shapes and the internal structures of satellites; (2) the tidal heating of Miranda; (3) the dynamics of arc-like rings; and (4) the structure of the zodiacal cloud that was revealed by the Infrared Astronomy Satellite. Significant progress was made in determining the shape and internal structure of Mimas and in understanding the dynamical evolution of Miranda's orbit

  15. Tree Rings: Timekeepers of the Past.

    Science.gov (United States)

    Phipps, R. L.; McGowan, J.

    One of a series of general interest publications on science issues, this booklet describes the uses of tree rings in historical and biological recordkeeping. Separate sections cover the following topics: dating of tree rings, dating with tree rings, tree ring formation, tree ring identification, sample collections, tree ring cross dating, tree…

  16. Small-angle X-ray scattering analysis reveals the ATP-bound monomeric state of the ATPase domain from the homodimeric MutL endonuclease, a GHKL phosphotransferase superfamily protein.

    Science.gov (United States)

    Iino, Hitoshi; Hikima, Takaaki; Nishida, Yuya; Yamamoto, Masaki; Kuramitsu, Seiki; Fukui, Kenji

    2015-05-01

    DNA mismatch repair is an excision system that removes mismatched bases chiefly generated by replication errors. In this system, MutL endonucleases direct the excision reaction to the error-containing strand of the duplex by specifically incising the newly synthesized strand. Both bacterial homodimeric and eukaryotic heterodimeric MutL proteins belong to the GHKL ATPase/kinase superfamily that comprises the N-terminal ATPase and C-terminal dimerization regions. Generally, the GHKL proteins show large ATPase cycle-dependent conformational changes, including dimerization-coupled ATP binding of the N-terminal domain. Interestingly, the ATPase domain of human PMS2, a subunit of the MutL heterodimer, binds ATP without dimerization. The monomeric ATP-bound state of the domain has been thought to be characteristic of heterodimeric GHKL proteins. In this study, we characterized the ATP-bound state of the ATPase domain from the Aquifex aeolicus MutL endonuclease, which is a homodimeric GHKL protein unlike the eukaryotic MutL. Gel filtration, dynamic light scattering, and small-angle X-ray scattering analyses clearly showed that the domain binds ATP in a monomeric form despite its homodimeric nature. This indicates that the uncoupling of dimerization and ATP binding is a common feature among bacterial and eukaryotic MutL endonucleases, which we suggest is closely related to the molecular mechanisms underlying mismatch repair.

  17. Sequence analyses reveal that a TPR-DP module, surrounded by recombinable flanking introns, could be at the origin of eukaryotic Hop and Hip TPR-DP domains and prokaryotic GerD proteins.

    Science.gov (United States)

    Hernández Torres, Jorge; Papandreou, Nikolaos; Chomilier, Jacques

    2009-05-01

    The co-chaperone Hop [heat shock protein (HSP) organising protein] is known to bind both Hsp70 and Hsp90. Hop comprises three repeats of a tetratricopeptide repeat (TPR) domain, each consisting of three TPR motifs. The first and last TPR domains are followed by a domain containing several dipeptide (DP) repeats called the DP domain. These analyses suggest that the hop genes result from successive recombination events of an ancestral TPR-DP module. From a hydrophobic cluster analysis of homologous Hop protein sequences derived from gene families, we can postulate that shifts in the open reading frames are at the origin of the present sequences. Moreover, these shifts can be related to the presence or absence of biological function. We propose to extend the family of Hop co-chaperons into the kingdom of bacteria, as several structurally related genes have been identified by hydrophobic cluster analysis. We also provide evidence of common structural characteristics between hop and hip genes, suggesting a shared precursor of ancestral TPR-DP domains.

  18. Sequence analyses reveal that a TPR–DP module, surrounded by recombinable flanking introns, could be at the origin of eukaryotic Hop and Hip TPR–DP domains and prokaryotic GerD proteins

    Science.gov (United States)

    Papandreou, Nikolaos; Chomilier, Jacques

    2008-01-01

    The co-chaperone Hop [heat shock protein (HSP) organising protein] is known to bind both Hsp70 and Hsp90. Hop comprises three repeats of a tetratricopeptide repeat (TPR) domain, each consisting of three TPR motifs. The first and last TPR domains are followed by a domain containing several dipeptide (DP) repeats called the DP domain. These analyses suggest that the hop genes result from successive recombination events of an ancestral TPR–DP module. From a hydrophobic cluster analysis of homologous Hop protein sequences derived from gene families, we can postulate that shifts in the open reading frames are at the origin of the present sequences. Moreover, these shifts can be related to the presence or absence of biological function. We propose to extend the family of Hop co-chaperons into the kingdom of bacteria, as several structurally related genes have been identified by hydrophobic cluster analysis. We also provide evidence of common structural characteristics between hop and hip genes, suggesting a shared precursor of ancestral TPR–DP domains. Electronic supplementary material The online version of this article (doi:10.1007/s12192-008-0083-8) contains supplementary material, which is available to authorized users. PMID:18987995

  19. SOR-ring failure

    International Nuclear Information System (INIS)

    Kitamura, Hideo

    1981-01-01

    It was in the autumn of 1976 that the SOR-ring (synchrotron radiation storage ring) has commenced the regular operation. Since then, the period when the operation was interrupted due to the failures of SOR-ring itself is in total about 8 weeks. Failures and accidents have occurred most in the vacuum system. Those failure experiences are described on the vacuum, electromagnet, radio-frequency acceleration and beam transport systems with their interrupted periods. The eleven failures in the vacuum system have been reported, such as bellows breakage in a heating-evacuating period, leakage from the bellows of straight-through valves (made in U.S.A. and Japan), and leakage from the joint flange of the vacuum system. The longest interruption was 5 weeks due to the failure of a domestically manufactured straight-through valve. The failures of the electromagnet system involve the breakage in a cooling water system, short circuit of a winding in the Q magnet power transformer, blow of a fuse protecting the deflection magnet power source by the current less than the rating, and others. The failures of the RF acceleration system include the breakage of an output electronic tube the breakage of a cavity ceramic, RF voltage fluctuation due to the contact deterioration at a cavity electrode, and the failure of grid bias power source. It is necessary to select the highly reliable components for the vacuum system because the vacuum system failures require longer time for recovery, and very likely to induce secondary and tertiary failures. (Wakatsuki, Y.)

  20. Vibration of Elastic Functionally Graded Thick Rings

    Directory of Open Access Journals (Sweden)

    Guang-Hui Xu

    2017-01-01

    Full Text Available The free vibration behaviors of functionally graded rings were investigated theoretically. The material graded in the thickness direction according to the power law rule and the rings were assumed to be in plane stress and plane strain states. Based on the first-order shear deformation theory and the kinetic relation of von Kárman type, the frequency equation for free vibration of functionally graded ring was derived. The derived results were verified by those in literatures which reveals that the present theory can be appropriate to predict the free vibration characteristics for quite thick rings with the radius-to-thickness ratio from 60 down to 2.09. Comparison between the plane stress case and the plane strain case indicates a slight difference. Meanwhile, the effects of the structural dimensional parameters and the material inhomogeneous parameter are examined. It is interesting that the value of the logarithmic form of vibration frequency is inversely proportional to the logarithmic form of the radius-to-thickness ratio or the mean radius.

  1. Structure of a Glomulin-RBX1-CUL1 complex: inhibition of a RING E3 ligase through masking of its E2-binding surface

    Science.gov (United States)

    Duda, David M.; Olszewski, Jennifer L.; Tron, Adriana E.; Hammel, Michal; Lambert, Lester J.; Waddell, M. Brett; Mittag, Tanja; DeCaprio, James A.; Schulman, Brenda A.

    2012-01-01

    Summary The ~300 human Cullin-RING ligases (CRLs) are multisubunit E3s in which a RING protein, either RBX1 or RBX2, recruits an E2 to catalyze ubiquitination. RBX1-containing CRLs also can bind Glomulin (GLMN), which binds RBX1’s RING domain, regulates the RBX1-CUL1-containing SCFFBW7 complex, and is disrupted in the disease Glomuvenous Malformation. Here we report the crystal structure of a complex between GLMN, RBX1, and a fragment of CUL1. Structural and biochemical analyses reveal that GLMN adopts a HEAT-like repeat fold that tightly binds the E2-interacting surface of RBX1, inhibiting CRL-mediated chain formation by the E2 CDC34. The structure explains the basis for GLMN’s selectivity toward RBX1 over RBX2, and how disease-associated mutations disrupt GLMN-RBX1 interactions. Our study reveals a mechanism for RING E3 ligase regulation whereby an inhibitor blocks E2 access, and raises the possibility that other E3s are likewise controlled by cellular proteins that mask E2-binding surfaces to mediate inhibition. PMID:22748924

  2. Proton storage rings

    International Nuclear Information System (INIS)

    Rau, R.R.

    1978-04-01

    A discussion is given of proton storage ring beam dynamic characteristics. Topics considered include: (1) beam energy; (2) beam luminosity; (3) limits on beam current; (4) beam site; (5) crossing angle; (6) beam--beam interaction; (7) longitudinal instability; (8) effects of scattering processes; (9) beam production; and (10) high magnetic fields. Much of the discussion is related to the design parameters of ISABELLE, a 400 x 400 GeV proton---proton intersecting storage accelerator to be built at Brookhaven National Laboratory

  3. Ring-constrained Join

    DEFF Research Database (Denmark)

    Yiu, Man Lung; Karras, Panagiotis; Mamoulis, Nikos

    2008-01-01

    . This new operation has important applications in decision support, e.g., placing recycling stations at fair locations between restaurants and residential complexes. Clearly, RCJ is defined based on a geometric constraint but not on distances between points. Thus, our operation is fundamentally different......We introduce a novel spatial join operator, the ring-constrained join (RCJ). Given two sets P and Q of spatial points, the result of RCJ consists of pairs (p, q) (where p ε P, q ε Q) satisfying an intuitive geometric constraint: the smallest circle enclosing p and q contains no other points in P, Q...

  4. Femtoslicing in Storage Rings

    CERN Document Server

    Khan, Shaukat

    2005-01-01

    The generation of ultrashort synchrotron radiation pulses by laser-induced energy modulation of electrons and their subsequent transverse displacement, now dubbed "femtoslicing," was demonstrated at the Advanced Light Source in Berkeley. More recently, a femtoslicing user facility was commissioned at the BESSY storage ring in Berlin, and another project is in progress at the Swiss Light Source. The paper reviews the principle of femtoslicing, its merits and shortcomings, as well as the variations of its technical implementation. Various diagnostics techniques to detect successful laser-electron interaction are discussed and experimental results are presented.

  5. Viscosity of ring polymer melts

    KAUST Repository

    Pasquino, Rossana

    2013-10-15

    We have measured the linear rheology of critically purified ring polyisoprenes, polystyrenes, and polyethyleneoxides of different molar masses. The ratio of the zero-shear viscosities of linear polymer melts η0,linear to their ring counterparts η0,ring at isofrictional conditions is discussed as a function of the number of entanglements Z. In the unentangled regime η0,linear/η 0,ring is virtually constant, consistent with the earlier data, atomistic simulations, and the theoretical expectation η0,linear/ η0,ring = 2. In the entanglement regime, the Z-dependence of ring viscosity is much weaker than that of linear polymers, in qualitative agreement with predictions from scaling theory and simulations. The power-law extracted from the available experimental data in the rather limited range 1 < Z < 20, η0,linear/η0,ring ∼ Z 1.2±0.3, is weaker than the scaling prediction (η0,linear/η0,ring ∼ Z 1.6±0.3) and the simulations (η0,linear/ η0,ring ∼ Z2.0±0.3). Nevertheless, the present collection of state-of-the-art experimental data unambiguously demonstrates that rings exhibit a universal trend clearly departing from that of their linear counterparts, and hence it represents a major step toward resolving a 30-year-old problem. © 2013 American Chemical Society.

  6. Viscosity of ring polymer melts

    KAUST Repository

    Pasquino, Rossana; Vasilakopoulos, Thodoris C.; Jeong, Youncheol; Lee, Hyojoon; Rogers, Simon A.; Sakellariou, Georgios; Allgaier, Jü rgen B.; Takano, Atsushi; Brá s, Ana Rita E; Chang, Taihyun; Gooß en, Sebastian; Pyckhout-Hintzen, Wim; Wischnewski, Andreas; Hadjichristidis, Nikolaos; Richter, Dieter R.; Rubinstein, Michael H.; Vlassopoulos, Dimitris

    2013-01-01

    We have measured the linear rheology of critically purified ring polyisoprenes, polystyrenes, and polyethyleneoxides of different molar masses. The ratio of the zero-shear viscosities of linear polymer melts η0,linear to their ring counterparts η0,ring at isofrictional conditions is discussed as a function of the number of entanglements Z. In the unentangled regime η0,linear/η 0,ring is virtually constant, consistent with the earlier data, atomistic simulations, and the theoretical expectation η0,linear/ η0,ring = 2. In the entanglement regime, the Z-dependence of ring viscosity is much weaker than that of linear polymers, in qualitative agreement with predictions from scaling theory and simulations. The power-law extracted from the available experimental data in the rather limited range 1 < Z < 20, η0,linear/η0,ring ∼ Z 1.2±0.3, is weaker than the scaling prediction (η0,linear/η0,ring ∼ Z 1.6±0.3) and the simulations (η0,linear/ η0,ring ∼ Z2.0±0.3). Nevertheless, the present collection of state-of-the-art experimental data unambiguously demonstrates that rings exhibit a universal trend clearly departing from that of their linear counterparts, and hence it represents a major step toward resolving a 30-year-old problem. © 2013 American Chemical Society.

  7. Alpha - Skew Pi - Armendariz Rings

    Directory of Open Access Journals (Sweden)

    Areej M Abduldaim

    2018-03-01

    Full Text Available In this article we introduce a new concept called Alpha-skew Pi-Armendariz rings (Alpha - S Pi - ARas a generalization of the notion of Alpha-skew Armendariz rings.Another important goal behind studying this class of rings is to employ it in order to design a modern algorithm of an identification scheme according to the evolution of using modern algebra in the applications of the field of cryptography.We investigate general properties of this concept and give examples for illustration. Furthermore, this paperstudy the relationship between this concept and some previous notions related to Alpha-skew Armendariz rings. It clearly presents that every weak Alpha-skew Armendariz ring is Alpha-skew Pi-Armendariz (Alpha-S Pi-AR. Also, thisarticle showsthat the concepts of Alpha-skew Armendariz rings and Alpha-skew Pi- Armendariz rings are equivalent in case R is 2-primal and semiprime ring.Moreover, this paper proves for a semicommutative Alpha-compatible ringR that if R[x;Alpha] is nil-Armendariz, thenR is an Alpha-S Pi-AR. In addition, if R is an Alpha - S Pi -AR, 2-primal and semiprime ring, then N(R[x;Alpha]=N(R[x;Alpha]. Finally, we look forwardthat Alpha-skew Pi-Armendariz rings (Alpha-S Pi-ARbe more effect (due to their properties in the field of cryptography than Pi-Armendariz rings, weak Armendariz rings and others.For these properties and characterizations of the introduced concept Alpha-S Pi-AR, we aspire to design a novel algorithm of an identification scheme.

  8. Synthesis of 2-arylidenebenzocycloalkanones containing N-donor heterocyclic rings

    Energy Technology Data Exchange (ETDEWEB)

    Sun, S.-W., E-mail: sunsw0819@163.com [Yuncheng University, Department of Applied Chemistry (China); Zhang, X., E-mail: zhangx@hit.edu.cn [Harbin Institute of Technology, Academy of Fundamental and Interdisciplinary Science (China); Wang, G.-F. [Yuncheng University, Department of Applied Chemistry (China)

    2016-12-15

    A series of 2-arylidenebenzocycloalkanones containing heterocyclic rings 1–8 were prepared and characterized by IR, {sup 1}H NMR and elemental analyses. X-ray diffraction study of 6 reveals that the cyclohexyl ring of the 3,4-dihydronaphthalen-1(2H)-one adopts a chair conformation with a maximum deviation of 0.547(3) Å and makes dihedral angles of 52.24(17)° and 11.23(16)°, respectively, with the benzene plane and the mean plane of the benzimidazole ring.

  9. NRL ion ring program

    International Nuclear Information System (INIS)

    Kapetanakos, C.A.; Golden, J.; Drobot, A.; Mahaffey, R.A.; Marsh, S.J.; Pasour, J.A.

    1977-01-01

    An experiment is under way to form a storng proton ring using the 200 ka, 1.2 MeV, 50 nsec hollow proton beam recently generated at NRL. The 5 m long magnetic field configuration consists of a magnetic cusp, a compressing magnetic field, a gate field and a magnetic mirror. The midplane value of the magnetic mirror is such that the major radius of the ring will be about 10 cm. The degree of field reversal that will be achieved with 5 x 10 16 protons per pulse from the existing beam depends upon the field reversal is possible with the 600 kA proton beam that would be generated from the low inductance coaxial triode coupled to the upgraded Gamble II generator. The propagation and trapping of an intense proton beam in the experimental magnetic field configuration is investigated numerically. The results show that the self magnetic has a very pronounced effect on the dynamics of the gyrating protons

  10. Flexible ring seal

    International Nuclear Information System (INIS)

    Abbes, Claude; Gournier, Andre; Rouaud, Christian; Villepoix, Raymond de.

    1976-01-01

    The invention concerns a flexible metal ring seal, able to ensure a perfect seal between two bearings due to the crushing and elastic deformation properties akin to similar properties in elastomers. Various designs of seal of this kind are already known, particularly a seal made of a core formed by a helical wire spring with close-wound turns and with high axial compression ratio, closed on itself and having the shape of an annulus. This wire ring is surrounded by at least one envelope having at rest the shape of a toroidal surface of which the generating circle does not close on itself. In a particular design mode, the seal in question can include, around the internal spring, two envelopes of which one in contact with the spring is composed of a low ductility elastic metal, such as mild steel or stainless steel and the other is, on the contrary, made of a malleable metal, such as copper or nickel. The first envelope evenly distributes the partial crushing of the spring, when the seal is tightened, on the second envelope which closely fits the two surfaces between which the seal operates. The stress-crushing curve characteristic of the seal comprises two separate parts, the first with a relatively sharp slope corresponds to the start of the seal compression phase, enabling at least some of these curves to reach the requisite seal threshold very quickly, then, beyond this, a second part, practically flat, where the stress is appreciably constant for a wide operating bracket [fr

  11. Magnetization of two coupled rings

    International Nuclear Information System (INIS)

    Avishai, Y; Luck, J M

    2009-01-01

    We investigate the persistent currents and magnetization of a mesoscopic system consisting of two clean metallic rings sharing a single contact point in a magnetic field. Many novel features with respect to the single-ring geometry are underlined, including the explicit dependence of wavefunctions on the Aharonov-Bohm fluxes, the complex pattern of two-fold and three-fold degeneracies, the key role of length and flux commensurability, and in the case of commensurate ring lengths the occurrence of idle levels which do not carry any current. Spin-orbit interactions, induced by the electric fields of charged wires threading the rings, give rise to a peculiar version of the Aharonov-Casher effect where, unlike for a single ring, spin is not conserved. Remarkably enough, this can only be realized when the Aharonov-Bohm fluxes in both rings are neither integer nor half-integer multiples of the flux quantum

  12. Rings Research in the Next Decade

    Science.gov (United States)

    Burns, J. A.; Tiscareno, M. S.

    2009-12-01

    The study of planetary ring systems forms a key component of planetary science for several reasons: 1) The evolution and current states of planets and their satellites are affected in many ways by rings, while 2) conversely, properties of planets and moons and other solar system populations are revealed by their effects on rings; 3) highly structured and apparently delicate ring systems may be bellwethers, constraining various theories of the origin and evolution of their entire planetary system; and finally, 4) planetary rings provide an easily observable analogue to other astrophysical disk systems, enabling real “ground truth” results applicable to disks much more remote in space and/or time, including proto-planetary disks, circum-stellar disks, and even galaxies. Significant advances have been made in rings science in the past decade. The highest-priority rings research recommendations of the last Planetary Science Decadal Survey were to operate and extend the Cassini orbiter mission at Saturn; this has been done with tremendous success, accounting for much of the progress made on key science questions, as we will describe. Important progress in understanding the rings of Saturn and other planets has also come from Earth-based observational and theoretical work, again as prioritized by the last Decadal Survey. However, much important work remains to be done. At Saturn, the Cassini Solstice Mission must be brought to a successful completion. Priority should also be placed on sending spacecraft to Neptune and/or Uranus, now unvisited for more than 20 years. At Jupiter and Pluto, opportunities afforded by visiting spacecraft capable of studying rings should be exploited. On Earth, the need for continued research and analysis remains strong, including in-depth analysis of rings data already obtained, numerical and theoretical modeling work, laboratory analysis of materials and processes analogous to those found in the outer solar system, and continued Earth

  13. Split ring containment attachment device

    International Nuclear Information System (INIS)

    Sammel, A.G.

