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Sample records for s6 ring motif

  1. 2-[(2,4,4,6,6-Pentachloro-1,3,5,2λ5,4λ5,6λ5-triazatriphosphinin-2-ylazanidyl]pyridinium

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    Safaa A. Ahmed

    2012-02-01

    Full Text Available The title compound, C5H5Cl5N5P3, crystallizes as a zwitterion in which the pyridine N atom is protonated. An S(6 ring motif is formed via an intramolecular C—H...N hydrogen bond. The triazatriphosphinine ring adopts an envelope conformation, with one N atom displaced by 0.145 (1 Å from the other atoms. In the crystal, N—H...N and C—H...N hydrogen bonds link the molecules into centrosymmetric dimers containing one R22(7 ring motif and two R22(8 ring motifs.

  2. 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.

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    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.

  3. 7α-Methoxycarbonyl-6,7,8,14-tetrahydro-6,14-endo-ethenothebaine

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    Mustafa Odabaşoğlu

    2009-04-01

    Full Text Available In the molecule of the title compound, C23H27NO5, the furan ring adopts an envelope conformation. Intramolecular C—H...O interactions result in the formation of S(5 and S(6 motifs. In the crystal structure, weak intermolecular C—H...O hydrogen bonds link the molecules through C(6 and C(8 chains along the [100] and [010] directions, generating a two-dimensional network.

  4. Identification of the Raptor-binding motif on Arabidopsis S6 kinase and its use as a TOR signaling suppressor

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    Son, Ora; Kim, Sunghan; Hur, Yoon-Sun; Cheon, Choong-Ill, E-mail: ccheon@sookmyung.ac.kr

    2016-03-25

    TOR (target of rapamycin) kinase signaling plays central role as a regulator of growth and proliferation in all eukaryotic cells and its key signaling components and effectors are also conserved in plants. Unlike the mammalian and yeast counterparts, however, we found through yeast two-hybrid analysis that multiple regions of the Arabidopsis Raptor (regulatory associated protein of TOR) are required for binding to its substrate. We also identified that a 44-amino acid region at the N-terminal end of Arabidopsis ribosomal S6 kinase 1 (AtS6K1) specifically interacted with AtRaptor1, indicating that this region may contain a functional equivalent of the TOS (TOR-Signaling) motif present in the mammalian TOR substrates. Transient over-expression of this 44-amino acid fragment in Arabidopsis protoplasts resulted in significant decrease in rDNA transcription, demonstrating a feasibility of developing a new plant-specific TOR signaling inhibitor based upon perturbation of the Raptor-substrate interaction. - Highlights: • Multiple regions on the Arabidopsis Raptor protein were found to be involved in substrate binding. • N-terminal end of the Arabidopsis ribosomal S6 kinase 1 (AtS6K1) was responsible for interacting with AtRaptor1. • The Raptor-interacting fragment of AtS6K1 could be utilized as an effective inhibitor of plant TOR signaling.

  5. Identification of the Raptor-binding motif on Arabidopsis S6 kinase and its use as a TOR signaling suppressor

    International Nuclear Information System (INIS)

    Son, Ora; Kim, Sunghan; Hur, Yoon-Sun; Cheon, Choong-Ill

    2016-01-01

    TOR (target of rapamycin) kinase signaling plays central role as a regulator of growth and proliferation in all eukaryotic cells and its key signaling components and effectors are also conserved in plants. Unlike the mammalian and yeast counterparts, however, we found through yeast two-hybrid analysis that multiple regions of the Arabidopsis Raptor (regulatory associated protein of TOR) are required for binding to its substrate. We also identified that a 44-amino acid region at the N-terminal end of Arabidopsis ribosomal S6 kinase 1 (AtS6K1) specifically interacted with AtRaptor1, indicating that this region may contain a functional equivalent of the TOS (TOR-Signaling) motif present in the mammalian TOR substrates. Transient over-expression of this 44-amino acid fragment in Arabidopsis protoplasts resulted in significant decrease in rDNA transcription, demonstrating a feasibility of developing a new plant-specific TOR signaling inhibitor based upon perturbation of the Raptor-substrate interaction. - Highlights: • Multiple regions on the Arabidopsis Raptor protein were found to be involved in substrate binding. • N-terminal end of the Arabidopsis ribosomal S6 kinase 1 (AtS6K1) was responsible for interacting with AtRaptor1. • The Raptor-interacting fragment of AtS6K1 could be utilized as an effective inhibitor of plant TOR signaling.

  6. Crystal structure of 2-methylamino-4-(6-methyl-4-oxo-4H-chromen-3-yl-3-nitropyrano[3,2-c]chromen-5(4H-one with an unknown solvate

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    Rajamani Raja

    2015-09-01

    Full Text Available In the title compound, C23H16N2O7, the mean planes of the two chromene units (r.m.s. deviations = 0.031 and 0.064 Å are almost normal to one another with a dihedral angle of 85.59 (6°. The central six-membered pyran ring has a distorted envelope conformation, with the methine C atom at the flap. There is an intramolecular N—H...O hydrogen bond, which generates an S(6 ring motif. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(12 ring motif. The dimers are linked by pairs of C—H...O hydrogen bonds, enclosing R22(6 ring motifs, forming zigzag chains along [001]. The chains are linked by a second pair of C—H...O hydrogen bonds, forming slabs parallel to (110. Within the slabs there are C—H...π interactions present. A region of disordered electron density was treated with the SQUEEZE procedure in PLATON [Spek (2015. Acta Cryst. C71, 9–18] following unsuccessful attempts to model it as plausible solvent molecule(s. The given chemical formula and other crystal data do not take into account the unknown solvent molecule(s.

  7. Identification of the Raptor-binding motif on Arabidopsis S6 kinase and its use as a TOR signaling suppressor.

    Science.gov (United States)

    Son, Ora; Kim, Sunghan; Hur, Yoon-Sun; Cheon, Choong-Ill

    2016-03-25

    TOR (target of rapamycin) kinase signaling plays central role as a regulator of growth and proliferation in all eukaryotic cells and its key signaling components and effectors are also conserved in plants. Unlike the mammalian and yeast counterparts, however, we found through yeast two-hybrid analysis that multiple regions of the Arabidopsis Raptor (regulatory associated protein of TOR) are required for binding to its substrate. We also identified that a 44-amino acid region at the N-terminal end of Arabidopsis ribosomal S6 kinase 1 (AtS6K1) specifically interacted with AtRaptor1, indicating that this region may contain a functional equivalent of the TOS (TOR-Signaling) motif present in the mammalian TOR substrates. Transient over-expression of this 44-amino acid fragment in Arabidopsis protoplasts resulted in significant decrease in rDNA transcription, demonstrating a feasibility of developing a new plant-specific TOR signaling inhibitor based upon perturbation of the Raptor-substrate interaction. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Homeric Motifs in Cavafy’s Poem »Priam’s Night Journey«

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    Dragica Fabjan Andritsakos

    2016-12-01

    Full Text Available The paper discusses Homeric motifs in ‘Priam’s Night Journey’, a poem by the contemporary Greek poet Constantine P. Cavafy and, more precisely, one of the ten poems composed by Cavafy on mythological themes. The discussion begins by comparing Cavafy’s treatment of a motif from the Iliad, Canto 24 – Priam’s journey to Achilles – with its ancient counterpart. The question of Cavafy’s sources is addressed as well: does the poet draw on the Ancient Greek original or on the Modern Greek translation? The second part of the article analyses in detail those passages which closely lean on the ancient epic, and concludes by illustrating Cavafy’s departure from the myth, which emerges most radically in the close of the poem.

  9. 2-Amino-4-methoxy-6-methylpyrimidinium hydrogen phthalate

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    Ramalingam Sangeetha

    2016-05-01

    Full Text Available In the hydrogen phthalate anion of the title molecular salt, C6H10N3O+·C8H5O4−, the dihedral angles formed by the benzene ring and the mean planes of the –COOH and –COO− groups are 16.1 (3 and 19.8 (3°, respectively. There is an intramolecular O—H...O hydrogen bond in the anion generating an S(7 ring motif. In the crystal, the protonated N atom of the pyrimidinium ring and the 2-amino group of the cation are hydrogen bonded to the carboxylate O atoms of the anion via a pair of N—H...O hydrogen bonds, forming an R22(8 ring motif. The ion pairs are further connected via N—H...O and C—H...O hydrogen bonds, forming ribbons parallel to the [01-1] direction. The ribbons are linked by off-set π–π stacking interactions [intercentroid distances = 3.8279 (16 and 3.6074 (15 Å], forming a three-dimensional structure.

  10. 2-Carboxy-6-(quinolin-1-ium-8-yloxybenzoate

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    Jin Xie

    2012-05-01

    Full Text Available In the zwitterionic title compound, C17H11NO5, the dihedral angle between the two aromatic rings is 76.90 (7°. The dihedral angles between the carboxyl groups and the benzene ring are 64.02 (9 and 21.67 (9°, the larger angle being associated with an intramolecular N—H...Ocarboxyl hydrogen bond, resulting from proton transfer from the carboxylic acid group to the quinoline N atom and giving an S(9 ring motif. In the crystal, molecules are connected by O—H...O hydrogen bonds into chains extending along the b-axis direction. An overall two-dimensional network structure is formed through π–π interactions between the quinoline rings [minimum ring-centroid separation = 3.6068 (6 Å].

  11. A ROBUST EIGHT–MEMBERED RING MOTIF IN THE HYDROGEN-BONDED STRUCTURE OF -(PHENYLAMINOPYRIDINIUM- DI(METHANESULFONYLAMIDATE

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    Karna Wijaya

    2002-03-01

    Full Text Available The compound was prepared by dissolving 2-(phenylaminopyridine (0.52 g ; 3.0 mmol and di(methanesulfonylamine (0.51 g; 3.0 mmol in 5 mL methanol. Slow partial evaporation of the solvent at low tempertaure (-30 oC gave a yield of 0.66 g (64% and crystals suitable for X-ray study (m.p. 150-152 oC. The single crystal X-ray result showed that the crystal system was trikline with space group P. The crystal structure of the title compound 2-(phenylaminopyridinium-di(methane-sulfonylamidate forms a robust antidromic ring motif type. The structure testifies to the persistence of the  in question, which was previously detected as a robust supramolecular synthon in 2-aminopyridinium di(benzenesulfonylamidate and in a series of onium di(methane-sulfonylamidates.   Keywords: supramolecule, hydrogen-bond

  12. (E-4-Hydroxy-6-methyl-3-[1-(2-phenylhydrazinylideneethyl]-2H-pyran-2-one

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    Samra Rahmouni

    2016-05-01

    Full Text Available The title compound, C14H14N2O3, crystallized with three crystallographically independent molecules (A, B and C in the asymmetric unit. The three molecules each have an E conformation about the C=N bond but differ in the orientation of the phenyl and pyran rings. The dihedral angles between the phenyl and pyran ring planes are 14.30 (1, 28.38 (1 and 25.58 (1° in molecules A, B and C, respectively. There is an intramolecular O—H...N hydrogen bond in each molecule with an S(6 ring motif. In the crystal, molecules are linked by N—H...O and C—H...O hydrogen bonds, forming layers parallel to (001, enclosing R22(8 and R33(21 ring motifs. The layers are linked via C—H...π interactions, forming bilayers, which are joined by a further C—H...π interaction, forming a three-dimensional structure.

  13. Supramolecular architecture in a co-crystal of the N(7—H tautomeric form of N6-benzoyladenine with adipic acid (1/0.5

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    Robert Swinton Darious

    2016-06-01

    Full Text Available The asymmetric unit of the title co-crystal, C12H9N5O·0.5C6H10O4, consists of one molecule of N6-benzoyladenine (BA and one half-molecule of adipic acid (AA, the other half being generated by inversion symmetry. The dihedral angle between the adenine and phenyl ring planes is 26.71 (7°. The N6-benzoyladenine molecule crystallizes in the N(7—H tautomeric form with three non-protonated N atoms. This tautomeric form is stabilized by intramolecular N—H...O hydrogen bonding between the carbonyl (C=O group and the N(7—H hydrogen atom on the Hoogsteen face of the purine ring, forming an S(7 ring motif. The two carboxyl groups of adipic acid interact with the Watson–Crick face of the BA molecules through O—H...N and N—H...O hydrogen bonds, generating an R22(8 ring motif. The latter units are linked by N—H...N hydrogen bonds, forming layers parallel to (10-5. A weak C—H...O hydrogen bond is also present, linking adipic acid molecules in neighbouring layers, enclosing R22(10 ring motifs and forming a three-dimensional structure. C=O...π and C—H...π interactions are also present in the structure.

  14. Supra-molecular architecture in a co-crystal of the N(7)-H tautomeric form of N (6)-benzoyl-adenine with adipic acid (1/0.5).

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    Swinton Darious, Robert; Thomas Muthiah, Packianathan; Perdih, Franc

    2016-06-01

    The asymmetric unit of the title co-crystal, C12H9N5O·0.5C6H10O4, consists of one mol-ecule of N (6)-benzoyl-adenine (BA) and one half-mol-ecule of adipic acid (AA), the other half being generated by inversion symmetry. The dihedral angle between the adenine and phenyl ring planes is 26.71 (7)°. The N (6)-benzoyl-adenine mol-ecule crystallizes in the N(7)-H tautomeric form with three non-protonated N atoms. This tautomeric form is stabilized by intra-molecular N-H⋯O hydrogen bonding between the carbonyl (C=O) group and the N(7)-H hydrogen atom on the Hoogsteen face of the purine ring, forming an S(7) ring motif. The two carboxyl groups of adipic acid inter-act with the Watson-Crick face of the BA mol-ecules through O-H⋯N and N-H⋯O hydrogen bonds, generating an R 2 (2)(8) ring motif. The latter units are linked by N-H⋯N hydrogen bonds, forming layers parallel to (10-5). A weak C-H⋯O hydrogen bond is also present, linking adipic acid mol-ecules in neighbouring layers, enclosing R (2) 2(10) ring motifs and forming a three-dimensional structure. C=O⋯π and C-H⋯π inter-actions are also present in the structure.

  15. 4,4-Dimethyl-3,4-dihydropyrido[2′,3′:3,4]pyrazolo[1,5-a][1,3,5]triazin-2-amine ethanol monosolvateFused heterocyclic systems with s-triazine ring. Part 16. for part 15, see Sachdeva et al. (2010.

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    Lip Lin Koh

    2011-01-01

    Full Text Available In the title compound, C10H12N6·C2H5OH, the planarity of the heterocyclic system is slightly distorted at the triazine ring (r.m.s. deviation = 0.1191 Å, which adopts a conformation best described as intermediate between a flattened twisted boat and a half-boat with the tertiary Csp3 atom at the bow. In the crystal, molecules form centrosymmetric dimers connected by N...H—O and O...H—N hydrogen bonds between the amino group H atom, the ethanol solvent molecule and the triazine N atom, making an R44(12 graph-set motif. The other H atom of the amino group and the H atom on the endocyclic N atom form N...H—N hydrogen bonds with the N atoms of the pyrazole and pyridine rings, respectively, linking the molecules into C(7C(7 chains with the R22(8 binary graph-set motif running along [010].

  16. Crystal structure of (1S,3R,8R,10S-2,2-dichloro-10-hydroxy-3,7,7,10-tetramethyltricyclo[6.4.0.01,3]dodecan-9-one

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    Ahmed Benzalim

    2016-05-01

    Full Text Available The asymmetric unit of the title compound, C16H24Cl2O2, contains two independent molecules (A and B which are built from three fused rings, viz. a seven-membered heptane ring, a six-membered cyclohexyl ring bearing a ketone and an alcohol group, and a cyclopropane ring bearing two Cl atoms. In the crystal, the two molecules are linked via two O—H...O hydrogen bonds, forming an A–B dimer with an R22(10 ring motif. The A molecules of these dimers are linked via a C—H...O hydrogen bond, forming chains propagating along the a-axis direction. Both molecules have the same absolute configuration, i.e. 1S,3R,8R,10S, which is based on the synthetic pathway and further confirmed by resonant scattering [Flack parameter = 0.03 (5].

  17. Crystal structure of (Z-3-benzyloxy-6-[(2-hydroxy-5-methylanilinomethylidene]cyclohexa-2,4-dien-1-one

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    Nadir Ghichi

    2014-09-01

    Full Text Available In the title Schiff base compound, C21H19NO3, the conformation about the C=C bond is Z. The N—H group and carbonyl O atom form an intramolecular N—H...O hydrogen bond with an S(6 ring motif. The benzyloxy ring and the 2-hydroxy-5-methylphenyl ring are inclined to the central six-membered ring by 13.68 (9 and 9.13 (8°, respectively, and to one another by 21.95 (9°. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming helical chains along [010].

  18. NANOGRAIN DENSITY OUTSIDE SATURN’S A RING

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    Johnson, Robert E. [Engineering Physics, University of Virginia, Charlottesville, VA 22902 (United States); Tseng, Wei-Ling [National Taiwan Normal University, No. 88, Sec. 4, Tingzhou Road, Wenshan District, Taipei 11677, Taiwan (China); Elrod, M. K. [NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Persoon, A. M., E-mail: rej@virginia.edu, E-mail: wltseng@ntnu.edu.tw, E-mail: meredith.k.elrod@nasa.gov, E-mail: ann-persoon@uiowa.edu [Department of Physics and Astronomy, University of Iowa, Iowa City, IA 52242 (United States)

    2017-01-01

    The observed disparity between the radial dependence of the ion and electron densities measured by the Cassini plasma (CAPS) and radio (RPWS) science instruments are used to show that the region between the outer edge of Saturn’s main rings and its tenuous G ring is permeated with small charged grains (nanograins). These grains emanate from the edge of the A ring and from the tenuous F and G rings. This is a region of Saturn’s magnetosphere that is relatively unexplored, but will be a focus of Cassini ’s F ring orbits prior to the end of mission in 2017 September. Confirmation of the grain densities predicted here will enhance our ability to describe the formation and destruction of material in this important region of Saturn’s magnetosphere.

  19. Dimethyl 4,4′-dihydroxy-3,3′-{[(3aRS,7aRS-2,3,3a,4,5,6,7,7a-octahydro-1H-1,3-benzimidazole-1,3-diyl]bis(methylene}dibenzoate

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    Augusto Rivera

    2011-11-01

    Full Text Available The title compound, C25H30N2O6, has the imidazolidine ring in an envelope conformation. There are two intramolecular O—H...N hydrogen-bond interactions with graph-set motif S(6. The cyclohexane ring adopts a slightly distorted chair conformation. One methyl carboxylate substituent forms a dihedral angle of 12.00 (5° with the plane of the benzene ring, while the other methyl carboxylate group is almost coplanar, making a dihedral angle of 2.26 (9°. In the crystal, pairs of intermolecular C—H...O hydrogen bonds form racemic dimers, corresponding to an R22(18 graph-set motif. Further weak C—H...O interactions generate a chain running along the c axis.

  20. Ring-shaped functions and Wigner 6j-symbols

    International Nuclear Information System (INIS)

    Mardoyan, L.G.; Erevanskij Gosudarstvennyj Univ., Erevan

    2006-01-01

    The explicit expression for the ring-shaped matrix connecting the ring-shaped functions relating to different values of the axial parameter is obtained. The connection of this matrix with Wigner 6j-symbols is found out. The motion of quantum particle in the ring-shaped model with the zero priming potential is investigated. The bases of this model, which are factored in spherical cylindrical coordinates, are obtained. The formula generalizing the Rayleigh expansion of a plane wave with respect to spherical waves in the ring-shaped model is deduced [ru

  1. Methyl 2-({6-[(1-methoxy-2-methyl-1-oxopropan-2-ylcarbamoyl]pyridin-2-yl}formamido-2-methylpropanoate

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    Abdel-Galil E. Amr

    2012-05-01

    Full Text Available In the title compound, C17H23N3O6, the two methoxycarbonyl C—O—C=O planes are inclined at dihedral angles of 5.3 (4 and 83.9 (4° with respect to the central pyridine ring. An intramolecular N—H...O hydrogen bond generates an S(5 ring motif. In the crystal, molecules are linked into a chain along the c axis via C—H...O hydrogen bonds.

  2. meso-4,4′-Dimethoxy-2,2′-{[(3aR,7aS-2,3,3a,4,5,6,7,7a-octahydro-1H-benzimidazole-1,3-diyl]bis(methylene}diphenol

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    Augusto Rivera

    2013-07-01

    Full Text Available The title compound, C23H30N2O4, a di-Mannich base derived from 4-methoxyphenol and cis-1,2-diaminecyclohexane, has a perhydrobenzimidazolidine nucleus, in which the cyclohexane ring adopts a chair conformation and the heterocyclic ring has a half-chair conformation with a C—N—C—C torsion angles of −48.14 (15 and −14.57 (16°. The mean plane of the heterocycle makes dihedral angles of 86.29 (6 and 78.92 (6° with the pendant benzene rings. The molecular structure of the title compound shows the presence of two interactions between the N atoms of the imidazolidine ring and the hydroxyl groups through intramolecular O—H...N hydrogen bonds with graph-set motif S(6. The unobserved lone pairs of the N atoms are presumed to be disposed in a syn conformation, being only the second example of an exception to the typical `rabbit-ears' effect in 1,2-diamines.

  3. Remnants of black rings from gravity’s rainbow

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    Ali, Ahmed Farag [Center for Fundamental Physics, Zewail City of Science and Technology,6th of October City, Giza 12588 (Egypt); Department of Physics, Faculty of Science, Benha University,Benha 13518 (Egypt); Faizal, Mir [Department of Physics and Astronomy, University of Waterloo,Waterloo, Ontario, N2L 3G1 (Canada); Khalil, Mohammed M. [Department of Electrical Engineering, Alexandria University,El-Horreya Rd., Alexandria 12544 (Egypt)

    2014-12-29

    In this paper, we investigate a spinning black ring and a charged black ring in the context of gravity’s rainbow. By incorporating rainbow functions proposed by Amelino-Camelia, et al. in http://dx.doi.org/10.1142/S0217751X97000566 http://dx.doi.org/10.12942/lrr-2013-5 in the metric of the black rings, a considerable modification happens to their thermodynamical properties. We calculate corrections to the temperature, entropy and heat capacity of the black rings. These calculations demonstrate that the behavior of Hawking radiation changes considerably near the Planck scale in gravity’s rainbow, where it is shown that black rings do not evaporate completely and a remnant is left as the black rings evaporate down to Planck scale.

  4. 11-[(E-Benzylidene]-14-hydroxy-8-phenyl-6-thia-3,13-diazaheptacyclo[13.7.1.19,13.02,9.02,14.03,7.019,23]tetracosa-1(22,15(23,16,18,20-pentaen-10-one

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    Raju Suresh Kumar

    2012-07-01

    Full Text Available In the title compound, C34H28N2O2S, the piperidine ring adopts a chair conformation. One of the pyrrolidine rings adopts an envelope conformation with the methylene C atom at the flap whereas the other pyrrolidine ring and the thiazolidine ring adopt half-chair conformations. The mean plane of the dihydroacenaphthylene ring system [maximum deviation = 0.067 (1 Å] makes dihedral angles of 28.31 (5 and 31.32 (6° with the two terminal benzene rings. An intramolecular O—H...N hydrogen bond forms an S(5 ring motif. In the crystal, molecules are linked by C—H...O and C—H...S hydrogen bonds into layers lying parallel to the ac plane.

  5. Kopi dan Kakao dalam Kreasi Motif Batik Khas Jember

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    Irfa'ina Rohana Salma

    2015-06-01

    Full Text Available ABSTRAK Batik Jember selama ini identik dengan motif daun tembakau. Visualisasi daun tembakau dalam motif Batik Jember cukup lemah, yaitu kurang berkarakter karena motif yang muncul adalah seperti gambar daun pada umumnya. Oleh karena itu perlu diciptakan desain motif batik khas Jember yang sumber inspirasinya digali dari kekayaan alam lainnya dari Jember yang mempunyai bentuk spesifik dan karakteristik sehingga identitas motif bisa didapatkan dengan lebih kuat. Hasil alam khas Jember tersebut adalah kopi dan kakao. Tujuan penciptaan seni ini adalah untuk menghasilkan motif batik  baru yang mempunyai ciri khas Jember. Metode yang digunakan yaitu pengumpulan data, pengamatan mendalam terhadap objek penciptaan, pengkajian sumber inspirasi, pembuatan desain motif, dan perwujudan menjadi batik. Dari penciptaan seni ini berhasil dikreasikan 6 (enam motif batik yaitu: (1 Motif Uwoh Kopi; (2 Motif Godong Kopi;  (3 Motif Ceplok Kakao; (4 Motif Kakao Raja; (5 Motif Kakao Biru; dan (6 Motif Wiji Mukti. Berdasarkan hasil penilaian “Selera Estetika” diketahui bahwa motif yang paling banyak disukai adalah Motif Uwoh Kopi dan Motif Kakao Raja. Kata kunci: Motif Woh Kopi, Motif Godong Kopi, Motif Ceplok Kakao, Motif Kakao Raja, Motif Kakao Biru, Motif Wiji Mukti ABSTRACTBatik Jember is synonymous with tobacco leaf motif. Tobacco leaf shape is quite weak in the visual appearance characterized as that motif emerges like a picture of leaves in general. Therefore, it is necessary to create a distinctive design motif extracted from other natural resources of Jember that have specific shapes and characteristics that can be obtained as the stronger motif identity. The typical natural resources from Jember are coffee and cocoa. The purpose of the creation of this art is to produce the unique, creative and innovative batik and have specific characteristics of Jember. The method used are data collection, observation of the object, reviewing inspiration sources

  6. S100A6 - New facts and features

    Energy Technology Data Exchange (ETDEWEB)

    Lesniak, Wieslawa; Slomnicki, Lukasz P. [Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw (Poland); Filipek, Anna, E-mail: a.filipek@nencki.gov.pl [Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw (Poland)

    2009-12-25

    S100A6 (calcyclin) is a 10.5 kDa Ca{sup 2+}-binding protein that belongs to the S100 protein family. S100A6 contains two EF-hand motifs responsible for binding of Ca{sup 2+}. It also binds Zn{sup 2+} through not yet identified structures. Binding of Ca{sup 2+} induces a conformational change in the S100A6 molecule which in consequence increases its overall hydrophobicity and allows for interaction with target proteins. S100A6 was found in different mammalian and avian (chicken) tissues. A high level of S100A6 is observed in epithelial cells, fibroblasts and in different kinds of cancer cells. The function of S100A6 is not clear at present, but it has been suggested that it may be involved in cell proliferation, cytoskeletal dynamics and tumorigenesis. Additionally, S100A6 might have some extracellular activities. This review presents new facts and features concerning the S100A6 protein.

  7. Phospholipid composition and a polybasic motif determine D6 PROTEIN KINASE polar association with the plasma membrane and tropic responses.

    Science.gov (United States)

    Barbosa, Inês C R; Shikata, Hiromasa; Zourelidou, Melina; Heilmann, Mareike; Heilmann, Ingo; Schwechheimer, Claus

    2016-12-15

    Polar transport of the phytohormone auxin through PIN-FORMED (PIN) auxin efflux carriers is essential for the spatiotemporal control of plant development. The Arabidopsis thaliana serine/threonine kinase D6 PROTEIN KINASE (D6PK) is polarly localized at the plasma membrane of many cells where it colocalizes with PINs and activates PIN-mediated auxin efflux. Here, we show that the association of D6PK with the basal plasma membrane and PINs is dependent on the phospholipid composition of the plasma membrane as well as on the phosphatidylinositol phosphate 5-kinases PIP5K1 and PIP5K2 in epidermis cells of the primary root. We further show that D6PK directly binds polyacidic phospholipids through a polybasic lysine-rich motif in the middle domain of the kinase. The lysine-rich motif is required for proper PIN3 phosphorylation and for auxin transport-dependent tropic growth. Polybasic motifs are also present at a conserved position in other D6PK-related kinases and required for membrane and phospholipid binding. Thus, phospholipid-dependent recruitment to membranes through polybasic motifs might not only be required for D6PK-mediated auxin transport but also other processes regulated by these, as yet, functionally uncharacterized kinases. © 2016. Published by The Company of Biologists Ltd.

  8. Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus)

    Science.gov (United States)

    Suntronpong, Aorarat; Thapana, Watcharaporn; Twilprawat, Panupon; Prakhongcheep, Ornjira; Somyong, Suthasinee; Muangmai, Narongrit; Surin Peyachoknagul; Srikulnath, Kornsorn

    2017-01-01

    Abstract Among teleost fishes, Asian swamp eel (Monopterus albus Zuiew, 1793) possesses the lowest chromosome number, 2n = 24. To characterize the chromosome constitution and investigate the genome organization of repetitive sequences in M. albus, karyotyping and chromosome mapping were performed with the 18S – 28S rRNA gene, telomeric repeats, microsatellite repeat motifs, and Rex retroelements. The 18S – 28S rRNA genes were observed to the pericentromeric region of chromosome 4 at the same position with large propidium iodide and C-positive bands, suggesting that the molecular structure of the pericentromeric regions of chromosome 4 has evolved in a concerted manner with amplification of the 18S – 28S rRNA genes. (TTAGGG)n sequences were found at the telomeric ends of all chromosomes. Eight of 19 microsatellite repeat motifs were dispersedly mapped on different chromosomes suggesting the independent amplification of microsatellite repeat motifs in M. albus. Monopterus albus Rex1 (MALRex1) was observed at interstitial sites of all chromosomes and in the pericentromeric regions of most chromosomes whereas MALRex3 was scattered and localized to all chromosomes and MALRex6 to several chromosomes. This suggests that these retroelements were independently amplified or lost in M. albus. Among MALRexs (MALRex1, MALRex3, and MALRex6), MALRex6 showed higher interspecific sequence divergences from other teleost species in comparison. This suggests that the divergence of Rex6 sequences of M. albus might have occurred a relatively long time ago. PMID:29093797

  9. 1-[3-(2-Benzyloxy-6-hydroxy-4-methylphenyl-5-[3,5-bis(trifluoromethylphenyl]-4,5-dihydro-1H-pyrazol-1-yl]propane-1-one

    Directory of Open Access Journals (Sweden)

    U. H. Patel

    2013-06-01

    Full Text Available In the title compound, C28H24F6N2O3, the mean plane of the central pyrazoline ring forms dihedral angles of 2.08 (9 and 69.02 (16° with the 2-benzyloxy-6-hydroxy-4-methylphenyl and 3,5-bis(trifluoromethylphenyl rings, respectively. The dihedral angle between the mean planes of the pyrazoline and 3,5-bis(trifluoromethylphenyl rings is 68.97 (9°. An intramolecular O—H...N hydrogen bond is observed, which forms an S(6 graph-set motif. In the crystal, pairs of weak C—H...F halogen interactions link the molecules into inversion dimers while molecular chains along [100] are formed by C—H...O contacts.

  10. A novel RNA-recognition-motif protein is required for premeiotic G1/S-phase transition in rice (Oryza sativa L..

    Directory of Open Access Journals (Sweden)

    Ken-Ichi Nonomura

    2011-01-01

    Full Text Available The molecular mechanism for meiotic entry remains largely elusive in flowering plants. Only Arabidopsis SWI1/DYAD and maize AM1, both of which are the coiled-coil protein, are known to be required for the initiation of plant meiosis. The mechanism underlying the synchrony of male meiosis, characteristic to flowering plants, has also been unclear in the plant kingdom. In other eukaryotes, RNA-recognition-motif (RRM proteins are known to play essential roles in germ-cell development and meiosis progression. Rice MEL2 protein discovered in this study shows partial similarity with human proline-rich RRM protein, deleted in Azoospermia-Associated Protein1 (DAZAP1, though MEL2 also possesses ankyrin repeats and a RING finger motif. Expression analyses of several cell-cycle markers revealed that, in mel2 mutant anthers, most germ cells failed to enter premeiotic S-phase and meiosis, and a part escaped from the defect and underwent meiosis with a significant delay or continued mitotic cycles. Immunofluorescent detection revealed that T7 peptide-tagged MEL2 localized at cytoplasmic perinuclear region of germ cells during premeiotic interphase in transgenic rice plants. This study is the first report of the plant RRM protein, which is required for regulating the premeiotic G1/S-phase transition of male and female germ cells and also establishing synchrony of male meiosis. This study will contribute to elucidation of similarities and diversities in reproduction system between plants and other species.

  11. Multiple TPR motifs characterize the Fanconi anemia FANCG protein.

    Science.gov (United States)

    Blom, Eric; van de Vrugt, Henri J; de Vries, Yne; de Winter, Johan P; Arwert, Fré; Joenje, Hans

    2004-01-05

    The genome protection pathway that is defective in patients with Fanconi anemia (FA) is controlled by at least eight genes, including BRCA2. A key step in the pathway involves the monoubiquitylation of FANCD2, which critically depends on a multi-subunit nuclear 'core complex' of at least six FANC proteins (FANCA, -C, -E, -F, -G, and -L). Except for FANCL, which has WD40 repeats and a RING finger domain, no significant domain structure has so far been recognized in any of the core complex proteins. By using a homology search strategy comparing the human FANCG protein sequence with its ortholog sequences in Oryzias latipes (Japanese rice fish) and Danio rerio (zebrafish) we identified at least seven tetratricopeptide repeat motifs (TPRs) covering a major part of this protein. TPRs are degenerate 34-amino acid repeat motifs which function as scaffolds mediating protein-protein interactions, often found in multiprotein complexes. In four out of five TPR motifs tested (TPR1, -2, -5, and -6), targeted missense mutagenesis disrupting the motifs at the critical position 8 of each TPR caused complete or partial loss of FANCG function. Loss of function was evident from failure of the mutant proteins to complement the cellular FA phenotype in FA-G lymphoblasts, which was correlated with loss of binding to FANCA. Although the TPR4 mutant fully complemented the cells, it showed a reduced interaction with FANCA, suggesting that this TPR may also be of functional importance. The recognition of FANCG as a typical TPR protein predicts this protein to play a key role in the assembly and/or stabilization of the nuclear FA protein core complex.

  12. CompariMotif: quick and easy comparisons of sequence motifs.

    Science.gov (United States)

    Edwards, Richard J; Davey, Norman E; Shields, Denis C

    2008-05-15

    CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/

  13. The crystal structure of 6-(4-chlorophenyl-2-(4-methylbenzylimidazo[2,1-b][1,3,4]thiadiazole-5-carbaldehyde

    Directory of Open Access Journals (Sweden)

    A. Sowmya

    2016-10-01

    Full Text Available In the title imidazo[2,1-b][1,3,4]thiadiazole derivative, C19H14ClN3OS, the 4-methylbenzyl and chlorophenyl rings are inclined to the planar imidazo[2,1-b][1,3,4]thiadiazole moiety (r.m.s. deviation = 0.012 Å by 64.5 (1 and 3.7 (1°, respectively. The molecular structure is primarily stabilized by a strong intramolecular C—H...O hydrogen bond, leading to the formation of a pseudo-seven-membered S(7 ring motif, and a short intramolecular C—H...N contact forming an S(5 ring motif. In the crystal, molecules are linked by pairs of C—H...S hydrogen bonds, forming inversion dimers. The dimers are linked by C—H...O and C—H...π interactions, forming chains propagating along [110].

  14. 9-(3-Bromo-5-chloro-2-hydroxyphenyl-10-(2-hydroxyethyl-3,6-diphenyl-3,4,9,10-tetrahydroacridine-1,8(2H,5H-dione

    Directory of Open Access Journals (Sweden)

    Mehmet Akkurt

    2014-06-01

    Full Text Available In the title compound, C33H27BrClNO4, the dihydropyridine ring adopts a flattened boat conformation. The molecular conformation is stabilized by an intramolecular O—H...O hydrogen bond, with an S(8 ring motif. In the crystal, O—H...O, C—H...O and C—H...Cl hydrogen bonds, and C—H...π interactions link the molecules, forming a three-dimensional network. In the acridinedione ring system, the two ring C atoms at the 2- and 3-positions, and the C atom at the 6-position and the atoms of the phenyl ring attached to the C atom at the 6-position are disordered over two sets of sites with occupancy ratios of 0.783 (5:0.217 (5 and 0.526 (18:0.474 (18, respectively.

  15. On commutativity of one-sided s-unital rings

    Directory of Open Access Journals (Sweden)

    H. A. S. Abujabal

    1992-01-01

    Full Text Available The following theorem is proved: Let r=r(y>1, s, and t be non-negative integers. If R is a left s-unital ring satisfies the polynomial identity [xy−xsyrxt,x]=0 for every x,y∈R, then R is commutative. The commutativity of a right s-unital ring satisfying the polynomial identity [xy−yrxt,x]=0 for all x,y∈R, is also proved.

  16. 4,5,7,8,17-Pentahydroxy-14,18-dimethyl-6-methylene-3,10-dioxapentacyclo[9.8.0.01,7.04,19.013,18]nonadec-14-ene-9,16-dione methanol solvate dihydrate

    Directory of Open Access Journals (Sweden)

    Chin Hoe Teh

    2009-04-01

    Full Text Available The title quassinoid compound, C20H24O9·CH3OH·2H2O, is a natural eurycomanone isolated from the roots of Eurycoma longifolia. The molecules contain a fused five-ring system, with one tetrahydrofuran ring adopting an envelope conformation, one tetrahydropyran-2-one ring in a screw boat conformation, one cyclohexenone ring in a half-chair conformation and two cyclohexane rings in chair conformations. Intramolecular C—H...O interactions generate S(5 ring motifs and an O—H...O interaction generates an S(7 ring motif. In the crystal, molecules are linked via intermolecular O—H...O interactions along the b axis and further stacked along a axis. The absolute configuration of the title compound was inferred from previously solved structures of its analogues.

  17. Non-Linear Dynamics of Saturn’s Rings

    Science.gov (United States)

    Esposito, Larry W.

    2015-11-01

    Non-linear processes can explain why Saturn’s rings are so active and dynamic. Ring systems differ from simple linear systems in two significant ways: 1. They are systems of granular material: where particle-to-particle collisions dominate; thus a kinetic, not a fluid description needed. We find that stresses are strikingly inhomogeneous and fluctuations are large compared to equilibrium. 2. They are strongly forced by resonances: which drive a non-linear response, pushing the system across thresholds that lead to persistent states.Some of this non-linearity is captured in a simple Predator-Prey Model: Periodic forcing from the moon causes streamline crowding; This damps the relative velocity, and allows aggregates to grow. About a quarter phase later, the aggregates stir the system to higher relative velocity and the limit cycle repeats each orbit.Summary of Halo Results: A predator-prey model for ring dynamics produces transient structures like ‘straw’ that can explain the halo structure and spectroscopy: This requires energetic collisions (v ≈ 10m/sec, with throw distances about 200km, implying objects of scale R ≈ 20km).Transform to Duffing Eqn : With the coordinate transformation, z = M2/3, the Predator-Prey equations can be combined to form a single second-order differential equation with harmonic resonance forcing.Ring dynamics and history implications: Moon-triggered clumping at perturbed regions in Saturn’s rings creates both high velocity dispersion and large aggregates at these distances, explaining both small and large particles observed there. We calculate the stationary size distribution using a cell-to-cell mapping procedure that converts the phase-plane trajectories to a Markov chain. Approximating the Markov chain as an asymmetric random walk with reflecting boundaries allows us to determine the power law index from results of numerical simulations in the tidal environment surrounding Saturn. Aggregates can explain many dynamic aspects

  18. Graphical linking of MO multicenter bond index and VB structures. II-5-c rings and 6-c heterocyclic rings

    International Nuclear Information System (INIS)

    Bollini, Carlos Guido; Giambiagi, Mario; Giambiagi, Myriam Segre de; Figueiredo, Aloysio Paiva de

    2001-02-01

    Through the graphical method proposed it is possible to set a link between an MO multicenter bond index and VB structures. The value of the index depends on the order of the atoms involved if they are more than three. For 5-c rings three basic structures are required; the eventually different values are 12. Unlike the 6-c case it may happen that different pairs of basic structures are used to build the same polygon. For the 6-c rings including heteroatoms the original degeneracy of benzene splits leading eventually to 60 different I ring values. (author)

  19. Supra-molecular hydrogen-bonding patterns in the N(9)-H protonated and N(7)-H tautomeric form of an N(6) -benzoyl-adenine salt: N (6)-benzoyl-adeninium nitrate.

    Science.gov (United States)

    Karthikeyan, Ammasai; Jeeva Jasmine, Nithianantham; Thomas Muthiah, Packianathan; Perdih, Franc

    2016-02-01

    In the title molecular salt, C12H10N5O(+)·NO3 (-), the adenine unit has an N (9)-protonated N(7)-H tautomeric form with non-protonated N(1) and N(3) atoms. The dihedral angle between the adenine ring system and the phenyl ring is 51.10 (10)°. The typical intra-molecular N(7)-H⋯O hydrogen bond with an S(7) graph-set motif is also present. The benzoyl-adeninium cations also form base pairs through N-H⋯O and C-H⋯N hydrogen bonds involving the Watson-Crick face of the adenine ring and the C and O atoms of the benzoyl ring of an adjacent cation, forming a supra-molecular ribbon with R 2 (2)(9) rings. Benzoyl-adeninum cations are also bridged by one of the oxygen atoms of the nitrate anion, which acts as a double acceptor, forming a pair of N-H⋯O hydrogen bonds to generate a second ribbon motif. These ribbons together with π-π stacking inter-actions between the phenyl ring and the five- and six-membered adenine rings of adjacent mol-ecules generate a three-dimensional supra-molecular architecture.

  20. N,N-Diethylanilinium 2,4-dioxo-5-(2,4,6-trinitrophenyl-1,2,3,4-tetrahydropyrimidin-6-olate

    Directory of Open Access Journals (Sweden)

    Manickam Buvaneswari

    2011-12-01

    Full Text Available In the crystal structure of the title molecular salt, C10H16N+·C10H4N5O9−, the components are linked through a N—H...O hydrogen bonds. R22(8 ring motifs are formed between inversion-related barbiturate residues. Two intramoleculer N—H...O hydrogen bonds are observed in the anion. The dihedral angle between 2,4,6-trinitrophenyl and barbiturate rings is 53.6 (2°. The N,N-diethylamine substituent is disordered and was modeled as two geometrically equivalent conformers with occupancies of 0.737 (2 and 0.273 (2.

  1. 2-Hydroxy-16-[(E-4-methylbenzylidene]-13-(4-methylphenyl-12-phenyl-1,11-diazapentacyclo[12.3.1.02,10.03,8.010,14]octadeca-3(8,4,6-triene-9,15-dione

    Directory of Open Access Journals (Sweden)

    Raju Suresh Kumar

    2010-08-01

    Full Text Available In the title compound, C37H32N2O3, an intramolecular O—H...N hydrogen bond generates a five-membered ring, producing an S(5 motif. The piperidone ring adopts a half-chair conformation. The two fused pyrrolidine rings have similar envelope conformations. The interplanar angles between the benzene rings A/B and C/D are 75.68 (7 and 30.22 (6°, respectively. In the crystal structure, adjacent molecules are interconnected into chains propagating along the [010] direction via intermolecular C—H...O hydrogen bonds. Further stabilization is provided by weak C—H...π interactions.

  2. (E-2-(5-Chloro-2-hydroxybenzylidene-N-cyclohexylhydrazine-1-carbothioamide

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    Md. Azharul Arafath

    2017-01-01

    Full Text Available In the title compound, C14H18ClN3OS, the phenol ring is almost coplanar with the hydrazinecarbothioamide moiety, making a dihedral angle of 6.92 (8°. The cyclohexane ring has a chair conformation and the conformation about the C=N bond is E. In the crystal, molecules are linked by N—H...O and O—H...S hydrogen bonds, forming inversion dimers with an R22(14 ring motif flanked by two R22(6 ring motifs. The dimers are linked by short Cl...Cl interactions, forming layers parallel to the ab plane.

  3. Crystal structure of ethyl (2S-9-methoxy-2-methyl-4-oxo-3,4,5,6-tetrahydro-2H- 2,6-methanobenzo[g][1,3,5]oxadiazocine-11-carboxylate

    Directory of Open Access Journals (Sweden)

    A. Dhandapani

    2015-02-01

    Full Text Available In the title compound, C15H18N2O5, the methoxyphenyl ring makes a dihedral angle of 84.70 (12° with the mean plane of the tetrahydropyrimidin-2(1H-one ring. Both the pyran and tetrahydropyrimidin-2(1H-one rings have distorted envelope conformations with the carboxylate-substituted C atom as the flap. In the crystal, molecules are linked via pairs of N—H...O hydrogen bonds, forming zigzag chains propagating along [010], which enclose R22(8 ring motifs. The chains are linked by C—H...π interactions, forming a two-dimensional network parallel to (100.

  4. 6-Bromo-1,3-di-2-propynyl-1H-imidazo[4,5-b]pyridin-2(3H-one

    Directory of Open Access Journals (Sweden)

    S. Dahmani

    2010-04-01

    Full Text Available The room-temperature reaction of propargyl bromide and 6-bromo-1,3-dihydroimidazo[4,5-b]pyridin-2-one in dimethylformamide yields the title compound, C12H8BrN3O, which features nitrogen-bound propynyl substituents. The imidazopyridine fused ring is almost planar (r.m.s. deviation = 0.011 Å; the propynyl chains point in opposite directions relative to the fused ring. One acetylenic H atom is hydrogen bonded to the carbonyl O atom of an inversion-related molecule, forming a dimer; adjacent dimers are linked by a second acetylene–pyridine C—H...N interaction, forming a layer motif.

  5. A new type of Na(+-driven ATP synthase membrane rotor with a two-carboxylate ion-coupling motif.

    Directory of Open Access Journals (Sweden)

    Sarah Schulz

    Full Text Available The anaerobic bacterium Fusobacterium nucleatum uses glutamate decarboxylation to generate a transmembrane gradient of Na⁺. Here, we demonstrate that this ion-motive force is directly coupled to ATP synthesis, via an F₁F₀-ATP synthase with a novel Na⁺ recognition motif, shared by other human pathogens. Molecular modeling and free-energy simulations of the rotary element of the enzyme, the c-ring, indicate Na⁺ specificity in physiological settings. Consistently, activity measurements showed Na⁺ stimulation of the enzyme, either membrane-embedded or isolated, and ATP synthesis was sensitive to the Na⁺ ionophore monensin. Furthermore, Na⁺ has a protective effect against inhibitors targeting the ion-binding sites, both in the complete ATP synthase and the isolated c-ring. Definitive evidence of Na⁺ coupling is provided by two identical crystal structures of the c₁₁ ring, solved by X-ray crystallography at 2.2 and 2.6 Å resolution, at pH 5.3 and 8.7, respectively. Na⁺ ions occupy all binding sites, each coordinated by four amino acids and a water molecule. Intriguingly, two carboxylates instead of one mediate ion binding. Simulations and experiments demonstrate that this motif implies that a proton is concurrently bound to all sites, although Na⁺ alone drives the rotary mechanism. The structure thus reveals a new mode of ion coupling in ATP synthases and provides a basis for drug-design efforts against this opportunistic pathogen.

  6. Motif-role-fingerprints: the building-blocks of motifs, clustering-coefficients and transitivities in directed networks.

    Directory of Open Access Journals (Sweden)

    Mark D McDonnell

    Full Text Available Complex networks are frequently characterized by metrics for which particular subgraphs are counted. One statistic from this category, which we refer to as motif-role fingerprints, differs from global subgraph counts in that the number of subgraphs in which each node participates is counted. As with global subgraph counts, it can be important to distinguish between motif-role fingerprints that are 'structural' (induced subgraphs and 'functional' (partial subgraphs. Here we show mathematically that a vector of all functional motif-role fingerprints can readily be obtained from an arbitrary directed adjacency matrix, and then converted to structural motif-role fingerprints by multiplying that vector by a specific invertible conversion matrix. This result demonstrates that a unique structural motif-role fingerprint exists for any given functional motif-role fingerprint. We demonstrate a similar result for the cases of functional and structural motif-fingerprints without node roles, and global subgraph counts that form the basis of standard motif analysis. We also explicitly highlight that motif-role fingerprints are elemental to several popular metrics for quantifying the subgraph structure of directed complex networks, including motif distributions, directed clustering coefficient, and transitivity. The relationships between each of these metrics and motif-role fingerprints also suggest new subtypes of directed clustering coefficients and transitivities. Our results have potential utility in analyzing directed synaptic networks constructed from neuronal connectome data, such as in terms of centrality. Other potential applications include anomaly detection in networks, identification of similar networks and identification of similar nodes within networks. Matlab code for calculating all stated metrics following calculation of functional motif-role fingerprints is provided as S1 Matlab File.

  7. GRAVITATIONAL ACCRETION OF PARTICLES ONTO MOONLETS EMBEDDED IN SATURN's RINGS

    International Nuclear Information System (INIS)

    Yasui, Yuki; Ohtsuki, Keiji; Daisaka, Hiroshi

    2014-01-01

    Using a local N-body simulation, we examine gravitational accretion of ring particles onto moonlet cores in Saturn's rings. We find that gravitational accretion of particles onto moonlet cores is unlikely to occur in the C ring and probably difficult in the inner B ring as well provided that the cores are rigid water ice. Dependence of particle accretion on ring thickness changes when the radial distance from the planet and/or the density of particles is varied: the former determines the size of the core's Hill radius relative to its physical size, while the latter changes the effect of self-gravity of accreted particles. We find that particle accretion onto high-latitude regions of the core surface can occur even if the rings' vertical thickness is much smaller than the core radius, although redistribution of particles onto the high-latitude regions would not be perfectly efficient in outer regions of the rings such as the outer A ring, where the size of the core's Hill sphere in the vertical direction is significantly larger than the core's physical radius. Our results suggest that large boulders recently inferred from observations of transparent holes in the C ring are not formed locally by gravitational accretion, while propeller moonlets in the A ring would be gravitational aggregates formed by particle accretion onto dense cores. Our results also imply that the main bodies of small satellites near the outer edge of Saturn's rings may have been formed in rather thin rings

  8. GRAVITATIONAL ACCRETION OF PARTICLES ONTO MOONLETS EMBEDDED IN SATURN's RINGS

    Energy Technology Data Exchange (ETDEWEB)

    Yasui, Yuki; Ohtsuki, Keiji [Department of Earth and Planetary Sciences, Kobe University, Kobe 657-8501 (Japan); Daisaka, Hiroshi, E-mail: y.yasui@whale.kobe-u.ac.jp, E-mail: ohtsuki@tiger.kobe-u.ac.jp [Graduate School of Commerce and Management, Hitotsubashi University, Tokyo 186-8601 (Japan)

    2014-12-20

    Using a local N-body simulation, we examine gravitational accretion of ring particles onto moonlet cores in Saturn's rings. We find that gravitational accretion of particles onto moonlet cores is unlikely to occur in the C ring and probably difficult in the inner B ring as well provided that the cores are rigid water ice. Dependence of particle accretion on ring thickness changes when the radial distance from the planet and/or the density of particles is varied: the former determines the size of the core's Hill radius relative to its physical size, while the latter changes the effect of self-gravity of accreted particles. We find that particle accretion onto high-latitude regions of the core surface can occur even if the rings' vertical thickness is much smaller than the core radius, although redistribution of particles onto the high-latitude regions would not be perfectly efficient in outer regions of the rings such as the outer A ring, where the size of the core's Hill sphere in the vertical direction is significantly larger than the core's physical radius. Our results suggest that large boulders recently inferred from observations of transparent holes in the C ring are not formed locally by gravitational accretion, while propeller moonlets in the A ring would be gravitational aggregates formed by particle accretion onto dense cores. Our results also imply that the main bodies of small satellites near the outer edge of Saturn's rings may have been formed in rather thin rings.

  9. (1S,3S,8R,9S,10R-9,10-Epoxy-3,7,7,10-tetramethyltricyclo[6.4.0.01,3]dodecane

    Directory of Open Access Journals (Sweden)

    Abdoullah Bimoussa

    2014-04-01

    Full Text Available The title compound, C16H26O, was synthesized by treating (1S,3S,8R-3,7,7,10-tetramethyltricyclo[6.4.0.01,3]dodec-9-ene with metachloroperbenzoic acid. The molecule is built up from two fused six- and seven-membered rings. The six-membered ring has a half-chair conformation, whereas the seven-membered ring displays a boat conformation. In the crystal, there are no significant intermolecular interactions present.

  10. A 6-Nucleotide Regulatory Motif within the AbcR Small RNAs of Brucella abortus Mediates Host-Pathogen Interactions.

    Science.gov (United States)

    Sheehan, Lauren M; Caswell, Clayton C

    2017-06-06

    In Brucella abortus , two small RNAs (sRNAs), AbcR1 and AbcR2, are responsible for regulating transcripts encoding ABC-type transport systems. AbcR1 and AbcR2 are required for Brucella virulence, as a double chromosomal deletion of both sRNAs results in attenuation in mice. Although these sRNAs are responsible for targeting transcripts for degradation, the mechanism utilized by the AbcR sRNAs to regulate mRNA in Brucella has not been described. Here, two motifs (M1 and M2) were identified in AbcR1 and AbcR2, and complementary motif sequences were defined in AbcR-regulated transcripts. Site-directed mutagenesis of M1 or M2 or of both M1 and M2 in the sRNAs revealed transcripts to be targeted by one or both motifs. Electrophoretic mobility shift assays revealed direct, concentration-dependent binding of both AbcR sRNAs to a target mRNA sequence. These experiments genetically and biochemically characterized two indispensable motifs within the AbcR sRNAs that bind to and regulate transcripts. Additionally, cellular and animal models of infection demonstrated that only M2 in the AbcR sRNAs is required for Brucella virulence. Furthermore, one of the M2-regulated targets, BAB2_0612, was found to be critical for the virulence of B. abortus in a mouse model of infection. Although these sRNAs are highly conserved among Alphaproteobacteria , the present report displays how gene regulation mediated by the AbcR sRNAs has diverged to meet the intricate regulatory requirements of each particular organism and its unique biological niche. IMPORTANCE Small RNAs (sRNAs) are important components of bacterial regulation, allowing organisms to quickly adapt to changes in their environments. The AbcR sRNAs are highly conserved throughout the Alphaproteobacteria and negatively regulate myriad transcripts, many encoding ABC-type transport systems. In Brucella abortus , AbcR1 and AbcR2 are functionally redundant, as only a double abcR1 abcR2 ( abcR1 / 2 ) deletion results in attenuation in

  11. MotifNet: a web-server for network motif analysis.

    Science.gov (United States)

    Smoly, Ilan Y; Lerman, Eugene; Ziv-Ukelson, Michal; Yeger-Lotem, Esti

    2017-06-15

    Network motifs are small topological patterns that recur in a network significantly more often than expected by chance. Their identification emerged as a powerful approach for uncovering the design principles underlying complex networks. However, available tools for network motif analysis typically require download and execution of computationally intensive software on a local computer. We present MotifNet, the first open-access web-server for network motif analysis. MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes. The output motifs are presented graphically and the user can interactively filter them by their significance, number of instances, node and edge labels, and node identities, and view their instances. MotifNet also allows the user to distinguish between motifs that are centered on specific nodes and motifs that recur in distinct parts of the network. MotifNet is freely available at http://netbio.bgu.ac.il/motifnet . The website was implemented using ReactJs and supports all major browsers. The server interface was implemented in Python with data stored on a MySQL database. estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  12. Supramolecular patterns and Hirshfeld surface analysis in the crystal structure of bis(2-amino-4-methoxy-6-methylpyrimidinium isophthalate

    Directory of Open Access Journals (Sweden)

    Muthaiah Jeevaraj

    2017-10-01

    Full Text Available In the title molecular salt, 2C6H10N3O+·C8H4O42−, the N atom of each of the two 2-amino-4-methoxy-6-methylpyrimidine molecules lying between the amine and methyl groups has been protonated. The dihedral angles between the pyrimidine rings of the cations and the benzene ring of the succinate dianion are 5.04 (8 and 7.95 (8°. Each of the cations is linked to the anion through a pair of N—H...O(carboxylate hydrogen bonds, forming cyclic R22(8 ring motifs which are then linked through inversion-related N—H...O hydrogen bonds, giving a central R24(8 motif. Peripheral amine N—H...O hydrogen-bonding interactions on either side of the succinate anion, also through centrosymmetric R22(8 extensions, form one-dimensional ribbons extending along [211]. The crystal structure also features π–π stacking interactions between the aromatic rings of the pyrimidine cations [minimum ring centroid separation = 3.6337 (9 Å]. The intermolecular interactions were also investigated using Hirshfeld surface studies and two-dimensional fingerprint images.

  13. 3-(4-Fluorobenzoyl-4-(4-fluorophenyl-4-hydroxy-2,6-diphenylcyclohexane-1,1-dicarbonitrile

    Directory of Open Access Journals (Sweden)

    B. Narayana

    2014-06-01

    Full Text Available In the title compound, C33H24F2N2O2, the cyclohexane ring adopts a slightly distorted chair conformation. The dihedral angle between the planes of the phenyl rings is 71.80 (9°, while the planes of the fluorophenyl and fluorobenzoyl rings are inclined to one another by 31.04 (10°. The dihedral angles between the planes of the phenyl ring adjacent to the 4-hydroxy group and those of the the fluorophenyl and fluorobenzoyl rings are 51.64 (10 and 34.31 (10°, respectively, while the corresponding angles for the phenyl ring adjacent to the 3-(4-fluorobenzoyl group are 57.51 (9 and 85.02 (10°, respectively. An intramolecular O—H...O hydrogen bond generates an S(6 ring motif. In the crystal, molecules are linked via pairs of O—H...N hydrogen bonds, forming inversion dimers. The dimers are linked via C—H...N and C—H...O hydrogen bonds, forming chains along the c-axis direction. C—H...F hydrogen bonds link the chains into sheets lying parallel to the bc plane.

  14. Mechanism for activation of the growth factor-activated AGC kinases by turn motif phosphorylation

    DEFF Research Database (Denmark)

    Hauge, Camilla; Antal, Torben L; Hirschberg, Daniel

    2007-01-01

    investigated the role of the third, so-called turn motif phosphate, also located in the tail, in the AGC kinases PKB, S6K, RSK, MSK, PRK and PKC. We report cooperative action of the HM phosphate and the turn motif phosphate, because it binds a phosphoSer/Thr-binding site above the glycine-rich loop within...

  15. Semiconductor ring lasers coupled by a single waveguide

    Science.gov (United States)

    Coomans, W.; Gelens, L.; Van der Sande, G.; Mezosi, G.; Sorel, M.; Danckaert, J.; Verschaffelt, G.

    2012-06-01

    We experimentally and theoretically study the characteristics of semiconductor ring lasers bidirectionally coupled by a single bus waveguide. This configuration has, e.g., been suggested for use as an optical memory and as an optical neural network motif. The main results are that the coupling can destabilize the state in which both rings lase in the same direction, and it brings to life a state with equal powers at both outputs. These are both undesirable for optical memory operation. Although the coupling between the rings is bidirectional, the destabilization occurs due to behavior similar to an optically injected laser system.

  16. Residual stresses determination by neutron diffraction in a 100Cr6 chromium steel bearing ring

    Czech Academy of Sciences Publication Activity Database

    Rogante, M.; Martinat, G.; Mikula, Pavol; Vrána, Miroslav

    2013-01-01

    Roč. 51, č. 5 (2013), s. 275-281 ISSN 0023-432X R&D Projects: GA MŠk(XE) LM2011019 Institutional support: RVO:61389005 Keywords : 100Cr6 steel * rings * martensitic hardening * tempering * residual stress es * neutron diffraction Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.546, year: 2013

  17. Improved i-motif thermal stability by insertion of anthraquinone monomers

    DEFF Research Database (Denmark)

    Gouda, Alaa S; Amine, Mahasen S.; Pedersen, Erik Bjerregaard

    2017-01-01

    In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA...... loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends...... unlocked nucleic acid monomers or twisted intercalating nucleic acid. The 2,6-disubstituted anthraquinone linker replacing T10 enabled a significant increase of i-motif thermal melting by 8.2 °C. A substantial increase of 5.0 °C in i-motif thermal melting was recorded when both A6 and T16 were modified...

  18. XRD, vibrational spectra and quantum chemical studies of an anticancer drug: 6-Mercaptopurine.

    Science.gov (United States)

    Kumar, S Suresh; Athimoolam, S; Sridhar, B

    2015-07-05

    The single crystal of the hydrated anticancer drug, 6-Mercaptopurine (6-MP), has been grown by slow evaporation technique under room temperature. The structure was determined by single crystal X-ray diffraction. The vibrational spectral analysis was carried out using Laser Raman and FT-IR spectroscopy in the range of 3300-100 and 4000-400 cm(-1). The single crystal X-ray studies shows that the crystal packing is dominated by N-H⋯O and O-H⋯N classical hydrogen bonds leading to a hydrogen bonded ensemble. This classical hydrogen bonds were further connected through O-H⋯S hydrogen bond to form two primary ring R4(4)(16) and R4(4)(12) motifs. These two primary ring motifs are interlinked with each other to build a ladder like structure. These ladders are connected through N-H⋯N hydrogen bond along c-axis of the unit cell through chain C(5) motifs. Further, the strength of the hydrogen bonds is studied through vibrational spectral measurements. The shifting of bands due to the intermolecular interactions was also analyzed in the solid crystalline state. Geometrical optimizations of the drug molecule were done by Density Functional Theory (DFT) using the B3LYP function and Hartree-Fock (HF) level with 6-311++G(d,p) basis set. The optimized molecular geometry and computed vibrational spectra are compared with experimental results which show significant agreement. The natural bond orbital (NBO) analysis was carried out to interpret hyperconjugative interaction and intramolecular charge transfer (ICT). The chemical hardness, electro-negativity and chemical potential of the molecule are carried out by HOMO-LUMO plot. In which, the frontier orbitals has lower band gap value indicating the possible pharmaceutical activity of the molecule. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. BayesMotif: de novo protein sorting motif discovery from impure datasets.

    Science.gov (United States)

    Hu, Jianjun; Zhang, Fan

    2010-01-18

    Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms. We formulated the protein sorting motif discovery problem as a classification problem and proposed a Bayesian classifier based algorithm (BayesMotif) for de novo identification of a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions. A false positive removal procedure is developed to iteratively remove sequences that are unlikely to contain true motifs so that the algorithm can identify motifs from impure input sequences. Experiments on both implanted motif datasets and real-world datasets showed that the enhanced BayesMotif algorithm can identify anchored sorting motifs from pure or impure protein sequence dataset. It also shows that the false positive removal procedure can help to identify true motifs even when there is only 20% of the input sequences containing true motif instances. We proposed BayesMotif, a novel Bayesian classification based algorithm for de novo discovery of a special category of anchored protein sorting motifs from impure datasets. Compared to conventional motif discovery algorithms such as MEME, our algorithm can find less-conserved motifs with short highly conserved anchors. Our algorithm also has the advantage of easy incorporation of additional meta-sequence features such as hydrophobicity or charge of the motifs which may help to overcome the limitations of

  20. UKIRAN KERAWANG ACEH GAYO SEBAGAI INSPIRASI PENCIPTAAN MOTIF BATIK KHAS GAYO

    Directory of Open Access Journals (Sweden)

    Irfa ina Rohana Salma

    2016-12-01

    Full Text Available ABSTRAK Industri batik mulai berkembang di Gayo, tetapi belum memiliki motif batik khas daerah. Oleh karena itu perlu diciptakan motif batik khas Gayo, dengan mengambil inspirasi dari ukiran yang terdapat pada rumah tradisional yang biasa disebut ukiran kerawang Gayo. Tujuan penciptaan seni ini adalah untuk menciptakan motif batik yang memiliki ciri khas Gayo. Metode yang digunakan yaitu eksplorasi ide, perancangan, dan perwujudan menjadi motif batik. Dalam kegiatan ini telah diciptakan enam motif batik khas Gayo yaitu: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif Gayo Lurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. Hasil uji kesukaan terhadap motif kepada lima puluh responden menunjukkan bahwa Motif Ceplok Gayo paling banyak dipilih oleh responden yaitu sebesar 19%, sedangkan Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo Lurus 15% dan Motif Gayo Tegak 14%. Rata-rata motif yang dihasilkan mendapatkan apresiasi yang baik dari responden, sehingga semua motif layak diproduksi sebagai batik khas Gayo.Kata kunci: batik Gayo, Motif Ceplok Gayo, Motif Parang Gayo.ABSTRACTBatik industry began to develop in Gayo, but have not had a typical batik motif itself. Therefore, it is necessary to create batik motifs of Gayo, by taking inspiration from the carvings found in traditional houses commonly called kerawang Gayo. The purpose of this art is to create motifs those have a Gayo characteristic. The method used are the idea exploration, design, and motifs embodiment. In this activity has created six Gayo batik motifs, namely: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif GayoLurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. The test results fondness of the motives to fifty respondents indicated that the Motif Ceplok Gayo most preferred by respondents ie 19%, while Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo

  1. Colliding and merging galaxies. II. S0 galaxies with polar rings

    International Nuclear Information System (INIS)

    Schweizer, F.; Whitmore, B.D.; Rubin, V.C.

    1983-01-01

    We first present a detailed optical study of A0136-0801, a 16 1/2 -mag ''spindle'' galaxy girdled by a ring of gas, dust, and young stars. The spindle is a normal S0 disk seen nearly edge-on, as shown by its photometric profile and fast rotation (v/sub rot//sigma/sub v/ = 2.2); a prolate structure seems to be ruled out. The surrounding ring runs over the poles of this S0 disk and serves as a probe of the vertical potential. The ring motions suggest that a massive halo extends far beyond the S0 disk (out to 3R 25 ) and that this halo is more nearly spherical than flat. We then list 22 related galaxies and derive that a few percent of all field S0's possess near-polar rings or disks. We suggest that these structures are due to a second event, most likely the transfer of mass from a companion galaxy during a close encounter and occasionally also the merger of a companion. Although accretion occurs presumably at random angles, polar rings are favored statistically because of their slow differential precession and consequent longevity. Alternate evolutionary schemes are also discussed. Finally, we suggest that M82 may be forming a polar ring from former M81 material, and predict that the ''tilted bulge'' of UGC 7576 is an S0 disk seen nearly edge-on

  2. 2-(4-Methylphenyl-7-(2-methylpropoxy-4H-chromen-4-one–6-chloro-2-(4-methylphenyl-7-(2-methylpropoxy-4H-chromen-4-one (19/1

    Directory of Open Access Journals (Sweden)

    Vijay M. Barot

    2012-08-01

    Full Text Available The title co-crystal, 0.95C20H20O3·0.05C20H19ClO3, arises as the chloride carried over during the synthesis shares a position with an aromatic H atom; the partial occupancies are 0.947 (2 and 0.053 (2 for H and Cl, respectively. The molecular structure is stabilized by intramolecular C—H...O contacts, forming pseudo five- and six-membered rings with S(5 and S(6 graph-set motifs, respectively. The crystal structure features π–π stacking interactions between the centroids of the central fused ring systems [centroid–centroid distance = 3.501 (2 Å].

  3. 3-Phenyl-6-(2-pyridyl-1,2,4,5-tetrazine

    Directory of Open Access Journals (Sweden)

    Daniel Chartrand

    2008-01-01

    Full Text Available The title compound, C13H9N5, is the first asymmetric diaryl-1,2,4,5-tetrazine to be crystallographically characterized. We have been interested in this motif for incorporation into supramolecular assemblies based on coordination chemistry. The solid state structure shows a centrosymmetric molecule, forcing a positional disorder of the terminal phenyl and pyridyl rings. The molecule is completely planar, unusual for aromatic rings with N atoms in adjacent ortho positions. The stacking observed is very common in diaryltetrazines and is dominated by π stacking [centroid-to-centroid distance between the tetrazine ring and the aromatic ring of an adjacent molecule is 3.6 Å, perpendicular (centroid-to-plane distance of about 3.3 Å].

  4. 200 MW S-band traveling wave resonant ring development at IHEP

    Science.gov (United States)

    Zhou, Zu-Sheng; Chi, Yun-Long; Git, Meng-Ping; Pei, Guo-Xi

    2010-03-01

    The resonant-ring is a traveling wave circuit, which is used to produce high peak power with comparatively smaller stored energy. The application to be considered is its use as a high power simulator mainly for testing the klystron ceramic output window, as well as for high power microwave transmission devices. This paper describes the principle of a resonant ring and introduces the structure and property of the newly constructed traveling wave resonant ring at IHEP. Our goal is to produce a 200 MW class resonant ring at 2.856 GHz with a pulse length of 2 μs and repetition rate of 25 Hz. The installation, commissioning and testing of the ring have been completed and a peak power of 200 MW at 3 μs has been achieved. The conditioning results show that all the parameters of the resonant ring reach the design goals.

  5. Motif enrichment tool.

    Science.gov (United States)

    Blatti, Charles; Sinha, Saurabh

    2014-07-01

    The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. MIGRATION OF SMALL MOONS IN SATURN's RINGS

    Energy Technology Data Exchange (ETDEWEB)

    Bromley, Benjamin C. [Department of Physics and Astronomy, University of Utah, 115 S 1400 E, Rm 201, Salt Lake City, UT 84112 (United States); Kenyon, Scott J., E-mail: bromley@physics.utah.edu, E-mail: skenyon@cfa.harvard.edu [Smithsonian Astrophysical Observatory, 60 Garden Street, Cambridge, MA 02138 (United States)

    2013-02-20

    The motions of small moons through Saturn's rings provide excellent tests of radial migration models. In theory, torque exchange between these moons and ring particles leads to radial drift. We predict that moons with Hill radii r {sub H} {approx} 2-24 km should migrate through the A ring in 1000 yr. In this size range, moons orbiting in an empty gap or in a full ring eventually migrate at the same rate. Smaller moons or moonlets-such as the propellers-are trapped by diffusion of disk material into corotating orbits, creating inertial drag. Larger moons-such as Pan or Atlas-do not migrate because of their own inertia. Fast migration of 2-24 km moons should eliminate intermediate-size bodies from the A ring and may be responsible for the observed large-radius cutoff of r {sub H} {approx} 1-2 km in the size distribution of the A ring's propeller moonlets. Although the presence of Daphnis (r {sub H} Almost-Equal-To 5 km) inside the Keeler gap challenges this scenario, numerical simulations demonstrate that orbital resonances and stirring by distant, larger moons (e.g., Mimas) may be important factors. For Daphnis, stirring by distant moons seems the most promising mechanism to halt fast migration. Alternatively, Daphnis may be a recent addition to the ring that is settling into a low inclination orbit in {approx}10{sup 3} yr prior to a phase of rapid migration. We provide predictions of observational constraints required to discriminate among possible scenarios for Daphnis.

  7. (2aR*,5S*,6aS*,8aS*,E-Ethyl 5-hydroxy-7,7,8a-trimethyl-8-oxo-2,2a,6,6a,7,8,8a,8b-octahydro-1H-pentaleno[1,6-bc]oxepine-4-carboxylate

    Directory of Open Access Journals (Sweden)

    Goverdhan Mehta

    2012-12-01

    Full Text Available The title compound, C17H24O5, featuring a 2-carbethoxy-3-oxepanone unit in its intramolecularly O—H...O hydrogen-bonded enol form, was obtained via [(CF3CO22Rh]2-catalysed intramolecular O—H bond insertion in the α-diazo-ω-hydroxy-β-ketoester, ethyl 4-[(1S,3aS,6R,6aS-6-hydroxy-2,2,3a-trimethyl-3-oxo-octahydropentalen-1-yl]-2-diazo-3-oxobutanoate. The seven-membered oxacyclic ring, thus constructed on a cis-fused diquinane platform, was found to adopt a distorted boat–sofa conformation.

  8. Crystal structures and conformations of two Diels–Alder adduct derivatives: 1,8-bis(thiophen-2-yl-14-oxatetracyclo[6.5.1.02,7.09,13]tetradeca-2(7,3,5-trien-10-one and 1,8-diphenyl-14-oxatetracyclo[6.5.1.02,7.09,13] tetradeca-2,4,6-trien-10-one

    Directory of Open Access Journals (Sweden)

    S. Gopinath

    2015-02-01

    Full Text Available The title compounds, C21H16O2S2 (I and C25H20O2 (II, are products of a tandem `pincer' Diels–Alder reaction consisting of [2 + 2] cycloadditions between benzo[c]furan and cyclopentanone. Each comprises a fused tetracyclic ring system containing two five-membered rings (in envelope conformations with the O atom as the flap and six-membered rings (in boat conformations. In addition, two thiophene rings in (I and two phenyl rings in (II are attached to the tetracyclic ring system. The cyclopentanone ring adopts a twisted conformation in (I and an envelope conformation in (II. In (I, the thiophene rings are positionally disordered over two sets of sites, with occupancy ratios of 0.901 (2:0.099 (2 and 0.666 (2:0.334 (2. In (II, the oxygen atom of the cyclopentanone ring is rotationally disordered over two sites with an occupancy ratio of 0.579 (4:0.421 (4. The molecular structure of (I is stabilized by an intramolecular C—H...O hydrogen bond, which generates an S(7 ring motif. In the crystal, the molecules are linked via weak C—H...O hydrogen bonds, which generate R22(16 ring motifs in (I and C(8 chains in (II. In both structures, the crystal packing also features C—H...π interactions. The crystal studied of compound (I was twinned by non-merohedry. The twin component is related by the twin law [−1 0 0 −0.101 1 −0.484 0 0 −1] operated by a twofold rotation axis parallel to the b axis. The structure of (I was refined with a twin scale factor of 0.275 (2.

  9. Periventricular heterotopia and white matter abnormalities in a girl with mosaic ring chromosome 6.

    Science.gov (United States)

    Nishigaki, Satsuki; Hamazaki, Takashi; Saito, Mika; Yamamoto, Toshiyuki; Seto, Toshiyuki; Shintaku, Haruo

    2015-01-01

    Ring chromosome 6 is a rare chromosome abnormality that arises typically de novo. The phenotypes can be highly variable, ranging from almost normal to severe malformations and neurological defects. We report a case of a 3-year-old girl with mosaic ring chromosome 6 who presented with being small for gestational age and intellectual disability, and whose brain MRI later revealed periventricular heterotopia and white matter abnormalities. Mosaicism was identified in peripheral blood cells examined by standard G-bands, mos 46,XX,r(6)(p25q27)[67]/45,XX,-6[25]/46,XX,dic r(6:6)(p25q27:p25q27)[6]/47,XX,r(6)(p25q27) × 2[2]. Using array-comparative genomic hybridization, we identified terminal deletion of 6q27 (1.5 Mb) and no deletion on 6p. To our knowledge, this is the first report of periventricular heterotopia and white matter abnormalities manifested in a patient with ring chromosome 6. These central nervous system malformations are further discussed in relation to molecular genetics.

  10. Spin dynamics in a molecular ferrimagnetic ring, [Mn(hfac)2NITPh]6

    International Nuclear Information System (INIS)

    Itou, T.; Funahashi, S.; Oyamada, A.; Maegawa, S.; Fujita, K.; Amezawa, K.; Yamaguchi, R.

    2007-01-01

    We studied the spin dynamics of a ferrimagnetic ring [Mn(hfac) 2 NITPh] 6 with an S=12 ground state by means of H-NMR1 experiments under several fields. The spin-lattice relaxation rate increases monotonically with increasing temperature. This monotonous behavior is not reproduced by the calculation based on the lifetimes of eigenstates caused by the spin-phonon interaction. The relaxation rate is possibly caused by the dispersion resulting from the interaction between the clusters, which is far smaller than the interaction in the cluster but comparable to the nuclear Zeeman energy

  11. 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.

  12. The Human Papillomavirus E6 PDZ Binding Motif: From Life Cycle to Malignancy

    Directory of Open Access Journals (Sweden)

    Ketaki Ganti

    2015-07-01

    Full Text Available Cancer-causing HPV E6 oncoproteins are characterized by the presence of a PDZ binding motif (PBM at their extreme carboxy terminus. It was long thought that this region of E6 had a sole function to confer interaction with a defined set of cellular substrates. However, more recent studies have shown that the E6 PBM has a complex pattern of regulation, whereby phosphorylation within the PBM can regulate interaction with two classes of cellular proteins: those containing PDZ domains and the members of the 14-3-3 family of proteins. In this review, we explore the roles that the PBM and its ligands play in the virus life cycle, and subsequently how these can inadvertently contribute towards the development of malignancy. We also explore how subtle alterations in cellular signal transduction pathways might result in aberrant E6 phosphorylation, which in turn might contribute towards disease progression.

  13. Graphical linking of MO multicenter bond index and VB structures. II-5-c rings and 6-c heterocyclic rings

    CERN Document Server

    Bollini, C G; Giambiagi, M

    2001-01-01

    Through the graphical method proposed it is possible to set a link between an MO multicenter bond index and VB structures. The value of the index depends on the order of the atoms involved if they are more than three. For 5-c rings three basic structures are required; the eventually different values are 12. Unlike the 6-c case it may happen that different pairs of basic structures are used to build the same polygon. For the 6-c rings including heteroatoms the original degeneracy of benzene splits leading eventually to 60 different I sub r sub i sub n sub g values.

  14. Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries

    DEFF Research Database (Denmark)

    Nielsen, Jeppe Lund; Schramm, Andreas; Bernhard, Anne E.

    2004-01-01

    for Systems Biology,3 Seattle, Washington, and Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany2 A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting......  FLOW CYTOMETRY-ASSISTED CLONING OF SPECIFIC SEQUENCE MOTIFS FROM COMPLEX 16S RRNA GENE LIBRARIES Jeppe L. Nielsen,1 Andreas Schramm,1,2 Anne E. Bernhard,1 Gerrit J. van den Engh,3 and David A. Stahl1* Department of Civil and Environmental Engineering, University of Washington,1 and Institute......-assisted cloning, was used to recover sequences affiliated with a unique lineage within the Bacteroidetes not abundant in a clone library of environmental 16S rRNA genes.  ...

  15. Identity and functions of CxxC-derived motifs.

    Science.gov (United States)

    Fomenko, Dmitri E; Gladyshev, Vadim N

    2003-09-30

    Two cysteines separated by two other residues (the CxxC motif) are employed by many redox proteins for formation, isomerization, and reduction of disulfide bonds and for other redox functions. The place of the C-terminal cysteine in this motif may be occupied by serine (the CxxS motif), modifying the functional repertoire of redox proteins. Here we found that the CxxC motif may also give rise to a motif, in which the C-terminal cysteine is replaced with threonine (the CxxT motif). Moreover, in contrast to a view that the N-terminal cysteine in the CxxC motif always serves as a nucleophilic attacking group, this residue could also be replaced with threonine (the TxxC motif), serine (the SxxC motif), or other residues. In each of these CxxC-derived motifs, the presence of a downstream alpha-helix was strongly favored. A search for conserved CxxC-derived motif/helix patterns in four complete genomes representing bacteria, archaea, and eukaryotes identified known redox proteins and suggested possible redox functions for several additional proteins. Catalytic sites in peroxiredoxins were major representatives of the TxxC motif, whereas those in glutathione peroxidases represented the CxxT motif. Structural assessments indicated that threonines in these enzymes could stabilize catalytic thiolates, suggesting revisions to previously proposed catalytic triads. Each of the CxxC-derived motifs was also observed in natural selenium-containing proteins, in which selenocysteine was present in place of a catalytic cysteine.

  16. MotifMark: Finding regulatory motifs in DNA sequences.

    Science.gov (United States)

    Hassanzadeh, Hamid Reza; Kolhe, Pushkar; Isbell, Charles L; Wang, May D

    2017-07-01

    The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.

  17. Long-term evaluation of fluoroelastomer O-rings in UF6

    International Nuclear Information System (INIS)

    Russell, R.G.; Otey, M.G.; Dippo, G.L.

    1986-01-01

    A major component in the gaseous centrifuge enrichment plant (GCEP) was fluoroelastomer O-rings, which were used to seal the uranium hexafluoride (UF 6 ) gas system. A program utilizing accelerated test conditions was used to help identify the best material out of four selected candidates and to predict the service life of these materials at GCEP conditions. The tests included accelerated temperatures, mechanical stress, and UF 6 exposure. Data were evaluated using the Newman--Keuls 1 ranking system to identify the best material and a zero-order reaction rate equation to help predict service life. This presentation includes a description of the test facility, the materials tested, the types of tests, objectives of the study, service life predictions, and conclusions. The O-rings are predicted to last approx. 30 years, and a high-molecular-weight polymer had the best performance ranking

  18. Crystal structure of diethyl 2-amino-6-[(thiophen-3-ylethynyl]azulene-1,3-dicarboxylate

    Directory of Open Access Journals (Sweden)

    Sebastian Förster

    2015-03-01

    Full Text Available The title compound, C22H19NO4S, has an almost planar geometry supported by intramolecular N—H...O and C—H...O hydrogen bonds. The thiophene ring is inclined to the azulene ring by 4.85 (16°, while the ethoxycarbonyl groups are inclined to the azulene ring by 7.0 (2 and 5.7 (2°. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with an R22(12 ring motif. The dimers are linked via C—H...π interactions, forming sheets parallel to (10-1.

  19. Parole, Sintagmatik, dan Paradigmatik Motif Batik Mega Mendung

    Directory of Open Access Journals (Sweden)

    Rudi - Nababan

    2012-04-01

    Full Text Available ABSTRACT   Discussing traditional batik is related a lot to the organization system of fine arts element ac- companying it, either the pattern of the motif or the technique of the making. In this case, the motif of Mega Mendung Cirebon certainly has patterns and rules which are traditionally different from the other motifs in other areas. Through  semiotics analysis especially with Saussure and Pierce concept, it can be traced that batik with Cirebon motif, in this case Mega Mendung motif, has parole and langue system, as unique fine arts language in batik, and structure of visual syntagmatic and paradigmatic. In the context of batik motif as fine arts language, it is surely related to sign system as symbol and icon.       Keywords: visual semiotic, Cirebon’s batik.

  20. RingSys-Scheduler User`s manual. Information terminal for town monitoring; Brukermanual for RingSys-Scheduler. Informasjonsterminal for byovervaaking

    Energy Technology Data Exchange (ETDEWEB)

    Marsteen, L.

    1996-02-01

    This report is a User`s manual. It describes RingSys Scheduler, a computer system for continuous display of time series, public information and static pictures. The computer is connected to a host machine via modem and time series, and public information are automatically updated once an hour. RingSys-Scheduler is PC based. It is developed using Excel`s macro language as well as the asynchronous communication program Dynacomm`s script language. 12 figs.

  1. 4,6-Dichloro-2-((E-{4-[(E-3,5-dichloro-2-hydroxybenzylideneamino]butylimino}methylphenol

    Directory of Open Access Journals (Sweden)

    Hadi Kargar

    2012-07-01

    Full Text Available The asymmetric unit of the title compound, C18H16Cl4N2O2, comprises half of a potentially tetradentate Schiff base ligand. It is located about a twofold rotation axis that bisects the central C—C bond of the butane-1,4-diamine group. There are two intramolecular O—H...N hydrogen bonds making S(6 ring motifs. In the crystal, molecules are linked by pairs of weak C—H...Cl interactions, forming inversion dimers, which are further connected by C—H...O hydrogen bonds into two-dimensional frameworks that lie parallel to (001.

  2. (3R,6S,7aS-3-Phenyl-6-(phenylsulfanylperhydropyrrolo[1,2-c]oxazol-5-one

    Directory of Open Access Journals (Sweden)

    Anthony D. Woolhouse

    2009-05-01

    Full Text Available Molecules of the title compound [systematic name: (2R,5S,7S-2-phenyl-7-phenylsulfanyl-1-aza-3-oxabicyclo[3.3.0]octan-8-one], C18H17NO2S, form high quality crystals even though they are only packed using C—H...O(carbonyl and weak C—H...S interactions. The dihedral angle between the aromatic rings is 85.53 (5°. The fused rings adopt envelope and twist conformations.

  3. Saturn’s ring temperatures at equinox

    Science.gov (United States)

    Spilker, Linda J.; Ferrari, C.; Morishima, R.

    2013-10-01

    Modeling the thermal emission of Saturn's rings is challenging due to the numerous heating sources as well as the structural properties of the disk and of the particles that are closely related. At equinox, however, the main rings are externally heated by Saturn alone and the problem is somewhat simplified. We test the abilities of our current models to reproduce the temperatures observed with the Cassini CIRS instrument around equinox in August 2009. A simple semi-analytic model which includes mutual shadowing effects can mostly explain the radial profile of the equinox ring temperatures, except the model predicts lower temperatures than those observed for the A ring. The temperature variation at a given saturnocentric radius is primarily caused by observational geometry variations relative to Saturn. The observed temperature increases with decreasing Saturn-ring-observer angle. In addition, we found evidence that the leading hemispheres of particles are warmer than the trailing hemispheres at least for the C ring and probably for the A and B rings as well. This is explained if some fraction of particles has spin rates lower than the synchronous rotation rate as predicted by N-body simulations. The spin model for a monolayer ring (Ferrari, C., Leyrat, C., 2006, Astron. Astrophys. 447, 745-760) can fit the temperature variations with spacecraft longitude observed in the C ring with currently known thermal properties and a mixing of slow and fast rotators. The multilayer model (Morishima, R., Salo, H., Ohtsuki, K., 2009, Icarus 201, 634-654) can reproduce the temperatures of the B and C rings but gives A ring temperatures that are significantly lower than those observed as does the simple semi-analytic model. More advanced models which take into account self-gravity wakes may explain the A ring temperature behavior.

  4. ARCHETYPES AND MYTHOLOGICAL MOTIFS: JOHN UPDIKE’S LEGACY REVISITED

    Directory of Open Access Journals (Sweden)

    Loreta Ulvydienė

    2018-04-01

    Full Text Available John Updike is widely considered to be one of the greatest, one of the most popular and sometimes most controversial writers concerned with the American small town and middle-class materialism. A lot of literary critics and researchers observe that Updike’s finest work came from his exploration of ordinary America and from his use of elegant prose, rich with metaphor, to portray the public and private feelings of Americans, their daily rounds of life. In addition, discussing Updike’s individual works a lot of literary critics and researchers have observed the writer’s attempts to re-write myth in “the mythical age”1 of the twentieth century. Naturally enough, as the return to myth is assumed to be a certain feature of the Modernist movement, half a century later since Updike’s famous novel Centaur was penned, it is indispensable to re-examine the writer’s fictional intentions in the usage of myth. More importantly, it is needful to determine whether we can see the mythic elements and realistic details as a continuum or as the contrasted opposites in his so called “historical chronicles”. Updike’s novels and stories are filled with mythological motifs and character archetypes. Thus, the study aims at revisiting John Updike’s creation considering mythological elements and archetypal images of his heroes alongside with heroic masculinity, war, terrorism and American perfectionism.

  5. Mapping the Thermal Inertia of Saturn’s Rings with Cassini CIRS

    Science.gov (United States)

    Brooks, Shawn M.; Spilker, L. J.; PIlorz, S. H.; Showalter, M. R.

    2013-10-01

    We use data from Cassini's Composite Infrared Spectrometer to map out the thermal response of Saturn's ring particles passing through Saturn's shadow and to determine variations in ring thermal inertia. CIRS records far infrared radiation in three separate detectors, each of which covers a distinct wavelength range. In this work, we analyze rings spectra recorded at focal plane 1 (FP1), as its wavelength response (16.7-1000 microns) is well suited to detecting direct thermal emission from Saturn's rings. The thermal budget of the rings is typically dominated by solar radiation. When ring particles enter Saturn’s shadow this source of energy is abruptly cut off with a consequential drop in ring temperature. Likewise, temperatures rebound when particles exit the shadow. To characterize these heating and cooling events, FP1 was repeatedly scanned across the main rings. Each scan was offset from either the ingress or egress shadow boundary by an amount corresponding to a fraction of a Keplerian orbit. By resampling these scans onto a common radial grid, we can map out the rings’ response to the abrupt changes in insolation at shadow ingress and egress. Periods near equinox represent a unique situation. During this time the Sun's disk crosses the ring plane and its rays strike the rings at zero incidence. Solar heating is virtually absent, and thermal radiation from Saturn and sunlight reflected by Saturn dominate the thermal environment. While ring temperature variations at equinox are much more subtle, they represent temperature contrasts that vary at the unique timescale corresponding to variations in Saturn contributions to the rings’ thermal budget. By analyzing CIRS data at a variety of locations and epochs, we will map out thermal inertia across the rings and attempt to tease out structural information about the particles which comprise Saturn’s rings. This presentation will report upon our progress towards these ends. This research was carried out at the

  6. Belisa-Dido’s Suicide: Variations on a Vergilian Motif in Lope de Vega’s Non-Dramatic Works

    Directory of Open Access Journals (Sweden)

    Antonio Sánchez Jiménez

    2018-05-01

    Full Text Available This article examines the theme of the abandoned beloved in four texts by Lope de Vega in which the motif combines subtexts of different origin: on the one hand, a conspicuous biographical key, filtered by literature (Belisa’s and Filis’ attempted suicide; on the other, erudite sources (Dido’s suicide. Analyzing these four texts, dating from Lope’s youth and de senectute periods, we also suggest how Lope could have come up with the idea of combining these strains inspiring himself in an anonymous romance (La desesperada Dido that appears to be the source of the famous De pechos sobre una torre.

  7. Open Sores of a Republic: Injustice and Poverty as Motifs in Alex La Guma’s First Three Novels

    Directory of Open Access Journals (Sweden)

    OGBEIDE, O. Victor

    2013-11-01

    Full Text Available This paper examines injustice and poverty as motifs in Alex La Guma’s first three novels. A motif is a recurrent formal element in a work of art. The foundation of apartheid is injustice which often leads to massive poverty on the part of the non-white community whose members are hapless victims of marginalization and disfranchisement in the Republic of South Africa. The prevalence of the twin forces of injustice and poverty in apartheid South Africa which La Guma artistically portrays in his first three novels confers on them the status of a motif. This, in itself, is a function of the novelist’s deference to realism and artistic relevance. The paper discovers that the unrelenting travesty of justice and the prevalence of destitution which describe so many unsavoury scenes in the novels in focus are due to the non-whites’ lack of meaningful political consciousness which itself is a function of the racist government’s stamp on oppositional discourse. It is this vacuum that the puny and ineffective pockets of individual acts of courage attempt to fill in the three novels to no avail.

  8. 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...

  9. Crystal structure of 26-(4-methylphenyl-8,11,14,17-tetraoxa-28-azatetracyclo[22.3.1.02,7.018,23]hexacosa-2,4,6,18(23,19,21,24(1,25,27-nonaene

    Directory of Open Access Journals (Sweden)

    T. Thanh Van Tran

    2016-05-01

    Full Text Available The title compound, C30H29NO4, is a tetracyclic system containing a 4-arylpyridine fragment, two benzene rings and an aza-17-crown-5 ether moiety, in a bowl-like arrangement. The pyridine ring is inclined to the 4-methylphenyl ring by 26.64 (6°, and by 57.43 (6 and 56.81 (6° to the benzene rings. The benzene rings are inclined to one another by 88.32 (6°. In the crystal, molecules are linked by pairs of C—H...N hydrogen bonds, forming inversion dimers with an R22(14 ring motif. The dimers are linked via a number of C—H...π interactions, forming a three-dimensional architecture.

  10. On commutativity of right s-unital rings with some polynomial constraints

    International Nuclear Information System (INIS)

    Khan, M.A.

    1994-08-01

    We study the commutativity of certain class of rings, namely rings with unity 1 and right s-unital rings under each of the following properties [yx m - x n f(y)x p ,x]=0, [yx m +x n f(y)x p ,x]=0, where f(t) is a polynomial in t 2 Z[t] varying with pair of ring elements x,y and m,n,p are fixed non-negative integers. Moreover, the results have been extended to the case when m and n depend on the choice of x and y and the ring satisfies the Chacron's Theorem. (author). 14 refs

  11. Nicotine induced CpG methylation of Pax6 binding motif in StAR promoter reduces the gene expression and cortisol production

    International Nuclear Information System (INIS)

    Wang, Tingting; Chen, Man; Liu, Lian; Cheng, Huaiyan; Yan, You-E; Feng, Ying-Hong; Wang, Hui

    2011-01-01

    Steroidogenic acute regulatory protein (StAR) mediates the rate-limiting step in the synthesis of steroid hormones, essential to fetal development. We have reported that the StAR expression in fetal adrenal is inhibited in a rat model of nicotine-induced intrauterine growth retardation (IUGR). Here using primary human fetal adrenal cortex (pHFAC) cells and a human fetal adrenal cell line NCI-H295A, we show that nicotine inhibits StAR expression and cortisol production in a dose- and time-dependent manner, and prolongs the inhibitory effect on cells proliferating over 5 passages after termination of nicotine treatment. Methylation detection within the StAR promoter region uncovers a single site CpG methylation at nt -377 that is sensitive to nicotine treatment. Nicotine-induced alterations in frequency of this point methylation correlates well with the levels of StAR expression, suggesting an important role of the single site in regulating StAR expression. Further studies using bioinformatics analysis and siRNA approach reveal that the single CpG site is part of the Pax6 binding motif (CGCCTGA) in the StAR promoter. The luciferase activity assays validate that Pax6 increases StAR gene expression by binding to the glucagon G3-like motif (CGCCTGA) and methylation of this site blocks Pax6 binding and thus suppresses StAR expression. These data identify a nicotine-sensitive CpG site at the Pax6 binding motif in the StAR promoter that may play a central role in regulating StAR expression. The results suggest an epigenetic mechanism that may explain how nicotine contributes to onset of adult diseases or disorders such as metabolic syndrome via fetal programming. -- Highlights: ► Nicotine-induced StAR inhibition in two human adrenal cell models. ► Nicotine-induced single CpG site methylation in StAR promoter. ► Persistent StAR inhibition and single CpG methylation after nicotine termination. ► Single CpG methylation located at Pax6 binding motif regulates St

  12. Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Joshi NV

    2009-01-01

    Full Text Available Abstract Background Regulation of gene expression in Plasmodium falciparum (Pf remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS; this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

  13. Crystal structures of N-(4-chlorophenyl-2-[(4,6-diaminopyrimidin-2-ylsulfanyl]acetamide and N-(3-chlorophenyl-2-[(4,6-diaminopyrimidin-2-ylsulfanyl]acetamide

    Directory of Open Access Journals (Sweden)

    S. Subasri

    2017-04-01

    Full Text Available The title compounds, C12H12ClN5OS, (I, and C12H12ClN5OS, (II, are 2-[(diaminopyrimidin-2-ylsulfanyl]acetamides. Compound (II, crystallizes with two independent molecules (A and B in the asymmetric unit. In each of the molecules, in both (I and (II, an intramolecular N—H...N hydrogen bond forms an S(7 ring motif. The pyrimidine ring is inclined to the benzene ring by 42.25 (14° in (I, and by 59.70 (16 and 62.18 (15° in molecules A and B, respectively, of compound (II. In the crystal of (I, molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with an R22(8 ring motif. The dimers are linked via bifurcated N—H...O and C—H...O hydrogen bonds, forming corrugated layers parallel to the ac plane. In the crystal of (II, the A molecules are linked through N—H...O and N—H...Cl hydrogen bonds, forming layers parallel to (100. The B molecules are also linked by N—H...O and N—H...Cl hydrogen bonds, also forming layers parallel to (100. The parallel layers of A and B molecules are linked via N—H...N hydrogen bonds, forming a three-dimensional structure.

  14. A Conserved GPG-Motif in the HIV-1 Nef Core Is Required for Principal Nef-Activities.

    Directory of Open Access Journals (Sweden)

    Marta Martínez-Bonet

    Full Text Available To find out new determinants required for Nef activity we performed a functional alanine scanning analysis along a discrete but highly conserved region at the core of HIV-1 Nef. We identified the GPG-motif, located at the 121-137 region of HIV-1 NL4.3 Nef, as a novel protein signature strictly required for the p56Lck dependent Nef-induced CD4-downregulation in T-cells. Since the Nef-GPG motif was dispensable for CD4-downregulation in HeLa-CD4 cells, Nef/AP-1 interaction and Nef-dependent effects on Tf-R trafficking, the observed effects on CD4 downregulation cannot be attributed to structure constraints or to alterations on general protein trafficking. Besides, we found that the GPG-motif was also required for Nef-dependent inhibition of ring actin re-organization upon TCR triggering and MHCI downregulation, suggesting that the GPG-motif could actively cooperate with the Nef PxxP motif for these HIV-1 Nef-related effects. Finally, we observed that the Nef-GPG motif was required for optimal infectivity of those viruses produced in T-cells. According to these findings, we propose the conserved GPG-motif in HIV-1 Nef as functional region required for HIV-1 infectivity and therefore with a potential interest for the interference of Nef activity during HIV-1 infection.

  15. 8-{(E-[(4-Chlorophenylimino]methyl}-1,1,7,7-tetramethyl-1,2,3,5,6,7-hexahydropyrido[3,2,1-ij]quinolin-9-ol

    Directory of Open Access Journals (Sweden)

    Esen Nur Kantar

    2013-06-01

    Full Text Available The title Schiff base, C23H27ClN2O adopts the phenol–imine tautomeric form, with an intramolecular O—H...N hydrogen bond, which generates an S(6 ring motif. Three C atoms of the heterocyclic moiety of the hexahydropyridoquinoline unit, as well as the two methyl groups bonded to one of these C atoms, are disordered over two set of sites, with anoccupancy ratio of 0.740 (4:0.260 (4.

  16. Mechanical loading of the gymnast’s motor system during swings on rings

    Directory of Open Access Journals (Sweden)

    R Serafin

    2008-12-01

    Full Text Available The aim of this work was to identify the mechanical loading of the gymnast’s motor system during forward and backward swings on gymnastic rings. A junior gymnast of the First Class, aged 14, with body mass 53.1 kg and body length 1.61 m, participated in the study. He executed a series of ten cyclic swing movements on rings with his maximum amplitude. Kinematic variables of the gymnast’s centre of mass (COM as well as reaction forces in the cables were measured and synchronized using the SIMI MOTION movement analysis system. Two separate phases of mechanical loading of the motor system have been identified: resistance phase and non resistance phase. In the non resistance phase the gymnast attains similar values of the COM’s momentum but different angular displacements. In the resistance phase the forces acting on the motor system have their maximum. They amount to 5.5 BW for the forward swing and 6.5 BW for the backward swing movement. The maximum rate of change of the force for forward and backward swing is 42.6 BWs-1 and 67.4 BWs-1, respectively. These two variables differentiate the mechanical loading of the gymnast’s motor system between forward and backward swings. The reaction force produced by the gymnast is significantly greater during the execution of forward swings. It seems probable that horizontal displacements of COM may be the factor responsible for reduction of the mechanical loading experienced by the gymnast.

  17. 4-({[6-(4-Chlorobenzyl-4-methyl-5-oxo-4,5-dihydro-1,2,4-triazin-3-yl]sulfanyl}acetyl-3-phenylsydnone

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2011-04-01

    Full Text Available In the title syndone (1,2,3-oxadiazol-3-ylium-5-olate compound, C21H16ClN5O4S, the dihedral angle between the benzene and oxadiazole rings is 55.62 (11° and that between the triazine and the chloro-substituted phenyl rings is 82.45 (9°. There is an intramolecular C—H...S hydrogen bond, which generates an S(5 ring motif. In the crystal, inversion dimers linked by pairs of C—H...O hydrogen bonds generate R22(20 loops. The dimers are connected by C—H...N and C—H...O hydrogen bonds.

  18. Black rings in Taub-NUT and D0-D6 interactions

    International Nuclear Information System (INIS)

    Camps, Joan; Emparan, Roberto; Figueras, Pau; Giusto, Stefano; Saxena, Ashish

    2009-01-01

    We analyze the dynamics of neutral black rings in Taub-NUT spaces and their relation to systems of D0 and D6 branes in the supergravity approximation. We employ several recent techniques, both perturbative and exact, to construct solutions in which thermal excitations of the D0-branes can be turned on or off, and the D6-brane can have B-fluxes turned on or off in its worldvolume. By explicit calculation of the interaction energy between the D0 and D6 branes, we can study equilibrium configurations and their stability. We find that although D0 and D6 branes (in the absence of B fields, and at zero temperature) repeal each other at non-zero separation, as they get together they go over continuously to an unstable bound state of an extremal singular Kaluza-Klein black hole. We also find that, for B-fields larger than a critical value, or sufficiently large thermal excitation, the D0 and D6 branes form stable bound states. The bound states with thermally excited D0 branes are black rings in Taub-NUT, and we provide an analysis of their phase diagram.

  19. Tyrocidine A Analogues Bearing the Planar d-Phe-2-Abz Turn Motif: How Conformation Impacts Bioactivity.

    Science.gov (United States)

    Cameron, Alan J; Edwards, Patrick J B; Harjes, Elena; Sarojini, Vijayalekshmi

    2017-12-14

    The d-Phe-Pro β-turn of the cyclic β-hairpin antimicrobial decapeptide tyrocidine A, (Tyrc A) was substituted with the d-Phe-2-aminobenzoic acid (2-Abz) motif in a synthetic analogue (1). The NMR structure of 1 demonstrated that compound 1 retained the β-hairpin structure of Tyrc A with additional planarity, resulting in approximately 30-fold reduced hemolysis than Tyrc A. Although antibacterial activity was partially compromised, a single Gln to Lys substitution (2) restored activity equivalent to Tyrc A against S. aureus, enhanced activity against two Gram negative strains and maintained the reduced hemeloysis of 1. Analysis by transmission electron microscopy (TEM) suggested a membrane lytic mechanism of action for these peptides. Compound 2 also exhibits nanomolar antifungal activity in synergy with amphotericin B. The d-Phe-2-Abz turn may serve as a tool for the synthesis of structurally predictable β-hairpin libraries. Unlike traditional β-turn motifs such as d-Pro-Gly, both the 2-Abz and d-Phe rings may be further functionalized.

  20. Nicotine induced CpG methylation of Pax6 binding motif in StAR promoter reduces the gene expression and cortisol production

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Tingting [Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071 (China); Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, Maryland (United States); Chen, Man; Liu, Lian [Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071 (China); Cheng, Huaiyan [Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, Maryland (United States); Yan, You-E [Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071 (China); Feng, Ying-Hong, E-mail: yhfeng@usuhs.edu [Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, Maryland (United States); Wang, Hui, E-mail: wanghui19@whu.edu.cn [Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan 430071 (China); Research Center of Food and Drug Evaluation, Wuhan University, Wuhan 430071 (China)

    2011-12-15

    Steroidogenic acute regulatory protein (StAR) mediates the rate-limiting step in the synthesis of steroid hormones, essential to fetal development. We have reported that the StAR expression in fetal adrenal is inhibited in a rat model of nicotine-induced intrauterine growth retardation (IUGR). Here using primary human fetal adrenal cortex (pHFAC) cells and a human fetal adrenal cell line NCI-H295A, we show that nicotine inhibits StAR expression and cortisol production in a dose- and time-dependent manner, and prolongs the inhibitory effect on cells proliferating over 5 passages after termination of nicotine treatment. Methylation detection within the StAR promoter region uncovers a single site CpG methylation at nt -377 that is sensitive to nicotine treatment. Nicotine-induced alterations in frequency of this point methylation correlates well with the levels of StAR expression, suggesting an important role of the single site in regulating StAR expression. Further studies using bioinformatics analysis and siRNA approach reveal that the single CpG site is part of the Pax6 binding motif (CGCCTGA) in the StAR promoter. The luciferase activity assays validate that Pax6 increases StAR gene expression by binding to the glucagon G3-like motif (CGCCTGA) and methylation of this site blocks Pax6 binding and thus suppresses StAR expression. These data identify a nicotine-sensitive CpG site at the Pax6 binding motif in the StAR promoter that may play a central role in regulating StAR expression. The results suggest an epigenetic mechanism that may explain how nicotine contributes to onset of adult diseases or disorders such as metabolic syndrome via fetal programming. -- Highlights: Black-Right-Pointing-Pointer Nicotine-induced StAR inhibition in two human adrenal cell models. Black-Right-Pointing-Pointer Nicotine-induced single CpG site methylation in StAR promoter. Black-Right-Pointing-Pointer Persistent StAR inhibition and single CpG methylation after nicotine termination

  1. Ethyl (E-2-(2,7-dimethyl-5-oxo-4H,5H-pyrano[4,3-b]pyran-4-ylideneacetate

    Directory of Open Access Journals (Sweden)

    Oulemda Bassou

    2017-02-01

    Full Text Available In the title compound, C14H14O5, the two heterocyclic rings are coplanar (r.m.s. deviation = 0.008 Å, with the largest deviation from the mean plane being 0.012 (1 Å. The mean plane through the acetate group is inclined slightly with respect to the oxopyrano[4,3-b]pyran-4-yl system, as indicated by the dihedral angle of 1.70 (7° between them. Two intramolecular hydrogen bonds, completing S(6 ring motifs, are observed in the molecule. In the crystal, molecules are linked by weak C—H...O hydrogen bonds involving the same acceptor atom, forming chains propagating along the c-axis direction and enclosing R21(6 ring motifs. The chains are linked via offset π–π interactions [intercentroid distance = 3.622 (1 Å], involving inversion-related oxopyrano[4,3-b]pyran-4-yl ring systems, forming slabs parallel to the bc plane.

  2. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

    Science.gov (United States)

    Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

    2013-01-01

    The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

  3. Resource-saving technology for manufacturing billets for piston’s rings

    Directory of Open Access Journals (Sweden)

    A. N. Krutilin

    2010-10-01

    Full Text Available Piston’s rings are one of the most critical parts of heavy-duty engines for wear-work in conditions of prolonged exposure of alternating loads and high temperatures. Currently in the world production of billets for piston’s rings is dominated by the two methods of casting: production of individual and oiling billets of gray and ductile cast iron in green-sand mold and shell mold and centrifugal casting method (intended primarily for oiling billets of ductile iron; the technology for individual production billets for piston’s rings with a diameter up to 250 mm, from 250 to 450 mm with individual and oiling ways, over 450 mm - preference of oiling billet. The best parameters of physical-mechanical and operational characteristics piston’s rings are in the case of manufacture of billets to the maximum extent approaching the configuration to the finished product. The rings made of shaped billets are characterized by uniform distribution of properties from the perimeter, provide a given diagram of pressures and full fit to the cylinder. Because of deficiencies of traditional methods of casting, continuous quality requirements for billets, the need for economy of material, fuel and energy resources, are finding new progressive technological processes of production of high-quality billets for piston’s rings. One of the most promising for piston rings billet is a method of casting consists of immersing the sand molds into the melt. It is interesting idea, expressed by A. Sutherland and subsequently patented in several countries in the way of casting method, called "immersion pouring technology" (ICT-Immersion Casting Technique [1]. Experiments, conducted in the laboratory of the Belarusian National Technical University, have identified significant shortcomings of immersion method of casting. When forms are immersing, have an intensive gassing in molten metal, and freezing of the metal on the out surface of the form. But despite some

  4. A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.

    Science.gov (United States)

    Tran, Ngoc Tam L; Huang, Chun-Hsi

    2014-02-20

    ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data.

  5. Photochemistry in Saturn’s Ring-Shadowed Atmosphere: Modulation of Hydrocarbons and Aerosols

    Science.gov (United States)

    Edgington, Scott G.; Atreya, Sushil K.; Wilson, Eric H.; Baines, Kevin H.; West, Robert A.; Bjoraker, Gordon L.; Fletcher, Leigh N.; Momary, Tom

    2015-11-01

    Cassini has been orbiting Saturn for over eleven years now. During this epoch, the ring shadow has moved from covering much of the northern hemisphere (the solar inclination was 24 degrees) to covering a large swath south of the equator and it continues to move southward. At Saturn Orbit Insertion in 2004, the projection of the A-ring onto Saturn reached as far as 40N along the central meridian (52N at the terminator). At its maximum extent, the ring shadow can reach as far as 48N/S (58N/S at the terminator). The net effect is that the intensity of both ultraviolet and visible sunlight penetrating through the rings to any particular latitude will vary depending on both Saturn’s axis relative to the Sun and the optical thickness of each ring system. In essence, the rings act like semi-transparent venetian blinds.Our previous work, examined the variation of the solar flux as a function of solar inclination, i.e. for each 7.25-year season at Saturn. Here, we report on the impact of the oscillating ring shadow on the photolysis and production rates of hydrocarbons (acetylene, ethane, propane, and benzene) and phosphine in Saturn’s stratosphere and upper troposphere. The impact of these production and loss rates on the abundance of long-lived photochemical products leading to haze formation are explored. Similarly, we assess their impact on phosphine abundance, a disequilibrium species whose presence in the upper troposphere can be used as a tracer of convective processes in the deeper atmosphere.We will also present our ongoing analysis of Cassini’s datasets that provide an estimate of the evolving haze content of the northern hemisphere and we will begin to assess the implications for dynamical mixing. In particular, we will examine how the now famous hexagonal jet stream acts like a barrier to transport, isolating Saturn’s north polar region from outside transport of photochemically-generated molecules and haze.The research described in this paper was carried

  6. 4′-Methyl-14′,19′-dioxa-4′-azaspiro[acenaphthylene-1,5′-tetracyclo[18.4.0.02,6.08,13]tetracosane]-1′(24′,8′,10′,12′,20′,22′-hexaene-2,7′(1H-dione

    Directory of Open Access Journals (Sweden)

    Sibi Narayanan

    2012-12-01

    Full Text Available In the title compound, C33H29NO4, the acenaphthylene ring system is essentially planar (r.m.s. deviation = 0.0290 Å. The pyrrolidine ring adopts a C-envelope conformation with a C atom displaced by 0.671 (2 Å from the mean-plane formed by the remaining ring atoms. The pyrrolidine ring is fused to acenaphthylene ring system making a dihedral angle of 88.0 (7°. In the crystal, molecules are linked into R22(9 dimers via C—H...N and C—H...O hydrogen bonds. Two C atoms act as donors to the same O atom acceptor, resulting in the formation of R21(7 ring motifs. These two motifs combine to form hydrogen-bonded sheets running along the a- and b-axis directions.

  7. 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)

  8. Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants

    Directory of Open Access Journals (Sweden)

    Ahmad A. Malik

    2017-05-01

    Full Text Available Dehydrins, a large family of abiotic stress proteins, are defined by the presence of a mostly conserved motif known as the K-segment, and may also contain two other conserved motifs known as the Y-segment and S-segment. Using the dehydrin literature, we developed a sequence motif definition of the K-segment, which we used to create a large dataset of dehydrin sequences by searching the Pfam00257 dehydrin dataset and the Phytozome 10 sequences of vascular plants. A comprehensive analysis of these sequences reveals that lysine residues are highly conserved in the K-segment, while the amino acid type is often conserved at other positions. Despite the Y-segment name, the central tyrosine is somewhat conserved, but can be substituted with two other small aromatic amino acids (phenylalanine or histidine. The S-segment contains a series of serine residues, but in some proteins is also preceded by a conserved LHR sequence. In many dehydrins containing all three of these motifs the S-segment is linked to the K-segment by a GXGGRRKK motif (where X can be any amino acid, suggesting a functional linkage between these two motifs. An analysis of the sequences shows that the dehydrin architecture and several biochemical properties (isoelectric point, molecular mass, and hydrophobicity score are dependent on each other, and that some dehydrin architectures are overexpressed during certain abiotic stress, suggesting that they may be optimized for a specific abiotic stress while others are involved in all forms of dehydration stress (drought, cold, and salinity.

  9. (3R,6R,12R,20S,24S-3,6,12-Triacetyl-20,24-epoxydammarane-3,6,12,25-tetraol

    Directory of Open Access Journals (Sweden)

    Qing-Guo Meng

    2011-01-01

    Full Text Available The title compound, C36H58O8, was prepared from 20(S-protopanaxatriol, which was degraded from Panax quinquefolium saponin with sodium in glycerine, extracted and seperated by flash chromatography. Three six-membered rings are in chair conformations, the five-membered ring is in an envelope form and the tetrahydrofuran ring has a conformation intermediate between half-chair and envelope. In the crystal, molecules are linked by O—H...O hydrogen bonds, and C—H...O contacts also occur. The absolute structure was assigned on the basis of the synthesis.

  10. 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.

  11. RNA recognition motif (RRM)-containing proteins in Bombyx mori

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... Recognition Motif (RRM), sometimes referred to as. RNP1, is one of the first identified domains for RNA interaction. RRM is very common ..... Apart from the RRM motif, eIF3-S9 has a Trp-Asp. (WD) repeat domain, Poly (A) ...

  12. Native characterization of nucleic acid motif thermodynamics via non-covalent catalysis

    Science.gov (United States)

    Wang, Chunyan; Bae, Jin H.; Zhang, David Yu

    2016-01-01

    DNA hybridization thermodynamics is critical for accurate design of oligonucleotides for biotechnology and nanotechnology applications, but parameters currently in use are inaccurately extrapolated based on limited quantitative understanding of thermal behaviours. Here, we present a method to measure the ΔG° of DNA motifs at temperatures and buffer conditions of interest, with significantly better accuracy (6- to 14-fold lower s.e.) than prior methods. The equilibrium constant of a reaction with thermodynamics closely approximating that of a desired motif is numerically calculated from directly observed reactant and product equilibrium concentrations; a DNA catalyst is designed to accelerate equilibration. We measured the ΔG° of terminal fluorophores, single-nucleotide dangles and multinucleotide dangles, in temperatures ranging from 10 to 45 °C. PMID:26782977

  13. DMINDA: an integrated web server for DNA motif identification and analyses.

    Science.gov (United States)

    Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

    2014-07-01

    DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. (4bS,8aS-1-Isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octahydrophenanthren-2-yl acetate

    Directory of Open Access Journals (Sweden)

    Radouane Oubabi

    2014-03-01

    Full Text Available The hemisynthesis of the title compound, C22H32O2, was carried out through direct acetylation reaction of the naturally occurring diterpene totarol [systematic name: (4bS,8aS-4b,8,8-trimethyl-1-propan-2-yl-5,6,7,8a,9,10-hexahydrophenanthren-2-ol]. The molecule is built up from three fused six membered rings, one saturated and two unsaturated. The central unsaturated ring has a half-chair conformation, whereas the other unsaturated ring displays a chair conformation. The absolute configuration is deduced from the chemical pathway. The value of the Hooft parameter [−0.10 (6] allowed this absolute configuration to be confirmed.

  15. Crystal structures of (RS-N-[(1R,2S-2-benzyloxy-1-(2,6-dimethylphenylpropyl]-2-methylpropane-2-sulfinamide and (RS-N-[(1S,2R-2-benzyloxy-1-(2,4,6-trimethylphenylpropyl]-2-methylpropane-2-sulfinamide: two related protected 1,2-amino alcohols

    Directory of Open Access Journals (Sweden)

    Matthew R. Carbone

    2014-11-01

    Full Text Available The title compounds, C22H31NO2S, (1, and C23H33NO2S, (2, are related protected 1,2-amino alcohols. They differ in the substituents on the benzene ring, viz. 2,6-dimethylphenyl in (1 and 2,4,6-trimethylphenyl in (2. The plane of the phenyl ring is inclined to that of the benzene ring by 28.52 (7° in (1 and by 44.65 (19° in (2. In the crystal of (1, N—H...O=S and C—H...O=S hydrogen bonds link molecules, forming chains along [100], while in (2, similar hydrogen bonds link molecules into chains along [010]. The absolute structures of both compounds were determined by resonance scattering.