    1996-01-01

    A containment attachment device is described for operatively connecting a glovebag to plastic sheeting covering hazardous material. The device includes an inner split ring member connected on one end to a middle ring member wherein the free end of the split ring member is inserted through a slit in the plastic sheeting to captively engage a generally circular portion of the plastic sheeting. A collar potion having an outer ring portion is provided with fastening means for securing the device together wherein the glovebag is operatively connected to the collar portion. 5 figs

  14. Radar imaging of Saturn's rings

    Science.gov (United States)

    Nicholson, Philip D.; French, Richard G.; Campbell, Donald B.; Margot, Jean-Luc; Nolan, Michael C.; Black, Gregory J.; Salo, Heikki J.

    2005-09-01

    We present delay-Doppler images of Saturn's rings based on radar observations made at Arecibo Observatory between 1999 and 2003, at a wavelength of 12.6 cm and at ring opening angles of 20.1°⩽|B|⩽26.7°. The average radar cross-section of the A ring is ˜77% relative to that of the B ring, while a stringent upper limit of 3% is placed on the cross-section of the C ring and 9% on that of the Cassini Division. These results are consistent with those obtained by Ostro et al. [1982, Icarus 49, 367-381] from radar observations at |B|=21.4°, but provide higher resolution maps of the rings' reflectivity profile. The average cross-section of the A and B rings, normalized by their projected unblocked area, is found to have decreased from 1.25±0.31 to 0.74±0.19 as the rings have opened up, while the circular polarization ratio has increased from 0.64±0.06 to 0.77±0.06. The steep decrease in cross-section is at variance with previous radar measurements [Ostro et al., 1980, Icarus 41, 381-388], and neither this nor the polarization variations are easily understood within the framework of either classical, many-particle-thick or monolayer ring models. One possible explanation involves vertical size segregation in the rings, whereby observations at larger elevation angles which see deeper into the rings preferentially see the larger particles concentrated near the rings' mid-plane. These larger particles may be less reflective and/or rougher and thus more depolarizing than the smaller ones. Images from all four years show a strong m=2 azimuthal asymmetry in the reflectivity of the A ring, with an amplitude of ±20% and minima at longitudes of 67±4° and 247±4° from the sub-Earth point. We attribute the asymmetry to the presence of gravitational wakes in the A ring as invoked by Colombo et al. [1976, Nature 264, 344-345] to explain the similar asymmetry long seen at optical wavelengths. A simple radiative transfer model suggests that the enhancement of the azimuthal

  15. Magnetic ring for stripping enhancement

    International Nuclear Information System (INIS)

    Selph, F.

    1992-10-01

    A ring designed to recycle ions through a stripping medium offers the possibility for increasing output of the desired charge state by up to 4x. This could be a very important component of a Radioactive Nuclear Beam Facility. In order for such a ring to work effectively it must satisfy certain design conditions. These include achromaticity at the stripper, a dispersed region for an extraction magnet, and a number of first and higher order optics constraints which are necessary to insure that the beam emittance is not degraded unduly by the ring. An example is given of a candidate design of a stripping ring

  16. Saturn's Rings Edge-on

    Science.gov (United States)

    1995-01-01

    In one of nature's most dramatic examples of 'now-you see-them, now-you-don't', NASA's Hubble Space Telescope captured Saturn on May 22, 1995 as the planet's magnificent ring system turned edge-on. This ring-plane crossing occurs approximately every 15 years when the Earth passes through Saturn's ring plane.For comparison, the top picture was taken by Hubble on December 1, 1994 and shows the rings in a more familiar configuration for Earth observers.The bottom picture was taken shortly before the ring plane crossing. The rings do not disappear completely because the edge of the rings reflects sunlight. The dark band across the middle of Saturn is the shadow of the rings cast on the planet (the Sun is almost 3 degrees above the ring plane.) The bright stripe directly above the ring shadow is caused by sunlight reflected off the rings onto Saturn's atmosphere. Two of Saturn's icy moons are visible as tiny starlike objects in or near the ring plane. They are, from left to right, Tethys (slightly above the ring plane) and Dione.This observation will be used to determine the time of ring-plane crossing and the thickness of the main rings and to search for as yet undiscovered satellites. Knowledge of the exact time of ring-plane crossing will lead to an improved determination of the rate at which Saturn 'wobbles' about its axis (polar precession).Both pictures were taken with Hubble's Wide Field Planetary Camera 2. The top image was taken in visible light. Saturn's disk appears different in the bottom image because a narrowband filter (which only lets through light that is not absorbed by methane gas in Saturn's atmosphere) was used to reduce the bright glare of the planet. Though Saturn is approximately 900 million miles away, Hubble can see details as small as 450 miles across.The Wide Field/Planetary Camera 2 was developed by the Jet Propulsion Laboratory and managed by the Goddard Spaced Flight Center for NASA's Office of Space Science.This image and other images and

  17. Acceleration of magnetized plasma rings

    International Nuclear Information System (INIS)

    Hartman, D.; Eddleman, J.; Hammer, J.H.

    1982-01-01

    One scheme is considered, acceleration of a ring between coaxial electrodes by a B/sub theta/ field as in a coaxial rail-gun. If the electrodes are conical, a ring accelerated towards the apex of the cone undergoes self-similar compression (focussing) during acceleration. Because the allowable acceleration force F/sub a/ = kappa U/sub m//R (kappa - 2 , the accelerating distance for conical electrodes is considerably shortened over that required for coaxial electrodes. In either case however, since the accelerating flux can expand as the ring moves, most of the accelerating field energy can be converted into kinetic energy of the ring leading to high efficiency

  18. Ground Movement in SSRL Ring

    International Nuclear Information System (INIS)

    Sunikumar, Nikita

    2011-01-01

    Users of the Stanford Synchrotron Radiation Lightsource (SSRL) are being affected by diurnal motion of the synchrotron's storage ring, which undergoes structural changes due to outdoor temperature fluctuations. In order to minimize the effects of diurnal temperature fluctuations, especially on the vertical motion of the ring floor, scientists at SSRL tried three approaches: painting the storage ring white, covering the asphalt in the middle of the ring with highly reflective Mylar and installing Mylar on a portion of the ring roof and walls. Vertical motion in the storage ring is measured by a Hydrostatic Leveling System (HLS), which calculates the relative height of water in a pipe that extends around the ring. The 24-hr amplitude of the floor motion was determined using spectral analysis of HLS data, and the ratio of this amplitude before and after each experiment was used to quantitatively determine the efficacy of each approach. The results of this analysis showed that the Mylar did not have any significant effect on floor motion, although the whitewash project did yield a reduction in overall HLS variation of 15 percent. However, further analysis showed that the reduction can largely be attributed to a few local changes rather than an overall reduction in floor motion around the ring. Future work will consist of identifying and selectively insulating these local regions in order to find the driving force behind diurnal floor motion in the storage ring.

  19. ring og refleksion

    DEFF Research Database (Denmark)

    Wahlgren, B.; Rattleff, Pernille; Høyrup, S.

    State of the art inden for forskning om læring på arbejdspladsen samt gennemgang af læringsteori og refleksionsbegrebet hos Dewey, Dreyfus, Schön, Argyris, Kolb, Jarvis, Mezirow og Brookfield. Afsluttes med diskussion af syntetiseret model for læring på arbejdspladsen.......State of the art inden for forskning om læring på arbejdspladsen samt gennemgang af læringsteori og refleksionsbegrebet hos Dewey, Dreyfus, Schön, Argyris, Kolb, Jarvis, Mezirow og Brookfield. Afsluttes med diskussion af syntetiseret model for læring på arbejdspladsen....

  20. Ring artifacts removal from synchrotron CT image slices

    International Nuclear Information System (INIS)

    Wei Zhouping; Chapman, Dean; Wiebe, Sheldon

    2013-01-01

    Ring artifacts can occur in reconstructed images from x-ray Computerized Tomography (CT) as full or partial concentric rings superimposed on the scanned structures. Due to the data corruption by those ring artifacts in CT images, qualitative and quantitative analysis of these images are compromised. In this paper, we propose to correct the ring artifacts on the reconstructed synchrotron radiation (SR) CT image slices. The proposed correction procedure includes the following steps: (1). transform the reconstructed CT images into polar coordinates; (2) apply discrete two-dimensional (2D) wavelet transform to the polar image to decompose it into four image components: low pass band image component, as well as the components from horizontal, vertical and diagonal details bands; (3). apply 2D Fourier transform to the vertical details band image component only, since the ring artifacts become vertical lines in the polar coordinates; (4). apply Gaussian filtering in Fourier domain along the abscissa direction to suppress the vertical lines, since the information of the vertical lines in Fourier domain is completely condensed to that direction; (5). perform inverse Fourier transform to get the corrected vertical details band image component; (6). perform inverse wavelet transform to get the corrected polar image; (7). transform the corrected polar image back to Cartesian coordinates to get the CT image slice with reduced ring artifacts. This approach has been successfully used on CT data acquired from the Biomedical Imaging and Therapy (BMIT) beamline in Canadian Light Source (CLS), and the results show that the ring artifacts in original SR CT images have been effectively suppressed with all the structure information in the image preserved.

  1. Corneal ring infiltration in contact lens wearers

    Directory of Open Access Journals (Sweden)

    Seyed Ali Tabatabaei

    2017-01-01

    Full Text Available To report a case of atypical sterile ring infiltrates during wearing soft silicone hydrogel contact lens due to poor lens care. A 29-year-old woman presented with complaints of pain, redness, and morning discharge. She was wearing soft silicone hydrogel contact lens previously; her current symptoms began 1 week before presentation. On examination, best-corrected visual acuity was 20/40 in that eye. Slit-lamp examination revealed dense, ring-shaped infiltrate involving both the superficial and deep stromal layers with lucid interval to the limbus, edema of the epithelium, epithelial defect, and vascularization of the superior limbus. Cornea-specific in vivo laser confocal microscopy (Heidelberg Retina Tomograph 2 Rostock Cornea Module, HRT 2-RCM, Heidelberg Engineering GmbH, Dossenheim, Germany revealed Langerhans cells and no sign of Acanthamoeba or fungal features, using lid scraping and anti-inflammatory drops; her vision completely recovered. We reported an atypical case of a sterile corneal ring infiltrate associated with soft contact lens wearing; smear, culture, and confocal microscopy confirmed a sterile inflammatory reaction.

  2. Texture of lipid bilayer domains

    DEFF Research Database (Denmark)

    Jensen, Uffe Bernchou; Brewer, Jonathan R.; Midtiby, Henrik Skov

    2009-01-01

    We investigate the texture of gel (g) domains in binary lipid membranes composed of the phospholipids DPPC and DOPC. Lateral organization of lipid bilayer membranes is a topic of fundamental and biological importance. Whereas questions related to size and composition of fluid membrane domain...... are well studied, the possibility of texture in gel domains has so far not been examined. When using polarized light for two-photon excitation of the fluorescent lipid probe Laurdan, the emission intensity is highly sensitive to the angle between the polarization and the tilt orientation of lipid acyl...... chains. By imaging the intensity variations as a function of the polarization angle, we map the lateral variations of the lipid tilt within domains. Results reveal that gel domains are composed of subdomains with different lipid tilt directions. We have applied a Fourier decomposition method...

  3. Magnetically pinned ring dots for spin valve or magnetic tunnel junction memory cells

    International Nuclear Information System (INIS)

    Nakatani, Ryoichi; Yoshida, Tetsuo; Endo, Yasushi; Kawamura, Yoshio; Yamamoto, Masahiko; Takenaga, Takashi; Aya, Sunao; Kuroiwa, Takeharu; Beysen, Sadeh; Kobayashi, Hiroshi

    2005-01-01

    Ni-Fe/Mn-Ir asymmetric ring dots with partially planed outer sides are investigated in order to confirm a method for obtaining pinned layers in magnetic memories with asymmetric ring shapes. Magnetic force microscopy revealed that the direction of vortical magnetization is pinned in Ni-Fe/Mn-Ir asymmetric ring dots despite the direction of the magnetic fields. This investigation shows that the Ni-Fe/Mn-Ir asymmetric ring dots can be applied to pinned layers in magnetic memories with asymmetric ring shapes

  4. Fast and accurate focusing analysis of large photon sieve using pinhole ring diffraction model.

    Science.gov (United States)

    Liu, Tao; Zhang, Xin; Wang, Lingjie; Wu, Yanxiong; Zhang, Jizhen; Qu, Hemeng

    2015-06-10

    In this paper, we developed a pinhole ring diffraction model for the focusing analysis of a large photon sieve. Instead of analyzing individual pinholes, we discuss the focusing of all of the pinholes in a single ring. An explicit equation for the diffracted field of individual pinhole ring has been proposed. We investigated the validity range of this generalized model and analytically describe the sufficient conditions for the validity of this pinhole ring diffraction model. A practical example and investigation reveals the high accuracy of the pinhole ring diffraction model. This simulation method could be used for fast and accurate focusing analysis of a large photon sieve.

  5. Rotating ring-ring electrode theory and experiment

    NARCIS (Netherlands)

    Kuiken, H.K.; Bakkers, E.P.A.M.; Ligthart, H.; Kellyb, J.J.

    2000-01-01

    A model is presented for the rotating ring-ring electrode. Although the electrode is defined by four characteristic lengths, it is shown that the collection efficiency depends on only two dimensionless parameters. A simple relationship between these and the corresponding parameters for the rotating

  6. The Rotating Ring-Ring Electrode. Theory and Experiment

    NARCIS (Netherlands)

    Kuiken, H.K.; Bakkers, E.P.A.M.; Ligthart, H.; Kelly, J.J.

    2000-01-01

    A model is presented for the rotating ring-ring electrode. Although the electrode is defined by four characteristic lengths, it is shown that the collection efficiency depends on only two dimensionless parameters. A simple relationship between these and the corresponding parameters for the rotating

  7. "Ring" in the solo child singing voice.

    Science.gov (United States)

    Howard, David M; Williams, Jenevora; Herbst, Christian T

    2014-03-01

    Listeners often describe the voices of solo child singers as being "pure" or "clear"; these terms would suggest that the voice is not only pleasant but also clearly audible. The audibility or clarity could be attributed to the presence of high-frequency partials in the sound: a "brightness" or "ring." This article aims to investigate spectrally the acoustic nature of this ring phenomenon in children's solo voices, and in particular, relating it to their "nonring" production. Additionally, this is set in the context of establishing to what extent, if any, the spectral characteristics of ring are shared with those of the singer's formant cluster associated with professional adult opera singers in the 2.5-3.5kHz region. A group of child solo singers, acknowledged as outstanding by a singing teacher who specializes in teaching professional child singers, were recorded in a major UK concert hall performing Come unto him, all ye that labour, from the aria He shall feed his flock from The Messiah by GF Handel. Their singing was accompanied by a recording of a piano played through in-ear headphones. Sound pressure recordings were made from well within the critical distance in the hall. The singers were observed to produce notes with and without ring, and these recordings were analyzed in the frequency domain to investigate their spectra. The results indicate that there is evidence to suggest that ring in child solo singers is carried in two areas of the output spectrum: first in the singer's formant cluster region, centered around 4kHz, which is more than 1000Hz higher than what is observed in adults; and second in the region around 7.5-11kHz where a significant strengthening of harmonic presence is observed. A perceptual test has been carried out demonstrating that 94% of 62 listeners label a synthesized version of the calculated overall average ring spectrum for all subjects as having ring when compared with a synthesized version of the calculated overall average nonring

  8. .Gov Domains API

    Data.gov (United States)

    General Services Administration — This dataset offers the list of all .gov domains, including state, local, and tribal .gov domains. It does not include .mil domains, or other federal domains outside...

  9. Damping rings for CLIC

    CERN Document Server

    Jowett, John M; Zimmermann, Frank; Owen, H

    2001-01-01

    The Compact Linear Colider (CLIC) is designed to operate at 3 TeV centre-of-mass energy with a total luminosity of 10^35 cm^-2 s^-1. The overall system design leads to extremely demanding requirements on the bunch trains injected into the main libac at frequency of 100 Hz. In particular, the emittances of the intense bunches have to be about an order of magnitude smaller than presently achieved. We describe our approach to finding a damping ring design capable of meeting these requirements. Besides lattice design, emittance and damping rate considerations, a number of scattering and instability effects have to be incorporated into the optimisation of parameters. Among these, intra-bem scattering and the electron cloud effect are two of the most significant.

  10. Does the sun ring

    International Nuclear Information System (INIS)

    Isaak, G.R.

    1978-01-01

    The work of various groups, which have been investigating the possibility of measuring the periodicities of solar oscillations in an attempt to test theoretical models of the sun, is reported. In particular the observation of small velocity oscillations of the surface layers of the sun that permits the measurement of the sound waves (or phonons) in the solar atmosphere, is discussed. Oscillations with periods of 2.65 h, 58 and 40 min and amplitudes of 2.7, 0.8 and 0.7 ms -1 respectively are reported. Support for a periodicity at about 2.65 h from a number of other groups using other measuring techniques are considered. It is felt that the most probable interpretation of the observed solar oscillations is that the sun is a resonator which is ringing. (UK)

  11. Katanin spiral and ring structures shed light on power stroke for microtubule severing

    Energy Technology Data Exchange (ETDEWEB)

    Zehr, Elena; Szyk, Agnieszka; Piszczek, Grzegorz; Szczesna, Ewa; Zuo, Xiaobing; Roll-Mecak, Antonina

    2017-08-07

    Microtubule-severing enzymes katanin, spastin and fidgetin are AAA ATPases critical for the biogenesis and maintenance of complex microtubule arrays in axons, spindles and cilia. Because of a lack of 3D structures, their mechanism has remained poorly understood. We report the first X-ray structure of the monomeric AAA katanin module and cryo-EM reconstructions of the hexamer in two conformations. These reveal an unexpected asymmetric arrangement of the AAA domains mediated by structural elements unique to severing enzymes and critical for their function. Our reconstructions show that katanin cycles between open spiral and closed ring conformations, depending on the ATP occupancy of a gating protomer that tenses or relaxes inter-protomer interfaces. Cycling of the hexamer between these conformations would provide the power stroke for microtubule severing.

  12. How Jupiter's Ring Was Discovered.

    Science.gov (United States)

    Elliot, James; Kerr, Richard

    1985-01-01

    "Rings" (by astronomer James Elliot and science writer Richard Kerr) is a nontechnical book about the discovery and exploration of ring systems from the time of Galileo to the era of the Voyager spacecraft. One of this book's chapters is presented. (JN)

  13. Pyrimidine-pyridine ring interconversion

    NARCIS (Netherlands)

    Plas, van der H.C.

    2003-01-01

    This chapter discusses the pyrimidine-to-pyridine ring transformation and pyridine-to-pyrimidine ring transformation. In nucleophile-induced pyrimidine-to-pyridine rearrangements, two types of reactions can be distinguished depending on the structure of the nucleophile: (1) reactions in which the

  14. Binomial Rings: Axiomatisation, Transfer and Classification

    OpenAIRE

    Xantcha, Qimh Richey

    2011-01-01

    Hall's binomial rings, rings with binomial coefficients, are given an axiomatisation and proved identical to the numerical rings studied by Ekedahl. The Binomial Transfer Principle is established, enabling combinatorial proofs of algebraical identities. The finitely generated binomial rings are completely classified. An application to modules over binomial rings is given.

  15. Ionization cooling ring for muons

    Directory of Open Access Journals (Sweden)

    R. Palmer

    2005-06-01

    Full Text Available Practical ionization cooling rings could lead to lower cost or improved performance in neutrino factory or muon collider designs. The ring modeled here uses realistic three-dimensional fields. The performance of the ring compares favorably with the linear cooling channel used in the second U.S. Neutrino Factory Study. The normalized 6D emittance of an ideal ring is decreased by a factor of approximately 240, compared with a factor of only 15 for the linear channel. We also examine such real-world effects as windows on the absorbers and rf cavities and leaving empty lattice cells for injection and extraction. For realistic conditions the ring decreases the normalized 6D emittance by a factor of 49.