  16. Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

    Science.gov (United States)

    Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

    2012-01-01

    To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

  17. The identification of functional motifs in temporal gene expression analysis

    Directory of Open Access Journals (Sweden)

    Michael G. Surette

    2005-01-01

    Full Text Available The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.

  18. 6D “Garren” snake cooler and ring cooler for µ{sup ±} cooling of a muon collider

    Energy Technology Data Exchange (ETDEWEB)

    Ding, X., E-mail: xding@bnl.gov [UCLA, Los Angeles, CA 90095 (United States); Berg, J.S. [Brookhaven National Laboratory, Upton, NY 11973 (United States); Cline, D. [UCLA, Los Angeles, CA 90095 (United States); Garren, Al [Particle Beam Lasers, Inc., Northridge, CA 91324 (United States); Kirk, H.G. [Brookhaven National Laboratory, Upton, NY 11973 (United States)

    2014-12-21

    Six dimensional cooling of large emittance µ{sup +} and µ{sup −} beams is required in order to obtain the desired luminosity for a muon collider. In our previous study, we demonstrated that a 6D “Garren” ring cooler using both dipoles and solenoids in four 90{sup 0} achromatic arcs can give substantial cooling in all six phase space dimensions. In this paper, we describe the injection/extraction requirements of this four-sided ring. We also present the performance of an achromat-based 6D “Garren” snake cooler. The achromatic design permits the design to easily switch between a closed ring and a snaking geometry on injection or extraction from the ring.

  19. (S,Z-3-Phenyl-2-[(1,1,1-trichloro-7-methoxy-2,7-dioxohept-3-en-4-ylamino]propanoic acid monohydrate

    Directory of Open Access Journals (Sweden)

    Alex Fabiani Claro Flores

    2014-02-01

    Full Text Available In the title compound, C17H18Cl3NO5·H2O, intramolecular N—H...O and C—H...Cl hydrogen bonds form S(6 and S(5 ring motifs, respectively. The chiral organic molecule is connected to the solvent water molecule by a short O—H...O hydrogen bond. In the crystal, a weak C—H...Cl interaction connects the organic molecules along [100] while the water molecules act as bridges between the organic molecules in both the [100] and [010] directions, generating layers parallel to the ab plane.

  20. Benzo[4,5]cyclohepta[1,2-b]fluorene: an isomeric motif for pentacene containing linearly fused five-, six- and seven-membered rings

    KAUST Repository

    Yang, Xuejin

    2016-06-07

    Benzo[4,5]cyclohepta[1,2-b]fluorene (5a), a new π-conjugated polycyclic hydrocarbon containing linearly fused six-, five-, six-, seven- and six-membered rings (C6-C5-C6-C7-C6), was designed and its stable derivatives 5b and 5c were synthesized. With 22 π electrons, 5a is an isomer of pentacene with quinoidal, dipolar ionic and diradical resonance forms. Molecules 5b and 5c were experimentally investigated with cyclic voltammetry, electronic absorption spectroscopy and X-ray crystallographic analysis, and theoretically studied by calculating the NICS value, diradical character and dipole moment. A comparison of 5a–c with pentacene and other pentacene analogues containing linearly fused five- or seven- membered rings was also conducted and discussed. It was found that 5b behaved as a p-type organic semiconductor in solution-processed thin film transistors with field effect mobility of up to 0.025 cm2/Vs.

  1. Benzo[4,5]cyclohepta[1,2-b]fluorene: an isomeric motif for pentacene containing linearly fused five-, six- and seven-membered rings

    KAUST Repository

    Yang, Xuejin; Shi, Xueliang; Aratani, Naoki; Goncalves, Theo; Huang, Kuo-Wei; Yamada, Hiroko; Chi, Chunyan; Miao, Qian

    2016-01-01

    Benzo[4,5]cyclohepta[1,2-b]fluorene (5a), a new π-conjugated polycyclic hydrocarbon containing linearly fused six-, five-, six-, seven- and six-membered rings (C6-C5-C6-C7-C6), was designed and its stable derivatives 5b and 5c were synthesized. With 22 π electrons, 5a is an isomer of pentacene with quinoidal, dipolar ionic and diradical resonance forms. Molecules 5b and 5c were experimentally investigated with cyclic voltammetry, electronic absorption spectroscopy and X-ray crystallographic analysis, and theoretically studied by calculating the NICS value, diradical character and dipole moment. A comparison of 5a–c with pentacene and other pentacene analogues containing linearly fused five- or seven- membered rings was also conducted and discussed. It was found that 5b behaved as a p-type organic semiconductor in solution-processed thin film transistors with field effect mobility of up to 0.025 cm2/Vs.

  2. The Arabidopsis GAGA-Binding Factor BASIC PENTACYSTEINE6 Recruits the POLYCOMB-REPRESSIVE COMPLEX1 Component LIKE HETEROCHROMATIN PROTEIN1 to GAGA DNA Motifs.

    Science.gov (United States)

    Hecker, Andreas; Brand, Luise H; Peter, Sébastien; Simoncello, Nathalie; Kilian, Joachim; Harter, Klaus; Gaudin, Valérie; Wanke, Dierk

    2015-07-01

    Polycomb-repressive complexes (PRCs) play key roles in development by repressing a large number of genes involved in various functions. Much, however, remains to be discovered about PRC-silencing mechanisms as well as their targeting to specific genomic regions. Besides other mechanisms, GAGA-binding factors in animals can guide PRC members in a sequence-specific manner to Polycomb-responsive DNA elements. Here, we show that the Arabidopsis (Arabidopsis thaliana) GAGA-motif binding factor protein basic pentacysteine6 (BPC6) interacts with like heterochromatin protein1 (LHP1), a PRC1 component, and associates with vernalization2 (VRN2), a PRC2 component, in vivo. By using a modified DNA-protein interaction enzyme-linked immunosorbant assay, we could show that BPC6 was required and sufficient to recruit LHP1 to GAGA motif-containing DNA probes in vitro. We also found that LHP1 interacts with VRN2 and, therefore, can function as a possible scaffold between BPC6 and VRN2. The lhp1-4 bpc4 bpc6 triple mutant displayed a pleiotropic phenotype, extreme dwarfism and early flowering, which disclosed synergistic functions of LHP1 and group II plant BPC members. Transcriptome analyses supported this synergy and suggested a possible function in the concerted repression of homeotic genes, probably through histone H3 lysine-27 trimethylation. Hence, our findings suggest striking similarities between animal and plant GAGA-binding factors in the recruitment of PRC1 and PRC2 components to Polycomb-responsive DNA element-like GAGA motifs, which must have evolved through convergent evolution. © 2015 American Society of Plant Biologists. All Rights Reserved.

  3. Annotating RNA motifs in sequences and alignments.

    Science.gov (United States)

    Gardner, Paul P; Eldai, Hisham

    2015-01-01

    RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterize RNA motifs, which are critical components of many RNA structure-function relationships. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterized RNAs. Moreover, we introduce a new profile-based database of RNA motifs--RMfam--and illustrate some applications for investigating the evolution and functional characterization of RNA. All the data and scripts associated with this work are available from: https://github.com/ppgardne/RMfam. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Christian J. Michel

    2017-12-01

    Full Text Available A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C 3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X , using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X , in the complete genome of the yeast Saccharomyces cerevisiae. Several properties of X motifs are identified by basic statistics (at the frequency level, and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R . We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae. We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae, but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions. This property is true for all cardinalities of X motifs (from 4 to 20 and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non- X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together

  5. Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Michel, Christian J; Ngoune, Viviane Nguefack; Poch, Olivier; Ripp, Raymond; Thompson, Julie D

    2017-12-03

    A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading) frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X, using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X, in the complete genome of the yeast Saccharomyces cerevisiae . Several properties of X motifs are identified by basic statistics (at the frequency level), and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R. We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae . We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae , but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions). This property is true for all cardinalities of X motifs (from 4 to 20) and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non-X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together, represent the first

  6. 1,4a-Dimethyl-6-methyl-ene-5-(5,5,6,6-tetra-cyano-2-methyl-cyclo-hex-2-enylmeth-yl)deca-hydro-naphthalene-1-carboxylic acid: a trans-communic acid derivative.

    Science.gov (United States)

    Rejouani, Nezha; Auhmani, Aziz; Ait Itto, My Youssef; Benharref, Ahmed; Daran, Jean-Claude

    2008-01-18

    In the search for cancer chemopreventive agents, we have studied the Diels-Alder reaction of trans-communic acid with tetra-cyano-ethyl-ene in the presence of SiO(2) as catalyst. The title cycloadduct, C(26)H(30)N(4)O(2), was obtained in 75% yield. The mol-ecules are arranged in pairs through O-H⋯O hydrogen bonds, forming an R(2) (2)(8) ring motif. Both the fused cyclohexyl rings adopt a chair conformation, whereas the nonfused ring adopts a half-chair conformation.

  7. Photochemistry in Saturn’s Ring-Shadowed Atmosphere: Photochemistry and Haze Observations

    Science.gov (United States)

    Edgington, Scott G.; Atreya, Sushil K.; Baines, Kevin H.; West, Robert A.; Bjoraker, Gordon L.; Fletcher, Leigh; Momary, Thomas W.; Wilson, Eric; CIRS, ISS, UVIS, VIMS

    2017-10-01

    After 13 years of observing Saturn, Cassini would have ended nearly a half Saturnian year. During this epoch, the ring shadow has moved from covering much of the northern hemisphere to covering a large swath southern hemisphere. The net effect is that the intensity of both ultraviolet and visible sunlight penetrating through the rings to any particular latitude will vary depending on both Saturn’s axis relative to the Sun and the optical thickness of each ring system. In essence, the rings act like semi-transparent venetian blinds. This effect magnifies the effect due to axial tilt alone and acts to turn off photochemistry and haze generation. This effect is seen in both the presence of a bluish Rayleigh-scattering atmosphere in 2004 in the northern hemisphere and color change to blue in the northern hemisphere.Previous work examined the variation of the solar flux as a function of solar inclination, i.e. for each 7.25-year season at Saturn. We report on the impact of the oscillating ring shadow, in addition to variation due to axial tilt, on photolysis and production rates of hydrocarbons and phosphine in Saturn’s stratosphere and upper troposphere. The impact of these production and loss rates on the abundance of long-lived photochemical products leading to haze formation are explored. We assess their impact on a disequilibrium species whose presence in the upper troposphere can be used as a tracer of convective processes in the deeper atmosphere.We will also present our ongoing analysis of Cassini’s CIRS, UVIS, and VIMS datasets that provide an estimate of the evolving haze content. In particular, we will examine how the region inside Saturn’s famous hexagonal jet stream changes over time from a relatively clear atmosphere to a hazy one. We also explore how the hexagon acts like a barrier to transport, isolating Saturn’s north polar region from outside influences of photochemically-generated molecules and haze.The research described in this paper was

  8. Manufacturing processes of S-shaped temple rings from Vrbno, Central Bohemia

    Czech Academy of Sciences Publication Activity Database

    Ottenwelter, Estelle; Hošek, Jiří; Děd, J.; Štefan, I.

    2012-01-01

    Roč. 64, č. 3 (2012), s. 525-533 ISSN 0323-1267 Institutional research plan: CEZ:AV0Z80020508 Keywords : S-shaped temple rings * Early Middle Ages * Vrbno * tinning * gilding * silver plating Subject RIV: AC - Archeology, Anthropology, Ethnology

  9. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-01-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  10. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun

    2013-06-29

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors\\' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  11. 4-(3-Bromopropyloxy-1-hydroxy-9,10-anthraquinone

    Directory of Open Access Journals (Sweden)

    Natsumi Ohira

    2016-05-01

    Full Text Available In the molecule of the title compound, C17H13BrO4, the anthraquinone ring system is slightly bent, with a dihedral angle of 169.99 (7° between the planes of the two benzene rings. The side chain (O—C—C—C—Br has a gauche–gauche conformation, as indicated by the O—C—C—C and C—C—C—Br torsion angles of −66.9 (2 and −65.8 (2°, respectively. In addition, there is an intramolecular O—H...O hydrogen bond enclosing an S(6 ring motif. The hydrogen-bond donor is bifurcated; in the crystal, a pair of O—H...O hydrogen bonds connects two molecules, forming an inversion dimer with an R22(12 ring motif.

  12. Transduction motif analysis of gastric cancer based on a human signaling network

    Energy Technology Data Exchange (ETDEWEB)

    Liu, G.; Li, D.Z.; Jiang, C.S.; Wang, W. [Fuzhou General Hospital of Nanjing Command, Department of Gastroenterology, Fuzhou, China, Department of Gastroenterology, Fuzhou General Hospital of Nanjing Command, Fuzhou (China)

    2014-04-04

    To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD) scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs.

  13. AtalaphyllineThis paper is dedicated to the late His Royal Highness Prince Mahidol of Songkla for his contributions to the development of medical education in Thailand.

    Directory of Open Access Journals (Sweden)

    Suchada Chantrapromma

    2010-01-01

    Full Text Available The title acridone alkaloid [systematic name: 1,3,5-trihydroxy-2,4-bis(3-methylbut-2-enylacridin-9(10H-one], C23H25NO4, known as atalaphylline, was isolated from Atalantia monophylla Corrêa, a mangrove plant. The molecule contains three fused planar rings with an r.m.s. deviation of 0.026 (2 Å. Both 3-methylbut-2-enyl substituents are in a (−anticlinal conformation. An intramolecular N—H...O hydrogen bond generates an S(5 ring motif, while an intramolecular O—H...O hydrogen bond generates an S(6 ring motif. In the crystal structure, the molecules are linked into screw chains along [010] by intermolecular O—H...O hydrogen bonds. These chains are stacked along the a axis by π–π interactions with centroid–centroid distances of 3.6695 (13 and 3.6696 (13 Å.

  14. The MHC motif viewer: a visualization tool for MHC binding motifs

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Hoof, Ilka; Lund, Ole

    2010-01-01

    is hampered by the lack of tools for browsing and comparing specificity of these molecules. We have developed a Web server, MHC Motif Viewer, which allows the display of the binding motif for MHC class I proteins for human, chimpanzee, rhesus monkey, mouse, and swine, as well as HLA-DR protein sequences...

  15. Methyl 2-acetamido-2-(4-hydroxy-2-methyl-1,3-dioxo-1,2,3,4-tetrahydroisoquinolin-4-yl-4-methylpentanoate

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2011-07-01

    Full Text Available In the isoquinoline ring system of the title molecule, C19H24N2O6, the N-heterocyclic ring is in a half-boat conformation. The molecular structure is stabilized by an intramolecular O—H...O hydrogen bond, which generates an S(7 ring motif. In the crystal, molecules are linked via intermolecular bifurcated N—H...(O,O and weak C—H...O hydrogen bonds into a three-dimensional network.

  16. Spectral signature barcodes based on S-shaped Split Ring Resonators (S-SRRs

    Directory of Open Access Journals (Sweden)

    Herrojo Cristian

    2016-01-01

    Full Text Available In this paper, it is shown that S-shaped split ring resonators (S-SRRs are useful particles for the implementation of spectral signature (i.e., a class of radiofrequency barcodes based on coplanar waveguide (CPW transmission lines loaded with such resonant elements. By virtue of its S shape, these resonators are electrically small. Hence S-SRRs are of interest for the miniaturization of the barcodes, since multiple resonators, each tuned at a different frequency, are used for encoding purposes. In particular, a 10-bit barcode occupying 1 GHz spectral bandwidth centered at 2.5 GHz, with dimensions of 9 cm2, is presented in this paper.

  17. 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.

  18. (E-Methyl 3-(3,4-dimethoxyphenyl-2-[(1,3-dioxoisoindolin-2-ylmethyl]acrylate

    Directory of Open Access Journals (Sweden)

    D. Kannan

    2012-04-01

    Full Text Available In the title compound, C21H19NO6, the isoindole ring system is essentially planar [maximum deviation = 0.019 (2 Å for the N atom] and is oriented at a dihedral angle of 51.3 (1° with respect to the benzene ring. The two methoxy groups are almost coplanar with the attached benzene ring [C—O—C—C = 3.7 (4 and 4.3 (4°]. The molecular conformation is stabilized by an intramolecular C—H...O hydrogen bond, which generates an S(9 ring motif. In the crystal, molecules are linked through bifurcated C—H...(O,O hydrogen bonds having R12(5 ring motifs, forming chains along the b-axis direction. The crystal packing is further stabilzed by π–π interactions [centriod–centroid distance = 3.463 (1 Å].

  19. (E)-Methyl 3-(3,4-dimeth-oxy-phen-yl)-2-[(1,3-dioxoisoindolin-2-yl)meth-yl]acrylate.

    Science.gov (United States)

    Kannan, D; Bakthadoss, M; Lakshmanan, D; Murugavel, S

    2012-04-01

    In the title compound, C(21)H(19)NO(6), the isoindole ring system is essentially planar [maximum deviation = 0.019 (2) Å for the N atom] and is oriented at a dihedral angle of 51.3 (1)° with respect to the benzene ring. The two meth-oxy groups are almost coplanar with the attached benzene ring [C-O-C-C = 3.7 (4) and 4.3 (4)°]. The mol-ecular conformation is stabilized by an intra-molecular C-H⋯O hydrogen bond, which generates an S(9) ring motif. In the crystal, mol-ecules are linked through bifurcated C-H⋯(O,O) hydrogen bonds having R(1) (2)(5) ring motifs, forming chains along the b-axis direction. The crystal packing is further stabilzed by π-π inter-actions [centriod-centroid distance = 3.463 (1) Å].

  20. Conserved XPB Core Structure and Motifs for DNA Unwinding:Implications for Pathway Selection of Transcription or ExcisionRepair

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Li; Arval, Andrew S.; Cooper, Priscilla K.; Iwai, Shigenori; Hanaoka, Fumio; Tainer, John A.

    2005-04-01

    The human xeroderma pigmentosum group B (XPB) helicase is essential for transcription, nucleotide excision repair, and TFIIH functional assembly. Here, we determined crystal structures of an Archaeoglobus fulgidus XPB homolog (AfXPB) that characterize two RecA-like XPB helicase domains and discover a DNA damage recognition domain (DRD), a unique RED motif, a flexible thumb motif (ThM), and implied conformational changes within a conserved functional core. RED motif mutations dramatically reduce helicase activity, and the DRD and ThM, which flank the RED motif, appear structurally as well as functionally analogous to the MutS mismatch recognition and DNA polymerase thumb domains. Substrate specificity is altered by DNA damage, such that AfXPB unwinds dsDNA with 3' extensions, but not blunt-ended dsDNA, unless it contains a lesion, as shown for CPD or (6-4) photoproducts. Together, these results provide an unexpected mechanism of DNA unwinding with Implications for XPB damage verification in nucleotide excision repair.

  1. MODA: an efficient algorithm for network motif discovery in biological networks.

    Science.gov (United States)

    Omidi, Saeed; Schreiber, Falk; Masoudi-Nejad, Ali

    2009-10-01

    In recent years, interest has been growing in the study of complex networks. Since Erdös and Rényi (1960) proposed their random graph model about 50 years ago, many researchers have investigated and shaped this field. Many indicators have been proposed to assess the global features of networks. Recently, an active research area has developed in studying local features named motifs as the building blocks of networks. Unfortunately, network motif discovery is a computationally hard problem and finding rather large motifs (larger than 8 nodes) by means of current algorithms is impractical as it demands too much computational effort. In this paper, we present a new algorithm (MODA) that incorporates techniques such as a pattern growth approach for extracting larger motifs efficiently. We have tested our algorithm and found it able to identify larger motifs with more than 8 nodes more efficiently than most of the current state-of-the-art motif discovery algorithms. While most of the algorithms rely on induced subgraphs as motifs of the networks, MODA is able to extract both induced and non-induced subgraphs simultaneously. The MODA source code is freely available at: http://LBB.ut.ac.ir/Download/LBBsoft/MODA/

  2. CombiMotif: A new algorithm for network motifs discovery in protein-protein interaction networks

    Science.gov (United States)

    Luo, Jiawei; Li, Guanghui; Song, Dan; Liang, Cheng

    2014-12-01

    Discovering motifs in protein-protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.

  3. MSDmotif: exploring protein sites and motifs

    Directory of Open Access Journals (Sweden)

    Henrick Kim

    2008-07-01

    Full Text Available Abstract Background Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. Results We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS protocol. An additional entry point facilitates XML requests with XML responses. Conclusion MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.

  4. 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.

  5. Study of improvement in 1st ring`s gas-seal; Top ring no gas seal seino kojo no kento

    Energy Technology Data Exchange (ETDEWEB)

    Ando, H; Tateishi, Y; Fujimura, K; Hitosugi, H [Nippon Piston Ring Co. Ltd., Tokyo (Japan)

    1997-10-01

    The authors studied the effect of an angle of 1st ring twist on the amount of blow-by concerning higher speed/higher output engines for motorcycles. As a result, the authors found the twist made the ring restrained in a ring groove of piston , and confirmed its suitable range for blow-by. By means of the developed optimization method, the authors have achieved significant reduction in blow-by at high engine speed. 1 ref., 9 figs., 2 tabs.

  6. Ethyl 4′-ethenyl-2′-oxo-4-phenyl-2-(3,4,5-trimethoxyphenylspiro[pyrrolidine-3,3′-indoline]-5-carboxylate monohydrate

    Directory of Open Access Journals (Sweden)

    P. Ramesh

    2008-11-01

    Full Text Available In the title compound, C31H32N2O6·H2O, the pyrrolidine ring adopts an envelope conformation. The ethyl C atoms of the ethoxycabonyl group are disordered over two positions with occupancies of ca 0.80 and 0.20. Intramolecular N—H...O hydrogen bonds form S(5 and S(6 ring motifs. Molecules are linked into a three-dimensional framework by O—H...O, N—H...O and C—H...O hydrogen bonds, and by C—H...π interactions.

  7. Leucine-based receptor sorting motifs are dependent on the spacing relative to the plasma membrane

    DEFF Research Database (Denmark)

    Geisler, C; Dietrich, J; Nielsen, B L

    1998-01-01

    Many integral membrane proteins contain leucine-based motifs within their cytoplasmic domains that mediate internalization and intracellular sorting. Two types of leucine-based motifs have been identified. One type is dependent on phosphorylation, whereas the other type, which includes an acidic...... amino acid, is constitutively active. In this study, we have investigated how the spacing relative to the plasma membrane affects the function of both types of leucine-based motifs. For phosphorylation-dependent leucine-based motifs, a minimal spacing of 7 residues between the plasma membrane...... and the phospho-acceptor was required for phosphorylation and thereby activation of the motifs. For constitutively active leucine-based motifs, a minimal spacing of 6 residues between the plasma membrane and the acidic residue was required for optimal activity of the motifs. In addition, we found that the acidic...

  8. Review article: The mountain motif in the plot of Matthew

    Directory of Open Access Journals (Sweden)

    Gert J. Volschenk

    2010-09-01

    Full Text Available This article reviewed T.L. Donaldson’s book, Jesus on the mountain: A study in Matthean theology, published in 1985 by JSOT Press, Sheffield, and focused on the mountain motif in the structure and plot of the Gospel of Matthew, in addition to the work of Donaldson on the mountain motif as a literary motif and as theological symbol. The mountain is a primary theological setting for Jesus’ ministry and thus is an important setting, serving as one of the literary devices by which Matthew structured and progressed his narrative. The Zion theological and eschatological significance and Second Temple Judaism serve as the historical and theological background for the mountain motif. The last mountain setting (Mt 28:16–20 is the culmination of the three theological themes in the plot of Matthew, namely Christology, ecclesiology and salvation history.

  9. A cyclic nucleotide-gated channel mutation associated with canine daylight blindness provides insight into a role for the S2 segment tri-Asp motif in channel biogenesis.

    Directory of Open Access Journals (Sweden)

    Naoto Tanaka

    Full Text Available Cone cyclic nucleotide-gated channels are tetramers formed by CNGA3 and CNGB3 subunits; CNGA3 subunits function as homotetrameric channels but CNGB3 exhibits channel function only when co-expressed with CNGA3. An aspartatic acid (Asp to asparagine (Asn missense mutation at position 262 in the canine CNGB3 (D262N subunit results in loss of cone function (daylight blindness, suggesting an important role for this aspartic acid residue in channel biogenesis and/or function. Asp 262 is located in a conserved region of the second transmembrane segment containing three Asp residues designated the Tri-Asp motif. This motif is conserved in all CNG channels. Here we examine mutations in canine CNGA3 homomeric channels using a combination of experimental and computational approaches. Mutations of these conserved Asp residues result in the absence of nucleotide-activated currents in heterologous expression. A fluorescent tag on CNGA3 shows mislocalization of mutant channels. Co-expressing CNGB3 Tri-Asp mutants with wild type CNGA3 results in some functional channels, however, their electrophysiological characterization matches the properties of homomeric CNGA3 channels. This failure to record heteromeric currents suggests that Asp/Asn mutations affect heteromeric subunit assembly. A homology model of S1-S6 of the CNGA3 channel was generated and relaxed in a membrane using molecular dynamics simulations. The model predicts that the Tri-Asp motif is involved in non-specific salt bridge pairings with positive residues of S3/S4. We propose that the D262N mutation in dogs with CNGB3-day blindness results in the loss of these inter-helical interactions altering the electrostatic equilibrium within in the S1-S4 bundle. Because residues analogous to Tri-Asp in the voltage-gated Shaker potassium channel family were implicated in monomer folding, we hypothesize that destabilizing these electrostatic interactions impairs the monomer folding state in D262N mutant CNG

  10. Statistical tests to compare motif count exceptionalities

    Directory of Open Access Journals (Sweden)

    Vandewalle Vincent

    2007-03-01

    Full Text Available Abstract Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.

  11. Analisis Peranan Franchisor Terhadap Suksesnya Bisnis Franchise Pada Mc. Donald’s Cabang Ring Road Medan

    OpenAIRE

    Simarmata, Leonardo

    2012-01-01

    Tujuan penelitian ini adalah untuk mengetahui dan menganalisis peranan franchisor dalam promotion, support service, training, control system dan communication terhadap suksesnya bisnis franchise pada Mc Donald’s Cabang Ring Road Medan. Pengumpulan data primer diperoleh dengan cara memberikan daftar pertanyaan (questionaire) dan melakukan wawancara (interview) secara mendalam (depth interview) kepada pemilik usaha M. Donald’s Cabang Ring Road Medan. Teknik analisis data penelitian ini ad...

  12. Thomson's Jumping Ring over a Long Coil

    Science.gov (United States)

    Jeffery, Rondo N.; Amiri, Farhang

    2018-01-01

    The classic jumping ring apparatus consists of a coil with an iron core that extends out of the coil. A copper or aluminum ring placed over the iron core jumps upward when AC power is applied to the coil. In this paper we will examine a modified design of the jumping ring apparatus, called the "long-coil design." It allows the ring to…

  13. Prestressed Ring Beam in the Church of St. Peter’s and Paul’s in Bodzanow, Design and Realization

    Science.gov (United States)

    Szydlowski, Rafal; Labuzek, Barbara; Turcza, Monika

    2017-10-01

    The present trend in architecture is designing thin. slender and spacious architectural forms. It has become the reason for searching for new solutions and finding new ways of use of the existing construction ones. Recently, the first time in Poland, the post-tensioning has been used in realization of church building. In the Church of St. Peter’s and Paul’s in Bodzanow (near Cracow) was designed circumferential ring beam post-tensioned with 4 unbounded tendons to transfer peripheral tensile forces from the roof. Thanks to the use of a prestressed ring beam hidden in the wall, large cross-section of roof girders was possible to be avoided, as well as a massive reinforced concrete ring or additional steel tie-rods. The paper presents the applied solutions in details with the theoretical calculated results as well as the results of prestressing measured in site during tensioning of tendons. Based on presented results some conclusions have been drawn.

  14. Crystal structure of 3-methoxy-2-[5-(naphthalen-1-yl-4,5-dihydro-1H-pyrazol-3-yl]phenol

    Directory of Open Access Journals (Sweden)

    Dongsoo Koh

    2015-11-01

    Full Text Available In the title compound, C20H18N2O2, the central pyrazoline ring has an envelope conformation with the atom substituted by the naphthalene ring as the flap. It bridges a benzene ring and a naphthalene ring system which are almost normal to one another, making a dihedral angle of 82.03 (6 °. There is an intramolecular O—H...N hydrogen bond forming an S(6 ring motif. In the crystal, molecules are linked by pairs of N—H...π interactions, forming inversion dimers. There are also C—H...π interactions present and the dimers are linked via C—H...O hydrogen bonds, forming ribbons propagating along the a-axis direction.

  15. Crystal structure of 2-[(3aS,6R-3,3,6-trimethyl-3,3a,4,5,6,7-hexahydro-2H-indazol-2-yl]thiazol-4(5H-one

    Directory of Open Access Journals (Sweden)

    Abdellah N'ait Ousidi

    2016-03-01

    Full Text Available The title compound, C13H19N3OS, is a new thiazolidin-4-one derivative prepared and isolated as the pure (3aS,6R-diastereisomer from (R-thiosemicarbazone pulegone. It crystallized with two independent molecules (A and B in the asymmetric unit. The compound is composed of a hexhydroindazole ring system (viz. a five-membered dihydropyrazole ring fused to a cyclohexyl ring with a thiazole-4-one ring system attached to one of the pyrazole N atoms (at position 2. The overall geometry of the two molecules differs slightly, with the mean planes of the pyrazole and thiazole rings being inclined to one another by 10.4 (1° in molecule A and 0.9 (1° in molecule B. In the crystal, the A and B molecules are linked via C—H...O hydrogen bonds, forming slabs parallel to the ab plane. There are C—H...π interactions present within the layers, and between the layers, so forming a three-dimensional structure.

  16. (E)-Methyl 3-(3,4-dimeth­oxy­phen­yl)-2-[(1,3-dioxoisoindolin-2-yl)meth­yl]acrylate

    Science.gov (United States)

    Kannan, D.; Bakthadoss, M.; Lakshmanan, D.; Murugavel, S.

    2012-01-01

    In the title compound, C21H19NO6, the isoindole ring system is essentially planar [maximum deviation = 0.019 (2) Å for the N atom] and is oriented at a dihedral angle of 51.3 (1)° with respect to the benzene ring. The two meth­oxy groups are almost coplanar with the attached benzene ring [C—O—C—C = 3.7 (4) and 4.3 (4)°]. The mol­ecular conformation is stabilized by an intra­molecular C—H⋯O hydrogen bond, which generates an S(9) ring motif. In the crystal, mol­ecules are linked through bifurcated C—H⋯(O,O) hydrogen bonds having R 1 2(5) ring motifs, forming chains along the b-axis direction. The crystal packing is further stabilzed by π–π inter­actions [centriod–centroid distance = 3.463 (1) Å]. PMID:22589965

  17. On propagating direction of ring current proton ULF waves observed by ATS 6 at 6.6 R/sub e/

    International Nuclear Information System (INIS)

    Su, S.; Konradi, A.; Fritz, T.A.

    1977-01-01

    From June 11 to September 16, 1974, the NOAA low-energy proton detector on board the ATS 6 satellite observed 71 cases of ultralow-frequency oscillations of proton flux intensities. The oscillation periods varied from 40 s to 6 min, and the events were observed most frequently during moderate geomagnetic conditions. The flux oscillations occurred at various local times, yet almost two thirds of the events were detected in the near-dusk region of the magentosphere. For a majority of the events in this set a substantial phase shift in flux oscillation was detected between different energy channels and/or between two oppositely oriented detector telescopes. The phase shift is mainly due to the finite gyroradius effect of the protons gyrating in the geomagnetic field. By examining this finite gyroradius effect on the perturbed particle distribution function associated with the wave in a nonuniform magnetic field we are able to determine the propagation direction of the wave from particle observations made by a single spacecraft. Although the type of wave and its excitation mechanism can only be conjectured at the present time, it is concluded that the wave propagates in the westward direction with a phase velocity of about 13 km/s. Furthermore, it also has a very small phase velocity approx.0.15 km/s propagating toward the earth. If the wave had been traveling 1 hour or so before it was observed near the dusk magnetosphere, it might have originated in the dark magnetosphere in associating with some changes in geophysical conditions. The statistical correlation between the times of the observed wave events and the onsets of the auroral magnetic bays indicates that although they seldom occurred simultaneously, 80% of the waves were observed within 1 hour of the bay onset. Therefore it is concluded that the condition of the magnetosphere after a substorm is favorable for the occurrence of the ring current proton ultralow-frequency waves

  18. Polarization and pressure effects in caesium 6S-8S two-photon spectroscopy

    International Nuclear Information System (INIS)

    Lee, Yi-Chi; Tsai, Chin-Chun; Chui, Hsiang-Chen; Chang, Yi-Hsiu; Chen, Ying-Yu

    2010-01-01

    This work analyses the effects of polarization and pressure in caesium 6S-8S two-photon spectroscopy. The linewidth was broadened and the frequency was shifted by a change of polarization states. The frequency shift and the linewidth broadening of the caesium 6S-8S two-photon transition were measured as a function of laser power using one single-frequency Ti:sapphire ring cavity laser, two caesium cells and two quarter-wave plates to ensure polarization states of light, and we showed that the linewidth cannot be evaluated just by fitting data to a Lorentzian shape. As determined by fitting the data to a Voigt profile, the natural linewidth is independent of the polarization states of the pump beams, the laser power and the pressure. Caesium 6S-8S two-photon transitions pumped by a circularly polarized beam have narrower linewidths and smaller shifts than those pumped by a linearly polarized beam. The light shift obtained by pumping with the circularly polarized beam is -6.75(57) Hz (mW mm -2 ) -1 , and that obtained by pumping with a linearly polarized beam is -7.25(45) Hz (mW mm -2 ) -1 . These results agree closely with theoretical calculations. The pressure shift is -588(387) Hz mPa -1 . This work shows how to evaluate two-photon transitions with a Voigt profile, and then helps us to understand two-photon transitions with different polarization states, and improve the signal quality obtained when they are used as frequency markers.

  19. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

  20. Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Hanke, S.; Hinsby, A. M.

    2008-01-01

    set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr......(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified...

  1. (E-4-Amino-N′-(2-hydroxy-5-methylbenzylidenebenzohydrazide

    Directory of Open Access Journals (Sweden)

    Hadi Kargar

    2012-07-01

    Full Text Available The asymmetric unit of the title compound, C15H15N3O2, comprises two crystallographically independent molecules (A and B, each having an E conformation around the C=N bond. In each molecule, there is an intramolecular O—H...N hydrogen bond making an S(6 ring motif. The dihedral angles between the substituted phenyl rings are 17.49 (9 and 10.03 (9°. In the crystal, N—H...O hydrogen bonds link neighbouring independent molecules into infinite chains, of the type –A–B–A–B–, along the a axis, enclosing R21(7 ring motifs. The chains are linked by N—H...O hydrogen bonds and C—H...O interactions, leading to the formation of a three-dimensional network.

  2. Investigations into the construction of the pentasubstituted ring C of Neosurugatoxin – a crystallographic study

    Directory of Open Access Journals (Sweden)

    Alan M. Jones

    2016-01-01

    Full Text Available The crystal structures of three cyclopenta[c]furans with various substituents at the 4-, 5- and 6-positions of the ring system are reported, namely, (±-(3aR,4S,5S,6aS-4-methyl-5-phenylhexahydro-1H-cyclopenta[c]furan-4,5-diol, C14H18O3, (I, (±-(3aR,4S,5S,6aS-4-benzyloxy-4-methyl-5-phenylhexahydro-1H-cyclopenta[c]furan-5-ol, C21H24O3, (II, and (±-(1aR,1bS,4aR,5S,5aR-5-benzyloxy-5-methyl-5a-phenylhexahydro-2H-oxireno[2′,3′:3,4]cyclopenta[1,2-c]furan, C21H22O3, (III. The dominant interaction in (I and (II is an O—H...O hydrogen bond across the bicyclic 5,5-ring system between the non-functionalized hydroxy group and the tetrahydrofuran O atom, which appears to influence the envelope conformations of the fused five-membered rings, whereas in (III, the rings have different conformations. A weak intramolecular C—H...O interaction appears to influence the degree of tilt of the phenyl ring attached to the 5-position and is different in (I compared to (II and (III.

  3. 4-{(E-[2-(4-Iodobutoxybenzylidene]amino}-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H-one

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2010-07-01

    Full Text Available The title Schiff base compound, C22H24IN3O2, adopts an E configuration about the central C=N bond. The pyrazolone ring makes a dihedral angle of 49.68 (10° with its attached phenyl ring. The phenolate plane makes dihedral angles of 16.78 (9 and 50.54 (9°, respectively, with the pyrazolone ring and the terminal phenyl ring. An intramolecular C—H...O hydrogen bond generates an S(6 ring motif. In the crystal structure, an intermolecular C—H...O hydrogen bond is also observed.

  4. (E-1-(2,4-Dinitrophenyl-2-(3-ethoxy-4-hydroxybenzylidenehydrazine

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2014-01-01

    Full Text Available The molecule of the title hydrazine derivative, C15H14N4O6, is essentially planar, the dihedral angle between the substituted benzene rings being 2.25 (9°. The ethoxy and hydroxy groups are almost coplanar with their bound benzene ring [r.m.s. deviation = 0.0153 (2 Å for the ten non-H atoms]. Intramolecular N—H...O and O—H...Oethoxy hydrogen bonds generate S(6 and S(5 ring motifs, respectively. In the crystal, molecules are linked by O—H...Onitro hydrogen bonds into chains propagating in [010]. Weak aromatic π–π interactions, with centroid–centroid distances of 3.8192 (19 and 4.0491 (19 Å, are also observed.

  5. Hard x-ray measurements of the hot-electron rings in EBT-S

    International Nuclear Information System (INIS)

    Hillis, D.L.

    1982-06-01

    A thorough understanding of the hot electron rings in ELMO Bumpy Torus-Scale (EBT-S) is essential to the bumpy torus concept of plasma production, since the rings provide bulk plasma stability. The hot electrons are produced via electron cyclotron resonant heating using a 28-GHz cw gyrotron, which has operated up to power levels of 200 kW. The parameters of the energetic electron rings are studied via hard x-ray measurement techniques and with diamagnetic pickup coils. The hard x-ray measurements have used collimated NaI(Tl) detectors to determine the electron temperature T/sub e/ and electron density n/sub e/ for the hot electron annulus. Typical values of T/sub e/ are 400 to 500 keV and of n/sub e/ 2 to 5 x 10 11 cm -3 . The total stored energy of a single energetic electron ring as measured by diamagnetic pickup loops approaches approx. 40 J and is in good agreement with that deduced from hard x-ray measurements. By combining the experimental measurements from hard x-rays and the diamagnetic loops, an estimate can be obtained for the volume of a single hot electron ring. The ring volume is determined to be approx. 2.2 litres, and this volume remains approximately constant over the T-mode operating regime. Finally, the power in the electrons scattered out of the ring is measured indirectly by measuring the x-ray radiation produced when those electrons strike the chamber walls. The variation of this radiation with increasing microwave power levels is found to be consistent with classical scattering estimates

  6. [Personal motif in art].

    Science.gov (United States)

    Gerevich, József

    2015-01-01

    One of the basic questions of the art psychology is whether a personal motif is to be found behind works of art and if so, how openly or indirectly it appears in the work itself. Analysis of examples and documents from the fine arts and literature allow us to conclude that the personal motif that can be identified by the viewer through symbols, at times easily at others with more difficulty, gives an emotional plus to the artistic product. The personal motif may be found in traumatic experiences, in communication to the model or with other emotionally important persons (mourning, disappointment, revenge, hatred, rivalry, revolt etc.), in self-searching, or self-analysis. The emotions are expressed in artistic activity either directly or indirectly. The intention nourished by the artist's identity (Kunstwollen) may stand in the way of spontaneous self-expression, channelling it into hidden paths. Under the influence of certain circumstances, the artist may arouse in the viewer, consciously or unconsciously, an illusionary, misleading image of himself. An examination of the personal motif is one of the important research areas of art therapy.

  7. Temporal motifs in time-dependent networks

    International Nuclear Information System (INIS)

    Kovanen, Lauri; Karsai, Márton; Kaski, Kimmo; Kertész, János; Saramäki, Jari

    2011-01-01

    Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as telecommunication, neural signal processing, biochemical reaction and human social interaction networks. We introduce the framework of temporal motifs to study the mesoscale topological–temporal structure of temporal networks in which the events of nodes do not overlap in time. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences to coloured directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network

  8. Current’s Fluctuations through Molecular Wires Composed of Thiophene Rings

    Directory of Open Access Journals (Sweden)

    Judith Helena Ojeda Silva

    2018-04-01

    Full Text Available We study theoretically the electronic transport and quantum fluctuations in single-molecule systems using thiophene rings as integrated elementary functions, as well as the dependence of these properties with the increase of the coupled rings, i.e., as a quantum wire. In order to analyze the current flow through these molecular systems, the thiophene rings are considered to be connected to metal contacts, which, in general terms, will be related to the application of voltages (bias voltages or gate voltages to generate non-equilibrium behavior between the contacts. Due to the nonlinear behavior that is generated when said voltages are applied, it is possible to observe quantum fluctuations in the transport properties of these molecular wires. For the calculation of the transport properties, we applied a tight-binding approach using the Landauer–Büttiker formalism and the Fischer–Lee relationship, by means of a semi-analytic Green’s function method within a real-space renormalization (decimation procedure. Our results showed an excellent agreement with results using a tight-binding model with a minimal number of parameters reported so far for these molecular systems.

  9. Robustness and backbone motif of a cancer network regulated by miR-17-92 cluster during the G1/S transition.

    Directory of Open Access Journals (Sweden)

    Lijian Yang

    Full Text Available Based on interactions among transcription factors, oncogenes, tumor suppressors and microRNAs, a Boolean model of cancer network regulated by miR-17-92 cluster is constructed, and the network is associated with the control of G1/S transition in the mammalian cell cycle. The robustness properties of this regulatory network are investigated by virtue of the Boolean network theory. It is found that, during G1/S transition in the cell cycle process, the regulatory networks are robustly constructed, and the robustness property is largely preserved with respect to small perturbations to the network. By using the unique process-based approach, the structure of this network is analyzed. It is shown that the network can be decomposed into a backbone motif which provides the main biological functions, and a remaining motif which makes the regulatory system more stable. The critical role of miR-17-92 in suppressing the G1/S cell cycle checkpoint and increasing the uncontrolled proliferation of the cancer cells by targeting a genetic network of interacting proteins is displayed with our model.

  10. Crystal structure of (1S,3R,8R,9R,10S-2,4,6-tris(2,2-dichloro-3,7,7,10-tetramethyltricyclo[6.4.0.01,3]dodec-9-ylcyclotriboroxane

    Directory of Open Access Journals (Sweden)

    Ahmed Benharref

    2015-08-01

    Full Text Available The title compound, C48H75B3Cl6O3, was synthesized in two steps from β-himachalene (3,5,5,9-tetramethyl-2,4a,5,6,7,8-hexahydro-1H-benzocycloheptene, which was isolated from the essential oil of the Atlas cedar (Cedrus Atlantica. The molecule consists of an almost planar cyclotriboroxane ring [maximum deviation = 0.036 (2 Å] linked to three identical fused ring systems with different conformations. Each of the three attached ring systems is built up from a seven-membered ring to which a six- and a three-membered ring are fused. The three six-membered rings have a twist-boat conformation, whereas the seven-membered rings display boat, chair and twist-boat conformations. The dihedral angles between the central boroxane ring and the mean planes of the attached six-membered rings are 63.67 (18, 54.89 (2 and 56.57 (19°. The crystal packing is governed only by van der Waals interactions.

  11. 4,4′-Dimethoxy-2,2′-[(butane-1,4-diyldioxybis(nitrilomethylidyne]diphenol

    Directory of Open Access Journals (Sweden)

    Yin-Xia Sun

    2010-11-01

    Full Text Available The title Schiff base bisoxime compound, C20H24N2O6, lies across an inversion centre and adopts an E configuration with respect to the C=N bond. In the molecule, the oxime group is roughly coplanar with the benzene ring, forming a dihedral angle of 1.77 (2°. An intramolecular O—H...N hydrogen bond forms a six-membered ring with an S(6 motif. Weak intermolecular C—H...O hydrogen bonding is present in the crystal structure.

  12. Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif

    Directory of Open Access Journals (Sweden)

    Launey Thomas

    2011-06-01

    Full Text Available Abstract Background The interactions between PDZ (PSD-95, Dlg, ZO-1 domains and PDZ-binding motifs play central roles in signal transductions within cells. Proteins with PDZ domains bind to PDZ-binding motifs almost exclusively when the motifs are located at the carboxyl (C- terminal ends of their binding partners. However, it remains little explored whether PDZ-binding motifs show any preferential location at the C-terminal ends of proteins, at genome-level. Results Here, we examined the distribution of the type-I (x-x-S/T-x-I/L/V or type-II (x-x-V-x-I/V PDZ-binding motifs in proteins encoded in the genomes of five different species (human, mouse, zebrafish, fruit fly and nematode. We first established that these PDZ-binding motifs are indeed preferentially present at their C-terminal ends. Moreover, we found specific amino acid (AA bias for the 'x' positions in the motifs at the C-terminal ends. In general, hydrophilic AAs were favored. Our genomics-based findings confirm and largely extend the results of previous interaction-based studies, allowing us to propose refined consensus sequences for all of the examined PDZ-binding motifs. An ontological analysis revealed that the refined motifs are functionally relevant since a large fraction of the proteins bearing the motif appear to be involved in signal transduction. Furthermore, co-precipitation experiments confirmed two new protein interactions predicted by our genomics-based approach. Finally, we show that influenza virus pathogenicity can be correlated with PDZ-binding motif, with high-virulence viral proteins bearing a refined PDZ-binding motif. Conclusions Our refined definition of PDZ-binding motifs should provide important clues for identifying functional PDZ-binding motifs and proteins involved in signal transduction.

  13. (5S,6R-6-Bromo-6-methyl-5-phenyl-3,4,5,6-tetrahydro-2H-cyclopenta[b]pyran-7-one

    Directory of Open Access Journals (Sweden)

    Winai Ieawsuwan

    2011-10-01

    Full Text Available The title compound, C15H15BrO2, was synthesized by a Brønsted acid-catalysed domino electrocyclization-halogenation reaction. The five-membered ring is essentially planar (r.m.s. deviation 0.006 Å and forms a dihedral angle of 72.7 (3° with the attached phenyl ring. The six-membered heterocycle adopts a half-chair conformation. The crystal packing is stabilized by a C—H...O contact.

  14. Continuously tunable S and C+L bands ultra wideband erbium-doped fiber ring laser

    International Nuclear Information System (INIS)

    Wang, Q; Yu, Q X

    2009-01-01

    This paper presents an ultra wideband tunable silica-based erbium doped fiber ring laser (EDFRL) that can be continuously tuned in S and C+L bands from 1475 to 1619 nm. It is the first time that a fiber ring laser's tuning range reaches 144 nm using a standard silica-based C-band erbium-doped fiber as gain media. In the laser configuration two isolators are used in the fiber loop for suppressing the ASE in C-band and elevating the lasing gain in S-band. As a result the available lasing wavelength is extended toward the shorter wavelength of the gain bandwidth. The optimized erbium-doped fiber length, output coupling ratio and pumping laser power have been obtained through experimental study. This ring fiber laser has simple configuration, low threshold, flat laser spectral distribution and high signal-to-ASE-noise ratio. The laser will have many potential applications in fiber sensor wavelength interrogation, high-resolution spectroscopy and fiber optic communications

  15. Crystal structure of 2-cyano-N-(furan-2-ylmethyl-3-(3-nitrophenylpropanamide

    Directory of Open Access Journals (Sweden)

    Shivanna Subhadramma

    2015-08-01

    Full Text Available In the title compound, C15H11N3O4, the acetamide group is inclined to the furan ring by 66.5 (1°. The dihedral angle between the furan ring and the benzene ring is 66.8 (1°. In the crystal, molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with an R22(12 ring motif. The dimers are linked via two pairs of C—H...O hydrogen bonds to the same acceptor oxygen atom, enclosing R21(6 ring motifs, forming chains along the [101] direction.

  16. Functional Characterization of the Apple RING E3 Ligase MdMIEL1 in Transgenic Arabidopsis

    Directory of Open Access Journals (Sweden)

    Jianping AN

    2017-03-01

    Full Text Available E3 ubiquitin ligases are involved in various physiological processes, and they play pivotal roles in growth and development. In this study, we identified a previously unknown gene in the apple fruit (Malus × domestica and named it MdMIEL1. The MdMIEL1 gene encoded a protein that contained a zinc-finger domain at its N-terminus and a RING-finger motif at its C-terminus. To investigate MdMIEL1 functions, we generated transgenic Arabidopsis lines expressing the MdMIEL1 gene under the control of the Cauliflower mosaic virus 35S promoter. Interestingly, ectopic expression of MdMIEL1 in Arabidopsis produced multiple phenotypes, including early germination, early flowering and a lateral root number increase relative to wild-type plants. Further analysis indicated that MdMIEL1 regulated lateral root initiation by increasing auxin accumulation in the roots. In a word, these results suggest that, MdMIEL1 as a novel RING-finger ubiquitin ligase influences plant growth and development, and highlight that MdMIEL1 regulates lateral root growth.

  17. Large-scale discovery of promoter motifs in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Thomas A Down

    2007-01-01

    Full Text Available A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.

  18. Crystal structure of 4-(4-chlorophenyl-6-(morpholin-4-ylpyridazin-3(2H-one

    Directory of Open Access Journals (Sweden)

    Abdullah Aydın

    2015-08-01

    Full Text Available In the title compound, C14H14ClN3O2, the morpholine ring adopts a chair conformation, with the exocyclic N—C bond in an equatorial orientation. The 1,6-dihydropyridazine ring is essentially planar, with a maximum deviation of 0.014 (1 Å, and forms a dihedral angle of 40.16 (7° with the plane of the benzene ring. In the crystal, pairs of centrosymmetrically related molecules are linked into dimers via N—H...O hydrogen bonds, forming R22(8 ring motifs. The dimers are connected via C—H...O and C—H...Cl hydrogen bonds, forming a three-dimensional network. Aromatic π–π stacking interactions [centroid–centroid distance = 3.6665 (9 Å] are also observed. Semi-empirical molecular orbital calculations were carried out using the AM1 method. The calculated dihedral angles between the pyridizine and benzene rings and between the pyridizine and morpholine (all atoms rings are 34.49 and 76.96°, respectively·The corresponding values obtained from the X-ray structure determination are 40.16 (7 and 12.97 (9°, respectively. The morpholine ring of the title compound in the calculated gas-phase seems to have a quite different orientation compared to that indicated by the X-ray structure determination.

  19. 4-(4-Bromophenyl-7,7-dimethyl-2-methylamino-3-nitro-7,8-dihydro-4H-chromen-5(6H-one including an unknown solvate

    Directory of Open Access Journals (Sweden)

    S. Antony Inglebert

    2014-05-01

    Full Text Available In the title compound, C18H19BrN2O4, the chromene unit is not quite planar (r.m.s. deviation = 0.199 Å, with the methyl C atoms lying 0.027 (4 and 1.929 (4 Å from the mean plane of the chromene unit. The six-membered carbocyclic ring of the chromene moiety adopts an envelope conformation, with the dimethyl-substituted C atom as the flap. The methylamine and nitro groups are slightly twisted from the chromene moiety, with C—N—C—O and O—N—C—C torsion angles of 2.7 (4 and −0.4 (4°, respectively. The dihedral angle between the mean plane of the chromene unit and the benzene ring is 85.61 (13°. An intramolecular N—H...O hydrogen bond generates an S(6 ring motif, which stabilizes the molecular conformation. In the crystal, molecules are linked via N—H...O hydrogen bonds, forming hexagonal rings lying parallel to the ab plane. A region of disordered electron density, most probably disordered ethanol solvent molecules, occupying voids of ca 432 Å3 for an electron count of 158, was treated using the SQUEEZE routine in PLATON [Spek (2009. Acta Cryst. D65, 148–155]. Their formula mass and unit-cell characteristics were not taken into account during refinement.

  20. MHC motif viewer

    DEFF Research Database (Denmark)

    Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole

    2008-01-01

    . Algorithms that predict which peptides MHC molecules bind have recently been developed and cover many different alleles, but the utility of these algorithms is hampered by the lack of tools for browsing and comparing the specificity of these molecules. We have, therefore, developed a web server, MHC motif....... A special viewing feature, MHC fight, allows for display of the specificity of two different MHC molecules side by side. We show how the web server can be used to discover and display surprising similarities as well as differences between MHC molecules within and between different species. The MHC motif...

  1. Motif discovery in ranked lists of sequences

    DEFF Research Database (Denmark)

    Nielsen, Morten Muhlig; Tataru, Paula; Madsen, Tobias

    2016-01-01

    Motif analysis has long been an important method to characterize biological functionality and the current growth of sequencing-based genomics experiments further extends its potential. These diverse experiments often generate sequence lists ranked by some functional property. There is therefore...... advantage of the regular expression feature, including enrichments for combinations of different microRNA seed sites. The method is implemented and made publicly available as an R package and supports high parallelization on multi-core machinery....... a growing need for motif analysis methods that can exploit this coupled data structure and be tailored for specific biological questions. Here, we present an exploratory motif analysis tool, Regmex (REGular expression Motif EXplorer), which offers several methods to evaluate the correlation of motifs...

  2. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

    Science.gov (United States)

    Castro-Mondragon, Jaime Abraham; Jaeger, Sébastien; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

    2017-07-27

    Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. 2-Amino-5-bromopyridinium 2-hydroxybenzoate

    Directory of Open Access Journals (Sweden)

    Ching Kheng Quah

    2010-08-01

    Full Text Available In the title compound, C5H6BrN2+·C7H5O3−, the 2-amino-5-bromopyridinium cation and 2-hydroxybenzoate anion are essentially planar with maximum deviations of 0.020 (1 and 0.018 (2 Å, respectively. The anion is stabilized by an intramolecular O—H...O hydrogen bond, which generates an S(6 ring motif. In the crystal, the cations and anions are linked by N—H...O hydrogen bonds into chains propagating along [010]. The chains contain R22(8 ring motifs. The structure is further stabilized by π–π stacking interactions [centroid–centroid distances = 3.4908 (10 and 3.5927 (10 Å] and also features short Br...O contacts [2.9671 (13 Å].

  4. Deciphering functional glycosaminoglycan motifs in development.

    Science.gov (United States)

    Townley, Robert A; Bülow, Hannes E

    2018-03-23

    Glycosaminoglycans (GAGs) such as heparan sulfate, chondroitin/dermatan sulfate, and keratan sulfate are linear glycans, which when attached to protein backbones form proteoglycans. GAGs are essential components of the extracellular space in metazoans. Extensive modifications of the glycans such as sulfation, deacetylation and epimerization create structural GAG motifs. These motifs regulate protein-protein interactions and are thereby repsonsible for many of the essential functions of GAGs. This review focusses on recent genetic approaches to characterize GAG motifs and their function in defined signaling pathways during development. We discuss a coding approach for GAGs that would enable computational analyses of GAG sequences such as alignments and the computation of position weight matrices to describe GAG motifs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Fitness for synchronization of network motifs

    DEFF Research Database (Denmark)

    Vega, Y.M.; Vázquez-Prada, M.; Pacheco, A.F.

    2004-01-01

    We study the synchronization of Kuramoto's oscillators in small parts of networks known as motifs. We first report on the system dynamics for the case of a scale-free network and show the existence of a non-trivial critical point. We compute the probability that network motifs synchronize, and fi...... that the fitness for synchronization correlates well with motifs interconnectedness and structural complexity. Possible implications for present debates about network evolution in biological and other systems are discussed....

  6. N-(2,4-Dichlorophenyl-1,3-thiazol-2-amine

    Directory of Open Access Journals (Sweden)

    Ayesha Babar

    2012-09-01

    Full Text Available In the title molecule, C9H6Cl2N2S, the mean planes of the benzene and thiazole rings make a dihedral angle of 54.18 (8°. In the crystal, molecules are joined into dimers with an R22(8 ring motif by pairs of N—H...N hydrogen bonds. These dimers are linked by C—H...Cl interactions into layers parallel to (011. The thiazole rings form columns along the c-axis direction, with a centroid–centroid separation of 3.8581 (9 Å, indicating π–π interactions. An intramolecular C—H...S contact also occurs.

  7. 4-Benzyl-6-bromo-2-(4-chlorophenyl)-4H-imidazo[4,5-b]pyridine

    OpenAIRE

    Selma Bourichi; Youssef Kandri Rodi; Jerry P. Jasinski; Manpreet Kaur; Younes Ouzidan; El Mokhtar Essassi

    2017-01-01

    In the title compound, C19H13BrClN3, the chlorophenyl ring occupies an equatorial position with respect to the mean plane of the imidazopyridine unit, while the other phenyl ring is twisted by 4.1 (2)° with respect to the mean plane of the imidazopyridine unit. In the crystal, pairwise C—H...Br interactions link the molecules into dimers, forming an R22(16) ring motif. In addition, weak π–π stacking interactions stabilize the crystal packing.

  8. 4-Benzyl-6-bromo-2-(4-chlorophenyl-4H-imidazo[4,5-b]pyridine

    Directory of Open Access Journals (Sweden)

    Selma Bourichi

    2017-06-01

    Full Text Available In the title compound, C19H13BrClN3, the chlorophenyl ring occupies an equatorial position with respect to the mean plane of the imidazopyridine unit, while the other phenyl ring is twisted by 4.1 (2° with respect to the mean plane of the imidazopyridine unit. In the crystal, pairwise C—H...Br interactions link the molecules into dimers, forming an R22(16 ring motif. In addition, weak π–π stacking interactions stabilize the crystal packing.

  9. Aplikasi Ornamen Khas Maluku untuk Pengembangan Desain Motif Batik

    Directory of Open Access Journals (Sweden)

    Masiswo Masiswo

    2016-04-01

    Full Text Available ABSTRAKMaluku memiliki banyak ragam hias budaya warisan nilai leluhur berupa ornamen etnis yang merupakan kesenian dan keterampilan kerajinan. Hasil warisan tersebut sampai saat ini masih lestari hidup serta dapat dinikmati sebagai konsumsi rohani yang memuaskan manusia. Berkaitan dengan keberlangsungan nilai-nilai tradisi etnis yang berwujud pada ornamen-ornamen daerah Maluku, maka dikembangkan untuk kebutuhan manusia berupa motif batik pada kain. Pengembangan ornamen ini lebih menekankan pada representasi akan bentuk-bentuk ornamen yang diterapkan pada kerajinan batik berupa motif khas Maluku. Pengembangan alternatif desain motif batik dibuat tiga variasi yang bersumber dari ornamen khas Maluku dibuat prototipe produknya dan diuji ketahanan luntur warnanya. Hasil uji ketahanan luntur warna terhadap gosokan basah dari tiga prototipe produk berpredikat baik sekali terdapat pada “Motif Siwa” dan predikat baik pada motif “Siwa Talang” dan motif “Matahari Siwa Talang”.Kata kunci: desain, Maluku, motif batik, ornamenABSTRACTMaluku has much decorative ancestral cultural heritage value in the form of ornament ethnic arts and crafts skills. The result of the legacy is still sustainable living can be enjoyed as well as satisfying spiritual human consumption.Related to the sustainability of traditional values in the form of ethnic ornaments Maluku, it was developed for human needs in the form of batik cloth . The development of these ornaments will be more emphasis on the representation forms of ornamentation that is applied to a batik motif Maluku. Development of alternative design motif made three variations. The development of three alternative design motifs derived from the Maluku ornaments made and tested a prototype product color fastness. The test results of color fastness to wet rubbing of the three prototypes are excellent products predicated on the "Motif Siwa" and a good rating on the motif "Siwa Talang" and motif "Matahari Siwa

  10. Development of high-speed reactive processing system for carbon fiber-reinforced polyamide-6 composite: In-situ anionic ring-opening polymerization

    International Nuclear Information System (INIS)

    Kim, Sang-Woo; Seong, Dong Gi; Yi, Jin-Woo; Um, Moon-Kwang

    2016-01-01

    In order to manufacture carbon fiber-reinforced polyamide-6 (PA-6) composite, we optimized the reactive processing system. The in-situ anionic ring-opening polymerization of ε-caprolactam was utilized with proper catalyst and initiator for PA-6 matrix. The mechanical properties such as tensile strength, inter-laminar shear strength and compressive strength of the produced carbon fiber-reinforced PA-6 composite were measured, which were compared with the corresponding scanning electron microscope (SEM) images to investigate the polymer properties as well as the interfacial interaction between fiber and polymer matrix. Furthermore, kinetics of in-situ anionic ring-opening polymerization of ε-caprolactam will be discussed in the viewpoint of increasing manufacturing speed and interfacial bonding between PA-6 matrix and carbon fiber during polymerization.

  11. Development of high-speed reactive processing system for carbon fiber-reinforced polyamide-6 composite: In-situ anionic ring-opening polymerization

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sang-Woo; Seong, Dong Gi; Yi, Jin-Woo; Um, Moon-Kwang [Composites Research Division, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 642–831 (Korea, Republic of)

    2016-05-18

    In order to manufacture carbon fiber-reinforced polyamide-6 (PA-6) composite, we optimized the reactive processing system. The in-situ anionic ring-opening polymerization of ε-caprolactam was utilized with proper catalyst and initiator for PA-6 matrix. The mechanical properties such as tensile strength, inter-laminar shear strength and compressive strength of the produced carbon fiber-reinforced PA-6 composite were measured, which were compared with the corresponding scanning electron microscope (SEM) images to investigate the polymer properties as well as the interfacial interaction between fiber and polymer matrix. Furthermore, kinetics of in-situ anionic ring-opening polymerization of ε-caprolactam will be discussed in the viewpoint of increasing manufacturing speed and interfacial bonding between PA-6 matrix and carbon fiber during polymerization.

  12. The limits of de novo DNA motif discovery.

    Directory of Open Access Journals (Sweden)

    David Simcha

    Full Text Available A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of

  13. Tricuspid annuloplasty with the MC3 ring and septal plication technique.

    Science.gov (United States)

    Isomura, Tadashi; Hirota, Masanori; Hoshino, Joji; Fukada, Yasuhisa; Kondo, Taichi; Takahashi, Yu

    2015-01-01

    Functional tricuspid regurgitation is caused by annular dilation mainly in the posterior annulus. However, ring annuloplasty does not always prevent the recurrence of tricuspid regurgitation due to dilation of the septal annulus. We developed a septal plication technique with a 3-dimensional MC3 ring. Between 2006 and 2011, 76 patients (male/female 30/46; mean age 68 ± 11 years) with functional tricuspid regurgitation received tricuspid ring annuloplasty. After placement of the annular sutures, the 3 commissural ring portions were fixed on the equivalent commissures to plicate the anterior and posterior annulus. The end of the septal ring portion was fixed at the optimal annular position to obtain minimal tricuspid regurgitation. All patients were followed-up for a mean of 47 ± 18 months; the longest duration was 79 months. Although there was no operative death, one patient died of sepsis during hospitalization (hospital mortality 1.3%). After implantation of the MC3 ring (mean size 31.0 ± 3.3 mm), additional edge-to-edge sutures were required for minor leakage in 5 (7%) patients. The degree of tricuspid regurgitation was significantly reduced at discharge (0.5 ± 0.6) and midterm (0.6 ± 0.6) compared to 2.5 ± 0.7 before the operation (p tricuspid ring annuloplasty with a 3-dimensional MC3 ring. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  14. A novel fibronectin binding motif in MSCRAMMs targets F3 modules.

    Directory of Open Access Journals (Sweden)

    Sabitha Prabhakaran

    Full Text Available BBK32 is a surface expressed lipoprotein and fibronectin (Fn-binding microbial surface component recognizing adhesive matrix molecule (MSCRAMM of Borrelia burgdorferi, the causative agent of Lyme disease. Previous studies from our group showed that BBK32 is a virulence factor in experimental Lyme disease and located the Fn-binding region to residues 21-205 of the lipoprotein.Studies aimed at identifying interacting sites between BBK32 and Fn revealed an interaction between the MSCRAMM and the Fn F3 modules. Further analysis of this interaction showed that BBK32 can cause the aggregation of human plasma Fn in a similar concentration-dependent manner to that of anastellin, the superfibronectin (sFn inducing agent. The resulting Fn aggregates are conformationally distinct from plasma Fn as indicated by a change in available thermolysin cleavage sites. Recombinant BBK32 and anastellin affect the structure of Fn matrices formed by cultured fibroblasts and inhibit endothelial cell proliferation similarly. Within BBK32, we have located the sFn-forming activity to a region between residues 160 and 175 which contains two sequence motifs that are also found in anastellin. Synthetic peptides mimicking these motifs induce Fn aggregation, whereas a peptide with a scrambled sequence motif was inactive, suggesting that these motifs represent the sFn-inducing sequence.We conclude that BBK32 induces the formation of Fn aggregates that are indistinguishable from those formed by anastellin. The results of this study provide evidence for how bacteria can target host proteins to manipulate host cell activities.

  15. 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.

  16. N′-(3,5-Dibromo-2-hydroxybenzylidene-2-methylbenzohydrazide

    Directory of Open Access Journals (Sweden)

    Chun-Bao Tang

    2010-12-01

    Full Text Available The asymmetric unit of the title compound, C15H12Br2N2O2, contains two independent molecules in which the dihedral angles between the benzene rings are 49.5 (7 and 66.4 (7°. Intramolecular O—H...N hydrogen bonds generate S(6 ring motifs in each molecule. In the crystal, molecules are linked through intermolecular N—H...O hydrogen bonds, forming chains along the b axis.

  17. Weyl Exceptional Rings in a Three-Dimensional Dissipative Cold Atomic Gas (Author’s Manuscript)

    Science.gov (United States)

    2017-01-27

    in a dissipative system with particle gain and loss, we discover a new type of topological ring, dubbed Weyl exceptional ring consisting of...valued. On the other hand , the Chern number is zero when the surface S does not enclose any part of the ring even when it is located inside it...k)〉 and Ãθ(k) = i〈ũθ(k)|∂kuθ(k)〉, where 〈ũθ(k)| is the normalized left eigenstate of H [i.e., 〈ũθ(k)|H(k) = 〈ũθ(k)|Eθ(k) and 〈ũθ(k)|uθ(k)〉 = 1

  18. Motif statistics and spike correlations in neuronal networks

    International Nuclear Information System (INIS)

    Hu, Yu; Shea-Brown, Eric; Trousdale, James; Josić, Krešimir

    2013-01-01

    Motifs are patterns of subgraphs of complex networks. We studied the impact of such patterns of connectivity on the level of correlated, or synchronized, spiking activity among pairs of cells in a recurrent network of integrate and fire neurons. For a range of network architectures, we find that the pairwise correlation coefficients, averaged across the network, can be closely approximated using only three statistics of network connectivity. These are the overall network connection probability and the frequencies of two second order motifs: diverging motifs, in which one cell provides input to two others, and chain motifs, in which two cells are connected via a third intermediary cell. Specifically, the prevalence of diverging and chain motifs tends to increase correlation. Our method is based on linear response theory, which enables us to express spiking statistics using linear algebra, and a resumming technique, which extrapolates from second order motifs to predict the overall effect of coupling on network correlation. Our motif-based results seek to isolate the effect of network architecture perturbatively from a known network state. (paper)

  19. Bayesian centroid estimation for motif discovery.

    Science.gov (United States)

    Carvalho, Luis

    2013-01-01

    Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

  20. Bayesian centroid estimation for motif discovery.

    Directory of Open Access Journals (Sweden)

    Luis Carvalho

    Full Text Available Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

  1. N,N-Diethyl-2-[5-(4-methoxybenzylidene-2,4-dioxo-1,3-thiazolidin-3-yl]acetamide

    Directory of Open Access Journals (Sweden)

    Vijayan Viswanathan

    2017-05-01

    Full Text Available In the title compound, C17H20N2O4S, the thiazolidine (r.m.s. deviation = 0.022 Å and phenyl rings (major and minor occupancies are inclined to one another by 6.3 (3 and 10.5 (3°, respectively. The molecular conformation is stabilized by an intramolecular C—H...S interaction. In the crystal, molecules are linked by C—H...O hydrogen bonds, which generate R22(18, R22(24 and R21(7 ring motifs. Aromatic π–π stacking interactions are also observed.

  2. Ethyl 27-oxo-15-oxa-2,20-diazahexacyclo[18.6.1.01,8.02,6.09,14.021,26]heptacosa-9,11,13,21,23,25-hexaene-7-carboxylate

    Directory of Open Access Journals (Sweden)

    Devadasan Velmurugan

    2013-01-01

    Full Text Available In the title compound, C27H30N2O4, the pyrrolidine ring adopts a twisted conformation. The indoline ring system is almost perpendicular to the mean plane of the pyrrolidine ring, making a dihedral angle of 81.7 (8°. In the crystal, molecules are linked into centrosymmetric dimers with graph-set motif R22(16 via pairs of C—H...O hydrogen bonds. The terminal ethyl group of the ester group is disordered over two sets of sites, with a site-occupancy ratio of 0.587 (11:0.413 (11.

  3. 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.

  4. CONTEMPORARY USAGE OF TRADITIONAL TURKISH MOTIFS IN PRODUCT DESIGNS

    Directory of Open Access Journals (Sweden)

    Tulay Gumuser

    2012-12-01

    Full Text Available The aim of this study is to identify the traditional Turkish motifs and its relations among present industrial designs. Traditional Turkish motifs played a very important role in 16th century onwards. The arts of the Ottoman Empire were used because of their symbolic meanings and unique styles. When we examine these motifs we encounter; Tiger Stripe, Three Spot (Çintemani, Rumi, Hatayi, Penç, Cloud, Crescent, Star, Crown, Hyacinth, Tulip and Carnation motifs. Nowadays, Turkish designers have begun to use these traditional Turkish motifs in their designs so as to create differences and awareness in the world design. The examples of these industrial designs, using the Turkish motifs, have survived and have Ottoman heritage and historical value. In this study, the Turkish motifs will be examined along with their focus on contemporary Turkish industrial designs used today.

  5. RNA motif search with data-driven element ordering.

    Science.gov (United States)

    Rampášek, Ladislav; Jimenez, Randi M; Lupták, Andrej; Vinař, Tomáš; Brejová, Broňa

    2016-05-18

    In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .

  6. Conserved binding of GCAC motifs by MEC-8, couch potato, and the RBPMS protein family

    Science.gov (United States)

    Soufari, Heddy

    2017-01-01

    Precise regulation of mRNA processing, translation, localization, and stability relies on specific interactions with RNA-binding proteins whose biological function and target preference are dictated by their preferred RNA motifs. The RBPMS family of RNA-binding proteins is defined by a conserved RNA recognition motif (RRM) domain found in metazoan RBPMS/Hermes and RBPMS2, Drosophila couch potato, and MEC-8 from Caenorhabditis elegans. In order to determine the parameters of RNA sequence recognition by the RBPMS family, we have first used the N-terminal domain from MEC-8 in binding assays and have demonstrated a preference for two GCAC motifs optimally separated by >6 nucleotides (nt). We have also determined the crystal structure of the dimeric N-terminal RRM domain from MEC-8 in the unbound form, and in complex with an oligonucleotide harboring two copies of the optimal GCAC motif. The atomic details reveal the molecular network that provides specificity to all four bases in the motif, including multiple hydrogen bonds to the initial guanine. Further studies with human RBPMS, as well as Drosophila couch potato, confirm a general preference for this double GCAC motif by other members of the protein family and the presence of this motif in known targets. PMID:28003515

  7. Amine-free melanin-concentrating hormone receptor 1 antagonists: Novel 1-(1H-benzimidazol-6-yl)pyridin-2(1H)-one derivatives and design to avoid CYP3A4 time-dependent inhibition.

    Science.gov (United States)

    Igawa, Hideyuki; Takahashi, Masashi; Shirasaki, Mikio; Kakegawa, Keiko; Kina, Asato; Ikoma, Minoru; Aida, Jumpei; Yasuma, Tsuneo; Okuda, Shoki; Kawata, Yayoi; Noguchi, Toshihiro; Yamamoto, Syunsuke; Fujioka, Yasushi; Kundu, Mrinalkanti; Khamrai, Uttam; Nakayama, Masaharu; Nagisa, Yasutaka; Kasai, Shizuo; Maekawa, Tsuyoshi

    2016-06-01

    Melanin-concentrating hormone (MCH) is an attractive target for antiobesity agents, and numerous drug discovery programs are dedicated to finding small-molecule MCH receptor 1 (MCHR1) antagonists. We recently reported novel pyridine-2(1H)-ones as aliphatic amine-free MCHR1 antagonists that structurally featured an imidazo[1,2-a]pyridine-based bicyclic motif. To investigate imidazopyridine variants with lower basicity and less potential to inhibit cytochrome P450 3A4 (CYP3A4), we designed pyridine-2(1H)-ones bearing various less basic bicyclic motifs. Among these, a lead compound 6a bearing a 1H-benzimidazole motif showed comparable binding affinity to MCHR1 to the corresponding imidazopyridine derivative 1. Optimization of 6a afforded a series of potent thiophene derivatives (6q-u); however, most of these were found to cause time-dependent inhibition (TDI) of CYP3A4. As bioactivation of thiophenes to form sulfoxide or epoxide species was considered to be a major cause of CYP3A4 TDI, we introduced electron withdrawing groups on the thiophene and found that a CF3 group on the ring or a Cl adjacent to the sulfur atom helped prevent CYP3A4 TDI. Consequently, 4-[(5-chlorothiophen-2-yl)methoxy]-1-(2-cyclopropyl-1-methyl-1H-benzimidazol-6-yl)pyridin-2(1H)-one (6s) was identified as a potent MCHR1 antagonist without the risk of CYP3A4 TDI, which exhibited a promising safety profile including low CYP3A4 inhibition and exerted significant antiobesity effects in diet-induced obese F344 rats. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. (S,S,S,S-Nebivolol hydrochloride hemihydrate

    Directory of Open Access Journals (Sweden)

    Yoann Rousselin

    2012-12-01

    Full Text Available The asymmetric unit of the title hydrated salt, C22H26F2NO4+·Cl−·0.5H2O, consists of an (S,S,S,S-nebivolol {nebivol = bis[2-(6-fluoro-3,4-dihydro-2H-1-benzopyran-2-yl-2-hydroxyethyl]ammonium} cation, a chloride anion and a half-occupancy water molecule. The dihedral angle between the mean planes of the benzene rings is 50.34 (12°. The pyran rings adopt half-chair conformations. The crystal packing features O—H...O hydrogen bonds and weak N—H...Cl, O—H...Cl, and O—H...Cl interactions, producing layers along (010.

  9. 3-{2-[2-(2-Fluorobenzylidenehydrazinyl]-1,3-thiazol-4-yl}-2H-chromen-2-one

    Directory of Open Access Journals (Sweden)

    Afsheen Arshad

    2010-06-01

    Full Text Available In the title compound, C19H12FN3O2S, the chromene ring system and the thiazole ring are approximately planar [maximum deviations of 0.023 (3 Å and 0.004 (2 Å, respectively]. The chromene ring system is inclined at angles of 4.78 (10 and 26.51 (10° with respect to the thiazole and benzene rings, respectively, while the thiazole ring makes a dihedral angle of 23.07 (12° with the benzene ring. The molecular structure is stabilized by an intramolecular C—H...O hydrogen bond, which generates an S(6 ring motif. The crystal packing is consolidated by intermolecular N—H...O hydrogen bonds, which link the molecules into chains parallel to [100], and by C—H...π and π–π [centroid–centroid distance = 3.4954 (15 Å] stacking interactions.

  10. A Woman Voice in an Epic: Tracing Gendered Motifs in Anne Vabarna's Peko

    Directory of Open Access Journals (Sweden)

    Andreas Kalkun

    2008-12-01

    Full Text Available In the article the gendered motifs found in Anne Vabarna’s Seto epic Peko are analysed. Besides the narrative telling of the life of the male hero, the motives regarding eating, refusing to eat or offering food, and the aspect of the female body or its control deserve to be noticed. These scenes do not communicate the main plot, they are often related to minor characters of the epic and slow down the narrative, but at the same time they clearly carry artistic purpose and meaning. I consider these motifs, present in the liminal parts of the epic, to be the dominant symbols of the epic where the author’s feminine world is being exposed. Observing these motifs of Peko in the context of Seto religious worldview, the life of Anne Vabarna and the social position of Seto women, the symbols become eloquent and informative.

  11. Identification of sequence motifs significantly associated with antisense activity

    Directory of Open Access Journals (Sweden)

    Peek Andrew S

    2007-06-01

    Full Text Available Abstract Background Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the model to be efficient we must know what properties do not associate significantly and can be omitted from the model. This paper will discuss the results of a randomization procedure to find motifs that associate significantly with either high or low antisense suppression activity, analysis of their properties, as well as the results of support vector machine modelling using these significant motifs as features. Results We discovered 155 motifs that associate significantly with high antisense suppression activity and 202 motifs that associate significantly with low suppression activity. The motifs range in length from 2 to 5 bases, contain several motifs that have been previously discovered as associating highly with antisense activity, and have thermodynamic properties consistent with previous work associating thermodynamic properties of sequences with their antisense activity. Statistical analysis revealed no correlation between a motif's position within an antisense sequence and that sequences antisense activity. Also, many significant motifs existed as subwords of other significant motifs. Support vector regression experiments indicated that the feature set of significant motifs increased correlation compared to all possible motifs as well as several subsets of the significant motifs. Conclusion The thermodynamic properties of the significantly associated motifs support existing data correlating the thermodynamic properties of the antisense oligonucleotide with antisense efficiency, reinforcing our hypothesis that antisense suppression is strongly associated with probe/target thermodynamics, as there are no enzymatic

  12. rac-1-[6-Hydroxy-4-(4-methoxyphenyl-3,6-dimethyl-4,5,6,7-tetrahydro-2H-indazol-5-yl]ethanone

    Directory of Open Access Journals (Sweden)

    Konstantin A. Potekhin

    2013-02-01

    Full Text Available The title compound, C18H22N2O3, represents a (4S,5R,6S-stereoisomer, crystallizing as a racemate in a centrosymmetric space group. The six-membered aliphatic ring adopts a half-chair conformation, with the hydroxy- and acetyl-substituted C atoms deviating by 0.458 (2 and −0.366 (2 Å, respectively, from the plane defined by other four ring atoms. The pyrazole ring is essentially planar [r.m.s deviation = 0.004 (2 Å]. In the crystal, the molecules are linked into chains along the b axis by N—H...N hydrogen bonds. The chains are linked by O—H...N hydrogen bonds into layers parallel to the bc plane.

  13. The Coagulant Type Influence on Removal Efficiency of 5- and 6-Ring Pahs During Water Coagulation Process

    Directory of Open Access Journals (Sweden)

    Nowacka Anna

    2014-12-01

    Full Text Available The article presents results on investigation of the removal efficiency of selected 5- and 6-ring polycyclic aromatic hydrocarbons (benzo[a]pyrene, benzo[b]fluoranthene, benzo[k]fluoranthene, benzo[j]fluoranthene, benzo[g,h,i]perylene, indeno[1,2,3-cd]pyrene, dibenzo[a,h]anthracene from water during coagulation and sedimentation process. Two pre-hydrolyzed aluminum coagulants: PAX XL 19H and FLOKOR 105V were chosen for research. Process was carried out at optimum process parameters: rapid-mixing - 3 min at the rotational speed of 200 rpm, slow mixing - 10 min at 30 rpm, sedimentation - 60 min. The removal effectiveness was dependant on coagulant type and its composition. Better results in the removal of 5-and 6-ring PAHs were obtained after application of FLOKOR 105V (lower aluminum content than after using PAX XL 19H.

  14. Fluorinated cyclohexanes: Synthesis of amine building blocks of the all-cis 2,3,5,6-tetrafluorocyclohexylamine motif

    Directory of Open Access Journals (Sweden)

    Tetiana Bykova

    2017-04-01

    Full Text Available This paper reports the synthesis of three amine stereoisomers 5a–c of the tetrafluorocyclohexyl ring system, as building blocks for discovery chemistry programmes. The synthesis starts from a Birch reduction of benzonitrile, followed by an in situ methyl iodide quench. The resultant 2,5-cyclohexadiene was progressed via double epoxidations and then hydrofluorination ring opening reactions. The resultant fluorohydrin moieties were then converted to different stereoisomers of the tetrafluorocyclohexyl ring system, and then reductive hydrogenation of the nitrile delivered three amine stereoisomers. It proved necessary to place a methyl group on the cyclohexane ring in order to stabilise the compound against subsequent HF elimination. The two all-cis tetrafluorocyclohexyl isomers 5a and 5b constitute facially polarized cyclohexane rings, with fluorines on the electronegative face and hydrogens on the electropositive face.

  15. APOCALYPTIC MOTIFS IN THE CYCLE OF STORIES BY M.A. BULGAKOV «NOTES OF A YOUNG DOCTOR»

    Directory of Open Access Journals (Sweden)

    Evgeniy Igorevich Erokhov

    2015-10-01

    Full Text Available The motif analysis of a cycle of stories by M.A. Bulgakov «Notes of a Young Doctor» from the point of view of their apocalyptic problematics was first performed in this article. To identify apocalyptic motifs the method of motif analysis, developed by B.M. Gasparov, was used which will also help to prove the interpenetration of motifs in the cycle of stories. The result of the research work is the identification of apocalyptic motifs which are manifested in the experiences of the main character and the events taking place around him and passing through the prism of physician’s perception of the world. Our identified motifs show that the stories in the cycle are united not only thematically and with the help of the image of the main character, but with the help of the motifs which reflect interpenetration of apocalyptic motifs in the stories of one cycle. There are the following apocalyptic motifs in the cycle of stories by Bulgakov: diseases, darkness (as part of the landscape, resurrection from the dead and beast. They all belong to the biblical type which is allocated on the basis of the associative bond of these motifs with the biblical texts.

  16. 2-(1H-Benzimidazol-2-ylphenol

    Directory of Open Access Journals (Sweden)

    S. M. Prakash

    2014-02-01

    Full Text Available The title molecule, C13H10N2O, is essentially planar, the maximum deviation from the plane of the non-H atoms being 0.016 (2 Å. The imidazole ring makes a dihedral angle of 0.37 (13° with the attached benzene ring. An intramolecular O—H...N hydrogen bond generates an S(6 ring motif. In the crystal, molecules are linked through N—H...O hydrogen bonds, forming chains propagating in [001]. The crystal packing also features four π–π stacking interactions involving the imidazole ring, fused benzene ring and attached benzene ring system [centroid–centroid distances = 3.6106 (17, 3.6108 (17, 3.6666 (17 and 3.6668 (17 Å].

  17. Implications of Liebig’s law of the minimum for tree-ring reconstructions of climate

    Science.gov (United States)

    Stine, A. R.; Huybers, P.

    2017-11-01

    A basic principle of ecology, known as Liebig’s Law of the Minimum, is that plant growth reflects the strongest limiting environmental factor. This principle implies that a limiting environmental factor can be inferred from historical growth and, in dendrochronology, such reconstruction is generally achieved by averaging collections of standardized tree-ring records. Averaging is optimal if growth reflects a single limiting factor and noise but not if growth also reflects locally variable stresses that intermittently limit growth. In this study a collection of Arctic tree ring records is shown to follow scaling relationships that are inconsistent with the signal-plus-noise model of tree growth but consistent with Liebig’s Law acting at the local level. Also consistent with law-of-the-minimum behavior is that reconstructions based on the least-stressed trees in a given year better-follow variations in temperature than typical approaches where all tree-ring records are averaged. Improvements in reconstruction skill occur across all frequencies, with the greatest increase at the lowest frequencies. More comprehensive statistical-ecological models of tree growth may offer further improvement in reconstruction skill.

  18. (1S*,2S*,4R*,5R*-Cyclohexane-1,2,4,5-tetracarboxylic acid

    Directory of Open Access Journals (Sweden)

    Akira Uchida

    2014-01-01

    Full Text Available The title compound, C10H12O8, a prospective raw material for colourless polyimides which are applied to electronic and microelectronic devices, lies about an inversion centre and the cyclohexane ring adopts a chair conformation. Two crystallographycally independent carboxylic acid groups on adjacent C atoms are in equatorial positions, resulting in a mutually trans conformation. In the crystal, O—H...O hydrogen bonds around an inversion centre and a threefold rotoinversion axis, respectively, form an inversion dimer with an R22(8 motif and a trimer with an R33(12 motif.

  19. Modelling of the ring current in Saturn's magnetosphere

    Directory of Open Access Journals (Sweden)

    G. Giampieri

    2004-01-01

    Full Text Available The existence of a ring current inside Saturn's magnetosphere was first suggested by Smith et al. (1980 and Ness et al. (1981, 1982, in order to explain various features in the magnetic field observations from the Pioneer 11 and Voyager 1 and 2 spacecraft. Connerney et al. (1983 formalized the equatorial current model, based on previous modelling work of Jupiter's current sheet and estimated its parameters from the two Voyager data sets. Here, we investigate the model further, by reconsidering the data from the two Voyager spacecraft, as well as including the Pioneer 11 flyby data set.

    First, we obtain, in closed form, an analytic expression for the magnetic field produced by the ring current. We then fit the model to the external field, that is the difference between the observed field and the internal magnetic field, considering all the available data. In general, through our global fit we obtain more accurate parameters, compared to previous models. We point out differences between the model's parameters for the three flybys, and also investigate possible deviations from the axial and planar symmetries assumed in the model. We conclude that an accurate modelling of the Saturnian disk current will require taking into account both of the temporal variations related to the condition of the magnetosphere, as well as non-axisymmetric contributions due to local time effects.

    Key words. Magnetospheric physics (current systems; planetary magnetospheres; plasma sheet

  20. Synthesis of carboxylic acids, esters, alcohols and ethers containing a tetrahydropyran ring derived from 6-methyl-5-hepten-2-one.

    Science.gov (United States)

    Hanzawa, Yohko; Hashimoto, Kahoko; Kasashima, Yoshio; Takahashi, Yoshiko; Mino, Takashi; Sakamoto, Masami; Fujita, Tsutomu

    2012-01-01

    3-hydroxy acids, 3-hydroxy-3,7-dimethyloct-6-enoic acid (1) and 3-hydroxy-2,2,3,7-tetramethyloct-6-enoic acid (2), were prepared from 6-methyl-5-hepten-2-one, and they were subsequently used to prepare (2,6,6-trimethyltetrahydropyran-2-yl)acetic acid (3) and 2-methyl-2-(2,6,6-trimethyltetrahydropyran-2-yl)propanoic acid (4), respectively, via cyclization with an acidic catalyst such as boron trifluoride diethyl etherate or iodine. The reaction of carboxylic acids 3 and 4 with alcohols, including methanol, ethanol, and 1-propanol, produced the corresponding methyl, ethyl, and propyl esters, which all contained a tetrahydropyran ring. Reduction of carboxylic acids 3 and 4 afforded the corresponding alcohols. Subsequent reactions of these alcohols with several acyl chlorides produced novel esters. The alcohols also reacted with methyl iodide and sodium hydride to provide novel ethers. A one-pot cyclization-esterification of 1 to produce esters containing a tetrahydropyran ring, using iodine as a catalyst, was also investigated.

  1. 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)

  2. Methyl 11-hydroxy-9-[1-(4-methoxyphenyl-4-oxo-3-phenoxyazetidin-2-yl]-18-oxo-10-oxa-2-azapentacyclo[9.7.0.01,8.02,6.012,17]octadeca-12(17,13,15-triene-8-carboxylate

    Directory of Open Access Journals (Sweden)

    S. Sundaramoorthy

    2012-07-01

    Full Text Available In the title compound, C34H32N2O8, one of the pyrrolidine rings in the pyrrolizidine ring system adopts a twist conformation, whereas the other ring adopts an envelope conformation (C atom as flap. The five-membered ring in the indene ring system and the fused furan ring also adopt envelope conformations (C and O atoms as flaps, respectively. The β-lactam ring makes dihedral angles of 23.41 (2 and 25.98 (2°, respectively, with the attached methoxyphenyl and phenoxy rings. The molecular conformation is stabilized by an intramolecular O—H...N hydrogen bond, generating an S(5 motif. In the crystal, molecules are linked into C(12 chains running along the a axis by C—H...O hydrogen bonds. The structure is further consolidated by weak intermolecular C—H...π and π–π interactions [centroid–centroid distance = 3.7987 (14 Å].

  3. rac-Dimethyl 2-(tert-butylamino-5-oxo-4,5-dihydropyrano[3,2-c]chromene-3,4-dicarboxylate

    Directory of Open Access Journals (Sweden)

    S. Antony Inglebert

    2011-11-01

    Full Text Available The title compound, C20H21NO7, is asymmetric with a chiral centre located in the pyran ring and crystallizes as a racemate. The molecular framework is somewhat bent; the coumarin moiety and the pyran ring are inclined by 7.85 (5°. The molecular structure is characterized by an intramolecular N—H...O hydrogen bond, which generates an S(6 ring motif, and the crystal packing is stabilized by intermolecular C—H...O hydrogen bonds. The 3-carboxylate O atom is involved in both of them, having a bifurcated character.

  4. 2-Hydroxy-5-nitrobenzaldehyde 2,4-dinitrophenylhydrazone

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2008-04-01

    Full Text Available In the title compound, C13H9N5O7, one of the nitro groups is twisted away from the attached benzene ring by 16.21 (8°. The dihedral angle between the two benzene rings is 4.63 (1°. The molecular structure is stabilized by intramolecular N—H...O and O—H...N hydrogen bonds which generate an S(6 ring motif. The molecules pack as layers parallel to the ab plane; molecules of adjacent layers are linked into chains along the [101] direction through N—H...O hydrogen bonds.

  5. Analisis Unsur Matematika pada Motif Sulam Usus

    Directory of Open Access Journals (Sweden)

    Fredi Ganda Putra

    2017-12-01

    Full Text Available Based on interviews with researchers sources said that the beginning of the intestine embroidery is an art of genuine crafts. Called the intestine embroidery because this technique is a technique of combining a strand of cloth resembling the intestine formed according to the pattern by means of embroidered using a thread. Intestinal embroidery techniques were originally used to create a cover of the women's customary wardrobe of Lampung or often referred to as bebe. But not many people in Lampung, especially people who live in Lampung are still many who do not know and recognize the intestine embroidery because most only know tapis only characteristic of Lampung, besides that there are other cultural results that is embroidered intestine. There are still many who do not know that the intestine motif there is a knowledge of mathematics. The researcher's problem formulation is whether there are mathematical elements contained in the intestine embroidery motif based on the concept of geometry. The purpose of this study is to determine whether there are elements of mathematics contained in the intestine motif based on the concept of geometry. Subjects in this study consisted of 4 people obtained by purposive sampling technique. From the results of data analysis conducted by using descriptive analysis and discussion as follows: (1 Intestinal embroidery motif contains the meaning of mathematics and culture or often called Etnomatematika. On the meaning of culture there is a link between the embroidery intestine with a culture that has been there before as the existence of cultural linkage between Hindu belief Buddhism and there are similarities of motifs and decorative patterns contained in the motif embroidery intestine with ornamental variety in Indonesia. (2 The relationship between the intestine with mathematical motifs there are elements of mathematics such as geometry elements in the form of geometry of dimension one and dimension two, and the

  6. The phase structure of higher-dimensional black rings and black holes

    International Nuclear Information System (INIS)

    Emparan, Roberto; Harmark, Troels; Niarchos, Vasilis; Obers, Niels A.; RodrIguez, Maria J.

    2007-01-01

    We construct an approximate solution for an asymptotically flat, neutral, thin rotating black ring in any dimension D ≥ 5 by matching the near-horizon solution for a bent boosted black string, to a linearized gravity solution away from the horizon. The rotating black ring solution has a regular horizon of topology S 1 x S D-3 and incorporates the balancing condition of the ring as a zero-tension condition. For D = 5 our method reproduces the thin ring limit of the exact black ring solution. For D ≥ 6 we show that the black ring has a higher entropy than the Myers-Perry black hole in the ultra-spinning regime. By exploiting the correspondence between ultra-spinning black holes and black membranes on a two-torus, we take steps towards qualitatively completing the phase diagram of rotating blackfolds with a single angular momentum. We are led to propose a connection between MP black holes and black rings, and between MP black holes and black Saturns, through merger transitions involving two kinds of 'pinched' black holes. More generally, the analogy suggests an infinite number of pinched black holes of spherical topology leading to a complicated pattern of connections and mergers between phases

  7. Wideband Circularly Polarized Printed Ring Slot Antenna for 5 GHz – 6 GHz

    Science.gov (United States)

    Nasrun Osman, Mohamed; Rahim, Mohamad Helmi A.; Jusoh, Muzammil; Sabapathy, Thennarasan; Rahim, Mohamad Kamal A.; Norlyana Azemi, Saidatul

    2018-03-01

    This paper presents the design of circularly polarized printed slot antenna operating at 5 – 6 GHz. The proposed antenna consists of L-shaped feedline on the top of structure and circular ring slot positioned at the ground plane underneath the substrate as a radiator. A radial and narrow slot in the ground plane provides coupling between the L-shaped feedline and circular ring slot. The circular polarization is realized by implementing the slits perturbation located diagonally to perturb the current flow on the slot structure. The antenna prototype is fabricated on FR4 substrate. The simulated and measured results are compared and analyzed to demonstrate the performance of the antenna. Good measured of simulated results are obtained at the targeted operating frequency. The simulated -10dB reflection coefficient bandwidths and axial ratio are 750 MHz and 165 MHz, respectively. The investigation on the affect of the important parameters towards the reflection coefficient and axial are also presented. The proposed antenna is highly potential to be used for wireless local area network (WLAN) and wireless power transfer (WPT).

  8. Crystal structure of (1S,3R,8R,9R-2,2-dichloro-3,7,7-trimethyl-10-methylenetricyclo[6.4.0.01,3]dodecan-9-ol

    Directory of Open Access Journals (Sweden)

    Ahmed Benzalim

    2016-08-01

    Full Text Available The title compound, C16H24Cl2O, was synthesized by treating (1S,3R,8S,9R,10S-2,2-dichloro-3,7,7,10-tetramethyl-9,10-epoxytricyclo[6.4.0.01,3]dodecane with a concentrated solution of hydrobromic acid. It is built up from three fused rings: a cycloheptane ring, a cyclohexyl ring bearing alkene and hydroxy substituents, and a cyclopropane ring bearing two chlorine atoms. The asymmetric unit contains two molecules linked by an O—H...O hydrogen bond. In the crystal, further O—H...O hydrogen bonds build up an R44(8 cyclic tetramer. One of the molecules presents disorder that affects the seven-membered ring. In both molecules, the six-membered rings display a chair conformation, whereas the seven-membered rings display conformations intermediate between boat and twist-boat for the non-disordered molecule and either a chair or boat and twist-boat for the disordered molecule owing to the disorder. The absolute configuration for both molecules is 1S,3R,8R,9R and was deduced from the chemical pathway and further confirmed by the X-ray structural analysis.

  9. Tablets, læring og nye forretningsmodeller

    DEFF Research Database (Denmark)

    Andersen, Pernille Viktoria Kathja

    2011-01-01

    D. 6 oktober satte Netværk om E-Læring (NoEL) i samarbejde med InVIO fokus på Tablet-computing igennem et heldagsarrangement i Aalborg Universitets nye omgivelser på Nyhavnsgade 14. Formålet med dagen var, at stille skarpt på tablet formatet og udforske potentialerne og udfordringerne med særligt...... vægt på iPads til mobillæring og nye forretningsmodeller. Tablet –computing er de seneste år blevet mere og mere udbredt indenfor både uddannelse, arbejdsliv og i fritiden. Ønsket for dagen var derfor at bidrage med diskussion og videndeling omkring, hvad den nye håndholdte touch teknologi kommer til...... at betyde for læring, samarbejde og forretningsmodeller og dermed hvilke nye vilkår tablet computing kan bidrage med indenfor arbejdsliv og uddannelse....

  10. Effects of pH, temperature, and chemical structure on the stability of S-(purin-6-yl)-L-cysteine: evidence for a novel molecular rearrangement mechanism to yield N-(purin-6-yl)-L-cysteine.

    Science.gov (United States)

    Elfarra, A A; Hwang, I Y

    1996-01-01

    The stability of S-(purin-6-yl)-L-cysteine (SPC), a kidney-selective prodrug of 6-mercaptopurine and a putative metabolite of 6-chloropurine, was investigated under various pH and temperature conditions. At room temperature, the half-life (t 1/2) of SPC at either highly acidic (pH 3.6) or basic conditions (pH 9.6) was longer than at neutral or slightly acidic or basic conditions (pH 5.7-8.75). The primary degradation product, N-(purin-6-yl)-L-cysteine (NPC), was isolated using Sephadex LH-20 chromatography and characterized by 1H NMR and FAB/MS after derivatization with 2-iodoacetic acid. These results reveal novel stability requirements and implicate the cysteinyl amino group and the purinyl N-1 nitrogen in the mechanism of SPC rearrangement to NPC. Further evidence for this hypothesis was provided by the findings that the stability of SPC in phosphate buffer (pH 7.4) at 37 degrees C was similar to that of S-(guanin-6-yl)-L-cysteine, whereas S-(purin-6-yl)-N-acetyl-L-cysteine and S-(purin-6-yl)glutathione which have their cysteine amino groups blocked were much more stable than SPC. S-(Purin-6-yl)-L-homocysteine (SPHC) was also more stable than SPC, possibly because the formation of a 6-membered ring transition state as would be expected with SPHC is kinetically less favored than the formation of a 5-membered ring transition state as would be expected with SPC. These results may explain previous in vivo metabolism results of SPC and its analogs and may contribute to a better understanding of stability of structurally related cysteine S-conjugates.

  11. Motif signatures of transcribed enhancers

    KAUST Repository

    Kleftogiannis, Dimitrios

    2017-09-14

    In mammalian cells, transcribed enhancers (TrEn) play important roles in the initiation of gene expression and maintenance of gene expression levels in spatiotemporal manner. One of the most challenging questions in biology today is how the genomic characteristics of enhancers relate to enhancer activities. This is particularly critical, as several recent studies have linked enhancer sequence motifs to specific functional roles. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers genomic code in a more systematic way. To address this problem, we developed a novel computational method, TELS, aimed at identifying predictive cell type/tissue specific motif signatures. We used TELS to compile a comprehensive catalog of motif signatures for all known TrEn identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that distinct cell type/tissue specific motif signatures characterize TrEn. These signatures allow discriminating successfully a) TrEn from random controls, proxy of non-enhancer activity, and b) cell type/tissue specific TrEn from enhancers expressed and transcribed in different cell types/tissues. TELS codes and datasets are publicly available at http://www.cbrc.kaust.edu.sa/TELS.

  12. TOPDOM: database of conservatively located domains and motifs in proteins.

    Science.gov (United States)

    Varga, Julia; Dobson, László; Tusnády, Gábor E

    2016-09-01

    The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in α-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins. TOPDOM database is available at http://topdom.enzim.hu The webpage utilizes the common Apache, PHP5 and MySQL software to provide the user interface for accessing and searching the database. The database itself is generated on a high performance computer. tusnady.gabor@ttk.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  13. 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 ...

  14. Physiological Responses during Cycling With Oval Chainrings (Q-Ring and Circular Chainrings

    Directory of Open Access Journals (Sweden)

    Alfredo Cordova

    2014-06-01

    Full Text Available The aim of this study was to compare the physiological responses of cyclists using round (C-ring or oval (Q-ring chainrings during an incremental test until exhaustion. Following a randomized design, fourteen male elite cyclists [age (mean ± SD: 21.1 ± 2.1 yr; VO2max: 78.5 ± 5.3 mL·kg-1min-1] performed two incremental maximal tests separated by 48 h (one with C-rings, the other with Q-rings. Starting at 100 W, the workload was increased by 25 W every 3 min until volitional exhaustion. Maximal heart rate, power output and oxygen consumption were compared. Blood lactate was monitored throughout the test. After the incremental test, 4 intermittent 20-s maximal sprints with a 60-s recovery period in between were performed. Maximal isometric voluntary contractions were performed at rest and immediately after each 20-s maximal sprint, and the force and EMG RMS amplitude were recorded from the vastus medialis and vastus lateralis muscles. For the incremental exercise test, no significant differences were found in the maximal power output (P=0.12, oxygen consumption (P=0.39, and heart rate (P=0.32 between Q-rings and C-rings. Throughout the incremental test, lactate levels were comparable when using both the C-rings and Q-rings (P=0.47. During the short sprints, power output was 2.5–6.5% greater for Q-rings than for C-rings (P=0.22. The decline in EMG RMS amplitude observed during the incremental tests was comparable for Q-rings and C-rings (0.42. These findings indicate that the oval chainring design, presented here as “Q-rings”, did not significantly influence the physiological response to an incremental exercise test as compared to a conventional chainring.

  15. Through the Portal: Viking Motifs Incorporated in the Romanesque Style in Telemark, Norway

    Directory of Open Access Journals (Sweden)

    Kristine Ødeby

    2013-09-01

    Full Text Available This paper presents the results of an analysis of motifs identified on six carved wooden Romanesque portal panels from the Norwegian county of Telemark. The findings suggest that animal motifs in the Late Viking style survived long into the Late Medieval period and were reused on these medieval portals. Stylistically, late expressions of Viking animal art do not differ a great deal from those of the subsequent Romanesque style. However, their symbolical differences are considered to be significant. The motifs themselves, and the issue of whether the Romanesque style adopted motifs from pre-Christian art, have attracted less attention. The motif portraying Sigurd slaying the dragon is considered in depth. It will be suggested that Sigurd, serving as a mediator between the old and the new beliefs when he appeared in late Viking contexts, was given a new role when portrayed in Christian art. Metaphor and liminality are a central part of this paper, and the theories of Alfred Gell and Margrete Andås suggest that the portal itself affects those who pass through it, and that the iconography is meaningful from a liminal perspective.

  16. Dragon polya spotter: Predictor of poly(A) motifs within human genomic DNA sequences

    KAUST Repository

    Kalkatawi, Manal M.

    2011-11-15

    Motivation: Recognition of poly(A) signals in mRNA is relatively straightforward due to the presence of easily recognizable polyadenylic acid tail. However, the task of identifying poly(A) motifs in the primary genomic DNA sequence that correspond to poly(A) signals in mRNA is a far more challenging problem. Recognition of poly(A) signals is important for better gene annotation and understanding of the gene regulation mechanisms. In this work, we present one such poly(A) motif prediction method based on properties of human genomic DNA sequence surrounding a poly(A) motif. These properties include thermodynamic, physico-chemical and statistical characteristics. For predictions, we developed Artificial Neural Network and Random Forest models. These models are trained to recognize 12 most common poly(A) motifs in human DNA. Our predictors are available as a free web-based tool accessible at http://cbrc.kaust.edu.sa/dps. Compared with other reported predictors, our models achieve higher sensitivity and specificity and furthermore provide a consistent level of accuracy for 12 poly(A) motif variants. The Author(s) 2011. Published by Oxford University Press. All rights reserved.

  17. 2-Oxo-2H-chromen-7-yl 4-tert-butylbenzoate

    Directory of Open Access Journals (Sweden)

    Mohammad Ouédraogo

    2018-04-01

    Full Text Available In the title compound, C20H18O4, the benzoate ring is oriented at an acute angle of 33.10 (12° with respect to the planar (r.m.s deviation = 0.016 Å coumarin ring system. An intramolecular C—H...O hydrogen bond closes an S(6 ring motif. In the crystal, C—H...O contacts generate infinite C(6 chains along the b-axis direction. Also present are π–π stacking interactions between neighbouring pyrone and benzene rings [centroid–centroid distance = 3.7034 (18 Å] and C=O...π interactions [O...centroid = 3.760 (3 Å]. The data obtained from quantum chemical calculations performed on the title compound are in good agreement with the observed structure, although the calculated C—O—C—C torsion angle between the coumarin ring system and the benzoate ring (129.1° is somewhat lower than the observed value [141.3 (3°]. Hirshfeld surface analysis has been used to confirm and quantify the supramolecular interactions.

  18. Electron-deficient N-alkyloyl derivatives of thieno[3,4-c]pyrrole-4,6-dione yield efficient polymer solar cells with open-circuit voltages > 1 v

    KAUST Repository

    Warnan, Julien

    2014-05-13

    Poly(benzo[1,2-b:4,5-b′]dithiophene-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymer donors yield some of the highest open-circuit voltages (V OC, ca. 0.9 V) and fill factors (FF, ca. 70%) in conventional bulk-heterojunction (BHJ) solar cells with PCBM acceptors. Recent work has shown that the incorporation of ring substituents into the side chains of the BDT motifs in PBDTTPD can induce subtle variations in material properties, resulting in an increase of the BHJ device VOC to ∼1 V. In this contribution, we report on the synthesis of N-alkyloyl-substituted TPD motifs (TPD(CO)) and show that the electron-deficient motifs can further lower both the polymer LUMO and HOMO levels, yielding device VOC > 1 V (up to ca. 1.1 V) in BHJ solar cells with PCBM. Despite the high VOC achieved (i.e., low polymer HOMO), BHJ devices cast from TPD(CO)-based polymer donors can reach power conversion efficiencies (PCEs) of up to 6.7%, making these promising systems for use in the high-band-gap cell of tandem solar cells. © 2014 American Chemical Society.

  19. 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)

  20. Triadic motifs in the dependence networks of virtual societies

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-01

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  1. Triadic motifs in the dependence networks of virtual societies.

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-10

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  2. Direct AUC optimization of regulatory motifs.

    Science.gov (United States)

    Zhu, Lin; Zhang, Hong-Bo; Huang, De-Shuang

    2017-07-15

    The discovery of transcription factor binding site (TFBS) motifs is essential for untangling the complex mechanism of genetic variation under different developmental and environmental conditions. Among the huge amount of computational approaches for de novo identification of TFBS motifs, discriminative motif learning (DML) methods have been proven to be promising for harnessing the discovery power of accumulated huge amount of high-throughput binding data. However, they have to sacrifice accuracy for speed and could fail to fully utilize the information of the input sequences. We propose a novel algorithm called CDAUC for optimizing DML-learned motifs based on the area under the receiver-operating characteristic curve (AUC) criterion, which has been widely used in the literature to evaluate the significance of extracted motifs. We show that when the considered AUC loss function is optimized in a coordinate-wise manner, the cost function of each resultant sub-problem is a piece-wise constant function, whose optimal value can be found exactly and efficiently. Further, a key step of each iteration of CDAUC can be efficiently solved as a computational geometry problem. Experimental results on real world high-throughput datasets illustrate that CDAUC outperforms competing methods for refining DML motifs, while being one order of magnitude faster. Meanwhile, preliminary results also show that CDAUC may also be useful for improving the interpretability of convolutional kernels generated by the emerging deep learning approaches for predicting TF sequences specificities. CDAUC is available at: https://drive.google.com/drive/folders/0BxOW5MtIZbJjNFpCeHlBVWJHeW8 . dshuang@tongji.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  3. Southwestern (U.S.A. Archaeological Tree-Ring Dating: 1930-1942

    Directory of Open Access Journals (Sweden)

    Stephen E. Nash

    1997-11-01

    Full Text Available Dendrochronology, the science of assigning precise and accurate calendar dates to annual growth rings in trees (Stokes and Smiley 1968, was the first independent dating technique available to prehistorians. Ar­chaeological tree-ring dating came of age at a time when North American archaeologists concerned them­selves primarily with time/space systematics (Willey and Sabloff 1980 and yet had no absolute and inde­pendent dating techniques available to guide their analyses. Histories of archaeology typically have not considered the development of archaeological tree-ring dating in detail. Willey and Sabloff (1980:12 devote one paragraph to the development of Southwestern archaeological tree-ring dating, as does Steibing (1993:261. Trigger (1989:305 considers dendrochronology (in the sense of the Douglass method only in light of radiocarbon dating. Textbooks and regional histories of archaeology do a little better in their treat­ment of dendrochronology, though discussions typically focus on the interpretation of tree-ring dates and not on the developmental history of the technique itself (e.g. Cordell 1984:88-90; Fagan 1991:129-133; Lyon 1996:46; Michels 1973:116; Thomas 1979:190-194. Scott (1966:9 argues that 'the story of the discovery of archaeological tree-ring dating by A E. Douglass and others has been told and retold and is now familiar to scientists and laymen alike'. I beg to differ.

  4. Ethyl (E)-2-(2,7-dimethyl-5-oxo-4H,5H-pyrano[4,3-b]pyran-4-ylidene)acetate

    OpenAIRE

    Oulemda Bassou; Hakima Chicha; Latifa Bouissane; El Mostapha Rakib; Mohamed Saadi; Lahcen El Ammari

    2017-01-01

    In the title compound, C14H14O5, the two heterocyclic rings are coplanar (r.m.s. deviation = 0.008 Å), with the largest deviation from the mean plane being 0.012 (1) Å. The mean plane through the acetate group is inclined slightly with respect to the oxopyrano[4,3-b]pyran-4-yl system, as indicated by the dihedral angle of 1.70 (7)° between them. Two intramolecular hydrogen bonds, completing S(6) ring motifs, are observed in the molecule. In the crystal, molecules are linked by weak C—H...O hy...

  5. Mechanisms of ring chromosome formation in 11 cases of human ring chromosome 21

    DEFF Research Database (Denmark)

    McGinniss, M J; Kazazian, H H; Stetten, G

    1992-01-01

    We studied the mechanism of ring chromosome 21 (r(21)) formation in 13 patients (11 unique r(21)s), consisting of 7 from five families with familial r(21) and 6 with de novo r(21). The copy number of chromosome 21 sequences in the rings of these patients was determined by quantitative dosage......), resulting in deletion of varying amounts of 21q22.1 to 21qter. The data from one individual who had a Down syndrome phenotype were consistent with asymmetric breakage and reunion of 21q sequences from an intermediate isochromosome or Robertsonian translocation chromosome as reported by Wong et al. Another......). The phenotype of patients correlated well with the extent of deletion or duplication of chromosome 21 sequences. These data demonstrate three mechanisms of r(21) formation and show that the phenotype of r(21) patients varies with the extent of chromosome 21 monosomy or trisomy....

  6. 3-Phenyl-6-(2-pyrid­yl)-1,2,4,5-tetra­zine

    OpenAIRE

    Chartrand, Daniel; Laverdière, François; Hanan, Garry

    2007-01-01

    The title compound, C13H9N5, is the first asymmetric diaryl-1,2,4,5-tetrazine to be crystallographically characterized. We have been interested in this motif for incorporation into supramolecular assemblies based on coordination chemistry. The solid state structure shows a centrosymmetric molecule, forcing a positional disorder of the terminal phenyl and pyridyl rings. The molecule is completely planar, unusual for aromatic rings with N atoms in adjacent ortho positions. The stacking observed...

  7. Efficient motif finding algorithms for large-alphabet inputs

    Directory of Open Access Journals (Sweden)

    Pavlovic Vladimir

    2010-10-01

    Full Text Available Abstract Background We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. Results The proposed algorithm (1 improves search efficiency compared to existing algorithms, and (2 scales well with the size of alphabet. On a synthetic planted DNA motif finding problem our algorithm is over 10× more efficient than MITRA, PMSPrune, and RISOTTO for long motifs. Improvements are orders of magnitude higher in the same setting with large alphabets. On benchmark TF-binding site problems (FNP, CRP, LexA we observed reduction in running time of over 12×, with high detection accuracy. The algorithm was also successful in rapidly identifying protein motifs in Lipocalin, Zinc metallopeptidase, and supersecondary structure motifs for Cadherin and Immunoglobin families. Conclusions Our algorithm reduces computational complexity of the current motif finding algorithms and demonstrate strong running time improvements over existing exact algorithms, especially in important and difficult cases of large-alphabet sequences.

  8. RMOD: a tool for regulatory motif detection in signaling network.

    Directory of Open Access Journals (Sweden)

    Jinki Kim

    Full Text Available Regulatory motifs are patterns of activation and inhibition that appear repeatedly in various signaling networks and that show specific regulatory properties. However, the network structures of regulatory motifs are highly diverse and complex, rendering their identification difficult. Here, we present a RMOD, a web-based system for the identification of regulatory motifs and their properties in signaling networks. RMOD finds various network structures of regulatory motifs by compressing the signaling network and detecting the compressed forms of regulatory motifs. To apply it into a large-scale signaling network, it adopts a new subgraph search algorithm using a novel data structure called path-tree, which is a tree structure composed of isomorphic graphs of query regulatory motifs. This algorithm was evaluated using various sizes of signaling networks generated from the integration of various human signaling pathways and it showed that the speed and scalability of this algorithm outperforms those of other algorithms. RMOD includes interactive analysis and auxiliary tools that make it possible to manipulate the whole processes from building signaling network and query regulatory motifs to analyzing regulatory motifs with graphical illustration and summarized descriptions. As a result, RMOD provides an integrated view of the regulatory motifs and mechanism underlying their regulatory motif activities within the signaling network. RMOD is freely accessible online at the following URL: http://pks.kaist.ac.kr/rmod.

  9. Crystal structures of 2-benzylamino-4-(4-bromophenyl-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridine-3-carbonitrile and 2-benzylamino-4-(4-chlorophenyl-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridine-3-carbonitrile

    Directory of Open Access Journals (Sweden)

    R. A. Nagalakshmi

    2015-01-01

    Full Text Available In the title compounds, C24H22BrN3, (I, and C24H22ClN3, (II, the 2-aminopyridine ring is fused with a cycloheptane ring, which adopts a half-chair conformation. The planes of the phenyl and benzene rings are inclined to that of the central pyridine ring [r.m.s. deviations = 0.0083 (1 and 0.0093 (1 Å for (I and (II, respectively] by 62.47 (17 and 72.51 (14°, respectively, in (I, and by 71.44 (9 and 54.90 (8°, respectively, in (II. The planes of the aromatic rings are inclined to one another by 53.82 (17° in (I and by 58.04 (9° in (II. In the crystals of both (I and (II, pairs of N—H...Nnitrile hydrogen bonds link the molecules, forming inversion dimers with R22(12 ring motifs. In (I, the resulting dimers are connected through C—H...Br hydrogen bonds, forming sheets parallel to (10-1, and π–π interactions [inter-centroid distance = 3.7821 (16 Å] involving inversion-related pyridine rings, forming a three-dimensional network. In (II, the resulting dimers are connected through π–π interactions [inter-centroid distance = 3.771 (2 Å] involving inversion-related pyridine rings, forming a two-dimensional network lying parallel to (001.

  10. Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.

    Science.gov (United States)

    Michael, Sushama; Travé, Gilles; Ramu, Chenna; Chica, Claudia; Gibson, Toby J

    2008-02-15

    KEN-box-mediated target selection is one of the mechanisms used in the proteasomal destruction of mitotic cell cycle proteins via the APC/C complex. While annotating the Eukaryotic Linear Motif resource (ELM, http://elm.eu.org/), we found that KEN motifs were significantly enriched in human protein entries with cell cycle keywords in the UniProt/Swiss-Prot database-implying that KEN-boxes might be more common than reported. Matches to short linear motifs in protein database searches are not, per se, significant. KEN-box enrichment with cell cycle Gene Ontology terms suggests that collectively these motifs are functional but does not prove that any given instance is so. Candidates were surveyed for native disorder prediction using GlobPlot and IUPred and for motif conservation in homologues. Among >25 strong new candidates, the most notable are human HIPK2, CHFR, CDC27, Dab2, Upf2, kinesin Eg5, DNA Topoisomerase 1 and yeast Cdc5 and Swi5. A similar number of weaker candidates were present. These proteins have yet to be tested for APC/C targeted destruction, providing potential new avenues of research.