  16. The unique N-terminal zinc finger of synaptotagmin-like protein 4 reveals FYVE structure.

    Science.gov (United States)

    Miyamoto, Kazuhide; Nakatani, Arisa; Saito, Kazuki

    2017-12-01

    Synaptotagmin-like protein 4 (Slp4), expressed in human platelets, is associated with dense granule release. Slp4 is comprised of the N-terminal zinc finger, Slp homology domain, and C2 domains. We synthesized a compact construct (the Slp4N peptide) corresponding to the Slp4 N-terminal zinc finger. Herein, we have determined the solution structure of the Slp4N peptide by nuclear magnetic resonance (NMR). Furthermore, experimental, chemical modification of Cys residues revealed that the Slp4N peptide binds two zinc atoms to mediate proper folding. NMR data showed that eight Cys residues coordinate zinc atoms in a cross-brace fashion. The Simple Modular Architecture Research Tool database predicted the structure of Slp4N as a RING finger. However, the actual structure of the Slp4N peptide adopts a unique C 4 C 4 -type FYVE fold and is distinct from a RING fold. To create an artificial RING finger (ARF) with specific ubiquitin-conjugating enzyme (E2)-binding capability, cross-brace structures with eight zinc-ligating residues are needed as the scaffold. The cross-brace structure of the Slp4N peptide could be utilized as the scaffold for the design of ARFs. © 2017 The Protein Society.

  17. Domain wall motion in magnetically frustrated nanorings

    Science.gov (United States)

    Lubarda, M. V.; Escobar, M. A.; Li, S.; Chang, R.; Fullerton, E. E.; Lomakin, V.

    2012-06-01

    We describe a magnetically frustrated nanoring (MFNR) configuration which is formed by introducing antiferromagnetic coupling across an interface orthogonal to the ring's circumferential direction. Such structures have the unique characteristic that only one itinerant domain wall (DW) can exist in the ring, which does not need to be nucleated or injected into the structure and can never escape making it analogous to a magnetic Möbius strip. Numerical simulations show that the DW in a MFNR can be driven consecutively around the ring with a prescribed cyclicity, and that the frequency of revolutions can be controlled by the applied field. The energy landscapes can be controlled to be flat allowing for low fields of operation or to have a barrier for thermal stability. Potential logic and memory applications of MFNRs are considered and discussed.

  18. Evidence of Accretion in Saturn's F Ring (Invited)

    Science.gov (United States)

    Agnor, C. B.; Buerle, K.; Murray, C. D.; Evans, M. W.; Cooper, N. J.; Williams, G. W.

    2010-12-01

    Lying slightly outside the classical Roche radius and being strongly perturbed by the adjacent moons Prometheus and Pandora, Saturn's F ring represents a unique astrophysical laboratory for examining the processes of mass accretion and moonlet formation. Recent images from the Cassini spacecraft reveal optically thick clumps, capable of casting shadows, and associated structures in regions of the F ring following close passage by Prometheus. Here we examine the accretion environment of the F ring and Prometheus' role in moonlet formation and evolution. Using the observed structures adjacent to these clumps and dynamical arguments we estimate the masses of these clumps and find them comparable to that of ~10-20-km contiguous moonlets. Further, we show that Prometheus' perturbations on the F ring create regions of enhanced density and low relative velocity that may accelerate the accretion of clumps and moonlets.

  19. Evaluation of ring impedance of the Photon Factory storage ring

    International Nuclear Information System (INIS)

    Kiuchi, T.; Izawa, M.; Tokumoto, S.; Hori, Y.; Sakanaka, S.; Kobayashi, M.; Kobayakawa, H.

    1992-05-01

    The loss parameters of the ducts in the Photon Factory (PF) storage ring were evaluated using the wire method and the code TBCI. Both the measurement and the calculation were done for a different bunch length (σ) ranging from 23 to 80 ps. The PF ring impedance was estimated to be |Z/n|=3.2 Ω using the broadband impedance model. The major contribution to the impedance comes from the bellows and the gate valve sections. Improvements of these components will lower the ring impedance by half. (author)

  20. Sequence similarity between the erythrocyte binding domain 1 of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals binding residues for the Duffy Antigen Receptor for Chemokines

    OpenAIRE

    Bolton, Michael J; Garry, Robert F

    2011-01-01

    Abstract Background The surface glycoprotein (SU, gp120) of the human immunodeficiency virus (HIV) must bind to a chemokine receptor, CCR5 or CXCR4, to invade CD4+ cells. Plasmodium vivax uses the Duffy Binding Protein (DBP) to bind the Duffy Antigen Receptor for Chemokines (DARC) and invade reticulocytes. Results Variable loop 3 (V3) of HIV-1 SU and domain 1 of the Plasmodium vivax DBP share a sequence similarity. The site of amino acid sequence similarity was necessary, but not sufficient, ...

  1. Sequence similarity between the erythrocyte binding domain of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals a functional heparin binding motif involved in binding to the Duffy antigen receptor for chemokines

    OpenAIRE

    Bolton, Michael J; Garry, Robert F

    2011-01-01

    Abstract Background The HIV surface glycoprotein gp120 (SU, gp120) and the Plasmodium vivax Duffy binding protein (PvDBP) bind to chemokine receptors during infection and have a site of amino acid sequence similarity in their binding domains that often includes a heparin binding motif (HBM). Infection by either pathogen has been found to be inhibited by polyanions. Results Specific polyanions that inhibit HIV infection and bind to the V3 loop of X4 strains also inhibited DBP-mediated infectio...

  2. Evidence of benzenoid domains in nanographenes.

    Science.gov (United States)

    Baldoni, Matteo; Mercuri, Francesco

    2015-01-21

    Calculations based on density functional theory demonstrate the occurrence of local deformations of the perfect honeycomb lattice in nanographenes to form arrangements, with triangular symmetry, composed of six-membered ring patterns. The formation of these locally regular superstructures, which can be considered as benzenoid-like domains on the 2D graphene lattice, is ascribed to the gain in resonance energy deriving from aromaticity. The relationship between the atomic morphology of nanographenes and details of the relaxed structure is rationalized in terms of Clar's theory of the aromatic sextet and by extending concepts borrowed from valence bond theory to 2D carbon nanostructures. Namely, two regular arrangements can be evidenced, defined as Clar (fully benzenoid) and Kekulé domains, which correspond to two different regular bond patterns in sets of adjacent six-membered rings. Our findings are compatible with recent experiments and have potentially relevant consequences in the development of novel electronic devices based on graphene materials.

  3. Tinkering at the main-ring lattice

    Energy Technology Data Exchange (ETDEWEB)

    Ohnuma, S.

    1982-08-23

    To improve production of usable antiprotons using the proton beam from the main ring and the lossless injection of cooled antiprotons into the main ring, modifications of the main ring lattice are recommended.

  4. Is the bell ringing?

    CERN Multimedia

    Francesco Poppi

    2010-01-01

    During the Nobel prize-winning UA1 experiment, scientists in the control room used to ring a bell if a particularly interesting event had occurred. Today, the “CMS Exotica hotline” routine produces a daily report that lists the exotic events that were recorded the day before.   Display of an event selected by the Exotica routine. Take just a very small fraction of the available data (max. 5%); define the events that you want to keep and set the parameters accordingly; run the Exotica routine and only look at the very few images that the system has selected for you. This is the recipe that a small team of CMS researchers has developed to identify the signals coming from possible new physics processes. “This approach does not replace the accurate data analysis on the whole set of data. However, it is a very fast and effective way to focus on just a few events that are potentially very interesting”, explains Maurizio Pierini (CERN), who developed the...

  5. Moving ring reactor 'Karin-1'

    International Nuclear Information System (INIS)

    1983-12-01

    The conceptual design of a moving ring reactor ''Karin-1'' has been carried out to advance fusion system design, to clarify the research and development problems, and to decide their priority. In order to attain these objectives, a D-T reactor with tritium breeding blanket is designed, a commercial reactor with net power output of 500 MWe is designed, the compatibility of plasma physics with fusion engineering is demonstrated, and some other guideline is indicated. A moving ring reactor is composed mainly of three parts. In the first formation section, a plasma ring is formed and heated up to ignition temperature. The plasma ring of compact torus is transported from the formation section through the next burning section to generate fusion power. Then the plasma ring moves into the last recovery section, and the energy and particles of the plasma ring are recovered. The outline of a moving ring reactor ''Karin-1'' is described. As a candidate material for the first wall, SiC was adopted to reduce the MHD effect and to minimize the interaction with neutrons and charged particles. The thin metal lining was applied to the SiC surface to solve the problem of the compatibility with lithium blanket. Plasma physics, the engineering aspect and the items of research and development are described. (Kako, I.)

  6. Drop impact entrapment of bubble rings

    KAUST Repository

    Thoraval, M.-J.

    2013-04-29

    We use ultra-high-speed video imaging to look at the initial contact of a drop impacting on a liquid layer. We observe experimentally the vortex street and the bubble-ring entrapments predicted numerically, for high impact velocities, by Thoraval et al. (Phys. Rev. Lett., vol. 108, 2012, article 264506). These dynamics mainly occur within 50 -s after the first contact, requiring imaging at 1 million f.p.s. For a water drop impacting on a thin layer of water, the entrapment of isolated bubbles starts through azimuthal instability, which forms at low impact velocities, in the neck connecting the drop and pool. For Reynolds number Re above -12 000, up to 10 partial bubble rings have been observed at the base of the ejecta, starting when the contact is -20% of the drop size. More regular bubble rings are observed for a pool of ethanol or methanol. The video imaging shows rotation around some of these air cylinders, which can temporarily delay their breakup into micro-bubbles. The different refractive index in the pool liquid reveals the destabilization of the vortices and the formation of streamwise vortices and intricate vortex tangles. Fine-scale axisymmetry is thereby destroyed. We show also that the shape of the drop has a strong influence on these dynamics. 2013 Cambridge University Press.

  7. Evaluation of ring tensile test results

    International Nuclear Information System (INIS)

    Chatterjee, S.; Anantharaman, S.; Balakrishnan, K.S.; Sivaramakrish, K.S.

    1990-01-01

    Ring specimens of 5-mm width cut from Zircaloy-2 cladding of reactor operated fuel elements that had experienced 5000 to 15,000 MWD/T of fuel burnup were subjected to ring tensile testing. The true stress-true strain data points up to the onset of necking from the individual load-elongation curves of these specimens were used as input data in Voce's equation. The results reveal that the uniform elongation (UE) values generated using Voce's equation were within (UE-2)% of the experimental percent uniform elongation (UE%). The corresponding ultimate tensile strength values were within ±1%. The uncertainty inherently associated in the determination of gauge length introduces extraneous deformation in the rings tested. Previous results had shown that a 14% increase in cladding diameter caused the gauge length to increase by 40%. To simulate the contribution of extraneous deformation due to an increase in cladding diameter, an analysis of the variation of the tensile parameters (uniform elongation and ultimate tensile strength) due to increase in the gauge length in the range of 10 to 40% was carried out. The results are discussed

  8. Sequence similarity between the erythrocyte binding domain 1 of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals binding residues for the Duffy Antigen Receptor for Chemokines

    Directory of Open Access Journals (Sweden)

    Garry Robert F

    2011-01-01

    Full Text Available Abstract Background The surface glycoprotein (SU, gp120 of the human immunodeficiency virus (HIV must bind to a chemokine receptor, CCR5 or CXCR4, to invade CD4+ cells. Plasmodium vivax uses the Duffy Binding Protein (DBP to bind the Duffy Antigen Receptor for Chemokines (DARC and invade reticulocytes. Results Variable loop 3 (V3 of HIV-1 SU and domain 1 of the Plasmodium vivax DBP share a sequence similarity. The site of amino acid sequence similarity was necessary, but not sufficient, for DARC binding and contained a consensus heparin binding site essential for DARC binding. Both HIV-1 and P. vivax can be blocked from binding to their chemokine receptors by the chemokine, RANTES and its analog AOP-RANTES. Site directed mutagenesis of the heparin binding motif in members of the DBP family, the P. knowlesi alpha, beta and gamma proteins abrogated their binding to erythrocytes. Positively charged residues within domain 1 are required for binding of P. vivax and P. knowlesi erythrocyte binding proteins. Conclusion A heparin binding site motif in members of the DBP family may form part of a conserved erythrocyte receptor binding pocket.

  9. Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 Å resolution

    Energy Technology Data Exchange (ETDEWEB)

    Tu, Chao [Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702 (United States); Tan, Yu-Hong [Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA 92697 (United States); Shaw, Gary [Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702 (United States); Zhou, Zheng; Bai, Yawen [Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, MD 20892 (United States); Luo, Ray [Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA 92697 (United States); Ji, Xinhua, E-mail: jix@ncifcrf.gov [Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702 (United States)

    2008-05-01

    The impact of hotspot mutation R282Q on the structure of human p53 DNA-binding domain has been characterized by X-ray crystallography and molecular-dynamics simulations. Tumor suppressor p53 is a sequence-specific DNA-binding protein and its central DNA-binding domain (DBD) harbors six hotspots (Arg175, Gly245, Arg248, Arg249, Arg273 and Arg282) for human cancers. Here, the crystal structure of a low-frequency hotspot mutant, p53DBD(R282Q), is reported at 1.54 Å resolution together with the results of molecular-dynamics simulations on the basis of the structure. In addition to eliminating a salt bridge, the R282Q mutation has a significant impact on the properties of two DNA-binding loops (L1 and L3). The L1 loop is flexible in the wild type, but it is not flexible in the mutant. The L3 loop of the wild type is not flexible, whereas it assumes two conformations in the mutant. Molecular-dynamics simulations indicated that both conformations of the L3 loop are accessible under biological conditions. It is predicted that the elimination of the salt bridge and the inversion of the flexibility of L1 and L3 are directly or indirectly responsible for deactivating the tumor suppressor p53.

  10. Quantum Fourier Transform Over Galois Rings

    OpenAIRE

    Zhang, Yong

    2009-01-01

    Galois rings are regarded as "building blocks" of a finite commutative ring with identity. There have been many papers on classical error correction codes over Galois rings published. As an important warm-up before exploring quantum algorithms and quantum error correction codes over Galois rings, we study the quantum Fourier transform (QFT) over Galois rings and prove it can be efficiently preformed on a quantum computer. The properties of the QFT over Galois rings lead to the quantum algorit...

  11. Polarized particles in storage rings

    International Nuclear Information System (INIS)

    Derbenev, Ya.S.; Kondratenko, A.M.; Serednyakov, S.I.; Skrinskij, A.N.; Tumajkin, G.M.; Shatunov, Yu.M.

    1977-01-01

    Experiments with polarized beams on the VEPP-2M and SPEAK storage rings are described. Possible methods of producing polarized particle beams in storage rings as well as method of polarization monitoring are counted. Considered are the processes of radiation polarization of electrons and positrons. It is shown, that to preserve radiation polarization the introduction of regions with a strong sign-variable magnetic field is recommended. Methods of polarization measurement are counted. It is suggested for high energies to use dependence of synchrotron radiation power on transverse polarization of electrons and positrons. Examples of using polarizability of colliding beams in storage rings are presented

  12. Researches on the Piston Ring

    Science.gov (United States)

    Ehihara, Keikiti

    1944-01-01

    In internal combustion engines, steam engines, air compressors, and so forth, the piston ring plays an important role. Especially, the recent development of Diesel engines which require a high compression pressure for their working, makes, nowadays, the packing action of the piston ring far more important than ever. Though a number of papers have been published in regard to researches on the problem of the piston ring, none has yet dealt with an exact measurement of pressure exerted on the cylinder wall at any given point of the ring. The only paper that can be traced on this subject so far is Mr. Nakagawa's report on the determination of the relative distribution of pressure on the cylinder wall, but the measuring method adopted therein appears to need further consideration. No exact idea has yet been obtained as to how the obturation of gas between the piston and cylinder, the frictional resistance of the piston, and the wear of the cylinder wall are affected by the intensity and the distribution of the radial pressure of the piston ring. Consequently, the author has endeavored, by employing an apparatus of his own invention, to get an exact determination of the pressure distribution of the piston ring. By means of a newly devised ring tester, to which piezoelectricity of quartz was applied, the distribution of the radial pressure of many sample rings on the market was accurately determined. Since many famous piston rings show very irregular pressure distribution, the author investigated and achieved a manufacturing process of the piston ring which will exert uniform pressure on the cylinder wall. Temperature effects on the configuration and on the mean spring power have also been studied. Further, the tests were performed to ascertain how the gas tightness of the piston ring may be affected by the number or spring power. The researches as to the frictional resistance between the piston ring and the cylinder wall were carried out, too. The procedure of study, and

  13. Soft Congruence Relations over Rings

    Science.gov (United States)

    Xin, Xiaolong; Li, Wenting

    2014-01-01

    Molodtsov introduced the concept of soft sets, which can be seen as a new mathematical tool for dealing with uncertainty. In this paper, we initiate the study of soft congruence relations by using the soft set theory. The notions of soft quotient rings, generalized soft ideals and generalized soft quotient rings, are introduced, and several related properties are investigated. Also, we obtain a one-to-one correspondence between soft congruence relations and idealistic soft rings and a one-to-one correspondence between soft congruence relations and soft ideals. In particular, the first, second, and third soft isomorphism theorems are established, respectively. PMID:24949493

  14. Distributively generated matrix near rings

    International Nuclear Information System (INIS)

    Abbasi, S.J.

    1993-04-01

    It is known that if R is a near ring with identity then (I,+) is abelian if (I + ,+) is abelian and (I,+) is abelian if (I*,+) is abelian [S.J. Abbasi, J.D.P. Meldrum, 1991]. This paper extends these results. We show that if R is a distributively generated near ring with identity then (I,+) is included in Z(R), the center of R, if (I + ,+) is included in Z(M n (R)), the center of matrix near ring M n (R). Furthermore (I,+) is included in Z(R) if (I*,+) is included in Z(M n (R)). (author). 5 refs

  15. SMARANDACHE NON-ASSOCIATIVE RINGS

    OpenAIRE

    Vasantha, Kandasamy

    2002-01-01

    An associative ring is just realized or built using reals or complex; finite or infinite by defining two binary operations on it. But on the contrary when we want to define or study or even introduce a non-associative ring we need two separate algebraic structures say a commutative ring with 1 (or a field) together with a loop or a groupoid or a vector space or a linear algebra. The two non-associative well-known algebras viz. Lie algebras and Jordan algebras are mainly built using a vecto...

  16. The SPOR Domain, a Widely Conserved Peptidoglycan Binding Domain That Targets Proteins to the Site of Cell Division.

    Science.gov (United States)

    Yahashiri, Atsushi; Jorgenson, Matthew A; Weiss, David S

    2017-07-15

    Sporulation-related repeat (SPOR) domains are small peptidoglycan (PG) binding domains found in thousands of bacterial proteins. The name "SPOR domain" stems from the fact that several early examples came from proteins involved in sporulation, but SPOR domain proteins are quite diverse and contribute to a variety of processes that involve remodeling of the PG sacculus, especially with respect to cell division. SPOR domains target proteins to the division site by binding to regions of PG devoid of stem peptides ("denuded" glycans), which in turn are enriched in septal PG by the intense, localized activity of cell wall amidases involved in daughter cell separation. This targeting mechanism sets SPOR domain proteins apart from most other septal ring proteins, which localize via protein-protein interactions. In addition to SPOR domains, bacteria contain several other PG-binding domains that can exploit features of the cell wall to target proteins to specific subcellular sites. Copyright © 2017 American Society for Microbiology.

  17. Modeling and Simulation of Longitudinal Dynamics for Low Energy Ring-High Energy Ring at the Positron-Electron Project

    International Nuclear Information System (INIS)

    Rivetta, Claudio; Mastorides, T.; Fox, J.D.; Teytelman, D.; Van Winkle, D.

    2007-01-01

    A time domain dynamic modeling and simulation tool for beam-cavity interactions in the Low Energy Ring (LER) and High Energy Ring (HER) at the Positron-Electron Project (PEP-II) is presented. Dynamic simulation results for PEP-II are compared to measurements of the actual machine. The motivation for this tool is to explore the stability margins and performance limits of PEP-II radio-frequency (RF) systems at future higher currents and upgraded RF configurations. It also serves as a test bed for new control algorithms and can define the ultimate limits of the low-level RF (LLRF) architecture. The time domain program captures the dynamic behavior of the beam-cavity-LLRF interaction based on a reduced model. The ring current is represented by macrobunches. Multiple RF stations in the ring are represented via one or two macrocavities. Each macrocavity captures the overall behavior of all the 2 or 4 cavity RF stations. Station models include nonlinear elements in the klystron and signal processing. This enables modeling the principal longitudinal impedance control loops interacting via the longitudinal beam model. The dynamics of the simulation model are validated by comparing the measured growth rates for the LER with simulation results. The simulated behavior of the LER at increased operation currents is presented via low-mode instability growth rates. Different control strategies are compared and the effects of both the imperfections in the LLRF signal processing and the nonlinear drivers and klystrons are explored

  18. Prototype moving-ring reactor

    International Nuclear Information System (INIS)

    Smith, A.C. Jr.; Ashworth, C.P.; Abreu, K.E.