  11. Open-ring enhancement sign in diagnosing demyelinating pseudotumor

    International Nuclear Information System (INIS)

    Fang Liting; Wang Zhiping; Wang Linyou

    2010-01-01

    Objective: To describe open-ring enhancement sign on MRI of demyelinating pseudotumor. Methods: Contrast-enhanced MRI of histologically confirmed demyelinating pseudotumors (14 patients) and astrocytomas (21) was reviewed. Results: Of the 14 cases of demyelinating pseudotumor, open-ring enhancement pattern was observed in 6; closed ring enhancement in 2; nodular enhancement in 3; patchy enhancement in 1; slight enhancement in 1; and no enhancement in 1. Of the 21 cases of astrocytoma, there was complete ring or lace-like enhancement in 13, no contrast enhancement in 6, patchy enhancement in 2, and none with open-ring enhancement pattern. Conclusion: Open-ring enhancement is a valuable sign in differential diagnosis between demyelinating pseudotumor and astrocytoma. (authors)

  12. Disparate requirements for the Walker A and B ATPase motifs ofhuman RAD51D in homologous recombination

    Energy Technology Data Exchange (ETDEWEB)

    Wiese, Claudia; Hinz, John M.; Tebbs, Robert S.; Nham, Peter B.; Urbin, Salustra S.; Collins, David W.; Thompson, Larry H.; Schild, David

    2006-04-21

    In vertebrates, homologous recombinational repair (HRR) requires RAD51 and five RAD51 paralogs (XRCC2, XRCC3, RAD51B, RAD51C, and RAD51D) that all contain conserved Walker A and B ATPase motifs. In human RAD51D we examined the requirement for these motifs in interactions with XRCC2 and RAD51C, and for survival of cells in response to DNA interstrand crosslinks. Ectopic expression of wild type human RAD51D or mutants having a non-functional A or B motif was used to test for complementation of a rad51d knockout hamster CHO cell line. Although A-motif mutants complement very efficiently, B-motif mutants do not. Consistent with these results, experiments using the yeast two- and three-hybrid systems show that the interactions between RAD51D and its XRCC2 and RAD51C partners also require a functional RAD51D B motif, but not motif A. Similarly, hamster Xrcc2 is unable to bind to the non-complementing human RAD51D B-motif mutants in co-immunoprecipitation assays. We conclude that a functional Walker B motif, but not A motif, is necessary for RAD51D's interactions with other paralogs and for efficient HRR. We present a model in which ATPase sites are formed in a bipartite manner between RAD51D and other RAD51 paralogs.

  13. THE EFFECTS OF CRACKING ON THE SURFACE POTENTIAL OF ICY GRAINS IN SATURN’S E-RING: LABORATORY STUDIES

    Energy Technology Data Exchange (ETDEWEB)

    Bu, Caixia; Bahr, David A.; Dukes, Catherine A.; Baragiola, Raúl A., E-mail: cb8nw@virginia.edu [Laboratory for Astrophysics and Surface Physics, Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904 (United States)

    2016-07-10

    Within Saturn's E-ring, dust grains are coated by water vapor co-released with ice grains from the geyser-like eruptions of Enceladus. These ice-coated grains have intrinsic surface potential and interact synergistically with the ions and electrons of Saturn's magnetospheric plasmas. We perform laboratory experiments to investigate the effects of water-ice growth on the surface potential, using amorphous solid water (ASW) films. We estimate the growth of the surface potential to be ∼ 2.5 mV (Earth) yr{sup 1} and 112 mV yr{sup 1} for E-ring grains at ∼4.5 R {sub s} and 3.95 R {sub s} outside Enceladus’s plume, respectively. In addition, our measurements show that the linear relationship between the surface potential and the film thickness, as described in previous studies, has an upper limit, where the film spontaneously cracks above a porosity-dependent critical thickness. Heating of the cracked films with (and without) deposited charge shows that significant positive (and negative) surface potentials are retained at temperatures above 110 K, contrary to the minimal values (roughly zero) for thin, transparent ASW films. The significant surface potentials observed on micron-scale cracked ice films after thermal cycling, (5–20) V, are consistent with Cassini measurements, which indicate a negative charge of up to 5 V for E-ring dust particles at ∼5 R {sub s}. Therefore, the native grain surface potential resulting from water-vapor coating must be included in modeling studies of interactions between E-ring icy surfaces and Saturn's magnetospheric plasma.

  14. DNA motif alignment by evolving a population of Markov chains.

    Science.gov (United States)

    Bi, Chengpeng

    2009-01-30

    Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

  15. (1S,3R,8S,9R,10S-2,2-Dichloro-3,7,7,10-tetramethyl-9,10-epoxytricyclo[6.4.0.01,3]dodecane

    Directory of Open Access Journals (Sweden)

    Moha Berraho

    2010-12-01

    Full Text Available The title compound, C16H24Cl2O, was synthesized from β-himachalene (3,5,5,9-tetramethyl-2,4a,5,6,7,8-hexahydro-1H-benzocycloheptene, which was isolated from the essential oil of the Atlas cedar (cedrus atlantica. The molecule forms an extended sheet of two fused rings which exhibit different conformations. The six-membered ring has a half-chair conformation, while the seven-membered ring displays a chair conformation; the dihedral angle between the two rings is 38.2 (1°.

  16. Physiological Responses during Cycling With Oval Chainrings (Q-Ring) and Circular Chainrings.

    Science.gov (United States)

    Cordova, Alfredo; Latasa, Iban; Seco, Jesus; Villa, Gerardo; Rodriguez-Falces, Javier

    2014-05-01

    The aim of this study was to compare the physiological responses of cyclists using round (C-ring) or oval (Q-ring) chainrings during an incremental test until exhaustion. Following a randomized design, twelve male elite cyclists [age (mean ± SD): 21.1 ± 2.1 yr; VO2max: 78.1 ± 5.3 mL·kg(-1)min(-1)] performed two incremental maximal tests separated by 48 h (one with C-rings, the other with Q-rings). Starting at 100 W, the workload was increased by 25 W every 3 min until volitional exhaustion. Maximal heart rate, power output and oxygen consumption were compared. Blood lactate was monitored throughout the test. After the incremental test, 4 intermittent 20-s maximal sprints with a 60-s recovery period in between were performed. Maximal isometric voluntary contractions were performed at rest and immediately after each 20-s maximal sprint, and the force and EMG RMS amplitude were recorded from the vastus medialis and vastus lateralis muscles. For the incremental exercise test, no significant differences were found in the maximal power output (P=0.12), oxygen consumption (P=0.39), and heart rate (P=0.32) between Q-rings and C-rings. Throughout the incremental test, lactate levels were comparable when using both the C-rings and Q-rings (P=0.47). During the short sprints, power output was 2.5-6.5% greater for Q-rings than for C-rings (P=0.22). The decline in EMG RMS amplitude observed during the incremental tests was comparable for Q-rings and C-rings (0.42). These findings indicate that the oval chainring design, presented here as "Q-rings", did not significantly influence the physiological response to an incremental exercise test as compared to a conventional chainring. Key pointsDuring the incremental exercise test, no significant differences were found in power output, oxygen consumption or heart rate between oval "Q-rings" and conventional chainrings.Over the course of the incremental test, blood lactate levels were comparable for the oval "Q-rings" and

  17. Micro-ring sensor used in the diagnosis of gastric cancer

    Science.gov (United States)

    Shi, Sichao; Cheng, Qing; Lin, Rong; Su, Da; Huang, Ying

    2016-01-01

    To find a detecting method that can be applied to the clinical screening and diagnosis, the cascaded micro-ring sensor with Vernier effect was used to distinguish gastric cancerous and normal cells. The simulation by FDTD of the cascaded microring sensor with different refractive indexes of the analyte (normal cells and gastric cancer cells) will be presented. In the simulation, with the refractive index's change Δn=0.02 for the two different analyte, the shift of sensor's resonant wavelength is 6.71nm. And the cascaded micro-ring sensor's sensitivity S is 335.5nm/RIU, and it is much larger compared to 19nm/RIU for a single ring sensor.

  18. Comparison of different mass spectrometry techniques in the measurement of L-[ring-13C6]phenylalanine incorporation into mixed muscle proteins

    Science.gov (United States)

    Zabielski, Piotr; Ford, G. Charles; Persson, X. Mai; Jaleel, Abdul; Dewey, Jerry D.; Nair, K Sreekumaran

    2013-01-01

    Precise measurement of low enrichment of stable isotope labeled amino-acid tracers in tissue samples is a prerequisite in measuring tissue protein synthesis rates. The challenge of this analysis is augmented when small sample size is a critical factor. Muscle samples from human participants following an 8 hour intravenous infusion of L-[ring-13C6]phenylalanine and a bolus dose of L-[ring-13C6]phenylalanine in a mouse were utilized. Liquid Chromatography tandem mass spectrometry (LC/MS/MS), Gas Chromatography tandem mass spectrometry (GC/MS/MS) and Gas Chromatography/Mass spectrometry (GC/MS) were compared to the Gas Chromatography-Combustion-Isotope Ratio mass spectrometry (GC/C/IRMS), to measure mixed muscle protein enrichment of [ring13C6]phenylalanine enrichment. The sample isotope enrichment ranged from 0.0091 to 0.1312 Molar Percent excess (MPE). As compared with GC/C/IRMS, LC/MS/MS, GC/MS/MS and GC/MS showed coefficients of determination of R2 = 0.9962 and R2 = 0.9942, and 0.9217 respectively. However, the precision of measurements (coefficients of variation) for intra-assay are 13.0%, 1.7%, 6.3% and 13.5% and for inter-assay are 9.2%, 3.2%, 10.2% and 25% for GC/C/IRMS, LC/MS/MS, GC/MS/MS and GC/MS respectively. The muscle sample sizes required to obtain these results were 8μg, 0.8μg, 3μg and 3μg for GC/C/IRMS, LC/MS/MS, GC/MS/MS, and GC/MS respectively. We conclude that LC/MS/MS is optimally suited for precise measurements of L-[ring-13C6]phenylalanine tracer enrichment in low abundance and in small quantity samples. PMID:23378099

  19. 25Gb/s 1V-driving CMOS ring modulator with integrated thermal tuning.

    Science.gov (United States)

    Li, Guoliang; Zheng, Xuezhe; Yao, Jin; Thacker, Hiren; Shubin, Ivan; Luo, Ying; Raj, Kannan; Cunningham, John E; Krishnamoorthy, Ashok V

    2011-10-10

    We report a high-speed ring modulator that fits many of the ideal qualities for optical interconnect in future exascale supercomputers. The device was fabricated in a 130 nm SOI CMOS process, with 7.5 μm ring radius. Its high-speed section, employing PN junction that works at carrier-depletion mode, enables 25 Gb/s modulation and an extinction ratio >5 dB with only 1V peak-to-peak driving. Its thermal tuning section allows the device to work in broad wavelength range, with a tuning efficiency of 0.19 nm/mW. Based on microwave characterization and circuit modeling, the modulation energy is estimated ~7 fJ/bit. The whole device fits in a compact 400 μm2 footprint.

  20. DNA motif elucidation using belief propagation.

    Science.gov (United States)

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-09-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.

  1. Crystal structures of 2-[(4,6-diaminopyrimidin-2-ylsulfanyl]-N-(naphthalen-1-ylacetamide and 2-[(4,6-diaminopyrimidin-2-ylsulfanyl]-N-(4-fluorophenylacetamide

    Directory of Open Access Journals (Sweden)

    S. Subasri

    2017-02-01

    Full Text Available The title compounds, C16H15N5OS, (I, and C12H12FN5OS, (II, are [(diaminopyrimidinesulfanyl]acetamide derivatives. In (I, the pyrimidine ring is inclined to the naphthalene ring system by 55.5 (1°, while in (II, the pyrimidine ring is inclined to the benzene ring by 58.93 (8°. In (II, there is an intramolecular N—H...N hydrogen bond and a short C—H...O contact. In the crystals of (I and (II, molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with R22(8 ring motifs. In the crystal of (I, the dimers are linked by bifurcated N—H...(O,O and C—H...O hydrogen bonds, forming layers parallel to (100. In the crystal of (II, the dimers are linked by N—H...O hydrogen bonds, also forming layers parallel to (100. The layers are linked by C—H...F hydrogen bonds, forming a three-dimensional architecture.

  2. CD3 gamma contains a phosphoserine-dependent di-leucine motif involved in down-regulation of the T cell receptor

    DEFF Research Database (Denmark)

    Dietrich, J; Hou, X; Wegener, A M

    1994-01-01

    -regulation of the TCR. Furthermore, analysis of a series of CD3 gamma truncation mutants indicated that in addition to S126 phosphorylation a motif C-terminal of S126 was required for TCR down-regulation. Point mutation analyses confirmed this observation and demonstrated that a membrane-proximal di-leucine motif (L131......, indicating that the TCR was down-regulated by endocytosis via clathrin coated pits. Based on the present results and previously published observations on intracellular receptor sorting, a general model for intracellular sorting of receptors containing di-leucine- or tyrosine-based motifs is proposed....

  3. 1-(6-Chloro-2-methyl-4-phenylquinolin-3-yl-3-(3-methoxyphenylprop-2-en-1-one

    Directory of Open Access Journals (Sweden)

    Wan-Sin Loh

    2010-01-01

    Full Text Available In the title compound, C26H20ClNO2, the quinoline ring system is approximately planar with a maximum deviation of 0.028 (2 Å and forms a dihedral angle of 73.84 (5° with the phenyl ring. Two neighbouring molecules are arranged into a centrosymmetric dimer through a pair of intermolecular C—H...Cl interactions. A pair of intermolecular C—H...O hydrogen bonds link two methoxyphenyl groups into another centrosymmetric dimer, generating an R22(8 ring motif. The structure is further stabilized by C—H...π interactions.

  4. 2-Hydroxy-5-nitrobenzaldehyde

    Directory of Open Access Journals (Sweden)

    Şamil Işık

    2009-12-01

    Full Text Available The title compound, C7H5NO4, is essentially planar, with a maximum deviation from the mean plane of 0.0116 (11 Å for the hydroxy O atom. The molecular and crystal structure are stabilized by intra- and intermolecular interactions. An intramolecular O—H...O hydrogen bond generates a six-membered ring, producing an S(6 ring motif. The C—H...O interactions result in the formation of C(5 chains and R22(8 rings forming an approximately planar network parallel to (10overline{1}. These planes are interconnected through π–π interactions [centroid–centroid distance 3.582 (2 Å].

  5. Functional motifs responsible for human metapneumovirus M2-2-mediated innate immune evasion.

    Science.gov (United States)

    Chen, Yu; Deng, Xiaoling; Deng, Junfang; Zhou, Jiehua; Ren, Yuping; Liu, Shengxuan; Prusak, Deborah J; Wood, Thomas G; Bao, Xiaoyong

    2016-12-01

    Human metapneumovirus (hMPV) is a major cause of lower respiratory infection in young children. Repeated infections occur throughout life, but its immune evasion mechanisms are largely unknown. We recently found that hMPV M2-2 protein elicits immune evasion by targeting mitochondrial antiviral-signaling protein (MAVS), an antiviral signaling molecule. However, the molecular mechanisms underlying such inhibition are not known. Our mutagenesis studies revealed that PDZ-binding motifs, 29-DEMI-32 and 39-KEALSDGI-46, located in an immune inhibitory region of M2-2, are responsible for M2-2-mediated immune evasion. We also found both motifs prevent TRAF5 and TRAF6, the MAVS downstream adaptors, to be recruited to MAVS, while the motif 39-KEALSDGI-46 also blocks TRAF3 migrating to MAVS. In parallel, these TRAFs are important in activating transcription factors NF-kB and/or IRF-3 by hMPV. Our findings collectively demonstrate that M2-2 uses its PDZ motifs to launch the hMPV immune evasion through blocking the interaction of MAVS and its downstream TRAFs. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Crystal structure of 3,5-dimethoxy-2-[5-(naphthalen-1-yl-4,5-dihydro-1H-pyrazol-3-yl]phenol

    Directory of Open Access Journals (Sweden)

    Dongsoo Koh

    2015-10-01

    Full Text Available In the title compound, C21H20N2O3, the planes of the benzene ring and the naphthalene ring system are inclined to one another by 70.95°, and by 4.99 (6 and 75.93 (5°, respectively, to the mean plane of the pyrazoline ring. The latter has an envelope conformation with the methine (CH C atom as the flap. There is an intramolecular O—H...N hydrogen bond that forms an S(6 ring motif. In the crystal, molecules are linked by C—H...O hydrogen bonds, forming chains along [100]. The chains are linked via C—H...N hydrogen bonds, forming sheets parallel to the ab plane. The sheets are linked by a series of N—H...π and C—H...π interactions forming a three-dimensional structure.

  7. 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.

  8. Hunting Motifs in Situla Art

    Directory of Open Access Journals (Sweden)

    Andrej Preložnik

    2013-07-01

    Full Text Available Situla art developed as an echo of the toreutic style which had spread from the Near East through the Phoenicians, Greeks and Etruscans as far as the Veneti, Raeti, Histri, and their eastern neighbours in the region of Dolenjska (Lower Carniola. An Early Iron Age phenomenon (c. 600—300 BC, it rep- resents the major and most arresting form of the contemporary visual arts in an area stretching from the foot of the Apennines in the south to the Drava and Sava rivers in the east. Indeed, individual pieces have found their way across the Alpine passes and all the way north to the Danube. In the world and art of the situlae, a prominent role is accorded to ani- mals. They are displayed in numerous representations of human activities on artefacts crafted in the classic situla style – that is, between the late 6th  and early 5th centuries BC – as passive participants (e.g. in pageants or in harness or as an active element of the situla narrative. The most typical example of the latter is the hunting scene. Today we know at least four objects decorat- ed exclusively with hunting themes, and a number of situlae and other larger vessels where hunting scenes are embedded in composite narratives. All this suggests a popularity unparallelled by any other genre. Clearly recognisable are various hunting techniques and weapons, each associated with a particu- lar type of game (Fig. 1. The chase of a stag with javelin, horse and hound is depicted on the long- familiar and repeatedly published fibula of Zagorje (Fig. 2. It displays a hound mauling the stag’s back and a hunter on horseback pursuing a hind, her neck already pierced by the javelin. To judge by the (so far unnoticed shaft end un- der the stag’s muzzle, the hunter would have been brandishing a second jave- lin as well, like the warrior of the Vače fibula or the rider of the Nesactium situla, presumably himself a hunter. Many parallels to his motif are known from Greece, Etruria, and

  9. Mutagenic and cytotoxic properties of 6-thioguanine, S6-methylthioguanine, and guanine-S6-sulfonic acid.

    Science.gov (United States)

    Yuan, Bifeng; Wang, Yinsheng

    2008-08-29

    Thiopurine drugs, including 6-thioguanine ((S)G), 6-mercaptopurine, and azathioprine, are widely employed anticancer agents and immunosuppressants. The formation of (S)G nucleotides from the thiopurine prodrugs and their subsequent incorporation into nucleic acids are important for the drugs to exert their cytotoxic effects. (S)G in DNA can be methylated by S-adenosyl-l-methionine to give S(6)-methylthioguanine (S(6)mG) and oxidized by UVA light to render guanine-S(6)-sulfonic acid ((SO3H)G). Here, we constructed single-stranded M13 shuttle vectors carrying a (S)G, S(6)mG, or (SO3H)G at a unique site and allowed the vectors to propagate in wild-type and bypass polymerase-deficient Escherichia coli cells. Analysis of the replication products by using the competitive replication and adduct bypass and a slightly modified restriction enzyme digestion and post-labeling assays revealed that, although none of the three thionucleosides considerably blocked DNA replication in all transfected E. coli cells, both S(6)mG and (SO3H)G were highly mutagenic, which resulted in G-->A mutation at frequencies of 94 and 77%, respectively, in wild-type E. coli cells. Deficiency in bypass polymerases does not result in alteration of mutation frequencies of these two lesions. In contrast to what was found from previous steady-state kinetic analysis, our data demonstrated that 6-thioguanine is mutagenic, with G-->A transition occurring at a frequency of approximately 10%. The mutagenic properties of 6-thioguanine and its derivatives revealed in the present study offered important knowledge about the biological implications of these thionucleosides.

  10. The Lord of Rings - the mysterious case of the stolen rings: a critical analysis

    Science.gov (United States)

    Sandrelli, S.

    The Lord of Rings - the mysterious case of the stolen rings: a critical analysis S. Sandrelli INAF - Osservatorio Astronomico di Brera, Milano, Italy (stefano.sandrelli@brera.inaf.it / Fax: 02 72001600 / Phone: +39 02 72320337) "The Lord of Rings - the mysterious case of the stolen rings" is a live astronomical role-playing game for kids aged 10 -13. Its goal is to introduce them to some of the main topics of the Solar System: a) the role of gravity; b) the distribution of mass & light; c) the effects of rotation; d) the distribution of water. The game was held both at the Perugia (2004) and the Genova Science Festival (2005), obtaining great success. Teams of about 6-8 members are introduced to Mr Schioppanelli, the astro-detective of the town (the name is a pun: it reminds Schiaparelli, the famous italian astronomer, and it is a slang expression meaning "ring-breaker"). Mr Schioppanelli has his office in an "gastronomical astronomical observatory", known as The Red Giant Pizzeria. Schioppanelli informs the kids that a mysterious Centaur succeded in stealing the rings of Saturn. The partecipants are appointed astro-detectives in-charge and asked to find the rings by browsing around the Solar System, which is scaled so as to fit the town historical centre or a pedestrian area, going from the Sun to Saturn or beyond, depending on the actual area at disposal. Great care must be taken allowing children playing only in a car-free area of the town. At the right scaled distances, the partecipants meet characters playing as the various planets. The kids can talk to them after solving a riddle, obtaining useful informations. A special characters play as a comet, timely going in and out of the inner solar system. The teams can also talk to some shepherd-moons of the rings. They easily discover that the rings were totally destroyed by the Centaur: a real disaster! They are also suggested to gather the necessary ingredients (gravity, light, rotation, inclination, dust and

  11. 4-[(5-Hydroxy-3-methyl-1-phenyl-1H-pyrazol-4-ylphenylmethyl]-5-methyl-2-phenyl-1H-pyrazol-3(2H-one ethanol hemisolvate

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2009-01-01

    Full Text Available The asymmetric unit of the title compound, C27H24N4O2·0.5C2H6O, comprises two crystallographically independent molecules (A and B with slightly different conformations, and one ethanol molecule of crystallization. Intramolecular C—H...O and O—H...O hydrogen bonds generate six- and eight-membered rings, producing S(6 and S(8 ring motifs, respectively. In molecule A, one of the benzene rings is disordered over two positions, with site-occupancy factors of 0.542 (11 and 0.458 (11. The dihedral angles between the central benzene ring and the two outer benzene rings are 73.88 (9 and 82.6 (2/88.9 (2° in molecule A, and 80.81 (8 and 79.38 (8° in molecule B. In the crystal structure, molecules form infinite one-dimensional chains in the (101 plane. The crystal structure is stabilized by intermolecular O—H...N, N—H...N, N—H...O and C—H...O hydrogen bonds, weak C—H...π and π–π [centroid–centroid = 3.5496 (1 Å] interactions.

  12. Hybrid DNA i-motif: Aminoethylprolyl-PNA (pC5) enhance the stability of DNA (dC5) i-motif structure.

    Science.gov (United States)

    Gade, Chandrasekhar Reddy; Sharma, Nagendra K

    2017-12-15

    This report describes the synthesis of C-rich sequence, cytosine pentamer, of aep-PNA and its biophysical studies for the formation of hybrid DNA:aep-PNAi-motif structure with DNA cytosine pentamer (dC 5 ) under acidic pH conditions. Herein, the CD/UV/NMR/ESI-Mass studies strongly support the formation of stable hybrid DNA i-motif structure with aep-PNA even near acidic conditions. Hence aep-PNA C-rich sequence cytosine could be considered as potential DNA i-motif stabilizing agents in vivo conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Automatic annotation of protein motif function with Gene Ontology terms

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Vanathi

    2004-09-01

    Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.

  14. Verification of the MOTIF code version 3.0

    International Nuclear Information System (INIS)

    Chan, T.; Guvanasen, V.; Nakka, B.W.; Reid, J.A.K.; Scheier, N.W.; Stanchell, F.W.

    1996-12-01

    As part of the Canadian Nuclear Fuel Waste Management Program (CNFWMP), AECL has developed a three-dimensional finite-element code, MOTIF (Model Of Transport In Fractured/ porous media), for detailed modelling of groundwater flow, heat transport and solute transport in a fractured rock mass. The code solves the transient and steady-state equations of groundwater flow, solute (including one-species radionuclide) transport, and heat transport in variably saturated fractured/porous media. The initial development was completed in 1985 (Guvanasen 1985) and version 3.0 was completed in 1986. This version is documented in detail in Guvanasen and Chan (in preparation). This report describes a series of fourteen verification cases which has been used to test the numerical solution techniques and coding of MOTIF, as well as demonstrate some of the MOTIF analysis capabilities. For each case the MOTIF solution has been compared with a corresponding analytical or independently developed alternate numerical solution. Several of the verification cases were included in Level 1 of the International Hydrologic Code Intercomparison Project (HYDROCOIN). The MOTIF results for these cases were also described in the HYDROCOIN Secretariat's compilation and comparison of results submitted by the various project teams (Swedish Nuclear Power Inspectorate 1988). It is evident from the graphical comparisons presented that the MOTIF solutions for the fourteen verification cases are generally in excellent agreement with known analytical or numerical solutions obtained from independent sources. This series of verification studies has established the ability of the MOTIF finite-element code to accurately model the groundwater flow and solute and heat transport phenomena for which it is intended. (author). 20 refs., 14 tabs., 32 figs

  15. Suppressing band gap of MoS{sub 2} by the incorporation of four- and eight-membered rings

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Liyan; Zhang, Tingting, E-mail: ttzhang@hytc.edu.cn [Huaiyin Normal University, School of Physics and Electronic & Electrical Engineering, and Jiangsu Key Laboratory of Modern Measurement Technology and Intelligent Systems (China)

    2015-05-15

    A stable planar allotrope of MoS{sub 2}, formed by introducing four- and eight-membered rings into its hexagonal network (H468), is identified to be a narrow direct-band-gap semiconductor by first principle calculations, which is remarkably different from the large band gap semiconductor of conventional MoS{sub 2} and also the zero band gap allotrope consisting of four- and eight-membered rings (H48) only. The medium-sized direct band gap indicates that H468 would find applications in nanoelectronics and near-infrared optoelectronic devices. Furthermore, the distinctive simulated scanning tunneling microscope images under positive and negative biases might be a unique characteristic for the experimental identification of such an allotrope of MoS{sub 2}.

  16. 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

  17. Purification and functional motifs of the recombinant ATPase of orf virus.

    Science.gov (United States)

    Lin, Fong-Yuan; Chan, Kun-Wei; Wang, Chi-Young; Wong, Min-Liang; Hsu, Wei-Li

    2011-10-01

    Our previous study showed that the recombinant ATPase encoded by the A32L gene of orf virus displayed ATP hydrolysis activity as predicted from its amino acids sequence. This viral ATPase contains four known functional motifs (motifs I-IV) and a novel AYDG motif; they are essential for ATP hydrolysis reaction by binding ATP and magnesium ions. The motifs I and II correspond with the Walker A and B motifs of the typical ATPase, respectively. To examine the biochemical roles of these five conserved motifs, recombinant ATPases of five deletion mutants derived from the Taiping strain were expressed and purified. Their ATPase functions were assayed and compared with those of two wild type strains, Taiping and Nantou isolated in Taiwan. Our results showed that deletions at motifs I-III or IV exhibited lower activity than that of the wild type. Interestingly, deletion of AYDG motif decreased the ATPase activity more significantly than those of motifs I-IV deletions. Divalent ions such as magnesium and calcium were essential for ATPase activity. Moreover, our recombinant proteins of orf virus also demonstrated GTPase activity, though weaker than the original ATPase activity. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. Mutagenic and Cytotoxic Properties of 6-Thioguanine, S6-Methylthioguanine, and Guanine-S6-sulfonic Acid*S⃞

    OpenAIRE

    Yuan, Bifeng; Wang, Yinsheng

    2008-01-01

    Thiopurine drugs, including 6-thioguanine (SG), 6-mercaptopurine, and azathioprine, are widely employed anticancer agents and immunosuppressants. The formation of SG nucleotides from the thiopurine prodrugs and their subsequent incorporation into nucleic acids are important for the drugs to exert their cytotoxic effects. SG in DNA can be methylated by S-adenosyl-l-methionine to give S6-methylthioguanine (S6mG) and oxidized by UVA light to render guanine-S6-sulfonic acid ...

  19. Generation of stable mixed-compact-toroid rings by inducing plasma currents in strong E rings

    International Nuclear Information System (INIS)

    Jayakumar, R.; Taggart, D.P.; Parker, M.R.; Fleischmann, H.H.

    1989-01-01

    In the RECE-Christa device, hybrid-type compact toroid rings are generated by inducing large toroidal plasma currents I rho in strong electron rings using a thin induction coil positioned along the ring axis. Starting from field-reversal values δ ο = 50 - 120 percent of the original pure fast-electron ring, the induced plasma current I rho raises δ to a maximum value of up to 240 percent with I rho contributing more than 50 percent of the total ring current. Quite interestingly, the generated hybrid compact toroid configurations appear gross-stable during the full I rho pulse length (half-amplitude width about 100 μs)

  20. Requirement for asparagine in the aquaporin NPA sequence signature motifs for cation exclusion

    DEFF Research Database (Denmark)

    Wree, Dorothea; Wu, Binghua; Zeuthen, Thomas

    2011-01-01

    Two highly conserved NPA motifs are a hallmark of the aquaporin (AQP) family. The NPA triplets form N-terminal helix capping structures with the Asn side chains located in the centre of the water or solute-conducting channel, and are considered to play an important role in AQP selectivity. Although...... interchangeable at both NPA sites without affecting protein expression or water, glycerol and methylamine permeability. However, other mutations in the NPA region led to reduced permeability (S186C and S186D), to nonfunctional channels (N64D), or even to lack of protein expression (S186A and S186T). Using...... electrophysiology, we found that an analogous mammalian AQP1 N76S mutant excluded protons and potassium ions, but leaked sodium ions, providing an argument for the overwhelming prevalence of Asn over other amino acids. We conclude that, at the first position in the NPA motifs, only Asn provides efficient helix cap...

  1. rac-6-Hydroxy-4-(4-nitrophenyl-5-(2-thienylcarbonyl-6-(trifluoromethyl-3,4,5,6-tetrahydropyrimidin-2(1H-one monohydrate

    Directory of Open Access Journals (Sweden)

    Jian-Li Zhang

    2010-11-01

    Full Text Available The title compound, C16H12F3N3O5S·H2O, was prepared by reaction of 4-nitrobenzaldehyde, 4,4,4-trifluoro-1-(thiophen-2-ylbutane-1,3-dione and urea. The asymmetric unit contains two independent molecules, with essentially identical geometries and conformations. The dihydropyrimidine rings adopt a half-chair conformation. The dihedral angles between the benzene ring and the thiophene ring are 54.82 (8 and 58.72 (8° in the two molecules. The molecular conformation of one of the molecules is stabilized by two intramolecular O—H...O hydrogen bonds, generating an S(6 ring. The crystal structure is stabilized by intermolecular O—H...O and N—H...O hydrogen bonds.

  2. An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers.

    Science.gov (United States)

    Wang, Rang Jian; Gao, Xiang Feng; Kong, Xiang Rui; Yang, Jun

    2016-01-01

    Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.

  3. Radiology of posterior lumbar apophyseal ring fractures: Report of 13 cases

    Energy Technology Data Exchange (ETDEWEB)

    Dietemann, J.L.; Beaujeux, R.; Wackenheim, A.; Runge, M.; Bonneville, J.F.; Badoz, A.; Dosch, J.C.

    1988-08-01

    The authors report radiological findings in 13 cases of avulsion of the posterior lumbar apophyseal ring. The lesion affected young adults in 10 cases and adolescents in 3 cases. The lesion involved the inferior endplate of L4 in 11, and of L5 in 2 patients. 6 patients presented with unilateral sciatica, 3 with bilateral sciatica, and 4 with low back pain. Acute spinal trauma was evident only in 2 adolescents. Radiological recognition of the lesion was possible on plain films in 9 cases. CT demonstrates association of avulsion of the posterior vertebral apophyseal ring and herniated disc in all cases. Avulsion of the posterior apophyseal ring has to be differentiated from posterior longitudinal ligament, annulus, or herniated disc calcifications, as well as from posterior degenerative ridge osteophytes. Controversy about physiopathology of the lesion remains: Weakness of the apophyseal ring during childhood and in patients with Scheuermann's disease may explain avulsion of the apophyseal ring in association with median disc herniation.

  4. Fifth Interim Status Report: Model 9975 PCV O-Ring Fixture Long-Term Leak Performance

    International Nuclear Information System (INIS)

    Daugherty, W.; Hoffman, E.

    2010-01-01

    A series of experiments to monitor the aging performance of Viton reg. GLT O-rings used in the Model 9975 package has been ongoing for six years at the Savannah River National Laboratory. Sixty-seven mock-ups of 9975 Primary Containment Vessels (PCVs) were assembled and heated to temperatures ranging from 200 to 450 F. They were leak-tested initially and have been tested at nominal six month intervals to determine if they meet the criterion of leaktightness defined in ANSI standard N14.5-97. Fourteen additional tests were initiated in 2008 with GLT-S O-rings heated to temperatures ranging from 200 to 400 F. High temperature aging continues for 36 GLT O-ring fixtures at 200--350 F. Room temperature leak test failures have been experienced in 5 of the GLT O-ring fixtures aging at 300 and 350 F, and in all 3 of the GLT O-ring fixtures aging at higher temperatures. No failures have yet been observed in GLT O-ring fixtures aging at 200 F for 30--48 months, which is still bounding to O-ring temperatures during storage in KAMS. High temperature aging continues for 6 GLT-S O-ring fixtures at 200--300 F. Room temperature leak test failures have been experienced in all 8 of the GLT-S O-ring fixtures aging at 350 and 400 F. No failures have yet been observed in GLT-S O-ring fixtures aging at 200 or 300 F for 19 months. For O-ring fixtures that have failed the room temperature leak test and been disassembled, the O-rings displayed a compression set ranging from 51--95%. This is significantly greater than seen to date for packages inspected during KAMS field surveillance (23% average). For GLT O-rings, service life based on the room temperature leak rate criterion is comparable to that predicted by compression stress relaxation (CSR) data at higher temperatures (350--400 F). While there are no comparable failure data yet at aging temperatures below 300 F, extrapolations of the data for GLT O-rings suggests that CSR model predictions provide a conservative prediction of service

  5. 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.

  6. An experimental test of a fundamental food web motif.

    Science.gov (United States)

    Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia

    2010-06-07

    Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.

  7. Structure-activity relationship studies of 1,7-diheteroarylhepta-1,4,6-trien-3-ones with two different terminal rings in prostate epithelial cell models.

    Science.gov (United States)

    Wang, Rubing; Zhang, Xiaojie; Chen, Chengsheng; Chen, Guanglin; Sarabia, Cristian; Zhang, Qiang; Zheng, Shilong; Wang, Guangdi; Chen, Qiao-Hong

    2017-06-16

    To systematically investigate the structure-activity relationships of 1,7-diheteroarylhepta-1,4,6-trien-3-ones in three human prostate cancer cell models and one human prostate non-neoplastic epithelial cell model, thirty five 1,7-diarylhepta-1,4,6-trien-3-ones with different terminal heteroaromatic rings have been designed for evaluation of their anti-proliferative potency in vitro. These target compounds have been successfully synthesized through two sequential Horner-Wadsworth-Emmons reactions starting from the appropriate aldehydes and tetraethyl (2-oxopropane-1,3-diyl)bis(phosphonate). Their anti-proliferative potency against PC-3, DU-145 and LNCaP human prostate cancer cell lines can be significantly enhanced by the manipulation of the terminal heteroaromatic rings, further demonstrating the utility of 1,7-diarylhepta-1,4,6-trien-3-one as a potential scaffold for the development of anti-prostate cancer agents. The optimal analog 40 is 82-, 67-, and 39-fold more potent than curcumin toward the three prostate cancer cell lines, respectively. The experimental data also reveal that the trienones with two different terminal aromatic rings possess greater potency toward three prostate cancer cell lines, but also have greater capability of suppressing the proliferation of PWR-1E benign human prostate epithelial cells, as compared to the corresponding counterparts with two identical terminal rings and curcumin. The terminal aromatic rings also affect the cell apoptosis perturbation. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  8. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit; Bajic, Vladimir B.; Kaushik, Dinesh

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  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. Nuclear localization of the dehydrin OpsDHN1 is determined by histidine-rich motif

    Science.gov (United States)

    Hernández-Sánchez, Itzell E.; Maruri-López, Israel; Ferrando, Alejandro; Carbonell, Juan; Graether, Steffen P.; Jiménez-Bremont, Juan F.

    2015-01-01

    The cactus OpsDHN1 dehydrin belongs to a large family of disordered and highly hydrophilic proteins known as Late Embryogenesis Abundant (LEA) proteins, which accumulate during the late stages of embryogenesis and in response to abiotic stresses. Herein, we present the in vivo OpsDHN1 subcellular localization by N-terminal GFP translational fusion; our results revealed a cytoplasmic and nuclear localization of the GFP::OpsDHN1 protein in Nicotiana benthamiana epidermal cells. In addition, dimer assembly of OpsDHN1 in planta using a Bimolecular Fluorescence Complementation (BiFC) approach was demonstrated. In order to understand the in vivo role of the histidine-rich motif, the OpsDHN1-ΔHis version was produced and assayed for its subcellular localization and dimer capability by GFP fusion and BiFC assays, respectively. We found that deletion of the OpsDHN1 histidine-rich motif restricted its localization to cytoplasm, but did not affect dimer formation. In addition, the deletion of the S-segment in the OpsDHN1 protein affected its nuclear localization. Our data suggest that the deletion of histidine-rich motif and S-segment show similar effects, preventing OpsDHN1 from getting into the nucleus. Based on these results, the histidine-rich motif is proposed as a targeting element for OpsDHN1 nuclear localization. PMID:26442018

  11. Nuclear localization of the dehydrin OpsDHN1 is determined by histidine-rich motif

    Directory of Open Access Journals (Sweden)

    Itzell Euridice Hernández-Sánchez

    2015-09-01

    Full Text Available The cactus OpsDHN1 dehydrin belongs to a large family of disordered and highly hydrophilic proteins known as Late Embryogenesis Abundant (LEA proteins, which accumulate during the late stages of embryogenesis and in response to abiotic stresses. Herein, we present the in vivo OpsDHN1 subcellular localization by N-terminal GFP translational fusion; our results revealed a cytoplasmic and nuclear localization of the GFP::OpsDHN1 protein in Nicotiana benthamiana epidermal cells. In addition, dimer assembly of OpsDHN1 in planta using a Bimolecular Fluorescence Complementation (BiFC approach was demonstrated. In order to understand the in vivo role of the histidine-rich motif, the OpsDHN1-ΔHis version was produced and assayed for its subcellular localization and dimer capability by GFP fusion and BiFC assays, respectively. We found that deletion of the OpsDHN1 histidine-rich motif restricted its localization to cytoplasm, but did not affect dimer formation. In addition, the deletion of the S-segment in the OpsDHN1 protein affected its nuclear localization. Our data suggest that the deletion of histidine-rich motif and S-segment show similar effects, preventing OpsDHN1 from getting into the nucleus. Based on these results, the histidine rich motif is proposed as a targeting element for OpsDHN1 nuclear localization.

  12. Virtual Exploration of the Ring Systems Chemical Universe.

    Science.gov (United States)

    Visini, Ricardo; Arús-Pous, Josep; Awale, Mahendra; Reymond, Jean-Louis

    2017-11-27

    Here, we explore the chemical space of all virtually possible organic molecules focusing on ring systems, which represent the cyclic cores of organic molecules obtained by removing all acyclic bonds and converting all remaining atoms to carbon. This approach circumvents the combinatorial explosion encountered when enumerating the molecules themselves. We report the chemical universe database GDB4c containing 916 130 ring systems up to four saturated or aromatic rings and maximum ring size of 14 atoms and GDB4c3D containing the corresponding 6 555 929 stereoisomers. Almost all (98.6%) of these ring systems are unknown and represent chiral 3D-shaped macrocycles containing small rings and quaternary centers reminiscent of polycyclic natural products. We envision that GDB4c can serve to select new ring systems from which to design analogs of such natural products. The database is available for download at www.gdb.unibe.ch together with interactive visualization and search tools as a resource for molecular design.

  13. Mechanisms of zero-lag synchronization in cortical motifs.

    Directory of Open Access Journals (Sweden)

    Leonardo L Gollo

    2014-04-01

    Full Text Available Zero-lag synchronization between distant cortical areas has been observed in a diversity of experimental data sets and between many different regions of the brain. Several computational mechanisms have been proposed to account for such isochronous synchronization in the presence of long conduction delays: Of these, the phenomenon of "dynamical relaying"--a mechanism that relies on a specific network motif--has proven to be the most robust with respect to parameter mismatch and system noise. Surprisingly, despite a contrary belief in the community, the common driving motif is an unreliable means of establishing zero-lag synchrony. Although dynamical relaying has been validated in empirical and computational studies, the deeper dynamical mechanisms and comparison to dynamics on other motifs is lacking. By systematically comparing synchronization on a variety of small motifs, we establish that the presence of a single reciprocally connected pair--a "resonance pair"--plays a crucial role in disambiguating those motifs that foster zero-lag synchrony in the presence of conduction delays (such as dynamical relaying from those that do not (such as the common driving triad. Remarkably, minor structural changes to the common driving motif that incorporate a reciprocal pair recover robust zero-lag synchrony. The findings are observed in computational models of spiking neurons, populations of spiking neurons and neural mass models, and arise whether the oscillatory systems are periodic, chaotic, noise-free or driven by stochastic inputs. The influence of the resonance pair is also robust to parameter mismatch and asymmetrical time delays amongst the elements of the motif. We call this manner of facilitating zero-lag synchrony resonance-induced synchronization, outline the conditions for its occurrence, and propose that it may be a general mechanism to promote zero-lag synchrony in the brain.

  14. A speedup technique for (l, d-motif finding algorithms

    Directory of Open Access Journals (Sweden)

    Dinh Hieu

    2011-03-01

    Full Text Available Abstract Background The discovery of patterns in DNA, RNA, and protein sequences has led to the solution of many vital biological problems. For instance, the identification of patterns in nucleic acid sequences has resulted in the determination of open reading frames, identification of promoter elements of genes, identification of intron/exon splicing sites, identification of SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have proven to be extremely helpful in domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, etc. Motifs are important patterns that are helpful in finding transcriptional regulatory elements, transcription factor binding sites, functional genomics, drug design, etc. As a result, numerous papers have been written to solve the motif search problem. Results Three versions of the motif search problem have been proposed in the literature: Simple Motif Search (SMS, (l, d-motif search (or Planted Motif Search (PMS, and Edit-distance-based Motif Search (EMS. In this paper we focus on PMS. Two kinds of algorithms can be found in the literature for solving the PMS problem: exact and approximate. An exact algorithm identifies the motifs always and an approximate algorithm may fail to identify some or all of the motifs. The exact version of PMS problem has been shown to be NP-hard. Exact algorithms proposed in the literature for PMS take time that is exponential in some of the underlying parameters. In this paper we propose a generic technique that can be used to speedup PMS algorithms. Conclusions We present a speedup technique that can be used on any PMS algorithm. We have tested our speedup technique on a number of algorithms. These experimental results show that our speedup technique is indeed very

  15. Rotavirus NSP1 Requires Casein Kinase II-Mediated Phosphorylation for Hijacking of Cullin-RING Ligases.

    Science.gov (United States)

    Davis, Kaitlin A; Morelli, Marco; Patton, John T

    2017-08-29

    The rotavirus nonstructural protein NSP1 repurposes cullin-RING E3 ubiquitin ligases (CRLs) to antagonize innate immune responses. By functioning as substrate adaptors of hijacked CRLs, NSP1 causes ubiquitination and proteasomal degradation of host proteins that are essential for expression of interferon (IFN) and IFN-stimulated gene products. The target of most human and porcine rotaviruses is the β-transducin repeat-containing protein (β-TrCP), a regulator of NF-κB activation. β-TrCP recognizes a phosphorylated degron (DSGΦXS) present in the inhibitor of NF-κB (IκB); phosphorylation of the IκB degron is mediated by IκB kinase (IKK). Because NSP1 contains a C-terminal IκB-like degron (ILD; DSGXS) that recruits β-TrCP, we investigated whether the NSP1 ILD is similarly activated by phosphorylation and whether this modification is required to trigger the incorporation of NSP1 into CRLs. Based on mutagenesis and phosphatase treatment studies, we found that both serine residues of the NSP1 ILD are phosphorylated, a pattern mimicking phosphorylation of IκB. A three-pronged approach using small-molecule inhibitors, small interfering RNAs, and mutagenesis demonstrated that NSP1 phosphorylation is mediated by the constitutively active casein kinase II (CKII), rather than IKK. In coimmunoprecipitation assays, we found that this modification was essential for NSP1 recruitment of β-TrCP and induced changes involving the NSP1 N-terminal RING motif that allowed formation of Cul3-NSP1 complexes. Taken together, our results indicate a highly regulated stepwise process in the formation of NSP1-Cul3 CRLs that is initiated by CKII phosphorylation of NSP1, followed by NSP1 recruitment of β-TrCP and ending with incorporation of the NSP1-β-TrCP complex into the CRL via interactions dependent on the highly conserved NSP1 RING motif. IMPORTANCE Rotavirus is a segmented double-stranded RNA virus that causes severe diarrhea in young children. A primary mechanism used by the

  16. 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

  17. Armadillo motifs involved in vesicular transport.

    Directory of Open Access Journals (Sweden)

    Harald Striegl

    Full Text Available Armadillo (ARM repeat proteins function in various cellular processes including vesicular transport and membrane tethering. They contain an imperfect repeating sequence motif that forms a conserved three-dimensional structure. Recently, structural and functional insight into tethering mediated by the ARM-repeat protein p115 has been provided. Here we describe the p115 ARM-motifs for reasons of clarity and nomenclature and show that both sequence and structure are highly conserved among ARM-repeat proteins. We argue that there is no need to invoke repeat types other than ARM repeats for a proper description of the structure of the p115 globular head region. Additionally, we propose to define a new subfamily of ARM-like proteins and show lack of evidence that the ARM motifs found in p115 are present in other long coiled-coil tethering factors of the golgin family.

  18. Characterizing Motif Dynamics of Electric Brain Activity Using Symbolic Analysis

    Directory of Open Access Journals (Sweden)

    Massimiliano Zanin

    2014-10-01

    Full Text Available Motifs are small recurring circuits of interactions which constitute the backbone of networked systems. Characterizing motif dynamics is therefore key to understanding the functioning of such systems. Here we propose a method to define and quantify the temporal variability and time scales of electroencephalogram (EEG motifs of resting brain activity. Given a triplet of EEG sensors, links between them are calculated by means of linear correlation; each pattern of links (i.e., each motif is then associated to a symbol, and its appearance frequency is analyzed by means of Shannon entropy. Our results show that each motif becomes observable with different coupling thresholds and evolves at its own time scale, with fronto-temporal sensors emerging at high thresholds and changing at fast time scales, and parietal ones at low thresholds and changing at slower rates. Finally, while motif dynamics differed across individuals, for each subject, it showed robustness across experimental conditions, indicating that it could represent an individual dynamical signature.

  19. Discriminative motif discovery via simulated evolution and random under-sampling.

    Directory of Open Access Journals (Sweden)

    Tao Song

    Full Text Available Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

  20. Discriminative motif discovery via simulated evolution and random under-sampling.

    Science.gov (United States)

    Song, Tao; Gu, Hong

    2014-01-01

    Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs) training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

  1. Bacterial proteasome activator bpa (rv3780) is a novel ring-shaped interactor of the mycobacterial proteasome.

    Science.gov (United States)

    Delley, Cyrille L; Laederach, Juerg; Ziemski, Michal; Bolten, Marcel; Boehringer, Daniel; Weber-Ban, Eilika

    2014-01-01

    The occurrence of the proteasome in bacteria is limited to the phylum of actinobacteria, where it is maintained in parallel to the usual bacterial compartmentalizing proteases. The role it plays in these organisms is still not fully understood, but in the human pathogen Mycobacterium tuberculosis (Mtb) the proteasome supports persistence in the host. In complex with the ring-shaped ATPase Mpa (called ARC in other actinobacteria), the proteasome can degrade proteins that have been post-translationally modified with the prokaryotic ubiquitin-like protein Pup. Unlike for the eukaryotic proteasome core particle, no other bacterial proteasome interactors have been identified to date. Here we describe and characterize a novel bacterial proteasome activator of Mycobacterium tuberculosis we termed Bpa (Rv3780), using a combination of biochemical and biophysical methods. Bpa features a canonical C-terminal proteasome interaction motif referred to as the HbYX motif, and its orthologs are only found in those actinobacteria encoding the proteasomal subunits. Bpa can inhibit degradation of Pup-tagged substrates in vitro by competing with Mpa for association with the proteasome. Using negative-stain electron microscopy, we show that Bpa forms a ring-shaped homooligomer that can bind coaxially to the face of the proteasome cylinder. Interestingly, Bpa can stimulate the proteasomal degradation of the model substrate β-casein, which suggests it could play a role in the removal of non-native or damaged proteins.

  2. 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.

  3. 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.

  4. Hybrid macrocycle formation and spiro annulation on cis-syn-cis-tricyclo[6.3.0.02,6]undeca-3,11-dione and its congeners via ring-closing metathesis

    Directory of Open Access Journals (Sweden)

    Sambasivarao Kotha

    2015-07-01

    Full Text Available We have developed a simple methodology to transform cis-syn-cis-triquinane derivative 2 into the diindole based macrocycle 6 involving Fischer indolization and ring-closing metathesis (RCM. Various spiro-polyquinane derivatives have been assembled via RCM as a key step.

  5. FY2017 status report: Model 9975 O-ring fixture long-term leak performance

    Energy Technology Data Exchange (ETDEWEB)

    Daugherty, W. L. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2017-07-27

    A series of experiments to monitor the aging performance of Viton® GLT and GLT-S O-rings used in the Model 9975 shipping package has been ongoing since 2004 at the Savannah River National Laboratory. One approach has been to periodically evaluate the leak performance of O-rings being aged in mock-up 9975 Primary Containment Vessels (PCVs) at elevated temperature. Other methods such as compression-stress relaxation (CSR) tests and field surveillance are also on-going to evaluate O-ring behavior. Seventy tests using PCV mock-ups with GLT O-rings were assembled and heated to temperatures ranging from 200 to 450 ºF. They were leak-tested initially and have been tested periodically to determine if they continue to meet the leak-tightness criterion defined in ANSI standard N14.5-97. Due to material substitution, a smaller test matrix with fourteen additional tests was initiated in 2008 with GLT-S O-rings heated to temperatures ranging from 200 to 400 ºF. Leak test failures have been experienced in all of the GLT O-ring fixtures aging at 350 ºF and higher temperatures, and in 8 fixtures aging at 300 ºF. The 300 °F GLT O-ring fixtures failed after 2.8 to 5.7 years at temperature. The remaining GLT O-ring fixtures aging at 300 ºF were retired from testing following more than 5 years at temperature without failure. No failures have yet been observed in GLT O-ring fixtures aging at 200 ºF for 9 to 10.5 years, or in GLT O-ring fixtures aging at 270 ºF for 5.7 years. These aging temperatures bound O-ring temperatures anticipated during normal storage in K-Area Complex (KAC). Leak test failures have been experienced in all of the GLT-S O-ring fixtures aging at 300 ºF and above. No failures have yet been observed in GLT-S O-ring fixtures aging at 200 and 250 ºF for 6.9 to 7.5 years. Data from the O-ring fixtures are generally consistent with results from compression stress relaxation testing, and provide confidence in the predictive models based on those results

  6. The BsaHI restriction-modification system: Cloning, sequencing and analysis of conserved motifs

    Directory of Open Access Journals (Sweden)

    Roberts Richard J

    2008-05-01

    Full Text Available Abstract Background Restriction and modification enzymes typically recognise short DNA sequences of between two and eight bases in length. Understanding the mechanism of this recognition represents a significant challenge that we begin to address for the BsaHI restriction-modification system, which recognises the six base sequence GRCGYC. Results The DNA sequences of the genes for the BsaHI methyltransferase, bsaHIM, and restriction endonuclease, bsaHIR, have been determined (GenBank accession #EU386360, cloned and expressed in E. coli. Both the restriction endonuclease and methyltransferase enzymes share significant similarity with a group of 6 other enzymes comprising the restriction-modification systems HgiDI and HgiGI and the putative HindVP, NlaCORFDP, NpuORFC228P and SplZORFNP restriction-modification systems. A sequence alignment of these homologues shows that their amino acid sequences are largely conserved and highlights several motifs of interest. We target one such conserved motif, reading SPERRFD, at the C-terminal end of the bsaHIR gene. A mutational analysis of these amino acids indicates that the motif is crucial for enzymatic activity. Sequence alignment of the methyltransferase gene reveals a short motif within the target recognition domain that is conserved among enzymes recognising the same sequences. Thus, this motif may be used as a diagnostic tool to define the recognition sequences of the cytosine C5 methyltransferases. Conclusion We have cloned and sequenced the BsaHI restriction and modification enzymes. We have identified a region of the R. BsaHI enzyme that is crucial for its activity. Analysis of the amino acid sequence of the BsaHI methyltransferase enzyme led us to propose two new motifs that can be used in the diagnosis of the recognition sequence of the cytosine C5-methyltransferases.

  7. Indonesian Traditional Toys and the Development of Batik Motifs

    Directory of Open Access Journals (Sweden)

    Bagus Indrayana

    2016-06-01

    Full Text Available There is a wide array of traditional toys in Indonesia. In the past, traditional toys played an important role for skill and creativity development of children. Today, the position of traditional toys in the society is displaced by toys from large-scale manufacturers. Given the critical role of traditional toys for children’s motoric and social development, there is a need to develop media that can be used to promote these traditional products and strengthen their position in the public. We propose to use Batik as a way to effectively disseminate and promote traditional toys to the general public. Apart from this, using traditional toys to create new Batik motifs can have an economic value for the producers of Batik, promote Indonesian products and enrich the Indonesian Batik. This study aims to explore the variety of traditional toys, mainly from Klaten and Magelang, in the Central Java province of Indonesia, and use them as the basis for the development of Batik motif creation. This study used Trilogi Keseimbangan (or Harmony Trilogy aesthetic theory analytical approach that explains the creation of craft consists of the following phases: exploration, design, and materialization. The creation method in this study adopts Tiga Tahap Enam Langkah (Three Phases, Six Steps method offered in the theory. The finding in the field found that the traditional toys material used in Klaten and Magelang, mostly made from waste wood, plywood, and zinc. The manufacturing process is done manually by two or three craftsmen using a simple technology. The traditional toys are designed by the artisans mostly, although there may be designs from the clients. In addition, we also found that the traditional toys have never been used as a Batik motif. The traditional toys Batik motif presented in this work is researcher’s design. For the purposes of this study, we first research the variety of traditional toys available in the market today in Indonesia. We look

  8. Two structure types based on Si6O15 rings: synthesis and structural and spectroscopic characterisation of Cs1.86K1.14DySi6O15 and Cs1.6K1.4SmSi6O15

    International Nuclear Information System (INIS)

    Wierzbicka-Wieczorek, Maria; Goeckeritz, Martin; Kolitsch, Uwe; Lenz, Christoph; Giester, Gerald

    2015-01-01

    The silicate Cs 1.86 K 1.14 DySi 6 O 15 represents a mixed tetrahedral-octahedral framework structure type based on roughly circular Si 6 O 15 rings and isolated DyO 6 octahedra. The silicate Cs 1.6 K 1.4 SmSi 6 O 15 has a layered atomic arrangement built from corrugated Si 6 O 15 layers containing four-, six- and eight-membered rings. The layers are connected by isolated SmO 6 octahedra to form a mixed tetrahedral-octahedral framework. This structure shows a close structural relationship to β-K 3 NdSi 6 O 15 and a less close one to dehydrated elpidite (Na 2 ZrSi 6 O 15 ). In both structures, Cs/K atoms occupy large voids. The silicates were obtained through high-temperature flux syntheses. Their crystal structures have been determined from single-crystal X-ray diffraction data. Cs 1.86 K 1.14 DySi 6 O 15 crystallises in R32 (no. 155) with a = 13.896(2), c = 35.623(7) Aa and V = 5957.2(17) Aa 3 , whereas Cs 1.6 K 1.4 SmSi 6 O 15 crystallises in Cmca (no. 64) with a = 14.474(3), b = 14.718(3), c = 15.231(3) Aa and V = 3244.7(11) Aa 3 . The Dy 3+ and Sm 3+ cations present in the silicates cause PL emission bands in the visible yellow-to-orange spectral range. (Copyright copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  9. Enhanced thermal and mechanical properties of PLA/MoS2 nanocomposites synthesized via the in-situ ring-opening polymerization

    Science.gov (United States)

    Chen, Pengpeng; Liang, Xiao; Xu, Ying; Zhou, Yifeng; Nie, Wangyan

    2018-05-01

    In this work, MoS2 nanosheets were employed to reinforce PLA. In order to promote the homogeneous dispersion of MoS2 in PLA and form a strong interface between MoS2 and PLA, the MoS2 nanosheets were firstly modified by mercapto-ethylamine, and then functionalized with PLA chains through ring-opening polymerization of poly(L-lactide). The XRD, XPS, TGA and 1H NMR characterizations confirmed the successful amino and PLA functionalization of MoS2 nanosheets. The obtained MoS2-g-PLA nanosheets were then introduced to reinforce PLA. SEM images displayed that the MoS2-g-PLA nanosheets were dispersed in PLA matrix uniformly. TGA results showed that initial decomposition temperature was improved from 275.6 °C to 334.8 °C with 0.5 wt% of MoS2-g-PLA nanosheets. The storage modulus of PLA/MoS2-g-PLA-0.5 wt% in the glass state and rubber state were both greatly enhanced compared with neat PLA.