    1982-01-01

    We have completed a design of the Prototype Moving-Ring Reactor. The fusion fuel is confined in current-carrying rings of magnetically-field-reversed plasma (Compact Toroids). The plasma rings, formed by a coaxial plasma gun, undergo adiabatic magnetic compression to ignition temperature while they are being injected into the reactor's burner section. The cylindrical burner chamber is divided into three burn stations. Separator coils and a slight axial guide field gradient are used to shuttle the ignited toroids rapidly from one burn station to the next, pausing for 1/3 of the total burn time at each station. D-T- 3 He ice pellets refuel the rings at a rate which maintains constant radiated power

  19. Autumn study on storage rings

    CERN Multimedia

    1974-01-01

    The first two weeks of October have seen storage ring people from accelerator Laboratories throughout the world at CERN to study the fundamental problems of very high energy protonproton colliding beam machines.

  20. Minimal Gromov-Witten rings

    International Nuclear Information System (INIS)

    Przyjalkowski, V V

    2008-01-01

    We construct an abstract theory of Gromov-Witten invariants of genus 0 for quantum minimal Fano varieties (a minimal class of varieties which is natural from the quantum cohomological viewpoint). Namely, we consider the minimal Gromov-Witten ring: a commutative algebra whose generators and relations are of the form used in the Gromov-Witten theory of Fano varieties (of unspecified dimension). The Gromov-Witten theory of any quantum minimal variety is a homomorphism from this ring to C. We prove an abstract reconstruction theorem which says that this ring is isomorphic to the free commutative ring generated by 'prime two-pointed invariants'. We also find solutions of the differential equation of type DN for a Fano variety of dimension N in terms of the generating series of one-pointed Gromov-Witten invariants

  1. Cosmic rings from colliding galaxies

    Energy Technology Data Exchange (ETDEWEB)

    Mitton, S

    1976-11-18

    Research on two ring galaxies has led to the proposal of an interaction model to account for the rings. It is envisaged that this class of galaxy is created when a compact galaxy crashes through the disc of a spiral galaxy. The results of a spectroscopic investigation of the galaxy known as the Cartwheel and of another ring galaxy 11 NZ 4 are discussed. The general picture of ring galaxies which emerges from these studies of a massive starry nucleus with a necklace of emitting gas and some spokes and along the spin axis of the wheel a small companion galaxy that is devoid of interstellar gas. An explanation of these properties is considered.

  2. Ring lasers - a brief history

    Science.gov (United States)

    Klein, Tony

    2017-10-01

    Used these days in inertial navigation, ring lasers are also used in recording the tiniest variations in the Earth's spin, as well in detecting earthquakes and even the drift of continents. How did it all begin?

  3. Ring insertions as light sources

    International Nuclear Information System (INIS)

    Green, G.K.

    1975-01-01

    Bending magnets can be inserted in the long straight sections of electron storage rings to produce synchrotron radiation. If the design is carefully proportioned, the bending magnets create only a small perturbation of the properties of the ring. The resulting spectra have favorable optical properties as sources for spectroscopy and diffraction studies. The characteristics of the source are discussed, and the geometrical requirements of the magnets are presented

  4. Collector ring project at FAIR

    International Nuclear Information System (INIS)

    Dolinskii, A; Blell, U; Dimopoulou, C; Gorda, O; Leibrock, H; Litvinov, S; Laier, U; Schurig, I; Weinrich, U; Berkaev, D; Koop, I; Starostenko, A; Shatunov, P

    2015-01-01

    The collector ring is a dedicated ring for fast cooling of ions coming from separators at the FAIR project. To accommodate optimal technical solutions, a structure of a magnet lattice was recently reviewed and modified. Consequently, more appropriate technical solutions for the main magnets could be adopted. A general layout and design of the present machine is shown. The demanding extraction schemes have been detailed and open design issues were completed. (paper)

  5. Synlig læring

    DEFF Research Database (Denmark)

    Brandsen, Mads

    2017-01-01

    Introduktionen af John Hatties synlig læring i den danske skoleverden møder stadig meget kritik. Mange lærere og pædagoger oplever synlig læring som en tornado, der vil opsuge og ødelægge deres særlige danske udgave af den kontinentale dannelsestænkning, didaktik og pædagogik. Spørgsmålet er om...

  6. The circular RFQ storage ring

    International Nuclear Information System (INIS)

    Ruggiero, A.G.

    1998-01-01

    This paper presents a novel idea of storage ring for the accumulation of intense beams of light and heavy ions at low energy. The new concept is a natural development of the combined features used in a conventional storage ring and an ion trap, and is basically a linear RFQ bend on itself. In summary the advantages are: smaller beam dimensions, higher beam intensity, and a more compact storage device

  7. The Circular RFQ Storage Ring

    International Nuclear Information System (INIS)

    Ruggiero, A. G.

    1999-01-01

    This paper presents a novel idea of storage ring for the accumulation of intense beams of light and heavy ions at low energy. The new concept is a natural development of the combined features of conventional storage rings and ion traps, and is basically a linear RFQ bent on itself. The advantages are: smaller beam dimensions, higher beam intensity, and a more compact storage device

  8. Electrically charged dilatonic black rings

    International Nuclear Information System (INIS)

    Kunduri, Hari K.; Lucietti, James

    2005-01-01

    In this Letter we present (electrically) charged dilatonic black ring solutions of the Einstein-Maxwell-dilaton theory in five dimensions and we consider their physical properties. These solutions are static and as in the neutral case possess a conical singularity. We show how one may remove the conical singularity by application of a Harrison transformation, which physically corresponds to supporting the charged ring with an electric field. Finally, we discuss the slowly rotating case for arbitrary dilaton coupling

  9. Low emittance electron storage rings

    Science.gov (United States)

    Levichev, E. B.

    2018-01-01

    Low-emittance electron (positron) beams are essential for synchrotron light sources, linear collider damping rings, and circular Crab Waist colliders. In this review, the principles and methods of emittance minimization are discussed, prospects for developing relativistic electron storage rings with small beam phase volume are assessed, and problems related to emittance minimization are examined together with their possible solutions. The special features and engineering implementation aspects of various facilities are briefly reviewed.

  10. Resonance capture and Saturn's rings

    International Nuclear Information System (INIS)

    Patterson, C.W.

    1986-05-01

    We have assigned the resonances apparently responsible for the stabilization of the Saturn's shepherd satellites and for the substructure seen in the F-ring and the ringlets in the C-ring. We show that Saturn's narrow ringlets have a substructure determined by three-body resonances with Saturn's ringmoons and the sun. We believe such resonances have important implications to satellite formation. 17 refs., 1 fig., 1 tab

  11. Energy spectra of quantum rings.

    Science.gov (United States)

    Fuhrer, A; Lüscher, S; Ihn, T; Heinzel, T; Ensslin, K; Wegscheider, W; Bichler, M

    2001-10-25

    Quantum mechanical experiments in ring geometries have long fascinated physicists. Open rings connected to leads, for example, allow the observation of the Aharonov-Bohm effect, one of the best examples of quantum mechanical phase coherence. The phase coherence of electrons travelling through a quantum dot embedded in one arm of an open ring has also been demonstrated. The energy spectra of closed rings have only recently been studied by optical spectroscopy. The prediction that they allow persistent current has been explored in various experiments. Here we report magnetotransport experiments on closed rings in the Coulomb blockade regime. Our experiments show that a microscopic understanding of energy levels, so far limited to few-electron quantum dots, can be extended to a many-electron system. A semiclassical interpretation of our results indicates that electron motion in the rings is governed by regular rather than chaotic motion, an unexplored regime in many-electron quantum dots. This opens a way to experiments where even more complex structures can be investigated at a quantum mechanical level.

  12. The Dynamical History of Chariklo and Its Rings

    Energy Technology Data Exchange (ETDEWEB)

    Wood, Jeremy [Hazard Community and Technical College, Community College Drive, Hazard, KY 41701 (United States); Horner, Jonti; Marsden, Stephen C. [Computational Engineering and Science Research Centre, University of Southern Queensland, West Street, Toowoomba, QLD 4350 (Australia); Hinse, Tobias C., E-mail: jeremy.wood@kctcs.edu [Korea Astronomy and Space Science Institute, 776 Daedukdae-ro, Yuseong-gu, Daejeon 305-348 (Korea, Republic of)

    2017-06-01

    Chariklo is the only small solar system body confirmed to have rings. Given the instability of its orbit, the presence of rings is surprising, and their origin remains poorly understood. In this work, we study the dynamical history of the Chariklo system by integrating almost 36,000 Chariklo clones backward in time for 1 Gyr under the influence of the Sun and the four giant planets. By recording all close encounters between the clones and planets, we investigate the likelihood that Chariklo’s rings could have survived since its capture to the Centaur population. Our results reveal that Chariklo’s orbit occupies a region of stable chaos, resulting in its orbit being marginally more stable than those of the other Centaurs. Despite this, we find that it was most likely captured to the Centaur population within the last 20 Myr, and that its orbital evolution has been continually punctuated by regular close encounters with the giant planets. The great majority (>99%) of those encounters within 1 Hill radius of the planet have only a small effect on the rings. We conclude that close encounters with giant planets have not had a significant effect on the ring structure. Encounters within the Roche limit of the giant planets are rare, making ring creation through tidal disruption unlikely.

  13. A ring system detected around the Centaur (10199) Chariklo.

    Science.gov (United States)

    Braga-Ribas, F; Sicardy, B; Ortiz, J L; Snodgrass, C; Roques, F; Vieira-Martins, R; Camargo, J I B; Assafin, M; Duffard, R; Jehin, E; Pollock, J; Leiva, R; Emilio, M; Machado, D I; Colazo, C; Lellouch, E; Skottfelt, J; Gillon, M; Ligier, N; Maquet, L; Benedetti-Rossi, G; Ramos Gomes, A; Kervella, P; Monteiro, H; Sfair, R; El Moutamid, M; Tancredi, G; Spagnotto, J; Maury, A; Morales, N; Gil-Hutton, R; Roland, S; Ceretta, A; Gu, S-h; Wang, X-b; Harpsøe, K; Rabus, M; Manfroid, J; Opitom, C; Vanzi, L; Mehret, L; Lorenzini, L; Schneiter, E M; Melia, R; Lecacheux, J; Colas, F; Vachier, F; Widemann, T; Almenares, L; Sandness, R G; Char, F; Perez, V; Lemos, P; Martinez, N; Jørgensen, U G; Dominik, M; Roig, F; Reichart, D E; LaCluyze, A P; Haislip, J B; Ivarsen, K M; Moore, J P; Frank, N R; Lambas, D G

    2014-04-03

    Hitherto, rings have been found exclusively around the four giant planets in the Solar System. Rings are natural laboratories in which to study dynamical processes analogous to those that take place during the formation of planetary systems and galaxies. Their presence also tells us about the origin and evolution of the body they encircle. Here we report observations of a multichord stellar occultation that revealed the presence of a ring system around (10199) Chariklo, which is a Centaur--that is, one of a class of small objects orbiting primarily between Jupiter and Neptune--with an equivalent radius of 124 ±  9 kilometres (ref. 2). There are two dense rings, with respective widths of about 7 and 3 kilometres, optical depths of 0.4 and 0.06, and orbital radii of 391 and 405 kilometres. The present orientation of the ring is consistent with an edge-on geometry in 2008, which provides a simple explanation for the dimming of the Chariklo system between 1997 and 2008, and for the gradual disappearance of ice and other absorption features in its spectrum over the same period. This implies that the rings are partly composed of water ice. They may be the remnants of a debris disk, possibly confined by embedded, kilometre-sized satellites.

  14. Investigation of phosphotyrosine recognition by the SH2 domain of the Src kinase.

    Science.gov (United States)

    Bradshaw, J M; Mitaxov, V; Waksman, G

    1999-11-05

    The binding of tyrosine phosphorylated targets by SH2 domains is required for propagation of many cellular signals in higher eukaryotes; however, the determinants of phosphotyrosine (pTyr) recognition by SH2 domains are not well understood. In order to identify the attributes of pTyr required for high affinity interaction with SH2 domains, the binding of the SH2 domain of the Src kinase (Src SH2 domain) to a dephosphorylated peptide, a phosphoserine-containing peptide, and the amino acid pTyr was studied using titration calorimetry and compared with the binding of a high affinity tyrosyl phosphopeptide. The dephosphorylated peptide and the phosphoserine containing peptide both bind extremely weakly to the Src SH2 domain (DeltaGo (dephosphorylated)=-3.6 kcal/mol, DeltaGo (phosphoserine) >-3.7 kcal/mol); however, the DeltaGo value of pTyr binding is more favorable (-4.7 kcal/mol, or 50 % of the entire binding free energy of a high affinity tyrosyl phosphopeptide). These results indicate that both the phosphate and the tyrosine ring of the pTyr are critical determinants of high affinity binding. Alanine mutagenesis was also used to evaluate the energetic contribution to binding of ten residues located in the pTyr-binding site. Mutation of the strictly conserved Arg betaB5 resulted in a large increase in DeltaGo (DeltaDeltaGo=3.2 kcal/mol) while elimination of the other examined residues each resulted in a significantly smaller (DeltaDeltaGoSH2 domain, surprisingly increased affinity by eightfold (DeltaDeltaGo=-1.1 kcal/mol). Using a double mutant cycle analysis, it was revealed that residues of the pTyr-binding pocket are not coupled to the peptide residues C-terminal to the pTyr. In addition, comparison of each residue's DeltaDeltaGo value upon mutation with that residue's sequence conservation among SH2 domains revealed only a modest correlation between a residue's energetic contribution to pTyr recognition and its conservation throughout evolution. The results of

  15. Double acting stirling engine piston ring

    Science.gov (United States)

    Howarth, Roy B.

    1986-01-01

    A piston ring design for a Stirling engine wherein the contact pressure between the piston and the cylinder is maintained at a uniform level, independent of engine conditions through a balancing of the pressure exerted upon the ring's surface and thereby allowing the contact pressure on the ring to be predetermined through the use of a preloaded expander ring.

  16. Study for ILC Damping Ring at KEKB

    Energy Technology Data Exchange (ETDEWEB)

    Flanagan, J.W.; Fukuma, H.; Kanazawa, K.I.; Koiso, H.; Masuzawa, M.; Ohmi, Kazuhito; Ohnishi, Y.; Oide, Katsunobu; Suetsugu, Y.; Tobiyama, M.; /KEK, Tsukuba; Pivi, M.; /SLAC

    2011-11-04

    ILC damping ring consists of very low emittance electron and positron storage rings. It is necessary for ILC damping ring to study electron cloud effects in such low emittance positron ring. We propose a low emittance operation of KEKB to study the effects.

  17. Atomic structure of the sweet-tasting protein thaumatin I at pH 8.0 reveals the large disulfide-rich region in domain II to be sensitive to a pH change.

    OpenAIRE

    Masuda, Tetsuya; Ohta, Keisuke; Mikami, Bunzo; Kitabatake, Naofumi; Tani, Fumito

    2012-01-01

    Thaumatin, an intensely sweet-tasting plant protein, elicits a sweet taste at 50 nM. Although the sweetness remains when thaumatin is heated at 80 °C for 4h under acid conditions, it rapidly declines when heating at a pH above 6.5. To clarify the structural difference at high pH, the atomic structure of a recombinant thaumatin I at pH 8.0 was determined at a resolution of 1.0Å. Comparison to the crystal structure of thaumatin at pH 7.3 and 7.0 revealed the root-mean square deviation value of ...

  18. Manipulation of vortex rings for flow control

    International Nuclear Information System (INIS)

    Toyoda, Kuniaki; Hiramoto, Riho

    2009-01-01

    This paper reviews the dynamics of vortex rings and the control of flow by the manipulation of vortex rings. Vortex rings play key roles in many flows; hence, the understanding of the dynamics of vortex rings is crucial for scientists and engineers dealing with flow phenomena. We describe the structures and motions of vortex rings in circular and noncircular jets, which are typical examples of flows evolving into vortex rings. For circular jets the mechanism of evolving, merging and breakdown of vortex rings is described, and for noncircular jets the dynamics of three-dimensional deformation and interaction of noncircular vortex rings under the effect of self- and mutual induction is discussed. The application of vortex-ring manipulation to the control of various flows is reviewed with successful examples, based on the relationship between the vortex ring dynamics and the flow properties. (invited paper)

  19. Structure and dynamics of ringed galaxies

    International Nuclear Information System (INIS)

    Buta, R.J.

    1984-01-01

    In many spiral and SO galaxies, single or multiple ring structures are visible in the disk. These inner rings (r), outer rings (R), and nuclear rings (nr) were investigated by means of morphology, photometry, and spectroscopy in order to provide basic data on a long neglected phenomenon. The metric properties of each ring are investigated and found to correlate with the structure of the parent galaxy. When properly calibrated, inner rings in barred (SB) systems can be used as geometric extragalactic distance indicators to distances in excess of 100 Mpc. Other statistics are presented that confirm previous indications that the rings have preferred shapes, relative sizes, and orientations with respect to bars. A survey is made of the less homogeneous non-barred (SA) ringed systems, and the causes of the inhomogeneity are isolated. It is shown that rings can be identified in multiple-ring SA systems that are exactly analogous to those in barred spirals

  20. Sequence similarity between the erythrocyte binding domain of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals a functional heparin binding motif involved in binding to the Duffy antigen receptor for chemokines

    Directory of Open Access Journals (Sweden)

    Bolton Michael J

    2011-11-01

    Full Text Available Abstract Background The HIV surface glycoprotein gp120 (SU, gp120 and the Plasmodium vivax Duffy binding protein (PvDBP bind to chemokine receptors during infection and have a site of amino acid sequence similarity in their binding domains that often includes a heparin binding motif (HBM. Infection by either pathogen has been found to be inhibited by polyanions. Results Specific polyanions that inhibit HIV infection and bind to the V3 loop of X4 strains also inhibited DBP-mediated infection of erythrocytes and DBP binding to the Duffy Antigen Receptor for Chemokines (DARC. A peptide including the HBM of PvDBP had similar affinity for heparin as RANTES and V3 loop peptides, and could be specifically inhibited from heparin binding by the same polyanions that inhibit DBP binding to DARC. However, some V3 peptides can competitively inhibit RANTES binding to heparin, but not the PvDBP HBM peptide. Three other members of the DBP family have an HBM sequence that is necessary for erythrocyte binding, however only the protein which binds to DARC, the P. knowlesi alpha protein, is inhibited by heparin from binding to erythrocytes. Heparitinase digestion does not affect the binding of DBP to erythrocytes. Conclusion The HBMs of DBPs that bind to DARC have similar heparin binding affinities as some V3 loop peptides and chemokines, are responsible for specific sulfated polysaccharide inhibition of parasite binding and invasion of red blood cells, and are more likely to bind to negative charges on the receptor than cell surface glycosaminoglycans.

  1. Planetary Rings: a Brief History of Observation and Theory

    Science.gov (United States)

    Nicholson, P. D.

    2000-05-01

    Over several centuries, and extending down to today, the ring systems encircling Saturn and the other jovian planets have provided an endless source of speculation and theorizing for astronomers, theologians, and physicists. In the past two decades they have also become a testing ground for dynamical models of more distant astrophysical disks, such as those which surround protostars and even the stellar disks of spiral galaxies. I will review some of the early theories, and their sometimes rude confrontation with observational data, starting with Christiaan Huygens and touching on seminal contributions by Laplace, Bessel, Maxwell, Barnard, Russell (of H-R diagram fame) and Jeffreys. In the modern era, observations at infrared and radio wavelengths have revealed Saturn's rings to be composed of large chunks of almost pure water ice, and to have a vertical thickness measured in tens of meters. A renaissance in planetary rings studies occurred in the period 1977--1981, first with the discoveries of the narrow, dark and non-circular rings of Uranus and the tenuous jovian ring system, and capped off by the spectacular images returned during the twin Voyager flybys of Saturn. Along with the completely unsuspected wealth of detail these observations revealed came an unwelcome problem: are the rings ancient or are we privileged to live at a special time in history? The answer to this still-vexing question may lie in the complex gravitational interactions recent studies have revealed between the rings themselves and their retinues of attendant satellites. Between the four known ring systems, we see elegant examples of Lindblad and corotation resonances (first invoked in the galactic context), electromagnetic resonances, many-armed spiral density waves and bending waves, narrow ringlets which exhibit internal modes due to a collective instability, sharp-edged gaps maintained via tidal torques from embedded moonlets, and tenuous dust belts created by meteoroid impact onto

  2. Pure subrings of the rings

    International Nuclear Information System (INIS)

    Tsarev, Andrei V

    2009-01-01

    Pure subrings of finite rank in the Z-adic completion of the ring of integers and in its homomorphic images are considered. Certain properties of these rings are studied (existence of an identity element, decomposability into a direct sum of essentially indecomposable ideals, condition for embeddability into a csp-ring, etc.). Additive groups of these rings and conditions under which these rings are subrings of algebraic number fields are described. Bibliography: 12 titles.