  10. Orchestration of Structural, Stereoelectronic, and Hydrogen-Bonding Effects in Stabilizing Triplexes from Engineered Chimeric Collagen Peptides (Pro(X)-Pro(Y)-Gly)6 Incorporating 4(R/S)-Aminoproline.

    Science.gov (United States)

    Umashankara, Muddegowda; Sonar, Mahesh V; Bansode, Nitin D; Ganesh, Krishna N

    2015-09-04

    Collagens are an important family of structural proteins found in the extracellular matrix with triple helix as the characteristic structural motif. The collagen triplex is made of three left-handed polyproline II (PPII) helices with each PPII strand consisting of repetitive units of the tripeptide motif X-Y-Gly, where the amino acids X and Y are most commonly proline (Pro) and 4R-hydroxyproline (Hyp), respectively. A C4-endo pucker at X-site and C4-exo pucker at Y-site have been proposed to be the key for formation of triplex, and the nature of pucker is dependent on both the electronegativity and stereochemistry of the substituent. The present manuscript describes a new class of collagen analogues-chimeric cationic collagens-wherein both X- and Y-sites in collagen triad are simultaneously substituted by a combination of 4(R/S)-(OH/NH2/NH3(+)/NHCHO)-prolyl units and triplex stabilities measured at different pHs and in EG:H2O. Based on the results a model has been proposed with the premise that any factors which specifically favor the ring puckers of C4-endo at X-site and C4-exo at Y-site stabilize the PPII conformation and hence the derived triplexes. The pH-dependent triplex stability uniquely observed with ionizable 4-amino substituent on proline enables one to define the critical combination of factors C4-(exo/endo), intraresidue H-bonding, stereoelectronic (R/S) and n → π* interactions in dictating the triplex strength. The ionizable NH2 substituent at C4 in R/S configuration is thus a versatile probe for delineating the triplex stabilizing factors and the results have potential for designing of collagen analogues with customized properties for material and biological applications.

  11. Whole-body ring-shaped confocal photoacoustic computed tomography of small animals in vivo

    Science.gov (United States)

    Xia, Jun; Chatni, Muhammad R.; Maslov, Konstantin; Guo, Zijian; Wang, Kun; Anastasio, Mark; Wang, Lihong V.

    2012-05-01

    We report a novel small-animal whole-body imaging system called ring-shaped confocal photoacoustic computed tomography (RC-PACT). RC-PACT is based on a confocal design of free-space ring-shaped light illumination and 512-element full-ring ultrasonic array signal detection. The free-space light illumination maximizes the light delivery efficiency, and the full-ring signal detection ensures a full two-dimensional view aperture for accurate image reconstruction. Using cylindrically focused array elements, RC-PACT can image a thin cross section with 0.10 to 0.25 mm in-plane resolutions and 1.6 s/frame acquisition time. By translating the mouse along the elevational direction, RC-PACT provides a series of cross-sectional images of the brain, liver, kidneys, and bladder.

  12. On (weakly precious rings associated to central polynomials

    Directory of Open Access Journals (Sweden)

    Hani A. Khashan

    2018-04-01

    Full Text Available Let R be an associative ring with identity and let g(x be a fixed polynomial over the center of R. We define R to be (weakly g(x-precious if for every element a∈R, there are a zero s of g(x, a unit u and a nilpotent b such that (a=±s+u+b a=s+u+b. In this paper, we investigate many examples and properties of (weakly g(x-precious rings. If a and b are in the center of R with b-a is a unit, we give a characterizations for (weakly (x-a(x-b-precious rings in terms of (weakly precious rings. In particular, we prove that if 2 is a unit, then a ring is precious if and only it is weakly precious. Finally, for n∈ℕ, we study (weakly (xⁿ-x-precious rings and clarify some of their properties.

  13. Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

    Directory of Open Access Journals (Sweden)

    Farré Domènec

    2007-12-01

    Full Text Available Abstract Background The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.

  14. Atomic cranks and levers control sugar ring conformations

    International Nuclear Information System (INIS)

    Zhang Qingmin; Lee, Gwangrog; Marszalek, Piotr E

    2005-01-01

    In this paper we review the conformational analysis of sugar rings placed under tension during mechanical manipulations of single polysaccharide molecules with the atomic force microscope and during steered molecular dynamics simulations. We examine the role of various chemical bonds and linkages between sugar rings in inhibiting or promoting their conformational transitions by means of external forces. Small differences in the orientation of one chemical bond on the sugar ring can produce significantly different mechanical properties at the polymer level as exemplified by two polysaccharides: cellulose, composed of β-1→4-linked D-glucose, and amylose, composed of α-1→4-linked D-glucose. In contrast to β-glucose rings, which are mechanically stable and produce simple entropic elasticity of the chain, α-glucose rings flip under tension from their chair to a boat-like structure and these transitions produce deviations of amylose elasticity from the freely jointed chain model. We also examine the deformation of two mechanically complementary 1→6-linked polysaccharides: pustulan, a β-1→6-linked glucan, and dextran, a α-1→6-linked glucan. Forced rotations about the C 5 -C 6 bonds govern the elasticity of pustulan, and complex conformational transitions that involve simultaneous C 5 -C 6 rotations and chair-boat transitions govern the elasticity of dextran. Finally, we discuss the likelihood of various conformational transitions in sugar rings in biological settings and speculate on their significance

  15. Computational analyses of synergism in small molecular network motifs.

    Directory of Open Access Journals (Sweden)

    Yili Zhang

    2014-03-01

    Full Text Available Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically to alter the responses of the motifs to stimuli. Synergism (or antagonism was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions.

  16. Phyloproteomic Analysis of 11780 Six-Residue-Long Motifs Occurrences

    Directory of Open Access Journals (Sweden)

    O. V. Galzitskaya

    2015-01-01

    Full Text Available How is it possible to find good traits for phylogenetic reconstructions? Here, we present a new phyloproteomic criterion that is an occurrence of simple motifs which can be imprints of evolution history. We studied the occurrences of 11780 six-residue-long motifs consisting of two randomly located amino acids in 97 eukaryotic and 25 bacterial proteomes. For all eukaryotic proteomes, with the exception of the Amoebozoa, Stramenopiles, and Diplomonadida kingdoms, the number of proteins containing the motifs from the first group (one of the two amino acids occurs once at the terminal position made about 20%; in the case of motifs from the second (one of two amino acids occurs one time within the pattern and third (the two amino acids occur randomly groups, 30% and 50%, respectively. For bacterial proteomes, this relationship was 10%, 27%, and 63%, respectively. The matrices of correlation coefficients between numbers of proteins where a motif from the set of 11780 motifs appears at least once in 9 kingdoms and 5 phyla of bacteria were calculated. Among the correlation coefficients for eukaryotic proteomes, the correlation between the animal and fungi kingdoms (0.62 is higher than between fungi and plants (0.54. Our study provides support that animals and fungi are sibling kingdoms. Comparison of the frequencies of six-residue-long motifs in different proteomes allows obtaining phylogenetic relationships based on similarities between these frequencies: the Diplomonadida kingdoms are more close to Bacteria than to Eukaryota; Stramenopiles and Amoebozoa are more close to each other than to other kingdoms of Eukaryota.

  17. Examining the Effects of Different Ring Configurations and Equatorial Fluorine Atom Positions on CO 2 Sorption in [Cu(bpy) 2 SiF 6

    KAUST Repository

    Forrest, Katherine A.

    2013-10-02

    Simulations of CO2 sorption were performed in a metal-organic material (MOM) that is part of a "SIFSIX" family of compounds that has remarkable carbon dioxide capture and separation properties. The MOM considered here has the formula [Cu(bpy)2SiF6] (bpy = 4,4′-bipyridine). This hydrophobic MOM is both water-stable and CO 2-specific with significant sorption capacity under ambient conditions. The crystal structure reveals bpy rings and equatorial fluorine atoms in multiple possible orientations; the static disorder has been modeled based on single-crystal X-ray diffraction data revealing several possible relatives of atoms in the crystal structure. With regards to the bpy rings, the structure can be interpreted as two pyridyl rings with coplanar configurations within a unit cell (configuration 1), a twisted bpy ring conformation in which orthogonal pyridyl rings have C4 symmetry about the Cu2+ ion (configuration 2), and a twisted bpy ring conformation in which the two orthogonal pyridyl rings are facing one another within a unit cell (configuration 3). Further, the equatorial fluorine atoms can be positioned such that all atoms are eclipsed with the square grid (position A), oriented at a 21.3 angle with respect to the square grid (position B), and oriented at a 45 angle with respect to the square grid (position C). It was observed that experimental data for CO2 sorption were only consistent with sorption into configurations 1 and 3 with any of the possible equatorial fluorine atom positions at ambient temperatures, although simulations using position A produced slightly higher uptakes in these bpy ring configurations. It is demonstrated that the orientation of the bpy rings in configurations 1 and 3 allows more space for the sorbate molecules and thus promotes favorable MOM-sorbate interactions, resulting in isotherms in line with the experimental results. The results from this study suggests that [Cu(bpy)2SiF 6] in either configuration 1 or 3 with CO2 present in

  18. (2S,4aR,6aR,7R,9S,10aS,10bR-7-Carboxy-2-(3-furyl-6a,10b-dimethyl-4,10-dioxoperhydrobenzo[f]isochromen-9-yl acetate

    Directory of Open Access Journals (Sweden)

    2009-03-01

    Full Text Available The asymmetric unit of the title compound, C22H26O8, contains two crystallographically independent molecules with closely comparable conformations (r.m.s. overlay = 0.54 Å for 30 non-H atoms. All six-membered rings display chair conformations, with a slight distortion for the lactone ring. The molecules are connected by O—H...O hydrogen bonds into chains along [010], with the independent molecules segregated into separate chains. The two molecules in the asymmetric unit face each other in a head-to-tail fashion, with the furan ring of one molecule turned towards the carboxylic acid terminal of the other molecule.

  19. 5-Isobutyl-4-phenylsulfonyl-1H-pyrazol-3(2H-one

    Directory of Open Access Journals (Sweden)

    M. Venkatesh

    2010-12-01

    Full Text Available The title compound, C13H16N2O3S, consists of two crystallographically independent molecules with similar geometries and exists in a keto form, the C=O bond lengths being 1.267 (2 and 1.254 (2 Å. In both molecules, the pyrazole rings are approximately planar, with maximum deviations of 0.017 (2 and 0.010 (2 Å, and the dihedral angles between the pyrazole and phenyl rings are 83.63 (11 and 70.07 (12°. In one molecule, an intramolecular C—H...O hydrogen bond with an S(6 ring motif is observed. In the crystal, intermolecular N—H...O and C—H...O hydrogen bonds link the molecules into two-dimensional networks parallel to the ab plane.

  20. (4bS,8aS-1-Isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octahydrophenanthren-2-yl benzoate

    Directory of Open Access Journals (Sweden)

    Radouane Oubabi

    2014-08-01

    Full Text Available The title compound, C27H34O2, was hemisynthesized through direct benzoylation of the naturally occurring meroterpene totarol. The central fused six-membered ring has a half-chair conformation, whereas the terminal six-membered ring displays a chair conformation. The dihedral angle between the fused benzene ring and the benzoyl benzene ring is 73.05 (14°. The S,S chirality of the molecule is consistent with the synthetic pathway, and confirmed by the refinement of the Flack parameter.

  1. Convergent evolution and mimicry of protein linear motifs in host-pathogen interactions.

    Science.gov (United States)

    Chemes, Lucía Beatriz; de Prat-Gay, Gonzalo; Sánchez, Ignacio Enrique

    2015-06-01

    Pathogen linear motif mimics are highly evolvable elements that facilitate rewiring of host protein interaction networks. Host linear motifs and pathogen mimics differ in sequence, leading to thermodynamic and structural differences in the resulting protein-protein interactions. Moreover, the functional output of a mimic depends on the motif and domain repertoire of the pathogen protein. Regulatory evolution mediated by linear motifs can be understood by measuring evolutionary rates, quantifying positive and negative selection and performing phylogenetic reconstructions of linear motif natural history. Convergent evolution of linear motif mimics is widespread among unrelated proteins from viral, prokaryotic and eukaryotic pathogens and can also take place within individual protein phylogenies. Statistics, biochemistry and laboratory models of infection link pathogen linear motifs to phenotypic traits such as tropism, virulence and oncogenicity. In vitro evolution experiments and analysis of natural sequences suggest that changes in linear motif composition underlie pathogen adaptation to a changing environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. The positron accumulator ring for the APS

    International Nuclear Information System (INIS)

    Crosbie, E.A.

    1989-01-01

    The Positron Accumulator Ring (PAR) is designed to accumulate and damp positrons from the 450-MeV linac during the 0.5-s cycle time of the injector synchrotron for the APS 7-GeV storage ring. During 0.4 s of each synchrotron cycle, up to 24 linac pulses are injected into the horizontal phase space of the PAR at a 60-Hz rate. Each injected pulse occupies about 1.3 of the circumference of the accumulator ring. After 0.1 s for longitudinal damping, the single accumulated bunch is transferred to one of the 353-MHz buckets of the injector synchrotron RF system. The bunch is accelerated to 7 GeV and transferred to the storage ring, while the PAR accumulates the next bunch of positrons. 2 refs., 3 figs., 2 tabs

  3. The positron accumulator ring for the APS

    International Nuclear Information System (INIS)

    Crosbie, E.A.

    1989-01-01

    The Positron Accumulator Ring (PAR) is designed to accumulate and damp positrons from the 450-MeV linac during the 0.5-s cycle time of the injector synchrotron for the APS 7-GeV storage ring. During 0.4 s of each synchrotron cycle, up to 24 linac pulses are injected into the horizontal phase space of the PAR at a 60-Hz rate. Each injected pulse occupies about 1/3 of the circumference of the accumulator ring. After 0.1 s for longitudinal damping, the single accumulated bunch is transferred to one of the 353-MHz buckets of the injector synchrotron RF system. The bunch is accelerated to 7 GeV and transferred to the storage ring, while the PAR accumulates the next bunch of positrons. 2 refs., 3 figs., 2 tabs

  4. A Repeating Sulfated Galactan Motif Resuscitates Dormant Micrococcus luteus Bacteria.

    Science.gov (United States)

    Böttcher, Thomas; Szamosvári, Dávid; Clardy, Jon

    2018-07-01

    Only a small fraction of bacteria can autonomously initiate growth on agar plates. Nongrowing bacteria typically enter a metabolically inactive dormant state and require specific chemical trigger factors or signals to exit this state and to resume growth. Micrococcus luteus has become a model organism for this important yet poorly understood phenomenon. Only a few resuscitation signals have been described to date, and all of them are produced endogenously by bacterial species. We report the discovery of a novel type of resuscitation signal that allows M. luteus to grow on agar but not agarose plates. Fractionation of the agar polysaccharide complex and sulfation of agarose allowed us to identify the signal as highly sulfated saccharides found in agar or carrageenans. Purification of hydrolyzed κ-carrageenan ultimately led to the identification of the signal as a small fragment of a large linear polysaccharide, i.e., an oligosaccharide of five or more sugars with a repeating disaccharide motif containing d-galactose-4-sulfate (G4S) 1,4-linked to 3,6-anhydro-α-d-galactose (DA), G4S-(DA-G4S) n ≥2 IMPORTANCE Most environmental bacteria cannot initiate growth on agar plates, but they can flourish on the same plates once growth is initiated. While there are a number of names for and manifestations of this phenomenon, the underlying cause appears to be the requirement for a molecular signal indicating safe growing conditions. Micrococcus luteus has become a model organism for studying this growth initiation process, often called resuscitation, because of its apparent connection with the persistent or dormant form of Mycobacterium tuberculosis , an important human pathogen. In this report, we identify a highly sulfated saccharide from agar or carrageenans that robustly resuscitates dormant M. luteus on agarose plates. We identified and characterized the signal as a small repeating disaccharide motif. Our results indicate that signals inherent in or absent from the

  5. 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

  6. Methods and statistics for combining motif match scores.

    Science.gov (United States)

    Bailey, T L; Gribskov, M

    1998-01-01

    Position-specific scoring matrices are useful for representing and searching for protein sequence motifs. A sequence family can often be described by a group of one or more motifs, and an effective search must combine the scores for matching a sequence to each of the motifs in the group. We describe three methods for combining match scores and estimating the statistical significance of the combined scores and evaluate the search quality (classification accuracy) and the accuracy of the estimate of statistical significance of each. The three methods are: 1) sum of scores, 2) sum of reduced variates, 3) product of score p-values. We show that method 3) is superior to the other two methods in both regards, and that combining motif scores indeed gives better search accuracy. The MAST sequence homology search algorithm utilizing the product of p-values scoring method is available for interactive use and downloading at URL http:/(/)www.sdsc.edu/MEME.

  7. Powder metallurgy ferrous synchronizer ring with brass-based friction layer; Tetsu-do niso shoketsu synchronize ring no kaihatsu

    Energy Technology Data Exchange (ETDEWEB)

    Okajima, H; Yoshikawa, K; Miyajima, K; Sugiyama, M [Toyota Motor Corp., Aichi (Japan); Nakamura, M; Ito, M [Japan Powder Metallurgy Co. Ltd., Tokyo (Japan)

    1997-10-01

    Synchronizer rings for manual transmissions are generally made of brass or molybdenum coated brass. Powder metallurgy (PM) synchronizer ring was developed for the purpose of high performance and cost reduction. This synchronizer ring consists of the high strength PM ferrous ring that needs neither special densification nor heat treatment, and it has the brass-based friction layer. New joining technique was required because of that shape and two different materials. Powder of copper-phosphorus alloy are admixed with the friction material. While sintering, that melt and migrate to the interface. Then the friction layer and the ferrous ring are joined tightly. 7 refs., 9 figs., 6 tabs.

  8. MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.

    Science.gov (United States)

    Ozaki, Haruka; Iwasaki, Wataru

    2016-08-01

    As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory networks and evaluating mutations in cis-regulatory elements. Although chromatin immunoprecipitation sequencing (ChIP-seq) now provides abundant data on the genomic sequences to which a given TF binds, existing motif discovery methods are unable to directly answer whether a given TF can bind to a specific DNA-binding motif. Here, we report a method for clarifying the DNA-binding motif ambiguity, MOCCS. Given ChIP-Seq data of any TF, MOCCS comprehensively analyzes and describes every k-mer to which that TF binds. Analysis of simulated datasets revealed that MOCCS is applicable to various ChIP-Seq datasets, requiring only a few minutes per dataset. Application to the ENCODE ChIP-Seq datasets proved that MOCCS directly evaluates whether a given TF binds to each DNA-binding motif, even if known position weight matrix models do not provide sufficient information on DNA-binding motif ambiguity. Furthermore, users are not required to provide numerous parameters or background genomic sequence models that are typically unavailable. MOCCS is implemented in Perl and R and is freely available via https://github.com/yuifu/moccs. By complementing existing motif-discovery software, MOCCS will contribute to the basic understanding of how the genome controls diverse cellular processes via DNA-protein interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. A Ring-‘Rain’ influence for Saturn’s Cloud Albedo and Temperatures? Evidence Pro or Con from Voyager, HST, and Cassini

    Science.gov (United States)

    West, Robert A.; Li, Liming

    2015-11-01

    J. E. P. Connerney [Geophys. Res. Lett, 13, 773-776, 1986] pointed out that ‘latitudinal variations in images of Saturn’s disk, upper atmospheric temperatures, and ionospheric electron densities are found in magnetic conjugacy with features in Saturn’s ring plane’, and proposed ‘that these latitudinal variations are the result of a variable influx of water, transported along magnetic field lines from sources in Saturn’s ring plane’. Observations of H3+ support a ring-ionosphere connection [O'Donoghue et al., Nature 496, 7444, 2013]. What about cloud albedo and temperature? Connerney attributed a hemispheric asymmetry in haze and temperature to an asymmetry in water flux and predicted that ‘the presently-observed north-south asymmetry (upper tropospheric temperatures, aerosols) will persist throughout the Saturn year’. We can now test these ideas with data from the Cassini mission, from the Hubble Space Telescope, and from ground-based observations. Analyses of ground-based images and especially Hubble data established that the hemispheric asymmetry of the aerosol population does change, and seasonal effects are dominant, although non-seasonal variations are also observed [Karkoschka and Tomasko, Icarus 179, 195-221, 2005]. Upper tropospheric temperatures also vary as expected in response to seasonal forcing [Fletcher et al., Icarus 208, 337-352, 2009]. Connerney also identified dark bands in Voyager Green-filter images on magnetic conjugacy with the E ring and edges of the A and B rings. In Cassini Green-filter images there is some correspondence between dark bands and ring features in magnetic conjugacy, but collectively the correlation is not strong. Cassini 727-nm methane band images do not suggest depletion of aerosols in the upper troposphere at ring edge magnetic conjugacy latitudes as proposed by Connerney. We conclude that ring rain does not have a significant influence on upper tropospheric aerosols and temperatures on Saturn. Part of

  10. Discovery and validation of information theory-based transcription factor and cofactor binding site motifs.

    Science.gov (United States)

    Lu, Ruipeng; Mucaki, Eliseos J; Rogan, Peter K

    2017-03-17

    Data from ChIP-seq experiments can derive the genome-wide binding specificities of transcription factors (TFs) and other regulatory proteins. We analyzed 765 ENCODE ChIP-seq peak datasets of 207 human TFs with a novel motif discovery pipeline based on recursive, thresholded entropy minimization. This approach, while obviating the need to compensate for skewed nucleotide composition, distinguishes true binding motifs from noise, quantifies the strengths of individual binding sites based on computed affinity and detects adjacent cofactor binding sites that coordinate with the targets of primary, immunoprecipitated TFs. We obtained contiguous and bipartite information theory-based position weight matrices (iPWMs) for 93 sequence-specific TFs, discovered 23 cofactor motifs for 127 TFs and revealed six high-confidence novel motifs. The reliability and accuracy of these iPWMs were determined via four independent validation methods, including the detection of experimentally proven binding sites, explanation of effects of characterized SNPs, comparison with previously published motifs and statistical analyses. We also predict previously unreported TF coregulatory interactions (e.g. TF complexes). These iPWMs constitute a powerful tool for predicting the effects of sequence variants in known binding sites, performing mutation analysis on regulatory SNPs and predicting previously unrecognized binding sites and target genes. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Initial clinical experience with a novel biodegradable ring in patients with functional tricuspid insufficiency: Kalangos Biodegradable Tricuspid Ring.

    Science.gov (United States)

    Burma, O; Ustunsoy, H; Davutoglu, V; Celkan, M A; Kazaz, H; Pektok, E

    2007-08-01

    Tricuspid annuloplasty procedures have been widely performed in clinics for many years. The Kalangos Biodegradable Tricuspid Ring (Kalangos Biodegradable Tricuspid Ring, Bioring SA, Lonay, Switzerland) is a novel prosthesis for the treatment of tricuspid insufficiency. The aim of this study was to evaluate the clinical and echocardiographic results of this novel prosthesis for functional tricuspid insufficiency. Between October 2005 and May 2006, 15 patients with the diagnosis of moderate or severe functional tricuspid insufficiency were treated by implantation of a Kalangos Biodegradable Tricuspid Ring. All patients were evaluated clinically and by echocardiography preoperatively, and control tests were performed at the end of the 1st and 6th month following surgery. Moderate and severe insufficiency was documented in 11 and 4 patients, respectively, in the preoperative tests. 1 and 6 months after surgery, 4 patients had trace and 1 patient had mild tricuspid insufficiency, while 10 patients had none. At the 1st and 6th month follow-up, systolic pulmonary arterial pressure, right atrial dimension and right ventricular diastolic diameter were found to be significantly lower than the preoperative values ( P tricuspid valve area had decreased significantly at the end of the 1st month; however, no significant difference was found between the 1st and 6th month tests ( P > 0.05). Three-quarters of the annuloplasty ring had degraded at 6 months. No complications related to the prosthesis or the procedure occurred within this period. Kalangos Biodegradable Ring is a promising prosthesis in patients with functional tricuspid insufficiency, with encouraging initial results.

  12. Investigation of ‘Head-to-Tail’-Connected Oligoaryl N,O-Ligands as Recognition Motifs for Cancer-Relevant G-Quadruplexes

    Directory of Open Access Journals (Sweden)

    Natalia Rizeq

    2017-12-01

    Full Text Available Oligomeric compounds, constituted of consecutive N,O-heteroaromatic rings, introduce useful and tunable properties as alternative ligands for biomolecular recognition. In this study, we have explored a synthetic scheme relying on Van Leusen oxazole formation, in conjunction with C–H activation of the formed oxazoles and their subsequent C–C cross-coupling to 2-bromopyridines in order to assemble a library of variable-length, ‘head-to-tail’-connected, pyridyl-oxazole ligands. Through investigation of the interaction of the three longer ligands (5-mer, 6-mer, 7-mer with cancer-relevant G-quadruplex structures (human telomeric/22AG and c-Myc oncogene promoter/Myc2345-Pu22, the asymmetric pyridyl-oxazole motif has been demonstrated to be a prominent recognition element for G-quadruplexes. Fluorescence titrations reveal excellent binding affinities of the 7-mer and 6-mer for a Na+-induced antiparallel 22AG G-quadruplex (KD = 0.6 × 10−7 M−1 and 0.8 × 10−7 M−1, respectively, and satisfactory (albeit lower affinities for the 22AG/K+ and Myc2345-Pu22/K+ G-quadruplexes. All ligands tested exhibit substantial selectivity for G-quadruplex versus duplex (ds26 DNA, as evidenced by competitive Förster resonance energy transfer (FRET melting assays. Additionally, the 7-mer and 6-mer are capable of promoting a sharp morphology transition of 22AG/K+ G-quadruplex.

  13. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  14. Leisure/Crime, Immaterial Labor, and the Performance of the Teenage Girl in Harmony Korine’s Spring Breakers and Sofia Coppola’s The Bling Ring

    NARCIS (Netherlands)

    Wilkinson, M.

    2017-01-01

    Harmony Korine’s Spring Breakers (2012) and Sofia Coppola’s The Bling Ring (2013) introduced audiences to girls exploring criminal behavior both for and as leisure. The films introduce an idea of leisure/crime: criminal acts that appear to develop as natural, fruitful extensions of leisure

  15. Stability of driven systems with growing gaps, quantum rings, and Wannier ladders

    Czech Academy of Sciences Publication Activity Database

    Asch, J.; Duclos, P.; Exner, Pavel

    1998-01-01

    Roč. 92, 5/6 (1998), s. 1053-1070 ISSN 0022-4715 R&D Projects: GA AV ČR(CZ) IAA148409 Keywords : quantum stability * energy expectations * driven rings Subject RIV: BE - Theoretical Physics Impact factor: 1.469, year: 1998

  16. Low-dimensional morphospace of topological motifs in human fMRI brain networks

    Directory of Open Access Journals (Sweden)

    Sarah E. Morgan

    2018-06-01

    Full Text Available We present a low-dimensional morphospace of fMRI brain networks, where axes are defined in a data-driven manner based on the network motifs. The morphospace allows us to identify the key variations in healthy fMRI networks in terms of their underlying motifs, and we observe that two principal components (PCs can account for 97% of the motif variability. The first PC of the motif distribution is correlated with efficiency and inversely correlated with transitivity. Hence this axis approximately conforms to the well-known economical small-world trade-off between integration and segregation in brain networks. Finally, we show that the economical clustering generative model proposed by Vértes et al. (2012 can approximately reproduce the motif morphospace of the real fMRI brain networks, in contrast to other generative models. Overall, the motif morphospace provides a powerful way to visualize the relationships between network properties and to investigate generative or constraining factors in the formation of complex human brain functional networks. Motifs have been described as the building blocks of complex networks. Meanwhile, a morphospace allows networks to be placed in a common space and can reveal the relationships between different network properties and elucidate the driving forces behind network topology. We combine the concepts of motifs and morphospaces to create the first motif morphospace of fMRI brain networks. Crucially, the morphospace axes are defined by the motifs, in a data-driven manner. We observe strong correlations between the networks’ positions in morphospace and their global topological properties, suggesting that motif morphospaces are a powerful way to capture the topology of networks in a low-dimensional space and to compare generative models of brain networks. Motif morphospaces could also be used to study other complex networks’ topologies.

  17. 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...

  18. FORMATION OF CENTAURS’ RINGS THROUGH THEIR PARTIAL TIDAL DISRUPTION DURING PLANETARY ENCOUNTERS

    Energy Technology Data Exchange (ETDEWEB)

    Hyodo, Ryuki; Charnoz, Sébastien [Institut de Physique du Globe, F-75005 Paris, France (France); Genda, Hidenori [Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550 (Japan); Ohtsuki, Keiji [Department of Planetology, Kobe University, Kobe 657-8501 (Japan)

    2016-09-01

    Centaurs are minor planets orbiting between Jupiter and Neptune that have or had crossing orbits with one or more giant planets. Recent observations and reinterpretation of previous observations have revealed the existence of ring systems around 10199 Chariklo and 2060 Chiron. However, the origin of the ring systems around such a minor planet is still an open question. Here, we propose that the tidal disruption of a differentiated object that experiences a close encounter with a giant planet could naturally form diverse ring–satellite systems around the Centaurs. During the close encounter, the icy mantle of the passing object is preferentially ripped off by the planet's tidal force and the debris is distributed mostly within the Roche limit of the largest remnant body. Assuming the existence of a 20−50 wt% silicate core below the icy mantle, a disk of particles is formed when the objects pass within 0.4–0.8 of the planet's Roche limit with the relative velocity at infinity 3−6 km s{sup −1} and 8 hr initial spin period of the body. The resultant ring mass is 0.1%–10% of the central object's mass. Such particle disks are expected to spread radially, and materials spreading beyond the Roche limit would accrete into satellites. Our numerical results suggest that ring formation would be a natural outcome of such extreme close encounters, and Centaurs can naturally have such ring systems because they cross the orbits of the giant planets.

  19. 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.

  20. Memetic algorithms for de novo motif-finding in biomedical sequences.

    Science.gov (United States)

    Bi, Chengpeng

    2012-09-01

    The objectives of this study are to design and implement a new memetic algorithm for de novo motif discovery, which is then applied to detect important signals hidden in various biomedical molecular sequences. In this paper, memetic algorithms are developed and tested in de novo motif-finding problems. Several strategies in the algorithm design are employed that are to not only efficiently explore the multiple sequence local alignment space, but also effectively uncover the molecular signals. As a result, there are a number of key features in the implementation of the memetic motif-finding algorithm (MaMotif), including a chromosome replacement operator, a chromosome alteration-aware local search operator, a truncated local search strategy, and a stochastic operation of local search imposed on individual learning. To test the new algorithm, we compare MaMotif with a few of other similar algorithms using simulated and experimental data including genomic DNA, primary microRNA sequences (let-7 family), and transmembrane protein sequences. The new memetic motif-finding algorithm is successfully implemented in C++, and exhaustively tested with various simulated and real biological sequences. In the simulation, it shows that MaMotif is the most time-efficient algorithm compared with others, that is, it runs 2 times faster than the expectation maximization (EM) method and 16 times faster than the genetic algorithm-based EM hybrid. In both simulated and experimental testing, results show that the new algorithm is compared favorably or superior to other algorithms. Notably, MaMotif is able to successfully discover the transcription factors' binding sites in the chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) data, correctly uncover the RNA splicing signals in gene expression, and precisely find the highly conserved helix motif in the transmembrane protein sequences, as well as rightly detect the palindromic segments in the primary micro

  1. 3,3,4,4-Tetrafluoro-1-[2-(3,3,4,4-tetrafluoropyrrolidin-1-ylphenyl]pyrrolidine

    Directory of Open Access Journals (Sweden)

    Jin Wang

    2011-09-01

    Full Text Available The asymmetric unit of the title compound, C14H12F8N2, contains one tetrafluoropyrrolidine system and one half-molecule of benzene; the latter, together with a second heterocyclic unit, are completed by symmetry, with a twofold crystallographic axis crossing through both the middle of the bond between the C atoms bearing the heterocyclic rings and the opposite C—C bonds of the whole benzene molecule. The pyrrolidine ring shows an envelope conformation with the apex at the N atom. The dihedral angle between the least-squares plane of this ring and the benzene ring is 36.9 (5°. There are intramolecular C—H...N interactions generating S(6 ring motifs. In the crystal structure, the molecules are linked by C—H...F interactions, forming chains parallel to [010].

  2. Discovering Motifs in Biological Sequences Using the Micron Automata Processor.

    Science.gov (United States)

    Roy, Indranil; Aluru, Srinivas

    2016-01-01

    Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the (l, d) motif search problem of identifying one or more motifs of length l present in at least q of the n given sequences, with each occurrence differing from the motif in at most d substitutions. The problem is known to be NP-complete, and the largest solved instance reported to date is (26,11). We propose a novel algorithm for the (l,d) motif search problem using streaming execution over a large set of non-deterministic finite automata (NFA). This solution is designed to take advantage of the micron automata processor, a new technology close to deployment that can simultaneously execute multiple NFA in parallel. We demonstrate the capability for solving much larger instances of the (l, d) motif search problem using the resources available within a single automata processor board, by estimating run-times for problem instances (39,18) and (40,17). The paper serves as a useful guide to solving problems using this new accelerator technology.

  3. PISMA: A Visual Representation of Motif Distribution in DNA Sequences

    Directory of Open Access Journals (Sweden)

    Rogelio Alcántara-Silva

    2017-03-01

    Full Text Available Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. Results: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. Availability and Implementation: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf .

  4. Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network

    Directory of Open Access Journals (Sweden)

    Barabási Albert-László

    2004-01-01

    Full Text Available Abstract Background Transcriptional regulation of cellular functions is carried out through a complex network of interactions among transcription factors and the promoter regions of genes and operons regulated by them.To better understand the system-level function of such networks simplification of their architecture was previously achieved by identifying the motifs present in the network, which are small, overrepresented, topologically distinct regulatory interaction patterns (subgraphs. However, the interaction of such motifs with each other, and their form of integration into the full network has not been previously examined. Results By studying the transcriptional regulatory network of the bacterium, Escherichia coli, we demonstrate that the two previously identified motif types in the network (i.e., feed-forward loops and bi-fan motifs do not exist in isolation, but rather aggregate into homologous motif clusters that largely overlap with known biological functions. Moreover, these clusters further coalesce into a supercluster, thus establishing distinct topological hierarchies that show global statistical properties similar to the whole network. Targeted removal of motif links disintegrates the network into small, isolated clusters, while random disruptions of equal number of links do not cause such an effect. Conclusion Individual motifs aggregate into homologous motif clusters and a supercluster forming the backbone of the E. coli transcriptional regulatory network and play a central role in defining its global topological organization.

  5. Novel and deviant Walker A ATP-binding motifs in bacteriophage large terminase-DNA packaging proteins

    International Nuclear Information System (INIS)

    Mitchell, Michael S.; Rao, Venigalla B.

    2004-01-01

    Bacteriophage terminases constitute a very interesting class of viral-coded multifunctional ATPase 'motors' that apparently drive directional translocation of DNA into an empty viral capsid. A common Walker A motif and other conserved signatures of a critical ATPase catalytic center are identified in the N-terminal half of numerous large terminase proteins. However, several terminases, including the well-characterized λ and SPP1 terminases, seem to lack the classic Walker A in the N-terminus. Using sequence alignment approaches, we discovered the presence of deviant Walker A motifs in these and many other phage terminases. One deviation, the presence of a lysine at the beginning of P-loop, may represent a 3D equivalent of the universally conserved lysine in the Walker A GKT/S signature. This and other novel putative Walker A motifs that first came to light through this study help define the ATPase centers of phage and viral terminases as well as elicit important insights into the molecular functioning of this fundamental motif in biological systems

  6. Cave acoustics in prehistory: Exploring the association of Palaeolithic visual motifs and acoustic response.

    Science.gov (United States)

    Fazenda, Bruno; Scarre, Chris; Till, Rupert; Pasalodos, Raquel Jiménez; Guerra, Manuel Rojo; Tejedor, Cristina; Peredo, Roberto Ontañón; Watson, Aaron; Wyatt, Simon; Benito, Carlos García; Drinkall, Helen; Foulds, Frederick

    2017-09-01

    During the 1980 s, acoustic studies of Upper Palaeolithic imagery in French caves-using the technology then available-suggested a relationship between acoustic response and the location of visual motifs. This paper presents an investigation, using modern acoustic measurement techniques, into such relationships within the caves of La Garma, Las Chimeneas, La Pasiega, El Castillo, and Tito Bustillo in Northern Spain. It addresses methodological issues concerning acoustic measurement at enclosed archaeological sites and outlines a general framework for extraction of acoustic features that may be used to support archaeological hypotheses. The analysis explores possible associations between the position of visual motifs (which may be up to 40 000 yrs old) and localized acoustic responses. Results suggest that motifs, in general, and lines and dots, in particular, are statistically more likely to be found in places where reverberation is moderate and where the low frequency acoustic response has evidence of resonant behavior. The work presented suggests that an association of the location of Palaeolithic motifs with acoustic features is a statistically weak but tenable hypothesis, and that an appreciation of sound could have influenced behavior among Palaeolithic societies of this region.

  7. Tert-butyl 3-oxo-2,3,4,5,6,7-hexahydro-1H-pyrazolo[4,3-c]pyridine-5-carboxylate

    Directory of Open Access Journals (Sweden)

    Tara Shahani

    2010-01-01

    Full Text Available In the title compound, C11H17N3O3, the pyrazole ring is approximately planar, with a maximum deviation of 0.005 (2 Å, and forms a dihedral angle of 5.69 (13° with the plane through the six atoms of the piperidine ring. In the crystal, pairs of intermolecular N—H...O hydrogen bonds form dimers with neighbouring molecules, generating R22(8 ring motifs. These dimers are further linked into two-dimensional arrays parallel to the bc plane by intermolecular N—H...O and C—H...O hydrogen bonds.

  8. (1R,4R,6S,7R-5,5-Dibromo-1,4,8,8-tetramethyltricyclo[5.4.1.04,6]dodecan-12-one

    Directory of Open Access Journals (Sweden)

    Mohamed Zaki

    2014-05-01

    Full Text Available The title compound, C16H24Br2O, was synthesized from the reaction of β-himachalene (3,5,5,9-tetramethyl-2,4a,5,6,7,8-hexahydro-1H-benzocycloheptene, which was isolated from Atlas cedar (Cedrus atlantica. The asymmetric unit contains two independent molecules with similar conformations. Each molecule is built up from two fused seven-membered rings and an additional three-membered ring. In both molecules, one of the seven-membered rings has a chair conformation, whereas the other displays a screw-boat conformation.

  9. 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.

  10. Study on online community user motif using web usage mining

    Science.gov (United States)

    Alphy, Meera; Sharma, Ajay

    2016-04-01

    The Web usage mining is the application of data mining, which is used to extract useful information from the online community. The World Wide Web contains at least 4.73 billion pages according to Indexed Web and it contains at least 228.52 million pages according Dutch Indexed web on 6th august 2015, Thursday. It’s difficult to get needed data from these billions of web pages in World Wide Web. Here is the importance of web usage mining. Personalizing the search engine helps the web user to identify the most used data in an easy way. It reduces the time consumption; automatic site search and automatic restore the useful sites. This study represents the old techniques to latest techniques used in pattern discovery and analysis in web usage mining from 1996 to 2015. Analyzing user motif helps in the improvement of business, e-commerce, personalisation and improvement of websites.

  11. Dynamic motifs in socio-economic networks

    Science.gov (United States)

    Zhang, Xin; Shao, Shuai; Stanley, H. Eugene; Havlin, Shlomo

    2014-12-01

    Socio-economic networks are of central importance in economic life. We develop a method of identifying and studying motifs in socio-economic networks by focusing on “dynamic motifs,” i.e., evolutionary connection patterns that, because of “node acquaintances” in the network, occur much more frequently than random patterns. We examine two evolving bi-partite networks: i) the world-wide commercial ship chartering market and ii) the ship build-to-order market. We find similar dynamic motifs in both bipartite networks, even though they describe different economic activities. We also find that “influence” and “persistence” are strong factors in the interaction behavior of organizations. When two companies are doing business with the same customer, it is highly probable that another customer who currently only has business relationship with one of these two companies, will become customer of the second in the future. This is the effect of influence. Persistence means that companies with close business ties to customers tend to maintain their relationships over a long period of time.

  12. 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.

  13. Assessing local structure motifs using order parameters for motif recognition, interstitial identification, and diffusion path characterization

    Science.gov (United States)

    Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav; Haranczyk, Maciej

    2017-11-01

    Structure-property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal closed packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

  14. 3-Chloro-N-(4-sulfamoylphenylpropanamide

    Directory of Open Access Journals (Sweden)

    Mehmet Akkurt

    2010-07-01

    Full Text Available In the title compound, C9H11ClN2O3S, the dihedral angle between the benzene ring and the amido –NHCO– plane is 15.0 (2°. An intramolecular C—H...O hydrogen bond generates an S(6 ring motif. In the crystal structure, the amino NH2 group is involved in intermolecular N—H...O hydrogen bonds, which connect the molecules into a double layer structure expanding parallel to the bc plane. The layers are further linked by an amido N—H...O hydrogen bond. Between the layers, a weak π–π interaction with a centroid–centroid distance of 3.7447 (12 Å is also observed.

  15. Two genes in Balbiani ring 2 with metabolically different 75S transcripts

    OpenAIRE

    Galler, R.; Saiga, H.; Widmer, R. M.; Lezzi, M.; Edström, J.-E.

    1985-01-01

    Balbiani ring 2 (BR2) in salivary glands of Chironomus pallidivittatus and C. tentans (two sibling species of the subgenus Camptochironomus) is a favoured model system for studies of gene organization and transcript formation. Here we show that BR2 is more complex than hitherto believed, containing two 75S RNA-producing genes, BR2a and BR2b, present in different 35–40 kb blocks of DNA. The transcripts hybridizing to two different repeat units originating in BR2 differ in size. Further support...

  16. The PDZ Ligand Domain of the Human Papillomavirus Type 16 E6 Protein Is Required for E6's Induction of Epithelial Hyperplasia In Vivo

    Science.gov (United States)

    Nguyen, Marie L.; Nguyen, Minh M.; Lee, Denis; Griep, Anne E.; Lambert, Paul F.

    2003-01-01

    Human papillomaviruses (HPVs) are the causative agent of warts. Infections with high-risk HPVs are associated with anogenital and head and neck cancers. One of the viral genes responsible for HPV's oncogenic activity is E6. Mice expressing the HPV-16 E6 protein in their epidermis (K14E6WT) develop epithelial hyperplasia and squamous carcinomas. Numerous cellular proteins interact with E6, some of which can be grouped based on common amino acid motifs in their E6-binding domains. One such group, the PDZ partners, including hDLG, hSCRIBBLE, MUPP1, and MAGI, bind to the carboxy-terminal four amino acids of E6 through their PDZ domains. E6's interaction with the PDZ partners leads to their degradation. Additionally, E6's binding to PDZ proteins has been correlated with its ability to transform baby rat kidney cells in tissue culture and to confer tumorigenicity onto cells in xenograft experiments. To address whether the ability of E6 to bind PDZ domain partners is necessary for E6 to confer epithelial hyperproliferation in vivo, we generated transgenic mice that express in stratified squamous epithelia a mutant of E6 lacking the last six amino acids at its carboxyl terminus, E6Δ146-151, from the human keratin 14 (K14) promoter. The K14E6Δ146-151 mice exhibit a radiation response similar to that of the K14E6WT mice, demonstrating that this protein, as predicted, retains an ability to inactivate p53. However, the K14E6Δ146-151 mice fail to display epithelial hyperplasia. These results indicate that an interaction of E6 with PDZ partners is necessary for its induction of epithelial hyperplasia. PMID:12768014

  17. Regulation of amyloid precursor protein processing by its KFERQ motif.

    Science.gov (United States)

    Park, Ji-Seon; Kim, Dong-Hou; Yoon, Seung-Yong

    2016-06-01

    Understanding of trafficking, processing, and degradation mechanisms of amyloid precursor protein (APP) is important because APP can be processed to produce β-amyloid (Aβ), a key pathogenic molecule in Alzheimer's disease (AD). Here, we found that APP contains KFERQ motif at its C-terminus, a consensus sequence for chaperone-mediated autophagy (CMA) or microautophagy which are another types of autophagy for degradation of pathogenic molecules in neurodegenerative diseases. Deletion of KFERQ in APP increased C-terminal fragments (CTFs) and secreted N-terminal fragments of APP and kept it away from lysosomes. KFERQ deletion did not abolish the interaction of APP or its cleaved products with heat shock cognate protein 70 (Hsc70), a protein necessary for CMA or microautophagy. These findings suggest that KFERQ motif is important for normal processing and degradation of APP to preclude the accumulation of APP-CTFs although it may not be important for CMA or microautophagy. [BMB Reports 2016; 49(6): 337-342].

  18. Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

    Science.gov (United States)

    Kinjo, Akira R.; Nakamura, Haruki

    2012-01-01

    Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

  19. Crystal structures of (E-4-[1-(2-carbamothioylhydrazinylideneethyl]phenyl acetate and (E-4-[1-(2-carbamothioylhydrazinylideneethyl]phenyl benzoate

    Directory of Open Access Journals (Sweden)

    Vijayan Viswanathan

    2017-01-01

    Full Text Available In the title compounds, C11H13N3O2S, (I, and C16H15N3O2S, (II, the thiosemicarbazone group adopts an extended conformation. The acetate ester (I crystallizes with two independent molecules in the asymmetric unit. In the benzoate ester (II, the planes of the two aryl rings are inclined to one another by 46.70 (7°. In both compounds, there is a short intramolecular N—H...N contact present, forming an S(5 ring motif. In the crystals of both compounds, molecules are linked via pairs of N—H...S hydrogen bonds, forming dimers with R22(8 ring motifs. The dimers are linked by N—H...S and N—H...O hydrogen bonds, forming slabs parallel to (01-1. In (I, there are N—H...π and C—H...π interactions present within the slabs, while in (II, there are only N—H...π interactions present.

  20. Probing structural changes of self assembled i-motif DNA

    KAUST Repository

    Lee, Iljoon; Patil, Sachin; Fhayli, Karim; Alsaiari, Shahad K.; Khashab, Niveen M.

    2015-01-01

    We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change. This journal is

  1. Report of the eRHIC Ring-Ring Working Group

    Energy Technology Data Exchange (ETDEWEB)

    Aschenauer, E. C. [Brookhaven National Lab. (BNL), Upton, NY (United States); Berg, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Blaskiewicz, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Brennan, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Fedotov, A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Fischer, W. [Brookhaven National Lab. (BNL), Upton, NY (United States); Litvinenko, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Montag, C. [Brookhaven National Lab. (BNL), Upton, NY (United States); Palmer, R. [Brookhaven National Lab. (BNL), Upton, NY (United States); Parker, B. [Brookhaven National Lab. (BNL), Upton, NY (United States); Peggs, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Ptitsyn, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Ranjbar, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Tepikian, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Trbojevic, D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Willeke, F. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2015-10-13

    This report evaluates the ring-ring option for eRHIC as a lower risk alternative to the linac-ring option. The reduced risk goes along with a reduced initial luminosity performance. However, a luminosity upgrade path is kept open. This upgrade path consists of two branches, with the ultimate upgrade being either a ring-ring or a linac-ring scheme. The linac-ring upgrade could be almost identical to the proposed linac-ring scheme, which is based on an ERL in the RHIC tunnel. This linac-ring version has been studied in great detail over the past ten years, and its significant risks are known. On the other hand, no detailed work on an ultimate performance ring-ring scenario has been performed yet, other than the development of a consistent parameter set. Pursuing the ring-ring upgrade path introduces high risks and requires significant design work that is beyond the scope of this report.

  2. Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

    Directory of Open Access Journals (Sweden)

    Down Thomas A

    2010-09-01

    Full Text Available Abstract Background DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predicted TFBS" but the large majority of these are proven by chromatin immunoprecipitation and high throughput sequencing (ChIP-seq not to be biological transcription factor binding sites ("empirical TFBS". We hypothesize that DNA methylation at conserved consensus motifs prevents promiscuous or disorderly transcription factor binding. Results Using genome-wide methylation maps of the human heart and sperm, we found that all conserved consensus motifs as well as the subset of those that reside outside CpG islands have an aggregate profile of hyper-methylation. In contrast, empirical TFBS with conserved consensus motifs have a profile of hypo-methylation. 40% of empirical TFBS with conserved consensus motifs resided in CpG islands whereas only 7% of all conserved consensus motifs were in CpG islands. Finally we further identified a minority subset of TF whose profiles are either hypo-methylated or neutral at their respective conserved consensus motifs implicating that these TF may be responsible for establishing or maintaining an un-methylated DNA state, or whose binding is not regulated by DNA methylation. Conclusions Our analysis supports the hypothesis that at least for a subset of TF, empirical binding to conserved consensus motifs genome-wide may be controlled by DNA methylation.

  3. Calcium Sensing Receptor Mutations Implicated in Pancreatitis and Idiopathic Epilepsy Syndrome Disrupt an Arginine-rich Retention Motif

    Science.gov (United States)

    Stepanchick, Ann; McKenna, Jennifer; McGovern, Olivia; Huang, Ying; Breitwieser, Gerda E.

    2010-01-01

    Calcium sensing receptor (CaSR) mutations implicated in familial hypocalciuric hypercalcemia, pancreatitis and idiopathic epilepsy syndrome map to an extended arginine-rich region in the proximal carboxyl terminus. Arginine-rich motifs mediate endoplasmic reticulum retention and/or retrieval of multisubunit proteins so we asked whether these mutations, R886P, R896H or R898Q, altered CaSR targeting to the plasma membrane. Targeting was enhanced by all three mutations, and Ca2+-stimulated ERK1/2 phosphorylation was increased for R896H and R898Q. To define the role of the extended arginine-rich region in CaSR trafficking, we independently determined the contributions of R890/R891 and/or R896/K897/R898 motifs by mutation to alanine. Disruption of the motif(s) significantly increased surface expression and function relative to wt CaSR. The arginine-rich region is flanked by phosphorylation sites at S892 (protein kinase C) and S899 (protein kinase A). The phosphorylation state of S899 regulated recognition of the arginine-rich region; S899D showed increased surface localization. CaSR assembles in the endoplasmic reticulum as a covalent disulfide-linked dimer and we determined whether retention requires the presence of arginine-rich regions in both subunits. A single arginine-rich region within the dimer was sufficient to confer intracellular retention comparable to wt CaSR. We have identified an extended arginine-rich region in the proximal carboxyl terminus of CaSR (residues R890 - R898) which fosters intracellular retention of CaSR and is regulated by phosphorylation. Mutation(s) identified in chronic pancreatitis and idiopathic epilepsy syndrome therefore increase plasma membrane targeting of CaSR, likely contributing to the altered Ca2+ signaling characteristic of these diseases. PMID:20798521

  4. Use of a marshmallow bolus for evaluating lower esophageal mucosal rings.

    Science.gov (United States)

    Ott, D J; Kelley, T F; Chen, M Y; Gelfand, D W; Wu, W C

    1991-07-01

    Sixty-three patients (35 women, 28 men; mean age 55 yr) with lower esophageal mucosal ring shown radiographically were examined with a semi-solid bolus consisting of a portion of a standard marshmallow. The most common symptom was dysphagia, present in 46 (73%) patients. Impaction of the marshmallow bolus by the ring occurred in 40 (63%) of the 63 patients, and produced symptoms in 27 (68%) of these 40 patients. Nine (14%) rings were detected radiographically only with a solid bolus; eight of these patients had dysphagia and seven rings were 20 mm or less in caliber. Impaction related to ring caliber, and was found in all 17 (100%) rings that were 13 mm or less in diameter, in 17/24 (71%) 14- to 19-mm rings, and in 6/22 (27%) rings 20 mm or more in caliber. Endoscopy in 23 patients detected 16 (70%) rings, and also depended on ring caliber: less than or equal to 13 mm, 6/6 (100%); 14-19 mm, 5/9 (56%); greater than or equal to 20 mm, 5/8 (63%). Marshmallow impaction occurred in 17 (74%) of 23 patients who had endoscopy; three of the 23 patients had normal endoscopy. In conclusion, radiographic examination supplemented by the use of a marshmallow bolus best detects lower esophageal mucosal ring.

  5. Design of S-Band Phased Array Antenna with High Isolation Using Broadside Coupled Split Ring Resonator

    Directory of Open Access Journals (Sweden)

    Sungyoun Hwang

    2018-04-01

    Full Text Available In this paper, a method of designing a Vivaldi type phased array antenna (PAA which operates at S-band (2.8–3.3 GHz is presented. The presented antenna uses broadside coupled split ring resonators (BC-SRRs for high isolation, wide field of view, and good active S-parameter characteristics. As an example, we design a 1 × 8 array antenna with various BC-SRR structures using theory and EM simulations. The antenna is fabricated and measured to verify the design. With the BC-SRR implemented between the two radiating elements, the isolation is shown to be enhanced by 6 dB, up to 23 dB. The scan angle is shown to be within ±53° based on a −10 dB active reflection coefficient. The operation of the scan angle is possible within ±60° with a little larger reflection coefficient (−7 dB to −8 dB. The proposed design with BC-SRRs is expected to be useful for PAA applications.

  6. BlockLogo: Visualization of peptide and sequence motif conservation

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian

    2013-01-01

    BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, se...

  7. Numerical Simulations of Saturn's B Ring: Granular Friction as a Mediator between Self-gravity Wakes and Viscous Overstability

    Energy Technology Data Exchange (ETDEWEB)

    Ballouz, Ronald-Louis; Richardson, Derek C. [Department of Astronomy, University of Maryland, College Park, MD 20742-2421 (United States); Morishima, Ryuji [University of California, Los Angeles, Institute of Geophysics and Planetary Physics, Los Angeles, CA (United States)

    2017-04-01

    We study the B ring’s complex optical depth structure. The source of this structure may be the complex dynamics of the Keplerian shear and the self-gravity of the ring particles. The outcome of these dynamic effects depends sensitively on the collisional and physical properties of the particles. Two mechanisms can emerge that dominate the macroscopic physical structure of the ring: self-gravity wakes and viscous overstability. Here we study the interplay between these two mechanisms by using our recently developed particle collision method that allows us to better model the inter-particle contact physics. We find that for a constant ring surface density and particle internal density, particles with rough surfaces tend to produce axisymmetric ring features associated with the viscous overstability, while particles with smoother surfaces produce self-gravity wakes.

  8. THE MOTIF OF THE SECOND COMING IN RUSSIAN FANTASTIC FICTION

    Directory of Open Access Journals (Sweden)

    Tatyana I. Khoruzhenko

    2017-06-01

    Full Text Available The motif of the Second Coming of Christ takes a special place in Russian fantastic fiction at the turn of the millennium. In the recent decades allusions to the Gospel topic appears in increasing frequency in the genre of fantasy. The aim of the given article was to analyze the peculiarities of the depiction of the subject of Advent in Russian fantastic fiction. As the basis for the research the novels of Y. Voznesenskaya, N. Perumov, V. Khlumov, S. Lukyanenko and T. Ustimenko are of particular interest. The Advent motif appears in the story line of each of the novels in question. Though, the attitude of the authors to the image of the Savior and his second coming to the world fluctuates: from a respectful expectation (Y. Voznesenskaya, T. Ustimenko, S. Lukyanenko to the depiction of the Savior as a monster (N. Perumov. The possibility of an ambivalent interpretation of the Savior is the eloquent evidence of desacralization of this image. The profaning of the sacred is one of the tendencies of the modern popular culture. The genre of fantastic fiction, as a product of mass culture, has caught this trend quite precisely.

  9. Bimodality and the formation of Saturn's ring particles

    International Nuclear Information System (INIS)

    Gehrels, T.

    1980-01-01

    The F ring appears to have an outer and an inner rim, with only the latter observed by the imaging photopolarimeter (IPP) on the Pioneer Saturn spacecraft. The inside of the G ring, near 2.49 R/sub S/, may also be seen in the optical data. 1979S1 is red as well as dark. The light scattered through the B ring is noticeably red. The A ring has a dense outer rim. The Cassini Division and the French Division (Dollfus Division) have a dark gap near their centers. The C ring becomes weaker toward the center such that outer, middle, and inner C rings can be recognized. The Pioneer and earth-based observations are explained with a model for the B and A rings to some extent of a bimodal size distributions of particles; the larger ones may be original accretions, while small debris diffuses inward through the Cassini Division and the C ring. During the formation of the ring system, differential gravitation allowed only silicaceous grains of higher density (rho> or approx. =3 g cm -3 ) to coagulate. These serve as interstitial cores for snowy carbonaceous grains, between the times of accretion from interplanetary cometary grains and liberation by collision followed by diffusion inward to Saturn and final evaporation

  10. Antibody classes & subclasses induced by mucosal immunization of mice with Streptococcus pyogenes M6 protein & oligodeoxynucleotides containing CpG motifs.