  3. Primitivity and weak distributivity in near rings and matrix near rings

    International Nuclear Information System (INIS)

    Abbasi, S.J.

    1993-08-01

    This paper shows the structure of matrix near ring constructed over a weakly distributive and primative near ring. It is proved that a weakly distributive primitive near ring is a ring and the matrix near rings constructed over it is also a bag. (author). 14 refs

  4. Ring wormholes via duality rotations

    Directory of Open Access Journals (Sweden)

    Gary W. Gibbons

    2016-09-01

    Full Text Available We apply duality rotations and complex transformations to the Schwarzschild metric to obtain wormhole geometries with two asymptotically flat regions connected by a throat. In the simplest case these are the well-known wormholes supported by phantom scalar field. Further duality rotations remove the scalar field to yield less well known vacuum metrics of the oblate Zipoy–Voorhees–Weyl class, which describe ring wormholes. The ring encircles the wormhole throat and can have any radius, whereas its tension is always negative and should be less than −c4/4G. If the tension reaches the maximal value, the geometry becomes exactly flat, but the topology remains non-trivial and corresponds to two copies of Minkowski space glued together along the disk encircled by the ring. The geodesics are straight lines, and those which traverse the ring get to the other universe. The ring therefore literally produces a hole in space. Such wormholes could perhaps be created by negative energies concentrated in toroidal volumes, for example by vacuum fluctuations.

  5. The RING 2.0 web server for high quality residue interaction networks.

    Science.gov (United States)

    Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

    2016-07-08

    Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Energetic ion injection and formation of the storm-time symmetric ring current

    Directory of Open Access Journals (Sweden)

    L. Xie

    2006-12-01

    Full Text Available An extensive study of ring current injection and intensification of the storm-time ring current is conducted with three-dimensional (3-D test particle trajectory calculations (TPTCs. The TPTCs reveal more accurately the process of ring current injection, with the main results being the following: (1 an intense convection electric field can effectively energize and inject plasma sheet particles into the ring current region within 1–3 h. (2 Injected ions often follow chaotic trajectories in non-adiabatic regions, which may have implications in storm and ring current physics. (3 The shielding electric field, which arises as a consequence of enhanced convection and co-exists with the injection and convection electric field, may cause the original open trajectories of injected ions with higher energy to change into closed ones, thus playing a role in the formation of the symmetric ring current.

  7. Official regulations and perceptual aspects of bell ringing

    Directory of Open Access Journals (Sweden)

    Kovačič Mojca

    2017-01-01

    Full Text Available Through the analytical approach of studying official and perception-related discourse on bell ringing I accentuate the complexity of aspects that the sound of church bell presents in contemporary society. I point out the misleading officially defined level of noise nuisance and reveal how, when and why bell ringing is perceived as a positive or negative part of the acoustic environment. The study argues for a holistic approach to the noise nuisance issues, still much underestimated in the official discourse, that co-create our everyday soundscape.

  8. Abdominal compression during endoscopy (the Bolster technique) demonstrates hidden Schatzki rings (with videos).

    Science.gov (United States)

    Jouhourian, Caroline; Bonis, Peter A; Guelrud, Moises

    2016-05-01

    Schatzki rings are found in the distal esophagus, are associated with hiatal hernias, and present with intermittent dysphagia to solid foods. They can be identified by radiology (GI series or barium swallow studies) or endoscopy. Rings are not always visualized during endoscopy in patients in whom they are suspected clinically. The Bolster technique involves application of epigastric abdominal pressure, which offers the potential to reveal a Schatzki ring that is otherwise obscured within a reduced hiatal hernia. The aim of this study was to determine whether the Bolster technique improves endoscopic detection of Schatzki rings. We reviewed 30 symptomatic patients with a history of a Schatzki ring in a tertiary care center. The Bolster technique was applied to patients in whom the ring was not visible during standard endoscopy. The main outcome measurement was identification of the Schatzki ring after the Bolster technique. A Schatzki ring was visible during standard endoscopy in 26 of the 30 patients. In the remaining 4, the ring was visible only after the application of the Bolster technique. The Bolster technique is a simple maneuver that can increase detection rates of Schatzki rings during endoscopy. Copyright © 2016 American Society for Gastrointestinal Endoscopy. Published by Elsevier Inc. All rights reserved.

  9. CMB lensing and giant rings

    Energy Technology Data Exchange (ETDEWEB)

    Rathaus, Ben; Itzhaki, Nissan, E-mail: nitzhaki@post.tau.ac.il, E-mail: ben.rathaus@gmail.com [Raymond and Beverly Sackler Faculty of Exact Sciences, School of Physics and Astronomy, Tel-Aviv University, Ramat-Aviv, 69978 (Israel)

    2012-05-01

    We study the CMB lensing signature of a pre-inationary particle (PIP), assuming it is responsible for the giant rings anomaly that was found recently in the WMAP data. Simulating Planck-like data we find that generically the CMB lensing signal to noise ratio associated with such a PIP is quite small and it would be difficult to cross correlate the temperature giant rings with the CMB lensing signal. However, if the pre-inationary particle is also responsible for the bulk flow measured from the local large scale structure, which happens to point roughly at the same direction as the giant rings, then the CMB lensing signal to noise ratio is fairly significant.

  10. Proton storage ring summer workshop

    International Nuclear Information System (INIS)

    Lawrence, G.P.; Cooper, R.K.

    1977-10-01

    During the week of August 16, 1976 a Workshop was held at the Los Alamos Scientific Laboratory (LASL) on the Proton Storage Ring (PSR) for the Weapons Neutron Research Facility (WNRF). Written contributions were solicited from each of the participants in the Workshop, and the contributions that were received are presented. The papers do not represent polished or necessarily complete work, but rather represent ''first cuts'' at their respective areas. Topics covered include: (1) background information on the storage ring; (2) WNRF design; (3) rf transient during filling; (4) rf capture; (5) beam bunch compression; (6) transverse space charge limits; (7) transverse resistive instability in the PSR; (8) longitudinal resistive instability; (9) synchrotron frequency splitting; (10) E Quintus Unum--off resonance; (11) first harmonic bunching in the storage ring; (12) kicker considerations; (13) beam extraction; (14) ferrite kicker magnets; and (15) E Quintus Unum: a possible ejection scheme

  11. New Main Ring control system

    International Nuclear Information System (INIS)

    Seino, K.; Anderson, L.; Ducar, R.; Franck, A.; Gomilar, J.; Hendricks, B.; Smedinghoff, J.

    1990-03-01

    The Fermilab Main Ring control system has been operational for over sixteen years. Aging and obsolescence of the equipment make the maintenance difficult. Since the advent of the Tevatron, considerable upgrades have been made to the controls of all the Fermilab accelerators except the Main Ring. Modernization of the equipment and standardization of the hardware and software have thus become inevitable. The Tevatron CAMAC serial system has been chosen as a basic foundation in order to make the Main Ring control system compatible with the rest of the accelerator complex. New hardware pieces including intelligent CAMAC modules have been designed to satisfy unique requirements. Fiber optic cable and repeaters have been installed in order to accommodate new channel requirements onto the already saturated communication medium system. 8 refs., 2 figs

  12. A tree-ring perspective on the terrestrial carbon cycle

    International Nuclear Information System (INIS)

    Babst, F.; Alexander, M.R.; Szejner, P.; Trouet, V.; Alexander, M.R.; Moore, D.J.P.; Bouriaud, O.; Klesse, S.; Frank, D.; Roden, J.; Ciais, P.; Poulter, B.

    2014-01-01

    Tree-ring records can provide valuable information to advance our understanding of contemporary terrestrial carbon cycling and to reconstruct key metrics in the decades preceding monitoring data. The growing use of tree rings in carbon-cycle research is being facilitated by increasing recognition of reciprocal benefits among research communities. Yet, basic questions persist regarding what tree rings represent at the ecosystem level, how to optimally integrate them with other data streams, and what related challenges need to be overcome. It is also apparent that considerable unexplored potential exists for tree rings to refine assessments of terrestrial carbon cycling across a range of temporal and spatial domains. Here, we summarize recent advances and highlight promising paths of investigation with respect to (1) growth phenology, (2) forest productivity trends and variability, (3) CO 2 fertilization and water-use efficiency, (4) forest disturbances, and (5) comparisons between observational and computational forest productivity estimates. We encourage the integration of tree-ring data: with eddy-covariance measurements to investigate carbon allocation patterns and water-use efficiency; with remotely sensed observations to distinguish the timing of cambial growth and leaf phenology; and with forest inventories to develop continuous, annually resolved and long-term carbon budgets. In addition, we note the potential of tree-ring records and derivatives thereof to help evaluate the performance of earth system models regarding the simulated magnitude and dynamics of forest carbon uptake, and inform these models about growth responses to (non-)climatic drivers. Such efforts are expected to improve our understanding of forest carbon cycling and place current developments into a long-term perspective. (authors)

  13. Tree rings and radiocarbon calibration

    International Nuclear Information System (INIS)

    Barbetti, M.

    1999-01-01

    Only a few kinds of trees in Australia and Southeast Asia are known to have growth rings that are both distinct and annual. Those that do are therefore extremely important to climatic and isotope studies. In western Tasmania, extensive work with Huon pine (Lagarostrobos franklinii) has shown that many living trees are more than 1,000 years old, and that their ring widths are sensitive to temperature, rainfall and cloud cover (Buckley et al. 1997). At the Stanley River there is a forest of living (and recently felled) trees which we have sampled and measured. There are also thousands of subfossil Huon pine logs, buried at depths less than 5 metres in an area of floodplain extending over a distance of more than a kilometre with a width of tens of metres. Some of these logs have been buried for 50,000 years or more, but most of them belong to the period between 15,000 years and the present. In previous expeditions in the 1980s and 1990s, we excavated and sampled about 350 logs (Barbetti et al. 1995; Nanson et al. 1995). By measuring the ring-width patterns, and matching them between logs and living trees, we have constructed a tree-ring dated chronology from 571 BC to AD 1992. We have also built a 4254-ring floating chronology (placed by radiocarbon at ca. 3580 to 7830 years ago), and an earlier 1268-ring chronology (ca. 7,580 to 8,850 years ago). There are many individuals, or pairs of logs which match and together span several centuries, at 9,000 years ago and beyond

  14. Adiabatic compression of ion rings

    International Nuclear Information System (INIS)

    Larrabee, D.A.; Lovelace, R.V.

    1982-01-01

    A study has been made of the compression of collisionless ion rings in an increasing external magnetic field, B/sub e/ = zB/sub e/(t), by numerically implementing a previously developed kinetic theory of ring compression. The theory is general in that there is no limitation on the ring geometry or the compression ratio, lambdaequivalentB/sub e/ (final)/B/sub e/ (initial)> or =1. However, the motion of a single particle in an equilibrium is assumed to be completely characterized by its energy H and canonical angular momentum P/sub theta/ with the absence of a third constant of the motion. The present computational work assumes that plasma currents are negligible, as is appropriate for a low-temperature collisional plasma. For a variety of initial ring geometries and initial distribution functions (having a single value of P/sub theta/), it is found that the parameters for ''fat'', small aspect ratio rings follow general scaling laws over a large range of compression ratios, 1 3 : The ring radius varies as lambda/sup -1/2/; the average single particle energy as lambda/sup 0.72/; the root mean square energy spread as lambda/sup 1.1/; and the total current as lambda/sup 0.79/. The field reversal parameter is found to saturate at values typically between 2 and 3. For large compression ratios the current density is found to ''hollow out''. This hollowing tends to improve the interchange stability of an embedded low β plasma. The implications of these scaling laws for fusion reactor systems are discussed

  15. Superconducting proton ring for PETRA

    International Nuclear Information System (INIS)

    Baynham, E.

    1979-01-01

    A powerful new facility for colliding beam physics could be provided by adding a proton storage ring in the range of several hundred GeV to the electron-positron storage ring PETRA at DESY. This can be achieved in an economic way utilizing the PETRA tunnel and taking advantage of the higher magnetic fields of superconducting magnets which would be placed above or below the PETRA magnets. A central field of 4 Tesla in the bending magnets corresponds to a proton energy of 225 GeV. (orig.)

  16. The Cryogenic Storage Ring CSR

    OpenAIRE

    von Hahn, Robert; Becker, Arno; Berg, Felix; Blaum, Klaus; Breitenfeldt, Christian; Fadil, Hisham; Fellenberger, Florian; Froese, Michael; George, Sebastian; Göck, Jürgen; Grieser, Manfred; Grussie, Florian; Guerin, Elisabeth A.; Heber, Oded; Herwig, Philipp

    2016-01-01

    An electrostatic cryogenic storage ring, CSR, for beams of anions and cations with up to 300 keV kinetic energy per unit charge has been designed, constructed, and put into operation. With a circumference of 35 m, the ion-beam vacuum chambers and all beam optics are in a cryostat and cooled by a closed-cycle liquid helium system. At temperatures as low as (5.5 ± 1) K inside the ring, storage time constants of several minutes up to almost an hour were observed for atomic and molecular, anion a...

  17. Supersymmetric rings in field theory

    International Nuclear Information System (INIS)

    Blanco-Pillado, Jose J.; Redi, Michele

    2006-01-01

    We study the dynamics of BPS string-like objects obtained by lifting monopole and dyon solutions of N = 2 Super-Yang-Mills theory to five dimensions. We present exact traveling wave solutions which preserve half of the supersymmetries. Upon compactification this leads to macroscopic BPS rings in four dimensions in field theory. Due to the fact that the strings effectively move in six dimensions the same procedure can also be used to obtain rings in five dimensions by using the hidden dimension

  18. Damping ring designs and issues

    International Nuclear Information System (INIS)

    Wolski, Andrzej; Decking, Winfried

    2003-01-01

    The luminosity performance of a future linear collider (LC) will depend critically on the performance of the damping rings. The design luminosities of the current LC proposals require rings with very short damping times, large acceptance, low equilibrium emittance and high beam intensity. We discuss the design strategies for lattices achieving the goals of dynamical stability, examine the challenges for alignment and coupling correction, and consider a variety of collective effects that threaten to limit beam quality. We put the design goals in context by referring to the experience of operating facilities, and outline the further research and development that is needed

  19. Laparoscopic appendicectomy using endo-ring applicator and fallope rings

    International Nuclear Information System (INIS)

    Ali, Iyoob V; Maliekkal, Joji I

    2009-01-01

    Wider adoption of laparoscopic appendicectomy (LA) is limited by problems in securing the appendiceal base as well as the cost and the duration compared with the open procedure. The objective of this study was to assess the feasibility and efficacy of a new method for securing the appendiceal base in LA, so as to make the entire procedure simpler and cheaper, and hence, more popular. Twenty-five patients who were candidates for appendicectomy (emergency as well as elective) and willing for the laparoscopic procedure were selected for this study. Ports used were 10 mm at the umbilicus, 5 mm at the lower right iliac fossa, and 10 mm at the left iliac fossa. Extremely friable, ruptured, or turgid organs of diameters larger than 8 mm were excluded from the study. The mesoappendix was divided close to the appendix by diathermy. Fallope rings were applied to the appendiceal base using a special ring applicator, and the appendix was divided and extracted through the lumen of the applicator. The procedure was successful in 23 (92%) cases, and the mean duration of the procedure was 20 minutes (15-32 minutes). There were no procedural complications seen during a median follow-up of two weeks. The equipment and rings were cheaper when compared with that of the standard methods of securing the base of the appendix. LA using fallope rings is a safe, simple, easy-to-learn, and economically viable method. (author)

  20. Mutagenesis of Dengue Virus Protein NS2A Revealed a Novel Domain Responsible for Virus-Induced Cytopathic Effect and Interactions between NS2A and NS2B Transmembrane Segments.

    Science.gov (United States)

    Wu, Ren-Huang; Tsai, Ming-Han; Tsai, Kuen-Nan; Tian, Jia Ni; Wu, Jian-Sung; Wu, Su-Ying; Chern, Jyh-Haur; Chen, Chun-Hong; Yueh, Andrew

    2017-06-15

    The NS2A protein of dengue virus (DENV) has eight predicted transmembrane segments (pTMS1 to -8) and participates in RNA replication, virion assembly, and host antiviral response. However, the roles of specific amino acid residues within the pTMS regions of NS2A during the viral life cycle are not clear. Here, we explore the function of DENV NS2A by introducing a series of alanine substitutions into the N-terminal half (pTMS1 to -4) of the protein in the context of a DENV infectious clone or subgenomic replicon. Six NS2A mutants (NM5, -7, -9, and -17 to -19) around pTMS1 and -2 displayed a novel phenotype showing a >1,000-fold reduction in virus yield, an absence of plaque formation despite wild-type-like replicon activity, and infectious-virus-like particle yields. HEK-293 cells infected with the six NS2A mutant viruses failed to cause a virus-induced cytopathic effect (CPE) by MitoCapture staining, cell proliferation, and lactate dehydrogenase release assays. Sequencing analyses of pseudorevertant viruses derived from lethal-mutant viruses revealed two consensus reversion mutations, leucine to phenylalanine at codon 181 (L181F) within pTMS7 of NS2A and isoleucine to threonine at codon 114 (I114T) within NS2B. The introduction of an NS2A-L181F mutation into the lethal (NM15, -16, -25, and -33) and CPE-defective (NM7, -9, and -19) mutants substantially rescued virus infectivity and virus-induced CPE, respectively, whereas the NS2B-L114T mutation rescued the NM16, -25, and -33 mutants. In conclusion, the results revealed the essential roles of the N-terminal half of NS2A in RNA replication and virus-induced CPE. Intramolecular interactions between pTMSs of NS2A and intermolecular interactions between the NS2A and NS2B proteins were also implicated. IMPORTANCE The characterization of the N-terminal (current study) and C-terminal halves of DENV NS2A is the most comprehensive mutagenesis study to date to investigate the function of NS2A during the flaviviral life cycle

  1. Domain-to-domain coupling in voltage-sensing phosphatase.

    Science.gov (United States)

    Sakata, Souhei; Matsuda, Makoto; Kawanabe, Akira; Okamura, Yasushi

    2017-01-01

    Voltage-sensing phosphatase (VSP) consists of a transmembrane voltage sensor and a cytoplasmic enzyme region. The enzyme region contains the phosphatase and C2 domains, is structurally similar to the tumor suppressor phosphatase PTEN, and catalyzes the dephosphorylation of phosphoinositides. The transmembrane voltage sensor is connected to the phosphatase through a short linker region, and phosphatase activity is induced upon membrane depolarization. Although the detailed molecular characteristics of the voltage sensor domain and the enzyme region have been revealed, little is known how these two regions are coupled. In addition, it is important to know whether mechanism for coupling between the voltage sensor domain and downstream effector function is shared among other voltage sensor domain-containing proteins. Recent studies in which specific amino acid sites were genetically labeled using a fluorescent unnatural amino acid have enabled detection of the local structural changes in the cytoplasmic region of Ciona intestinalis VSP that occur with a change in membrane potential. The results of those studies provide novel insight into how the enzyme activity of the cytoplasmic region of VSP is regulated by the voltage sensor domain.

  2. Dependency of the regio- and stereoselectivity of intramolecular, ring-closing glycosylations upon the ring size

    Directory of Open Access Journals (Sweden)

    Patrick Claude

    2011-12-01

    Full Text Available Phenyl 3,4,6-tri-O-benzyl-2-O-(3-carboxypropionyl-1-thio-β-D-galactopyranoside (1 was condensed via its pentafluorophenyl ester 2 with 5-aminopentyl (4a, 4-aminobutyl (4b, 3-aminopropyl (4c and 2-aminoethyl 4,6-O-benzylidene-β-D-glucopyranoside (4d, prepared from the corresponding N-Cbz protected glucosides 3a–d, to give the corresponding 2-[3-(alkylcarbamoylpropionyl] tethered saccharides 5a–d. Intramolecular, ring closing glycosylation of the saccharides with NIS and TMSOTf afforded the tethered β(1→3 linked disaccharides 6a–c, the α(1→3 linked disaccharides 7a–d and the α(1→2 linked disaccharide 8d in ratios depending upon the ring size formed during glycosylation. No β(1→2 linked disaccharides were formed. Molecular modeling of saccharides 6–8 revealed that a strong aromatic stacking interaction between the aromatic parts of the benzyl and benzylidene protecting groups in the galactosyl and glucosyl moieties was mainly responsible for the observed regioselectivity and anomeric selectivity of the ring-closing glycosylation step.

  3. Electric dipole moment of magnetoexciton in concentric quantum rings

    Science.gov (United States)

    García, L. F.; Mikhailov, I. D.; Revinova, S. Yu

    2017-12-01

    We study properties of exciton in a weakly coupled concentric quantum rings, penetrated by an axially directed magnetic flux and subjected to an electric field in the ring’s plane. To this end, we adopt a simple model of quasi-one-dimensional rotator, for which the wave functions and the corresponding energies we found by using the double Fourier series expansion method. Revealed multiple intersections of the energy levels provide conditions for abrupt changes of the radial and the angular quantum numbers, making possible the tunnelling of carriers between rings and allowing the formation of a permanent large dipole moment. We show that the electric and magnetic polarizability of concentric quantum rings with a trapped exciton are very sensible to external electric and magnetic fields.

  4. Examination techniques for non-magnetic rings

    International Nuclear Information System (INIS)

    Metala, M.J.; Kilpatrick, N.L.; Frank, W.W.

    1990-01-01

    Until the introduction of 18Mn18Cr rings a few years ago, most non-magnetic steel rings for generator rotors were made from 18Mn5Cr alloy steel, which is highly susceptible to stress corrosion cracking in the presence of water. This, the latest in a series of papers on the subject of non-magnetic rings by the authors' company, provides a discussion of nondestructive examination of 18Mn5Cr rings for stress corrosion distress. With rings on the rotor, fluorescent penetrant, ultrasonic and special visual techniques are applied. With rings off the rotor, the fluorescent penetrant technique is used, with and without stress enhancement

  5. Ring diagrams and phase transitions

    International Nuclear Information System (INIS)

    Takahashi, K.

    1986-01-01

    Ring diagrams at finite temperatures carry most infrared-singular parts among Feynman diagrams. Their effect to effective potentials are in general so significant that one must incorporate them as well as 1-loop diagrams. The author expresses these circumstances in some examples of supercooled phase transitions

  6. WR stars with ring nebulae

    International Nuclear Information System (INIS)

    Tutukov, A.

    1982-01-01

    It is shown that most of usually apparently single nitrogen WR stars with ring emission nebulae around them (WN + Neb) are a probable product of the evolution of a massive close binary with initial masses of components exceeding approximately 20 solar masses. (Auth.)

  7. Alignment for new Subaru ring

    International Nuclear Information System (INIS)

    Zhang, Ch.; Matsui, S.; Hashimoto, S.

    1999-01-01

    The New SUBARU is a synchrotron light source being constructed at the SPring-8 site. The main facility is a 1.5 GeV electron storage ring that provides light beam in the region from VUV to soft X-ray using SPring-8's 1 GeV linac as an injector. The ring, with a circumference of about 119 meters, is composed of six bending cells. Each bending cell has two normal dipoles of 34 degree and one inverse dipole of -8 degree. The ring has six straight sections: two very long straight sections for a 11-m long undulator and an optical klystron, four short straight sections for a 2.3-m undulator, a super-conducting wiggler, rf cavity and injection, etc. The magnets of the storage ring are composed of 12 dipoles (BMs), 6 invert dipoles (BIs), 56 quadrupoles and 44 sextupoles, etc. For the magnet alignment, positions of the dipoles (the BMs and BIs) are determined by network survey method. The multipoles, which are mounted on girders between the dipoles, are aligned with a laser-CCD camera system. This article presents the methodology used to position the different components and particularly to assure the precise alignment of the multipoles. (authors)

  8. Characteristic of Rings. Prime Fields

    Directory of Open Access Journals (Sweden)

    Schwarzweller Christoph

    2015-12-01

    Full Text Available The notion of the characteristic of rings and its basic properties are formalized [14], [39], [20]. Classification of prime fields in terms of isomorphisms with appropriate fields (ℚ or ℤ/p are presented. To facilitate reasonings within the field of rational numbers, values of numerators and denominators of basic operations over rationals are computed.

  9. Ring laser frequency biasing mechanism

    International Nuclear Information System (INIS)

    McClure, R.E.

    1975-01-01

    A ring laser cavity including a magnetically saturable member for differentially phase shifting the contradirectional waves propagating in the laser cavity, the phase shift being produced by the magneto-optic interaction occurring between the light waves and the magnetization in the cavity forming component as the light waves are reflected therefrom is described

  10. Counting problems for number rings

    NARCIS (Netherlands)

    Brakenhoff, Johannes Franciscus

    2009-01-01

    In this thesis we look at three counting problems connected to orders in number fields. First we study the probability that for a random polynomial f in Z[X] the ring Z[X]/f is the maximal order in Q[X]/f. Connected to this is the probability that a random polynomial has a squarefree

  11. Progressiv læring

    DEFF Research Database (Denmark)

    Wahlgren, Bjarne

    2017-01-01

    SAMMENFATNING I denne evalueringsrapport præsenterer Nationalt Center for Kompetenceudvikling ved Aarhus Universitet (herefter NCK) og Rambøll Management Consulting (herefter Rambøll) den værktøjsspecifikke evaluering af Progressiv Læring som pædagogisk værktøj for de ni implementeringsskoler i s...

  12. Wands of the Black Ring

    Czech Academy of Sciences Publication Activity Database

    Pravda, Vojtěch; Pravdová, Alena

    2005-01-01

    Roč. 37, č. 7 (2005), s. 1277-1287 ISSN 0001-7701 R&D Projects: GA ČR GP202/03/P017; GA AV ČR KJB1019403 Institutional research plan: CEZ:AV0Z10190503 Keywords : algebraic classification * Petrov classification * black ring Subject RIV: BA - General Mathematics Impact factor: 1.550, year: 2005

  13. Substitution of matrices over rings

    NARCIS (Netherlands)

    Hautus, M.L.J.

    1995-01-01

    For a given commutative ring with an identity element, we define and study the substitution of a matrix with entries in into a matrix polynomial or rational function over . A Bezout-type remainder theorem and a "partial-substitution rule" are derived and used to obtain a number of results. The

  14. Exercises in modules and rings

    CERN Document Server

    Lam, TY

    2009-01-01

    This volume offers a compendium of exercises of varying degree of difficulty in the theory of modules and rings. All exercises are solved in full detail. Each section begins with an introduction giving the general background and the theoretical basis for the problems that follow.

  15. On commutativity theorems for rings

    Directory of Open Access Journals (Sweden)

    H. A. S. Abujabal

    1990-01-01

    Full Text Available Let R be an associative ring with unity. It is proved that if R satisfies the polynomial identity [xny−ymxn,x]=0(m>1,n≥1, then R is commutative. Two or more related results are also obtained.

  16. Conference on Arithmetic and Ideal Theory of Rings and Semigroups

    CERN Document Server

    Fontana, Marco; Geroldinger, Alfred; Olberding, Bruce

    2016-01-01

    This book consists of both expository and research articles solicited from speakers at the conference entitled "Arithmetic and Ideal Theory of Rings and Semigroups," held September 22–26, 2014 at the University of Graz, Graz, Austria. It reflects recent trends in multiplicative ideal theory and factorization theory, and brings together for the first time in one volume both commutative and non-commutative perspectives on these areas, which have their roots in number theory, commutative algebra, and algebraic geometry. Topics discussed include topological aspects in ring theory, Prüfer domains of integer-valued polynomials and their monadic submonoids, and semigroup algebras. It will be of interest to practitioners of mathematics and computer science, and researchers in multiplicative ideal theory, factorization theory, number theory, and algebraic geometry.

  17. Speckle reduction in digital holography with resampling ring masks

    Science.gov (United States)

    Zhang, Wenhui; Cao, Liangcai; Jin, Guofan

    2018-01-01

    One-shot digital holographic imaging has the advantages of high stability and low temporal cost. However, the reconstruction is affected by the speckle noise. Resampling ring-mask method in spectrum domain is proposed for speckle reduction. The useful spectrum of one hologram is divided into several sub-spectra by ring masks. In the reconstruction, angular spectrum transform is applied to guarantee the calculation accuracy which has no approximation. N reconstructed amplitude images are calculated from the corresponding sub-spectra. Thanks to speckle's random distribution, superimposing these N uncorrelated amplitude images would lead to a final reconstructed image with lower speckle noise. Normalized relative standard deviation values of the reconstructed image are used to evaluate the reduction of speckle. Effect of the method on the spatial resolution of the reconstructed image is also quantitatively evaluated. Experimental and simulation results prove the feasibility and effectiveness of the proposed method.

  18. Semistar-Krull and Valuative Dimension of Integral Domains

    OpenAIRE

    Sahandi, Parviz

    2008-01-01

    Given a stable semistar operation of finite type $\\star$ on an integral domain $D$, we show that it is possible to define in a canonical way a stable semistar operation of finite type $\\star[X]$ on the polynomial ring $D[X]$, such that, if $n:=\\star$-$\\dim(D)$, then $n+1\\leq \\star[X]\\text{-}\\dim(D[X])\\leq 2n+1$. We also establish that if $D$ is a $\\star$-Noetherian domain or is a Pr\\"{u}fer $\\star$-multiplication domain, then $\\star[X]\\text{-}\\dim(D[X])=\\star\\text{-}\\dim(D)+1$. Moreover we de...

  19. 21 CFR 870.3800 - Annuloplasty ring.

    Science.gov (United States)

    2010-04-01

    ...) Identification. An annuloplasty ring is a rigid or flexible ring implanted around the mitral or tricuspid heart valve for reconstructive treatment of valvular insufficiency. (b) Classification. Class II (special...

  20. International Tree Ring Data Bank (ITRDB)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives. Data include raw treering measurements (most are...

  1. Planetary ring systems properties, structures, and evolution

    CERN Document Server

    Murray, Carl D

    2018-01-01

    Planetary rings are among the most intriguing structures of our solar system and have fascinated generations of astronomers. Collating emerging knowledge in the field, this volume reviews our current understanding of ring systems with reference to the rings of Saturn, Uranus, Neptune, and more. Written by leading experts, the history of ring research and the basics of ring–particle orbits is followed by a review of the known planetary ring systems. All aspects of ring system science are described in detail, including specific dynamical processes, types of structures, thermal properties and their origins, and investigations using computer simulations and laboratory experiments. The concluding chapters discuss the prospects of future missions to planetary rings, the ways in which ring science informs and is informed by the study of other astrophysical disks, and a perspective on the field's future. Researchers of all levels will benefit from this thorough and engaging presentation.

  2. Vortex rings in classical and quantum systems

    International Nuclear Information System (INIS)

    Barenghi, C F; Donnelly, R J

    2009-01-01

    The study of vortex rings has been pursued for decades and is a particularly difficult subject. However, the discovery of quantized vortex rings in superfluid helium has greatly increased interest in vortex rings with very thin cores. While rapid progress has been made in the simulation of quantized vortex rings, there has not been comparable progress in laboratory studies of vortex rings in a viscous fluid such as water. This article overviews the history and current frontiers of classical and quantum vortex rings. After introducing the classical results, this review discusses thin-cored vortex rings in superfluid helium in section 2, and recent progress in understanding vortex rings of very thin cores propagating in water in section 3. (invited paper)

  3. Mathematical simulation of bearing ring grinding process

    Science.gov (United States)

    Koltunov, I. I.; Gorbunova, T. N.; Tumanova, M. B.

    2018-03-01

    The paper suggests the method of forming a solid finite element model of the bearing ring. Implementation of the model allowed one to evaluate the influence of the inner cylindrical surface grinding scheme on the ring shape error.

  4. Dynamics of long ring Raman fiber laser

    Science.gov (United States)

    Sukhanov, Sergey V.; Melnikov, Leonid A.; Mazhirina, Yulia A.

    2016-04-01

    The numerical model for dynamics of long fiber ring Raman laser is proposed. The model is based on the transport equations and Courant-Isaacson-Rees numerical method. Different regimes of a long ring fiber Raman laser are investigated.

  5. Genetics Home Reference: ring chromosome 20 syndrome

    Science.gov (United States)

    ... drugs. Prolonged seizure episodes known as non-convulsive status epilepticus also appear to be characteristic of ring chromosome ... K, Takahashi Y. Ring chromosome 20 and nonconvulsive status epilepticus. A new epileptic syndrome. Brain. 1997 Jun;120 ( ...

  6. Nonlinear analysis of ring oscillator circuits

    KAUST Repository

    Ge, Xiaoqing

    2010-06-01

    Using nonlinear systems techniques, we analyze the stability properties and synchronization conditions for ring oscillator circuits, which are essential building blocks in digital systems. By making use of its cyclic structure, we investigate local and global stability properties of an n-stage ring oscillator. We present a sufficient condition for global asymptotic stability of the origin and obtain necessity if the ring oscillator consists of identical inverter elements. We then give a synchronization condition for identical interconnected ring oscillators.

  7. On P-coherent endomorphism rings

    Indian Academy of Sciences (India)

    A ring is called right -coherent if every principal right ideal is finitely presented. Let M R be a right -module. We study the -coherence of the endomorphism ring of M R . It is shown that is a right -coherent ring if and only if every endomorphism of M R has a pseudokernel in add M R ; S is a left -coherent ring if and ...

  8. Nonlinear analysis of ring oscillator circuits

    KAUST Repository

    Ge, Xiaoqing; Arcak, Murat; Salama, Khaled N.

    2010-01-01

    Using nonlinear systems techniques, we analyze the stability properties and synchronization conditions for ring oscillator circuits, which are essential building blocks in digital systems. By making use of its cyclic structure, we investigate local and global stability properties of an n-stage ring oscillator. We present a sufficient condition for global asymptotic stability of the origin and obtain necessity if the ring oscillator consists of identical inverter elements. We then give a synchronization condition for identical interconnected ring oscillators.

  9. Beam dynamic issues in TESLA damping ring

    International Nuclear Information System (INIS)

    Shiltsev, V.

    1996-05-01

    In this paper we study general requirements on impedances of the linear collider TESLA damping ring design. Quantitative consideration is performed for 17-km long ''dog-bone'' ring. Beam dynamics in alternative options of 6.3 and 2.3-km long damping rings is briefly discussed. 5 refs., 2 tabs

  10. IAG ring test animal proteins 2014

    NARCIS (Netherlands)

    Raamsdonk, van L.W.D.; Pinckaers, V.G.Z.; Scholtens-Toma, I.M.J.; Prins, T.W.; Voet, van der H.; Vliege, J.J.M.

    2014-01-01

    A ring test was organized for the detection of animal proteins in animal feed by microscopy in the framework of the annual ring tests of the IAG – International Association for Feeding stuff Analysis, Section Feeding stuff Microscopy. The aim of the ring study was to provide the participants

  11. IAG ring test animal proteins 2015

    NARCIS (Netherlands)

    Raamsdonk, van L.W.D.; Rhee, van de N.E.; Scholtens-Toma, I.M.J.; Prins, T.W.; Vliege, J.J.M.; Pinckaers, V.G.Z.

    2015-01-01

    A ring test was organized for the detection of animal proteins in animal feed by microscopy in the framework of the annual ring tests of the IAG - International Association for Feeding stuff Analysis, Section Feeding stuff Microscopy. The organizer of the ring test was RIKILT - Wageningen UR, The

  12. IAG ring test animal proteins 2013

    NARCIS (Netherlands)

    Raamsdonk, van L.W.D.; Pinckaers, V.G.Z.; Scholtens-Toma, I.M.J.; Prins, T.W.; Vliege, J.J.M.

    2013-01-01

    A ring test was organized for the detection of animal proteins in animal feed by microscopy in the framework of the annual ring tests of the IAG - International Association for Feeding stuff Analysis, Section Feeding stuff Microscopy. The organizer of the the ring study was to provide the

  13. Self-gravitation in Saturn's rings

    International Nuclear Information System (INIS)

    Salo, H.; Lukkari, J.

    1982-01-01

    In a ring-shaped collisional system self-gravitation reduces the equilibrium values of the geometric and optical thickness. In Saturn's rings both effects are appreciable. The previously found discrepancy between the calculated profile and the observed profile of the rings is chiefly caused by the omission of self-gravitation. (Auth.)

  14. Domain structures of LiNbO3 crystals grown by a floating zone technique

    International Nuclear Information System (INIS)

    Kawakami, Shoji; Ishii, Eiichi; Tsuzuki, Akihiro; Sekiya, Tadashi; Torii, Yasuyoshi; Takahashi, Akio.

    1986-01-01

    LiNbO 3 single crystals were grown from the congruently melting composition by a floating zone technique. It was confirmed by etching that the single domain crystals were produced without applying any external electric field. When annealed above the Curie temperature, antiparallel domain appeared in the form of annual rings. (author)

  15. Aromatic amino acids in the cellulose binding domain of Penicillium crustosum endoglucanase EGL1 differentially contribute to the cellulose affinity of the enzyme.

    Directory of Open Access Journals (Sweden)

    Jiang-Ke Yang

    Full Text Available The cellulose binding domain (CBD of cellulase binding to cellulosic materials is the initiation of a synergistic action on the enzymatic hydrolysis of the most abundant renewable biomass resources in nature. The binding of the CBD domain to cellulosic substrates generally relies on the interaction between the aromatic amino acids structurally located on the flat face of the CBD domain and the glucose rings of cellulose. In this study, we found the CBD domain of a newly cloned Penicillium crustosum endoglucanase EGL1, which was phylogenetically related to Aspergillus, Fusarium and Rhizopus, and divergent from the well-characterized Trichoderma reeseis cellulase CBD domain, contain two conserved aromatic amino acid-rich regions, Y451-Y452 and Y477-Y478-Y479, among which three amino acids Y451, Y477, and Y478 structurally sited on a flat face of this domain. Cellulose binding assays with green fluorescence protein as the marker, adsorption isotherm assays and an isothermal titration calorimetry assays revealed that although these three amino acids participated in this process, the Y451-Y452 appears to contribute more to the cellulose binding than Y477-Y478-Y479. Further glycine scanning mutagenesis and structural modelling revealed that the binding between CBD domain and cellulosic materials might be multi-amino-acids that participated in this process. The flexible poly-glucose molecule could contact Y451, Y477, and Y478 which form the contacting flat face of CBD domain as the typical model, some other amino acids in or outside the flat face might also participate in the interaction. Thus, it is possible that the conserved Y451-Y452 of CBD might have a higher chance of contacting the cellulosic substrates, contributing more to the affinity of CBD than the other amino acids.

  16. Ultrasonic Resonance Spectroscopy of Composite Rings for Flywheel Rotors

    Science.gov (United States)

    Harmon, Laura M.; Baaklini, George Y.

    2001-01-01

    Flywheel energy storage devices comprising multilayered composite rotor systems are being studied extensively for utilization in the International Space Station. These composite material systems were investigated with a recently developed ultrasonic resonance spectroscopy technique. The system employs a swept frequency approach and performs a fast Fourier transform on the frequency spectrum of the response signal. In addition. the system allows for equalization of the frequency spectrum, providing all frequencies with equal amounts of energy to excite higher order resonant harmonics. Interpretation of the second fast Fourier transform, along with equalization of the frequency spectrum, offers greater assurance in acquiring and analyzing the fundamental frequency, or spectrum resonance spacing. The range of frequencies swept in a pitch-catch mode was varied up to 8 MHz, depending on the material and geometry of the component. Single and multilayered material samples, with and without known defects, were evaluated to determine how the constituents of a composite material system affect the resonant frequency. Amplitude and frequency changes in the spectrum and spectrum resonance spacing domains were examined from ultrasonic responses of a flat composite coupon, thin composite rings, and thick composite rings. Also, the ultrasonic spectroscopy responses from areas with an intentional delamination and a foreign material insert, similar to defects that may occur during manufacturing malfunctions, were compared with those from defect-free areas in thin composite rings. A thick composite ring with varying thickness was tested to investigate the full-thickness resonant frequency and any possible bulk interfacial bond issues. Finally, the effect on the frequency response of naturally occurring single and clustered voids in a composite ring was established.

  17. Fourth-generation storage rings

    International Nuclear Information System (INIS)

    Galayda, J. N.