    Science.gov (United States)

    Teloni, R; von Hunolstein, C; Mariotti, S; Donati, S; Orefici, G; Nisini, R

    2004-05-01

    Type-specific antibodies against M protein are critical for human protection as they enhance phagocytosis and are protective. An ideal vaccine for the protection against Streptococcus pyogenes would warrant mucosal immunity, but mucosally administered M-protein has been shown to be poorly immunogenic in animals. We used a recombinant M type 6 protein to immunize mice in the presence of synthetic oligodeoxynucleotides containing CpG motifs (immunostimulatory sequences: ISS) or cholera toxin (CT) to explore its possible usage in a mucosal vaccine. Mice were immunized by intranasal (in) or intradermal (id) administration with four doses at weekly intervals of M6-protein (10 microg/mouse) with or without adjuvant (ISS, 10 microg/mouse or CT, 0,5 microg/mouse). M6 specific antibodies were measured by enzyme linked immunosorbent assay using class and subclass specific monoclonal antibodies. The use of ISS induced an impressive anti M-protein serum IgG response but when id administered was not detectable in the absence of adjuvant. When used in, M-protein in the presence of both ISS and CT induced anti M-protein IgA in the bronchoalveolar lavage, as well as specific IgG in the serum. IgG were able to react with serotype M6 strains of S. pyogenes. The level of antibodies obtained by immunizing mice in with M-protein and CT was higher in comparison to M-protein and ISS. The analysis of anti-M protein specific IgG subclasses showed high levels of IgG1, IgG2a and IgG2b, and low levels of IgG3 when ISS were used as adjuvant. Thus, in the presence of ISS, the ratio IgG2a/IgG1 and (IgG2a+IgG3)/IgG1 >1 indicated a type 1-like response obtained both in mucosally or systemically vaccinated mice. Our study offers a reproducible model of anti-M protein vaccination that could be applied to test new antigenic formulations to induce an anti-group A Streptococcus (GAS) vaccination suitable for protection against the different diseases caused by this bacterium.

  11. Bond Energies and Thermochemical Properties of Ring-Opened Diradicals and Carbenes of exo-Tricyclo[5.2.1.0(2,6)]decane.

    Science.gov (United States)

    Hudzik, Jason M; Castillo, Álvaro; Bozzelli, Joseph W

    2015-09-24

    Exo-tricyclo[5.2.1.0(2,6)]decane (TCD) or exo-tetrahydrodicyclopentadiene is an interesting strained ring compound and the single-component high-energy density hydrocarbon fuel known as JP-10. Important initial reactions of TCD at high temperatures could cleave a strained carbon-carbon (C-C) bond in the ring system creating diradicals also constrained by the remaining ring system. This study determines the thermochemical properties of these diradicals (TCD-H2 mJ-nJ where m and n correspond to the cleaved carbons sites) including the carbon-carbon bond dissociation energy (C-C BDE) corresponding to the cleaved TCD site. Thermochemical properties including enthalpies (ΔH°f298), entropies (S(T)), heat capacities (Cp(T)), and C-H and C-C BDEs for the parent (TCD-H2 m-n), radical (TCD-H2 mJ-n and m-nJ), diradical (TCD-H2 mJ-nJ), and carbene (TCD-H2 mJJ-n and m-nJJ) species are determined. Structures, vibrational frequencies, moments of inertia, and internal rotor potentials are calculated at the B3LYP/6-31G(d,p) level of theory. Standard enthalpies of formation in the gas phase for the TCD-H2 m-n parent and radical species are determined using the B3LYP density functional theory and the higher level G3MP2B3 and CBS-QB3 composite methods. For singlet and triplet TCD diradicals and carbenes, M06-2X, ωB97X-D, and CCSD(T) methods are included in the analysis to determine ΔH°f298 values. The C-C BDEs are further calculated using CASMP2(2,2)/aug-cc-pvtz//CASSCF(2,2)/cc-pvtz and with the CASMP2 energies extrapolated to the complete basis set limit. The bond energies calculated with these methods are shown to be comparable to the other calculation methods. Isodesmic work reactions are used for enthalpy analysis of these compounds for effective cancelation of systematic errors arising from ring strain. C-C BDEs range from 77.4 to 84.6 kcal mol(-1) for TCD diradical singlet species. C-H BDEs for the parent TCD-H2 m-n carbon sites range from 93 to 101 kcal mol(-1) with a

  12. Forandringslæring med autismediagnoser?

    DEFF Research Database (Denmark)

    Gustafson, Kari Ingrid; Mørck, Line Lerche

    2013-01-01

    Artiklen drøfter en række aktuelle spørgsmål omkring læring hos børn og unge med autisme-spektrum-forstyrrelses diagnoser. Der introduceres til en social praksisteoretisk forståelse af forandringslæring, der diskuterer forandring ikke kun i relation til en persons identitet, men også aktuelle og...... potentielle forandringer, når det gælder overskridelse af binær logik i autisme versus normalitet, samt i relation til at overskride individualiserede og dualistiske problem-forståelser af fejl og mangler ved det autistiske barn. Det illustreres, hvordan disse former for dualistisk tænkning er forankret i et...... Rasmus’ ændringer i læring, selvforståelse og tilhørsforhold perspektiveres med andre ASF-diagnostiseredes læring udforsket bl.a. gennem gruppeinterviews i regi af Asperger-foreningen. Artiklen byder således på et alternativ i form af at forstå forandringslæring som overskridende læring, med langt større...

  13. Warden’s Five-Ring System Theory: Legitimate Wartime Military Targeting or an Increased Potential to Violate the Law and Norms of Expected Behavior?

    Science.gov (United States)

    2000-04-01

    the five-ring system theory that dramatically improves the warfighters ability to systematically identify wartime targets. However, for all of its...acclaim, little has been written about Warden’s five-ring system theory . Even less has been written about the legal and moral implications of using Warden’s theory to identify wartime targets.

  14. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements

    OpenAIRE

    Huang, Hsi-Yuan; Chien, Chia-Hung; Jen, Kuan-Hua; Huang, Hsien-Da

    2006-01-01

    Numerous regulatory structural motifs have been identified as playing essential roles in transcriptional and post-transcriptional regulation of gene expression. RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (i) motifs in mRNA 5′-untra...

  15. 5-[(E-(2-Hydroxybenzylideneamino]-1H-1,3-benzimidazole-2(3H-thione

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2011-01-01

    Full Text Available There are two molecules in the asymmetric unit of the title compound, C14H11N3OS. In each, the benzimidazole ring system is essentially planar, with maximum deviations of 0.010 (2 and 0.006 (2 Å, and makes dihedral angles of 8.70 (9 and 13.75 (8°, respectively, with the hydroxy-substituted benzene rings. Each molecule adopts an E configuration about the central C=N double bond. In the crystal, the two independent molecules are connected via intermolecular N—H...S hydrogen bonds, forming dimers. Furthermore, the dimers are connected by N—H...O hydrogen bonds into molecular ribbons along the c axis. There is an intramolecular O—H...N hydrogen bond in each molecule, which generates an S(6 ring motif.

  16. Inhomogeneous molecular ring around the B[e] supergiant LHA 120-S 73

    Science.gov (United States)

    Kraus, M.; Cidale, L. S.; Arias, M. L.; Maravelias, G.; Nickeler, D. H.; Torres, A. F.; Borges Fernandes, M.; Aret, A.; Curé, M.; Vallverdú, R.; Barbá, R. H.

    2016-10-01

    Context. B[e] supergiants are evolved massive stars, enshrouded in a dense wind and surrounded by a molecular and dusty disk. The mechanisms that drive phases of enhanced mass loss and mass ejections, responsible for the shaping of the circumstellar material of these objects, are still unclear. Aims: We aim to improve our knowledge on the structure and dynamics of the circumstellar disk of the Large Magellanic Cloud B[e] supergiant LHA 120-S 73. Methods: High-resolution optical and near-infrared spectroscopic data were obtained over a period of 16 and 7 yr, respectively. The spectra cover the diagnostic emission lines from [Ca II] and [O I], as well as the CO bands. These features trace the disk at different distances from the star. We analyzed the kinematics of the individual emission regions by modeling their emission profiles. A low-resolution mid-infrared spectrum was obtained as well, which provides information on the composition of the dusty disk. Results: All diagnostic emission features display double-peaked line profiles, which we interpret as due to Keplerian rotation. We find that the profile of each forbidden line contains contributions from two spatially clearly distinct rings. In total, we find that LHA 120-S 73 is surrounded by at least four individual rings of material with alternating densities (or by a disk with strongly non-monotonic radial density distribution). Moreover, we find that the molecular ring must have gaps or at least strong density inhomogeneities, or in other words, a clumpy structure. The optical spectra additionally display a broad emission feature at 6160-6180 Å, which we interpret as molecular emission from TiO. The mid-infrared spectrum displays features of oxygen- and carbon-rich grain species, which indicates a long-lived, stable dusty disk. We cannot confirm the previously reported high value for the stellar rotation velocity. He I λ 5876 is the only clearly detectable pure atmospheric absorption line in our data. Its

  17. Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization

    Directory of Open Access Journals (Sweden)

    Nils E. R. Zimmermann

    2017-11-01

    Full Text Available Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP database (61,422 compounds for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

  18. A Bacon Tone Ring on an Open-Back Banjo

    OpenAIRE

    Politzer, David

    2016-01-01

    Head taps on a new Goodtime banjo rim fitted with a reproduction Bacon Professional ff tone ring are contrasted with a new Goodtime, a 2002 Goodtime, and a 1999 Goodtime fitted with a 1/4′′ diameter brass ring. Conclusions: The 1/4" ring does what’s commonly imagined, the upgrades to the Goodtime over the years are not merely cosmetic, and the Bacon ring’s biggest effect is to damp head ringing and suppress high harmonics. Detailed comparisons of the new Goodtimes with and without the Bacon r...

  19. Small horizontal emittance in the TESLA damping ring

    International Nuclear Information System (INIS)

    Decking, W.

    2001-01-01

    The present TESLA damping ring is designed for a normalized horizontal emittance of 8x10 -6 m. γ-γ collisions at the TESLA linear collider will benefit from a further decrease of the horizontal emittance. This paper reviews the processes which limit the horizontal emittance in the damping ring. Preliminary estimates on the smallest horizontal emittance for the present TESLA damping ring design as well as an ultimate limit of the emittance reachable with the TESLA damping ring concept will be given

  20. S-Nitrosothiols Observed Using Cavity Ring-Down Spectroscopy

    Science.gov (United States)

    Rad, Mary Lynn; Gaston, Benjamin M.; Lehmann, Kevin

    2017-06-01

    The biological importance of nitric oxide has been known for nearly forty years due to its role in cardiovascular and nervous signaling. The main carrier molecules, s-nitrosothiols (RSNOs), are of additional interest due to their role in signaling reactions. Additionally, these compounds are related to several diseases including muscular dystrophy, stroke, myocardial infarction, Alzheimer's disease, Parkinson's disease, cystic fibrosis, asthma, and pulmonary arterial hypertension. One of the main barriers to elucidating the role of these RSNOs is the low (nanomolar) concentration present in samples of low volume (typically ˜100 μL). To this end we have set up a cavity ring-down spectrometer tuned to observe ^{14}NO and ^{15}NO released from cell growth samples. To decrease the limit of detection we have implemented a laser locking scheme employing Zeeman modulation of NO in a reference cell and have tuned the polarization of the laser using a half wave plate to optimize the polarization for the inherent birefringence of the CRDS mirrors. Progress toward measuring RSNO concentration in biological samples will be presented.

  1. 2-Hydroxy-4-(prop-2-ynyloxybenzaldehyde

    Directory of Open Access Journals (Sweden)

    D. Velmurugan

    2013-01-01

    Full Text Available The asymmetric unit of the title compound, C10H8O3, contains two independent molecules, both of which are almost planar (r.m.s deviations for all non-H atoms of 0.044 and 0.053 Å. The dihedral angles between the benzene ring and the prop-1-yne group are 3.47 (1 and 3.07 (1° in the two molecules, and the prop-1-yne groups adopt extended conformations. In each molecule, an intramolecular O—H...O hydrogen bond involving the OH and aldehyde substituents forms an S(6 ring. In the crystal, molecules are linked into cyclic centrosymmetric dimers via C—H...O hydrogen bonds, generating R22(14 ring motifs. The crystal structure is further stabilized by aromatic π–π stacking interactions between the benzene rings [centroid–centroid distances = 3.813 (2 and 3.843 (2 Å

  2. Observations of ions of ionospheric origin in the storm-time ring current

    International Nuclear Information System (INIS)

    Johnson, R.G.; Sharp, R.D.; Shelley, E.G.

    1977-01-01

    O + , He + , and H + ions in the energy range 0.5 to 16 keV have been observed in the storm-time ring current with an energetic ion mass spectrometer aboard the polar-orbiting S3-3 satellite. During the main phases of the 29 December 1976, 6 April 1977, and 19 April 1977 magnetic storms, the O + number density within the instrument energy range in the inner ring current (L=2.8--4.0) was larger than the H + density in the altitude range from about 5000--7000 km. At two days after the main phase of the 29 December 1976 storm, O + was still the dominant ion at MLT=14.5 hours in the L=2.6--3.4 range at altitudes near 6000 km

  3. The Fine Structure of Herman Rings

    DEFF Research Database (Denmark)

    Fagella, Nuria; Henriksen, Christian

    2017-01-01

    We study the geometric structure of the boundary of Herman rings in a model family of Blaschke products of degree 3 (up to quasiconformal deformation). Shishikura’s quasiconformal surgery relates the Herman ring to the Siegel disk of a quadratic polynomial. By studying the regularity properties...

  4. Rings with involution whose symmetric elements are central

    Directory of Open Access Journals (Sweden)

    Taw Pin Lim

    1980-01-01

    Full Text Available In a ring R with involution whose symmetric elements S are central, the skew-symmetric elements K form a Lie algebra over the commutative ring S. The classification of such rings which are 2-torsion free is equivalent to the classification of Lie algebras K over S equipped with a bilinear form f that is symmetric, invariant and satisfies [[x,y],z]=f(y,zx−f(z,xy. If S is a field of char ≠2, f≠0 and dimK>1 then K is a semisimple Lie algebra if and only if f is nondegenerate. Moreover, the derived algebra K′ is either the pure quaternions over S or a direct sum of mutually orthogonal abelian Lie ideals of dim≤2.

  5. One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs.

    Science.gov (United States)

    Lock, Antonia; Forfar, Rachel; Weston, Cathryn; Bowsher, Leo; Upton, Graham J G; Reynolds, Christopher A; Ladds, Graham; Dixon, Ann M

    2014-12-01

    G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins and well-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the full-length protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conserved mechanism for assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs. Copyright © 2014. Published by Elsevier B.V.

  6. 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

  7. 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

  8. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

    LENUS (Irish Health Repository)

    Casey, Fergal

    2011-08-22

    Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

  9. Fingerprint motifs of phytases | Fan | African Journal of Biotechnology

    African Journals Online (AJOL)

    Among the total of potential 173 phytases gained in 11 plant genomes through MAST, PAPhys are the major phytases, and HAPhys are the minor, and other phytase groups are not found in planta. Keywords: Phytase, fingerprint motif, multiple EM for motif elicitation (MEME), MAST African Journal of Biotechnology Vol.

  10. A [Mo{sub 2}O{sub 2}S{sub 2}]-based ring system incorporating tartrate as the bridging ligand. Synthesis, structure and catalytic activity of Cs{sub 4}[Mo{sub 2}O{sub 2}(μ-S){sub 2}]{sub 2}(μ{sub 4}-tart){sub 2} (tart=[C{sub 4}H{sub 2}O{sub 6}]{sup 4-})

    Energy Technology Data Exchange (ETDEWEB)

    Qian, Ting-Ting; Cui, Yu-Jie; Xin, Zhifeng; Jia, Ai-Quan; Zhang, Qian-Feng [Anhui Univ. of Technology, Anhui (China). Inst. of Molecular Engineering and Applied Chemistry and Anhui Province Key Lab. of Metallurgy Engineering and Resources Recycling

    2017-08-01

    Treatment of [Mo{sub 2}S{sub 2}O{sub 2}(H{sub 2}O){sub 6}]{sup 2+} with racemic tartaric acid (tartH{sub 4}) in the presence of sodium hydroxide and cesium chloride in aqueous solution led to the isolation of a new tetra-molybdenum ring cluster Cs{sub 4}[Mo{sub 2}O{sub 2}(μ-S){sub 2}]{sub 2}(μ{sub 4}-tart){sub 2}. The cyclic cluster polyanion consists of two dinuclear [Mo{sub 2}O{sub 2}(μ-S){sub 2}]{sup 2+} moieties and two bridging tart{sup 4-} ligands. The cyclic polyoxothiomolybdate cluster, supported on the mesoporous silica SBA-15, was tested for heterogenerous catalysis in thiophene hydrodesulfurization.

  11. The PDZ-binding motif of Yes-associated protein is required for its co-activation of TEAD-mediated CTGF transcription and oncogenic cell transforming activity

    International Nuclear Information System (INIS)

    Shimomura, Tadanori; Miyamura, Norio; Hata, Shoji; Miura, Ryota; Hirayama, Jun; Nishina, Hiroshi

    2014-01-01

    Highlights: •Loss of the PDZ-binding motif inhibits constitutively active YAP (5SA)-induced oncogenic cell transformation. •The PDZ-binding motif of YAP promotes its nuclear localization in cultured cells and mouse liver. •Loss of the PDZ-binding motif inhibits YAP (5SA)-induced CTGF transcription in cultured cells and mouse liver. -- Abstract: YAP is a transcriptional co-activator that acts downstream of the Hippo signaling pathway and regulates multiple cellular processes, including proliferation. Hippo pathway-dependent phosphorylation of YAP negatively regulates its function. Conversely, attenuation of Hippo-mediated phosphorylation of YAP increases its ability to stimulate proliferation and eventually induces oncogenic transformation. The C-terminus of YAP contains a highly conserved PDZ-binding motif that regulates YAP’s functions in multiple ways. However, to date, the importance of the PDZ-binding motif to the oncogenic cell transforming activity of YAP has not been determined. In this study, we disrupted the PDZ-binding motif in the YAP (5SA) protein, in which the sites normally targeted by Hippo pathway-dependent phosphorylation are mutated. We found that loss of the PDZ-binding motif significantly inhibited the oncogenic transformation of cultured cells induced by YAP (5SA). In addition, the increased nuclear localization of YAP (5SA) and its enhanced activation of TEAD-dependent transcription of the cell proliferation gene CTGF were strongly reduced when the PDZ-binding motif was deleted. Similarly, in mouse liver, deletion of the PDZ-binding motif suppressed nuclear localization of YAP (5SA) and YAP (5SA)-induced CTGF expression. Taken together, our results indicate that the PDZ-binding motif of YAP is critical for YAP-mediated oncogenesis, and that this effect is mediated by YAP’s co-activation of TEAD-mediated CTGF transcription

  12. The PDZ-binding motif of Yes-associated protein is required for its co-activation of TEAD-mediated CTGF transcription and oncogenic cell transforming activity

    Energy Technology Data Exchange (ETDEWEB)

    Shimomura, Tadanori; Miyamura, Norio; Hata, Shoji; Miura, Ryota; Hirayama, Jun, E-mail: hirayama.dbio@mri.tmd.ac.jp; Nishina, Hiroshi, E-mail: nishina.dbio@mri.tmd.ac.jp

    2014-01-17

    Highlights: •Loss of the PDZ-binding motif inhibits constitutively active YAP (5SA)-induced oncogenic cell transformation. •The PDZ-binding motif of YAP promotes its nuclear localization in cultured cells and mouse liver. •Loss of the PDZ-binding motif inhibits YAP (5SA)-induced CTGF transcription in cultured cells and mouse liver. -- Abstract: YAP is a transcriptional co-activator that acts downstream of the Hippo signaling pathway and regulates multiple cellular processes, including proliferation. Hippo pathway-dependent phosphorylation of YAP negatively regulates its function. Conversely, attenuation of Hippo-mediated phosphorylation of YAP increases its ability to stimulate proliferation and eventually induces oncogenic transformation. The C-terminus of YAP contains a highly conserved PDZ-binding motif that regulates YAP’s functions in multiple ways. However, to date, the importance of the PDZ-binding motif to the oncogenic cell transforming activity of YAP has not been determined. In this study, we disrupted the PDZ-binding motif in the YAP (5SA) protein, in which the sites normally targeted by Hippo pathway-dependent phosphorylation are mutated. We found that loss of the PDZ-binding motif significantly inhibited the oncogenic transformation of cultured cells induced by YAP (5SA). In addition, the increased nuclear localization of YAP (5SA) and its enhanced activation of TEAD-dependent transcription of the cell proliferation gene CTGF were strongly reduced when the PDZ-binding motif was deleted. Similarly, in mouse liver, deletion of the PDZ-binding motif suppressed nuclear localization of YAP (5SA) and YAP (5SA)-induced CTGF expression. Taken together, our results indicate that the PDZ-binding motif of YAP is critical for YAP-mediated oncogenesis, and that this effect is mediated by YAP’s co-activation of TEAD-mediated CTGF transcription.

  13. Cancer caused by radioactive gold rings

    International Nuclear Information System (INIS)

    Callary, E.M.

    1989-01-01

    Two recent cases of skin cancer caused by radioactive gold rings are described. The gold was contaminated with radon daughters from hollow goldseeds used to hold radon, back in the 1930s or possibly later. Other radioactive gold rings are probably being worn. The Canadian AECB offers free testing

  14. Mitochondrial and Y chromosome haplotype motifs as diagnostic markers of Jewish ancestry: a reconsideration.

    Directory of Open Access Journals (Sweden)

    Sergio eTofanelli

    2014-11-01

    Full Text Available Several authors have proposed haplotype motifs based on site variants at the mitochondrial genome (mtDNA and the non-recombining portion of the Y chromosome (NRY to trace the genealogies of Jewish people. Here, we analyzed their main approaches and test the feasibility of adopting motifs as ancestry markers through construction of a large database of mtDNA and NRY haplotypes from public genetic genealogical repositories. We verified the reliability of Jewish ancestry prediction based on the Cohen and Levite Modal Haplotypes in their classical 6 STR marker format or in the extended 12 STR format, as well as four founder mtDNA lineages (HVS-I segments accounting for about 40% of the current population of Ashkenazi Jews. For this purpose we compared haplotype composition in individuals of self-reported Jewish ancestry with the rest of European, African or Middle Eastern samples, to test for non-random association of ethno-geographic groups and haplotypes. Overall, NRY and mtDNA based motifs, previously reported to differentiate between groups, were found to be more represented in Jewish compared to non-Jewish groups. However, this seems to stem from common ancestors of Jewish lineages being rather recent respect to ancestors of non-Jewish lineages with the same haplotype signatures. Moreover, the polyphyly of haplotypes which contain the proposed motifs and the misuse of constant mutation rates heavily affected previous attempts to correctly dating the origin of common ancestries. Accordingly, our results stress the limitations of using the above haplotype motifs as reliable Jewish ancestry predictors and show its inadequacy for forensic or genealogical purposes.

  15. 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

  16. Structural Analysis of the Bacterial Proteasome Activator Bpa in Complex with the 20S Proteasome.

    Science.gov (United States)

    Bolten, Marcel; Delley, Cyrille L; Leibundgut, Marc; Boehringer, Daniel; Ban, Nenad; Weber-Ban, Eilika

    2016-12-06

    Mycobacterium tuberculosis harbors proteasomes that recruit substrates for degradation through an ubiquitin-like modification pathway. Recently, a non-ATPase activator termed Bpa (bacterial proteasome activator) was shown to support an alternate proteasomal degradation pathway. Here, we present the cryo-electron microscopy (cryo-EM) structure of Bpa in complex with the 20S core particle (CP). For docking into the cryo-EM density, we solved the X-ray structure of Bpa, showing that it forms tight four-helix bundles arranged into a 12-membered ring with a 40 Å wide central pore and the C-terminal helix of each protomer protruding from the ring. The Bpa model was fitted into the cryo-EM map of the Bpa-CP complex, revealing its architecture and striking symmetry mismatch. The Bpa-CP interface was resolved to 3.5 Å, showing the interactions between the C-terminal GQYL motif of Bpa and the proteasome α-rings. This docking mode is related to the one observed for eukaryotic activators with features specific to the bacterial complex. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Short Arginine Motifs Drive Protein Stickiness in the Escherichia coli Cytoplasm.

    Science.gov (United States)

    Kyne, Ciara; Crowley, Peter B

    2017-09-19

    Although essential to numerous biotech applications, knowledge of molecular recognition by arginine-rich motifs in live cells remains limited. 1 H, 15 N HSQC and 19 F NMR spectroscopies were used to investigate the effects of C-terminal -GR n (n = 1-5) motifs on GB1 interactions in Escherichia coli cells and cell extracts. While the "biologically inert" GB1 yields high-quality in-cell spectra, the -GR n fusions with n = 4 or 5 were undetectable. This result suggests that a tetra-arginine motif is sufficient to drive interactions between a test protein and macromolecules in the E. coli cytoplasm. The inclusion of a 12 residue flexible linker between GB1 and the -GR 5 motif did not improve detection of the "inert" domain. In contrast, all of the constructs were detectable in cell lysates and extracts, suggesting that the arginine-mediated complexes were weak. Together these data reveal the significance of weak interactions between short arginine-rich motifs and the E. coli cytoplasm and demonstrate the potential of such motifs to modify protein interactions in living cells. These interactions must be considered in the design of (in vivo) nanoscale assemblies that rely on arginine-rich sequences.

  18. An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom.

    Science.gov (United States)

    Vujaklija, Ivan; Bielen, Ana; Paradžik, Tina; Biđin, Siniša; Goldstein, Pavle; Vujaklija, Dušica

    2016-02-18

    The massive accumulation of protein sequences arising from the rapid development of high-throughput sequencing, coupled with automatic annotation, results in high levels of incorrect annotations. In this study, we describe an approach to decrease annotation errors of protein families characterized by low overall sequence similarity. The GDSL lipolytic family comprises proteins with multifunctional properties and high potential for pharmaceutical and industrial applications. The number of proteins assigned to this family has increased rapidly over the last few years. In particular, the natural abundance of GDSL enzymes reported recently in plants indicates that they could be a good source of novel GDSL enzymes. We noticed that a significant proportion of annotated sequences lack specific GDSL motif(s) or catalytic residue(s). Here, we applied motif-based sequence analyses to identify enzymes possessing conserved GDSL motifs in selected proteomes across the plant kingdom. Motif-based HMM scanning (Viterbi decoding-VD and posterior decoding-PD) and the here described PD/VD protocol were successfully applied on 12 selected plant proteomes to identify sequences with GDSL motifs. A significant number of identified GDSL sequences were novel. Moreover, our scanning approach successfully detected protein sequences lacking at least one of the essential motifs (171/820) annotated by Pfam profile search (PfamA) as GDSL. Based on these analyses we provide a curated list of GDSL enzymes from the selected plants. CLANS clustering and phylogenetic analysis helped us to gain a better insight into the evolutionary relationship of all identified GDSL sequences. Three novel GDSL subfamilies as well as unreported variations in GDSL motifs were discovered in this study. In addition, analyses of selected proteomes showed a remarkable expansion of GDSL enzymes in the lycophyte, Selaginella moellendorffii. Finally, we provide a general motif-HMM scanner which is easily accessible through

  19. On zero divisor graph of unique product monoid rings over Noetherian reversible ring

    Directory of Open Access Journals (Sweden)

    Ebrahim Hashemi

    2016-02-01

    Full Text Available Let $R$ be an associative ring with identity and $Z^*(R$ be its set of non-zero zero divisors.  The zero-divisor graph of $R$, denoted by $Gamma(R$, is the graph whose vertices are the non-zero  zero-divisors of  $R$, and two distinct vertices $r$ and $s$ are adjacent if and only if $rs=0$ or $sr=0$.  In this paper, we bring some results about undirected zero-divisor graph of a monoid ring over reversible right (or left Noetherian ring $R$. We essentially classify the diameter-structure of this graph and show that $0leq mbox{diam}(Gamma(Rleq mbox{diam}(Gamma(R[M]leq 3$. Moreover, we give a characterization for the possible diam$(Gamma(R$ and diam$(Gamma(R[M]$, when $R$ is a reversible Noetherian ring and $M$ is a u.p.-monoid. Also, we study relations between the girth of $Gamma(R$ and that of $Gamma(R[M]$.

  20. Syntheses and Tribological Property of CrMoN/MoS2 Multilayer Films on Piston Rings of Heavy Vehicle Engine

    Institute of Scientific and Technical Information of China (English)

    WANG Xiancheng; LI Qi; LI Ruoting; DI Yuelan

    2016-01-01

    In order to prolong the service life of piston rings of heavy vehicle engine and decrease the friction and wear of piston rings and cylinder liner, CrMoN/MoS2 multilayer iflms were deposited on the surface of rings by magnetron sputtering and low temperature ion sulfuration. FESEM equipped with EDX was adopted to analyze the compositions and morphologies of surface, cross-section, and wear scars of the multilayer iflms. The nano-hardness and Young’s modulus of the iflms were measured by a nano tester. Tribological properties of the iflms were tested by an SRV®4 wear tester. The experimental results indicate that the structures of the multilayer films are dense and compact. The films possess nano hardness value of approximately 26.7 GPa and superior ability of plastic deformation resistance. The multilayer iflms can activate solid lubricating, and possess an excellent antifriction and wear resistance under the conditions of heavy load, high frequency, high temperature, and dynamic load.

  1. Anion induced conformational preference of Cα NN motif residues in functional proteins.

    Science.gov (United States)

    Patra, Piya; Ghosh, Mahua; Banerjee, Raja; Chakrabarti, Jaydeb

    2017-12-01

    Among different ligand binding motifs, anion binding C α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion. © 2017 Wiley Periodicals, Inc.

  2. Crystal structure of 4-allylsulfanyl-1H-pyrazolo[3,4-d]pyrimidine

    Directory of Open Access Journals (Sweden)

    Mohammed El Fal

    2014-09-01

    Full Text Available In the title compound, C8H8N4S, the pyrazolo[3,4-d]pyrimidine ring system is essentially planar, with a maximum deviation from the mean plane of 0.025 (3 Å. The allyl group is disordered over two sites in a 0.512 (6:0.488 (6 ratio. In the crystal, molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with an R22(8 graph-set motif.

  3. Gene regulatory and signaling networks exhibit distinct topological distributions of motifs

    Science.gov (United States)

    Ferreira, Gustavo Rodrigues; Nakaya, Helder Imoto; Costa, Luciano da Fontoura

    2018-04-01

    The biological processes of cellular decision making and differentiation involve a plethora of signaling pathways and gene regulatory circuits. These networks in turn exhibit a multitude of motifs playing crucial parts in regulating network activity. Here we compare the topological placement of motifs in gene regulatory and signaling networks and observe that it suggests different evolutionary strategies in motif distribution for distinct cellular subnetworks.

  4. Finding a Leucine in a Haystack: Searching the Proteome for ambigous Leucine-Aspartic Acid motifs

    KAUST Repository

    Arold, Stefan T.

    2016-01-25

    Leucine-aspartic acid (LD) motifs are short helical protein-protein interaction motifs involved in cell motility, survival and communication. LD motif interactions are also implicated in cancer metastasis and are targeted by several viruses. LD motifs are notoriously difficult to detect because sequence pattern searches lead to an excessively high number of false positives. Hence, despite 20 years of research, only six LD motif–containing proteins are known in humans, three of which are close homologues of the paxillin family. To enable the proteome-wide discovery of LD motifs, we developed LD Motif Finder (LDMF), a web tool based on machine learning that combines sequence information with structural predictions to detect LD motifs with high accuracy. LDMF predicted 13 new LD motifs in humans. Using biophysical assays, we experimentally confirmed in vitro interactions for four novel LD motif proteins. Thus, LDMF allows proteome-wide discovery of LD motifs, despite a highly ambiguous sequence pattern. Functional implications will be discussed.

  5. Corneal iron ring after hyperopic photorefractive keratectomy.

    Science.gov (United States)

    Bilgihan, K; Akata, F; Gürelik, G; Adigüzel, U; Akpinar, M; Hasanreisoğlu, B

    1999-05-01

    To report the incidence and course of corneal iron deposition after hyperopic photorefractive keratectomy (PRK). Gazi University, Medical School, Department of Ophthalmology, Ankara, Turkey. Between January 1995 and December 1997, 62 eyes had PRK to correct hyperopia. Nine eyes developed corneal iron ring 5 to 8 months (mean 6.25 months +/- 1.3 [SD]) after PRK for hyperopia. The rings persisted during the mean follow-up of 19 +/- 11.09 months. The ring-shaped iron deposition after PRK for hyperopia must be differentiated from the Fleischer ring. Our results suggest that the slitlamp findings of peripheral corneal iron deposition in hyperopic PRK patients correlate with achieved correction.

  6. Permuting the PGF Signature Motif Blocks both Archaeosortase-Dependent C-Terminal Cleavage and Prenyl Lipid Attachment for the Haloferax volcanii S-Layer Glycoprotein.

    Science.gov (United States)

    Abdul Halim, Mohd Farid; Karch, Kelly R; Zhou, Yitian; Haft, Daniel H; Garcia, Benjamin A; Pohlschroder, Mechthild

    2015-12-28

    For years, the S-layer glycoprotein (SLG), the sole component of many archaeal cell walls, was thought to be anchored to the cell surface by a C-terminal transmembrane segment. Recently, however, we demonstrated that the Haloferax volcanii SLG C terminus is removed by an archaeosortase (ArtA), a novel peptidase. SLG, which was previously shown to be lipid modified, contains a C-terminal tripartite structure, including a highly conserved proline-glycine-phenylalanine (PGF) motif. Here, we demonstrate that ArtA does not process an SLG variant where the PGF motif is replaced with a PFG motif (slg(G796F,F797G)). Furthermore, using radiolabeling, we show that SLG lipid modification requires the PGF motif and is ArtA dependent, lending confirmation to the use of a novel C-terminal lipid-mediated protein-anchoring mechanism by prokaryotes. Similar to the case for the ΔartA strain, the growth, cellular morphology, and cell wall of the slg(G796F,F797G) strain, in which modifications of additional H. volcanii ArtA substrates should not be altered, are adversely affected, demonstrating the importance of these posttranslational SLG modifications. Our data suggest that ArtA is either directly or indirectly involved in a novel proteolysis-coupled, covalent lipid-mediated anchoring mechanism. Given that archaeosortase homologs are encoded by a broad range of prokaryotes, it is likely that this anchoring mechanism is widely conserved. Prokaryotic proteins bound to cell surfaces through intercalation, covalent attachment, or protein-protein interactions play critical roles in essential cellular processes. Unfortunately, the molecular mechanisms that anchor proteins to archaeal cell surfaces remain poorly characterized. Here, using the archaeon H. volcanii as a model system, we report the first in vivo studies of a novel protein-anchoring pathway involving lipid modification of a peptidase-processed C terminus. Our findings not only yield important insights into poorly understood

  7. 2,4,6-Trimethyl-3,5-bis[(phenylcarbonothioylsulfanylmethyl]benzyl benzenecarbodithioate

    Directory of Open Access Journals (Sweden)

    M. Kannan

    2010-06-01

    Full Text Available In the title compound C33H30S6, the three pendant methylene benzodithioate groups lie to one side of the central benzene ring in a cis-cis-cis `tripod' arrangement. The dihedral angles between the central benzene ring and the three pendant rings are 72.54 (4, 89.68 (4 and 86.74 (4°. In the crystal structure, one of the benzene rings is disordered over two orientations in a 0.559 (13:0.441 (13 ratio.

  8. A proposed vestigial translation initiation motif in VP1 of hepatitis A virus.

    Science.gov (United States)

    Kang, Jeong-Ah; Funkhouser, Ann W

    2002-07-01

    The internal ribosome entry site (IRES) of picornaviruses has a 3' polypyrimidine tract (PPT) 16-24 bases upstream of an AUG triplet (PPT/AUG motif). This motif is critical in determining the efficiency of cap-independent translation. HAV has a conserved PPT/AUG motif consisting of a nine base sequence (AGGUUUUUC) 23 bases upstream of the preferred AUG start codon. This HAV-specific PPT/AUG motif is repeated and conserved in VP1 of HAV, but not of other picornaviruses. We proposed that the PPT/AUG motif in the open reading frame initiated translation and/or had an impact on the life cycle of the virus. In vitro translation of mutant bicistronic mRNAs and growth in cell culture of mutant viruses provided no evidence that the VP1 PPT/AUG motif had any impact on either translation or growth. HAV differs from other picornaviruses in its inefficient growth in cell culture. Since the HAV-specific PPT/AUG motif is found in only 1 in 300,000 reported viral sequences outside the hepatovirus genus, this motif may be a vestigial translation initiation element and may have played a role in determining the unusual phenotype of HAV.

  9. CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures

    Directory of Open Access Journals (Sweden)

    Hamed Bostan

    2012-01-01

    Full Text Available Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.

  10. 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

  11. BEAM web server: a tool for structural RNA motif discovery.

    Science.gov (United States)

    Pietrosanto, Marco; Adinolfi, Marta; Casula, Riccardo; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2018-03-15

    RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. marco.pietrosanto@uniroma2.it. Supplementary data are available at Bioinformatics online.

  12. Study of lead free ferroelectrics using overlay technique on thick film microstrip ring resonator

    Directory of Open Access Journals (Sweden)

    Shridhar N. Mathad

    2016-03-01

    Full Text Available The lead free ferroelectrics, strontium barium niobates, were synthesized via the low cost solid state reaction method and their fritless thick films were fabricated by screen printing technique on alumina substrate. The X band response (complex permittivity at very high frequencies of Ag thick film microstrip ring resonator perturbed with strontium barium niobates (SrxBa1-xNb2O6 in form of bulk and thick film was measured. A new approach for determination of complex permittivity (ε′ and ε′′ in the frequency range 8–12 GHz, using perturbation of Ag thick film microstrip ring resonator (MSRR, was applied for both bulk and thick film of strontium barium niobates (SrxBa1-xNb2O6. The microwave conductivity of the bulk and thick film lie in the range from 1.779 S/cm to 2.874 S/cm and 1.364 S/cm to 2.296 S/cm, respectively. The penetration depth of microwave in strontium barium niobates is also reported.

  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. Scanning Tunneling Microscopic Observation of Adatom-Mediated Motifs on Gold-Thiol Self-assembled Monolayers at High Coverage

    DEFF Research Database (Denmark)

    Wang, Yun; Chi, Qijin; Hush, Noel S.

    2009-01-01

    the structural motifs observed on surfaces at low coverage and on gold nanoparticles to the observed spectroscopic properties of high-coverage SAMs formed by methanethiol. However, the significant role attributed to intermolecular steric packing effects suggests a lack of generality for the adatom-mediated motif......Self-assembled monolayers (SAMs) formed by chemisorption of a branched-chain alkanethiol, 2-methyl-1-propanethiol, on Au(111) surfaces were studied by in situ scanning tunneling microscopy (STM) under electrochemical potential control and analyzed using extensive density functional theory (DFT...... two R−S−Au−S−R adatom-mediated motifs per surface cell, with steric-induced variations in the adsorbate alignment inducing the observed STM image contrasts. Observed pits covering 5.6 ± 0.5% of the SAM surface are consistent with this structure. These results provide the missing link from...

  15. The Tribological Performance of CrMoN/MoS2 Solid Lubrication Coating on a Piston Ring

    Directory of Open Access Journals (Sweden)

    Yuelan Di

    2017-05-01

    Full Text Available In order to improve the tribological properties of an engine piston ring and enhance its service life, magnetron sputtering technology and low temperature ion sulphurizing treatment technology were used to prepare CrMoN/MoS2 solid lubricant coating on the surface of an engine piston ring. The morphologies and compositions of the surface and cross-section of the sulfuration layer were analyzed by field emission scanning electron microscopy (FESEM, and wear property under high load, high speed and high temperature conditions were tested by a SRV®4 friction and wear testing machine. The results show that the CrMoN/MoS2 composite coatings appear as a dense grain structure, and the coating is an ideal solid lubrication layer that possesses an excellent high temperature wear resistance, reducing the engine operating temperature abrasion effectively and prolonging the service life of the engine.

  16. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Science.gov (United States)

    Fauteux, François; Strömvik, Martina V

    2009-01-01

    Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L.) Heynh.), soybean (Glycine max (L.) Merr.) and rice (Oryza sativa L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs

  17. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Directory of Open Access Journals (Sweden)

    Fauteux François

    2009-10-01

    Full Text Available Abstract Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP gene promoters from three plant families, namely Brassicaceae (mustards, Fabaceae (legumes and Poaceae (grasses using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L. Heynh., soybean (Glycine max (L. Merr. and rice (Oryza sativa L. respectively. We have identified three conserved motifs (two RY-like and one ACGT-like in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination

  18. 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.

  19. Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification.

    Science.gov (United States)

    Wang, Yin; Li, Rudong; Zhou, Yuhua; Ling, Zongxin; Guo, Xiaokui; Xie, Lu; Liu, Lei

    2016-01-01

    Text data of 16S rRNA are informative for classifications of microbiota-associated diseases. However, the raw text data need to be systematically processed so that features for classification can be defined/extracted; moreover, the high-dimension feature spaces generated by the text data also pose an additional difficulty. Here we present a Phylogenetic Tree-Based Motif Finding algorithm (PMF) to analyze 16S rRNA text data. By integrating phylogenetic rules and other statistical indexes for classification, we can effectively reduce the dimension of the large feature spaces generated by the text datasets. Using the retrieved motifs in combination with common classification methods, we can discriminate different samples of both pneumonia and dental caries better than other existing methods. We extend the phylogenetic approaches to perform supervised learning on microbiota text data to discriminate the pathological states for pneumonia and dental caries. The results have shown that PMF may enhance the efficiency and reliability in analyzing high-dimension text data.

  20. Saturn's F Ring Core: Calm in the Midst of Chaos

    Science.gov (United States)

    Cuzzi, J. N.; Whizin, A. D.; Hogan, R. C.; Dobrovolskis, A. R.; Dones, L.; Showalter. M. R.; Colwell, J. E.; Scargle, J. D.

    2013-01-01

    The long-term stability of the narrow F Ring core has been hard to understand. Instead of acting as "shepherds", Prometheus and Pandora together stir the vast preponderance of the region into a chaotic state, consistent with the orbits of newly discovered objects like S/2004S6. We show how a comb of very narrow radial locations of high stability in semimajor axis is embedded within this otherwise chaotic region. The stability of these semimajor axes relies fundamentally on the unusual combination of rapid apse precession and long synodic period which characterizes the region. This situation allows stable "antiresonances" to fall on or very close to traditional Lindblad resonances which, under more common circumstances, are destabilizing. We present numerical integrations of tens of thousands of test particles over tens of thousands of Prometheus orbits that map out the effect. The stable antiresonance zones are most stable in a subset of the region where Prometheus first-order resonances are least cluttered by Pandora resonances. This region of optimum stability is paradoxically closer to Prometheus than a location more representative of "torque balance", helping explain a longstanding paradox. One stable zone corresponds closely to the currently observed semimajor axis of the F Ring core. While the model helps explain the stability of the narrow F Ring core, it does not explain why the F Ring material all shares a common apse longitude; we speculate that collisional damping at the preferred semimajor axis (not included in the current simulations) may provide that final step. Essentially, we find that the F Ring core is not confined by a combination of Prometheus and Pandora, but a combination of Prometheus and precession.

  1. On the origin of distribution patterns of motifs in biological networks

    Directory of Open Access Journals (Sweden)

    Lesk Arthur M

    2008-08-01

    Full Text Available Abstract Background Inventories of small subgraphs in biological networks have identified commonly-recurring patterns, called motifs. The inference that these motifs have been selected for function rests on the idea that their occurrences are significantly more frequent than random. Results Our analysis of several large biological networks suggests, in contrast, that the frequencies of appearance of common subgraphs are similar in natural and corresponding random networks. Conclusion Indeed, certain topological features of biological networks give rise naturally to the common appearance of the motifs. We therefore question whether frequencies of occurrences are reasonable evidence that the structures of motifs have been selected for their functional contribution to the operation of networks.

  2. Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences

    Science.gov (United States)

    König, Sebastian L. B.; Huppert, Julian L.; Sigel, Roland K. O.; Evans, Amanda C.

    2013-01-01

    G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions. PMID:23771141

  3. Systematic comparison of the response properties of protein and RNA mediated gene regulatory motifs.

    Science.gov (United States)

    Iyengar, Bharat Ravi; Pillai, Beena; Venkatesh, K V; Gadgil, Chetan J

    2017-05-30

    We present a framework enabling the dissection of the effects of motif structure (feedback or feedforward), the nature of the controller (RNA or protein), and the regulation mode (transcriptional, post-transcriptional or translational) on the response to a step change in the input. We have used a common model framework for gene expression where both motif structures have an activating input and repressing regulator, with the same set of parameters, to enable a comparison of the responses. We studied the global sensitivity of the system properties, such as steady-state gain, overshoot, peak time, and peak duration, to parameters. We find that, in all motifs, overshoot correlated negatively whereas peak duration varied concavely with peak time. Differences in the other system properties were found to be mainly dependent on the nature of the controller rather than the motif structure. Protein mediated motifs showed a higher degree of adaptation i.e. a tendency to return to baseline levels; in particular, feedforward motifs exhibited perfect adaptation. RNA mediated motifs had a mild regulatory effect; they also exhibited a lower peaking tendency and mean overshoot. Protein mediated feedforward motifs showed higher overshoot and lower peak time compared to the corresponding feedback motifs.

  4. Fast social-like learning of complex behaviors based on motor motifs

    Science.gov (United States)

    Calvo Tapia, Carlos; Tyukin, Ivan Y.; Makarov, Valeri A.

    2018-05-01

    Social learning is widely observed in many species. Less experienced agents copy successful behaviors exhibited by more experienced individuals. Nevertheless, the dynamical mechanisms behind this process remain largely unknown. Here we assume that a complex behavior can be decomposed into a sequence of n motor motifs. Then a neural network capable of activating motor motifs in a given sequence can drive an agent. To account for (n -1 )! possible sequences of motifs in a neural network, we employ the winnerless competition approach. We then consider a teacher-learner situation: one agent exhibits a complex movement, while another one aims at mimicking the teacher's behavior. Despite the huge variety of possible motif sequences we show that the learner, equipped with the provided learning model, can rewire "on the fly" its synaptic couplings in no more than (n -1 ) learning cycles and converge exponentially to the durations of the teacher's motifs. We validate the learning model on mobile robots. Experimental results show that the learner is indeed capable of copying the teacher's behavior composed of six motor motifs in a few learning cycles. The reported mechanism of learning is general and can be used for replicating different functions, including, for example, sound patterns or speech.

  5. Adsorption and ring-opening of lactide on the chiral metal surface Pt(321){sup S} studied by density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Franke, J.-H.; Kosov, D. S. [Department of Physics, Campus Plaine - CP 231, Universite Libre de Bruxelles, 1050 Brussels (Belgium)

    2015-01-28

    We study the adsorption and ring-opening of lactide on the naturally chiral metal surface Pt(321){sup S}. Lactide is a precursor for polylactic acid ring-opening polymerization, and Pt is a well known catalyst surface. We study, here, the energetics of the ring-opening of lactide on a surface that has a high density of kink atoms. These sites are expected to be present on a realistic Pt surface and show enhanced catalytic activity. The use of a naturally chiral surface also enables us to study potential chiral selectivity effects of the reaction at the same time. Using density functional theory with a functional that includes the van der Waals forces in a first-principles manner, we find modest adsorption energies of around 1.4 eV for the pristine molecule and different ring-opened states. The energy barrier to be overcome in the ring-opening reaction is found to be very small at 0.32 eV and 0.30 eV for LL- and its chiral partner DD-lactide, respectively. These energies are much smaller than the activation energy for a dehydrogenation reaction of 0.78 eV. Our results thus indicate that (a) ring-opening reactions of lactide on Pt(321) can be expected already at very low temperatures, and Pt might be a very effective catalyst for this reaction; (b) the ring-opening reaction rate shows noticeable enantioselectivity.

  6. 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...

  7. G345.45+1.50: an expanding ring-like structure with massive star formation

    Science.gov (United States)

    López-Calderón, Cristian; Bronfman, Leonardo; Nyman, Lars-Åke; Garay, Guido; de Gregorio-Monsalvo, Itziar; Bergman, Per

    2016-11-01

    Context. Ring-like structures in the interstellar medium (ISM) are commonly associated with high-mass stars. Kinematic studies of large structures in giant molecular clouds (GMCs) toward these ring-like structures may help us to understand how massive stars form. Aims: The origin and properties of the ring-like structure G345.45+1.50 is investigated through observations of the 13CO(3-2) line. The aim of the observations is to determine the kinematics in the region and to compare physical characteristics estimated from gas emission with those previously determined using dust continuum emission. This area in the sky is well suited for studies like this because the ring is located 1.5° above the Galactic plane at 1.8 kpc from the Sun, thus molecular structures are rarely superposed on our line of sight, which minimizes confusion effects that might hinder identifying of individual molecular condensations. Methods: The 13CO(3-2) line was mapped toward the whole ring using the Atacama Pathfinder Experiment (APEX) telescope. The observations cover 17' × 20' in the sky with a spatial resolution of 0.2 pc and an rms of 1 K at a spectral resolution of 0.1 km s-1. Results: The ring is found to be expanding with a velocity of 1.0 km s-1, containing a total mass of 6.9 × 103M⊙, which agrees well with that determined using 1.2 mm dust continuum emission. An expansion timescale of 3 × 106 yr and a total energy of 7 × 1046 erg are estimated. The origin of the ring might have been a supernova explosion, since a 35.5 cm source, J165920-400424, is located at the center of the ring without an infrared counterpart. The ring is fragmented, and 104 clumps were identified with diameters of between 0.3 and 1.6 pc, masses of between 2.3 and 7.5 × 102M⊙, and densities of between 102 and 104 cm-3. At least 18% of the clumps are forming stars, as is shown in infrared images. Assuming that the clumps can be modeled as Bonnor-Ebert spheres, 13 clumps are collapsing, and the rest of

  8. Thermal Stability of Modified i-Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

    DEFF Research Database (Denmark)

    El-Sayed, Ahmed Ali; Pedersen, Erik B.; Khaireldin, Nahid Y.

    2016-01-01

    In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion of naphtha......In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion...... of naphthalimide (1H-benzo[de]isoquinoline-1,3(2H)-dione) as the intercalating nucleic acid. The stabilities of i-motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures (Tm) and circular dichroism spectra at different pH values and conditions (crowding...

  9. WildSpan: mining structured motifs from protein sequences

    Directory of Open Access Journals (Sweden)

    Chen Chien-Yu

    2011-03-01

    Full Text Available Abstract Background Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. Discovering such patterns is time-consuming because abundant combinations exist when long gaps (a gap consists of one or more successive wildcards are considered. Mining algorithms often employ constraints to narrow down the search space in order to increase efficiency. However, improper constraint models might degrade the sensitivity and specificity of the motifs discovered by computational methods. We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. The patterns that satisfy the proposed constraint model are called W-patterns. A W-pattern is a structured motif that groups motif symbols into pattern blocks interleaved with large irregular gaps. Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions that incorporates several pruning strategies to largely reduce the mining cost. Results WildSpan is shown to efficiently find W-patterns containing conserved residues that are far separated in sequences. We conducted experiments with two mining strategies, protein-based and family-based mining, to evaluate the usefulness of W-patterns and performance of WildSpan. The protein-based mining mode

  10. Motif formation and industry specific topologies in the Japanese business firm network

    Science.gov (United States)

    Maluck, Julian; Donner, Reik V.; Takayasu, Hideki; Takayasu, Misako

    2017-05-01

    Motifs and roles are basic quantities for the characterization of interactions among 3-node subsets in complex networks. In this work, we investigate how the distribution of 3-node motifs can be influenced by modifying the rules of an evolving network model while keeping the statistics of simpler network characteristics, such as the link density and the degree distribution, invariant. We exemplify this problem for the special case of the Japanese Business Firm Network, where a well-studied and relatively simple yet realistic evolving network model is available, and compare the resulting motif distribution in the real-world and simulated networks. To better approximate the motif distribution of the real-world network in the model, we introduce both subgraph dependent and global additional rules. We find that a specific rule that allows only for the merging process between nodes with similar link directionality patterns reduces the observed excess of densely connected motifs with bidirectional links. Our study improves the mechanistic understanding of motif formation in evolving network models to better describe the characteristic features of real-world networks with a scale-free topology.

  11. Containing Ebola at the Source with Ring Vaccination.

    Directory of Open Access Journals (Sweden)

    Stefano Merler

    2016-11-01

    Full Text Available Interim results from the Guinea Ebola ring vaccination trial suggest high efficacy of the rVSV-ZEBOV vaccine. These findings open the door to the use of ring vaccination strategies in which the contacts and contacts of contacts of each index case are promptly vaccinated to contain future Ebola virus disease outbreaks. To provide a numerical estimate of the effectiveness of ring vaccination strategies we introduce a spatially explicit agent-based model to simulate Ebola outbreaks in the Pujehun district, Sierra Leone, structurally similar to previous modelling approaches. We find that ring vaccination can successfully contain an outbreak for values of the effective reproduction number up to 1.6. Through an extensive sensitivity analysis of parameters characterising the readiness and capacity of the health care system, we identify interventions that, alongside ring vaccination, could increase the likelihood of containment. In particular, shortening the time from symptoms onset to hospitalisation to 2-3 days on average through improved contact tracing procedures, adding a 2km spatial component to the vaccination ring, and decreasing human mobility by quarantining affected areas might contribute increase our ability to contain outbreaks with effective reproduction number up to 2.6. These results have implications for future control of Ebola and other emerging infectious disease threats.

  12. Two-dimensional hydrogen-bonded polymers in the crystal structures of the ammonium salts of phenoxyacetic acid, (4-fluorophenoxyacetic acid and (4-chloro-2-methylphenoxyacetic acid

    Directory of Open Access Journals (Sweden)

    Graham Smith

    2014-12-01

    Full Text Available The structures of the ammonium salts of phenoxyacetic acid, NH4+·C8H6O3−, (I, (4-fluorophenoxyacetic acid, NH4+·C8H5FO3−, (II, and the herbicidally active (4-chloro-2-methylphenoxyacetic acid (MCPA, NH4+·C9H8ClO3−·0.5H2O, (III have been determined. All have two-dimensional layered structures based on inter-species ammonium N—H...O hydrogen-bonding associations, which give core substructures consisting primarily of conjoined cyclic motifs. The crystals of (I and (II are isomorphous with the core comprising R12(5, R12(4 and centrosymmetric R42(8 ring motifs, giving two-dimensional layers lying parallel to (100. In (III, the water molecule of solvation lies on a crystallographic twofold rotation axis and bridges two carboxyl O atoms in an R44(12 hydrogen-bonded motif, creating two R43(10 rings, which together with a conjoined centrosymmetric R42(8 ring incorporating both ammonium cations, generate two-dimensional layers lying parallel to (100. No π–π ring associations are present in any of the structures.

  13. A Convenient Approach to Heterocyclic Building Blocks: Synthesis of Novel Ring Systems Containing a [5,6]Pyrano[2,3-c]pyrazol-4(1H-one Moiety

    Directory of Open Access Journals (Sweden)

    Wolfgang Holzer

    2007-01-01

    Full Text Available Starting from commercially available educts, a straightforward synthetic route to new heterocyclic building blocks is exemplified with the one- or two-step synthesis of tri-, tetra-, or pentacyclic ring systems. Representatives of the following novel ring systems are prepared from 3-methyl-1-phenyl-2-pyrazolin-5-one and the corresponding o-halo-arenecarbonyl chloride using calcium hydroxide in refluxing 1,4-dioxane: pyrimidino[4',5':5,6]pyrano[2,3-c]pyrazol-4(1H-one, thieno[3',2':5,6]pyrano[2,3c]pyrazol- 4-(1H-one, thieno[3',4':5,6]pyrano[2,3-c]pyrazol-4(1H-one, thieno[3'',2'':4',5']thieno[2',3':5,6]-pyrano[2,3-c]pyrazol-4(1H-one, [1,3]dioxolo[5',6'][1]benzothieno[2',3':5,6]pyrano-[2,3-c]- pyrazol-4(1H-one, pyridazino[4',3':5,6]pyrano[2,3-c]pyrazol-4(1H-one and pyrazolo-[4'',3'':5',6']pyrido[3',4':5,6]pyrano[2,3-c]pyrazol-4(1H-one. While the latter two ring systems are directly obtained due to a spontaneous intramolecular substitution reaction, in the other reactions uncyclised 4-aroylpyrazol-5-ols are produced, which are cyclised into the target heterocycles in a subsequent synthetic step (i.e. treatment with NaH in DMF. Detailed NMR spectroscopic investigations (1H-, 13C-, 15N- with the obtained compounds were undertaken to unambiguously prove the new structures.

  14. Binding properties of SUMO-interacting motifs (SIMs) in yeast.

    Science.gov (United States)

    Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

    2015-03-01

    Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

  15. Ultra-low energy storage ring at FLAIR

    International Nuclear Information System (INIS)

    Welsch, Carsten P.; Papash, A. I.; Gorda, O.; Harasimowicz, J.; Karamyshev, O.; Karamysheva, G.; Newton, D.; Panniello, M.; Putignano, M.; Siggel-King, M. R. F.; Smirnov, A.