    1999-01-01

    It seems clear that a linac-driven free-electron laser is the accepted prototype of a fourth-generation facility. This raises two questions: can a storage ring-based light source join the fourth generation? Has the storage ring evolved to its highest level of performance as a synchrotrons light source? The answer to the second question is clearly no. The author thinks the answer to the first question is unimportant. While the concept of generations has been useful in motivating thought and effort towards new light source concepts, the variety of light sources and their performance characteristics can no longer be usefully summed up by assignment of a ''generation'' number

  18. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  19. Spectroscopy of annular drums and quantum rings: Perturbative and nonperturbative results

    International Nuclear Information System (INIS)

    Alvarado, Carlos; Amore, Paolo

    2011-01-01

    We obtain systematic approximations to the states (energies and wave functions) of quantum rings (annular drums) of arbitrary shape by conformally mapping the annular domain to a simply connected domain. Extending the general results of Amore [J. Math. Phys. 51, 052105 (2010)], we obtain an analytical formula for the spectrum of quantum ring of arbitrary shape: for the cases of a circular annulus and of an asymmetric annulus considered here this formula is remarkably simple and precise. We also obtain precise variational bounds for the ground state of different quantum rings. Finally, we extend the conformal collocation method of Amore [J. Math. Phys. 51, 052105 (2010); J. Phys. A 41, 265206 (2008)] to the class of problems considered here and calculate precise numerical solutions for a large number of states (≅2000).

  20. ring mellem elever

    DEFF Research Database (Denmark)

    Davidsen, Jacob; Georgsen, Marianne

    I denne rapport tilbyder vi et indblik i det gennemførte projekt, og forfatterne har valgt nogle forhold ud, som belyses og diskuteres, mens andre ikke berøres eller diskuteres nævneværdigt i denne rapport. Det skyldes blandt andet projektets mange facetter, som dækker både læring, teknologi, pæd...

  1. ring mellem elever

    DEFF Research Database (Denmark)

    Georgsen, Marianne; Davidsen, Jacob

    2010-01-01

    I denne rapport præsenteres resultater fra følgeforskningen til projektet Læring gennem Bevægelse, som er gennemført på Søndervangskolen i Hammel i perioden august 2009 - maj 2010. Projektet er gennemført i samspil mellem lærere, it-vejleder, elever og skolens ledelse. Projektets overordnede formål...

  2. Two superconducting storage rings: ISABELLE

    International Nuclear Information System (INIS)

    Sanford, J.R.

    1978-01-01

    The general features of the design and the status of the ISABELLE storage ring project at the present time are reported. It brings up to date the results reported at the National Particle Accelerator Conference in March 1977. The most significant change since that time has been an upgrading of the energy of the overall facility, and acceptance of the project by the Department of Energy

  3. ring og it

    DEFF Research Database (Denmark)

      Antologien er et bidrag til didaktiske diskussioner om brug af f.eks. programpakker til sprogundervisning, præsentationsprogrammel og konferencesystemer på de videregående uddannelser. Antologien diskuterer ideen om, at multimediale medier og internettet kan understøtte læring, undervisning og ...... samarbejde ud fra konkrete eksempler på it-anvendelser, hvor fokus er på potentialer, barrierer og faldgruber....

  4. Carbon-14 in tree rings

    International Nuclear Information System (INIS)

    Cain, W.F.; Suess, H.E.

    1976-01-01

    In order to investigate how reliably the carbon 14 content of tree rings reflects that of atmospheric carbon dioxide, two types of determinations were carried out: (1) carbon 14 determinations in annual rings from the beginning of this century until 1974 and (2) carbon 14 determinations in synchronous wood from the North American bristlecone pine and from European oak trees, dendrochronologically dated to have grown in the third and fourth century B.C. The first series of measurements showed that bomb-produced radiocarbon was incorporated in wood at a time when it was converted from sapwood to heartwood, whenever radiocarbon from bomb testing was present in the atmosphere. The second series showed that wood more than 2000 years old and grown on two different continents at different altitudes had, within the limits of experimental error, the same radiocarbon content. This work and other experimental evidence, obtained in part by other laboratories, show that tree rings reflect the average radiocarbon content of global atmospheric carbon dioxide accurately within several parts per mil. In rare cases, deviations of up to 10 parts per thousand may be possible. This means that a typical single radiocarbon date for wood or charcoal possesses an intrinsic uncertainty (viz., an estimated ''one-sigma error'' in addition to all the other errors) of the order of +-50 years. This intrinsic uncertainty is independent of the absolute age of the sample. More accurate dates can, in principle, be obtained by the so-called method of ''wiggle matching.''

  5. Evaluated Rayleigh integrals for pulsed planar expanding ring sources

    International Nuclear Information System (INIS)

    Warshaw, S.I.

    1985-01-01

    Time-domain analytic and semianalytic pressure fields acoustically radiated from expanding pulsed ring sources imbedded in a planar rigid baffle have been calculated. The source functions are radially symmetric delta-function distributions whose amplitude and argument have simple functional dependencies on radius and time. Certain cases yield closed analytic results, while others result in elliptic integrals, which are evaluated to high accuracy by Gauss-Chebyshev and modified Gauss-Legendre quadrature. These results are of value for calibrating computer simulations and convolution procedures, and estimating fields from more complex planar radiators. 3 refs., 4 figs

  6. Cell culture arrays using micron-sized ferromagnetic ring-shaped thin films

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Chen-Yu; Wei, Zung-Hang, E-mail: wei@pme.nthu.edu.tw [Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu City 300, Taiwan (China); Lai, Mei-Feng; Ger, Tzong-Rong [Institute of NanoEngineering and MicroSystems, National Tsing Hua University, Hsinchu City 300, Taiwan (China)

    2015-05-07

    Cell patterning has become an important technology for tissue engineering. In this research, domain walls are formed at the two ends of a ferromagnetic ring thin film after applying a strong external magnetic field, which can effectively attract magnetically labeled cells and control the position for biological cell. Magnetophoresis experiment was conducted to quantify the magnetic nanoparticle inside the cells. A ring-shaped magnetic thin films array was fabricated through photolithography. It is observed that magnetically labeled cells can be successfully attracted to the two ends of the ring-shaped magnetic thin film structure and more cells were attracted and further attached to the structures. The cells are co-cultured with the structure and kept proliferating; therefore, such ring thin film can be an important candidate for in-vitro biomedical chips or tissue engineering.

  7. Cell culture arrays using micron-sized ferromagnetic ring-shaped thin films

    International Nuclear Information System (INIS)

    Huang, Chen-Yu; Wei, Zung-Hang; Lai, Mei-Feng; Ger, Tzong-Rong

    2015-01-01

    Cell patterning has become an important technology for tissue engineering. In this research, domain walls are formed at the two ends of a ferromagnetic ring thin film after applying a strong external magnetic field, which can effectively attract magnetically labeled cells and control the position for biological cell. Magnetophoresis experiment was conducted to quantify the magnetic nanoparticle inside the cells. A ring-shaped magnetic thin films array was fabricated through photolithography. It is observed that magnetically labeled cells can be successfully attracted to the two ends of the ring-shaped magnetic thin film structure and more cells were attracted and further attached to the structures. The cells are co-cultured with the structure and kept proliferating; therefore, such ring thin film can be an important candidate for in-vitro biomedical chips or tissue engineering

  8. Size dependence of magnetization reversal of ring shaped magnetic tunnel junction

    International Nuclear Information System (INIS)

    Chen, C.C.; Kuo, C.Y.; Chang, Y.C.; Chang, C.C.; Horng, Lance; Wu, Teho; Chern, G.; Huang, C.Y.; Tsunoda, M.; Takahashi, M.; Wu, J.C.

    2007-01-01

    The size dependence of magnetization reversal of magnetic tunnel junction (MTJ) rings has been investigated. The MTJ rings, with outer diameter of 4, 2 and 1 μm and inner diameter of 1.5, 1 and 0.5 μm were fabricated by a top-down technique. The magnetoresistance curves manifest all of the magnetic domain configurations during magnetization reversal in different sized rings. Various transition processes were observed, such as four transition, three transition and two transition in the largest, middle and smallest MTJ ring, respectively. Furthermore, the biasing fields observed from major loops decrease with decreasing size, which may result from edge roughness produced in the ion-milling process

  9. Evidence for Quantisation in Planetary Ring Systems

    OpenAIRE

    WAYTE, RICHARD

    2017-01-01

    Absolute radial positions of the main features in Saturn's ring system have been calculated by adapting the quantum theory of atomic spectra. Fine rings superimposed upon broad rings are found to be covered by a harmonic series of the form N α A(r)1/2, where N and A are integers. Fourier analysis of the ring system shows that the spectral amplitude fits a response profile which is characteristic of a resonant system. Rings of Jupiter, Uranus and Neptune also obey the same rules. Involvement o...

  10. Vaginal rings for delivery of HIV microbicides.

    Science.gov (United States)

    Malcolm, R Karl; Fetherston, Susan M; McCoy, Clare F; Boyd, Peter; Major, Ian

    2012-01-01

    Following the successful development of long-acting steroid-releasing vaginal ring devices for the treatment of menopausal symptoms and contraception, there is now considerable interest in applying similar devices to the controlled release of microbicides against HIV. In this review article, the vaginal ring concept is first considered within the wider context of the early advances in controlled-release technology, before describing the various types of ring device available today. The remainder of the article highlights the key developments in HIV microbicide-releasing vaginal rings, with a particular focus on the dapivirine ring that is presently in late-stage clinical testing.

  11. WW Domain Folding Complexity Revealed by Infrared Spectroscopy

    OpenAIRE

    Davis, Caitlin M.; Dyer, R. Brian

    2014-01-01

    Although the intrinsic tryptophan fluorescence of proteins offers a convenient probe of protein folding, interpretation of the fluorescence spectrum is often difficult because it is sensitive to both global and local changes. Infrared (IR) spectroscopy offers a complementary measure of structural changes involved in protein folding, because it probes changes in the secondary structure of the protein backbone. Here we demonstrate the advantages of using multiple probes, infrared and fluorescen...

  12. Leapfrogging of multiple coaxial viscous vortex rings

    International Nuclear Information System (INIS)

    Cheng, M.; Lou, J.; Lim, T. T.

    2015-01-01

    A recent theoretical study [Borisov, Kilin, and Mamaev, “The dynamics of vortex rings: Leapfrogging, choreographies and the stability problem,” Regular Chaotic Dyn. 18, 33 (2013); Borisov et al., “The dynamics of vortex rings: Leapfrogging in an ideal and viscous fluid,” Fluid Dyn. Res. 46, 031415 (2014)] shows that when three coaxial vortex rings travel in the same direction in an incompressible ideal fluid, each of the vortex rings alternately slips through (or leapfrogs) the other two ahead. Here, we use a lattice Boltzmann method to simulate viscous vortex rings with an identical initial circulation, radius, and separation distance with the aim of studying how viscous effect influences the outcomes of the leapfrogging process. For the case of two identical vortex rings, our computation shows that leapfrogging can be achieved only under certain favorable conditions, which depend on Reynolds number, vortex core size, and initial separation distance between the two rings. For the case of three coaxial vortex rings, the result differs from the inviscid model and shows that the second vortex ring always slips through the leading ring first, followed by the third ring slipping through the other two ahead. A simple physical model is proposed to explain the observed behavior

  13. Evaluation of the two-photon absorption characteristics of GaSb/GaAs quantum rings

    Energy Technology Data Exchange (ETDEWEB)

    Wagener, M. C.; Botha, J. R. [Department of Physics, Nelson Mandela Metropolitan University, Port Elizabeth 6031 (South Africa); Carrington, P. J. [Department of Electronic and Electrical Engineering, University College London, London (United Kingdom); Krier, A. [Department of Physics, Lancaster University, Lancaster LA1 4YB (United Kingdom)

    2014-07-28

    The optical parameters describing the sub-bandgap response of GaSb/GaAs quantum rings solar cells have been obtained from photocurrent measurements using a modulated pseudo-monochromatic light source in combination with a second, continuous photo-filling source. By controlling the charge state of the quantum rings, the photoemission cross-sections describing the two-photon sub-bandgap transitions could be determined independently. Temperature dependent photo-response measurements also revealed that the barrier for thermal hole emission from the quantum rings is significantly below the quantum ring localisation energy. The temperature dependence of the sub-bandgap photo-response of the solar cell is also described in terms of the photo- and thermal-emission characteristics of the quantum rings.

  14. Schatzki ring in children and young adults: clinical and radiologic findings

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, K.; Buonomo, C. [Department of Radiology, Children`s Hospital, Boston, MA (United States); Husain, K.; Nurko, S. [Division of Gastroenterology, Children`s Hospital, Boston, MA (United States)

    1998-11-01

    Background. The Schatzki ring is a well-known clinical and radiologic entity in adults, but is thought to be rare in childhood. Objective. To review the clinical presentations and radiologic findings of children and young adults with Schatzki rings. Materials and methods. A retrospective review of all barium swallow examinations done between 1990 and 1996 revealed 20 patients with Schatzki rings. Results. The most frequent presenting symptoms of these patients were progressive dysphagia with solid food and acute food impaction. Radiographic findings of Schatzki rings were typical in all cases. Twelve patients had endoscopy and all had evidence of esophagitis. Conclusion. Schatzki rings are not rare in childhood. The patients are symptomatic, presenting with either progressive dysphagia with solids or acute food impaction. A thorough evaluation of the distal esophagus should be performed in patients with a suggestive clinical history. (orig.) With 2 figs., 8 refs.

  15. METER-SIZED MOONLET POPULATION IN SATURN'S C RING AND CASSINI DIVISION

    International Nuclear Information System (INIS)

    Baillié, Kévin; Colwell, Joshua E.; Esposito, Larry W.; Lewis, Mark C.

    2013-01-01

    Stellar occultations observed by the Cassini Ultraviolet Imaging Spectrograph reveal the presence of transparent holes a few meters to a few tens of meters in radial extent in otherwise optically thick regions of the C ring and the Cassini Division. We attribute the holes to gravitational disturbances generated by a population of ∼10 m boulders in the rings that is intermediate in size between the background ring particle size distribution and the previously observed ∼100 m propeller moonlets in the A ring. The size distribution of these boulders is described by a shallower power-law than the one that describes the ring particle size distribution. The number and size distribution of these boulders could be explained by limited accretion processes deep within Saturn's Roche zone.

  16. Fabrication and Characterization of Ultrathin-ring Electrodes for Pseudo-steady-state Amperometric Detection.

    Science.gov (United States)

    Kitazumi, Yuki; Hamamoto, Katsumi; Noda, Tatsuo; Shirai, Osamu; Kano, Kenji

    2015-01-01

    The fabrication of ultrathin-ring electrodes with a diameter of 2 mm and a thickness of 100 nm is established. The ultrathin-ring electrodes provide a large density of pseudo-steady-state currents, and realize pseudo-steady-state amperometry under quiescent conditions without a Faraday cage. Under the limiting current conditions, the current response at the ultrathin-ring electrode can be well explained by the theory of the microband electrode response. Cyclic voltammograms at the ultrathin-ring electrode show sigmoidal characteristics with some hysteresis. Numerical simulation reveals that the hysteresis can be ascribed to the time-dependence of pseudo-steady-state current. The performance of amperometry with the ultrathin-ring electrode has been verified in its application to redox enzyme kinetic measurements.

  17. Plasma-ring, fast-opening switch

    International Nuclear Information System (INIS)

    Hartman, C.W.; Eddleman, J.; Hammer, J.H.

    1986-01-01

    The authors discuss a fast-opening switch concept based on magnetically confined plasma rings, PROS (for Plasma Ring Opening Switch). In PROS, the plasma ring, confined by Bθ /sub and B/poloidal /sub fields of a compact torus, provide a low mass, localized conduction path between coaxial electrodes. To operate the switch, driver current is passed across the electrodes through the ring, storing inductive energy in external inductance and between the electrodes on the driver side of the ring. The ring is accelerated away from the driver by the field of the driver current and passes over a load gap transferring the current to the load. The authors distinguish two configurations in PROS, straight PROS where the electrodes are coaxial cylinders, and cone PROS with conical electrodes. In straight PROS ring acceleration takes place during the inductive store period as in foil switches, but with the localized ring providing the current path. Increased performance is predicted for the cone PROS (see figure) which employs compression of the ring in the cone during the inductive store period. Here, the B/θ /sub field of the driver forces the ring towards the apex of the cone but the force is in near balance with the opposing component of the radial equilibrium force of the ring along the cone. As a result, the ring undergoes a slow, quasistatic compression limited only by resistive decay of the ring field. Slow compression allows inductive storage with low-power drivers (homopoloar, magneto cumulative generators, high C-low V capacitor banks, etc.). Near the apex of the cone, near peak compression, the ring is allowed to enter a straight coaxial section where, because of low-mass, it rapidly accelerates to high velocity and crosses the load gap

  18. Variations in Ring Particle Cooling across Saturn's Rings with Cassini CIRS

    Science.gov (United States)

    Brooks, S. M.; Spilker, L. J.; Pilorz, S.; Edgington, S. G.; Déau, E.; Altobelli, N.

    2010-12-01

    Cassini's Composite Infrared Spectrometer has recorded over two million of spectra of Saturn's rings in the far infrared since arriving at Saturn in 2004. CIRS records far infrared radiation between 10 and 600 cm-1 ( 16.7 and 1000 μ {m} ) at focal plane 1 (FP1), which has a field of view of 3.9 mrad. Thermal emission from Saturn’s rings peaks in this wavelength range. Ring temperatures can be inferred from FP1 data. By tracking how ring temperatures vary, we can determine the thermal inertia of the rings. Previous studies have shown that the rings' thermal inertia, a measure of their response to changes in the thermal environment, varies from ring to ring. Thermal inertia can provide insight into the physical structure of Saturn's ring particles and their regoliths. Low thermal inertia and rapidly changing temperatures are suggestive of ring particles that have more porous or fluffy regoliths or that are riddled with cracks. Solid particles can be expected to have higher thermal inertias. Ferrari et al. (2005) fit thermal inertia values of 5218 {Jm)-2 {K}-1 {s}-1/2 to their B ring data and 6412 {Jm)-2 {K}-1 {s}-1/2 to their C ring data. In this work we focus on CIRS observations of the shadowed portion of Saturn's rings. The rings’ thermal budget is dominated by its absorption of solar radiation. As a result, ring particles abruptly cool as they traverse Saturn's shadow. From these shadow observations we can create cooling curves at specific locations across the rings. We will show that the rings' cooling curves and thus their thermal inertia vary not only from ring to ring, but by location within the individual rings. This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA. Copyright 2010 California Institute of Technology. Government sponsorship acknowledged.

  19. The dynamics of rings around small, irregular bodies

    Science.gov (United States)

    Sicardy, Bruno

    2017-06-01

    Stellar occultations revealed the presence of two dense rings around the Centaur object (10199) Chariklo (Braga-Ribas et al., Nature 508, 72, 2014). This is the first ring system discovered around an object that is not a giant planet, suggesting that rings may exist around numerous bodies in the solar system. Chariklo's rings roughly reside at the outer limit of the Roche zone of the body. Moreover, the main ring has sharp edges, which call for the presence of putative shepherd satellites. Those characteristics give an image of Chariklo's rings that are rather similar, in terms of dynamics, to those surrounding the gaseous planets.An important difference exists, however, between giant planets and small bodies: the formers are highly axisymmetric, while the latters can support mass anomalies (eg surface topographic features) or non-spherical shapes (eg an ellipsoidal figure of equilibrium) that involve masses, relative to the body itself, as large as 10-4-10-3.We investigate the effect of non-axisymmetric terms in the potential of the body upon a collisional debris disk that initially surrounds a small irregular body. We show that the corotation points being maxima of energy, dissipative collisions remove the particles from the corotation zone over short time scales (< 106 years). Moreover, the Lindblad resonances inside the corotation radius create torques that drive the particles onto the surface of the central body. Conversely, the outer Lindblad resonances push the disk material beyond the outer 3/2 and 2/1 Lindblad resonances.Taking as an example Chariklo's ring system, for which recent data have been obtained from stellar occultations, we show that the Lindblad resonant torques actuate over short time scales (< 106 years). This general picture offers a natural explanation of the presence of dense rings at the outer limit of Chariklo's Roche zone, and their absence closer to the body.The work leading to this results has received funding from the European

  20. Characterization of domain reorientation in Pzt ceramics

    International Nuclear Information System (INIS)

    Lente, Manuel Henrique; Povoa, Jose Marques; Eiras, Jose Antonio

    1997-01-01

    The dynamic of domains in ferroelectric materials has been intensively studied due to its importance in applications like non volatile memories. Domain reorientation was characterized in lead zirconate titanate samples, pure and doped, through measurements of the transient current, after reversal a electric field. The reorientation behavior of the domains showed to be influenced by type of impurity (Nb or Fe) and by the electrical field intensity. Analysis of the experimental results reveals mainly the existence of two contributions: a dependent (t 0.1 s) of the field intensity. (author)

  1. Proton accumulator ring injection studies

    International Nuclear Information System (INIS)

    Cooper, R.K.; Neil, V.K.