    2012-01-01

    The Ultra-low energy electrostatic Storage Ring (USR) at the future Facility for Low-energy Antiproton and Ion Research (FLAIR) will provide cooled beams of antiprotons in the energy range between 300 keV down to 20 keV and possibly less. The USR has been completely redesigned over the past three years. The ring structure is based on a “split achromat” lattice that allows in-ring experiments with internal gas jet target. Beam parameters might be adjusted in a wide range: from very short pulses in the nanosecond regime to a Coasting beam. In addition, a combined fast and slow extraction scheme was developed that allows for providing external experiments with cooled beams of different time structure. Detailed investigations of the USR, including studies into the ring’s long term beam dynamics, life time, equilibrium momentum spread and equilibrium lateral spread during collisions with an internal target were carried out. New tools and beam handling techniques for diagnostics of ultra-low energy ions at beam intensities less than 10 6 were developed by the QUASAR Group. In this paper, progress on the USR project will be presented with an emphasis on the expected beam parameters available to the experiments at FLAIR.

  16. De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences

    DEFF Research Database (Denmark)

    Ruzzo, Walter L; Gorodkin, Jan

    2014-01-01

    De novo discovery of "motifs" capturing the commonalities among related noncoding ncRNA structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphas...... on an approach based on the CMfinder CMfinder program as a case study. Applications to genomic screens for novel de novo structured ncRNA ncRNA s, including structured RNA elements in untranslated portions of protein-coding genes, are presented.......De novo discovery of "motifs" capturing the commonalities among related noncoding ncRNA structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphasis...

  17. Flupentixol tartrate.

    Science.gov (United States)

    Yamuna, Thammarse S; Kaur, Manpreet; Anderson, Brian J; Jasinski, Jerry P; Yathirajan, H S

    2014-02-01

    In the title salt, C23H26F3N2OS(+)·C4H5O6 (-) [systematic name: 1-(2-hy-droxy-eth-yl)-4-[3-(2-(tri-fluoro-meth-yl)thioxanthen-9-yl-idene)prop-yl]piperazin-1-ium 3-carb-oxy-2,3-di-hydroxy-pro-pion-ate], the monoprotonated piperazine ring in the cation adopts a chair conformation, while the thio-pyran ring of the thioxanthene group has a boat conformation. The dihedral angle between the mean planes of the two outer aromatic rings of the thioxanthene groups is 31.6 (2)°. In the crystal, the cations and anions are linked via O-H⋯O, N-H⋯O, O-H⋯N and C-H⋯O hydrogen bonds, forming chains propagating along [100]. In addition, R (2) 2(7), R (2) 2(11), R (2) 2(10) and R (2) 2(12) graph-set ring motifs involving the anions, and R (2) 2(9) graph-set ring motifs involving both the cations and anions are observed. The three F atoms of the tri-fluoro-methyl group are disordered over two sets of sites and the individual atoms were refined with occupancy ratios of 0.54 (6):0.46 (6), 0.72 (2):0.28 (2) and 0.67 (3):0.33 (3).

  18. The astrosphere of the asymptotic giant branch star CIT 6

    Energy Technology Data Exchange (ETDEWEB)

    Sahai, Raghvendra [Jet Propulsion Laboratory, MS 183-900, California Institute of Technology, Pasadena, CA 91109 (United States); Mack-Crane, Galen P., E-mail: sahai@jpl.nasa.gov [Department of Physics, Occidental College, Los Angeles, CA 90041 (United States)

    2014-10-01

    We have discovered two extended half-ring structures in a far-ultraviolet image taken with the GALEX satellite of the well-known mass-losing carbon star CIT 6 (RW LMi). The northern (southern) ring is brighter (fainter) with a diameter of ∼15' (∼18'). These structures most likely represent the astrosphere resulting from the shock interaction of CIT 6's molecular wind with the warm interstellar medium (ISM), as it moves through the latter. These data provide a direct estimate of the size of CIT 6's circumstellar envelope that is a factor ∼20 larger than previous estimates based on CO millimeter-wave line data. We find that CIT 6 has been undergoing heavy mass-loss for at least 93,000 yr and the total envelope mass is 0.29 M {sub ☉} or larger, assuming a constant mass-loss rate of 3.2 × 10{sup –6} M {sub ☉} yr{sup –1}. Assuming that the shock front has reached a steady state and CIT 6's motion relative to the ISM is in the sky plane, we measure the termination-shock standoff distance directly from the image and find that CIT 6 is moving at a speed of about ≳39 (0.17 cm{sup –3}/n {sub ISM}){sup 1/2} km s{sup –1} through the ISM around it. However, comparisons with published numerical simulations and analytical modeling shows that CIT 6's forward shock (the northern ring) departs from the parabolic shape expected in steady state. We discuss several possible explanations for this departureþ.

  19. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin

    2015-01-01

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  20. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun

    2015-09-27

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  1. (1S,3S,4S-tert-Butyl N-[1-benzyl-3-hydroxy-5-phenyl-4-(picolinamidopentyl]carbamate

    Directory of Open Access Journals (Sweden)

    Jian-Feng Zheng

    2008-07-01

    Full Text Available The title compound, C29H35N3O4, was obtained by the reaction of (2S,4S,5S-tert-butyl N-(4-amino-1-benzyl-3-hydroxy-5-phenylpentylcarbamate and picolinic acid using oxalyl chloride as a chlorinating reagent to activate the carboxyl group. In the crystal structure there are two molecules in the asymmetric unit, which are aligned edge-to-face. In one molecule, the pyridyl ring forms a dihedral angle of 22.0 (1° with the phenyl ring of the terminal benzyl group and 14.3 (1° with the other phenyl ring; in the other molecule, the corresponding angles are 12.1 (1 and 10.6 (1°, respectively. The packing is stabilized by intermolecular hydrogen bonds and C—H...π interactions.

  2. Crystal structures of 2-[(4,6-di-amino-pyrimidin-2-yl)sulfan-yl]-N-(naphthalen-1-yl)acetamide and 2-[(4,6-di-amino-pyrimidin-2-yl)sulfan-yl]-N-(4-fluoro-phen-yl)acetamide.

    Science.gov (United States)

    Subasri, S; Kumar, Timiri Ajay; Sinha, Barij Nayan; Jayaprakash, Venkatesan; Viswanathan, Vijayan; Velmurugan, Devadasan

    2017-02-01

    The title compounds, C 16 H 15 N 5 OS, (I), and C 12 H 12 FN 5 OS, (II), are [(di-amino-pyrimidine)-sulfan-yl]acetamide derivatives. In (I), the pyrimidine ring is inclined to the naphthalene ring system by 55.5 (1)°, while in (II), the pyrimidine ring is inclined to the benzene ring by 58.93 (8)°. In (II), there is an intra-molecular N-H⋯N hydrogen bond and a short C-H⋯O contact. In the crystals of (I) and (II), mol-ecules are linked by pairs of N-H⋯N hydrogen bonds, forming inversion dimers with R 2 2 (8) ring motifs. In the crystal of (I), the dimers are linked by bifurcated N-H⋯(O,O) and C-H⋯O hydrogen bonds, forming layers parallel to (100). In the crystal of (II), the dimers are linked by N-H⋯O hydrogen bonds, also forming layers parallel to (100). The layers are linked by C-H⋯F hydrogen bonds, forming a three-dimensional architecture.

  3. Catch history of ringed seals (Phoca hispida in Canada

    Directory of Open Access Journals (Sweden)

    Randall R Reeves

    1998-06-01

    Full Text Available The ringed seal (Phoca hispida has always been a staple in the diet and household economy of Inuit in Canada. The present paper was prepared at the request of the NAMMCO Scientific Committee to support their assessment of ringed seal stocks in the North Atlantic Basin and adjacent arctic and subarctic waters. Specifically, our objective was to evaluate recent and current levels of use of ringed seals by Canadian Inuit. Annual removals probably were highest (possibly greater than 100,000 in the 1960s and 1970s, a period when sealskin prices were particularly strong. Catches declined substantially in the 1980s following a collapse in sealskin prices, presumably related to the European trade ban on skins from newborn harp and hooded seals (Phoca groenlandica and Cystophora cristata, respectively. Recent catch levels throughout Canada (1980s and early 1990s are believed to be in the order of 50,000 to 65,000 ringed seals, with a total average annual kill (including hunting loss in the high tens of thousands. No reliable system is in place to monitor catches of ringed seals, so any estimate must be derived from a heterogeneous array of sources.

  4. Crystal structure of 2-hydroxyimino-2-(pyridin-2-yl-N′-[1-(pyridin-2-ylethylidene]acetohydrazide

    Directory of Open Access Journals (Sweden)

    Maxym O. Plutenko

    2014-12-01

    Full Text Available The molecule of the title compound, C14H13N5O2, is approximately planar (r.m.s deviation for all non-H atoms = 0.093 Å, with the planes of the two pyridine rings inclined to one another by 5.51 (7°. The oxime group is syn to the amide group, probably due to the formation of an intramolecular N—H...N hydrogen bond that forms an S(6 ring motif. In the crystal, molecules are linked by pairs of bifurcated O—H...(O,N hydrogen bonds, forming inversion dimers. The latter are linked via C—H...O and C—H...N hydrogen bonds, forming sheets lying parallel to (502. The sheets are linked via π–π stacking interactions [inter-centroid distance = 3.7588 (9 Å], involving the pyridine rings of inversion-related molecules, forming a three-dimensional structure.

  5. Efficient sequential and parallel algorithms for finding edit distance based motifs.

    Science.gov (United States)

    Pal, Soumitra; Xiao, Peng; Rajasekaran, Sanguthevar

    2016-08-18

    Motif search is an important step in extracting meaningful patterns from biological data. The general problem of motif search is intractable and there is a pressing need to develop efficient, exact and approximation algorithms to solve this problem. In this paper, we present several novel, exact, sequential and parallel algorithms for solving the (l,d) Edit-distance-based Motif Search (EMS) problem: given two integers l,d and n biological strings, find all strings of length l that appear in each input string with atmost d errors of types substitution, insertion and deletion. One popular technique to solve the problem is to explore for each input string the set of all possible l-mers that belong to the d-neighborhood of any substring of the input string and output those which are common for all input strings. We introduce a novel and provably efficient neighborhood exploration technique. We show that it is enough to consider the candidates in neighborhood which are at a distance exactly d. We compactly represent these candidate motifs using wildcard characters and efficiently explore them with very few repetitions. Our sequential algorithm uses a trie based data structure to efficiently store and sort the candidate motifs. Our parallel algorithm in a multi-core shared memory setting uses arrays for storing and a novel modification of radix-sort for sorting the candidate motifs. The algorithms for EMS are customarily evaluated on several challenging instances such as (8,1), (12,2), (16,3), (20,4), and so on. The best previously known algorithm, EMS1, is sequential and in estimated 3 days solves up to instance (16,3). Our sequential algorithms are more than 20 times faster on (16,3). On other hard instances such as (9,2), (11,3), (13,4), our algorithms are much faster. Our parallel algorithm has more than 600 % scaling performance while using 16 threads. Our algorithms have pushed up the state-of-the-art of EMS solvers and we believe that the techniques introduced in

  6. Physical-chemical property based sequence motifs and methods regarding same

    Science.gov (United States)

    Braun, Werner [Friendswood, TX; Mathura, Venkatarajan S [Sarasota, FL; Schein, Catherine H [Friendswood, TX

    2008-09-09

    A data analysis system, program, and/or method, e.g., a data mining/data exploration method, using physical-chemical property motifs. For example, a sequence database may be searched for identifying segments thereof having physical-chemical properties similar to the physical-chemical property motifs.

  7. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

    Science.gov (United States)

    Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

    2011-06-20

    One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

  8. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2011-06-01

    Full Text Available Abstract Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet, which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i ubiquitous motifs, shared by several superfamilies and (ii superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

  9. Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks.

    Science.gov (United States)

    Gorochowski, Thomas E; Grierson, Claire S; di Bernardo, Mario

    2018-03-01

    Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli . Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution.

  10. Storm-time ring current: model-dependent results

    Directory of Open Access Journals (Sweden)

    N. Yu. Ganushkina

    2012-01-01

    Full Text Available The main point of the paper is to investigate how much the modeled ring current depends on the representations of magnetic and electric fields and boundary conditions used in simulations. Two storm events, one moderate (SymH minimum of −120 nT on 6–7 November 1997 and one intense (SymH minimum of −230 nT on 21–22 October 1999, are modeled. A rather simple ring current model is employed, namely, the Inner Magnetosphere Particle Transport and Acceleration model (IMPTAM, in order to make the results most evident. Four different magnetic field and two electric field representations and four boundary conditions are used. We find that different combinations of the magnetic and electric field configurations and boundary conditions result in very different modeled ring current, and, therefore, the physical conclusions based on simulation results can differ significantly. A time-dependent boundary outside of 6.6 RE gives a possibility to take into account the particles in the transition region (between dipole and stretched field lines forming partial ring current and near-Earth tail current in that region. Calculating the model SymH* by Biot-Savart's law instead of the widely used Dessler-Parker-Sckopke (DPS relation gives larger and more realistic values, since the currents are calculated in the regions with nondipolar magnetic field. Therefore, the boundary location and the method of SymH* calculation are of key importance for ring current data-model comparisons to be correctly interpreted.

  11. Some commutativity theorems for a certain class of rings

    International Nuclear Information System (INIS)

    Khan, M.A.

    1994-08-01

    In the present paper we first establish the commutativity theorem for semiprime ring satisfying the polynomial identity [x n ,y]x r = ±y s [x,y m ]y t for all x,y in R, where m,n,r,s and t are fixed nonnegative integers, and further, we investigate commutativity of rings with unity under some additional hypothesis. Moreover, it is also shown that the above result is true for s-unital. Also, we provide some counter examples which show that the hypothesis of our theorems are not altogether superfluous. The results of this paper generalize some of the well-known commutativity theorems for rings which are right s-unital. (author). 21 refs

  12. Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

    Directory of Open Access Journals (Sweden)

    Vassilev Boris

    2010-04-01

    Full Text Available Abstract Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94% appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1 a dimer interface motif found in voltage-gated chloride channels, (2 a proton transfer motif found in heme-copper oxidases, and (3 a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

  13. The heptanucleotide motif GAGACGC is a key component of a cis-acting promoter element that is critical for SnSAG1 expression in Sarcocystis neurona.

    Science.gov (United States)

    Gaji, Rajshekhar Y; Howe, Daniel K

    2009-07-01

    The apicomplexan parasite Sarcocystis neurona undergoes a complex process of intracellular development, during which many genes are temporally regulated. The described study was undertaken to begin identifying the basic promoter elements that control gene expression in S. neurona. Sequence analysis of the 5'-flanking region of five S. neurona genes revealed a conserved heptanucleotide motif GAGACGC that is similar to the WGAGACG motif described upstream of multiple genes in Toxoplasma gondii. The promoter region for the major surface antigen gene SnSAG1, which contains three heptanucleotide motifs within 135 bases of the transcription start site, was dissected by functional analysis using a dual luciferase reporter assay. These analyses revealed that a minimal promoter fragment containing all three motifs was sufficient to drive reporter molecule expression, with the presence and orientation of the 5'-most heptanucleotide motif being absolutely critical for promoter function. Further studies should help to identify additional sequence elements important for promoter function and for controlling gene expression during intracellular development by this apicomplexan pathogen.

  14. A 250-Mbit/s ring local computer network using 1.3-microns single-mode optical fibers

    Science.gov (United States)

    Eng, S. T.; Tell, R.; Andersson, T.; Eng, B.

    1985-01-01

    A 250-Mbit/s three-station fiber-optic ring local computer network was built and successfully demonstrated. A conventional token protocol was employed for bus arbitration to maximize the bus efficiency under high loading conditions, and a non-return-to-zero (NRS) data encoding format was selected for simplicity and maximum utilization of the ECL-circuit bandwidth.

  15. Pr4N2S3 and Pr4N2Se3: two non-isostructural praseodymium(iii) nitride chalcogenides

    International Nuclear Information System (INIS)

    Lissner, Falk; Schleid, Thomas

    2005-01-01

    The non-isostructural nitride chalcogenides of praseodymium, Pr 4 N 2 S 3 and Pr 4 N 2 Se 3 , are formed by the reaction of the praseodymium metal with sodium azide (NaN 3 ), praseodymium trihalide (PrX 3 ; X = Cl, Br, I) and the respective chalcogen (sulfur or selenium) at 900 C in evacuated silica ampoules after seven days. Both crystallize monoclinically in space group C2/c (Pr 4 N 2 S 3 : a = 1788.57(9), b = 986.04(5), c = 1266.49(6) pm, β = 134.546(7) , Z = 8; Pr 4 N 2 Se 3 : a = 1311.76(7), b = 1017.03(5), c = 650.42(3) pm, β = 90.114(6) , Z = 4). The crystal structures of both compounds show a layered construction, dominated by N 3- -centred (Pr 3+ ) 4 tetrahedra which share a common edge first. Continuing linkage of the so resulting bitetrahedral [N 2 Pr 6 ] 12+ units via the non-connected vertices to layers according to [stack ∞ 2 ]{[N(Pr) 2/2 e (Pr') 2/2 v ] 3+ } forms different kinds of tetrahedral nets which can be described as layers consisting of ''four- and eight-rings'' for Pr 4 N 2 S 3 and as layers of ''six-rings'' for Pr 4 N 2 Se 3 . Whereas the crystal structure of Pr 4 N 2 S 3 exhibits four different Pr 3+ cations with coordination numbers of six (2 x) and seven (2 x) against N 3- and S 2- , the number of cations in the nitride selenide (Pr 4 N 2 Se 3 ) is reduced to half (Pr1 and Pr2) also having six- and sevenfold anionic coordination spheres. Further motifs for the connection of [NM 4 ] 9+ tetrahedra in crystal structures of nitride chalcogenides and halides of the rare-earth elements with ratios of N: M = 1: 2 are presented and discussed. (Abstract Copyright [2005], Wiley Periodicals, Inc.) [de

  16. Development of high-performance sintered friction material for synchronizer ring; Koseino shoketsu synchronizer ring masatsu zairyo no kaihatsu

    Energy Technology Data Exchange (ETDEWEB)

    Miyajima, K; Fuwa, Y; Okajima, H; Yoshikawa, K [Toyota Motor Corp., Aichi (Japan); Nakamura, M [Japan Powder Metallurgy Co. Ltd., Tokyo (Japan)

    1997-10-01

    Increasing vehicle speed and power, high-performance synchronizer ring of manual transmission is required. We develop double layer sintered synchronizer ring for high performance and cost reduction. The main structure is consisted of ferrous sinter for high strength. In this paper, friction materials of sintered synchronizer ring are studied. We can get the good friction and anti-wear property by means of hard particles (FeTi, ZrO2), solid lubricant (Graphite) and suitable porosity in brass sinter matrix. And we also achieve high joining strength between double layers adding Cu-P material. 6 refs., 13 figs., 2 tabs.

  17. 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.

  18. [Cover motifs of the Tidsskrift. A 14-year cavalcade].

    Science.gov (United States)

    Nylenna, M

    1998-12-10

    In 1985 the Journal of the Norwegian Medical Association changed its cover policy, moving the table of contents inside the Journal and introducing cover illustrations. This article provides an analysis of all cover illustrations published over this 14-year period, 420 covers in all. There is a great variation in cover motifs and designs and a development towards more general motifs. The initial emphasis on historical and medical aspects is now less pronounced, while the use of works of art and nature motifs has increased, and the cover now more often has a direct bearing on the specific contents of the issue. Professor of medical history Oivind Larsen has photographed two thirds of the covers and contributed 95% of the inside essay-style reflections on the cover motif. Over the years, he has expanded the role of the historian of medicine disseminating knowledge to include that of the raconteur with a personal tone of voice. The Journal's covers are now one of its most characteristic features, emblematic of the Journal's ambition of standing for quality and timelessness vis-à-vis the news media, and of its aim of bridging the gap between medicine and the humanities.

  19. Insights into the motif preference of APOBEC3 enzymes.

    Directory of Open Access Journals (Sweden)

    Diako Ebrahimi

    Full Text Available We used a multivariate data analysis approach to identify motifs associated with HIV hypermutation by different APOBEC3 enzymes. The analysis showed that APOBEC3G targets G mainly within GG, TG, TGG, GGG, TGGG and also GGGT. The G nucleotides flanked by a C at the 3' end (in +1 and +2 positions were indicated as disfavoured targets by APOBEC3G. The G nucleotides within GGGG were found to be targeted at a frequency much less than what is expected. We found that the infrequent G-to-A mutation within GGGG is not limited to the inaccessibility, to APOBEC3, of poly Gs in the central and 3'polypurine tracts (PPTs which remain double stranded during the HIV reverse transcription. GGGG motifs outside the PPTs were also disfavoured. The motifs GGAG and GAGG were also found to be disfavoured targets for APOBEC3. The motif-dependent mutation of G within the HIV genome by members of the APOBEC3 family other than APOBEC3G was limited to GA→AA changes. The results did not show evidence of other types of context dependent G-to-A changes in the HIV genome.

  20. Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs

    DEFF Research Database (Denmark)

    van Beest, M; Dooijes, D; van De Wetering, M

    2000-01-01

    Sequence-specific high mobility group (HMG) box factors bind and bend DNA via interactions in the minor groove. Three-dimensional NMR analyses have provided the structural basis for this interaction. The cognate HMG domain DNA motif is generally believed to span 6-8 bases. However, alignment...

  1. Modification of Titanium Substrates with Chimeric Peptides Comprising Antimicrobial and Titanium-Binding Motifs Connected by Linkers To Inhibit Biofilm Formation.

    Science.gov (United States)

    Liu, Zihao; Ma, Shiqing; Duan, Shun; Xuliang, Deng; Sun, Yingchun; Zhang, Xi; Xu, Xinhua; Guan, Binbin; Wang, Chao; Hu, Meilin; Qi, Xingying; Zhang, Xu; Gao, Ping

    2016-03-02

    Bacterial adhesion and biofilm formation are the primary causes of implant-associated infection, which is difficult to eliminate and may induce failure in dental implants. Chimeric peptides with both binding and antimicrobial motifs may provide a promising alternative to inhibit biofilm formation on titanium surfaces. In this study, chimeric peptides were designed by connecting an antimicrobial motif (JH8194: KRLFRRWQWRMKKY) with a binding motif (minTBP-1: RKLPDA) directly or via flexible/rigid linkers to modify Ti surfaces. We evaluated the binding behavior of peptides using quartz crystal microbalance (QCM) and atomic force microscopy (AFM) techniques and investigated the effect of the modification of titanium surfaces with these peptides on the bioactivity of Streptococcus gordonii (S. gordonii) and Streptococcus sanguis (S. sanguis). Compared with the flexible linker (GGGGS), the rigid linker (PAPAP) significantly increased the adsorption of the chimeric peptide on titanium surfaces (p chimeric peptide with the rigid linker exhibited more effective antimicrobial ability than the peptide with the flexible linker. This finding was ascribed to the ability of the rigid linker to separate functional domains and reduce their interference to the maximum extent. Consequently, the performance of chimeric peptides with specific titanium-binding motifs and antimicrobial motifs against bacteria can be optimized by the proper selection of linkers. This rational design of chimeric peptides provides a promising alternative to inhibit the formation of biofilms on titanium surfaces with the potential to prevent peri-implantitis and peri-implant mucositis.

  2. I-motif DNA structures are formed in the nuclei of human cells

    Science.gov (United States)

    Zeraati, Mahdi; Langley, David B.; Schofield, Peter; Moye, Aaron L.; Rouet, Romain; Hughes, William E.; Bryan, Tracy M.; Dinger, Marcel E.; Christ, Daniel

    2018-06-01

    Human genome function is underpinned by the primary storage of genetic information in canonical B-form DNA, with a second layer of DNA structure providing regulatory control. I-motif structures are thought to form in cytosine-rich regions of the genome and to have regulatory functions; however, in vivo evidence for the existence of such structures has so far remained elusive. Here we report the generation and characterization of an antibody fragment (iMab) that recognizes i-motif structures with high selectivity and affinity, enabling the detection of i-motifs in the nuclei of human cells. We demonstrate that the in vivo formation of such structures is cell-cycle and pH dependent. Furthermore, we provide evidence that i-motif structures are formed in regulatory regions of the human genome, including promoters and telomeric regions. Our results support the notion that i-motif structures provide key regulatory roles in the genome.

  3. Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop.

    Science.gov (United States)

    Dembska, Anna; Juskowiak, Bernard

    2015-01-01

    In this work, we present a spectral characterization of pH-sensitive system, which combines the i-motif properties with the spatially sensitive fluorescence signal of pyrene molecules attached to hairpin ends. The excimer production (fluorescence max. ∼480 nm) by pyrene labels at the ends of the molecular beacon is driven by pH-dependent i-motif formation in the loop. To illustrate the performance and reversible work of our systems, we performed the experiments with repeatedly pH cycling between pH values of 7.5±0.3 and 6.5±0.3. The sensor gives analytical response in excimer-monomer switching mode in narrow pH range (1.5 pH units) and exhibits high pH resolution (0.1 pH unit). Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Variability of the tree-rings structure of Gmelin’s larch at northern tree line (peninsula of Taymyr

    Directory of Open Access Journals (Sweden)

    V. V. Fakhrutdinova

    2017-04-01

    Full Text Available The study of tree-ring cell structure changes as the result of tree adaptation to varying environmental conditions becomes increasingly important to predict future vegetation shifts under projected climate changes. The estimate of intrapopulation annual variability of wood anatomy characteristics is particularly informative. It helps to divide the contribution of different ecological factors to total features dispersion. In this work, a comparative analysis of individual and climatic variability of tree ring structure characteristics of Gmelin’s larch Larix gmelinii (Rupr. growth within northernmost forest was carried out. The trees from forest-tundra boundary has greater radial growth intensity, forms the bigger conductive zone in rings with wider mean lumen area in comparison with trees from closed forest. This result can be explained by adaptive features and height ecological xylem plasticity of larch. The tree rings structure of larch from boundary with tundra is determined by largely current weather conditions. Is because these ones evince high adaptive plasticity on the level of xylem structure. The xylem reflects joint changes of climate factors and local ecological conditions. The trees from closed forest are characterized by larger individual variability. The local conditions in oldest forest (for example, bad hydrothermal soil conditions inhibit the radial growth and sensitivity to environmental factors. In this case, the trees on individual level are tended to save the normal functioning of water-transport system. The significant differences in ratio individual to climate variability of tree ring structure characteristics can be caused by the different in the level of ecological habitat heterogeneity or the different in the level genetic within-population heterogeneity.

  5. Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

    KAUST Repository

    Alam, Tanvir

    2018-03-11

    Short Linear Motifs (SLiMs) contribute to almost every cellular function by connecting appropriate protein partners. Accurate prediction of SLiMs is difficult due to their shortness and sequence degeneracy. Leucine-aspartic acid (LD) motifs are SLiMs that link paxillin family proteins to factors controlling (cancer) cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. To enable a proteome-wide assessment of these motifs, we developed an active-learning based framework that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome identified a dozen proteins that contain LD motifs, all being involved in cell adhesion and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter-species comparison revealed a conserved LD signalling core, and reveals the emergence of species-specific adaptive connections, while maintaining a strong functional focus of the LD motif interactome. Collectively, our data elucidate the mechanisms underlying the origin and adaptation of an ancestral SLiM.

  6. Crystal structure of bis(1,4-diazabicyclo[2.2.2]octan-1-ium thiosulfate dihydrate

    Directory of Open Access Journals (Sweden)

    Gorgui Awa Seck

    2016-03-01

    Full Text Available The crystal structure of the hydrated title salt, 2C6H13N2+·S2O32−·2H2O, contains a centrosymmetric cyclic motif of eight hydrogen-bonded molecular subunits. Two DABCOH+ cations (DABCO = 1,4-diazabicyclo[2.2.2]octane are linked to two water molecules and two thiosulfate anions via O—H...N and O—H...O hydrogen bonds, respectively. Two other water molecules close the cyclic motif through O—H...O contacts to the first two water molecules and to the two thiosulfate anions. A second pair of DABCOH+ cations is N—H...O hydrogen bonded to the two anions and is pendant to the ring. Adjacent cyclic motifs are bridged into a block-like arrangement extending along [100] through O—H...O interactions involving the second pair of water molecules and neighbouring thiosulfate anions.

  7. Characterization of sulfur deposition over the period of industrialization in Japan using sulfur isotope ratio in Japanese cedar tree rings taken from stumps.

    Science.gov (United States)

    Ishida, Takuya; Tayasu, Ichiro; Takenaka, Chisato

    2015-07-01

    We characterized the sulfur deposition history over the period of industrialization in Japan based on the sulfur isotope ratio (δ(34)S) in tree rings of Japanese cedar (Cryptomeria japonica D. Don) stumps. We analyzed and compared δ(34)S values in the rings from two types of disk samples from 170-year-old stumps that had been cut 5 years earlier (older forest stand) and from 40-year-old living trees (younger forest stand) in order to confirm the validity of using stump disks for δ(34)S analysis. No differences in δ(34)S values by age were found between the sample types, indicating that stump disks can be used for δ(34)S analysis. The δ(34)S profile in tree rings was significantly correlated with anthropogenic SO2 emissions in Japan (r = -0.76, p tree rings serve as a record of anthropogenic sulfur emissions. In addition, the values did not change largely from pre-industrialization to the 1940s (+4.2 to +6.1‰). The values before the 1940s are expected to reflect the background sulfur conditions in Japan and, thus, disks containing rings formed before the 1940s contain information about the natural environmental sulfur, which is useful for biogeochemical studies.

  8. Fiber-ring laser-based intracavity photoacoustic spectroscopy for trace gas sensing.

    Science.gov (United States)

    Wang, Qiang; Wang, Zhen; Chang, Jun; Ren, Wei

    2017-06-01

    We demonstrated a novel trace gas sensing method based on fiber-ring laser intracavity photoacoustic spectroscopy. This spectroscopic technique is a merging of photoacoustic spectroscopy (PAS) with a fiber-ring cavity for sensitive and all-fiber gas detection. A transmission-type PAS gas cell (resonant frequency f0=2.68  kHz) was placed inside the fiber-ring laser to fully utilize the intracavity laser power. The PAS signal was excited by modulating the laser wavelength at f0/2 using a custom-made fiber Bragg grating-based modulator. We used this spectroscopic technique to detect acetylene (C2H2) at 1531.6 nm as a proof of principle. With a low Q-factor (4.9) of the PAS cell, our sensor achieved a good linear response (R2=0.996) to C2H2 concentration and a minimum detection limit of 390 ppbv at 2-s response time.

  9. Identification of a putative nuclear export signal motif in human NANOG homeobox domain

    International Nuclear Information System (INIS)

    Park, Sung-Won; Do, Hyun-Jin; Huh, Sun-Hyung; Sung, Boreum; Uhm, Sang-Jun; Song, Hyuk; Kim, Nam-Hyung; Kim, Jae-Hwan

    2012-01-01

    Highlights: ► We found the putative nuclear export signal motif within human NANOG homeodomain. ► Leucine-rich residues are important for human NANOG homeodomain nuclear export. ► CRM1-specific inhibitor LMB blocked the potent human NANOG NES-mediated nuclear export. -- Abstract: NANOG is a homeobox-containing transcription factor that plays an important role in pluripotent stem cells and tumorigenic cells. To understand how nuclear localization of human NANOG is regulated, the NANOG sequence was examined and a leucine-rich nuclear export signal (NES) motif ( 125 MQELSNILNL 134 ) was found in the homeodomain (HD). To functionally validate the putative NES motif, deletion and site-directed mutants were fused to an EGFP expression vector and transfected into COS-7 cells, and the localization of the proteins was examined. While hNANOG HD exclusively localized to the nucleus, a mutant with both NLSs deleted and only the putative NES motif contained (hNANOG HD-ΔNLSs) was predominantly cytoplasmic, as observed by nucleo/cytoplasmic fractionation and Western blot analysis as well as confocal microscopy. Furthermore, site-directed mutagenesis of the putative NES motif in a partial hNANOG HD only containing either one of the two NLS motifs led to localization in the nucleus, suggesting that the NES motif may play a functional role in nuclear export. Furthermore, CRM1-specific nuclear export inhibitor LMB blocked the hNANOG potent NES-mediated export, suggesting that the leucine-rich motif may function in CRM1-mediated nuclear export of hNANOG. Collectively, a NES motif is present in the hNANOG HD and may be functionally involved in CRM1-mediated nuclear export pathway.

  10. Gray Matter Heterotopia, Mental Retardation, Developmental Delay, Microcephaly, and Facial Dysmorphisms in a Boy with Ring Chromosome 6: A 10-Year Follow-Up and Literature Review.

    Science.gov (United States)

    Liu, Shu; Wang, Zhiqing; Wei, Sisi; Liang, Jinqun; Chen, Nuan; OuYang, Haimei; Zeng, Weihong; Chen, Liying; Xie, Xunjie; Jiang, Jianhui

    2018-04-14

    Ring chromosome 6, r(6), is an extremely rare cytogenetic abnormality with clinical heterogeneity which arises typically de novo. The phenotypes of r(6) can be highly variable, ranging from almost normal to severe malformations and neurological defects. Up to now, only 33 cases have been reported in the literature. In this 10-year follow-up study, we report a case presenting distinctive facial features, severe developmental delay, and gray matter heterotopia with r(6) and terminal deletions of 6p25.3 (115426-384174, 268 kb) and 6q26-27 (168697778-170732033, 2.03 Mb) encompassing 2 and 15 candidate genes, respectively, which were detected using G-banding karyotyping, FISH, and chromosomal microarray analysis. We also analyzed the available information on the clinical features of the reported r(6) cases in order to provide more valuable information on genotype-phenotype correlations. To the best of our knowledge, this is the first report of gray matter heterotopia manifested in a patient with r(6) in China, and the deletions of 6p and 6q in our case are the smallest with the precise size of euchromatic material loss currently known. © 2018 S. Karger AG, Basel.

  11. Computerspil og læring

    Directory of Open Access Journals (Sweden)

    Lasse Juel Larsen

    2015-02-01

    Full Text Available Game-based learning og gamification er ord, der ofte optræder i forbindelse med computerspil og læring. Denne artikel vil analytisk undersøge, hvordan computerspil og læring går i forbindelse med hinanden. Artikel tager afsæt i Gregory Batesons læringsteori og læser denne igennem det kommercielle computerspil StarCraft 2 fra Blizzard Intertainment. Batesons læringsteori vil ikke alene blive gennemgået, men også udvidet og perspektiveret.  Formålet med denne indsats er at skabe et afsæt, der kan demonstrere, hvordan læring foregår i computerspil. Herefter vil afsættet blive anvendt til at destillere et læringsteoretisk udkast. Artiklen falder således i to dele, hvor den første analytisk adresserer, hvordan læring i computerspil foregår, mens den anden er teoriproducerende på baggrund af resultaterne fra første del.

  12. Photosonochemical catalytic ring opening of α-epoxyketones

    Directory of Open Access Journals (Sweden)

    Saffar-Teluri Ali

    2007-01-01

    Full Text Available Abstract The combination of ultrasound and photochemical methods has been used for the catalytic ring opening of α-epoxyketones by 1-benzyl-2,4,6-triphenylpyridinium tetrafluoroborate (NBTPT as photocatalyst in methanol. Sonication of these compounds in the presence of NBTPT did not result in the opening of epoxide ring, but the use of ultrasound increased the rate of photoreaction.

  13. 'On Earth as it is in Heaven...' The heavenly sanctuary motif in ...

    African Journals Online (AJOL)

    ... archetype] by Philo) and σκια [shadow] – is studied within the context of Hebrews 8:1–5. The purpose of this investigation is to explore the possible Graeco-Jewish background(s) of the 'heavenly sanctuary' motif in Hebrews 8:5, the presence of its key terminology and some of its intertextual occurrences in, amongst others ...

  14. Phase behaviour of polyethylene knotted ring chains

    International Nuclear Information System (INIS)

    Wen Xiao-Hui; Xia A-Gen; Chen Hong-Ping; Zhang Lin-Xi

    2011-01-01

    The phase behaviour of polyethylene knotted ring chains is investigated by using molecular dynamics simulations. In this paper, we focus on the collapse of the polyethylene knotted ring chain, and also present the results of linear and ring chains for comparison. At high temperatures, a fully extensive knot structure is observed. The mean-square radius of gyration per bond (S 2 )/(Nb 2 ) and the shape factor (δ*) depend on not only the chain length but also the knot type. With temperature decreasing, chain collapse is observed, and the collapse temperature decreases with the chain length increasing. The actual collapse transition can be determined by the specific heat capacity C v , and the knotted ring chain undergoes gas—liquid—solid-like transition directly. The phase transition of a knotted ring chain is only one-stage collapse, which is different from the polyethylene linear and ring chains. This investigation can provide some insights into the statistical properties of knotted polymer chains. (condensed matter: structural, mechanical, and thermal properties)

  15. 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

  16. Polarization Studies for the eRHIC Electron Storage Ring

    Energy Technology Data Exchange (ETDEWEB)

    Gianfelice-Wendt, Eliana [Fermilab; Tepikian, S. [Brookhaven

    2018-04-01

    A hadron/lepton collider with polarized beams has been under consideration by the scientific community since some years, in the U.S. and Europe. Among the various proposals, those by JLAB and BNL with polarized electron and proton beams are currently under closer study in the U.S. Experimenters call for the simultaneous storage of electron bunches with both spin helicity. In the BNL based Ring-Ring design, electrons are stored at top energy in a ring to be accommodated in the existing RHIC tunnel. The transversely polarized electron beam is injected into the storage ring at variable energies, between 5 and 18 GeV. Polarization is brought into the longitudinal direction at the IP by a couple of spin rotators. In this paper results of first studies of the attainable beam polarization level and lifetime in the storage ring at 18 GeV are presented.

  17. Ring structure amino acids affect the suppressor activity of melon aphid-borne yellows virus P0 protein.

    Science.gov (United States)

    Han, Yan-Hong; Xiang, Hai-Ying; Wang, Qian; Li, Yuan-Yuan; Wu, Wen-Qi; Han, Cheng-Gui; Li, Da-Wei; Yu, Jia-Lin

    2010-10-10

    Melon aphid-borne yellows virus (MABYV) is a newly identified polerovirus occurring in China. Here, we demonstrate that the MABYV encoded P0 (P0(MA)) protein is a strong suppressor of post-transcriptional gene silencing (PTGS) with activity comparable to tobacco etch virus (TEV) HC-Pro. In addition we have shown that the LP F-box motif present at the N-terminus of P0(MA) is required for suppressor activity. Detailed mutational analyses on P0(MA) revealed that changing the conserved Trp 212 with non-ring structured amino acids altered silencing suppressor functions. Ala substitutions at positions 12 and 211 for Phe had no effect on P0 suppression-activity, whereas Arg and Glu substitutions had greatly decreased suppressor activity. Furthermore, substitutions targeting Phe at position 30 also resulted in reduced P0 suppression-activity. Altogether, these results suggest that ring structured Trp/Phe residues in P0 have important roles in suppressor activity. Copyright © 2010 Elsevier Inc. All rights reserved.

  18. Spectrometer of Cherenkov radiation rings with hodoscopic photomultipliers

    International Nuclear Information System (INIS)

    Abramov, V.V.; Alekseev, A.V.; Baldin, B.Yu.

    1983-01-01

    Characteristics of SKOCH Cherenkov radiation ring spectrometer intended for identification of π- and K-mesons and protons in a wide divergent beam in the pulse range of 5.5-30 GeV/s are investigated. The spectrometer detecting system is based on using the hodoscopic photoelectron multipliers (HPEM). The HPEM specific feature is that they have an extended cathode and permit to determine the coordinate of an incident photon by measuring the time of photoelectron drift to a dinode system. The spectrometer has been tested at the FODS facility in the secondary particle beam with angular divergence equal to 16x6 mrad and aperture of 400x200 mm in the pulse range of 6-20 GeV/s. The range of Cherenkov radiation angle detection is 40-100 mrad which corresponds to the particle velocity range of 0.996-1. The angular and radial aperture is 30 mrad, the diameter is 420 mm. The obtained velocity resolution is 6x10 -5

  19. (6S,7S,8S,8aS-6-Ethyl-7,8-dihydroxy-1,5,6,7,8,8a-hexahydroindolizin-3(2H-one monohydrate

    Directory of Open Access Journals (Sweden)

    Jozefína Žúžiová

    2010-12-01

    Full Text Available The absolute configuration of the title compound, C10H17NO3·H2O, was assigned from the synthesis. In the molecular structure, the central six-membered ring of the indolizine moiety adopts a chair conformation, with two atoms displaced by −0.578 (2 and 0.651 (1 Å from the plane of the other four atoms [maximum deviation 0.019 (2 Å] The conformation of the fused oxopyrrolidine ring is close to that of a flat envelope, with the flap atom displaced by 0.294 (1 Å from the plane through the remaining four atoms. In the crystal, one of the hydroxy groups is hydrogen-bonded to two water molecules, while the other hydroxy group exhibits an intermolecular hydrogen bond to the carbonyl O atom, resulting in a chain parallel to the b axis.

  20. Requirements on internal targets for the Aladdin storage ring

    International Nuclear Information System (INIS)

    Holt, R.J.

    1984-01-01

    The feasibility of performing electron scattering experiments with polarized targets in electron storage rings is explored by considering an electron-deuteron scattering experiment at the Aladdin storage ring. It is noted that this new method is compatible with recent proposals for linac-stretcher-ring accelerator designs. A new method for producing a polarized hydrogen or deuterium target is proposed and some preliminary results are described. 21 references, 6 figures, 1 table

  1. Dual Functions of Lip6 and Its Regulation of Lipid Metabolism in the Oleaginous Fungus Mucor circinelloides.

    Science.gov (United States)

    Zan, Xinyi; Tang, Xin; Chu, Linfang; Song, Yuanda

    2018-03-21

    Although multiple roles of lipases have been reported in yeasts and microalgae, the functions of lipases have not been studied in oleaginous filamentous fungi. Lipase Lip6 has been reported in the oleaginous filamentous fungus Mucor circinelloides with the consensus lipase motif GXSXG and the typical acyltransferase motif of H-(X) 4 -D. To demonstrate that Lip6 might play dual roles as a lipase and an acyltransferase, we performed site-directed mutagenesis in the lipase motif and the acyltransferase motif of Lip6. Mutation in the lipase motif increased cell biomass by 12%-18% and promoted lipid accumulation by 9%-24%, while mutation in the acyltransferase motif induced lipid degradation. In vitro, purified Lip6 had a slight lipase activity but had a stronger phospholipid:DAG acyltransferase activity. Enzyme activity assays in vivo and phospholipid synthesis pathway analysis suggested that phosphatidyl serine and phosphatidyl ethanolamine can be the supplier of a fatty acyl moiety to form TAG in M. circinelloides.

  2. 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

  3. DistAMo: A web-based tool to characterize DNA-motif distribution on bacterial chromosomes

    Directory of Open Access Journals (Sweden)

    Patrick eSobetzko

    2016-03-01

    Full Text Available Short DNA motifs are involved in a multitude of functions such as for example chromosome segregation, DNA replication or mismatch repair. Distribution of such motifs is often not random and the specific chromosomal pattern relates to the respective motif function. Computational approaches which quantitatively assess such chromosomal motif patterns are necessary. Here we present a new computer tool DistAMo (Distribution Analysis of DNA Motifs. The algorithm uses codon redundancy to calculate the relative abundance of short DNA motifs from single genes to entire chromosomes. Comparative genomics analyses of the GATC-motif distribution in γ-proteobacterial genomes using DistAMo revealed that (i genes beside the replication origin are enriched in GATCs, (ii genome-wide GATC distribution follows a distinct pattern and (iii genes involved in DNA replication and repair are enriched in GATCs. These features are specific for bacterial chromosomes encoding a Dam methyltransferase. The new software is available as a stand-alone or as an easy-to-use web-based server version at http://www.computational.bio.uni-giessen.de/distamo.

  4. (25R-6α-Hydroxy-5α-spirostan-3β-yl tosylate

    Directory of Open Access Journals (Sweden)

    María A. Fernández-Herrera

    2012-12-01

    Full Text Available The title steroid, C34H50O6S, is an intermediate on the synthetic route between diosgenin and brassinosteroids, which possess the A ring modified with the 2α,3α-diol functionality. The polycyclic spirostan system has the expected conformation, with six-membered rings adopting chair forms and the five-membered rings envelope forms (flap atoms are the methine C atom in the C/D-ring junction and the spiro C atom connecting rings E and F. The 3β-tosylate group is oriented in such a way that S=O bonds are engaged in intermolecular hydrogen bonds with O—H and C—H donors. Chains of molecules are formed along [100] via O—H...O hydrogen bonds, and secondary weak C—H...O interactions connect two neighbouring chains in the [001] direction.

  5. Tyrosine phosphorylation of LRP6 by Src and Fer inhibits Wnt/β-catenin signalling

    Science.gov (United States)

    Chen, Qing; Su, Yi; Wesslowski, Janine; Hagemann, Anja I; Ramialison, Mirana; Wittbrodt, Joachim; Scholpp, Steffen; Davidson, Gary

    2014-01-01

    Low-density lipoprotein receptor-related proteins 5 and 6 (LRP5/6) function as transmembrane receptors to transduce Wnt signals. A key mechanism for signalling is Wnt-induced serine/threonine phosphorylation at conserved PPPSPxS motifs in the LRP6 cytoplasmic domain, which promotes pathway activation. Conserved tyrosine residues are positioned close to all PPPSPxS motifs, which suggests they have a functional significance. Using a cell culture-based cDNA expression screen, we identified the non-receptor tyrosine kinases Src and Fer as novel LRP6 modifiers. Both Src and Fer associate with LRP6 and phosphorylate LRP6 directly. In contrast to the known PPPSPxS Ser/Thr kinases, tyrosine phosphorylation by Src and Fer negatively regulates LRP6-Wnt signalling. Epistatically, they function upstream of β-catenin to inhibit signalling and in agreement with a negative role in regulating LRP6, MEF cells lacking these kinases show enhanced Wnt signalling. Wnt3a treatment of cells enhances tyrosine phosphorylation of endogenous LRP6 and, mechanistically, Src reduces cell surface LRP6 levels and disrupts LRP6 signalosome formation. Interestingly, CK1γ inhibits Fer-induced LRP6 phosphorylation, suggesting a mechanism whereby CK1γ acts to de-represses inhibitory LRP6 tyrosine phosphorylation. We propose that LRP6 tyrosine phosphorylation by Src and Fer serves a negative regulatory function to prevent over-activation of Wnt signalling at the level of the Wnt receptor, LRP6. Subject Categories Membrane & Intracellular Transport; Post-translational Modifications, Proteolysis & Proteomics PMID:25391905

  6. Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification

    Directory of Open Access Journals (Sweden)

    Yin Wang

    2016-01-01

    Full Text Available Background. Text data of 16S rRNA are informative for classifications of microbiota-associated diseases. However, the raw text data need to be systematically processed so that features for classification can be defined/extracted; moreover, the high-dimension feature spaces generated by the text data also pose an additional difficulty. Results. Here we present a Phylogenetic Tree-Based Motif Finding algorithm (PMF to analyze 16S rRNA text data. By integrating phylogenetic rules and other statistical indexes for classification, we can effectively reduce the dimension of the large feature spaces generated by the text datasets. Using the retrieved motifs in combination with common classification methods, we can discriminate different samples of both pneumonia and dental caries better than other existing methods. Conclusions. We extend the phylogenetic approaches to perform supervised learning on microbiota text data to discriminate the pathological states for pneumonia and dental caries. The results have shown that PMF may enhance the efficiency and reliability in analyzing high-dimension text data.

  7. Ménage à trois: the complex relationships between mitogen-activated protein kinases, WRKY transcription factors, and VQ-motif-containing proteins.

    Science.gov (United States)

    Weyhe, Martin; Eschen-Lippold, Lennart; Pecher, Pascal; Scheel, Dierk; Lee, Justin

    2014-01-01

    Out of the 34 members of the VQ-motif-containing protein (VQP) family, 10 are phosphorylated by the mitogen-activated protein kinases (MAPKs), MPK3 and MPK6. Most of these MPK3/6-targeted VQPs (MVQs) interacted with specific sub-groups of WRKY transcription factors in a VQ-motif-dependent manner. In some cases, the MAPK appears to phosphorylate either the MVQ or the WRKY, while in other cases, both proteins have been reported to act as MAPK substrates. We propose a network of dynamic interactions between members from the MAPK, MVQ and WRKY families - either as binary or as tripartite interactions. The compositions of the WRKY-MVQ transcriptional protein complexes may change - for instance, through MPK3/6-mediated modulation of protein stability - and therefore control defense gene transcription.

  8. The nature of hydrogen bonding in R-2(2)(8) crystal motifs - a computational exploration

    Czech Academy of Sciences Publication Activity Database

    Deepa, Palanisamy; Solomon, R. V.; Vedha, S. A.; Kolandaivel, P.; Venuvanalingam, P.

    2014-01-01

    Roč. 112, č. 24 (2014), s. 3195-3205 ISSN 0026-8976 Institutional support: RVO:61388963 Keywords : NCI plot * hydrogen bonds * R-2(2)(8) motif * organic crystals * NBO * QTAIM analysis Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.720, year: 2014

  9. The King's Ring: A Matter of Trust

    DEFF Research Database (Denmark)

    Sterrett, Joseph William

    2018-01-01

    This essay examines the material and social effects of an exchange of trust between a king, Henry VIII, and his counsellor, Thomas Cranmer in Shakespeare and Fletcher’s All is True. The ring that the King gives Cranmer is both nothing and everything: nothing in that it could be anything, any ring...

  10. Selection against spurious promoter motifs correlates withtranslational efficiency across bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Froula, Jeffrey L.; Francino, M. Pilar

    2007-05-01

    Because binding of RNAP to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of DNA motifs capable of RNAP-binding across the genome. Here we analyze the distribution of the -10 promoter motifs that bind the {sigma}{sup 70} subunit of RNAP in 42 bacterial genomes. We show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequences while eliminating them from the nonfunctional and, in most cases, from the protein coding regions. In some genomes, however, -10 sites are over-represented in the coding sequences; these sites could induce pauses effecting regulatory roles throughout the length of a transcriptional unit. For nonfunctional sequences, the extent of motif under-representation varies across genomes in a manner that broadly correlates with the number of tRNA genes, a good indicator of translational speed and growth rate. This suggests that minimizing the time invested in gene transcription is an important selective pressure against spurious binding. However, selection against spurious binding is detectable in the reduced genomes of host-restricted bacteria that grow at slow rates, indicating that components of efficiency other than speed may also be important. Minimizing the number of RNAP molecules per cell required for transcription, and the corresponding energetic expense, may be most relevant in slow growers. These results indicate that genome-level properties affecting the efficiency of transcription and translation can respond in an integrated manner to optimize gene expression. The detection of selection against promoter motifs in nonfunctional regions also implies that no sequence may evolve free of selective constraints, at least in the relatively small and unstructured genomes of bacteria.

  11. An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.

    Science.gov (United States)

    Liu, Bingqiang; Zhang, Hanyuan; Zhou, Chuan; Li, Guojun; Fennell, Anne; Wang, Guanghui; Kang, Yu; Liu, Qi; Ma, Qin

    2016-08-09

    Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif prediction. Here we present an integrative phylogenetic footprinting framework for accurate motif predictions in prokaryotic genomes (MP(3)). The framework includes a new orthologous data preparation procedure, an additional promoter scoring and pruning method and an integration of six existing motif finding algorithms as basic motif search engines. Specifically, we collected orthologous genes from available prokaryotic genomes and built the orthologous regulatory regions based on sequence similarity of promoter regions. This procedure made full use of the large-scale genomic data and taxonomy information and filtered out the promoters with limited contribution to produce a high quality orthologous promoter set. The promoter scoring and pruning is implemented through motif voting by a set of complementary predicting tools that mine as many motif candidates as possible and simultaneously eliminate the effect of random noise. We have applied the framework to Escherichia coli k12 genome and evaluated the prediction performance through comparison with seven existing programs. This evaluation was systematically carried out at the nucleotide and binding site level, and the results showed that MP(3) consistently outperformed other popular motif finding tools. We have integrated MP(3) into our motif identification and analysis server DMINDA, allowing users to efficiently identify and analyze motifs in 2,072 completely sequenced prokaryotic genomes. The performance evaluation indicated that MP(3) is effective for predicting regulatory motifs in prokaryotic genomes. Its application may enhance

  12. Regulation and function of the CD3¿ DxxxLL motif: a binding site for adaptor protein-1 and adaptor protein-2 in vitro

    DEFF Research Database (Denmark)

    Dietrich, J; Kastrup, J; Nielsen, B L

    1997-01-01

    /CD3gamma chimeras; and in vitro by binding CD3gamma peptides to clathrin-coated vesicle adaptor proteins (APs). We find that the CD3gamma D127xxxLL131/132 sequence represents one united motif for binding of both AP-1 and AP-2, and that this motif functions as an active sorting motif in monomeric CD4...... and for AP binding in vitro. Furthermore, we provide evidence indicating that phosphorylation of CD3gamma S126 in the context of the complete TCR induces a conformational change that exposes the DxxxLL sequence for AP binding. Exposure of the DxxxLL motif causes an increase in the TCR internalization rate...

  13. 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.

  14. Passive scalar transport mediated by laminar vortex rings

    Energy Technology Data Exchange (ETDEWEB)

    Hernández, R H; Rodríguez, G, E-mail: rohernan@ing.uchile.cl [LEAF-NL, Depto. Ingeniería Civil Mecánica, Universidad de Chile, Casilla 2777, Santiago (Chile)

    2017-04-15

    Numerical simulations were used to study the dynamics of a passive conserved scalar quantity entrained by a self-propelling viscous vortex ring. The transport and mixing process of the passive scalar variable were studied considering two initial scalar distributions: (i) The scalar substance was introduced into the ring during its formation, further focusing in the shedding into the wake of the ring; (ii) A disk-like scalar layer was placed in the ring’s path where the entrainment of the scalar substance into the ring bubble was studied as a function of the ring strength. In both cases, the scalar concentration inside the vortex bubble exhibits a steady decay with time. In the second case, it was shown that the entrained scalar mass grows with both the Reynolds number of the ring and the thickness of the scalar layer in the propagation direction. The ring can be viewed as a mechanism for scalar transportation along important distances. (paper)

  15. Dipropyl 3,6-diphenyl-1,2-dihydro-1,2,4,5-tetrazine-1,2-dicarboxylate.

    Science.gov (United States)

    Rao, Guo-Wu; Hu, Wei-Xiao

    2003-05-01

    The title compound, C(22)H(24)N(4)O(4), was prepared from propyl chloroformate and 3,6-diphenyl-1,2-dihydro-s-tetrazine. This reaction yields the title compound rather than dipropyl 3,6-diphenyl-1,4-dihydro-s-tetrazine-1,4-dicarboxylate. The 2,3-diazabutadiene group in the central six-membered ring is not planar; the C=N double-bond length is 1.285 (2) A, and the average N-N single-bond length is 1.401 (3) A, indicating a lack of conjugation. The ring has a twist conformation, in which adjacent N atoms lie +/- 0.3268 (17) A from the plane of the ring. The molecule has twofold crystallographic symmetry.

  16. The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element.

    Science.gov (United States)

    Fukunaga, Junichi; Nomura, Yusuke; Tanaka, Yoichiro; Amano, Ryo; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Sakamoto, Taiichi; Kozu, Tomoko

    2013-07-01

    AML1 (RUNX1) is a key transcription factor for hematopoiesis that binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. Aberrations in the AML1 gene are frequently found in human leukemia. To better understand AML1 and its potential utility for diagnosis and therapy, we obtained RNA aptamers that bind specifically to the AML1 Runt domain. Enzymatic probing and NMR analyses revealed that Apt1-S, which is a truncated variant of one of the aptamers, has a CACG tetraloop and two stem regions separated by an internal loop. All the isolated aptamers were found to contain the conserved sequence motif 5'-NNCCAC-3' and 5'-GCGMGN'N'-3' (M:A or C; N and N' form Watson-Crick base pairs). The motif contains one AC mismatch and one base bulged out. Mutational analysis of Apt1-S showed that three guanines of the motif are important for Runt binding as are the three guanines of RDE, which are directly recognized by three arginine residues of the Runt domain. Mutational analyses of the Runt domain revealed that the amino acid residues used for Apt1-S binding were similar to those used for RDE binding. Furthermore, the aptamer competed with RDE for binding to the Runt domain in vitro. These results demonstrated that the Runt domain of the AML1 protein binds to the motif of the aptamer that mimics DNA. Our findings should provide new insights into RNA function and utility in both basic and applied sciences.

  17. 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

  18. 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

  19. 2-[(1R*,4R*-1,4-Dihydroxycyclohexyl]acetic acid

    Directory of Open Access Journals (Sweden)

    Mohammad Arfan

    2011-04-01

    Full Text Available The title compound, C8H14O4, is an isolation product of the aerial parts of Senecio desfontanei. The acetic acid group is oriented at a dihedral angle of 48.03 (9° with respect to the basal plane of the cyclohexane-1,4-diol chair. An intramolecular O—H...O hydrogen bond generates an S(6 ring with an envelope conformation. In the crystal, molecules are linked by O—H...O hydrogen bonds, resulting in R33(20 ring motifs and C(2 O—H...O—H...O—H... chains. Overall, a three-dimensional polymeric network arises. A C—H...O contact is also present.

  20. Electronic de-multipliers II (ring-shape systems)

    International Nuclear Information System (INIS)

    Raievski, V.

    1948-09-01

    This report describes a new type of ring-shape fast electronic counter (de-multiplier) with a resolution capacity equivalent to the one made by Regener (Rev. of Scientific Instruments USA 1946, 17, 180-89) but requiring two-times less electronic valves. This report follows the general description of electronic de-multipliers made by J. Ailloud (CEA--001). The ring comprises 5 flip-flop circuits with two valves each. The different elements of the ring are calculated with enough details to allow the transfer of this calculation to different valve types. (J.S.)