    1977-01-01

    Protons may be created in an accelerator or storage ring by stripping electrons from neutral hydrogen atoms that have been injected into the machine. Because Liouville's theorem is violated by this type of injection, particles may be continually injected into a region of phase space that is already populated, and the density in that region increases with time. A computational investigation was made of the evolution of the distribution of particles in longitudinal phase space during such an injection process for a storage ring operating below the transition energy. In one calculation, an rf cavity is present in the ring and particles are injected into the stable phase region once each revolution. The purpose of this calculation is to determine the rf voltage necessary to overcome the longitudinal self-forces and contain the particles within the region of stable phase. In a second calculation, the rf is turned off, so that there is spreading in azimuth of the injected particles (i.e., de-bunching). The de-bunching occurs because of the initial energy spread and the action of the self-forces. One purpose of the calculation is to determine the total energy spread after a given number of revolutions. Another purpose is to elucidate the effect of finite resistance in the vacuum tank walls. For sufficiently high current, the finite resistance can cause bunching of a beam that is initially uniform in azimuth. Therefore it might be expected that the finite resistance would inhibit or prevent de-bunching once the number of particles injected reaches some threshold, and that this threshold would depend upon the energy spread in the beam

  2. 3-D studies of the formation and stability of strong ion rings

    International Nuclear Information System (INIS)

    Omelchenko, Yu.A.; Sudan, R.N.

    1996-01-01

    Complex 3-D simulations were conducted in support of the on-going experimental program, FIREX( (Field-Reversed Ion Ring Experiment) launched at the Cornell University to produce an ion ring magnetic field-reversed configuration by injecting an intense annular proton beam across a plasma-filled magnetic cusp region into a neutral gas immersed in a ramped solenoidal magnetic field. Previous axisymmetric PIC simulations performed with the FIRE code have demonstrated that strong ion rings (with a self-magnetic field large enough to reverse the applied field on axis) can be created using this technique on the equipment designed and assembled at Cornell. A new parallel object-oriented 3-D hybrid PIC code FLAME has been created to study questions of extreme importance to the success of the FIREX program, namely, the 3-D injection of a powerful ion beam into a strongly magnetized plasma, formation of a field-reversed ring, and the stability and equilibrium of such rings to toroidal perturbations. Using FLAME, the stability was studied of the ring formation during the injection phase and at later times when the ring is virtually stopped and the applied magnetic field is nearly reversed. The simulations revealed the effect of toroidal aberrations in the axially ramped magnetic field on the ion ring formation. (author). 4 figs., 4 refs

  3. 3-D studies of the formation and stability of strong ion rings

    Energy Technology Data Exchange (ETDEWEB)

    Omelchenko, Yu A; Sudan, R N [Cornell Univ., Ithaca, NY (United States). Laboratory of Plasma Studies

    1997-12-31

    Complex 3-D simulations were conducted in support of the on-going experimental program, FIREX( (Field-Reversed Ion Ring Experiment) launched at the Cornell University to produce an ion ring magnetic field-reversed configuration by injecting an intense annular proton beam across a plasma-filled magnetic cusp region into a neutral gas immersed in a ramped solenoidal magnetic field. Previous axisymmetric PIC simulations performed with the FIRE code have demonstrated that strong ion rings (with a self-magnetic field large enough to reverse the applied field on axis) can be created using this technique on the equipment designed and assembled at Cornell. A new parallel object-oriented 3-D hybrid PIC code FLAME has been created to study questions of extreme importance to the success of the FIREX program, namely, the 3-D injection of a powerful ion beam into a strongly magnetized plasma, formation of a field-reversed ring, and the stability and equilibrium of such rings to toroidal perturbations. Using FLAME, the stability was studied of the ring formation during the injection phase and at later times when the ring is virtually stopped and the applied magnetic field is nearly reversed. The simulations revealed the effect of toroidal aberrations in the axially ramped magnetic field on the ion ring formation. (author). 4 figs., 4 refs.

  4. Polyurethane Foams with Pyrimidine Rings

    Directory of Open Access Journals (Sweden)

    Kania Ewelina

    2014-09-01

    Full Text Available Oligoetherols based on pyrimidine ring were obtained upon reaction of barbituric acid with glycidol and alkylene carbonates. These oligoetherols were then used to obtain polyurethane foams in the reaction of oligoetherols with isocyanates and water. The protocol of foam synthesis was optimized by the choice of proper kind of oligoetherol and synthetic composition. The thermal resistance was studied by dynamic and static methods with concomitant monitoring of compressive strength. The polyurethane foams have similar physical properties as the classic ones except their enhanced thermal resistance. They stand long-time heating even at 200°C. Moreover thermal exposition of foams results generally in increase of their compressive strength.

  5. Longitudinal dynamics in storage rings

    International Nuclear Information System (INIS)

    Colton, E.P.

    1986-01-01

    The single-particle equations of motion are derived for charged particles in a storage ring. Longitudinal space charge is included in the potential assuming an infinitely conducting circular beam pipe with a distributed inductance. The framework uses Hamilton's equations with the canonical variables phi and W. The Twiss parameters for longitudinal motion are also defined for the small amplitude synchrotron oscillations. The space-charge Hamiltonian is calculated for both parabolic bunches and ''matched'' bunches. A brief analysis including second-harmonic rf contributions is also given. The final sections supply calculations of dynamical quantities and particle simulations with the space-charge effects neglected

  6. Storage ring proton EDM experiment

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    sensitivity of 10^-29 e-cm.  The strength of the method originates from the fact that there are high intensity polarized proton beams available and the fact that the so-called geometric phase systematic error background cancels with clock-wise and counter-clock-wise storage possible in electric rings. The ultimate sensitivity of the method is 10^-30 e-cm. At this level it will either detect a non-zero EDM or it will eliminate electro-weak baryogenesis.

  7. Ring with changeable radiation dosimeter

    International Nuclear Information System (INIS)

    Collica, C.; Epifano, L.; Farella, R.

    1976-01-01

    A ring for housing a disc of radiation measuring material is described comprising a band having a circular shape and a housing integral with the band. The housing comprises a hollow cylindrical section substantially normal to the band surface and terminating in an inwardly disposed annular flange which defines a substantially circular aperture. In a preferred embodiment of the invention a retaining protrusion formed on the inside of the cylindrical section and spaced from the annular flange is provided to retain a plurality of discs mounted in the housing in layered fashion

  8. Ring magnet firing angle control

    International Nuclear Information System (INIS)

    Knott, M.J.; Lewis, L.G.; Rabe, H.H.

    1975-01-01

    A device is provided for controlling the firing angles of thyratrons (rectifiers) in a ring magnet power supply. A phase lock loop develops a smooth ac signal of frequency equal to and in phase with the frequency of the voltage wave developed by the main generator of the power supply. A counter that counts from zero to a particular number each cycle of the main generator voltage wave is synchronized with the smooth AC signal of the phase lock loop. Gates compare the number in the counter with predetermined desired firing angles for each thyratron and with coincidence the proper thyratron is fired at the predetermined firing angle

  9. Interaction of Vortex Ring with Cutting Plate

    Science.gov (United States)

    Musta, Mustafa

    2015-11-01

    The interaction of a vortex ring impinging on a thin cutting plate was made experimentally using Volumetric 3-component Velocitmetry (v3v) technique. The vortex rings were generated with piston-cylinder vortex ring generator using piston stroke-to-diameter ratios and Re at 2-3 and 1500 - 3000, respectively. The cutting of vortex rings below center line leads to the formation of secondary vortices on each side of the plate which is look like two vortex rings, and a third vortex ring propagates further downstream in the direction of the initial vortex ring, which is previously showed by flow visualization study of Weigand (1993) and called ``trifurcation''. Trifurcation is very sensitive to the initial Reynolds number and the position of the plate with respect to the vortex ring generator pipe. The present work seeks more detailed investigation on the trifurcation using V3V technique. Conditions for the formation of trifurcation is analyzed and compared with Weigand (1993). The formed secondary vortex rings and the propagation of initial vortex ring in the downstream of the plate are analyzed by calculating their circulation, energy and trajectories.

  10. A structural analysis of the AAA+ domains in Saccharomyces cerevisiae cytoplasmic dynein.

    Science.gov (United States)

    Gleave, Emma S; Schmidt, Helgo; Carter, Andrew P

    2014-06-01

    Dyneins are large protein complexes that act as microtubule based molecular motors. The dynein heavy chain contains a motor domain which is a member of the AAA+ protein family (ATPases Associated with diverse cellular Activities). Proteins of the AAA+ family show a diverse range of functionalities, but share a related core AAA+ domain, which often assembles into hexameric rings. Dynein is unusual because it has all six AAA+ domains linked together, in one long polypeptide. The dynein motor domain generates movement by coupling ATP driven conformational changes in the AAA+ ring to the swing of a motile element called the linker. Dynein binds to its microtubule track via a long antiparallel coiled-coil stalk that emanates from the AAA+ ring. Recently the first high resolution structures of the dynein motor domain were published. Here we provide a detailed structural analysis of the six AAA+ domains using our Saccharomycescerevisiae crystal structure. We describe how structural similarities in the dynein AAA+ domains suggest they share a common evolutionary origin. We analyse how the different AAA+ domains have diverged from each other. We discuss how this is related to the function of dynein as a motor protein and how the AAA+ domains of dynein compare to those of other AAA+ proteins. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  11. Detection and direction discrimination of single vortex rings by harbour seals (Phoca vitulina).

    Science.gov (United States)

    Krüger, Yvonne; Hanke, Wolf; Miersch, Lars; Dehnhardt, Guido

    2018-04-25

    Harbour seals possess highly sensitive vibrissae that enable them to track hydrodynamic trails left behind by a swimming fish. Most of these trails contain vortex rings as a main hydrodynamic component. They may reveal information about their generator as the trails differ depending on the fish species, the fish's body shape, size and swimming style. In addition, fish generate single vortex rings in diverse natural situations. In this study, the ability of blindfolded stationary harbour seals to detect and analyse single vortex rings regarding directional information has been investigated. In three different behavioural experiments, the animals were trained to respond to single artificially generated vortex rings. The results show that harbour seals are able to respond to a variety of different vortex rings upon vibrissal stimulation. The investigation of the minimum hydrodynamically perceivable angle revealed that it is at least as small as 5.7 deg, which was the smallest adjustable angle. Moreover, harbour seals are capable of analysing the travel direction of a vortex ring perceived by the mystacial vibrissae irrespective of whether the vibrissae were stimulated ipsilaterally or contralaterally. In situations in which no complex hydrodynamic trail is available, it is advantageous for a hunting seal to be able to extract information from a single vortex ring. © 2018. Published by The Company of Biologists Ltd.

  12. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

  13. Ring-enhancing spinal cord lesions in neuromyelitis optica spectrum disorders.

    Science.gov (United States)

    Zalewski, Nicholas L; Morris, Padraig P; Weinshenker, Brian G; Lucchinetti, Claudia F; Guo, Yong; Pittock, Sean J; Krecke, Karl N; Kaufmann, Timothy J; Wingerchuk, Dean M; Kumar, Neeraj; Flanagan, Eoin P

    2017-03-01

    We assessed the frequency and characteristics of ring-enhancing spinal cord lesions in neuromyelitis optica spectrum disorder (NMOSD) myelitis and myelitis of other cause. We reviewed spinal cord MRIs for ring-enhancing lesions from 284 aquaporin-4 (AQP4)-IgG seropositive patients at Mayo Clinic from 1996 to 2014. Inclusion criteria were as follows: (1) AQP4-IgG seropositivity, (2) myelitis attack and (3) MRI spinal cord demonstrating ring-enhancement. We identified two groups of control patients with: (1) longitudinally extensive myelopathy of other cause (n=66) and (2) myelitis in the context of a concurrent or subsequent diagnosis of multiple sclerosis (MS) from a population-based cohort (n=30). Ring-enhancement was detected in 50 of 156 (32%) myelitis episodes in 41 patients (83% single; 17% multiple attacks). Ring-enhancement was noted on sagittal and axial images in 36 of 43 (84%) ring enhancing myelitis episodes and extended a median of two vertebral segments (range, 1-12); in 21 of 48 (44%) ring enhancing myelitis episodes, the ring extended greater than or equal to three vertebrae. Ring-enhancement was accompanied by longitudinally extensive (greater than or equal to three vertebral segments) T2-hyperintensity in 44 of 50 (88%) ring enhancing myelitis episodes. One case of a spinal cord biopsy during ring-enhancing myelitis revealed tissue vacuolation and loss of AQP4 immunoreactivity with preserved axons. The clinical characteristics of ring-enhancing myelitis episodes did not differ from non-ring-enhancing episodes. Ring-enhancing spinal cord lesions were more common in NMOSD than other causes of longitudinally extensive myelopathy (50/156 (32%) vs 0/66 (0%); p≤0.001) but did not differ between NMOSD and MS (50/156 (32%) vs 6/30 (20%); p=0.20). Spinal cord ring-enhancement accompanies one-third of NMOSD myelitis episodes and distinguishes NMOSD from other causes of longitudinally extensive myelopathies but not from MS. Published by the BMJ Publishing

  14. Supersymmetric domain walls

    NARCIS (Netherlands)

    Bergshoeff, Eric A.; Kleinschmidt, Axel; Riccioni, Fabio

    2012-01-01

    We classify the half-supersymmetric "domain walls," i.e., branes of codimension one, in toroidally compactified IIA/IIB string theory and show to which gauged supergravity theory each of these domain walls belong. We use as input the requirement of supersymmetric Wess-Zumino terms, the properties of

  15. TRIM37 defective in mulibrey nanism is a novel RING finger ubiquitin E3 ligase

    International Nuclear Information System (INIS)

    Kallijaervi, Jukka; Lahtinen, Ulla; Haemaelaeinen, Riikka; Lipsanen-Nyman, Marita; Palvimo, Jorma J.; Lehesjoki, Anna-Elina

    2005-01-01

    Mulibrey nanism is an autosomal recessive prenatal-onset growth disorder characterized by dysmorphic features, cardiomyopathy, and hepatomegaly. Mutations in TRIM37 encoding a tripartite motif (TRIM, RING-B-box-coiled-coil)-family protein underlie mulibrey nanism. We investigated the ubiquitin ligase activity predicted for the RING domain of TRIM37 by analyzing its autoubiquitination. Full-length TRIM37 and its TRIM domain were highly polyubiquitinated when co-expressed with ubiquitin. Polyubiquitination was decreased in a mutant protein with disrupted RING domain (Cys35Ser;Cys36Ser) and in the Leu76Pro mutant protein, a disease-associated missense mutation affecting the TRIM domain of TRIM37. Bacterially produced GST-TRIM domain fusion protein, but not its Cys35Ser;Cys36Ser or Leu76Pro mutants, were polyubiquitinated in cell-free conditions, implying RING-dependent modification. Ubiquitin was also identified as an interaction partner for TRIM37 in a yeast two-hybrid screen. Ectopically expressed TRIM37 rapidly formed aggregates that were ubiquitin-, proteasome subunit-, and chaperone-positive in immunofluorescence analysis, defining them as aggresomes. The Cys35Ser;Cys36Ser mutant and the Leu76Pro and Gly322Val patient mutant proteins were markedly less prone to aggregation, implying that aggresomal targeting reflects a physiological function of TRIM37. These findings suggest that TRIM37 acts as a TRIM domain-dependent E3 ubiquitin ligase and imply defective ubiquitin-dependent degradation of an as-yet-unidentified target protein in the pathogenesis of mulibrey nanism

  16. Transformation of self-assembled InAs/InP quantum dots into quantum rings without capping.

    Science.gov (United States)

    Sormunen, Jaakko; Riikonen, Juha; Mattila, Marco; Tiilikainen, Jouni; Sopanen, Markku; Lipsanen, Harri

    2005-08-01

    Transformation of self-assembled InAs quantum dots (QDs) on InP(100) into quantum rings (QRs) is studied. In contrast to the typical approach to III--V semiconductor QR growth, the QDs are not capped to form rings. Atomic force micrographs reveal a drastic change from InAs QDs into rings after a growth interruption in tertiarybutylphosphine ambient. Strain energy relief in the InAs QD is discussed and a mechanism for dot-to-ring transformation by As/P exchange reactions is proposed.

  17. Liesegang rings in tissue. How to distinguish Liesegang rings from the giant kidney worm, Dioctophyma renale.

    Science.gov (United States)

    Tuur, S M; Nelson, A M; Gibson, D W; Neafie, R C; Johnson, F B; Mostofi, F K; Connor, D H

    1987-08-01

    Liesegang rings (LRs) are periodic precipitation zones from supersaturated solutions in colloidal systems. They are formed by a process that involves an interplay of diffusion, nucleation, flocculation or precipitation, and supersaturation. Examples include LRs of calcium carbonate in oölitic limestone (in nature), LRs of silver chromate in gelatin (in vitro), and LRs of glycoprotein in pulmonary corpora amylacea (in vivo). Here we describe LRs in lesions from 29 patients--mostly lesions of the kidney, synovium, conjunctiva, and eyelid. The LRs formed in cysts, or in fibrotic, inflamed, or necrotic tissue. The LRs in this study varied greatly in shape and size, measuring 7-800 microns. Special stains and energy-dispersive radiographic analysis or scanning electron microscopy revealed that some LRs contained calcium, iron (hemosiderin), silicon, and sulfur. Some pathologists have mistaken LRs for eggs, larvae, or adults of the giant kidney worm, Dioctophyma renale. D. renale is a large blood-red nematode that infects a variety of fish-eating mammals, especially mink. Fourteen documented infections of humans have been recorded, usually with adult worms expelled from the urethra. The adult worms are probably the largest helminth to parasitize humans. Eggs of D. renale are constant in size (60-80 microns X 39-47 microns), contain an embryo, and have characteristic sculpturing of the shell. Liesegang rings should not be mistaken for eggs, larvae, or adults of D. renale, or for any other helminth.

  18. Domain wall engineering through exchange bias

    International Nuclear Information System (INIS)

    Albisetti, E.; Petti, D.

    2016-01-01

    The control of the structure and position of magnetic domain walls is at the basis of the development of different magnetic devices and architectures. Several nanofabrication techniques have been proposed to geometrically confine and shape domain wall structures; however, a fine tuning of the position and micromagnetic configuration is hardly achieved, especially in continuous films. This work shows that, by controlling the unidirectional anisotropy of a continuous ferromagnetic film through exchange bias, domain walls whose spin arrangement is generally not favored by dipolar and exchange interactions can be created. Micromagnetic simulations reveal that the domain wall width, position and profile can be tuned by establishing an abrupt change in the direction and magnitude of the exchange bias field set in the system. - Highlights: • Micromagnetic simulations study domain walls in exchange biased thin films. • Novel domain wall configurations can be stabilized via exchange bias. • Domain walls nucleate at the boundary of regions with different exchange bias. • Domain wall width and spin profile are controlled by tuning the exchange bias.

  19. A ring D chromosome in association with Down's syndrome-like phenotype

    Directory of Open Access Journals (Sweden)

    A. Wajntal

    1973-03-01

    Full Text Available The case of a ten-years-old mentally retarded girl with Down's syndrome-like features whose chromosome analysis revealed an unusual mosaicism including 10% mitosis with a ring chromosome replacing a D chromosome is reported. The clinical features of the patient were considered similar to those described by Jacobsen (1966 and Emberger et al. (1971 who interpreted the ring chromosome present in their patients as being chromosome 15.

  20. Microstructure, texture, and magnetic properties of backward extruded NdFeB ring magnets

    International Nuclear Information System (INIS)

    Gruenberger, W.; Hinz, D.; Schlaefer, D.; Schultz, L.

    1996-01-01

    Radially-oriented NdFeB ring magnets have been prepared by backward extrusion of melt-spun material. The average remanence measured in the radial direction reaches values above 1.2 T. Due to the inhomogeneity of the deformation, the magnetic properties and X-ray diffraction patterns revealed a gradual improvement of the alignment from the outer shell to regions near the inner surface of the ring. (orig.)